title: lncRNA profile of case388T


title: phs001866_AP_232

status: Public on Aug 31 2020

type: SRA

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

description: RNA-Seq of human breast metastatic tumor

library_source: transcriptomic

data_processing:
Quality-control-passed reads were aligned to the human reference CGRh38/hg38 genome using STAR.
The alignment profile was determined by Picard Tools v1.64 (http://broadinstitute.github.io/picard/). Transcript abundance estimates for each sample were performed using Salmon, an expectation-maximization algorithm using the UCSC gene definitions.
Genome_build: CGRh38/hg38 genome
Supplementary_files_format_and_content: Raw read counts for all RNAseq samples were normalized to a fixed upper quartile (166_AP206_UQN.final.tsv). RNAseq normalized gene counts from primary and metastatic tumors were log2 transformed, the zeros were added again after log transformation and the genes were filtered for those expressed in 70% of samples using the cluster 3.0 software and the samples were median centered. (166_AP206_UQN_w0_log2_70p_mdctr.final.tsv)

molecule: total RNA

organism: Homo sapiens

source_name: breast

extract_protocol:
Tumor tissue was disrupted using roto-stator homogenization. RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to manufacturer protocol. RNA was quantified using a NanoDrop® Spectrophotometer,  and the quality of RNA was  then  analyzed  via  2100 Bioanalyzer Instrumentwhich  using the  RNA 6000 Nano  assay (Agilent)  for determination  of  an  RNA  Integrity  Number  (RIN).
Briefly, 1 μg of total RNA was converted to RNAseq libraries using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold (Illumina) and sequenced on an Illumina HiSeq 2500 using a 2x50bp configuration with an average of 136 million read pairs per sample.

value: metastatic tumor


title: phs001866_AP_241

description: RNA-Seq of human breast primary tumor

value: primary tumor


title: phs001866_AP_234


title: lncRNA profile of case388N

type: RNA

city: GZ

first: Rui-qi

last: WANG

state: Guangdong

address: 651 DONGFENG EAST ROAD, GUANGZHOU 510060, P. R. CH

department: state key lab

country: China

institute: SUN YAN-SEN UNIVERSITY CANCER CENTER

description: The microarray was used to acquire lncRNA expression profiles of 2412 lncRNAs.

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a LuxScanTM -10K Scanner (capitalBio Inc.,Beijing, China).

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

source_name: non-small-cell lung cancer

label_protocol: 2.5 μg of total RNA of intrahepatic cholangiocarcinoma/normal intrahepatic bile duct tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (USB, Cleveland, Oh, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: status after 3 years

value: Dead


title: phs001866_AP_231

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_230


title: phs001866_AP_228


title: phs001866_AP_229

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_227

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case383T

value: Alive


title: phs001866_AP_224


title: lncRNA profile of case385T


title: phs001866_AP_236


title: genomic DNA from peripheral blood leukocytes 2

type: genomic

city: Ann Arbor

first: Minjung

last: Kho

state: Michigan

address: School of Public Health University of Michigan 1415 Washington Heights

institute: University of Michigan

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to IIllumina Infinium HumanMethylation450 BeadChip or EPIC BeadChip using standard Illumina protocol

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

data_processing: For each chip, the Minfi R package was used to perform background correction and normalization. The regression on correlated probes (RCP) method was then used to adjust probe-type bias, and ComBat was used to remove confounding effects due to batch or other technical covariates. Data from the two platforms were combined, and ComBat was used to remove the platform effect. Age, gender, and phase effect was preserved when removing platform difference.

label: Cy5 and Cy3

molecule: genomic DNA

source_name: peripheral blood leukocytes

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted from stored peripheral blood leukocytes using AutoGen FlexStar (AutoGen, Holliston, MA) and DNA was bisulfite converted using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA)

tag: tissue

value: peripheral blood leukocytes

tag: gender

value: F

tag: age(yrs)

tag: systolic blood pressure (mmhg)

tag: diastolic blood pressure (mmhg)


title: phs001866_AP_223

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case384T


title: lncRNA profile of case385N


title: lncRNA profile of case382T


title: lncRNA profile of case381T


title: phs001866_AP_221

description: RNA-Seq of human breast primary tumor


title: genomic DNA from peripheral blood leukocytes 1


title: phs001866_AP_233

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case387N


title: lncRNA profile of case380T


title: phs001866_AP_220


title: lncRNA profile of case380N


title: lncRNA profile of case387T


title: phs001866_AP_219

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_217

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_218


title: lncRNA profile of case373T


title: lncRNA profile of case369T


title: lncRNA profile of case376T


title: lncRNA profile of case384N


title: lncRNA profile of case366T


title: lncRNA profile of case383N


title: phs001866_AP_222


title: phs001866_AP_215

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_216


title: lncRNA profile of case366N


title: phs001866_AP_209

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_210


title: phs001866_AP_206


title: lncRNA profile of case364T


title: lncRNA profile of case357T


title: lncRNA profile of case357N


title: lncRNA profile of case355T


title: phs001866_AP_204


title: lncRNA profile of case351T


title: phs001866_AP_203

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case345T


title: phs001866_AP_197

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case345N


title: phs001866_AP_196


title: lncRNA profile of case342T


title: lncRNA profile of case342N


title: phs001866_AP_195

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_194


title: lncRNA profile of case339T


title: phs001866_AP_193

description: RNA-Seq of human breast primary tumor


title: WT rep1

city: Sendai

first: Yuta

last: Chiba

state: Miyagi

address: 4-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University

description: total RNA

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sequenced reads were mapped to GRCm38.vM11 mouse genome using STAR v2.5.2a in  single-pass mode. With the following parameters:  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField None --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.25 --outFilterScoreMinOverLread 0.25 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000  --outSAMtype BAM SortedByCoordinate --bamRemoveDuplicatesType UniqueIdentical --quantMode GeneCounts
Gene counts were generated with STAR v2.5.2a built-in counting option --quantMode GeneCounts against a customized Gencode GRCm38 vM11 genome annotation GTF which included ERCCs.
A expression matrix was assembled using R. Genes with less than 5 reads in at least one of the samples were filtered out before differential gene expression analysis.
Differential expression was performed using the DESeq2, EdgeR and Limma-Voom R packages.
Genome_build: Custom mm10/GRCm38.vM11+ERCCs
Supplementary_files_format_and_content: Tab delimited files include a raw counts and TMM-normalized expression matrices.

organism: Mus musculus

source_name: Tooth germ

extract_protocol:
To construct each cDNA library, total RNA in P7 first molars from littermate WT and Gpr115-KO mice was extracted using TRIzol reagent (Invitrogen).
cDNA libraries were produced using a Nextera XT library kit (Illumina), and samples were run on a HiSeq1500 (Illumina) configured for 150 x 150 pair-end reads.

tag: strain

tag: genotype

value: wild type

value: Tooth germ

tag: age

value: post natal day 7


title: WT rep3

description: total RNA


title: WT rep2

description: total RNA


title: Gpr115-KO rep2

description: total RNA


title: Gpr115-KO rep3

description: total RNA


title: phs001866_AP_192


title: Gpr115-KO rep1

description: total RNA


title: lncRNA profile of case338T


title: phs001866_AP_205

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case337N


title: phs001866_AP_191

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_198


title: lncRNA profile of case328T


title: phs001866_AP_190


title: lncRNA profile of case337T


title: 4c11plus_rep3

city: São Paulo

first: Eduardo

middle: Moraes

last: Reis

state: SP

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of São Paulo

data_processing:
Quality control and adaptor trimming was conducted with Fast-QC and Trimmomatic, respectively, using default parameters
data was mapped to the annotated mouse genome (Ensembl 90 version) using the STAR aligner
Reads mapped to gene annotations were quantified and summarized using the Rsubread R package. Genes with read counts less than 1 CPM (count per million) in at least 4 out of 11 libraries (35% of samples) were discarded; expression values of the remaining genes were normalized and log transformed through the voom function from the limma R package.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include mous gene annotation (Ensembl 90) and normalized  expression values (CPM, log transformed) for each sample

source_name: metastatic melanoma (4C11+)

growth_protocol: Non-tumorigenic melan-a cells was cultured in RPMI supplemented with 5% fetal bovine serum and 200 nM PMA at 37°C in a humidified atmosphere of 5% CO2 and 95% air. The melanoma cell lines derived from melan-a cells were cultured in the same conditions, without PMA.

extract_protocol:
Triplicate cultures of each of the four cell lines were used (12 samples in total). RNA was isolated using TRIzol reagent using the manufacturer's protocol (Thermo Fisher Scientific Inc.) and treated with RNAse-free DNAse.
RNA-Seq libraries were generated using the Illumina TruSeq Stranded Total RNA LT sample preparation kit with Ribo-Zero Gold (Cat# RS-122-2001) according to the standard manufacturer’s protocol (Part no. 15031048 Rev. D April 2013).

treatment_protocol: The murine model of melanoma progression has been previously described (Oba-Shinjo et al., 2006) and comprises spontaneously immortalized nonmalignant melanocytes (melan-a) (Bennett et al., 1987) and three cell lines with increasing malignant potential (4C, 4C11- and 4C11+) derived from melan-a after sequential cycles of forced anchorage impediment.

tag: cell type

value: metastatic melanoma (4C11+)


title: 4c11plus_rep2


title: 4c11minus_rep3

source_name: non-metastatic melanoma (4C11-)

value: non-metastatic melanoma (4C11-)


title: 4c11plus_rep1


title: phs001866_AP_189

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_188


title: lncRNA profile of case315T


title: 4c11minus_rep2


title: phs001866_AP_187

description: RNA-Seq of human breast primary tumor


title: 4c11minus_rep1


title: 4c_rep3

source_name: non-tumorigenic pre-malignant melanocytes (4C)


title: lncRNA profile of case307T


title: 4c_rep1

value: non-tumorigenic pre-malignant melanocytes (4C)


title: phs001866_AP_185

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_184


title: phs001866_AP_186


title: 4c_rep2


title: melan_rep3

source_name: melan-a melanocyte lineage

value: nonmalignant melanocytes (melan-a)


title: lncRNA profile of case305T


title: lncRNA profile of case297T


title: phs001866_AP_182


title: lncRNA profile of case304T


title: lncRNA profile of case298T


title: melan_rep2


title: phs001866_AP_183

description: RNA-Seq of human breast primary tumor


title: L-30-B rep2

city: Nanjing

first: Xiannan

last: Meng

address: Hankou Road 22

institute: Nanjing University

description: transcript_fpkm.txt, circRNA.txt

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
The reference genomes and the annotation file were downloaded from MM10. Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample
Mapping reads to mature miRNA and hairping which recorded in miRBase (release 21) to identiy known-miRNA. After excluded the reads mapped to known miRNA/ncRNA/repeat region/mRNA region, the remaining reads were used to predict novel miRNA, the keys of prediction is hairping structure and stability. The software for identification and prediction is miRDeep2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: testis

extract_protocol:
testes were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ RNA Library Prep Kit for Illumina®（ #E7530L， NEB） was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina

value: Balb/c

value: post natal six month

tag: treatment

value: 30 ug/L MC-LR exposure)


title: lncRNA profile of case325T


title: L-30-A rep1

description: transcript_fpkm.txt, circRNA.txt


title: lncRNA profile of case296T


title: phs001866_AP_181

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_180


title: lncRNA profile of case296N


title: L-con-A rep1

description: transcript_fpkm.txt, circRNA.txt

value: control


title: L-con-B rep2

description: transcript_fpkm.txt, circRNA.txt


title: phs001866_AP_179

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case295T


title: lncRNA profile of case292T


title: phs001866_AP_178

value: metastatic tumor


title: M63_13

city: Tsukuba

first: Bei-Wen

last: Ying

state: Ibaraki

address: 1-1-1 Tennoudai

institute: University of Tsukuba

data_processing:
Basecalls performed using RTA.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic v0.38.
Trimmed reads were mapped to reference genome with Bowtie v1.1.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using HTseq v0.10.0.
Genome_build: ASM75055v1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli BW25113

source_name: culture population

extract_protocol:
The cell cultures were mixed with the ice cold phenol ethanol solution (phenol: ethanol = 1: 9), and centrifuged at 16,000g for 5 min at 4°C. The pelleted cells were stored at -80°C for future use. Total RNAs were extracted using an RNeasy mini kit (QIAGEN Cat#74104), in accordance to the manufacturer’s instructions.
TruSeq Stranded mRNA Sample Preparation Guide, Part#15031047 Rev. E

tag: growth medium

tag: growth temperature

tag: growth phase

value: late exponential phase


title: lncRNA profile of case291T

value: Dead


title: phs001866_AP_177

description: RNA-Seq of human breast primary tumor

value: primary tumor


title: lncRNA profile of case290T

value: Alive


title: phs001866_AP_175

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_176


title: M63_11


title: LB_8

value: LB


title: LB_9


title: lncRNA profile of case286T


title: M63_12


title: LB_10


title: lncRNA profile of case285T


title: phs001866_AP_173

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case301T


title: phs001866_AP_174


title: lncRNA profile of case279T


title: phs001866_AP_171

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case270T


title: phs001866_AP_172


title: lncRNA profile of case26T


title: lncRNA profile of case266T


title: lncRNA profile of case270N


title: phs001866_AP_168


title: phs001866_AP_169

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case249T


title: phs001866_AP_167

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case238T


title: lncRNA profile of case238N


title: phs001866_AP_166


title: lncRNA profile of case237T


title: phs001866_AP_164


title: phs001866_AP_165

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_163

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case237N


title: lncRNA profile of case236T


title: lncRNA profile of case231T


title: phs001866_AP_162


title: lncRNA profile of case231N


title: phs001866_AP_161

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case230T


title: phs001866_AP_158


title: lncRNA profile of case230N


title: L_B60_37R3

city: Ames

first: Stephen

middle: H

last: Howell

state: Iowa

address: 1111 WOI Road

department: Plant Sciences Institute Department of Genetics, Development and Cell Biology

institute: Iowa State University

description: bzip60-2 maize leaf (V5, maximum daily temperature 37°C) replicate 3

data_processing: Sequencing data were filtered with SOAPnuke (v1.5.2, github.com/BGI-flexlab/SOAPnuke) by removing reads (1) containing sequencing adapters, (2) in which more than 20% of the bases have a quality score less than 5 or (3) in which 5% or more of the bases are unknown (represented by N).  Clean reads were stored in FASTQ format and mapped to the reference maize B73 genome using HISAT2 (v2.0.4, http://www.ccb.jhu.edu/software/hisat/index.shtml). Bowtie2 (v2.2.5, http://bowtiebio.sourceforge.net/%20Bowtie2%20/index.shtml) was used to align the clean reads to the reference coding gene set (plants.ensembl.org/info/website/ftp/index.html),and gene expression levels were calculated by RSEM (v1.2.12, github.com/deweylab/RSEM).  Differential expression analysis was performed using DESeq2 (v1.4.5, www.bioconductor.org/packages/release/bioc/html/ DESeq2.html) using a Q value ≤ 0.05. GO (http://www.geneontology.org/) enrichment analysis of annotated DEGs was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution).  The significant levels of terms were corrected by Log2Ratio ≥ 1 and Q value with a threshold (Q value ≤ 0.05) by Bonferroni (Abdi, 2007).

organism: Zea mays

growth_protocol: Seeds of maize W22 and bzip60 mutants were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition. The performance of plants under these conditions was monitored by a robot, equipped with various sensors, that travels from chamber to chamber (Bao et al., 2019).  The temperature and light cycles were offset by 40 min from chamber to chamber to allow the robot to enter the different chambers at the same time of virtual day. The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  Plant performance was assessed at three different stages of vegetative growth, V4, V5 and V13-R1 stages (He et al., 2010), with the most extensive analysis carried out at the mid vegetative stages (V4 and V5).  The stages are defined by the leaf numbers visible in the collars.  For example, the V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

extract_protocol:
RNA was extracted from small samples (0.1 g) of leaf lamina (avoiding the midrib) obtained from the middle of the first fully expanded leaves. The samples were taken in triplicate, one sample from each of three different plants, in the two chambers set for the same conditions.  The samples obtained from the plants in the two different chambers were taken at the same time of virtual day, because the temperature and light cycles are offset to allow for sampling at the same time of day. The samples were separately ground to a powder in liquid nitrogen, and RNA was isolated using a Plant RNeasy Mini Kit and treated with DNase (Qiagen, www.qiagen.com/us/) according to the manufacturer’s instructions. RNA quality and quantity were determined by the UV absorbance spectra, gel electrophoresis and Agilent 2000 BioAnalyzer (http://www.agilent.com).
For RNAseq analysis, poly A RNA was isolated from the purified RNA using oligo(dT)-attached magnetic beads and fragmented at elevated temperature with NEBNext RNA fragmentation buffer (New England BioLabs).  cDNA library construction, sequencing, and primary bioinformatics analysis were performed by BGI Tech Solutions Co., Ltd. (Beijing Genomic Institute (www.genomics.org.cn, BGI)) as follows:  First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by second-strand cDNA synthesis.  cDNA ends were repaired by A-Tailing followed by adding RNA Index Adapters. The cDNA fragments were amplified by PCR, and the products purified by Ampure XP Beads (Beckman Coulter).  The products were validated for quality control using an Agilent Technologies 2100 bioanalyzer. The double stranded PCR products were heat denatured and circularized using splint oligos (Diegelman and Kool, 2000). The single strand circular DNAs (ssCir DNAs) were amplified with phi29 (Blanco et al., 1989) to make DNA nanoballs (DNBs) (Porreca, 2010).  DNBs were loaded into the patterned nanoarray and single end 50 base reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Seeds of maize W22 and bzip60 mutants were germinated in soil in small pots with 13h light/11h dark at 26°C.  For experiments in the Enviratron, 7 day-old plants were transplanted in 9 inch pots and randomly placed into 12 set positions within each chamber. The eight growth chambers in the Enviratron were used to simulate 4 different environmental conditions, i.e., with duplicate chambers for each condition.  The daytime temperatures were ramped up over 6 hr to a maximum daily temperature (MDT) of 31°C, 33°C, 35°C or 37°C.  Nightime temperatures were ramped down over 8 hr to 10°C below the MDT.  Light intensities in a 16 hr/8 hr photoperiod cycle were also ramped up to 1200 µmol/m²/sec (measured 60 cm from the LED light source) or down over 2 hr periods to simulate dawn and dusk.  Water potential in the soil (Sunshine SB300 or MM900 Universal potting soil) was maintained at 50% VWC (volumetric water content) and relative humidity was held at 60%.  The V4 stage has leaf 4 visible in the collar. (The leaf collar is the light-colored band located at the base of an exposed leaf blade, where the leaf blade attaches to the plant stem.)  The middle part of the first (newest) fully expanded leaf from plants at the V4 (20 DAG) and V5 (27 DAG) stages were collected for RNAseq analysis.

value: bzip60-2 mutant

value: leaf

tag: vegetative stage

value: V5 stage

value: maximum daily temperature 37°C


title: L_B60_37R2

description: bzip60-2 maize leaf (V5, maximum daily temperature 37°C) replicate 2


title: phs001866_AP_156


title: phs001866_AP_157

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_155

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case217T


title: lncRNA profile of case216N


title: L_B60_35R3

description: bzip60-2 maize leaf (V5, maximum daily temperature 35°C) replicate 3

value: maximum daily temperature 35°C


title: lncRNA profile of case216T


title: L_B60_37R1

description: bzip60-2 maize leaf (V5, maximum daily temperature 37°C) replicate 1


title: L_B60_35R2

description: bzip60-2 maize leaf (V5, maximum daily temperature 35°C) replicate 2


title: lncRNA profile of case193T


title: L_B60_35R1

description: bzip60-2 maize leaf (V5, maximum daily temperature 35°C) replicate 1


title: lncRNA profile of case185T


title: lncRNA profile of case170T


title: phs001866_AP_154


title: phs001866_AP_151

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_152


title: L_B60_33R3

description: bzip60-2 maize leaf (V5, maximum daily temperature 33°C) replicate 3

value: maximum daily temperature 33°C


title: phs001866_AP_153

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_150


title: L_B60_33R1

description: bzip60-2 maize leaf (V5, maximum daily temperature 33°C) replicate 1


title: phs001866_AP_149

description: RNA-Seq of human breast primary tumor


title: L_B60_31R3

description: bzip60-2 maize leaf (V5, maximum daily temperature 31°C) replicate 3

value: maximum daily temperature 31°C


title: phs001866_AP_147

description: RNA-Seq of human breast primary tumor


title: L_B60_31R2

description: bzip60-2 maize leaf (V5, maximum daily temperature 31°C) replicate 2


title: L_B60_33R2

description: bzip60-2 maize leaf (V5, maximum daily temperature 33°C) replicate 2


title: L_B60_31R1

description: bzip60-2 maize leaf (V5, maximum daily temperature 31°C) replicate 1


title: lncRNA profile of case173T


title: lncRNA profile of case169N


title: lncRNA profile of case168T


title: phs001866_AP_146


title: lncRNA profile of case163T


title: phs001866_AP_144


title: phs001866_AP_143

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_142


title: lncRNA profile of case149T


title: lncRNA profile of case153T


title: lncRNA profile of case148T


title: phs001866_AP_145

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_141

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_148


title: phs001866_AP_136


title: lncRNA profile of case159T


title: phs001866_AP_135

description: RNA-Seq of human breast primary tumor


title: iPSC-derived neural cell wildtype 1

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

description: iPSC-derived neural cells after 10 days of differentiation

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

scan_protocol: Standard Infinium HD Methylation Assay protocol

data_processing: Initial analysis was performed by the Genomestudio 2010.3 (Modul M Version 1.8.5). Data were normalized with internal controls according to Illumina´s standard procedures. Methylation level at each locus was calculated with the GenomeStudio Methylation module as beta-value (ranging from 0 to 1). The number of beads per feature varies between chips and beta-values were calculated as average of at least three technical replica.

source_name: iPSC from bone marrow MSC_WT

growth_protocol: Neural differentiation of iPSCs was performed as previously described (Chambers et al. 2012; Meents et al. 2019). iPSCs were seeded as single cells at a density of 105 cells/cm2 in presence of 10 µM Y-27632. At 80-90% confluency, neural conversion was induced by dual-SMAD inhibition: For the first five days LDN-193189 (100 nM or 1 µM, Sigma-Aldrich) and SB431542 (10 µM, Miltenyi Biotec) were added to the basal culture medium consisting of knockout DMEM/F 12 containing 15% knockout serum replacement, 1 mM L-glutamine, 100 µM non-essential amino acids, 100 µM β mercaptoethanol, 100 U/mL penicillin and 100 µg/mL streptomycin (all Thermo Fisher Scientific). To accelerate neural crest specification three small molecules (3 µM CHIR99021, 10 µM DAPT, and 10 µM SU5402, all Tocris, Bristol, United Kingdom) were added between days 2 to 10. After four days, the medium was supplemented in increasing percentages with DMEM/F 12, containing 10 ml/L N2, 20 ml/L B27 minus vitamin A supplements and 100 U/mL penicillin, 100 µg/mL streptomycin (all Thermo Fisher Scientific). N2/B27 medium was added to the basal medium at 25% between days 4-5, 50% between days 6-7 and 75% between days 8-10. On day 10, cells were dissociated using Accutase and seeded on glass coverslips coated with 50 µg/mL Poly-L-Ornithine (Sigma-Aldrich) and 5 µg/mL Laminin (Thermo Fisher Scientific) and further cultured for up to three weeks with N2/B27 medium supplemented with 20 ng/mL NGF (R&D Systems, Minneapolis, Minnesota, USA), BDNF, GDNF (all PeproTech) and  200 ng/mL L ascorbic acid (Sigma-Aldrich). Medium was changed every 3-4 days.

extract_protocol: Genomic DNA of iPSC-derived neural cells was harvested with the NucleoSpin Tissue kit (Macherey-Nagel, Düren, Germany).

value: Induced pluripotent stem cell derived neural cells

tag: genotype/variation

value: wild type


title: lncRNA profile of case147T


title: phs001866_AP_134


title: phs001866_AP_133

description: RNA-Seq of human breast primary tumor


title: iPSC-derived neural cell wildtype 2

label_protocol: Standard Infinium HD Methylation Assay protocol


title: lncRNA profile of case145T


title: iPSC-derived neural cell PRDM8-/- derived from wildtype 1

source_name: iPSC from bone marrow MSC_PRDM8-/-


title: lncRNA profile of case147N


title: lncRNA profile of case145N


title: lncRNA profile of case143N


title: phs001866_AP_132


title: lncRNA profile of case143T


title: E_B60_37R3

description: bzip60-2 maize leaf (V4, maximum daily temperature 37°C) replicate 3

value: V4 stage


title: phs001866_AP_118


title: E_B60_37R2

description: bzip60-2 maize leaf (V4, maximum daily temperature 37°C) replicate 2


title: phs001866_AP_117

description: RNA-Seq of human breast primary tumor


title: iPSC-derived neural cell PRDM8+/- derived from wildtype 1

source_name: iPSC from bone marrow MSC_PRDM8+/-


title: iPSC-derived neural cell wildtype 3


title: phs001866_AP_116

description: RNA-Seq of human breast metastatic tumor


title: lncRNA profile of case138T

description: The microarray was used to acquire lncRNA expression profiles of 2412 lncRNAs.


title: phs001866_AP_131

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case135T


title: phs001866_AP_115

description: RNA-Seq of human breast primary tumor


title: E_B60_37R1

description: bzip60-2 maize leaf (V4, maximum daily temperature 37°C) replicate 1


title: lncRNA profile of case135N


title: phs001866_AP_114


title: adult human left ventricle (R1234138)

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

institute: Takeda pharmaceuticals

description: Sample 9

data_processing:
Base calling was performed using software provided with the Ion Torrent Proton sequencer ( Torrent suite ver.5.10.1 ) .
Sequenced reads were trimmed for adaptor sequence low-quality sequence, then mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using a combination of using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.10.1  )
RPM were calculated using software provided with the Ion Torrent Proton sequencer ( AmpliSeqRNA v5.0.4.0  )
Genome_build: hg19_AmpliSeq_Transcriptome_ERCC_v1
Supplementary_files_format_and_content: Tab-delimited text files include gene symbol and gene expression (RPM) for each sample.

source_name: total heart RNA

extract_protocol:
RNAs were extracted using a QIAGEN RNeasy Micro Kit following manufacturer's instructions.
Libraries were prepared according to the Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific). Briefly, cDNA was generated from 10ng of total RNA. The resulted cDNA was amplified and barcoded using Ion AmpliSeq™ technology to accurately maintain expression levels of all targeted genes. Barcoded cDNA Libraries were quantified using Ion Library TaqMan Quantitation Kit (Thermo Fisher Scientific). Libraries were then diluted to 45 pM and pooled  by combining an equal volume of each.

value: adult heart


title: adult human heart (Z6532N)

description: Sample 10


title: lncRNA profile of case133T


title: E_B60_35R2

description: bzip60-2 maize leaf (V4, maximum daily temperature 35°C) replicate 2


title: adult human Heart (AM7966)

description: Sample 8


title: phs001866_AP_113

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case142T


title: human Fetal Heart (Z6583N)

description: Sample 7

value: fetal heart


title: phs001866_AP_170

value: metastatic tumor


title: E_B60_33R3

description: bzip60-2 maize leaf (V4, maximum daily temperature 33°C) replicate 3


title: phs001866_AP_112


title: lncRNA profile of case131T


title: phs001866_AP_111

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case129T

value: Dead


title: lncRNA profile of case129N


title: E_B60_33R2

description: bzip60-2 maize leaf (V4, maximum daily temperature 33°C) replicate 2


title: phs001866_AP_109

description: RNA-Seq of human breast primary tumor

value: primary tumor


title: phs001866_AP_110


title: human iPSC (253G1)-3

description: Sample 6

source_name: iPS cells

value: 253G1 line


title: E_B60_33R1

description: bzip60-2 maize leaf (V4, maximum daily temperature 33°C) replicate 1


title: human iPSC (253G1)-2

description: Sample 5


title: E_B60_35R3

description: bzip60-2 maize leaf (V4, maximum daily temperature 35°C) replicate 3


title: iCell1 lot 1093711 (2/22)

description: Sample 3

source_name: cardiomyocytes

value: iPS cell-derived cardiomyocytes

tag: lot no


title: lncRNA profile of case128T

tag: status after 3 years


title: E_B60_31R2

description: bzip60-2 maize leaf (V4, maximum daily temperature 31°C) replicate 2

value: bzip60-2 mutant

tag: tissue


title: E_B60_35R1

description: bzip60-2 maize leaf (V4, maximum daily temperature 35°C) replicate 1

value: leaf


title: human iPSC (253G1)-1

description: Sample 4


title: lncRNA profile of case128N


title: iCell1 lot 1096654-2 (2/15)

description: Sample 2


title: E_B60_31R1

description: bzip60-2 maize leaf (V4, maximum daily temperature 31°C) replicate 1


title: phs001866_AP_107

description: RNA-Seq of human breast primary tumor


title: lncRNA profile of case132T

value: Alive


title: lncRNA profile of case126T


title: iCell1 lot 1096654-1  (2/8)

description: Sample 1


title: phs001866_AP_106


title: E_B60_31R3

description: bzip60-2 maize leaf (V4, maximum daily temperature 31°C) replicate 3


title: 129Sv_pMC+rGM-CSF_2

city: Tokyo

first: Minaho

last: Kawamura

address: BLICK GATE Suidobashi F2, Chiyodaku-kandamisakicho

data_processing:
Samples were sequenced using BGI-seq instrument with paired-end 2 x 100-bp cycle
Quality check for sequence reads using FastQC
Pre-processing of sequence reads using Trimmomatic version 0.36 with LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 as command option
Mapping of sequence reads using Hisat2 version 2.1.0
Raw read counts were determined using Feature Count version 0.10.0 with -m union -r pos -t exon --stranded=no as options
Differentially expressed genes were identified using DESeq2 version 1.20.0 (log fold change x>1, x<-1)
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts

growth_protocol: iPSC-pMCs or GM-pMCs (2 × 10^6 cells/well/48 well plate) were cultured for 6 h in MEM-alpha supplemented with 20%FBS. iPSC-pMCs treated with recombinant mouse GM-CSF (30 ng/mL) were served as a reference.

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit Plus (Qiagen, Valencia, CA, USA).
Libraries were prepared for sequencing using library creation kits (TruSeq Stranded mRNA sample prep kit, Illumina, San Diego, CA, USA)

value: peritoneal macrophage


title: lncRNA profile of case125T


title: phs001866_AP_105

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_108


title: 129Sv_GM-pMC_2


title: 129Sv_GM-pMC_1


title: phs001866_AP_104


title: phs001866_AP_102


title: 129Sv_pMC_2


title: 129Sv_pMC_1


title: lncRNA profile of case124T


title: phs001866_AP_101

description: RNA-Seq of human breast primary tumor


title: phs001866_AP_100


title: lncRNA profile of case124N


title: lncRNA profile of case121T


title: lncRNA profile of case122N


title: lncRNA profile of case122T


title: C57BL/6_pMC+rGM-CSF_1

value: embryonic fibroblast


title: lncRNA profile of case121N


title: C57BL/6_GM-pMC_2


title: lncRNA profile of case125N


title: 129Sv_pMC+rGM-CSF_1


title: lncRNA profile of case115T


title: lncRNA profile of case169T


title: phs001866_AP_103

description: RNA-Seq of human breast primary tumor


title: C57BL/6_GM-pMC_1


title: C57BL/6_pMC_2


title: lncRNA profile of case109T


title: C57BL/6_pMC_1


title: lncRNA profile of case106T


title: lncRNA profile of case105T


title: lncRNA profile of case109N


title: NC_4

city: Nanchang

first: xijuan

last: liu

state: Jiangxi

address: No. 1 Minde Road

institute: The Second Affiliated Hospital of Nanchang University

description:
C41
circRNA

hyb_protocol: Labeled cRNA samples were hybridized onto the Arraystar Human circRNAs Array v2 (8 ´ 15 K, Arraystar).

scan_protocol: After washing the slides, reactions were performed using an Agilent G2505C Microarray Scanner (Agilent Technologies, Inc. USA).

data_processing: To obtain raw expression data, the array images were processed using Agilent feature extraction software (v11.0.1.1; Agilent Technologies, Inc.). circRNA expression values were quantile normalized and analyzed using the R program with the limma package in R.

source_name: healthy control

label_protocol: The circRNAs samples were amplified and transcribed into fluorescently labeled cRNA using a random priming approach (Arraystar Super RNA Labeling Kit; Arraystar).

extract_protocol: RNA samples were prepared for microarray hybridization using Eastep Super RNA simple Total RNA Kit (Promega (Beijing) Biotech Co., Ltd.) according to the manufacturer’s protocol. Total RNA was digested using RNase R (Epicentre) to enrich the sample for circRNAs and eliminate linear RNAs.

treatment_protocol: All specimens were obtained from idiopathic short stature patients and healthy controls. They were immediately frozen in liquid nitrogen and 3-5ml stored at -80 °C until further analysis.

tag: diagnosis

value: healthy

value: blood

tag: gender

value: female


title: NC_3

description:
T38
circRNA


title: lncRNA profile of case104T


title: SAMPLE 1_iPSC-derived neural cell wildtype

description:
DE33NGSUKBR106279_1
iPSC-derived neural cells after 27 days of differentiation

data_processing:
Adapter trimming and rRNA removal in raw fastq files was performed using TrimGalore (Babraham Bioinformatics, Cambridge, UK) and SortMeRNA (Kopylova et al. 2012), respectively. Reads were aligned to the human genome build GRCh38 with STAR aligner (Dobin et al. 2013). Read counts were retrieved by HTSeq-count and further analyzed with the R package DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Read counts

source_name: iPSC from bone marrow MSC

extract_protocol:
RNA of iPSC-derived neural cells was isolated with the NucleoSpin RNA Plus kit (Macherey-Nagel, Düren, Germany).
QuantSeq 3´-mRNA Library Prep/Lexogen, Standard 3' Seq (SR, 50 cycles)

value: Induced pluripotent stem cell derived neural cells

value: wild type


title: lncRNA profile of case115N

source_name: non-small-cell lung cancer


title: lncRNA profile of case104N


title: TSS_2016_A2_RNA

city: Minneapolis

first: Frank

middle: Wolfgang

last: Albert

state: MN

address: 6-160 Jackson Hall, 321 Church St SE

department: Department of Genetics, Cell Biology, & Development

institute: University of Minnesota

description:
processed data file:
TSS_countedMappedBarcodes_200806.txt.gz
TSS_countedBarcodesMappedToDesign_200806.txt.gz

data_processing:
library strategy: amplicon sequencing of barcoded library
Barcodes with perfect matches in the annotation runs were counted
Genome_build: Annotation runs performed for this study; custom synthetic oligo design was based on sacCer3
Supplementary_files_format_and_content: The processed annotation files are tab separated txt files. There are two files for the TSS and Upstream libraries, respectively. Processed files named "countedMappedBarcodes" give the counts from each sample for every detected barcode (one row per barcode). Processed files named "countedBarcodesMappedToDesign" have the same format but only include barcodes mapped to oligos that matched the designed oligos perfectly (i.e., had no synthesis errors), along with their given oligo ID as provided in the oligo design given in the associated publication.

organism: Saccharomyces cerevisiae

source_name: Synthetic DNA oligo library with barcodes

growth_protocol: Yeast were grown to late log phase in YNB (MSG) + glucose + G418 at 30˚C

extract_protocol:
For DNA, plasmids were isolated using Qiagen kits (Qiaprep Spin Miniprep #27106, or Plasmid Plus Midi). Total RNA was extracted using a Zymo Research Fungal/Bacterial RNA Miniprep kit (ZR, #R2014) or a Qiagen RNeasy Maxi Kit. For some samples, polyA-RNA was isolated using an mRNA Purification kit (Ambion #61006).
Sequencing libraries were constructed by PCR targeted at the barcodes. For RNA samples, 1st-strand cDNA was created using a targeted primer and used as the template for the PCR.

value: TSS library

value: RNA


title: TSS_2016_B1_RNA


title: TSS_2016_6_RNA


title: TSS_2016_A1_RNA


title: NC_1

description:
C34
circRNA

value: male


title: NC_2

description:
T35
circRNA


title: TSS_2016_5_RNA


title: Ct_32cell_4

city: Saint Augustine

first: Elaine

middle: C

last: Seaver

state: Florida

address: 9505 Ocean Shore Blvd.

department: Whitney Laboratory for Marine Bioscience

institute: University of Florida

description:
Lanza_Seaver_Capitella_rawRNAcounts.txt
Capitella_teleta_early_cleavage_counts_normalized.txt
Lanza_Seaver_DESeq2_LRT_Capi.csv

data_processing:
CEL-Seq: demultiplexing and qualtity control
CEL-Seq: Bowtie2 mapping
CEL-Seq: UMIs generated using htseq-count
CEL-Seq: UMI to transcript count conversion
CEL-Seq: count normalization
Genome_build: GCA_000328365.1
Supplementary_files_format_and_content: tab deleniated text file of transcript counts
Supplementary_files_format_and_content: tab deleniated text file of normalized transcript counts
Supplementary_files_format_and_content: comma separated file of DESeq2 LRT across 3 time points

molecule: polyA RNA

organism: Capitella teleta

source_name: embryo

extract_protocol:
Total RNA was extracted from individual embryos at the 8-cell (n=4), 16-cell (n=3), and 32-cell (n=5) stage at 1/5th the recommended volume using TRIzol. Linear polyacrylamide and tRNA were added to help precipitate and visualize pellets, as well as 1μl of the External RNA Control Consortium spike-in kit (Baker et al., 2005) at a 1:500,000 dilution to help quantify amplified RNA. The TRIzol mix was added to each sample, and then frozen in liquid nitrogen and thawed in a 42 °C water bath five times immediately after adding TRIzol to ensure disruption of the egg membrane. Isolated RNA was eluted in ultrapure water.
A uniquely barcoded primer was added for reverse transcription, and amplified according to the CEL-Seq protocol (Hashimshony et al., 2012). Samples were then sequenced  on one lane as paired end data on the Illumina HISeq2000

tag: developmental stage

value: embryo

tag: embryonic stage

value: 32 cell


title: Ct_32cell_5


title: TSS_2016_B2_RNA

tag: strain


title: Healthy_CD45Neg_rep1

city: Philadelphia

first: Michael

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

data_processing:
The Cell Ranger Single Cell Software Suite was used to perform sample demultiplexing, barcode processing, and single cell 3’ gene counting (http://software.10xgenomics.com/single-cell/overview/welcome). 10bp UMI tags were extracted from Read2.  Genome_build: mm10  Supplementary_files_format_and_content: mtx: count matrix in a sparse matrix format; barcodes.tsv: barcode ids for each sample; genes.tsv: gene ids for each sample
Genome_build: GRCh38
Supplementary_files_format_and_content: HDF5;  Cell ranger HDF5 Feature Barcode Matrix Format, this file  contains a single HDF5 group, called matrix, and metadata stored as HDF5 attributes. Within the matrix group are datasets containing the dimensions of the matrix, the matrix entries, as well as the features and cell-barcodes associated with the matrix rows and columns, respectively.

source_name: Lung

extract_protocol: Cellular suspensions were loaded on a GemCode Single Cell Instrument (10x Genomics, Pleasanton, CA) to generate single cell GEMs. Approximately ~1200 to 2800 cells were loaded per channel. Two biological replicates were generated per sample. Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit (now sold as P/N 120230, 120231, 120232, 10x Genomics) following the protocols outlined in Zheng et. al. Sequencing libraries were loaded at 2.1pM on an Illumina Hiseq 2500  with 2 × 100 paired-end kits using the following read length: 98bp Read1, 14bp I7 Index, 8bp I5 Index and 5bp Read2.

tag: disease

value: Healthy


title: ISS_3

description:
C06
circRNA

source_name: idiopathic short stature patient

value: idiopathic short stature

tag: age


title: lncRNA profile of case105N


title: C57BL/6_pMC+rGM-CSF_2

tag: cell type


title: TSS_2016_4_RNA

tag: treatment


title: SAMPLE 2_iPSC-derived neural cell PRDM8-/-

description:
DE65NGSUKBR106285_1
iPSC-derived neural cells after 27 days of differentiation


title: Ct_32cell_3


title: LAM_CD45Neg_rep2

value: LAM


title: ISS_2

description:
T40
circRNA


title: Ct_32cell_2


title: TSS_2016_3_RNA


title: ISS_1

description:
T03
circRNA


title: LAM_CD45Neg_rep1


title: Healthy_CD45Neg_rep2


title: Kidney_5

city: Chengdu

first: Feng

last: Li

state: Sichuan

address: No.211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer protocol. RNA degradation and contamination were monitored using 1% agarose gels.
A NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) was used to check the purity of RNA, and a Qubit® RNA Assay Kit was used on samples, which were measured using a Qubit® 2.0 Flurometer (Life Technologies, CA, USA) to measure the concentration of RNA.
RNA integrity was assessed using an RNA Nano 6000 Assay Kit for the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
A total amount of 1 μg RNA per sample was used as input material for sequencing.
Libraries were generated using an NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations; index codes were added to the attribute sequences of each sample.
Index-coded samples were then clustered on a cBot Cluster Generation System using a TruSeq PE Cluster Kit v3-cBot-HS (Illumina) in accordance with the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 150 bp paired-end reads were generated
Fastq format raw data (raw reads) were processed firstly through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing sequence reads with adaptor or ploy-N sequences with an uncertain base ratio of more than 10%, or low quality reads (reads with Qphred < 20 bases accounting for more than 50% of total read length) from raw data.
Genome_build: ailMel1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Ailuropoda melanoleuca

source_name: kidney

growth_protocol: Collection of samples from newly dead pandas

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Stored in liquid nitrogen

tag: Sex

value: kidney

tag: Cause of death

value: coronavirus infection


title: Ct_32cell_1


title: ISS_4

description:
C09
circRNA


title: TSS_2016_2_RNA


title: Ct_16cell_3

value: 16 cell


title: TSS_2016_1_RNA


title: Kidney_4


title: GTX treated rep 2

city: Rotterdam

first: Robert-Jan

last: Palstra

address: Dr. Molewaterplein 40

country: Netherlands

institute: ErasmusMC

data_processing:
Reads were mapped against the GRCh38 human reference using HiSat2 (version 2.0.4).
We called gene expression values using htseq-count  (version 0.6.1), using Ensembl transcript annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include gene expression values for each Sample.

source_name: healthy donors

growth_protocol: Primary CD4+ T cells were isolated from buffy coats from healthy donors by Ficoll gradient (GE Healthcare) followed by negative selection with RosetteSep Human CD4+ T Cell Enrichment Cocktail (StemCells Technologies). Primary CD4+ T cells were cultured in RPMI-1640 media supplemented with 7% FBS and 100 µg/ml penicillin-streptomycin at 37 oC in a humidified 95%-air-5%CO2 incubator.

extract_protocol:
Cells were lysed in TRI reagent and RNA was isolated with Total RNA Zol-out kit (A&A Biotechnology).
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded mRNA Library Prep Kit. The resulting DNA libraries were sequenced according to the Illumina TruSeq Rapid  v2 protocol on an Illumina HiSeq2500 sequencer.

treatment_protocol: Primary CD4+ T cells from two healthy blood donors were left unstimulated or stimulated with GTX [20nM] for 4 hours.

value: primary CD4+ T cells

value: 20nM Glyotoxin


title: Kidney_3


title: TSS_2017_B_RNA


title: GTX treated rep 1


title: Ct_16cell_2


title: Ct_16cell_1


title: Mock rep 2

value: Mock


title: Kidney_2

value: female

value: ileac pssion


title: TSS_2017_A_RNA


title: Kidney_1

value: ovarian cancer


title: Mock rep 1


title: Ct_8cell_4

value: 8 cell


title: TSS_2018_B_RNA

value: TSS library

value: RNA


title: Lung_5

source_name: lung

value: male

value: lung


title: Ct_8cell_3

value: embryo


title: Nthy-SEC23B-V594G, Tunica, 30 hr

city: Cleveland

first: Charis

last: Eng

state: OH

address: 9500 Euclid Avenue

department: Genomic Medicine Institute

institute: Cleveland Clinic

data_processing:
Sequencing reads were aligned to the reference human transcriptome (Genome Reference Consortium human genome build 37, hg19) using Tophat/Bowtie and then assembled into RNA transcripts using the Cufflinks package
Following computation of FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values, we calculated differential gene expression using Cuffdiff 2
We compared the treatment response per genotype (Tunicamycin relative to DMSO untreated mock control), at each time point (30 hours and day 7)
Transcripts were considered differentially expressed at q < 0.05 following Benjamini-Hochberg multiple testing correction of the original p-values
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

source_name: Nthy-SEC23B-V594G, Tunica, 30 hr

extract_protocol:
Total RNA was extracted using GeneJET RNA Purification Kit (Thermo, Catalog number:  K0731)
RNA libraries were prepared for sequencing using standard Illumina protocols. TruSeq Stranded Total RNA library prep kit

tag: cell line

value: Nthy-ori 3-1 stable cell line

value: Non-malignant thyroid

tag: genotype

value: MUT

value: Tunica

tag: time

value: 30 hr


title: TSS_2018_A_RNA


title: Nthy-SEC23B-V594G, DMSO, 30 hr

source_name: Nthy-SEC23B-V594G, DMSO, 30 hr

value: DMSO


title: TSS_2016_B2_DNA

library_source: genomic

value: DNA

tag: molecule subtype

value: plasmid DNA


title: lncRNA profile of case148N

city: GZ

first: Rui-qi

last: WANG

address: 651 DONGFENG EAST ROAD, GUANGZHOU 510060, P. R. CH

data_processing: Quantile normalization across multiple arrays,GPR normailization software, log 2 transformation of expression levels was used.

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

tag: status after 3 years

value: Alive


title: Ct_8cell_2


title: Nthy-SEC23B-WT, Tunica, 30 hr

source_name: Nthy-SEC23B-WT, Tunica, 30 hr

value: WT


title: Ct_8cell_1


title: Lung_3

value: female

tag: tissue

value: coronavirus infection


title: Lung_2

value: ileac pssion


title: TSS_2016_A2_DNA

value: TSS library


title: Lung_1

value: ovarian cancer


title: Nthy-SEC23B-WT, DMSO, 30 hr

source_name: Nthy-SEC23B-WT, DMSO, 30 hr


title: Spleen_5

source_name: spleen

value: male

value: spleen


title: TSS_2016_B1_DNA


title: TSS_2016_6_DNA


title: Spleen_3


title: Spleen_4


title: giPSC_55C1

city: Planegg-Martinsried

first: Johanna

last: Geuder

address: Großhadernerstr. 2

institute: LMU

description:
GGCAAT
mRNA
UMI_counts.txt

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017).
cDNA reads were aligned to the Human Genome (hg38) with STAR 2.6.0a.
Quantification was done with ENSEMBL gene models (GRCh38.84).
Genome_build: Human: hg38 (GRCh38), Ensembl 84
Supplementary_files_format_and_content: Cell (columns) and gene (rows) -wise UMI expression table.

organism: Gorilla gorilla

growth_protocol: Urinary cells were cultured in RE/MC medium. iPSCs were routinely cultured in StemFit+bFGF and passaged every 5 days using EDTA.

extract_protocol:
One colony was picked with a pipet and directly transferred into RLT+.
Library was constructed using a modified mcSRB protocol.

value: iPSC


title: gUDC

description:
TAAACA
mRNA
UMI_counts.txt

value: Urinary cells


title: giPSC_55D1

description:
CCCCCA
mRNA
UMI_counts.txt


title: giPSC_55A1

description:
AAATGT
mRNA
UMI_counts.txt


title: oiPSC_69A1

description:
GGCGGA
mRNA
UMI_counts.txt

organism: Pongo abelii


title: TSS_2016_4_DNA


title: TSS_2016_5_DNA


title: TSS_2016_3_DNA


title: Spleen_2


title: TSS_2016_A1_DNA


title: oUDC_70

description:
GACCCG
mRNA
UMI_counts.txt


title: Lung_4

value: lung


title: oUDC_68

description:
CTCGGG
mRNA
UMI_counts.txt


title: Liver_5

source_name: liver

value: liver


title: TSS_2016_1_DNA


title: TSS_2016_2_DNA


title: oiPSC_68A20

description:
CCCGGA
mRNA
UMI_counts.txt


title: Liver_4


title: TSS_2017_B_DNA


title: T4LP5

city: Tucson

first: Seth

middle: Alan

last: Steichen

state: AZ

address: 1140 E South Campus Dr Room 425

department: Plant Sciences

institute: University of Arizona School of Plant Sciences

data_processing:
Illumina shotgun reads were filtered using BBDuk (filterk=27, trimk=27; http://jgi.doe.gov/data-and-tools/bb-tools/) to remove adapter sequences, low quality reads, and phix contamination.
QC filtered reads were mapped to the A. protothecoides reference genome sequence using the geneious RNA mapper algorithm with the option for partial read mapping across multiple CDS annotated exon regions. For each mapped replicate read set, FPKM, RPKM, and TPM were calculated separately using the calculate expression levels tool in Geneious Prime 2019.0.4 (https://www.geneious.com).
Expression level between the time points sampled in triplicate were compared using DESeq2 by comparing average FPKM values of the biological replicates from each sampling time point.
Genome_build: GCA_000733215.1
Supplementary_files_format_and_content: tab-delimited text file includes RPKM values for each Sample

organism: Auxenochlorella protothecoides

source_name: algal biomass

growth_protocol: Algal cultures were clonally propagated from a parental line of wild type A. protothecoides (UTEX 25) cells (WT) subcultered from proteose-peptone agar plate lines into 50 mL of liquid proteose-peptone media for scale up. Proteose-peptone medium was prepared by the addition of 10ml/L from the stock solutions: 3.7g/L MgSO4, 25g/L NaNO3, 2.5g/L CaCl2∙2H2O, 17.5g/L KH2PO4, 7.5g/L K2HPO4, and 2.5g/L NaCl in 1.0 g/L of proteose-peptone solution. The pH was adjusted to 7.0 using 1M NaOH and sterilized by autoclaving. Wild type cells were harvested by centrifugation, washed twice with deionized water before resuspension in preteose peptone media containing 100 times less PO4 (0.175 g/L KH2PO4 and 0.075 g/L respectively) and 5 times less proteose (100XLP)

extract_protocol:
All algae samples (6 time points; 3 biological replicates each; 18 samples) were collected by separating biomass from liquid culturing media by centrifugation and removal of media prior to flash freezing in liquid nitrogen and storage at -80 °C. 100 mg of each sample was used for total RNA extraction using the RNeasy Plant Mini Kit (Qiagen, Valencia, CA), according to manufacturer’s instructions.
The poly(A) RNA was isolated from 2 μg of the total RNA from each treatment sample using magnetic oligo (dT) beads. Following purification, the mRNA was fragmented by zinc treatment at 94 °C for 4 min and reverse-transcribed to synthesize first strand cDNA using SuperScript II reverse transcriptase (Invitrogen) and random primers. Second-strand cDNA synthesis was performed, with the products then being subjected to end-repair and phosphorylation, and addition of an “A” base to the 3´ end of the blunt phosphorylated DNA fragments. Illumina multiple indexing adapters were ligated to the fragments, as described by Illumina’s TruSeq RNA Sample Prep Kit v2 Guide (Illumina, Cat. # RS-122-2002). The cDNA fragments flanked by Illumina PE adapters were selected and purified by AMPure XP beads for downstream enrichment. The cDNA fragments were amplified by PCR Primers PE 1.0 and PE 2.0 (Illumina) that anneal to the ends of the adapters, using the PCR program of 30 s at 98 °C followed by 15 cycles of 10 s at 98 °C, 30 s at 60 °C, 30 s at 72 °C and a final elongation step of 5 min at 72 °C. The products were purified using AMPure XP beads to create an Illumina RNA-seq library.

treatment_protocol: The liquid cell cultures were normalized to 0.1 optical density at 750nm (OD 750) and inoculated into five replicated 1L photobioreactors (PBRs). Samples were collected on alternating days by removing 20% of the total culture volume and replacing it with the same volume of 100XLP media.

tag: media

tag: timepoint

tag: replicategroup


title: Liver_3


title: oiPSC_70Ab1

description:
ATATTC
mRNA
UMI_counts.txt


title: TSS_2017_A_DNA


title: Liver_2


title: Upstream_B_RNA

description:
processed data file:
Upstream_countedMappedBarcodes_200806.txt.gz
Upstream_countedBarcodesMappedToDesign_200806.txt.gz

value: Upstream library

value: RNA


title: T4LP4


title: T4LP1


title: Liver_1


title: Upstream_A_RNA


title: T3LP5


title: T3LP4


title: Upstream_3_RNA


title: Upstream_4_RNA


title: Heart_4

source_name: heart

value: heart


title: oiPSC_70Af1

description:
AACTAA
mRNA
UMI_counts.txt


title: Heart_3


title: T3LP1


title: Spleen_1


title: Heart_5


title: Upstream_2_RNA


title: T2LP5


title: Heart_2


title: Heart_1


title: Upstream_B_DNA

value: DNA

value: plasmid DNA


title: Upstream_1_RNA


title: T2LP1


title: T2LP4


title: sync64; 2_55hr

city: College Station

first: Thomas

middle: R

last: Ioerger

state: TX

address: 3112 TAMUS

department: Department of Computer Science

institute: Texas A&M University

data_processing:
The reads were mapped to the H37Rv genome using BWA (Burroughs Wheeler Aligner; Li and Durbin, 2009) with default parameter settings. Reads mapping to each ORF were totaled (sense-strand only). Because certain loci were over-represented (e.g. rrs, rnpB, ssr, Rv3661), with 0.5-1.0 million reads each, counts were truncated to a maximum coverage of 10,000 (reads/nt).  Gene abundances were normalized across all timepoints and replicates using DESeq2 (Love, Huber, Anders, 2014).
Genome_build: NC_000962.3
Supplementary_files_format_and_content: total_deseq_norm.xlsx contains normalized gene abundances for all samples

organism: Mycobacterium tuberculosis

source_name: in vitro thermal shift

growth_protocol: Cultures of Mtb H37Rv and dnaAcos115 (mutant strain generated in a previous study, Nair et al, 2009, Mol Micro, 71(2):291-304) were grown in standard culture media at 37ºC under shaking conditions till OD600 0.4.

extract_protocol:
At each timepoint, 45ml culture was pelleted and resuspended in 1ml of TRIzol (Invitrogen) and transferred to lysing matrix tubes (MP Biomedicals: Lysing Matrix B). Cells were lysed in a MP Biomedicals Fast Prep-24 homogenizer (maximum power-6.5, 4 X 30s cycles, rest on ice for 5 minutes in between cycles). RNA was purified according to the manufacturer?s directions. RNA cleanup was performed with Qiagen RNeasy Mini kit 27 (74104) omitting the DNase step. Instead, after elution, in-tube DNase treatment was performed using Ambion DNase Turbo. RNeasy cleanup was repeated again with double volumes of RLT and ethanol. RNA was subjected to rRNA removal with Ribozero Bacteria kit (Illumina-MRZB12424).
Deep sequencing library was prepared using KAPA Stranded RNASeq kit (KK8401).

treatment_protocol: The cells were shifted to 30ºC for 36 hours. The cultures were then shifted to 37ºC and the cultures were processed for  RNA isolation at the following times: 0h, 3h, 6.5h, 9h, 12h, 18.5h, 21h, 27h, 31h, 33h, 36h, 39.5h, 42h, 45.5h, 52h and 55h.

value: H37Rv (wt)

tag: replicate


title: sync63; 2_52hr


title: Upstream_3_DNA

tag: strain


title: T1LP5


title: T1LP4


title: Upstream_1_DNA


title: T1LP1


title: sync62; 2_45.5hr


title: T0LP5


title: sync59; 2_36hr


title: T0LP1


title: T0WT3

value: P


title: T0WT2


title: sync60; 2_38.5hr


title: T0LP4


title: sync58; 2_33h


title: sync57; 2_31hr


title: sync54; 2_18.5hr


title: sync55; 2_21hr


title: sync56; 2_27hr


title: hUDC_65

description:
CCGCGA
mRNA
UMI_counts.txt


title: hiPSC_11C2

description:
TCGAAG
mRNA
UMI_counts.txt


title: Upstream_A_DNA


title: hiPSC_1383D2

description:
TTATGT
mRNA
UMI_counts.txt


title: sync53; 2_12hr


title: hiPSC_64A1

description:
TAATCT
mRNA
UMI_counts.txt


title: sync52; 2_9hr


title: sync51; 2_6.5hr


title: sync61; 2_42hr


title: hiPSC_12C2

description:
ATTAAG
mRNA
UMI_counts.txt


title: No BirA

city: Berkeley, CA

first: Siheng

last: Xiang

state: California

address: 1 Barker Hall

institute: UC Berkeley

description: N

data_processing:
ChIP seq reads were aligned to yeast genome by bowtie2.
Trace file were generated using bamCoverage.
Genome_build: S288C (sacCer3)
Supplementary_files_format_and_content: Trace files in bigWig

source_name: nocodazole arrested yeast

growth_protocol: Cells grown in synthetic complete medium with low biotin and 2% Raffinose, arrested in 1.2 ug/ml nocodazole for 3 hours at 30 degree, and then in synthetic complete medium with low biotin and 2% galactose for one hour.

extract_protocol: Lysates were bead beated 40s x 2. Chromatin were harvested by centrifuge at 15000 rmp for 10 minutes, sheared on Bioruptor Pico, and clarified by centrifuge again at 15000 rpm for 10 minutes.

treatment_protocol: Cells were treated with 10 nM biotin for 10 minutes at 30 degree, then fixed with 1% formaldehyde for one hour at room temperature.

tag: background

tag: expression

value: No BirA

tag: ChIP

value: streptavidin


title: NLS-BirA

description: P

value: NLS-BirA


title: T0WT1


title: Smc3p-BirA

description: O


title: hiPSC_63Ab1

description:
GTGACT
mRNA
UMI_counts.txt

tag: cell type


title: C-Control

city: Guangzhou

first: Jingsong

last: Ou

state: Please Select

address: 58 Zhong Shan Er Road

department: Surgery/Cardiac Surgery

institute: The First Affiliated Hospital, Sun Yat-sen University

hyb_protocol: Hybridized to the miRCURY™ locked-nucleic acid arrays.

scan_protocol: Raw data were analysed using a Axon GenePix 4000B microarray scanner.

data_processing:
Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction.Replicated miRNAs were averaged and miRNAs that intensities>=50 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the median normalization. After normalization, differentially expressed miRNAs were identified through fold change filtering.
The threshold value used to screen differentially expressed miRNAs was a fold change of >=1.5 or <=0.5, and a normalized signal value indicating a relative abundance to the transcript of >=2.0.

source_name: Human umbilical vein endothelial cells

label_protocol: Total RNA was labeled with miRCURY™ Hy3™/Hy5™ Power labeling kit.

growth_protocol: HUVECs were cultured in a complete DMEM, supplemented with 25ml FBS (Fetal bovine serum, FBS), 5ml growth factor supplements (endothelial cell growth supplement, ECGS), 5ml penicillin/streptomycin double antibody), and maintained at 37℃ with 5% CO2.

extract_protocol: Total RNA was isolated from cell lysates by TRIzol® reagent (Invitrogen, 15596-026) and quantified using Nanodrop spectrophotometer.

treatment_protocol: Cultured passage 4-6 HUVECs were serum starved 12 hours, Cells were treated with PBS and HDL (100μg/ml) for 24 h.

value: Human umbilical vein endothelial cells

tag: treatment

value: C-Control


title: hUDC_63

description:
TAACTT
mRNA
UMI_counts.txt


title: myb30_systemic_30min_3

city: Memphis

first: Soham

last: Sengupta

state: TN

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description: myb30 systemic

data_processing:
Base calling was done with RTA3 implemeation software in the NovaSeq 6000 system
3' trimming for Illumina adapters was performed using cutadapt v1.18
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample

organism: Arabidopsis thaliana

source_name: Arabidopsis leaves

growth_protocol: 4-week-old plants grown on soil; 10hr/14hr light/dark regime; 21-24C

extract_protocol:
leaves were flash frozen in liquid nitrogen; frozen samples were ground and RNA was extracted using Qiagen Plant Rneasy kit (Cat#74904)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: repeat

value: No treatment

value: mutant

value: Leaves

tag: molecule

value: total RNA


title: sync48; 1_55hr

tag: genotype


title: P-Proinflammatory

value: P-Proinflammatory


title: hiPSC_64Ab1

description:
TTAGAA
mRNA
UMI_counts.txt

value: iPSC


title: myb30_systemic_30min_2

description: myb30 systemic

tag: time


title: sync50; 2_3hr


title: hiPSC_65A3

description:
GGACGC
mRNA
UMI_counts.txt


title: sync46; 1_45.5hr


title: sync47; 1_52hr


title: myb30_systemic_8min_3

description: myb30 systemic


title: sync45; 1_42hr


title: hiPSC_29B5

description:
CGTGCC
mRNA
UMI_counts.txt


title: myb30_systemic_8min_2

description: myb30 systemic


title: N-Normal

value: N-Normal


title: hiPSC_65B4

description:
TTAAGA
mRNA
UMI_counts.txt


title: sync49; 2_0hr


title: sync43; 1_36hr


title: myb30_systemic_30min_1

description: myb30 systemic


title: hiPSC_63Ab2.2

description:
AAACTA
mRNA
UMI_counts.txt


title: sync44; 1_38.5hr


title: lncRNA profile of case170N

state: Guangdong

institute: SUN YAN-SEN UNIVERSITY CANCER CENTER

source_name: non-small-cell lung cancer

value: Alive


title: myb30_systemic_2min_3

description: myb30 systemic


title: IC8-L1597H-4h-MAML1-input

city: Boston

first: Li

last: Pan

state: MA

address: 77 Ave Louis Pasteur

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Reads were trimmed with Trim Galore (v.0.3.7 using cutadapt v.1.8), assessed for quality with FastQC (v.0.11.3), and aligned to GRCh38/hg38 with bowtie (v.2.0.0).
Peaks were identified using MACS2 (v.2.1.1) and annotated using Homer (v3.12, 6-8-2012).
Genome_build: hg38
Supplementary_files_format_and_content: bw files

source_name: Squamous cell carcinoma (SCC) cells

growth_protocol: Cells were grown in keratinocyte medium with 1 μM GSI (compound E).

extract_protocol:
Chromatin was prepared and immunoprecipitated with antibodies against MAML1 or RBPJ and Dynabeads bearing sheep anti-rabbit Ig (Thermo Fisher Scientific).
NEBNext Ultra II DNA Library Prep Kit (New England BioLabs)

treatment_protocol: GSI washout was performed for 4 hours.

value: SCC IC8 cells

tag: cell line

tag: chip antibody

value: GSI washout for 4h


title: myb30_systemic_2min_2

description: myb30 systemic

tag: tissue


title: hUDC_64

description:
ATCTTA
mRNA
UMI_counts.txt

value: Urinary cells


title: sync42; 1_33h

value: H37Rv (wt)


title: sync40; 1_27hr


title: myb30_systemic_2min_1

description: myb30 systemic


title: myb30_systemic_0min_3

description: myb30 systemic


title: myb30_systemic_0min_1

description: myb30 systemic


title: myb30_systemic_0min_2

description: myb30 systemic


title: IC8-L1597H-0h-RBPJ-input

value: GSI (Compound E 1 microM)


title: sync38; 1_18.5hr


title: sync37; 1_12hr


title: myb30_local_30min_3

description: myb30 local

value: High light stress


title: sync35; 1_6.5hr


title: sync36; 1_9hr


title: lung_M2+V

city: Chicago

first: Joyce

middle: huanhuan

last: Chen

state: IL

address: 5801 S Ellis Ave, Chicago

department: Pritzker School of Molecular Engineering

institute: Uchicago

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus virus sequence and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: RUES2-derived lung cells and M2 macrophages co-culture with SARS-CoV-2 infection

growth_protocol: RUES2 cells were differentiated to endoderm, anterior foregut endoderm, lung progenitor cells and functional lung cells using growth factor cocktails inclduing Activin A, CHIR, DSW, IWP2, FGF10, KFG, DAPT  etc.RUES2 cells were differentiated to  functional macrophages using growth factor cocktails inclduing BMP, CHIR, FGF2,VEGF,SB431542,IL3,M-CSF  etc

extract_protocol:
Single-cell suspensions were generated by dissociating the cultured RUES2 cells with 0.05% Trypsin/0.02% EDTA for 10-15 min, followed with passing through 40µM strainer.
Single-cell capture, reverse transcription, cell lysis, and library preparation was performed using the Single Cell 3' version 2 kit and chip according to the manufacturer’s protocol (10x Genomics)
scRNA-seq

treatment_protocol: For macrophage polarization, monocytes from differentiating day13-15 were treated with 10ng/ml IFNγ+100ng/ml LPS to genarate M1 macrophages, 20ng/ml IL4 to generate M2 macrophages,respectively. To assay pseudotyped virus infection on co-culture system, Pseudotyped virus was added at MOI=0.01 plus polybrene at a final concentration of 8 μg/mL for 30hrs.

value: WT

tag: infection

value: SARS-CoV-2 infection


title: myb30_local_30min_2

description: myb30 local


title: myb30_systemic_8min_1

description: myb30 systemic


title: sync34; 1_3hr

tag: timepoint


title: myb30_local_30min_1

description: myb30 local


title: myb30_local_8min_3

description: myb30 local


title: lung_M1+V

source_name: RUES2-derived lung cells and M1 macrophages co-culture with SARS-CoV-2 infection


title: myb30_local_8min_2

description: myb30 local


title: sync33; 1_0hr


title: myb30_local_8min_1

description: myb30 local


title: IC8-L1597H-4h-RBPJ-input


title: sync41; 1_31hr


title: RA2d_SAG1_d21_2

city: Stockholm

first: Johan

last: Ericson

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Instituet

data_processing:
The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite
Gene level abundances were estimated as FPKMs using StringTie
The read summarization to each gene (i.e. counts) was calculated using featureCounts
Multiple ENSEMBL gene IDs were summed up per known HUGO gene symbol
Genome_build: Reads were mapped to the human genome assembly, build GRCh37 using STAR (v 2.6.1a)
Supplementary_files_format_and_content: FPKM in txt format

source_name: Neural progenitor cells

growth_protocol: hESCs were differentiated in N2B27 medium in different conditions.

extract_protocol:
total RNA, Quick-RNA Mini Prep Plus kit (Zymo Research)
Illumina TruSeq Stranded mRNA
poly-A selection

treatment_protocol: RA was added (or not added in the control) to culture for 1, 2, or 4 days of the differentiation. The cells were treated also with inhibitors of TGFb and BMP signaling and the activator of SHH signaling SAG1.3

tag: line

tag: Stage

value: 21 day

value: RA 2 days, SAG  d1-9


title: sync32; 2_55hr

value: dnaA cold-sensitive mutant (cos)

tag: replicate


title: sync39; 1_21hr


title: RA2d_SAG1_d21_1


title: myb30_local_2min_2

description: myb30 local

value: mutant

value: Leaves


title: sync31; 2_52hr


title: myb30_local_2min_3

description: myb30 local

value: total RNA


title: sync30; 2_45.5hr


title: sync29; 2_42hr


title: RA2d_SAG1_d14_2

value: 14 day


title: myb30_local_2min_1

description: myb30 local


title: RA2d_SAG1_d14_1


title: sync28; 2_38.5hr


title: sync26; 2_33h


title: sync27; 2_36hr


title: RA2d_SAG1_d12_2

value: 12 days


title: myb30_local_0min_3

description: myb30 local


title: myb30_local_0min_2

description: myb30 local


title: sync25; 2_31hr


title: RA4d_SAG0_d9_2

value: 9 days

value: RA 4 days, SAG  d0-9


title: RA2d_SAG1_d12_1


title: sync24; 2_27hr


title: Col_systemic_30min_3

description: Col systemic

value: No treatment

value: wild type


title: Col_systemic_30min_2

description: Col systemic


title: RA1d_SAG0_d9_2

value: RA 1 day, SAG  d0-9


title: Col_systemic_8min_3

description: Col systemic


title: sync22; 2_18.5hr


title: RA1d_SAG0_d9_1


title: RA0d_SAG0_d9_2

value: No RA, SAG  d0-9


title: sync21; 2_12hr


title: Col_systemic_30min_1

description: Col systemic


title: Col_systemic_8min_2

description: Col systemic


title: sync20; 2_9hr


title: Col_systemic_8min_1

description: Col systemic


title: sync19; 2_6.5hr


title: RA2d_SAG1_d9_2


title: RA0d_SAG0_d9_1


title: Col_systemic_2min_3

description: Col systemic


title: myb30_local_0min_1

description: myb30 local

value: High light stress


title: RA2d_SAG0_d9_2

value: RA 2 days, SAG  d0-9


title: sync18; 2_3hr


title: Col_systemic_2min_2

description: Col systemic


title: sync16; 1_55hr


title: sync17; 2_0hr


title: RA2d_SAG0_d9_1


title: sync23; 2_21hr


title: sync15; 1_52hr


title: Col_systemic_2min_1

description: Col systemic


title: RA4d_SAG0_d9_1


title: Col_systemic_0min_3

description: Col systemic


title: sync13; 1_42hr


title: sync12; 1_38.5hr


title: Col_local_30min_3

description: Col local


title: Col_local_30min_2

description: Col local


title: sync10; 1_33h


title: sync9; 1_31hr


title: Col_local_8min_3

description: Col local


title: sync8; 1_27hr


title: Col_local_8min_2

description: Col local


title: sync7; 1_21hr


title: Col_local_8min_1

description: Col local


title: RA2d_SAG1_d9_1


title: Col_local_2min_3

description: Col local


title: Col_local_2min_2

description: Col local


title: sync6; 1_18.5hr


title: SH2-PTK6 + HGF

type: protein

first: Carol

last: Lange

state: Minnesota

address: 2231 6th St SE

department: Medicine

scan_protocol: Sample spots in tiff images were identified and their densities quantified by Array-Pro Analyzer.

data_processing:
All relative protein level data points were normalized for protein loading and transformed to linear values, which are designated Normalized Linear in the Excel worksheet labeled “NormLinear.”
Relative protein levels for each sample were determined by interpolating each dilution curve produced from the densities of the 5-dilution sample spots using a standard curve (SuperCurve) for each slide (antibody).  SuperCurve is constructed by a script in R, written by Bioinformatics.  Relative protein levels are designated as log2 values and are in the Excel worksheet labeled RawLog2.

molecule: protein

source_name: human cell line_MDA-MB-231

label_protocol: Stained slides were scanned on a Huron TissueScope scanner to produce 16-bit tiff images.

growth_protocol: MDA-MB-231 expressing either wt-GR or S134A-GR were serum starved in IMEM containing 1% DCC for 18 hrs.

extract_protocol: Total protein was extracted with RIPA-lysis buffer and stained slides qauntification was doned by Array-Pro-Analyzer

treatment_protocol: Cells were treated with vehicle treatment or either 50 ng/mL of HGF for 6 hrs.

value: HGF


title: PTK6 KO + HGF


title: PTK6 KO + veh

value: Vehicle


title: KM-PTK6 + HGF


title: sync14; 1_45.5hr


title: sync5; 1_12hr


title: WT + veh


title: WT + HGF


title: Col_systemic_0min_1

description: Col systemic


title: sync11; 1_36hr


title: Col_local_0min_3

description: Col local


title: sync3; 1_6.5hr


title: sync4; 1_9hr


title: Col_local_0min_2

description: Col local


title: Col_local_30min_1

description: Col local


title: SH2-PTK6 + veh


title: sync1; 1_0hr


title: Col_local_0min_1

description: Col local


title: Col_systemic_0min_2

description: Col systemic


title: KM-PTK6 + veh


title: Col_local_2min_1

description: Col local


title: Ramos EBV-WT rep2

status: Public on Aug 30 2020

city: guangzhou

first: Ersheng

last: Kuang

address: No. 74, 2nd Yat-Sen Road Yuexiu District, Guangzhou City, Guangdong Province, 510080, PRC

institute: Sun Yat-Sen University

data_processing:
Molecule Annotation System 3.0 (MAS 3.0; Annoroad Gene Technology Co., Ltd, Beijing, China) software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
HTSeq was used for read count and RPKM calculation.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: wild type EBV primary infected B lymphoma cells

extract_protocol:
Ramos cells were left uninfected or infected with EBV-WT or EBV-ΔBRLF1 virus at a high titer (MOI=100). Twenty-four hour later, total RNAs were extracted in two independent experiments with TRIzol following the manufacturer’s procedure, and approximately 10 μg of total RNAs were subjected to deep RNA sequencing.
Library construction and sequencing were performed by Annoroad Gene Technology (Beijing, China). The libraries were sequenced on an Illumina HiSeq-Xten platform and 150 bp paired‐end reads were generated. Data analysis was performed with Molecule Annotation System 3.0 (MAS 3.0; Annoroad Gene Technology Co., Ltd, Beijing, China).

value: B lymphoma cell

value: Ramos cells

value: EBV-WT infected


title: Ramos WT rep1

source_name: primary mock infected B lymphoma cells

value: uninfected


title: Ramos EBV-WT rep1


title: Ramos EBV-ΔBRLF1 rep1

source_name: BRLF1-deficient EBV primary infected B lymphoma cells

value: EBV-delta_BRLF1 infected


title: Ramos EBV-ΔBRLF1 rep2


title: Healthy_conjunctiva_S4_replicate 4

city: Freiburg

first: Clemens

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human reference genome (hg38, gencode release 32) with RNA STAR Galaxy Version 2.7.2b (default parameters) using the Gencode annotation file (Gencode 32)
Reads mapped to the human reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL release 98 (Human genes, GRCh38.p12, download on 11/19/2019). Genes without ENTREZID were removed from analysis. Batch effects were removed by the limma function removeBatchEffect and by considerung in the linear model of Deseq2. After principal component analysis, differential gene expression with Benjamini-Hochberg adjusted (adj.) p-values was analyzed using the R package DESeq2 Version 1.22.2 24 with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: normalized reads

source_name: Healthy conjuncitva

extract_protocol:
Total RNA was isolated from ten to fifteen formalin-fixed and paraffin-embedded (FFPE) 4-µm-thick sections of all specimens using the Quick-RNA FFPE Kit (Zymo Research, USA). Following a DNAse I digestion using the Baseline-ZERO kit (Epicentre, USA), the RNA concentration was measured with the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, USA). The RNA quality was determined with the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, USA). The fragment size of all RNA samples ranged between 120 and 150 bp.
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3' RNA sequencing method. The preparation of MACE libraries was carried out using 1 µg of total RNA, as previously described. The barcoded libraries were sequenced simultaneously on the NextSeq 500 (Illumina, USA) with 1× 75 bp. PCR bias was removed using an unique molecular identifier.

value: Healthy conjuncitva


title: Healthy_conjunctiva_S8_replicate 8


title: Healthy_conjunctiva_S6_replicate 6


title: Healthy_conjunctiva_S7_replicate 7


title: Healthy_conjunctiva_S3_replicate 3


title: sync2; 1_3hr

value: dnaA cold-sensitive mutant (cos)


title: Melanoma_poor_prognosis_S6_replicate 6

source_name: Conjunctival melanoma

value: Conjunctival melanoma

tag: prognosis

value: poor


title: Melanoma_poor_prognosis_S4_replicate 4


title: Healthy_conjunctiva_S2_replicate 2


title: Silence_Gene_A_rep1

city: Shenyang

first: Ning

last: Sun

state: Liao Ning Province

address: No.77, Puhe Road

department: Institute of life sciences

institute: China Medical University

data_processing:
Illumina Hiseq X 10 sequencer used for basecalling.
Raw data clean: Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Parameter: ILLUMINACLIP:{adaptor.fa}:2:30:10  -phred33 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 HEADCROP:0 MINLEN:36 PE
UMI deduplication: For eliminating duplication using UMI, UMI_soft (in-house) (version.1.0) was used. Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster, resulting in 65,536 clusters. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. Parameter: Default Parameter (developed by Wuhan Seqhealth Co., Ltd.)
Clean data mapping: The de-duplicated consensus sequences were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters (--outSAMtype BAM SortedByCoordinate).
Gene expression calculation: Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated. Parameter: -T 10 -d 30 -D 1000 -C -s 1 -t {exon} -g {geneid} --primary -O -a {gff_annotation_file}
Differential expression analysis: Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). A FDR corrected p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Genome_build: Homo_sapiens.GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Hepatoma

growth_protocol: HCCLM3 cells were cultured in the incubator with 37℃ temperature and 5% CO2 supply. The cell cultrure medium was DMEM with 10% FBS serum.

extract_protocol:
The cell medium was removed and the cells were harvested with 1ml RNA Trizol reagent purchased from Ambion corporation. Finally the cell RNA extract was stored under -80℃ temperature and ready for further RNA purification and sequencing.
poly-A-tailed mRNA selection (PA)

treatment_protocol: HCCLM3 cells were separated into two groups named as shcontrol and shATXN7L3. two groups were cultured with 1mL antibiotic free medium and transfected with lentivirus-delivered shcontrol and lentivirus-delivered shATXN7L3 respectively. After 16 hours culture, the medium was removed and replaced with 2mL fresh medium.


title: Silence_control_rep2

value: shcontrol


title: Silence_control_rep3


title: Silence_control_rep1


title: Melanoma_poor_prognosis_S3_replicate 3


title: Silence_Gene_A_rep2


title: Silence_Gene_A_rep3


title: Ramos WT rep2


title: Melanoma_poor_prognosis_S2_replicate 2


title: Healthy_conjunctiva_S5_replicate 5


title: Melanoma_good_prognosis_S6_replicate 6

value: good


title: Melanoma_good_prognosis_S5_replicate 5


title: Melanoma_poor_prognosis_S1_replicate 1


title: Melanoma_good_prognosis_S4_replicate 4


title: Melanoma_good_prognosis_S2_replicate 2


title: Melanoma_poor_prognosis_S5_replicate 5


title: Healthy_conjunctiva_S1_replicate 1


title: Melanoma_good_prognosis_S1_replicate 1


title: EN5C389; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep13

city: San Francisco

first: Elphege

last: Nora

state: CA

address: 555 Mission Bay Boulevard South

department: Cardiovascular Research Institute

institute: University of California San Francisco

data_processing:
Library strategy: 5C
ChIP-seq. Fastq files were trimmed using the fastq-mcf program, aligned to the mm9 reference genome with bowtie2 (Langmead and Salzberg, 2012). Reads with a mapq score of 30 or greater were retained, using Samtools. PCR duplicates were filtered out.  CTCF (FLAG) peaks were called using the geome wide Event finding and Motif Discovery (GEM) algorithm.
We processed each Hi-C dataset using distiller (https://github.com/mirnylab/distiller, doi:10.5281/zenodo.3350937), mapping reads to mm10 and saving processed data in the cooler format.
5C. Adapters were trimmed and aligment was performed using Bowtie2 against a pseudo-genome composed of all possible Forward-Reverse pairs of 5C oligonucleotides and matrices were analyzed using my5C (Lajoie et al. 2009 Nature Methods).
Genome_build: mm9 for ChIP-seq
Genome_build: custon 5C genome for 5C (provided as supplementary information) positions referring to mm9
Genome_build: mm10 for Hi-C
Supplementary_files_format_and_content: Hi-C .cool: valid Hi-C pairs mapped at 10kb resolution
Supplementary_files_format_and_content: ChIP-seq .bed: position of the CTCF (FLAG) peaks.
Supplementary_files_format_and_content: 5C - for all forward-reverse possible ligation pair we provide one file with raw 5C counts (not read normalized, including anchors ultimately removed from analysis), and one file with filtered symmetrical read-normalized balanced (Iterative Correction method - ICE) matrices.

source_name: mouse ES cells, line EN133.10

growth_protocol: E14Tg2a (karyotype 19, XY; 129/Ola isogenic background) and subclones were cultured in DMEM+Glutamax (ThermoFisher cat 10566-016) supplemented with 15% Fetal Bovine Serum (ThermoFisher SH30071.03), 550µM b-mercaptoethanol (ThermoFisher 21985-023), 1mM Sodium Pyruvate (ThermoFisher 11360-070), 1X non-essential amino-acids (ThermoFisher 11140-50) and 104U of Leukemia inhibitory factor (Millipore ESG1107). Cells were maintained at a density of 0.2-1.5x105 cells / cm² by passaging using TrypLE (12563011) every 24-48h on 0.1% gelatin-coated dishes (Millipore cat ES-006-B) at 37°C and 7% CO2. Medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
For ChIP-seq and Hi-C cells were  trypsinized and fixed in suspension; For 5C cells were fixed in tissue culture plates and scrapped off
ChIP libraries were prepared using standard Illumina protocols;5C (in-situ ligation with HindIII) and Hi-C (dilution ligation, Arima genomics kit) were assembled based on Illumina-compatible protocols. Detailed experimental procedures can be found in the supplementary information of the linked manuscript

treatment_protocol: For induction of the auxin-inducible degron indole-3-acetic acid (IAA, chemical analog of auxin) was added in the medium at 500µM from a 1000X stock diluted in sterile water and kept at 4°C up to 4 weeks or -20°C for long term storage. Doxycycline was added at 1ug/ml final from a 1mg/ml stock.


title: EN5C394; 5C_CTCF-AID_TetO-CTCF(Y226A-F228A) clone 1_auxin+dox4days_rep1

source_name: mouse ES cells, line EN297.3


title: EN5C391; 5C_CTCF-AID_TetO-CTCF(Del_1-265)_auxin+dox4days_rep6

source_name: mouse ES cells, line EN186.4


title: EN5C388; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep12


title: EN5C390; 5C_CTCF-AID_TetO-CTCF(Del_1-265)_auxin+dox4days_rep5


title: EN5C368; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 2_auxin+dox4days_rep4

source_name: mouse ES cells, line EN281.2


title: EN5C396; 5C_CTCF-AID_TetO-CTCF(del_13-33-Y226A-F228A) clone 1_auxin+dox4days_rep1

source_name: mouse ES cells, line EN298.4


title: EN5C392; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep5

source_name: mouse ES cells, line EN281.1


title: EN5C397; 5C_CTCF-AID_TetO-CTCF(del_13-33-Y226A-F228A) clone 1_auxin+dox4days_rep2


title: EN5C395; 5C_CTCF-AID_TetO-CTCF(Y226A-F228A) clone 1_auxin+dox4days_rep2


title: EN5C365; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep3


title: EN5C363; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep3


title: EN5C366; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep4


title: EN5C361; 5C_endogenous CTCF(Delta13-33)-AID, Tir1 clone 2_untreated_rep3

source_name: mouse ES cells, line EN277.2

value: untreated


title: EN5C360; 5C_endogenous CTCF(Delta13-33)-AID, Tir1 clone 1_untreated_rep4

source_name: mouse ES cells, line EN277.1


title: EN5C362; 5C_endogenous CTCF(Delta13-33)-AID, Tir1 clone 2_untreated_rep4


title: Melanoma_good_prognosis_S3_replicate 3


title: EN5C367; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 2_auxin+dox4days_rep3


title: EN5C359; 5C_endogenous CTCF(Delta13-33)-AID, Tir1 clone 1_untreated_rep3


title: EN5C358; 5C_CTCF-AID, Tir1_untreated_rep4

source_name: mouse ES cells, line EN52.9.1

value: CTCF-AID, Tir1


title: EN5C356; 5C_endogenous CTCF(Delta13-33) clone 2_untreated_rep4

source_name: mouse ES cells, line EN276.5

value: endogenous CTCF(Delta13-33) clone 2


title: EN5C355; 5C_endogenous CTCF(Delta13-33) clone 2_untreated_rep3


title: EN5C393; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep6


title: EN5C354; 5C_endogenous CTCF(Delta13-33) clone 1_untreated_rep4

source_name: mouse ES cells, line EN276.4

value: endogenous CTCF(Delta13-33) clone 1


title: EN5C301; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 2_auxin+dox4days_rep2


title: EN5C352; 5C_WT parental_untreated_rep4

source_name: mouse ES cells, line E14Tg2a

value: WT parental


title: EN5C300; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 2_auxin+dox4days_rep1


title: EN5C299; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep2


title: EN5C364; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep4


title: EN5C298; 5C_CTCF-AID_TetO-CTCF(Del_13-33) clone 1_auxin+dox4days_rep1


title: EN5C297; 5C_CTCF-AID_TetO-CTCF(Del_1-31) clone 2_auxin+dox4days_rep2

source_name: mouse ES cells, line EN280.2


title: EN5C296; 5C_CTCF-AID_TetO-CTCF(Del_1-31) clone 2_auxin+dox4days_rep1


title: EN5C295; 5C_CTCF-AID_TetO-CTCF(Del_1-31) clone 1_auxin+dox4days_rep2

source_name: mouse ES cells, line EN280.1


title: EN5C280; 5C_endogenous CTCF(Del_13-33)-AID, Tir1 clone 1_untreated_rep2


title: EN5C294; 5C_CTCF-AID_TetO-CTCF(Del_1-31) clone 1_auxin+dox4days_rep1


title: EN5C283; 5C_endogenous CTCF(Del_13-33)-AID, Tir1  clone2_untreated_rep1


title: EN5C279; 5C_endogenous CTCF(Del_13-33)-AID, Tir1 clone 1_untreated_rep1


title: EN5C273; 5C_endogenous CTCF-Delta(13-33) clone 2_untreated_rep1

value: endogenous CTCF-Delta(13-33) clone 2


title: EN5C276; 5C_CTCF-AID, Tir1_untreated_rep2


title: EN5C274; 5C_endogenous CTCF-Delta(13-33) clone 2_untreated_rep2


title: EN5C275; 5C_CTCF-AID, Tir1_untreated_rep1


title: EN5C271; 5C_endogenous CTCF-Delta(13-33) clone 1_untreated_rep1

value: endogenous CTCF-Delta(13-33) clone 1


title: EN5C269; 5C_WT parental_untreated_rep1


title: EN5C291; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox4days_rep4


title: EN5C220; 5C_CTCF-AID_TetO-CTCF(N/C-term-swap)_auxin+dox4days_rep1

source_name: mouse ES cells, line EN187.3


title: EN5C289; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep11


title: EN5C219; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN186.6


title: EN5C290; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox4days_rep3


title: EN5C221; 5C_CTCF-AID_TetO-CTCF(N/C-term-swap)_auxin+dox4days_rep2


title: EN5C217; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox4days_rep2


title: EN5C216; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone1)_auxin+dox4days_rep1


title: EN5C293; 5C_CTCF-AID_TetO-CTCF(Del_1-265)_auxin+dox4days_rep4


title: EN5C218; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox4days_rep1


title: EN5C215; 5C_CTCF-AID_TetO-CTCF(Full-length_low_expression)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN133.6


title: EN5C212; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep8

source_name: mouse ES cells, line EN133.10


title: EN5C213; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep9


title: EN5C211-2; 5C_CTCF-AID_TetO-CTCF(Del_576-614)_auxin+dox4days_rep3

source_name: mouse ES cells, line EN142.1


title: EN5C214; 5C_CTCF-AID_TetO-CTCF(Full-length_low_expression)_auxin+dox4days_rep1


title: EN5C292; 5C_CTCF-AID_TetO-CTCF(Del_1-265_clone2)_auxin+dox4days_rep3


title: EN5C206; 5C_CTCF-AID_TetO-CTCF(Sumoylation_deficient_2_K74R_Del_615-736)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN254.1


title: EN5C205; 5C_CTCF-AID_TetO-CTCF(Sumoylation_deficient_2_K74R_Del_615-736)_auxin+dox4days_rep1


title: EN5C204; 5C_CTCF-AID_TetO-CTCF(Sumoylation_deficient_1_K74R_Del_576-614)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN253.2


title: EN5C210-2; 5C_CTCF-AID_TetO-CTCF(Del_576-614)_auxin+dox4days_rep2


title: EN5C208; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep6


title: EN5C203; 5C_CTCF-AID_TetO-CTCF(Sumoylation_deficient_1_K74R_Del_576-614)_auxin+dox4days_rep1


title: EN5C201; 5C_CTCF-AID_TetO-CTCF(Mut_Parylation)_auxin+dox4days_rep1

source_name: mouse ES cells, line EN252.4


title: EN5C202; 5C_CTCF-AID_TetO-CTCF(Mut_Parylation)_auxin+dox4days_rep2


title: EN5C200; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep5


title: EN5C161; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep3


title: EN5C195; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin4days_rep1


title: EN5C196; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin4days_rep2


title: EN5C199; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep4


title: EN5C159; 5C_CTCF-AID_TetO-CTCF(H288R)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN216.1


title: EN5C160; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep2


title: EN5C270; 5C_WT parental_untreated_rep2


title: EN5C158; 5C_CTCF-AID_TetO-CTCF(89-178)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN215.1


title: EN5C157; 5C_CTCF-AID_TetO-CTCF(Del_1-88)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN214.1


title: EN5C156; 5C_CTCF-AID_TetO-CTCF(264-288)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN213.1


title: EN5C155; 5C_CTCF-AID_TetO-CTCF(179-265)_auxin+dox4days_rep2

source_name: mouse ES cells, line EN212.1


title: EN5C288; 5C_CTCF-AID_TetO-CTCF(Full-length)_auxin+dox4days_rep10


title: EN5C154; 5C_CTCF-AID_TetO-CTCF(H288R)_auxin+dox4days_rep1


title: EN5C153; 5C_CTCF-AID_TetO-CTCF(89-178)_auxin+dox4days_rep1


title: EN5C152; 5C_CTCF-AID_TetO-CTCF(Del_1-88)_auxin+dox4days_rep1


title: EN5C151; 5C_CTCF-AID_TetO-CTCF(264-288)_auxin+dox4days_rep1


title: EN5C150; 5C_CTCF-AID_TetO-CTCF(179-265)_auxin+dox4days_rep1


title: EN5C89; 5C_CTCF-AID_TetO-CTCF(Del_615-736)_auxin+dox4days_rep1

source_name: mouse ES cells, line EN143.7


title: EN5C81; 5C_CTCF-AID_TetO-CTCF(Del_577-736)_auxin+dox4days_rep1

source_name: mouse ES cells, line EN141.5