title: siZCCHC8_noPAP_in_batch1

value: in


title: GF_DSS_6 [RNA-seq]

status: Public on Feb 06 2020

type: SRA

city: Heidelberg

first: Guenter

last: Raddatz

address: Im Neuenheimer Feld 580

country: Germany

institute: German Center for Cancer Research

description: counts.all

library_source: transcriptomic

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6
computation of count data: htseq.py
Genome_build: mm9
Supplementary_files_format_and_content: count table containing the count values for all genes in all samples

molecule: total RNA

organism: Mus musculus

source_name: colon epithel

extract_protocol:
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for RNA extraction. Only samples from distal colon were used in our study. Total RNA from the samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturer’s instructions. The Poly(A)Purist™ MAG Kit (Ambion) was used for mRNA selection.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.

tag: treatment

value: Germ-free, DSS-treatment


title: Huvec_9_Untreated

type: RNA

city: New York

first: Anne

middle: M

last: Bowcock

state: New York

address: One Gustave L. Levy Place, Box 1130

country: USA

institute: Icahn School of Medicine at Mount Sinai

hyb_protocol: Illumina hybridization protocol by Eurofins Genomics

scan_protocol: Illumina scanning protocol by Eurofins Genomics

data_processing: Gene expression data were processed with the limma R package. Outlier samples were detected with boxplots and classical multidimensional scaling (MDS) plots of the log2 probe intensities and removed from analysis. The neqc function was used to perform background correction and quantile normalization, log2 transformation of the probe intensities, and removal of control probes. Probes with expression detected (detection p<0.05) in less than half of the samples (n=28,386) were removed from analysis. The remaining 18,937 probes were collapsed to 14,019 genes by selecting the probe with the maximum mean intensity value for each gene using the collapseRows function. After quality control, 39 sample pairs (treated and untreated) remained for analysis.

label: biotin

organism: Homo sapiens

source_name: Umbilical vein endothelial cells (primary cell line), untreated

label_protocol: Biotinylated cRNAs were generated by Eurofins Genomics

growth_protocol: Forty deidentified primary human umbilical vein endothelial cell (HUVEC) lines were obtained from Promocell and were cultured until passage four.

extract_protocol: RNA was isolated from cell pellets with Quiagen kits according to the protocol provided, and quality control was performed with the Agilent Bioanalyzer.

treatment_protocol: Each cell line was split in half, and one half was treated with 20ng/mL TNFa for 24 hours while the other half was left untreated. Cells were then pelleted, and DNA and RNA were isolated.

value: untreated

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

value: newborn

tag: pedsex

value: male

tag: mds race

value: EUROPE

tag: cell type

value: Umbilical vein endothelial cells


title: siRRP40_xPAP_ip_batch3

city: Aarhus C

first: Manfred

last: Schmid

address: CF Møllers Alle bldg 1130

department: Molecular Biology and Genetics

country: Denmark

institute: Aarhus University

data_processing:
3'end seq reads were trimmed using the bbduk.sh script from BBMAP and homopolymeric A-stretches removed from reads.
The data was mapped using STAR against a compound index composed of hg38 merged with ERCC spike-ins.
5' ends of uniquely mapped reads were used for downstream analysis.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files were generated from bam files using a custom script. The score represents normalized counts per base.

source_name: tissue culture cells

growth_protocol: HeLa cells were cultured in standard DMEM medium supplemented with 10% FBS and penicillin-streptomycin mix.

extract_protocol:
RNAs were extracted using TRIzol (Invitrogen) according to the manufacturer’s protocol and then treated with TURBO DNase (Invitrogen) following the manufacturer’s instruction to remove contaminating genomic DNA. Six in vitro transcribed spike-in RNAs were added. Sequences for spike-ins are identical to ERCC spike-ins. ERCC-00092, ERCC-00136 and ERCC-00043 were transcribed in the presence of 4sU, whereas ERCC-00170, ERCC-00002 and ERCC-00145 were transcribed without 4sU and serve as negative control in the 4sU purification step.
An aliquot of  each RNA was analyzed as total RNA, spiked with an additional full complement of commercially available ERCC spike-ins. The remainder of RNA was used for 4sU purification. Half of all total and 4sU labelled RNA samples were 3'end polydenylated in vitro using E.coli poly(A) polymerase ('xPAP'). All samples were rRNA depleted and subjected to pA+ RNA 3'end sequencing using QuantSeq REV kit from Lexogen GmbH. 8 or 10 libraries were multiplexed and sequenced at the Vienna Biocenter Core Facilities with a NextSeq SR75 High Output run.
RNA 3'end seq, single-end

treatment_protocol: siRNA transfections were performed targeting EGFP(control), RBM7, RRP40,  ZCCHC8, ZFC3H1 or ZCCHC8+ZFC3H1. Cells were transfected with siRNAs twice with the second time repeated after two days, and then cell were cultured for another two days. 10 min before harvesting, 4-thiouridine (4sU) was added to the growth medium for metabolic labelling of early RNA.

tag: cell line

value: HeLa

tag: sirna

tag: rna fraction

value: xPAP

tag: pap treatment

value: ip

tag: batch


title: siZCCHC8_noPAP_in_batch2

value: noPAP


title: Map_Lane_4

city: Los Angeles

first: Nathan

last: Lubock

email: nlubock@ucla.edu, nate@octant.bio

state: CA

address: 607 Charles E Young Drive

institute: UCLA

library_source: genomic

data_processing:
For NextSeq_MiSeq.map.csv.gz - We used the BBTools suite(https://jgi.doe.gov/data-and-tools/bbtools/) of programs to  process our sequencing data using the default settings unless otherwise noted. First,  we used BBDuk2 to filter out any reads matching PhiX (k=23, mink=11, hdist=1) and to  trim off any Illumina sequencing adapters. We then used BBMerge to merge our paired  end reads. We performed another round of trimming with BBDuk2 to ensure no  adapters were left over after merging and to remove any sequence with an N base call.  After merging and trimming the reads, we used a custom Python script (bcmap.py) to  generate a consensus nucleotide sequence for each barcode.  Briefly the script works as follows. First, we split each read into the 15 nt barcode and its  corresponding variant. We then generate a dictionary that maps each barcode to its list  of unique sequences and their counts. To enable majority basecalls, we drop any  barcode that has less than 3 reads. We then pass the barcodes through a series of  filters to eliminate potential errors introduced by barcodes that are mapped to multiple  variants. Since we barcoded and mutagenized the ADRB2 gene in separate pieces,  barcodes can be contaminated with variants from different parts of the ADRB2 gene.  We address this case by using BBMap to align every barcode’s sequences to the  ADRB2 reference and consider that barcode to be contaminated if any sequence aligns  >5 nt away from the most common sequence. Another source of contamination comes  from the chip-synthesized library itself, which contains a significant number of single  base deletions. We consider a barcode contaminated if it has any sequences of  different lengths as it is unlikely that a single base deletion will come from an Illumina  sequencer by chance. However, these filters would not catch the case where a barcode  is contaminated with variants from the same piece of ADRB2. As we only synthesized  the missense variants, we expect variants within the same piece of ADRB2 to be a  Levenshtein distance of 4 from each other on average (approximately two changes to  WT and two changes to a new codon). Thus, we drop any barcode that has a sequence  with >1 read at a Levenshtein distance of 4 away from that barcode’s most common  sequence. Lastly, we generate a consensus sequence by taking the majority base call  at each position and call an N at any ties.
For drug-*_cond-bcs-counts.txt.gz we used awk to substring and count the first 15 nt, which corresponds to the barcode. We then join in addional information such as the drug condition and repeat.

molecule: other

organism: Escherichia coli

source_name: Escherichia coli

growth_protocol: Cells were HEK293T derived and grown in DMEM+10%FBS+PS

extract_protocol:
Qiagen Plasmid Plus Maxi Kit
Determining ADRB2 variant-barcode associations. After barcoding variants, the library was cloned, transformed into DH5alpha E. coli, and grown in LB overnight at 30 degrees before being extracted using a Qiagen Plasmid Plus Maxi Kit.
Cells were lysed (buffer supplied in the kit) on the dishes and prepped according to the manufacturer's protocol (RNeasy miniprep)
The plasmid DNA library construction is simple Illumina amplicon sequencing.
RNA was reverse transcribed (Superscript IV) with a gene specific primer and the resulting cDNA was amplified with primers containing necessary adaptors for illumina sequencing

treatment_protocol: Media was replaced with OptiMEM and treated with vehicle, isoproterenol (ADRB2 agonist), or forskolin (cAMP stimulant)

tag: strain

tag: growth medium

value: LB

tag: molecule

value: Plasmid DNA


title: Map_Lane_3


title: siRRP40_xPAP_ip_batch1


title: Map-2_Lane_4


title: GF_DSS_4 [RNA-seq]

description: counts.all


title: GF_4 [RNA-seq]

description: counts.all

value: Germ-free


title: Map_Lane_2


title: siRRP40_xPAP_in_batch1


title: siRRP40_xPAP_in_batch2


title: siRRP40_noPAP_ip_batch3


title: Map_Lane_1


title: siRRP40_noPAP_in_batch3


title: GF_3 [RNA-seq]

description: counts.all


title: GF_2 [RNA-seq]

description: counts.all


title: siRRP40_noPAP_in_batch2


title: siRRP40_noPAP_in_batch1


title: CNV_DSS_18 [RNA-seq]

description: counts.all

value: DSS-treatment


title: SGA CON rep 6

city: Urbana

first: Rodney

middle: W.

last: Johnson

state: IL

address: 1207 W. Gregory Dr.

department: Animal Sciences

institute: Univ of Illinois in Urbana

description: SGA from litter 12 brought in with other litters in cohort 2

data_processing:
The libraries were pooled in equimolar concentration and the pool was quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Each sample's fastq file run through trimmomatic 0.33 with the following parameters: ILLUMINACLIP:TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 SLIDINGWINDOW:4:15 MINLEN:30
NCBI's Sus scrofa 10.2 reference genome and annotation release 105 were indexed using STAR 2.5.2a with parameters --sjdbOverhang 99. Each sample was then aligned to the genome again using STAR 2.5.2a.
Read counts for each gene were generated using featureCounts (from subread v 1.5.0) with parameters -s 2 -g gene_id -t exon, where gene_id were Entrez Gene IDs that were manually pulled from the Dbxref attribute in the gene annotation release 105 gff file
Genome_build: Sus scrofa 10.2
Supplementary_files_format_and_content: tab-delimited text files of raw read counts per gene per sample were used directly in edgeR 3.16.5 for statistical analysis and thus are the "normalized" data.

molecule: polyA RNA

organism: Sus scrofa

source_name: hippocampus

extract_protocol:
Tissue (~50 mg) was homogenized in 1 mL TRIzol Reagent (ThermoFisher Scientific, Waltham, MA, USA) following manufacturer’s protocol steps 1-8. After step 8, 0.4 mL of 200 proof ethanol was added and the samples briefly vortexed. The samples were loaded into RNeasy Mini Kit columns (cat. No. 74104, Qiagen, Germantown, MD, USA) and the manufacturer’s protocol followed from Part 1 step 3. Genomic DNA was removed with the RNase-free DNase Set (cat. No. 79254, Qiagen, Germantown, MD, USA) following manufacturer’s protocol.
Libraries were constructed and sequenced using the TruSeq LT Stranded RNA Sample Preparation Kit (Illumina, Inc., San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries

treatment_protocol: Hippocampi were dissected and stabilized with RNAlater (Qiagen, Germantown, MD, USA), snap frozen, and stored at -80°C

tag: breed

value: PIC Camborough (dam) x PIC 359 (sire)

tag: tissue

value: brain

tag: age

value: post natal day 14

tag: size

value: SGA

tag: diet

value: CON

tag: Sex

value: F

tag: pair

tag: cohort


title: siZCCHC8_noPAP_in_batch3

value: in


title: SGA HF rep 6

description: SGA from litter 11 brought in with other litters in cohort 2

value: HF


title: siRBM7_xPAP_ip_batch1


title: SGA CON rep 5

description: SGA from litter 10 brought in with other litters in cohort 2

value: M


title: siRBM7_xPAP_in_batch2

value: HeLa


title: CNV_DSS_17 [RNA-seq]

description: counts.all

tag: treatment


title: GF_DSS_5 [RNA-seq]

description: counts.all

value: Germ-free, DSS-treatment


title: siRBM7_xPAP_in_batch1

tag: cell line

value: xPAP


title: siRBM7_noPAP_ip_batch1

tag: sirna

value: noPAP

value: ip


title: siRRP40_xPAP_in_batch3

tag: rna fraction


title: Apocrine glands of lesional skin-male 7

city: Dessau

first: Christos

middle: C

last: Zouboulis

address: Auenweg 38

department: Departments of Dermatology, Venereology, Allergology and Immunology

institute: Dessau Medical Center, Brandenburg Medical School Theodor Fontane

hyb_protocol: RNA fragmentation was performed by incubation with 10x GEX Blocking Agent and Fragmentation Buffer (Agilent) for 30 minutes at 60°C. Then, 2x GEX hybridization buffer (Agilent) was added and samples were loaded on array slides. Hybridization was performed at 65°C at 10 rpm for 17 h and then washed with GEX wash buffer 2 (Agilent).

scan_protocol: Arrays were scanned using the Agilent Scanner.

data_processing:
Images were processed using the Agilent Feature Extraction software to generate text files.
Raw transcriptome profile data were preprocessed using the limma package in R. Background correction was performed using the normexp convolution model and corrected data were subsequently normalized using Loess normalization. After preprocessing, the control and low intensity probe sets were filtered out to improve the signal of further analyses. Low intensity probe sets were defined as those with an intensity less than 10% brighter than the 95th percentile of the negative control probe sets in at least eight arrays. Ratios were computed using the RosettaResolver™ Software (Rosetta Inpharmatics, Seattle, WA, USA). The significant genes were investigated using Enrichr.

source_name: skin

label_protocol: The Low Input Quick Amp Labeling Kit, one-color (Agilent) including the dye cyanine 3-labeled CTP (Cy3-CTP) was used.

extract_protocol: RNA isolation from the homogenates was performed using the RNeasy® Mini Kit (Qiagen) including DNase I on column treatment following the manufacturer's protocol.

value: apocrine glands


title: SGA HF rep 5

description: SGA from litter 9 brought in with other litters in cohort 2


title: siRBM7_noPAP_in_batch2

tag: pap treatment


title: siRBM7_noPAP_in_batch1

tag: batch


title: CNV_DSS_16 [RNA-seq]

description: counts.all


title: siRRP40_noPAP_ip_batch1


title: CNV_6 [RNA-seq]

description: counts.all

value: No treatment


title: siGFP_xPAP_ip_batch4

value: siGFP


title: siGFP_xPAP_ip_batch3


title: SGA HF rep 4

description: SGA from litter 7 brought in with other litters in cohort 2

value: PIC Camborough (dam) x PIC 359 (sire)


title: CNV_5 [RNA-seq]

description: counts.all


title: SGA CON rep 3

description: SGA from litter 6 brought in with other litters in cohort 1

value: brain


title: SGA CON rep 4

description: SGA from litter 8 brought in with other litters in cohort 2

value: post natal day 14


title: siGFP_xPAP_ip_batch1


title: siGFP_xPAP_in_batch5


title: CNV_4 [RNA-seq]

description: counts.all


title: SGA HF rep 3

description: SGA from litter 5 brought in with other litters in cohort 1

value: SGA


title: GF_DSS_5 [BiSulfite-seq]

data_processing:
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming: shore 0.6.2
Preprocessing, quality filtering: shore 0.6.2
BS-mapping: bsmap 2.0
computation of methylation ratios: methratio.py (part of bsmap package)
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph-format containing the genomic methylation ratios and coverage values of the respective sample

molecule: genomic DNA

source_name: GF_DSS_colon epithel

extract_protocol:
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for DNA extraction. Only samples from distal colon were used in our study.
5 µg of high molecular weight DNA were used for fragmentation using the Covaris S2 AFA System in a total volume of 100 µl. Fragmentation-run parameters: Duty cycle 10%; Intensity: 5; Cycles/burst: 200; Time: 3 min; number of cycles: 3, resulting in a total fragmentation-time of 180 s. Fragmentation was confirmed with a 2100 Bioanalyzer (Agilent Technologies) using a DNA1000 chip. The fragmented DNAs were concentrated to a final volume of 75 µl using a DNA Speed Vac. End repair of fragmented DNA was carried out in a total volume of 100 µl using the Paired End DNA Sample Prep Kit (Illumina) as recommended by the manufacturer. For the ligation of the adaptors, the Illumina Early Access Methylation Adaptor Oligo Kit and the Paired End DNA Sample Prep Kit (Illumina) were used, as recommended by the manufacturer. For the size selection of the adaptor-ligated fragments, we used the E-Gel Electrophoresis System (Invitrogen) and a Size Select 2% precast agarose gel (Invitrogen). Each fragmented DNA was loaded on two lanes of the E-gel. Electrophoresis was carried out using the “Size Select” program for 16 min. According to the standard loaded (50 bp DNA Ladder, Invitrogen), 240 bp fragments were extracted from the gel, pooled, and directly transferred to bisulfite treatment without further purification. For the bisulfite treatment we used the EZ-DNA Methylation Kit (Zymo) as recommended by the manufacturer with the exception of a modified thermal profile for the bisulfite conversion reaction. The conversion was carried out in a thermal cycler using the following thermal profile: 95°C for 15 s, 50°C for 1 h, repeat from step 1, 15×, 4°C for at least 10 min. The libraries were subsequently amplified, using the Fast Start High Fidelity PCR System (Roche) with buffer 2, and Illuminas PE1.1 and PE2.1 amplification primers. PCR thermal profile: 95°C for 2 min, 95°C for 30 s, 65°C for 20 s, 72°C for 30 s, then repeat from step 2, 11×, 72°C for 7min, hold at 4°C. PCR reactions were purified on PCR purification columns (MinElute, Qiagen) and eluted in 20 µl elution buffer (Qiagen).

tag: strain

tag: tissue/cell type

value: colon epithelial cells


title: siGFP_xPAP_in_batch2


title: siGFP_xPAP_in_batch1


title: siGFP_xPAP_in_batch3


title: siGFP_xPAP_in_batch4


title: SGA CON rep 2

description: SGA from litter 4 brought in with other litters in cohort 1

value: CON

value: F


title: siGFP_noPAP_ip_batch4


title: GF_DSS_4 [BiSulfite-seq]


title: siGFP_noPAP_ip_batch3


title: siGFP_noPAP_ip_batch1


title: GF_3 [BiSulfite-seq]

source_name: GF_colon epithel

value: Germ-free


title: SGA HF rep 2

description: SGA from litter 3 brought in with other litters in cohort 1

value: HF


title: siGFP_noPAP_in_batch5

value: HeLa

value: in


title: GF_2 [BiSulfite-seq]


title: SGA CON rep 1

description: SGA from litter 2 brought in with other litters in cohort 1

value: M


title: siGFP_noPAP_in_batch3

value: noPAP


title: SGA HF rep 1

description: SGA from litter 1 brought in with other litters in cohort 1


title: siGFP_noPAP_in_batch2


title: CNV_DSS_18 [BiSulfite-seq]

source_name: CNV_DSS_colon epithel

value: DSS-treatment


title: siGFP_noPAP_in_batch1


title: FP_RO_3

city: Mannheim

first: Johanna

middle: Daniela

last: Schott

address: Franz-Volhard-Straße 6

department: Mannheim Institute for Innate Immunoscience

institute: Heidelberg University

description: cytoplasmic RNA

data_processing:
Basecalling was performed with CASAVA and demultiplexing with bcl2fastq.
The adapters were removed with the fastx_clipper function of the FASTX-toolkit version 0.0.11   (http://hannonlab.cshl.edu/fastx_toolkit/), retaining only reads of at least 28 nt  and discarding non-clipped reads.  Afterwards, the four random nucleotides at the beginning and the end of the reads were removed  with an in-house-developed perl script.
Alignment was performed with bowtie version 0.12.8. In the first step,  reads were mapped to a common reference of cytoplasmic and mitochondrial tRNAs   as downloaded from the UCSC Genome Browser (the hg38 track "tRNA genes"   and mitochondrial tRNAs from the wgEncodeGencodeBasicV26 table).   What did not map in this step was mapped to rRNA sequences (mitochondrial rRNA  and 5S rRNA as defined in the wgEncodeGencodeBasicV26 table and 45S precursor   sequences as defined in the refGene table). Remaining reads were mapped to   a common reference of a human transcriptome (wgEncodeGencodeBasicV27) and  a yeast transcriptome (sacCer3ensGene). In all mapping steps, up to three   mismatches were allowed and and all reads in the best stratum were reported.
Alignment was performed with bowtie version 0.12.8. In the first step,  reads were mapped to a common reference of cytoplasmic and mitochondrial tRNAs   as downloaded from the UCSC Genome Browser (the hg38 track "tRNA genes"   and mitochondrial tRNAs from the wgEncodeGencodeBasicV26 table).   What did not map in this step was mapped to rRNA sequences (mitochondrial rRNA  and 5S rRNA as defined in the wgEncodeGencodeBasicV26 table and 45S precursor   sequences as defined in the refGene table). Remaining reads were mapped to   a common reference of a human transcriptome (wgEncodeGencodeBasicV27) and  a yeast transcriptome (sacCer3ensGene). In all mapping steps, up to three   mismatches were allowed and and all reads in the best stratum were reported.
In order to summarize reads at the gene level, only reads that map to isoforms  of one specific gene (as defined by a common gene symbol) and are contained in   regions between 12 nt before annotated start and stop codons   (the observed P-site offset in this data set)  were counted with an in-house-developed perl script.
In order to identify individually regulated mRNAs at the translational level,  read counts of human genes were normalized with DESeq2 version 1.16.1.   Only genes with a log2 base mean of at least 8 were considered and   significant changes in ribosome density (input/ribosome protected footprints)  due to CDK1-inhibition were identified with a likelihood ratio test (LRT).
Genome_build: hg38/sacCer3
Supplementary_files_format_and_content: The csv file RiboSeq_CKD1i_human.csv contains raw read counts as determined for   human genes, mean fold-changes in input, footprint   and ribosome density as calculated from the DESeq2-normalized human read counts   and p-values for changes in ribosome density as determined with the DESeq2 package (raw and corrected  for multiple testing with the Benjamini-Hochberg method). In addition, fold-changes for ribosome density after normalization to the yeast spike-in are shown. The csv file RiboSeq_CDKi_yeast.csv contains the sum of read counts assigned to yeast or human ORFs, which was used in order to measure global changes in translation efficiency.

source_name: RPEI/yeast cells

extract_protocol:
Cells were washed once in ice-cold PBS supplemented with 100 µg/ml CHX and harvested by scraping in polysome lysis buffer (20 mM Tris HCl pH 7.5, 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 100 mg/ml CHX, 1% Triton X-100, 40 U/ml RNasin, EDTA-free complete protease inhibitors (Roche)). Lysates were incubated end over end for 10 min at 4°C and cleared by centrifugation at 10,000 rpm for 10 min at 4°C. The DMSO and Ro3306 treated sample was adjusted to the same OD260 and afterwards combined to one sample. Yeast polysome lysate (2% of the RPE1 lysate) was spiked in. 10% of the lysate was saved as input sample. The lysate was subsequently digested with RNase I (60 units/ per OD260) for 5 min at 4°C. The reaction was stopped by the addition of Superase Inhibitor (6 units/per sample). Samples were loaded onto linear 17 to 50% sucrose gradients (dissolved in 20 mM Tris-HCl pH 7.5, 5 mM MgCl2, 150 mM NaCl). Sucrose density gradient centrifugation was carried out at 35,000 rpm at 4°C using a SW60 rotor (Beckman) for 2.5 h. Sucrose gradients were fractionated by time (14 s/ fraction) using a Teledyne ISCO Foxy Jr. system.  RNA was purified from the cytoplasmic lysate (input) or from the monosomal fractions (ribosome protected fragments)  with Phenol:Chloroform:Isamylalcohol (25:24:1) by phase separation.  Both input and ribosome protected fragements were depleted of rRNA with the Ribo-Zero Gold Kit (Illumina).  Input RNA was randomly fragmented at pH ~10 for 12 min at 95°C.  Fragmented RNA and ribosome protected fragments were size-selected (25 - 35 nt) on a 15% polyacrylamide TBE-urea gel.  After end-repair with T4 PNK, 3 ng per sample were used for library preparation.
Small RNA libraries were prepared with the NEXTflex Small RNA-Seq Kit v3 according to the manufacturer’s manual.

treatment_protocol: RPE1 cells were cultured in in HAM’s F-12 medium (HAM’s F-12 (1:1), Millipore) containing 10% FCS, 2 mM L-glutamine, 100 U/ml penicillin and 100 μg/ml streptomycin. For the experiment RPE1 cells were seeded and kept in the absence of FBS for 48 h. Afterwards cells were incubated  in fresh medium without FBS supplemented with either DMSO or Ro3306 (Sigma, 10 µM) for 4 h.

tag: fraction

value: Ribosome protected fragments

tag: agent

tag: spike-in

value: Saccharomyces cerevisiae


title: CNV_DSS_16 [BiSulfite-seq]


title: FP_DMSO_3

description: cytoplasmic RNA

value: DMSO


title: AGA HF rep 6

description: AGA from litter 11 brought in with other litters in cohort 2

tag: breed

value: PIC Camborough (dam) x PIC 359 (sire)

tag: tissue

tag: age

value: AGA


title: FP_RO_2

description: cytoplasmic RNA


title: FP_DMSO_2

description: cytoplasmic RNA


title: AGA CON rep 5

description: AGA from litter 10 brought in with other litters in cohort 2

value: brain

value: post natal day 14

tag: size

tag: diet

tag: Sex


title: FP_RO_1

description: cytoplasmic RNA


title: CNV_4 [BiSulfite-seq]

source_name: CNV_colon epithel

tag: treatment

value: No treatment

value: colon epithelial cells


title: AGA HF rep 5

description: AGA from litter 9 brought in with other litters in cohort 2

value: F

tag: pair

tag: cohort


title: Input_RO_3

description: cytoplasmic RNA

value: cytoplasmic lysate (input)


title: Input_DMSO_3

description: cytoplasmic RNA


title: AGA CON rep 4

description: AGA from litter 8 brought in with other litters in cohort 2

value: CON


title: FP_DMSO_1

description: cytoplasmic RNA


title: Input_RO_2

description: cytoplasmic RNA


title: Input_RO_1

description: cytoplasmic RNA


title: siGFP_noPAP_in_batch4

tag: cell line

value: HeLa

tag: sirna

value: siGFP

tag: rna fraction


title: Input_DMSO_2

description: cytoplasmic RNA


title: Input_DMSO_1

description: cytoplasmic RNA


title: AGA HF rep 4

description: AGA from litter 7 brought in with other litters in cohort 2

value: HF

value: M


title: AGA CON rep 6

description: AGA from litter 12 brought in with other litters in cohort 2


title: AGA CON rep 3

description: AGA from litter 6 brought in with other litters in cohort 1


title: CNV_5 [BiSulfite-seq]

tag: strain


title: AGA HF rep 3

description: AGA from litter 5 brought in with other litters in cohort 1


title: AGA CON rep 1

description: AGA from litter 2 brought in with other litters in cohort 1


title: AGA CON rep 2

description: AGA from litter 4 brought in with other litters in cohort 1


title: Huvec-8_TNF

type: genomic

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using a HiScan Reader with standard recommended Illumina scanner settings

data_processing: The minfi R package was used for data preprocessing, normalization, and quality control of DNA methylation data. Background subtraction and dye bias correction was performed using the preprocessNoob function, followed by quantile normalization with preprocessQuantile. Samples with more than 5% poor detection p-values (>0.01) were removed from analysis. CpG sites with poor detection p-values across samples were removed from analysis (n=3,451 sites). Predicted sex based on X and Y chromosome methylation was checked against recorded sex. CpG sites with probes predicted to cross-hybridize to other genomic locations were removed from analysis (n=44,032 sites).

label: Cy5 and Cy3

source_name: Umbilical vein endothelial cells (primary cell line), treated with TNFa, 24 hours

label_protocol: Standard Illumina protocol

extract_protocol: DNA was isolated from cell line pellets with Quiagen kits according to the protocol provided

tag: cell type

value: Umbilical vein endothelial cells

value: treated with TNFa, 24 hours

tag: ChIP

tag: array

tag: slide

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

value: newborn

tag: promocell gender

value: female

tag: promocell race

value: caucasian

tag: pedsex

tag: mds race

value: EUROPE


title: AGA HF rep 2

description: AGA from litter 3 brought in with other litters in cohort 1

tag: breed

value: PIC Camborough (dam) x PIC 359 (sire)

tag: tissue

value: brain

tag: age

tag: size

value: AGA

tag: diet

tag: Sex

tag: pair


title: Huvec-9

tag: cell type

tag: treatment

value: untreated

tag: ChIP

value: male


title: RNA-seq.DR++-M344_rep2

first: Jianlong

last: Wang

department: Department of Medicine

institute: Columbia University Irving Medical Center

description: ESC.gene.rep.matrix.tsv

data_processing:
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings.
Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting.
Genome_build: mm9
Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.

source_name: DR++ population of CJ7 ESCs transfected with an miR-344-2-activation vector by CRISPR/SAM system

growth_protocol: Feeder-free mouse embryonic stem cells (mESCs) were cultured on 0.1% gelatin-coated plates under standard conditions: DMEM supplemented with 15% fetal calf serum (FBS), 1000 units/mL recombinant leukemia inhibitory factor (LIF), 0.1 mM 2-mercaptoethanol, 2 mM L-glutamine, 0.1 mM MEM non-essential amino acids (NEAA), 1% nucleoside mix (100X stock, Sigma), and 50 U/mL Penicillin/Streptomycin).

extract_protocol:
For ESCs, total RNAs were extracted using the RNeasy kit (#74136, Qiagen) according to the manufacturer’s instructions. For embryos, a total of 10-20 embryos with the same treatment and embryonic stage were pooled for each reaction. Injected embryos were harvested, washed several times in 0.5% BSA-PBS (Sigma) solution and subsequently picked and transferred into lysis buffer by a mouth pipette.
For ESCs, 1 µg total RNA from each sample was taken for the preparation of PolyA RNA-seq libraries, and massively parallel sequencing was performed with the HiSeq4000 platform. Paired-end 150 bp-length reads were produced. For embryos, RNA-seq libraries were prepared according to the Smart-seq2 protocol (Picelli et al., 2014) with minor modifications. After reverse transcription, cDNA was pre-amplified (10 PCR cycles) and purified with Ampure XP Beads (Agencourt) at 0.8 beads/1 DNA (v/v). One microliter (1 μl) cDNA, dulited by 19 μl nuclease-free water, was used for Real-time PCR quality check. The amplified cDNA was fragmented using a Covaris sonicator (Covaris S220). To generate the sequence libraries, the KAPA Hyper Prep Kit was used following the manufacturer’s instructions. NOVA pair-end 150-bp sequencing was performed on a HiSeq 2500 sequencer (Illumina) at Berry Genomics Corporation.

treatment_protocol: B6D2F1 (BDF1) female mice (7-8 weeks old) were superovulated by intraperitoneally injecting with pregnant mare serum gonadotropin (PMSG) and human chorionic gonadotropin (hCG), and then mated to BDF1 male mice. The fertilized embryos (zygotes) were collected from oviducts. A mixture of Zmym2 siRNA (20 µM), scramble siRNA (20 µM), miRNA (50 µM), or scramble miRNA (50 µM) was separately injected into the cytoplasm of fertilized eggs with visible pronuclei. The injected zygotes were then cultured in G1 plus medium (10128, Vitrolife), and 2-cell, 4-cell, 8-cell, morula and blastocyst embryos were obtained after culturing.

value: Embryonic stem cells (DR++ population)

tag: cell line

tag: strain

tag: genotype/variation


title: Huvec-8

tag: array

tag: slide

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

tag: promocell gender


title: Huvec-6_TNF

tag: promocell race

tag: pedsex

tag: mds race


title: Huvec-6


title: 373_Ctrl: Hdac2wt

city: Berlin

first: Matthias

last: Wirth

address: Hindenburgdamm 30

institute: Charité Berlin

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized on Affymetrix Mouse Gene 1.0 ST Array in the Affymetrix according to standard Affymetrix protocol.

scan_protocol: Affymetrix chips were scanned using the Affymetrix GeneChip Scanner 3000

data_processing: CEL files were imported into Affymetrix Expression Console software. RMA algorithm were used for normalizing probe-level intensity.

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol.

extract_protocol: RNA was extracted with the RNeasy microkit from Qiagen following manufacturer's instructions.

tag: tissue

value: pancreatic ductal adenocarcinoma cell line

tag: genotype


title: Huvec-5_TNF

tag: cell type


title: 1128_Hdac2KO: Hdac2ko


title: 1042_Hdac2KO: Hdac2ko


title: supporting cells

city: Neuherberg

first: Hernán

last: López-Schier

address: Ingolstaedter Landstr. 1

department: Research Unit Sensory Biology and Organogenesis

institute: Helmholtz Zentrum München

data_processing:
The 10X Genomics core computational software Cellranger v.2.1.1 was used for alignment and processing of next generation sequencing reads of the scRNA-seq data as recommended (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome).
Genome_build: GRCz11
Supplementary_files_format_and_content: Raw UMI count matrix (feature x cell barcode) from 10X Genomics single cell RNAseq experiments. gzipped files contains count matrix in market matrix format, cell barcodes as tab-delimited text file and feature names as tab-delimited text file.

organism: Danio rerio

source_name: zebrafish neuromast cells

growth_protocol: Standardized conditions at 28.5°C in the 0,3 x Danieau’s solution.

extract_protocol:
Enzymatic dissociation of larval trunks and isolation of green fluorescent protein-expressing cells by FAC-sorting.
Single cell libraries were generated using the ChromiumTM Single cell 3`library and gel bead kit v2 (PN #120237) from 10x Genomics. Libraries were sequenced on the HiSeq4000 (Illumina) with 150bp paired-end sequencing.
RNA Seq (10X Genomics)

tag: source tissue

value: neuromast

tag: developmental day

value: 7 days post fertilization

tag: treatment


title: 1146_Hdac2KO: Hdac2ko


title: hair cells


title: 50_Ctrl: Hdac2wt


title: AGA HF rep 1

description: AGA from litter 1 brought in with other litters in cohort 1

tag: breed

tag: age

value: post natal day 14

tag: size

tag: diet

value: HF

tag: Sex

tag: pair

tag: cohort


title: JRY11339, native MNase-seq

city: Berkeley

first: Daniel

middle: S

last: Saxton

address: 100 University Ave

department: MCB

institute: University of California Berkeley

data_processing:
Basecalls and alignment performed using Bowtie2
Python was used to:
eliminate reads less than 140bp and greater than 180bp in length
plot midpoints of reads
use a 25bp rolling mean to smooth out resulting peaks
Genome_build: S. cerevisiae S288C Genome (Genbank Accession number GCA_000146045.2)
Supplementary_files_format_and_content: Tab-delimited midpoints.stacked file

organism: Saccharomyces cerevisiae

growth_protocol: Grown in CSM overnight, then to log phase over the course of 4 hours.

extract_protocol:
Cells were spheroplasted and nuclei were purified. Nuclei were treated with Mnase.
Libraries were prepared with NEBnext UltraII library preparation kit.

tag: strain

tag: hml genotype

value: HMLα, hmlα2∆::CRE

tag: rap1 to abf1 distance


title: JRY11340, native MNase-seq


title: 4917_Ctrl: Hdac2wt


title: Huvec-5

value: Umbilical vein endothelial cells

tag: ChIP

tag: array

tag: slide

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

tag: promocell gender

tag: promocell race

tag: pedsex

tag: mds race


title: RNA-seq.DR++-EV_rep2

description: ESC.gene.rep.matrix.tsv

source_name: DR++ population of CJ7 ESCs transfected with an empty vector by CRISPR/SAM system

tag: cell type

tag: cell line

tag: genotype/variation

value: transfected with an empty vector


title: RNA-seq.DR++-MERVL_rep2

description: ESC.gene.rep.matrix.tsv

source_name: DR++ population of CJ7 ESCs transfected with an MERVL-activation vector by CRISPR/SAM system


title: RNA-seq.DR++-MERVL_rep1

description: ESC.gene.rep.matrix.tsv

value: transfected with an MERVL-activation vector


title: JRY11338, native MNase-seq


title: Huvec-9_TNF

tag: treatment

value: treated with TNFa, 24 hours

value: newborn

value: caucasian


title: RNA-seq.DR++-EV_rep1

description: ESC.gene.rep.matrix.tsv

tag: strain


title: Huvec-4_TNF

value: female

value: EUROPE


title: Huvec-4

value: untreated


title: JRY11337, native MNase-seq

tag: hml genotype


title: JRY11336, native MNase-seq

tag: rap1 to abf1 distance


title: RNA-seq.DR++-UT_rep2

description: ESC.gene.rep.matrix.tsv

source_name: DR++ population of CJ7 ESCs, untreated cells


title: RNA-seq.DR++-M344_rep1

description: ESC.gene.rep.matrix.tsv

value: transfected with an miR-344-2-activation vector


title: JRY11341, native MNase-seq


title: RNA-seq.DR++-UT_rep1

description: ESC.gene.rep.matrix.tsv

value: Embryonic stem cells (DR++ population)


title: Huvec-38_TNF

tag: ChIP

value: male


title: JRY11280, native MNase-seq


title: Huvec-38

tag: array


title: ChIP-seq.CCE-KO_LSD1_C

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads were aligned to the mouse genome (NCBI build 37, mm9) using the bowtie2 (v2.3.4) program, with parameters -X 1000 --no-mixed --no-discordant.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.

source_name: Embryonic stem cells

extract_protocol:
ChIP was performed with SimpleChIP Plus Enzymatic Chromatin IP Kit (Cell Signaling Tech. #9005) following the standard protocol.
About 4 million cells were used for each ChIP experiment, with two antibodies of LSD1 (Cell Signaling Tech. #2184, clone C69G12; and Abcam, ab17721). Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufacturer’s protocol, and paired-end 150 bp-length reads were produced.

value: mESC CCE

tag: antibody

value: LSD1, Cell Signaling Tech #2184, clone C69G12

tag: genotype


title: Huvec-37_TNF

tag: slide

tag: promocell catalogue number

tag: promocell lot number


title: Huvec-37

source_name: Umbilical vein endothelial cells (primary cell line), untreated

tag: promocell age

tag: promocell gender

tag: promocell race


title: ChIP-seq.CCE-KO_Input


title: JRY11334, native MNase-seq


title: JRY11333, native MNase-seq


title: JRY11335, native MNase-seq


title: JRY11332, native MNase-seq


title: ChIP-seq.CCE-KO_LSD1_A

value: LSD1, Abcam, ab17721


title: Huvec-36_TNF

tag: cell type

value: asian

tag: pedsex

tag: mds race


title: Huvec-36

tag: treatment


title: JRY11331, native MNase-seq

tag: strain

value: HMLα, hmlα2∆::CRE


title: ChIP-seq.CCE-WT_Input

tag: cell line

value: WT


title: JRY11330, native MNase-seq

tag: hml genotype

tag: rap1 to abf1 distance


title: RNA-seq.CRISPRa-M344_rep2

description:
ESC.gene.rep.matrix.tsv
Embryonic stem cells

source_name: CJ7 ESCs transfected with an miR-344-2-activation vector by CRISPR/SAM system

tag: tissue

value: mESC CJ7

tag: genotype/variation


title: Huvec-35

value: Umbilical vein endothelial cells

tag: ChIP

tag: array


title: Huvec-35_TNF

value: treated with TNFa, 24 hours

tag: slide

tag: promocell catalogue number


title: JRY11327, native MNase-seq


title: Huvec-34_TNF

tag: promocell lot number

tag: promocell age

value: newborn


title: RNA-seq.CRISPRa-M344_rep1


title: RNA-seq.CRISPRa-MERVL_rep2

source_name: CJ7 ESCs transfected with an MERVL-activation vector by CRISPR/SAM system

value: MERVL-activated


title: Huvec-34

tag: promocell gender

value: female

tag: promocell race

value: caucasian


title: Huvec-33_TNF

tag: cell type

tag: pedsex

value: EUROPE


title: RNA-seq.CRISPRa-MERVL_rep1


title: JRY11325, native MNase-seq


title: ChIP-seq.CCE-WT_LSD1_A

tag: antibody

tag: genotype


title: ChIP-seq.CCE-WT_LSD1_C

tag: cell line

tag: strain


title: JRY11323, native MNase-seq

tag: hml genotype

tag: rap1 to abf1 distance


title: RNA-seq.CRISPRa-EV_rep1

source_name: CJ7 ESCs transfected with an empty vector by CRISPR/SAM system

tag: tissue

tag: genotype/variation

value: empty vector


title: Huvec-32

tag: treatment

value: untreated

tag: ChIP

tag: array

tag: mds race


title: JRY11322, native MNase-seq


title: RNA-seq.CRISPRa-EV_rep2


title: RNA-seq.A7.6.Zmym2GtGt_rep1

source_name: Zmym2 Gt/Gt KO ESCs

value: mESC


title: Huvec-33

tag: slide

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age


title: JRY11297, native MNase-seq


title: RNA-seq.A7.6.Zmym2GtGt_rep2


title: JRY11321, native MNase-seq


title: Huvec-31_TNF

tag: cell type

tag: promocell gender

tag: promocell race

tag: pedsex


title: JRY11320, native MNase-seq

tag: strain


title: Huvec-30_TNF


title: RNA-seq.A7.3.Zmym2++_rep2

source_name: Zmym2 WT ESCs

value: wildtype


title: JRY11326, native MNase-seq

tag: hml genotype


title: Huvec-30


title: JRY11324, native MNase-seq

tag: rap1 to abf1 distance


title: RNA-seq.A7.3.Zmym2++_rep1

tag: tissue


title: Huvec-3_TNF

value: male


title: JRY11296, native MNase-seq

value: 99 bp


title: ChIP-seq.FLAG-Zmym2_rep1

description: A 3xFLAG-P2A-Neomycin fragment was knocked in at the C-term of Zmym2 endogenous locus in a CJ7 ESC line.

data_processing:
FastQC (v0.10.1) was used to check the sequencing quality
Reads of two biological replicates were combined.
Reads were aligned to the mouse genome (NCBI build 37, mm9) using the bowtie (v1.0.0) program, with parameters -M 1 --chunkmbs 200.
The mapped reads were sorted and converted to a binary bam file using samtools (v0.1.19)
ChIP-seq peaks were determined by the MACS program (v.2.0.10), using input as the control data, and all other parameters followed the default settings.
Genome_build: mm9
Supplementary_files_format_and_content: Bed file of MACS called peaks.

extract_protocol:
ChIP was performed as previously described (Lee et al., 2006) by using a FLAG antibody (Sigma F1804).
Two biological replicates were performed for Input and FLAG ChIPed DNA. 6 µl of 138 ng/µl and 9 µl of 232 ng/ul as input, 32 µl 0.184 ng/µl and 32 µl 0.266 ng/µl FLAG ChIPed DNA to prepare ZMYM2 ChIP-seq libraries. Massively parallel sequencing was performed with the Illumina HiSeq4000 according to the manufactory protocol, and single-end 50 bp-length reads were produced.

tag: cell line

tag: mouse strain

tag: antibody

value: Flag (Sigma F1804)


title: ChIP-seq.Input_rep2


title: Huvec-3

tag: treatment

tag: ChIP

tag: array


title: JRY11318, native MNase-seq

value: HMLα, hmlα2∆::CRE

value: 69 bp


title: ChIP-seq.Input_rep1

value: mESC CJ7


title: JRY11317, native MNase-seq

value: 39 bp


title: Huvec-29_TNF

value: Umbilical vein endothelial cells

value: treated with TNFa, 24 hours

tag: slide

tag: promocell catalogue number

tag: mds race


title: Huvec-29

tag: cell type

tag: promocell lot number

tag: promocell age

value: newborn


title: JRY11281, native MNase-seq

value: 24 bp


title: Huvec-28_TNF

tag: promocell gender

value: female

tag: promocell race

value: (blank)

tag: pedsex


title: JRY11259 (DSSY66)_2, native MNase-seq

tag: strain

tag: hml genotype

tag: rap1 to abf1 distance

value: 1460 bp (no deletion)


title: Huvec-31

value: untreated

value: caucasian

value: EUROPE


title: JRY11259 (DSSY66)_1, native MNase-seq


title: ChIP-seq.FLAG-Zmym2_rep2

tag: cell line

tag: mouse strain


title: Huvec-28

tag: treatment


title: JRY11319, native MNase-seq


title: Huvec-27_TNF

tag: ChIP


title: Trailblazer WW8 block5

city: Albany

first: Christian

last: Tobias

address: USDA-ARS, 800 Buchanan Street Rm 2101

institute: USDA-ARS

description:
sample name in processed data file:
a8h_trail_b5s45qb29

data_processing:
Run on Illumina HiSeq4000, base calling with RTA2 software from images using quality scores, demultplexed with bcl2fastq conversion software
Further data processing with CLC-genomics workbench  v11.0.1
Discard failed reads; trim nucleotides below quality threshold  (limit = 0.05)
Discard reads with greater than 2 ambiguous nucleotides
Trimming of read-through adapter sequences
Reads mapped in base space to reference using defaults for RNA-Seq analysis
Total counts were used as input for DESeq2
Genome_build: Panicum.virgatum Assembly v4.0 Annotation v4.1 (www.phytozome.net)
Supplementary_files_format_and_content: Table of total counts with gene identifier on vertical axis and individual sample identifier on horizontal axis

organism: Panicum virgatum

source_name: crown

growth_protocol: Greenhouse with supplemental LED lighting in 3.6 L pots, 14h day/10h night

extract_protocol:
Samples ground in liquid nitrogen, total RNA extracted with TRIzol reagent.
Kapa Biosystems library prep (Kapa Biosystems, USA)

treatment_protocol:
control: well watered 7 wk
treatment: water stress 7 wk  (WW7)
treatment: water stress 7 wk followed by recovery well watered 1 wk
control: well watered 8 wk (WW8)

tag: tissue

value: crown

tag: water status

value: well-watered

tag: ploidy

value: octoploid


title: 2-43 WW8 block5

description:
sample name in processed data file:
a8h_theo_b5s44qb28


title: 2-37 WW8 block5

description:
sample name in processed data file:
a8h_sim_b5s48qb32


title: Huvec-27

tag: array

tag: slide

tag: promocell catalogue number

tag: mds race


title: Sk-hep1-IL-37 rep2

city: singapore

first: Yu

last: Mei

state: Singapore

address: 28 medical drive, center for life sciences, 03/09

country: Singapore

institute: NUS

description:
Gene expression in SK-hep1-IL-37
SAMPLE2 REP2

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray C-Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Tiff at 20 bit, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters for gene expression 1 color according to grid: 723632 to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: HCC cell, IL-37, rep2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent: 5190-2331) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were cultured in DMEM media with 10% FBS at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: RNA was prepared using the Rneasy mini kit (Qiagen, Hilden, Germany) following the manufacturer's recommendations.

treatment_protocol: 1x10^5 cells were seeded in 6 well plate for 24 hours.

value: liver

value: HCC cell line Sk-hep1

tag: genotype

value: IL-37 overexpression


title: Huvec-26_TNF

tag: cell type

tag: promocell lot number

tag: promocell age

tag: promocell gender

tag: promocell race


title: RNA181102RH_26168_NAcCore_S19

city: Portland

first: Priscila

last: Darakjian

state: OR

address: 3181 SW Sam Jackson Park Road, L470

department: Behavioral Neuroscience

institute: Oregon Health and Science University

data_processing:
FastQC (Babraham Bioinformatics) was used for quality checks on the raw sequence data.
Reads were aligned to MacaM genome assembly  using STAR version 2.5.2b (Dobin et al., 2013) with default parameters except for the following: outFilterMismatchNmax = 2 and outFilterMultimapNmax = 1.
Using HTSeq version 0.6.1p1 (Anders et al., 2015) and the MacaM_Rhesus_Genome_Annotation_v7.8.1 GTF annotation file read counts were summarized at the gene level.
Generalized linear models, using DESeq2 (Love et al., 2014), were used to detect differential expression between High Drinkers and Controls (HDvsControls), Low Drinkers and Controls (LDvsControl), and High Drinkers and Low Drinkers (HDvsLD).
Genome_build: Macaca mulatta (MacaM)
Supplementary_files_format_and_content: Reads Counts normalized through DESeq2 (csv format)

organism: Macaca mulatta

source_name: Dissected Tissue (Brain) - Nucleus Accumbens

extract_protocol:
After the 12-month open access period, and without imposed abstinence, a previously described, detailed necropsy protocol (Daunais et al., 2010) was used to systematically collect tissues from all subjects. Briefly, monkeys were anesthetized with ketamine (10 mg kg − 1), maintained on isoflurane and perfused with ice-cold oxygenated monkey perfusion solution (containing [in mM] 124 NaCl, 23 NaHCO3, 3 NaH2PO4, 5 KCl, 2 MgSO4, 10 D-glucose, 2 CaCl2). Brains were quickly removed and sectioned along the coronal plane using a brain matrix (Daunais et al., 2010).The block containing the NAcc was initially selected by each individual’s magnetic resonance imaging and verified using visible landmarks. In macaques, the NAcc is ~ 2 mm × 2 mm and extends ~ 3 mm rostral/caudal (Daunais et al., 2010). The core is differentiated from the shell based on visible landmarks such as the curvature of the internal capsule in which the area just ventral to its end is the NAcc. From the frozen 4 mm coronal brain block maintained on dry ice, a small circular dissection of ~ 1 mm^3 was made, taking care to not collect white matter from the tract (dorsal to the core). This relatively small dissection avoids the NAc shell and yields enough tissue for nucleic acid isolation. RNA was extracted from the NAcc using the All Prep DNA/RNA/microRNA Universal Kit (Qiagen Sciences, Germantown, MD, USA) following the manufacturer’s recommendations.
RNA libraries were prepared from cDNA for sequencing using Illumina TruSeq DNA library kit.
Samples were multiplexed in 8 lanes with 3 samples per lane on an Illumina HiSeq 2500 sequencer. RNA-Seq type was strand-specific paired-end with PolyA+ strand-select protocol

treatment_protocol: SIP is an effective protocol to establish voluntary ethanol consumption through the use of interval schedules for food delivery. Briefly, banana-flavored food pellets (1 g) were delivered every 300 seconds until the preset volume of fluid was consumed. After SIP of water only, monkeys were induced to increasing volumes of 4% (w/v) ethanol in 30 day increments equivalent to: 0.5, 1.0, and 1.5 g/kg/day, respectively. Following induction, “open-access” (or 22 hr/day concurrent access to ethanol on one spout and water on the other spout) began. The subjects received three meals (approximately 2 hours apart) of banana pellets each session (day), with the first meal available at the session start. Each daily session of 22 hrs began in the late morning and ended early morning the following day. Ethanol was removed for 2 hours each day for cage cleaning, blood draws, and other routine procedures. During the 2 hours of ethanol removal, monkeys were pair-housed by removing a barrier between adjacent cages. The lighting schedule in the room was 11 hrs light, 13 hrs dark; the lights went off 7 hrs after the start of the open-access session. The details of the open-access protocol are discussed in Grant et al., (2008). Ethanol intake was recorded daily with a 0.5 second resolution. Control subjects were housed in the same room as the ethanol drinking subjects of the same cohort and participated in all experimental manipulations. For the controls, SIP and self-administration conditions were identical, with the exception that both spouts dispensed water. A maltose dextrin solution (10% in water) was given to the controls to calorically match the drinkers and controls. The dextrin solution was given at the beginning of each daily session by attaching a bottle to the front of the housing cage.

tag: cohort

tag: alcohol consumption group

value: VHD

tag: ethanol intake (g/kg)


title: Liberty WW8 block5

description:
sample name in processed data file:
a8h_lib_b5s46qb30

value: tetraploid


title: RNA181102RH_26148_NAcCore_S7

value: HD

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: RNA181102RH_26104_NAcCore_S22

value: Control


title: 1-78 WW8 block5

description:
sample name in processed data file:
a8h_alv_b5s47qb31


title: Sk-hep1-venus rep2

description:
Gene expression in SK-hep1-control
SAMPLE1 REP2

source_name: HCC cell, control, rep2

tag: cell line

value: control


title: RNA181102RH_26082_NAcCore_S21

tag: tissue


title: Trailblazer WW7 block1

description:
sample name in processed data file:
a7h_trail_b1s8qb8

tag: water status


title: Sk-hep1-venus rep1

description:
Gene expression in SK-hep1-control
SAMPLE1 REP1

source_name: HCC cell, control, rep1


title: 2-43 WW7 block1

description:
sample name in processed data file:
a7h_theo_b1s6qb6

tag: ploidy


title: Huvec-25

value: Umbilical vein endothelial cells

tag: treatment

tag: ChIP

tag: array

value: newborn

value: female

tag: pedsex


title: RNA181102RH_25882_NAcCore_S24


title: 2-37 WW7 block1

description:
sample name in processed data file:
a7h_sim_b1s9qb9


title: RNA181102RH_25811_NAcCore_S13

value: LD


title: Liberty WW7 block1

description:
sample name in processed data file:
a7h_lib_b1s10qb10


title: Huvec-22

value: untreated

tag: slide

tag: promocell catalogue number

value: caucasian

tag: mds race

value: EUROPE


title: Huvec-24

tag: cell type

tag: promocell lot number

tag: promocell age


title: Huvec-22_TNF

source_name: Umbilical vein endothelial cells (primary cell line), treated with TNFa, 24 hours

value: treated with TNFa, 24 hours

tag: promocell gender

tag: promocell race


title: Huvec-25_TNF


title: Huvec-26


title: RNA181102RH_25790_NAcCore_S18

tag: cohort

tag: alcohol consumption group

tag: ethanol intake (g/kg)


title: Sk-hep1-IL-37 rep1

description:
Gene expression in SK-hep1-IL-37
SAMPLE2 REP1

source_name: HCC cell, IL-37, rep1

tag: tissue

value: liver

tag: cell line

tag: genotype


title: Trailblazer Arid7-R1 block1

description:
sample name in processed data file:
dr_trail_b1s40qb24

value: crown

tag: water status

value: recovery

tag: ploidy

value: octoploid


title: 1-78 WW7 block1

description:
sample name in processed data file:
a7h_alv_b1s7qb7

value: well-watered


title: RNA181102RH_25207_NAcCore_S9


title: Huvec-21_TNF

tag: treatment

tag: ChIP

tag: array

tag: pedsex


title: Huvec-20_TNF

tag: cell type

tag: slide

tag: promocell catalogue number

value: male

tag: mds race


title: RNA181102RH_25407_NAcCore_S11

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: 2-43 Arid7-R1 block7

description:
sample name in processed data file:
dr_theo_b7s56qb37


title: RNA181102RH_25787_NAcCore_S3

value: HD


title: RNA181102RH_26016_NAcCore_S4


title: Huvec-21

tag: promocell lot number

tag: promocell age

tag: promocell gender

tag: promocell race


title: RNA181102RH_25184_NAcCore_S17

tag: cohort

tag: alcohol consumption group

tag: ethanol intake (g/kg)

tag: tissue


title: Huvec-20


title: 2-43 Arid7-R1 block5

description:
sample name in processed data file:
dr_theo_b5s50qb33

tag: water status

tag: ploidy


title: Huvec-2_TNF

tag: treatment

tag: ChIP


title: Huvec-24_TNF

tag: array

tag: pedsex


title: RNA181102RH_25240_NAcCore_S23


title: 2-43 Arid7-R1 block1

description:
sample name in processed data file:
dr_theo_b1s42qb26


title: RNA181102RH_24818_NAcCore_S15

value: Control


title: Trailblazer Arid7-R1 block5

description:
sample name in processed data file:
dr_trail_b5s52qb35


title: Huvec-19_TNF

tag: cell type

value: Umbilical vein endothelial cells

tag: slide

value: asian


title: Huvec-2

tag: promocell catalogue number

value: newborn

tag: mds race


title: 2-37 Arid7-R1 block1

description:
sample name in processed data file:
dr_sim_b1s39qb23


title: Liberty Arid7-R1 block5

description:
sample name in processed data file:
dr_lib_b5s51qb34

value: tetraploid


title: RNA181102RH_24698_NAcCore_S8


title: Huvec-19

value: untreated

tag: promocell lot number

tag: promocell age

value: female


title: 2-43 Arid7-R1 block11

description:
sample name in processed data file:
dr_theo_b11s63qb40


title: Liberty Arid7-R1 block1

description:
sample name in processed data file:
dr_lib_b1s41qb25


title: RNA181102RH_24340_NAcCore_S5


title: Huvec-18_TNF

tag: promocell gender

tag: promocell race

value: caucasian

value: EUROPE


title: 1-78 Arid7-R1 block9

description:
sample name in processed data file:
dr_alv_b9s61qb39


title: Huvec-18


title: 1-78 Arid7-R1 block7

description:
sample name in processed data file:
dr_alv_b7s57qb38


title: Huvec-17_TNF

value: treated with TNFa, 24 hours


title: RNA181102RH_23779_NAcCore_S14

tag: cohort

tag: alcohol consumption group


title: RNA181102RH_23778_NAcCore_S16

tag: ethanol intake (g/kg)

tag: tissue


title: RNA181102RH_23784_NAcCore_S6

value: VHD


title: RNA181102RH_23762_NAcCore_S12


title: 1-78 Arid7-R1 block1

description:
sample name in processed data file:
dr_alv_b1s43qb27

value: crown

tag: water status

value: recovery

tag: ploidy


title: 1-78 Arid7-R1 block5

description:
sample name in processed data file:
dr_alv_b5s53qb36

value: octoploid


title: RNA181102RH_25157_NAcCore_S10

value: LD


title: Trailblazer Arid7 block5

description:
sample name in processed data file:
d_trail_b5s20qb15

value: water-stressed


title: RNA181102RH_22770_NAcCore_S1

value: Dissected Tissue (Brain) - Nucleus Accumbens


title: Huvec-16_TNF

tag: treatment

tag: ChIP


title: Huvec-17

tag: array

tag: pedsex


title: Huvec-16

tag: cell type

tag: slide


title: drug-7_F_2

extract_protocol:
Qiagen RNeasy Mini Kit
We extracted RNA from HEK293 cells and used an RT to amplify out our barcode sequence
Cells were lysed (buffer supplied in the kit) on the dishes and prepped according to the manufacturer's protocol (RNeasy miniprep)
The plasmid DNA library construction is simple Illumina amplicon sequencing.
RNA was reverse transcribed (Superscript IV) with a gene specific primer and the resulting cDNA was amplified with primers containing necessary adaptors for illumina sequencing

value: agonist Isoproterenol + forskolin

tag: molecule

value: total RNA


title: Huvec-15_TNF

value: Umbilical vein endothelial cells

tag: promocell catalogue number

tag: promocell lot number

tag: mds race


title: Trailblazer Arid7 block1

description:
sample name in processed data file:
d_trail_b1s1qb1


title: 2-43 Arid7 block11

description:
sample name in processed data file:
d_theo_b11s32qb21


title: RNA181102RH_20336_NAcCore_S20


title: drug-7_F_1


title: Huvec-15

tag: promocell age

value: newborn

tag: promocell gender

tag: promocell race


title: drug-7_625_2

value: agonist Isoproterenol

tag: dosage


title: PP_r2

city: Manchester

first: Tim

last: Somervaille

address: Wilmslow Rd

department: Manchester Institute

country: United Kingdom

institute: Cancer Research UK

data_processing:
Library strategy: CRISPR screen
The original FASTQ file was demultiplexed according to the 10 samples barcodes and the adaptors were trimmed using cutadapt (version 1.7.1). Then, the sgRNA guide sequence (20-mer) was aligned to the GeCKO library index (Human GeCKOv2 half libraries A and B)  using bowtie by allowing up to one mismatch.
Supplementary_files_format_and_content: read counts

organism: synthetic construct

source_name: GECKO A+B plasmid library replicate 2

growth_protocol: Human THP1 cells were from DMSZ and were cultured under standard conditions (5% CO2, 37°C) in RPMI1640 supplemented with 10% FBS, 10U/mL penicillin, 10μg/mL streptomycin and 2mM L-glutamine. Culture densities were 5x10^4 - 5x10^5 for cells in liquid culture.

extract_protocol:
Genomic DNA was isolated using a QIAamp Blood Maxi kit as per manufacturer’s instructions.
To verify uniform representation of sgRNAs a two-step PCR was performed in which PCR1 amplifies the lentiviral sequence containing the 20bp sgRNA cassette and PCR2 attaches Illumina sequencing adapters and barcodes. In PCR#1, 50ng of each half library was amplified using V2 adaptor primers (http://genome-engineering.org/gecko/) using Phusion High Fidelity master mix (Thermo). The thermocycling conditions were: 98C for 3min, 15 cycles of (98C for 20s, 60C for 20s, 72C for 30s) and 72C for 7min. For each half library there were two PCR#1 replicates. 5uL of each #PCR1 product was run in 1.5% TAE-agarose ethidium bromide gel to verify amplicon length (~300bp). For the PCR#2 reaction, which is carried out to add appropriate Illumina sequencing adapters to the PCR#1 product, 5uL of each PCR#1 product was used as template. Unique barcoded forward and reverse primer combination were used for each PCR#2 reaction as described. Thermocycling conditions and cycle numbers were the same as for PCR#1. 5uL of PCR#2 product was run on a 1.5% TAE-agarose ethidium bromide gel to verify amplicon length (~350bp). All PCR#2 products were then pooled and gel purified from 2% TAE-agarose ethidium bromide gel using a QiaQuick kit, as per manufacturer’s instructions . The pooled library was then quantified by Qubit fluorometric quantitation and sequenced with 10% PhiX using a HiSeq 2500 System (Rapid v3). The sgRNA cassettes recovered from lentivirally-infected cells were amplified using PCR#1 and PCR#2 reactions as described above, but with some modifications. To preserve full library complexity and representation during sequencing, 244μg genomic DNA (~300-fold coverage) was used in each PCR#1 reaction per sample. For each PCR#1, we used 5ug gDNA using V2 adaptor primers and Phusion High Fidelity master mix (Thermo Fisher). The thermocycling conditions were: 98C for 30s, 19 cycles of (98C for 1s, 62C for 5s, 72C for 35s), 72C for 1min. 50 PCR#1 reactions were carried out per sample to capture the full representation of the screen. All the PCR#1 reactions for each biological sample were pooled together and 10uL of pooled #PCR1 product was used as template for PCR#2 reactions using barcoded primers for Illumina sequencing. The thermocycling conditions were: 98C for 30s, 19 cycles of (98C for 1s, 70C for 5s, and 72C for 35s), 72C for 1 min. For each sample, we performed at least 15 PCR#2 reactions (1 per 10K constructs). We included PCR#2 technical replicates for every sample (barcoded differently) to avoid duplicate sequences due to PCR over-amplification of constructs during sequencing. PCR#2 products of each technical replicate were pooled together and gel purified. The gel purified products were quantified by Qubit fluorometric quantitation (Thermo Fisher). Pooled PCR#2 products for each biological sample were then normalized before combining uniquely barcoded separate PCR replicates for all biological samples. The amount of amplifiable DNA was assessed by real time PCR using P5 and P7 Illumina primers. High throughput sequencing was performed with 15% PhiX and a HiSeq 2500 system.

treatment_protocol: 2x10^8 THP1 AML cells were infected with lentiviral particles at a multiplicity of infection of 0.3 and selected with 3ug/ml puromycin for seven days. 6×10^7 cells (representing 500-fold coverage of the library) were then washed with PBS and frozen for subsequent genomic DNA (gDNA) isolation. This was the early time point (Day 0). The remaining cells were treated with either DMSO or 250nM OG-86 for 18 days (sufficient for ten population doublings). Cells were divided between two groups of ten T225 flasks; each flask was seeded at 2×10^5 cells/mL in a total volume of 120mL. Cells were split every three days and medium and compound replaced. At the end of the experiment cells were frozen at -80°C for subsequent genomic DNA isolation using a QIAamp Blood Maxi kit as per manufacturer’s instructions.

tag: cell line

tag: sample type

value: plasmid


title: 2-43 Arid7 block9

description:
sample name in processed data file:
d_theo_b9s26qb19

tag: tissue

tag: water status

tag: ploidy


title: drug-7_625_1

tag: treatment


title: PP_r1

source_name: GECKO A+B plasmid library replicate 1


title: Huvec-14_TNF

tag: ChIP

tag: array

value: female

tag: pedsex


title: Huvec-14

tag: cell type

value: untreated

tag: slide

value: caucasian


title: drug-7_150_2

tag: molecule


title: D18_CompB_r1

source_name: Day 18 compound B replicate 1

value: monocytic cell line derived from an acute monocytic leukemia patient


title: RNA181102RH_21177_NAcCore_S2

tag: cohort

tag: alcohol consumption group

tag: ethanol intake (g/kg)


title: 2-43 Arid7 block1

description:
sample name in processed data file:
d_theo_b1s5qb5


title: drug-7_150_1


title: drug-7_0_2


title: Huvec-13_TNF

value: treated with TNFa, 24 hours

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

tag: promocell gender

tag: promocell race

tag: mds race

value: EUROPE


title: 2-37 Arid7 block7

description:
sample name in processed data file:
d_sim_b7s22qb17

tag: tissue

value: crown

tag: water status

tag: ploidy


title: Huvec-13

tag: treatment

tag: ChIP

tag: array


title: D18_DMSO_r2

source_name: Day 18 DMSO replicate 2

tag: cell line

tag: cell type


title: D18_DMSO_r1

source_name: Day 18 DMSO replicate 1


title: Huvec-12_TNF

tag: slide

value: male

tag: pedsex


title: drug-7_0_1

tag: dosage

tag: molecule


title: Huvec-12

source_name: Umbilical vein endothelial cells (primary cell line), untreated

tag: promocell catalogue number

tag: promocell lot number


title: drug-6_F_2


title: ET_r2

source_name: Early timepoint replicate 2


title: 2-37 Arid7 block1

description:
sample name in processed data file:
d_sim_b1s2qb2

value: octoploid


title: Huvec-11_TNF

tag: promocell age

tag: promocell gender


title: D18_CompB_r2

source_name: Day 18 compound B replicate 2


title: ET_r1

source_name: Early timepoint replicate 1


title: 2-43 Arid7 block7

description:
sample name in processed data file:
d_theo_b7s23qb18

value: water-stressed


title: drug-6_F_1


title: Huvec-11

tag: promocell race

tag: mds race


title: 2-43 Arid7 block5

description:
sample name in processed data file:
d_theo_b5s17qb12

tag: tissue

tag: water status


title: drug-6_625_2

tag: treatment


title: Liberty Arid7 block5

description:
sample name in processed data file:
d_lib_b5s16qb11

tag: ploidy

value: tetraploid


title: drug-2

value: unknown


title: Liberty Arid7 block1

description:
sample name in processed data file:
d_lib_b1s4qb4


title: drug-6_625_1

value: total RNA


title: drug-3


title: Huvec-10_TNF

value: Umbilical vein endothelial cells

tag: ChIP

tag: array


title: drug-6_150_2


title: 1-78 Arid7 block11

description:
sample name in processed data file:
d_alv_b11s33qb22


title: mix_glu_mal

city: Leuven

first: Abbas

last: Jariani

address: Gaston Geenslaan 1, box 2471

department: KU Leuven - VIB Centre for Microbiology

country: Belgium

institute: KU Leuven - VIB

description: Contains 50-50 mix of cells from two growth conditions: I) cells growing to glucose (identical to glu_12h) II) cells continuously growing on maltose

data_processing:
transcript counts were derrived from fastq files, using cellranger 2.0.0 software, with 'cellranger count' command. This command demultiplexes transcripts single cells based on the barcode in the reverse transcription primer. The demultiplexed reads were aligned to yeast reference genome (R64-1-1.90), and transcript counting is carried out based on the Unique Molecular Identifier (UMI) barcodes.
Genome_build: R64-1-1.90
Supplementary_files_format_and_content: one file per sample. Each row represents a gene, and each column represents a cell.

source_name: Baker's yeast, s288c

growth_protocol: Cells were grown in rich media with either glucose (YP-glucose-5%) or maltose (YP-maltose-10%) in turbido-stat conditions. The cell counts were kept below 10 million cells per ml.

extract_protocol: 10x Genomics, V2 chemistry, For each sequencing run (1 NextSeq & 1 HiSeq with 2 lanes) and each sequencing lane and each sample, three fastq files are provided. The first fastq file corresponds to i7 index (I1, 8bps) and indicates the sample index. The second fastq files corresponds to read 1 (R1, 26bps) and indicates the cell barcode and Unique Molecular Identifier (UMI). The 3rd fastq file corresponds to Read 2 (R2, 98 bps) and corresponds to cDNA sequence.

treatment_protocol: The cells were initially inoculated in YP-maltose-10% and grown in turbido-stat for 3 overnights. Afterwards they were washed into glucose media (3x, 5min, 3000rpm). After 6h of growth in glucose, the first sample was taken (glu_6h). After 12h of glucose growth the 2nd sample was taken (glu_12h). Afterwards the cells were washed into maltose media, were they cease to grow and enter lag phase. 1h after the shift to maltose the 3rd sample was taken (in_lag_1h). After 3h in lag phase the 4th sample was taken (in_lag_3h). The 5th sample is a  50-50 mix of cells from two growth stages: A part of it is the cells from maltose pregrowth, and another part is the cells from glu_12h sample.

tag: strain

value: BY4741, MAL13::HygR-MAL63_c9  SAL1+

tag: media

value: mix (glucose growth & maltose growth)

tag: timepoint


title: inlag_3h

description: Sampled 3h after shift from glucose to maltose, during lag phase

value: lag phase in maltose

value: 3h after shift from glucose


title: drug-6_150_1

data_processing:
For NextSeq_MiSeq.map.csv.gz - We used the BBTools suite(https://jgi.doe.gov/data-and-tools/bbtools/) of programs to  process our sequencing data using the default settings unless otherwise noted. First,  we used BBDuk2 to filter out any reads matching PhiX (k=23, mink=11, hdist=1) and to  trim off any Illumina sequencing adapters. We then used BBMerge to merge our paired  end reads. We performed another round of trimming with BBDuk2 to ensure no  adapters were left over after merging and to remove any sequence with an N base call.  After merging and trimming the reads, we used a custom Python script (bcmap.py) to  generate a consensus nucleotide sequence for each barcode.  Briefly the script works as follows. First, we split each read into the 15 nt barcode and its  corresponding variant. We then generate a dictionary that maps each barcode to its list  of unique sequences and their counts. To enable majority basecalls, we drop any  barcode that has less than 3 reads. We then pass the barcodes through a series of  filters to eliminate potential errors introduced by barcodes that are mapped to multiple  variants. Since we barcoded and mutagenized the ADRB2 gene in separate pieces,  barcodes can be contaminated with variants from different parts of the ADRB2 gene.  We address this case by using BBMap to align every barcode’s sequences to the  ADRB2 reference and consider that barcode to be contaminated if any sequence aligns  >5 nt away from the most common sequence. Another source of contamination comes  from the chip-synthesized library itself, which contains a significant number of single  base deletions. We consider a barcode contaminated if it has any sequences of  different lengths as it is unlikely that a single base deletion will come from an Illumina  sequencer by chance. However, these filters would not catch the case where a barcode  is contaminated with variants from the same piece of ADRB2. As we only synthesized  the missense variants, we expect variants within the same piece of ADRB2 to be a  Levenshtein distance of 4 from each other on average (approximately two changes to  WT and two changes to a new codon). Thus, we drop any barcode that has a sequence  with >1 read at a Levenshtein distance of 4 away from that barcode’s most common  sequence. Lastly, we generate a consensus sequence by taking the majority base call  at each position and call an N at any ties.
For drug-*_cond-bcs-counts.txt.gz we used awk to substring and count the first 15 nt, which corresponds to the barcode. We then join in addional information such as the drug condition and repeat.

value: agonist Isoproterenol

tag: dosage


title: Huvec-1_TNF

tag: cell type

tag: slide

value: newborn

value: female

value: caucasian

tag: pedsex


title: 2-37 Arid7 block5

description:
sample name in processed data file:
d_sim_b5s19qb14

source_name: crown


title: 1-78 Arid7 block7

description:
sample name in processed data file:
d_alv_b7s21qb16


title: Huvec-1

value: untreated

tag: promocell catalogue number

tag: promocell lot number

tag: promocell age

value: EUROPE


title: inlag_1h

description: Sampled 1h after shift from glucose to maltose, during lag phase

value: 1h after shift from glucose


title: 1-78 Arid7 block5

description:
sample name in processed data file:
d_alv_b5s18qb13

value: crown

value: octoploid


title: Huvec-0_TNF

value: treated with TNFa, 24 hours

tag: promocell gender

tag: promocell race

value: male

tag: mds race


title: Huvec-0

tag: treatment


title: drug-6_0_1

tag: molecule

value: total RNA


title: 1-78 Arid7 block1

description:
sample name in processed data file:
d_alv_b1s3qb3

tag: tissue

tag: water status

value: water-stressed

tag: ploidy


title: glu_12h

description: Sampled during glucose growth, 12h after shift from continuous maltose growth

tag: strain

value: BY4741, MAL13::HygR-MAL63_c9  SAL1+

tag: media

value: glucose growth

value: 12h after shift from maltose


title: glu_6h

description: Sampled during glucose growth, 6h after shift from continuous maltose growth

tag: timepoint

value: 6h after shift from maltose


title: Huvec-32_TNF

tag: cell type

value: Umbilical vein endothelial cells

tag: ChIP

tag: array


title: Huvec-10

tag: slide

tag: promocell catalogue number

value: newborn

tag: pedsex


title: AtopicW5

status: Public on Feb 05 2020

city: Seattle

first: Elia

last: Tait Wojno

state: WA

address: 750 Republican St.

department: Department of Immunology

institute: University of Washington

data_processing:
Drop-seq Core Computation Protocol (version 2.0.0, 9/28/18) with Drop-seq_tools-1-12; Default pipeline and settings unless noted otherwise.
FastqToSam (Picard-tools-2.8.2)
TagBamWithReadSequenceExtended (BASE_RANGE= 1-12, BASE_QUALITY= 10, BARCODED_READ= 1, DISCARD_READ= False, TAG_NAME= XC, NUM_BASES_BELOW_QUALITY= 1)
TagBamWithReadSequenceExtended (BASE_RANGE= 13-20, BASE_QUALITY= 10, BARCODED_READ= 1, DISCARD_READ= True, TAG_NAME= XM, NUM_BASES_BELOW_QUALITY= 1)
FilterBAM (TAG_REJECT= Q)
TrimStartingSequence (SEQUENCE= AAGCAGTGGTATCAACGCAGAGTGAATGGG, MISMATCHES=0, NUM_BASES= 5)
SamToFastq (Picard-tools-2.8.2)
STAR-2.7.0f alignment with CanFam3.1 and CanFam3.1.96 from ensembl
SortSam (SO= queryname) (Picard-tools-2.8.2)
MergeBamAlignment (INCLUDE_SECONDARY_ALIGNMENT= false, PAIRED_RUN= false) (Picard-tools-2.8.2)
TagReadWithGeneExon (TAG= GE)
DigitalExpression (MIN_NUM_GENES_PER_CELL= 10)
Genome_build: CanFam3.1 and CanFam3.1.96 from ensembl
Supplementary_files_format_and_content: .txt (single-cell digital gene expression matrix)

organism: Canis lupus familiaris

source_name: peripheral blood

extract_protocol:
Drop-seq protocol provided online by MacCarroll lab (version 3.1, 12/28/2015)
Nextera XT Library Preparation Kit

value: PBMCs

tag: allergy status

value: atopic dermatitis

tag: breed

value: West Highland White Terrier

tag: Sex

value: female

tag: age (years)


title: 1-78 Arid7 block9

description:
sample name in processed data file:
d_alv_b9s27qb20


title: AtopicW4


title: HealthyW5

value: healthy


title: HealthyW4


title: Healthy3

value: Mixed breed


title: Atopic1

value: Cocker Spaniel


title: Healthy2


title: Atopic2

value: German Shepherd


title: Healthy1

value: male


title: drug-6_0_2

tag: dosage

tag: molecule

value: total RNA


title: colorectal cancer_34

city: Beijing

first: Rui

last: Chen

address: No.10 Xitoutiao, You An Men

country: China

institute: Capital medical university

hyb_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 6 out of 12 samples have flags in “P” or “M” (“All Targets Value”) were retained for further analyses. When comparing two groups of profile differences (such as disease versus control), the “fold change” (i.e. the ratio of the group averages) between the groups for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test. circRNAs having fold changes 2 and p-values  0.05 are selected as the significantly differentially expressed. One can filter the analysis outputs and rank the differentially expressed circRNAs according to fold change, p-value etc, using Microsoft Excel’s Data/Sort & Filter functionalities.

source_name: colorectal cancer

label_protocol: Sample labeling and array hybridization were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

extract_protocol: Total RNA was isolated using TRIzol (Invitrogen) and purified with RNeasy mini kit (QIAGEN) according to manufacturer’s instructions. RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis.

tag: subject id

tag: age

tag: gender

tag: tissue

value: colorectal adenocarcinoma


title: WT_2

city: Calgary

first: Sarah

middle: J

last: Childs

state: AB

address: 3330 Hospital Drive NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

data_processing:
Basecalling: bcl2fastq v2.20.0.422
Transcript quantification: kallisto version 0.42.4
Transcript database: NCBI mRNA RefSeq (Feb 2016)
Genome_build: DanRer10

source_name: whole embryo

growth_protocol: ZF embryos were grown at 28°C in E3 media until 72hpf.

extract_protocol:
RNA extracted from 8 whole embryos (minus dissected tail) per sample using RNeasy Plus mini kit (QIAGEN)
NEBNext Ultra II Directional RNA Library Prep kit (New England Biolabs)

tag: genotype

value: wild type


title: DKO_3

value: double homozygous hnrnpul1/1l mutant


title: WT_1


title: DKO_1


title: DKO_2


title: Atopic3

value: Pug


title: WT_3


title: Imp::GFP RNAseq 3

city: Oxford

first: Aino

middle: Inkeri

last: Järvelin

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

data_processing:
Reads from three Imp RIP-seq libraries and three RNA-seq libraries were mapped to the D. melanogaster genome (BDGP6.22.97) downloaded from ENSEMBL using the STAR aligner (2.5.3a) (Dobin et al., 2013). The aligned reads were then assigned to genes using htseq-count (0.11.2) (Anders et al., 2015). Imp RIP-seq enrichment over baseline RNA expression (RNA-seq) was calculated from gene counts after library size correction, and genes were ranked according to this ratio. We additionally used DESeq2 (1.24.0) (Love et al., 2014) to determine statistically significant difference between the RIP-seq and RNA-seq. Genes with very low abundance (those with total count of less than 10 across 3 RNA-seq libraries) were ignored from ranking. Non-coding RNAs that overlap other genes were flagged up.
Genome_build: BDGP6.22.97
Supplementary_files_format_and_content: Coverage along D. melanogaster genome (bedgraph file). Count tables for D. melanogaster genes for all six samples (using htseq-count on exon annotations) with additional information including differential expression analysis with DESeq2 and flagging of overlapping gene regions.

organism: Drosophila melanogaster

source_name: L3 larval brain

growth_protocol: Drosophila melanogaster flies were grown at 25 °C on standard cornmeal-agar medium.

extract_protocol:
Brains were removed and flash frozen in liquid nitrogen before lysis. RNA was harvested using RNASpin Mini kit (GE Healthcare). polyA RNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to manufacturer’s instructions.
Poly(A) enriched RNA was then used for library production using the Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Life Technologies).
Libraries were prepared using Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Life Technologies) according to manufacturer's instructions.

value: brain

value: wandering L3 larva

tag: sample type

value: whole transcriptome


title: Imp::GFP RNAseq 2


title: Imp::GFP RNAseq 1


title: Imp RIPseq 3

extract_protocol:
Brains were removed and flash frozen in liquid nitrogen before lysis. Imp::GFP was immunoprecipitated using anti-GFP agarose beads. RNA was harvested using RNASpin Mini kit (GE Healthcare). polyA RNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to manufacturer’s instructions.
Poly(A) enriched RNA was then used for library production using the Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Life Technologies).
Libraries were prepared using Ion Total RNA-Seq Kit v2 for Whole Transcriptome Libraries (Life Technologies) according to manufacturer's instructions.

value: IP of Imp::GFP


title: Imp RIPseq 2


title: Imp RIPseq 1


title: colorectal cancer_23


title: normal mucosa-5

source_name: normal mucosa

value: normal mucosa


title: normal mucosa-23


title: colorectal cancer_5


title: colorectal cancer_26


title: normal mucosa-25


title: normal mucosa-34


title: colorectal cancer_25


title: normal mucosa-33


title: normal mucosa-26


title: RDIPseq_RNAseH1oe

first: Nicholas

last: Proudfoot

institute: Sir William Dunn School of Pathology,  University of Oxford

description: chromatin RNA

data_processing:
Library strategy: RDIP-seq
Raw reads from RDIP-seq were aligned to reference genome hg19/GRCh37 using bowtie2. Uniquely mapped reads with no mismatches were retained for further analysis. Plus and minus strand were assigned to mapped reads using SAMtools.
RDIP-seq peaks were called using MACS2 algorithm with default options.
Genome_build: hg19
Supplementary_files_format_and_content: peak file

source_name: HeLa cells

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and RNA:DNA hybrids were isolated with S9.6 antibody for RDIP-seq
The RNA component of the R-loop was used to prepare the library using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, (E7760S) according to manufacturer's guidelines.

treatment_protocol: For RDIP-seq experiments recombinant RNase H was added the sonicated HeLa cells before S9.6 immunoprecipitation.

tag: cell type

value: cervical cancer cells

tag: genotype/variation

value: RnaseH1 over-expression


title: Gua-U1snRNP-screen-30, 300 uM Guanine, rep 6

city: Biberach an der Riß

first: Holger

last: Klein

state: Baden-Württemberg

address: Birkendorfer Straße 65

department: Global Computational Biology and Data Sciences

institute: Boehringer-Ingelheim Pharma GmbH & Co KG

data_processing:
Basecalls performed using bcl2fastq2/2.17.1.14
Reads were search for the expected amplicon patterns
Genome_build: n/a
Supplementary_files_format_and_content: tab-delimited text files include abundance values for each Sample. Fields represent: [abundance] [amplicon_sequence_name] [amplicon_variable_part1] [amplicon_variable_part2]

source_name: HEK293 cell line

growth_protocol: HEK-293 cells were grown in DMEM + 10 % FCS at 37°C in an incubator. 24 h prior to transfection, 310.000 cells were seeded per well of a 12-well plate.

extract_protocol:
RNA was extracted using the Qiagen RNeasy 96 kit.
Following random priming-based reverse transcription to cDNA, sequence amplicons of interest were generated by non-saturating PCR and PCR amplicons were purified. DNA concentration was determined on the Fragment Analyzer with NGS StandardSensitivity according to manufacturer’s instructions. Subsequently, end repair was carried out using the Ovation Library System for Low Complexity Samples kit (NuGEN) with the manufacturer’s protocol, followed by adaptor ligation from the same kit. The libraries underwent cleanup again using the MagMAX Express-96 Magnetic Particle processor and the Agencourt RNAClean XP beads (Beckmann Coulter) following the manufacturer’s protocol. Subsequently, library amplification was carried out using the Ovation Library System for Low Complexity Samples kit (NuGEN) with manufacturer’s protocol, followed by a clean-up step with Agencourt AMPure XP Beads (Beckmann Coulter). The libraries were quantified with a Quant-iT PicoGreen dsDNA Assay kit (Invitrogen) according to manufacturer’s instructions and fragment size was determined with NGS Standard Sensitivity Kit (Advanced Analytical) on a Fragment Analyzer. Based on the concentrations obtained from the PicoGreen measurement, a 2 nM dilution of the libraries in Illumina Resuspension Buffer + 0.1% Tween20 preparation (Sigma) was prepared and in the following 10 µl of each sample were mixed with a unique reverse adaptor from the 2 nM dilution. Libraries were denatured by consecutive addition of 10 µl 0.2 N NaOH, µl of 200 mM Tris-HCl, pH 7.0 and 970 µl of prechilled HT1 buffer. In a new prechilled tube, 1183 µl of prechilled HT1 buffer were added. Subsequently 117 µl of the library pool dilution and 2 µl of 20 pM PhiX control were added. Finally, the libraries were sequenced on an Illumina NextSeq 500, using 10 million single-end reads of 154 bp length  per sample, using the NextSeq 500/550 High Output Kit v2.

treatment_protocol: Cells were transfected with 600 ng of DNA (plasmid library) per well, using Lipofectamine-3000 and incubated for 48 h. Cells were then stimulated with Tetracycline or Guanine at indicated doses for 3 h, before being lysed for RNA extraction.

value: HEK293 cell lysate

tag: treatment

value: 300 uM Guanine


title: Gua-U1snRNP-screen-29, 300 uM Guanine, rep 5


title: Gua-U1snRNP-screen-32, 300 uM Guanine, rep 8


title: Gua-U1snRNP-screen-26, 300 uM Guanine, rep 2


title: Gua-U1snRNP-screen-28, 300 uM Guanine, rep 4


title: Gua-U1snRNP-screen-27, 300 uM Guanine, rep 3


title: Gua-U1snRNP-screen-31, 300 uM Guanine, rep 7


title: colorectal cancer_33

value: female


title: Gua-U1snRNP-screen-21, 100 uM Guanine, rep 5

value: 100 uM Guanine


title: Gua-U1snRNP-screen-25, 300 uM Guanine, rep 1


title: Gua-U1snRNP-screen-24, 100 uM Guanine, rep 8


title: Gua-U1snRNP-screen-23, 100 uM Guanine, rep 7


title: Gua-U1snRNP-screen-22, 100 uM Guanine, rep 6


title: Gua-U1snRNP-screen-19, 100 uM Guanine, rep 3


title: Gua-U1snRNP-screen-17, 100 uM Guanine, rep 1


title: Gua-U1snRNP-screen-18, 100 uM Guanine, rep 2


title: Gua-U1snRNP-screen-15, 30 uM Guanine, rep 7

value: 30 uM Guanine


title: Gua-U1snRNP-screen-14, 30 uM Guanine, rep 6


title: Gua-U1snRNP-screen-9, 30 uM Guanine, rep 1


title: Gua-U1snRNP-screen-8, untreated, rep 8

value: untreated


title: Gua-U1snRNP-screen-13, 30 uM Guanine, rep 5


title: Gua-U1snRNP-screen-11, 30 uM Guanine, rep 3


title: Gua-U1snRNP-screen-16, 30 uM Guanine, rep 8


title: Gua-U1snRNP-screen-6, untreated, rep 6


title: Gua-U1snRNP-screen-7, untreated, rep 7


title: Gua-U1snRNP-screen-5, untreated, rep 5


title: Gua-U1snRNP-screen-4, untreated, rep 4


title: Gua-U1snRNP-screen-3, untreated, rep 3


title: Gua-U1snRNP-screen-1, untreated, rep 1


title: Gua-U1snRNP-screen-2, untreated, rep 2


title: Pooled Gua-HDV and Gua-hammerhead-screen-32, 300 uM Guanine, rep 8


title: Pooled Gua-HDV and Gua-hammerhead-screen-30, 300 uM Guanine, rep 6


title: Pooled Gua-HDV and Gua-hammerhead-screen-28, 300 uM Guanine, rep 4


title: Pooled Gua-HDV and Gua-hammerhead-screen-29, 300 uM Guanine, rep 5


title: Gua-U1snRNP-screen-20, 100 uM Guanine, rep 4


title: Pooled Gua-HDV and Gua-hammerhead-screen-25, 300 uM Guanine, rep 1


title: Pooled Gua-HDV and Gua-hammerhead-screen-27, 300 uM Guanine, rep 3


title: Pooled Gua-HDV and Gua-hammerhead-screen-23, 100 uM Guanine, rep 7


title: Pooled Gua-HDV and Gua-hammerhead-screen-31, 300 uM Guanine, rep 7


title: Pooled Gua-HDV and Gua-hammerhead-screen-26, 300 uM Guanine, rep 2


title: Gua-U1snRNP-screen-10, 30 uM Guanine, rep 2


title: Pooled Gua-HDV and Gua-hammerhead-screen-22, 100 uM Guanine, rep 6


title: Pooled Gua-HDV and Gua-hammerhead-screen-18, 100 uM Guanine, rep 2


title: Gua-U1snRNP-screen-12, 30 uM Guanine, rep 4


title: Pooled Gua-HDV and Gua-hammerhead-screen-21, 100 uM Guanine, rep 5


title: Pooled Gua-HDV and Gua-hammerhead-screen-16, 30 uM Guanine, rep 8


title: Pooled Gua-HDV and Gua-hammerhead-screen-17, 100 uM Guanine, rep 1


title: Pooled Gua-HDV and Gua-hammerhead-screen-13, 30 uM Guanine, rep 5


title: Pooled Gua-HDV and Gua-hammerhead-screen-19, 100 uM Guanine, rep 3


title: Pooled Gua-HDV and Gua-hammerhead-screen-15, 30 uM Guanine, rep 7


title: Pooled Gua-HDV and Gua-hammerhead-screen-12, 30 uM Guanine, rep 4


title: Pooled Gua-HDV and Gua-hammerhead-screen-10, 30 uM Guanine, rep 2


title: Pooled Gua-HDV and Gua-hammerhead-screen-14, 30 uM Guanine, rep 6


title: Pooled Gua-HDV and Gua-hammerhead-screen-11, 30 uM Guanine, rep 3


title: Pooled Gua-HDV and Gua-hammerhead-screen-7, untreated, rep 7


title: Pooled Gua-HDV and Gua-hammerhead-screen-24, 100 uM Guanine, rep 8


title: Pooled Gua-HDV and Gua-hammerhead-screen-5, untreated, rep 5


title: Pooled Gua-HDV and Gua-hammerhead-screen-4, untreated, rep 4


title: Pooled Gua-HDV and Gua-hammerhead-screen-1, untreated, rep 1


title: Tet-Twister-screen1-30, 50 uM Tetracycline, rep 6

value: 25 uM Tetracycline


title: Pooled Gua-HDV and Gua-hammerhead-screen-2, untreated, rep 2


title: Pooled Gua-HDV and Gua-hammerhead-screen-20, 100 uM Guanine, rep 4


title: Tet-Twister-screen1-29, 50 uM Tetracycline, rep 5


title: Pooled Gua-HDV and Gua-hammerhead-screen-3, untreated, rep 3


title: Tet-Twister-screen1-32, 50 uM Tetracycline, rep 8


title: Tet-Twister-screen1-28, 50 uM Tetracycline, rep 4


title: Tet-Twister-screen1-31, 50 uM Tetracycline, rep 7


title: Tet-Twister-screen1-26, 50 uM Tetracycline, rep 2


title: Pooled Gua-HDV and Gua-hammerhead-screen-6, untreated, rep 6


title: Tet-Twister-screen1-27, 50 uM Tetracycline, rep 3


title: Tet-Twister-screen1-24, 25 uM Tetracycline, rep 8


title: Tet-Twister-screen1-23, 25 uM Tetracycline, rep 7


title: Tet-Twister-screen1-20, 25 uM Tetracycline, rep 4


title: Tet-Twister-screen1-22, 25 uM Tetracycline, rep 6


title: Tet-Twister-screen1-21, 25 uM Tetracycline, rep 5


title: Tet-Twister-screen1-19, 25 uM Tetracycline, rep 3


title: Tet-Twister-screen1-25, 50 uM Tetracycline, rep 1


title: Tet-Twister-screen1-18, 25 uM Tetracycline, rep 2


title: Tet-Twister-screen1-17, 25 uM Tetracycline, rep 1


title: Tet-Twister-screen1-16, 12.5 uM Tetracycline, rep 8

value: 12.5 uM Tetracycline


title: Pooled Gua-HDV and Gua-hammerhead-screen-9, 30 uM Guanine, rep 1


title: Tet-Twister-screen1-14, 12.5 uM Tetracycline, rep 6


title: Tet-Twister-screen1-15, 12.5 uM Tetracycline, rep 7


title: Tet-Twister-screen1-13, 12.5 uM Tetracycline, rep 5


title: Tet-Twister-screen1-12, 12.5 uM Tetracycline, rep 4


title: Tet-Twister-screen1-10, 12.5 uM Tetracycline, rep 2


title: Tet-Twister-screen1-11, 12.5 uM Tetracycline, rep 3


title: Tet-Twister-screen1-9, 12.5 uM Tetracycline, rep 1


title: Tet-Twister-screen1-8, untreated, rep 8


title: Tet-Twister-screen1-7, untreated, rep 7


title: Tet-Twister-screen1-6, untreated, rep 6


title: Tet-Twister-screen1-5, untreated, rep 5


title: Tet-Twister-screen1-4, untreated, rep 4


title: Tet-Twister-screen1-3, untreated, rep 3


title: Tet-hammerhead-library post transf - spike in conc 1:100


title: Tet-Twister-screen1-2, untreated, rep 2


title: Tet-hammerhead-library post transf - spike in conc 1:10


title: Tet-hammerhead-original library


title: Tet-hammerhead-library post transf - spike in conc 1


title: Tet-hammerhead-24, 50 uM Tetracycline, rep 8


title: Tet-hammerhead-lib, Library, rep 1


title: Tet-hammerhead-19, 50 uM Tetracycline, rep 3


title: Tet-hammerhead-23, 50 uM Tetracycline, rep 7


title: Tet-hammerhead-21, 50 uM Tetracycline, rep 5


title: Tet-hammerhead-22, 50 uM Tetracycline, rep 6


title: Tet-hammerhead-20, 50 uM Tetracycline, rep 4


title: Tet-hammerhead-16, 25 uM Tetracycline, rep 8


title: Tet-hammerhead-18, 50 uM Tetracycline, rep 2


title: Tet-hammerhead-14, 25 uM Tetracycline, rep 6


title: Tet-hammerhead-15, 25 uM Tetracycline, rep 7


title: Tet-hammerhead-12, 25 uM Tetracycline, rep 4


title: Tet-hammerhead-11, 25 uM Tetracycline, rep 3


title: Tet-Twister-screen1-1, untreated, rep 1


title: Tet-hammerhead-10, 25 uM Tetracycline, rep 2


title: Tet-hammerhead-8, untreated, rep 8


title: Tet-hammerhead-9, 25 uM Tetracycline, rep 1


title: Tet-hammerhead-6, untreated, rep 6


title: Tet-hammerhead-2, untreated, rep 2


title: Tet-hammerhead-3, untreated, rep 3


title: SNU-C1_HiC

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
library strategy: HiC-seq
Hi-C libraries were sequenced on a NextSeq 500 or a HiSeq 4000. Reads were aligned to the hg19 reference genome using BWA-MEM, and PCR duplicates were removed with Picard.
Genome_build: hg19
Supplementary_files_format_and_content: Hi-C interaction matrices were generated using 40kb as window size, and matrices were normalized using the iterative correction method (Imakaev et al., 2012). Sparse matrices represent the normalized contact frequency between two interacting genomic loci. Genomic coordinates of the bin numbers can be found in hg19_40kb.txt file.

source_name: Colon cancer cell line

extract_protocol:
Hi-C was performed using the in situ Hi-C protocol as previously described in Rao et al., 2014, using 2-5 million cells per experiment digested with the MboI restriction enzyme.
The libraries were prepared according to Illumina's instructions accompanying the Illumina TruSeq LT adaptors.

tag: cell line

value: Colon cancer cell line


title: Tet-hammerhead-1, untreated, rep 1


title: Tet-hammerhead-7, untreated, rep 7


title: Tet-hammerhead-17, 50 uM Tetracycline, rep 1