title: aT40

city: Pullman

first: Michael

middle: K

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC. Trimmomatic was used to remove low quality reads and bases
The reads for each sample were mapped to the rat (Rattus norvegicus) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than an arbitrarily chosen threshold were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The selected DMR were then summarized and annotated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window and other summary values.

source_name: Sperm

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley®™SD®™ (Harlan) at about 70 to 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and changes in body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from F1 generation control or DDT lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring.

extract_protocol:
Fifty to hundred ul of rat sperm suspension were used for DNA extraction, then 820 uL DNA extraction buffer and 80 ul 0.1M DTT added. The sample was incubated at 65C for 15 minutes. Following this incubation 80 ul proteinase K (20 mg/ml) was added and the sample was incubated at 55C for 2 hours under constant rotation. Then 300 ul of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 minutes at 4C. One ml of the supernatant was transferred to a 2 ml tube and 2 ul of glycoblue and 1 ml of cold 100 % isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20C freezer for at least one hour. After precipitation the sample was centrifuged at 13,500 rpm for 20 min at 4C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500ul of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4C at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 ul of nuclease free water.
The MeDIP DNA was used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of DDT (25 mg/kg BW/day) or dimethyl sulfoxide (vehicle). The DDT was obtained from Chem Service, Westchester PA and was injected in DMSO vehicle. The F1- F3 generation offspring were not themselves treated directly with DDT

value: DDT

tag: generation


title: aT38

status: Public on Jul 31 2018

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Rattus norvegicus

tag: treatment


title: Stage 3 rep2 [mRNA]

city: Lindau

first: Stefan

middle: Michael

last: Bauersachs

state: Zurich

address: Eschikon 27 EHB 23.1

department: Department for Farm Animals

country: Switzerland

institute: University of Zurich

library_source: transcriptomic

data_processing:
Trim Galore!, remove low quality from the 3′ end, adapter sequences, and sequences below a minimal length of 50 nt after the trimming steps
FastUniq, removal of PCR duplicates
Trimmomatic, cut 9 bases from the start of the read (HEADCROP), these bases are derived from the molecular code contained in the adapter sequence
HISAT2 (v1.4.0), mapping to the bovine genome sequence assembly
QuasR Qcount, generation of read count table for all annotated bovine genes based on the NCBI GFF3 annotation file
Counts per million (CPM) per sample filtering tool (Chen et al. 2014), remove sequences with negligible read counts, CPM cutoff: 4.21 (corresponding to an average of 20 reads per library) for at least 3 out of 20 libraries
Genome_build: bosTau8, UMD_3.1.1
Supplementary_files_format_and_content: tab-delimited text files, mRNA-Seq_count_table.txt contains mapped read counts, mRNA-Seq_filtered_counts.txt contains mapped read counts of the genes that passed the CPM filter, mRNA-Seq_CPM.txt contains counts per million (cpm) values of the genes that passed the CPM filter

molecule: total RNA

organism: Bos taurus

source_name: oviduct luminal fluid

growth_protocol: EVs were isolated by ultracentrifugation (Théry et al., 2006; Almiñana et al., 2017). First, flushing samples were centrifuged at 300 g for 15 min, followed by 2,000 g for 15 min, and then at 12,000 g for 15 min to remove cells, blood, and cell debris and ultracentrifuged twice at 100,000 g for 90 min (BECKMAN L8-M; SW41T1 rotor) to pellet EVs. The pellets were resuspended in 50 µL of PBS and stored at -80ºC for further analysis. Oviductal flushings from 3 animals were pooled for each replicate.

extract_protocol:
RNA was isolated from a total of 20 EVs samples (5 replicates, 4 stages) using RNeasy Micro kit (QIAGEN) according to the manufacturer's instructions. RNA quality and concentration was evaluated by Agilent 2100 Bionalyzer (Agilent Technologies, Santa Clara, CA.) and NanoDrop (ThermoFisher).
Poly(A) RNA was isolated starting from of 450 ng of total RNA by the use of NEXTflex™ Poly(A) beads. Poly(A) RNA was used for the preparation of mRNA libraries with the NEXTflex™ Rapid Directional qRNA-Seq Kit (Bioo Scientific). Library preparation followed the manufacturer's instructions.

tag: estrous cycle stage

value: late luteal phase, days 11-17


title: aT37


title: D2239-Y-APOE3het-M-S

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
fastq to bam using subread v1.5.0
featurecounts usinge Rsubread v1.24.2
edgeR analysis using v3.16.5
Genome_build: mm10
Supplementary_files_format_and_content: raw expresison counts form featurecounts

organism: Mus musculus

source_name: brain

growth_protocol: All animal experiments were approved through the University of Pittsburgh Institutional Animal Care and Use Committee and carried out in accordance with PHS policies on the use of animals in research. All mice were on the C57BL/6 genetic background and experimental groups consisted of both genders. Experimental mice were kept on a 12 h light-dark cycle with ad libitum access to food and water.

extract_protocol:
Fourteen days post-injury, mice were anesthetized using Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with 20mL of cold 0.1M PBS pH 7.4. Brains were rapidly removed and a 1.5 mm coronal section of the brain, including the injury site, taken by slicing the brain at -2.5 mm and -4.0 mm from bregma. Within the coronal slice, the hemispheres were separated, and the subcortical tissue was dissected out; hippocampal and cortical tissue were snap-frozen together for RNA isolation and RNA-seq. RNA was isolated from frozen cortices and hippocampi at the injury site and purified using RNeasy kit (Qiagen) according to the manufacturer recommendations. Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction.
Quality control of all RNA samples was performed on a 2100 Bioanalyzer instrument (Agilent Technologies) and samples with RIN > 8 were further used for library construction using RNA Library Prep Reagent Set (Illumina). Libraries for Next Generation Sequencing were generated by PCR enrichment including incorporation of barcodes to enable multiplexing. Sequencing was performed by the Next Generation Sequencing Center (University of Pennsylvania, http://fgc.genomics.upenn.edu/) on HiSeq 2500 machine.

treatment_protocol: At 3 months of age, these mice were randomly assigned to either sham or controlled cortical impact (CCI) experimental group. Anesthesia was induced using 5% isoflurane, after which it was maintained at 1.5% isoflurane. The head was secured using a stereotaxic frame, and core body temperature was held at 37°C using a heating pad. After shaving the heads, two separate iodine - alcohol washes were performed to sterilize the surgical site. A 50% mixture of bupivacaine and lidocaine was applied to the area and ophthalmic ointment was applied to the eyes. The scalp was opened with a midline incision exposing the dorsal aspect of the skull and the skull leveled. A 4.5 mm diameter craniotomy was performed over the left parietal cortex using a dental drill. Once the bone flap was removed, mice in the CCI group received a single impact at 1.0 mm depth with a 3.0 mm diameter metal tip onto the cortex (3 m/s, 100 ms dwell time; Impact One, Leica). Sham mice received identical anesthesia and craniotomy, but did not receive impact and are considered negative controls.

tag: Sex

value: Male

tag: genotype/variation

value: Sham


title: Stage 3 rep1 [mRNA]


title: aT36


title: Fruit-set-grape_Seedless_rep5

type: RNA

city: Logrono

first: Pablo

last: Carbonell-Bejerano

state: La Rioja

address: Madre de Dios, 51

department: Instituto de las Ciencias de la Vid y del Vino

country: Spain

institute: CSIC

description:
671-34_seedless
This sample is of developing stenospermocarpic fruitlets from the 671-34 table grape Red Globe × Crimson Seedless F1 hybrid with sdi+ genotype collected on 3 June 2010 at 2 weeks after anthesis developmental stage

hyb_protocol: If the quality control was correct according to Bioanalyzer results, 4 µg of labelled cDNA were hybridized. Hybridization solution (NimbleGen Hybridization kit) was added to each labelled cDNA and hybridization was performed for 16 h at 42ºC in a HS 4 Hybridization station (NimbleGen-Roche).

scan_protocol: Hybridized microarrays were washed with Wash buffer kit (NimbleGen-Roche) and scanned at 532 nm and 2 µm resolution in a DNA Microarray Scanner with Surescan High-Resolution Technology (Agilent technologies).

data_processing: After evaluation of hybridization quality by Experimental metrics report implemented in NimbleScan Software version 2.6 (NimbleGen-Roche), probeset signal values from all the microarray hybridizations were background corrected and normalized together using Robust Microarray Average (RMA) (Irizarry et al., 2003) in NimbleScan Software, which produces a calls file for each sample with normalized expression data for each gene.

organism: Vitis vinifera

source_name: Vitis vinifera Red Globe × Crimson Seedless F1 sdi+ hybrid stenospermocarpic fruitlets collected 2 weeks after anthesis

label_protocol: cDNA was synthesized from 10 µg of total RNA using cDNA Synthesis System Kit (NimbleGen-Roche). The cDNA preparation (1 µg) was amplified and labelled with Cy3-random nonamers using One color labeling kit (NimbleGen-Roche).

growth_protocol: A Red Globe×Crimson Seedless F1 table grape cross populations was generated from controlled crosses carried out in 2003. Progeny plants were grown in the same experimental field belonging to Sociedad Murciana de Investigación y Tecnología de Uva de Mesa (ITUM) located in Blanca, Murcia, Spain. Plants were grafted onto 1103 Paulsen rootstock conducted under parral trellis, ferti-irrigated and cultivated under the same management practices.

extract_protocol: Total RNA was extracted from frozen fruitlets of Red Globe × Crimson Seedless F1 hybrids using the Spectrum™ Plant Total RNA kit (Sigma-Aldrich) with the manufacturer’s protocol. An in column DNase digestion step with the RNase-Free DNase Set (QIAGEN) was added.

treatment_protocol: Five sdi+ seedless (660-40, 660-41, 660-57, 669-19, 671-34) and four sdi- seeded (660-43, 660-50, 669-45, 671-19) Red Globe × Crimson Seedless F1 hybrids were compared using NimbleGen microarrays. RNA was obtained form fruit set green fruits collected simultaneously for every progeny individual around midday on 3 June 2010.

tag: variety background

value: Red Globe × Crimson Seedless F1

tag: planto id

tag: genotype in sdi qtl

value: sdi+

tag: developmental stage

value: 2 weeks after anthesis

tag: tissue

value: Fruit-set green fruit

tag: fruit type

value: stenospermocarpic


title: Stage 4 rep1 [mRNA]

value: pre-ovulatory stage, days 18-20


title: D1999-Y-M-APOE3-T

value: TBI


title: Stage 2 rep5 [mRNA]

value: early luteal phase, days 5-11


title: D1998-Y-M-APOE3-S


title: aT39


title: Stage 2 rep4 [mRNA]


title: D1989-Y-M-APOE3-T


title: Stage 3 rep4 [mRNA]


title: aT34


title: aT33


title: Stage 2 rep3 [mRNA]


title: D1988-Y-M-APOE3-S


title: Stage 2 rep2 [mRNA]


title: D1973-Y-M-APOE3-T


title: aT32


title: aT31


title: Stage 2 rep1 [mRNA]


title: D1956-Y-M-APOE3-S


title: D1943-Y-M-APOE3-T


title: aT30


title: Stage 1 rep4 [mRNA]

value: postovulatory-stage, days 1-4 of estrous cycle


title: Stage 1 rep5 [mRNA]


title: Stage 1 rep3 [mRNA]


title: aT29


title: aT28


title: aT35


title: aT27


title: Stage 1 rep2 [mRNA]


title: Stage 1 rep1 [mRNA]


title: aT23


title: aT24


title: aT25


title: aT26


title: Rad21-/-_unstimulated_H3K27Ac_ChIP_rep1

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description:
KO0 K27 Rep1
H3K27 acetylation ChIP-seq of unstimulated Rad21-/- macrophages

data_processing:
Reads were aligned to mouse genome mm9 using Bowtie version 0.12.8 with default parameters. Reads aligning to multiple positions in the genome were discarded from the analysis. Quality of the ChIP-Seq libraries were assessed using ChIPQC.
Duplicate reads were identified using Picard MarkDuplicates and excluded from the downstream analysis.
Genome wide coverage tracks were generated using ‘coverage’ function in ‘GenomicRanges’ R package and exported as bigwig. The tracks were visualised using UCSC genome browser.
Genome_build: mm9
Supplementary_files_format_and_content: Bigiwig

source_name: Bone marrow-derived macrophages

growth_protocol: Bone marrow cells were isolated from WT or Rad21-/- mice and plated in 10 cm dishes containing 10 ml medium (DMEM containing 10% FCS, 20% L929-conditioned media, 0.05 mM β-mercaptoethanol, PenStrep 1% and Sodium Pyruvate 1mM). 96 hours later media was replaced by fresh media containing 200nM 4-hydroxy-tamoxifen to induce nuclear translocation of ERt2-Cre. Experiments were done at day 7.

extract_protocol:
Cells were crosslinked with 1% formaldehyde, lysed and then sonicated using a Bioruptor instrument (Diagenode) for 40 cycles and power H in sonication buffer (1% Triton, 0.1% Sodium Deoxycholate, 0.5% SDS, 0.2M NaCl, 10mM Tris, 10mM EDTA). Lysates were immunoprecipitated overnight with a-H3 (Abcam ab1791) and a-H3K27Ac (Abcam ab4729) pre-bound to Dynabeads Protein G (Invitrogen 10004D) in RIPA buffer. Beads were washed and reverse-crosslinked by incubation at 65ºC in 10% SDS. DNA was purified using ChIP DNA clean & Concentrator Kit (Zymo D5205).
Libraries were prepared using a NEBNext Ultra DNA LIbrary Prep kit (New England Biolabs E7370) and assessed for quality and quantity with Bioanalyzer and Qubit.

treatment_protocol: Macrophages were subjected to LPS treatment (10ng/ml) at the indicated time points (see individual samples).

tag: cell type

value: Bone marrow-derived macrophages

tag: stimulation

value: unstimulated

tag: genotype

tag: chip antibody

value: H3K27 acetylation (Abcam ab4729)


title: WT_unstimulated_H3K27Ac_ChIP_rep1

description:
WT0 K27 Rep1
H3K27 acetylation ChIP-seq of unstimulated macrophages

value: wild-type


title: WT_unstimulated_H3K27Ac_ChIP_rep2

description:
WT0 K27 Rep2
H3K27 acetylation ChIP-seq of unstimulated macrophages


title: WT_LPS_1h_H3K27Ac_ChIP_rep1

description:
WT1 K27 Rep1
H3K27 acetylation ChIP-seq of 1h LPS-stimulated macrophages

value: 1 hour of LPS stimulation


title: Rad21-/-_LPS_6h_H3K27Ac_ChIP_rep2

description:
KO6 K27 Rep2
H3K27 acetylation ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages

value: 6 hours of LPS stimulation


title: WT_LPS_6h_H3K27Ac_ChIP_rep2

description:
WT6 K27 Rep2
H3K27 acetylation ChIP-seq of 6h LPS-stimulated macrophages


title: Rad21-/-_unstimulated_H3K27Ac_ChIP_rep2

description:
KO0 K27 Rep2
H3K27 acetylation ChIP-seq of unstimulated Rad21-/- macrophages


title: WT_LPS_6h_H3K27Ac_ChIP_rep1

description:
WT6 K27 Rep1
H3K27 acetylation ChIP-seq of 6h LPS-stimulated macrophages


title: Rad21-/-_LPS_1h_H3K27Ac_ChIP_rep1

description:
KO1 K27 Rep1
H3K27 acetylation ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages


title: WT_LPS_1h_H3K27Ac_ChIP_rep2

description:
WT1 K27 Rep2
H3K27 acetylation ChIP-seq of 1h LPS-stimulated macrophages


title: Rad21-/-_LPS_6h_H3K27Ac_ChIP_rep1

description:
KO6 K27 Rep1
H3K27 acetylation ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages


title: Rad21-/-_LPS_1h_H3K27Ac_ChIP_rep2

description:
KO1 K27 Rep2
H3K27 acetylation ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages


title: WT_LPS_6h_H3_K27Ac_input_rep2

description:
WT6 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of 6h LPS-stimulated macrophages


title: aT16

value: DDT


title: aT21


title: aT18


title: aT20


title: aT17


title: aT19


title: aT22


title: WT_LPS_1h_H3_K27Ac_input_rep2

description:
WT1 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of 1h LPS-stimulated macrophages


title: aT15


title: aT14


title: Rad21-/-_LPS_1h_H3_K27Ac_input_rep2

description:
KO1 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages


title: WT_unstimulated_H3_K27Ac_input_rep2

description:
WT0 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of unstimulated macrophages


title: aT13


title: Rad21-/-_LPS_6h_H3_K27Ac_input_rep2

description:
KO6 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages


title: aT12


title: Rad21-/-_unstimulated_H3_K27Ac_input_rep2

description:
KO0 Input Rep2
Input DNA for H3 and H3K27Ac ChIP-seq of unstimulated Rad21-/- macrophages


title: T11


title: mESnpD (icSHAPE)

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

country: China

institute: Shandong University

data_processing:
Library strategy: icSHAPE
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 or mouse mm10 reference genome with bowtie2 as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
calculate icSHAPE score as icshape pipeline
For irCLIP,Reads were mapped to mm10 assembly and PCR duplicates were removed using UMI-tools). Reproducible RT stops were identified using the FAST-iCLIP pipeline. Lin28a binding sites were called by Piranha with the parameter –s –b 50.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. CLIP bed files are formatted as Piranha software. The first three columns are the peaks sites [chromosome, start sites, end sites], the fifth column means support reads of its peaks, the seventh is peaks confident P-value as Piranha.

source_name: V6.5 ES cell line

growth_protocol: Human HEK293 cells were cultured in DMEM supplemented with 10% FBS at 37°C with 5% CO2 in 15-cm plates. V6.5 mouse ES cells were cultured at 37°C with 5% CO2 in 15-cm plates coated with 0.2% gelatin, in knockout DMEM (Gibco) media supplemented with 15% FBS, 1% PenStrep, 1% MEM NEAA, 1% Glutamax, 0.2% beta-mercaptoethanol, and 0.01% LIF. Cells were cultured to 80~90% confluency, then rinsed, collected and treated with NAI-N3 as previously described by Flynn et. al. (2016).To carry out CLIP-seq experiments, mettl3 WT and KO mESCs9 were grown on gelatinized plates in Knockout DMEM media (Gibco) supplemented with 15% FBS, 1% penicillin-streptomycin (Gibco), glutamate, non-essential amino acids (NEAA), basal medium eagle (BME, Thermo Fischer Scientific), and ESGRO LIF (EMD Millipore).

extract_protocol:
The  RNA or modified RNA was extracted or cleaned up and eluted in RNase-free water by using RNeasy mini columns (Qiagen).
10 µg of RNA from each subcellular fraction for HEK293 cells was depleted of ribosomal RNA (rRNA) using the mouse/human ribominus kit (Invitrogen). About 500 ng RNA was recovered in the nucleoplasmic and cytoplasmic samples and about 2 µg RNA in the chromatin fractions. RNA from mES-cell fractions were depleted using the ribominus eukaryotic system v2 kit (Thermo Fischer Scientific). IcSHAPE sequencing libraries were then constructed from these RNA samples as icSHAPE protocol. Libraries of mES-cells were sequenced on the Hiseq 4000 and libraries of HEK293 cells were sequenced on the Hiseq 2500 to ~200 million reads per replicate.For irCLIP, RNA trimming, on-bead biochemistry, and library generation was performed as irCLIP protocol. Reverse transcription of LIN28 bound RNA was performed with SuperScript IV (Thermo Fischer Scientific) at 53°C for 30 minutes. Library amplification was done for a total of 14 cycles using Phusion HF polymerase master mix (NEB). Libraries were gel purified and submitted for sequencing. Libraries were sequenced on NextSeq 500 with custom sequencing primer P6_seq.

treatment_protocol: For in vivo treatment, cells was incubated with NAI-N3 at 37°C for 5min, then subcellular fractionatio was performed. For in vitro treatment, RNA was extracted by RNeasy mini columns (Qiagen) after subcellular fractionation.For refolding, purified RNA was first denatured at 95°C for 1 min, quickly cooled to 4°C, and then incubated for 5 min in the folding buffer with 100 mM HEPES, 6 mM MgCl2, and 100 mM NaCl. Samples were then respectively modified for 5 minutes at 37°C with the NAI-N3 reagent and DMSO as control. For irCLIP, cells were initially washed with ice-cold PBS, then crosslinked on ice with UV-C (254 nm) at 0.3 J/cm2 in a Stratalinker, washed again with ice-cold PBS (+10 mM EDTA) for 5 minutes, and removed from the plate. Immunoprecipitation of crosslinked protein-RNA complexes was performed with anti-LIN28 antibody (Abcam ab46030), the control samples with anti-GFP antibody (Abcam).

tag: cell line

value: mouse embryonic stem cells

tag: cellular compartment

value: nucleoplasm(np)

value: DMSO (D)


title: mESchD (icSHAPE)

value: chromatin (ch)


title: mEScyT (icSHAPE)

value: cytoplasm (cy)

value: in vitro NAI-N3 treatment (T)


title: mESchT (icSHAPE)


title: Lin28_CLIP_Mettl3_WT_GFP_control (irCLIP)

data_processing:
remove duplicete reads as icshape pipeline
trimmed reads adaptor as icshape pipeline
mapping reads to human hg38 or mouse mm10 reference genome with bowtie2 as default parameters
calculate rpkm as icshape pipeline
calulate reverse transcript stop sites as icshape pipeline
calculate icSHAPE score as icshape pipeline
For irCLIP,Reads were mapped to mm10 assembly and PCR duplicates were removed using UMI-tools). Reproducible RT stops were identified using the FAST-iCLIP pipeline. Lin28a binding sites were called by Piranha with the parameter –s –b 50.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is RPKM, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score. CLIP bed files are formatted as Piranha software. The first three columns are the peaks sites [chromosome, start sites, end sites], the fifth column means support reads of its peaks, the seventh is peaks confident P-value as Piranha.

tag: rip antibody

value: anti-GFP


title: mEScyN (icSHAPE)

tag: treatment

value: in vivo NAI-N3 treatment (N)


title: mESnpT (icSHAPE)


title: mESchN (icSHAPE)


title: mEScyD (icSHAPE)


title: Lin28_CLIP_Mettl3_WT (irCLIP)


title: WT_LPS_6h_H3_K27Ac_input_rep1

description:
WT6 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of 6h LPS-stimulated macrophages


title: Lin28_CLIP_Mettl3_KO (irCLIP)


title: Lin28_CLIP_Mettl3_KO_GFP_control (irCLIP)


title: mESnpN (icSHAPE)


title: T10

tag: generation


title: WT_LPS_1h_H3_K27Ac_input_rep1

description:
WT1 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of 1h LPS-stimulated macrophages


title: T9


title: WT_unstimulated_H3_K27Ac_input_rep1

description:
WT0 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of unstimulated macrophages


title: Rad21-/-_LPS_1h_H3_K27Ac_input_rep1

description:
KO1 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages


title: T6


title: T8


title: T5


title: Rad21-/-_unstimulated_H3_K27Ac_input_rep1

description:
KO0 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of unstimulated Rad21-/- macrophages


title: T4


title: WT_LPS_6h_H3_ChIP_rep2

description:
WT6 H3 Rep2
H3 ChIP-seq of 6h LPS-stimulated macrophages

value: H3 (Abcam ab1791)


title: WT_LPS_1h_H3_ChIP_rep2

description:
WT1 H3 Rep2
H3 ChIP-seq of 1h LPS-stimulated macrophages


title: Rad21-/-_LPS_1h_H3_ChIP_rep2

description:
KO1 H3 Rep2
H3 ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages


title: T2


title: WT_unstimulated_H3_ChIP_rep2

description:
WT0 H3 Rep2
H3 ChIP-seq of unstimulated macrophages


title: Rad21-/-_LPS_6h_H3_ChIP_rep2

description:
KO6 H3 Rep2
H3 ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages


title: Rad21-/-_unstimulated_H3_ChIP_rep2

description:
KO0 H3 Rep2
H3 ChIP-seq of unstimulated Rad21-/- macrophages


title: T1


title: Healthy_M_id1642

city: Stanford

first: Stephen

last: Popper

state: CA

department: Division of Infectious Diseases, Dept. of Medicine

institute: Stanford University

description: Healthy_M_id1642 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

hyb_protocol: reference URL : http://dx.doi.org/10.1371/journal.pntd.0001966 Hybridization method : "8 ug of Cy5-labeled amplified RNA and 5 ug of Cy3-labeled Universal Human Reference aRNA (Stratagene) were hybridized to Human Exonic Evidence Based Oligonucleotide (HEEBO) microarrays at 65C using the HYBEX hybridization system (SciGene) for 14 hours. Following hybridization, microarrays were washed in a series of four solutions containing 2_ SSC with 0.05% SDS, 2x SSC, 1x SSC, and 0.2x SSC, respectively. The first wash was performed for 5 min at 60C; subsequent washes were performed at room temperature for 2 min each. "

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 204181 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 33.80 Scan Time : 22:07:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 440, 4600

organism: Homo sapiens

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled Winter 2012

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-25

extract_protocol: Extraction method : Human Universal Reference RNA (Stratagene)

tag: sample name

source_name: Healthy_M_id1642 paxgene RNA aa-aRNA Cy5 labeled

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

extract_protocol:
Extraction method : PreAnalytiX PAXgene Blood RNA Kit
Amplification method : Epicentre TargetAmp Aminoallyl aRNA Amp Kit

tag: disease state

value: Healthy

value: Whole Blood


title: Healthy_M_id1872

description: Healthy_M_id1872 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 507 Pixel Size : 10 Laser on time : 203987 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 34.41 Scan Time : 16:53:26 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-24

value: Human Universal Reference RNA (Stratagene)

source_name: Healthy_M_id1872 paxgene RNA aa-aRNA Cy5 labeled


title: Healthy_F_id2173

description: Healthy_F_id2173 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 205398 Laser Power : 3.11 Scan Date : 2013-05-16 Scan Temperature : 36.18 Scan Time : 12:27:58 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 960, 4640

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-32

source_name: Healthy_F_id2173 paxgene RNA aa-aRNA Cy5 labeled


title: Healthy_F_id3478

description: Healthy_F_id3478 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 501 Pixel Size : 10 Laser on time : 203949 Laser Power : 3.08 Scan Date : 2013-04-26 Scan Temperature : 33.62 Scan Time : 16:14:47 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-22

source_name: Healthy_F_id3478 paxgene RNA aa-aRNA Cy5 labeled


title: Rad21-/-_LPS_6h_H3_K27Ac_input_rep1

description:
KO6 Input Rep1
Input DNA for H3 and H3K27Ac ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages

value: Bone marrow-derived macrophages


title: T7


title: RKO_P4_day30_H3K27ac

city: Chiba

first: Masaki

last: Fukuyo

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

department: Department of Molecular Oncology

country: Japan

institute: Chiba University

data_processing:
Read were aligned with Hisat v2.2.1.0 for RNA-Seq and BWA (version 0.5.9) for ChIP-Seq.
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.2.1for RNA-seq and Aligned reads were converted to BedGraph format with bedtools v2.20.1 for ChIP-seq.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Bedgraph files are generated from bedtools and converted to bigwig file.

source_name: RKO

growth_protocol: RKO cells were cultured in MEM containing penicillin-streptomycin, supplemented with 10% fetal bovine serum.

extract_protocol:
ChIP samples were purified by QIAquick PCR purification kit (Qiagen, Hilden, Germany) and total RNAs were collected using RNeasy (Invitrogen, Carlsbad, CA)
Libraries were prepared using NEBNext ChIP-Seq Library Preparation Set for Illumina (New England Biolabs) for ChIP-seq. TruSeq Stranded mRNA Sample Prep Kit (Illumina) were used for RNA-seq following the manufacturer’s protocol.

treatment_protocol: RKO cells were treated with 2 mM P4, PPIP, NCD38, P4-NCD38, or PPIP-NCD38 with 0.1% DMSO for 4days or 30 days. The medium containing the compound was refreshed every 5 days.

value: RKO

value: colorectal cancer cells

tag: antibody

value: Anti-Acetyl Histone H3 [Lys27] (#39159, Active Motif, Lot#12613005)


title: Healthy_M_id3231

description: Healthy_M_id3231 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 199368 Laser Power : 3.10 Scan Date : 2013-01-30 Scan Temperature : 33.65 Scan Time : 17:31:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 5.0.0.51
Datafile type : GenePix Results 3
Image Origin : 1040, 4640

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-7

source_name: Healthy_M_id3231 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_PIPP_day30_H3K27ac


title: Healthy_M_id3001

description: Healthy_M_id3001 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 205415 Laser Power : 3.12 Scan Date : 2013-05-16 Scan Temperature : 36.31 Scan Time : 12:44:32 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-33

source_name: Healthy_M_id3001 paxgene RNA aa-aRNA Cy5 labeled


title: T3

value: DDT


title: RKO_PIPP_day30_H3K4me3

value: Histone H3K4me3 antibody [pAb] (#ab7766, Abcam, Lot#GR160184-2)


title: Healthy_M_id3417

description: Healthy_M_id3417 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 196717 Laser Power : 3.08 Scan Date : 2013-01-15 Scan Temperature : 30.14 Scan Time : 15:57:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-40

source_name: Healthy_M_id3417 paxgene RNA aa-aRNA Cy5 labeled


title: DHF_ab1272_F_d5_id1167

description: DHF_ab1272_F_d5_id1167 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 199350 Laser Power : 3.09 Scan Date : 2013-01-30 Scan Temperature : 33.38 Scan Time : 17:14:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-10

source_name: DHF_ab1272_F_d5_id1167 paxgene RNA aa-aRNA Cy5 labeled

value: Dengue Hemorrhagic Fever


title: RKO_P4_day30_H3K4me3


title: RKO_PIPP_day30_H3K4me2

value: Anti-H3K4me2 (#05-1334, Merck Millipore, Lot#2768425)


title: DF_ab1593_F_d5_id1220

description: DF_ab1593_F_d5_id1220 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 489 Pixel Size : 10 Laser on time : 203933 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 33.32 Scan Time : 15:59:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-21

source_name: DF_ab1593_F_d5_id1220 paxgene RNA aa-aRNA Cy5 labeled

value: Dengue Fever


title: WT_unstimulated_H3_ChIP_rep1

description:
WT0 H3 Rep1
H3 ChIP-seq of unstimulated macrophages

value: unstimulated

value: wild-type


title: DF_ab1558_F_d5_id1172

description: DF_ab1558_F_d5_id1172 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 511 Pixel Size : 10 Laser on time : 199030 Laser Power : 3.09 Scan Date : 2013-01-25 Scan Temperature : 33.29 Scan Time : 16:13:31 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-6

source_name: DF_ab1558_F_d5_id1172 paxgene RNA aa-aRNA Cy5 labeled


title: Healthy_F_id629

description: Healthy_F_id629 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 513 Pixel Size : 10 Laser on time : 203966 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 34.02 Scan Time : 16:32:40 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-23

source_name: Healthy_F_id629 paxgene RNA aa-aRNA Cy5 labeled


title: Healthy_F_id1649

description: Healthy_F_id1649 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 508 Pixel Size : 10 Laser on time : 196727 Laser Power : 3.09 Scan Date : 2013-01-15 Scan Temperature : 30.39 Scan Time : 16:07:29 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

source_name: Healthy_F_id1649 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_P4_day30_H3K4me2


title: RKO_PIPP_NCD38_day4_H3K27ac

treatment_protocol: RKO cells were treated with 2 µM P4, PPIP, NCD38, P4-NCD38, or PPIP-NCD38 with 0.1% DMSO for 4days or 30 days. The medium containing the compound was refreshed every 5 days.


title: Rad21-/-_unstimulated_H3_ChIP_rep1

description:
KO0 H3 Rep1
H3 ChIP-seq of unstimulated Rad21-/- macrophages


title: Rad21-/-_LPS_1h_H3_ChIP_rep1

description:
KO1 H3 Rep1
H3 ChIP-seq of 1h LPS-stimulated Rad21-/- macrophages

value: 1 hour of LPS stimulation


title: Rad21-/-_LPS_6h_H3_ChIP_rep1

description:
KO6 H3 Rep1
H3 ChIP-seq of 6h LPS-stimulated Rad21-/- macrophages

value: 6 hours of LPS stimulation


title: RKO_NCD38_day4_H3K27ac


title: WT_LPS_6h_H3_ChIP_rep1

description:
WT6 H3 Rep1
H3 ChIP-seq of 6h LPS-stimulated macrophages

value: H3 (Abcam ab1791)


title: Rad21-/-_LPS_6h_ATAC_rep1

description:
KO6H Rep1
KO6H Rep1
ATAC-seq of 6h LPS-stimulated Rad21-/- macrophages

data_processing:
Quality of sequencing reads were evaluated using FastQC and found that bases 35-100 of sequencing reads were enriched for “Nextera transposase adapter” sequences. Therefore, reads were aligned to Mouse genome mm9 using bowtie v0.12.8 with arguments “--chunkmbs 256 -S -n 2 -m 1 -p 8 -X 2000” by successively trimming 10bases from 3’ end until the read length reaches 40bp.
Only reads aligned uniquely in the genome were retained for downstream analysis. Duplicate reads were identified using Picard MarkDuplicates.
Aligned reads in Watson strand were offset by +4 bp and reads aligned to Crick strand were offset by -5 bp as previously described in (Buenrostro, J.D., P.G. Giresi, L.C. Zaba, H.Y. Chang, and W.J. Greenleaf. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods. 10:1213–1218. )
Genome_build: mm9
Supplementary_files_format_and_content: Bigiwig

extract_protocol:
Nuclei suspensions were prepared from 50,000 cells per biological replicate.
ATAC sequencing was performed as described in (Buenrostro, J.D., P.G. Giresi, L.C. Zaba, H.Y. Chang, and W.J. Greenleaf. 2013. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods. 10:1213–1218. )


title: Rad21-/-_LPS_6h_ATAC_rep2

description:
KO6H Rep2
KO6H Rep2
ATAC-seq of 6h LPS-stimulated Rad21-/- macrophages


title: WT_LPS_1h_H3_ChIP_rep1

description:
WT1 H3 Rep1
H3 ChIP-seq of 1h LPS-stimulated macrophages


title: DF_ab2291_F_d5_id1214

description: DF_ab2291_F_d5_id1214 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 498 Pixel Size : 10 Laser on time : 198811 Laser Power : 3.10 Scan Date : 2013-01-23 Scan Temperature : 35.02 Scan Time : 16:39:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-4

source_name: DF_ab2291_F_d5_id1214 paxgene RNA aa-aRNA Cy5 labeled


title: Rad21-/-_LPS_1h_ATAC_rep1

description:
KO1H Rep1
KO1H Rep1
ATAC-seq of 1h LPS-stimulated Rad21-/- macrophages

source_name: Bone marrow-derived macrophages


title: RKO_P4_NCD38_day4_H3K4me3


title: RKO_NCD38_day4_H3K4me3


title: RKO_DMSO_day4_H3K27ac


title: DHF_ab4067_M_d4_id1151

description: DHF_ab4067_M_d4_id1151 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 484 Pixel Size : 10 Laser on time : 204291 Laser Power : 3.09 Scan Date : 2013-04-26 Scan Temperature : 35.02 Scan Time : 23:58:44 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-38

source_name: DHF_ab4067_M_d4_id1151 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab270_F_d5_id1040

description: DF_ab270_F_d5_id1040 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 524 Pixel Size : 10 Laser on time : 205433 Laser Power : 3.12 Scan Date : 2013-05-16 Scan Temperature : 36.37 Scan Time : 13:02:17 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled Winter 2012

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-34

source_name: DF_ab270_F_d5_id1040 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab2300_M_d5_id1026

description: DF_ab2300_M_d5_id1026 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 10 Laser on time : 203740 Laser Power : 3.10 Scan Date : 2013-04-25 Scan Temperature : 35.54 Scan Time : 17:54:42 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-20

source_name: DF_ab2300_M_d5_id1026 paxgene RNA aa-aRNA Cy5 labeled


title: Rad21-/-_unstimulated_ATAC_rep2

description:
KOUT Rep2
KOUT Rep2
ATAC-seq of unstimulated Rad21-/- macrophages


title: DF_ab908_F_d4_id1073

description: DF_ab908_F_d4_id1073 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 204278 Laser Power : 3.10 Scan Date : 2013-04-26 Scan Temperature : 34.90 Scan Time : 23:44:38 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-37

source_name: DF_ab908_F_d4_id1073 paxgene RNA aa-aRNA Cy5 labeled


title: WT_LPS_6h_ATAC_rep2

description:
WT6H Rep2
WT6H Rep2
ATAC-seq of 6h LPS-stimulated macrophages


title: RKO_DMSO_day4_H3K4me3


title: DHF_ab1020_F_d4_id1135

description: DHF_ab1020_F_d4_id1135 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 197695 Laser Power : 3.09 Scan Date : 2013-01-18 Scan Temperature : 31.27 Scan Time : 11:51:29 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-13

source_name: DHF_ab1020_F_d4_id1135 paxgene RNA aa-aRNA Cy5 labeled

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1


title: DHF_ab741_M_d4_id1174

description: DHF_ab741_M_d4_id1174 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 204230 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 34.44 Scan Time : 22:56:14 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-27

source_name: DHF_ab741_M_d4_id1174 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab565_M_d4_id1106

description: DF_ab565_M_d4_id1106 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 472 Pixel Size : 10 Laser on time : 203449 Laser Power : 3.09 Scan Date : 2013-04-25 Scan Temperature : 35.27 Scan Time : 13:04:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-16

source_name: DF_ab565_M_d4_id1106 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_PIPP_NCD38_day4_H3K4me2

source_name: RKO


title: Rad21-/-_LPS_1h_ATAC_rep2

description:
KO1H Rep2
KO1H Rep2
ATAC-seq of 1h LPS-stimulated Rad21-/- macrophages


title: RKO_P4_NCD38_day4_H3K4me2


title: Rad21-/-_unstimulated_ATAC_rep1

description:
KOUT Rep1
KOUT Rep1
ATAC-seq of unstimulated Rad21-/- macrophages


title: RKO_PIPP_NCD38_day4_H3K4me3


title: RKO_NCD38_day4_H3K4me2


title: WT_LPS_6h_ATAC_rep1

description:
WT6H Rep1
WT6H Rep1
ATAC-seq of 6h LPS-stimulated macrophages


title: RKO_DMSO_day4_H3K4me2


title: DF_ab1343_F_d4_id1213

description: DF_ab1343_F_d4_id1213 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 499 Pixel Size : 10 Laser on time : 199316 Laser Power : 3.09 Scan Date : 2013-01-30 Scan Temperature : 32.83 Scan Time : 16:39:01 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-9

source_name: DF_ab1343_F_d4_id1213 paxgene RNA aa-aRNA Cy5 labeled


title: DHF_ab1362_F_d3_id1128

description: DHF_ab1362_F_d3_id1128 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 528 Pixel Size : 10 Laser on time : 205480 Laser Power : 3.12 Scan Date : 2013-05-16 Scan Temperature : 36.40 Scan Time : 13:49:36 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-36

source_name: DHF_ab1362_F_d3_id1128 paxgene RNA aa-aRNA Cy5 labeled


title: WT_LPS_1h_ATAC_rep2

description:
WT1H Rep2
WT1H Rep2
ATAC-seq of 1h LPS-stimulated macrophages


title: WT_unstimulated_ATAC_rep2

description:
WTUT Rep2
WTUT Rep2
ATAC-seq of unstimulated macrophages


title: WT_unstimulated_ATAC_rep1

description:
WTUT Rep1
WTUT Rep1
ATAC-seq of unstimulated macrophages


title: DF_ab438_F_d4_id1126

description: DF_ab438_F_d4_id1126 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 520 Pixel Size : 10 Laser on time : 197679 Laser Power : 3.10 Scan Date : 2013-01-18 Scan Temperature : 31.03 Scan Time : 11:34:52 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-12

source_name: DF_ab438_F_d4_id1126 paxgene RNA aa-aRNA Cy5 labeled


title: DHF_ab262_M_d3_id1143

description: DHF_ab262_M_d3_id1143 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 10 Laser on time : 198755 Laser Power : 3.08 Scan Date : 2013-01-23 Scan Temperature : 33.96 Scan Time : 15:42:57 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-39

source_name: DHF_ab262_M_d3_id1143 paxgene RNA aa-aRNA Cy5 labeled


title: WT_LPS_1h_ATAC_rep1

description:
WT1H Rep1
WT1H Rep1
ATAC-seq of 1h LPS-stimulated macrophages


title: RKO_NCD38_day4_RNAseq


title: RKO_PIPP_NCD38_day4_RNAseq


title: RKO_P4_NCD38_day4_H3K27ac


title: Rad21-/-_LPS_6h_GROseq_rep2

description:
KO6 Rep2
GRO-seq of 6h LPS-stimulated Rad21-/- macrophages

data_processing:
Library strategy: GRO-seq
All GRO-Seq libraries were sequenced as 50 bp single end reads in 2 biological replicates. The last 10 bp were excluded from the alignment.
Reads were aligned to mouse genome mm9 using bowtie with arguments “-l 30 -m 10 -n 2 –trim3 10”.
Genome wide coverage was generated using coverage function in GenomicRanges package and converted to bigwig.
Genome_build: mm9
Supplementary_files_format_and_content: Bigiwig

extract_protocol:
5 million cells were used per each biological replicate. After nuclear run-on reaction the RNA extracted using Trizol (Ambion), treated with Turbo DNAse (Ambion AM1907), fragmented using RNA Fragmentation Reagents (Ambion AM8740), purified by running through P-30 column (Bio-Rad 732-6250), dephosphorylated with PNK (New England Biolabs Y904L) and purified using anti-BrdU beads (SantaCruz sc-214314).
GRO-Seq libraries were prepared  as described in (Kaikkonen et al. Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription, Molecular Cell, 51 (2013)).


title: Rad21-/-_LPS_1h_GROseq_rep2

description:
KO1 Rep2
GRO-seq of 1h LPS-stimulated Rad21-/- macrophages


title: DF_ab416_M_d4_id1136

description: DF_ab416_M_d4_id1136 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 492 Pixel Size : 10 Laser on time : 198833 Laser Power : 3.10 Scan Date : 2013-01-23 Scan Temperature : 35.39 Scan Time : 17:01:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-5

source_name: DF_ab416_M_d4_id1136 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_DMSO_day4_RNAseq


title: Rad21-/-_unstimulated_GROseq_rep2

description:
KO0 Rep2
GRO-seq of unstimulated Rad21-/- macrophages


title: RKO_P4_NCD38_day4_RNAseq


title: RKO_P4_NCD38_day30_H3K27ac

value: conjugated NCD38 with Py-Im polyamide P4_NCD38


title: RKO_NCD38_day30_H3K27ac


title: Rad21-/-_LPS_1h_GROseq_rep1

description:
KO1 Rep1
GRO-seq of 1h LPS-stimulated Rad21-/- macrophages


title: RKO_PIPP_NCD38_day30_H3K27ac

value: conjugated NCD38 with Py-Im polyamide PPIP_NCD38


title: DF_ab6593_M_d3_id1068

description: DF_ab6593_M_d3_id1068 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 510 Pixel Size : 10 Laser on time : 196795 Laser Power : 3.10 Scan Date : 2013-01-15 Scan Temperature : 31.39 Scan Time : 17:15:59 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-3

value: Human Universal Reference RNA (Stratagene)

source_name: DF_ab6593_M_d3_id1068 paxgene RNA aa-aRNA Cy5 labeled

value: Whole Blood


title: Rad21-/-_LPS_6h_GROseq_rep1

description:
KO6 Rep1
GRO-seq of 6h LPS-stimulated Rad21-/- macrophages

value: Bone marrow-derived macrophages


title: DF_ab5567_F_d3_id1195

description: DF_ab5567_F_d3_id1195 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 505 Pixel Size : 10 Laser on time : 204261 Laser Power : 3.09 Scan Date : 2013-04-26 Scan Temperature : 34.75 Scan Time : 23:28:21 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-29

source_name: DF_ab5567_F_d3_id1195 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab3861_F_d3_id1149

description: DF_ab3861_F_d3_id1149 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 488 Pixel Size : 10 Laser on time : 203481 Laser Power : 3.10 Scan Date : 2013-04-25 Scan Temperature : 35.60 Scan Time : 13:35:17 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-18

source_name: DF_ab3861_F_d3_id1149 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_DMSO_day30_H3K27ac

value: RKO

value: colorectal cancer cells

value: DMSO


title: Rad21-/-_unstimulated_GROseq_rep1

description:
KO0 Rep1
GRO-seq of unstimulated Rad21-/- macrophages

source_name: Bone marrow-derived macrophages


title: DF_ab1502_F_d3_id1067

description: DF_ab1502_F_d3_id1067 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 503 Pixel Size : 10 Laser on time : 196757 Laser Power : 3.11 Scan Date : 2013-01-15 Scan Temperature : 31.00 Scan Time : 16:38:22 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled Winter 2012

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-2

source_name: DF_ab1502_F_d3_id1067 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab457_M_d3_id1105

description: DF_ab457_M_d3_id1105 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 469 Pixel Size : 10 Laser on time : 203407 Laser Power : 3.05 Scan Date : 2013-04-25 Scan Temperature : 34.69 Scan Time : 12:21:56 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-14

source_name: DF_ab457_M_d3_id1105 paxgene RNA aa-aRNA Cy5 labeled


title: DF_ab958_F_d3_id1196

description: DF_ab958_F_d3_id1196 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 490 Pixel Size : 10 Laser on time : 203466 Laser Power : 3.09 Scan Date : 2013-04-25 Scan Temperature : 35.45 Scan Time : 13:21:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-17

source_name: DF_ab958_F_d3_id1196 paxgene RNA aa-aRNA Cy5 labeled


title: WT_LPS_6h_GROseq_rep2

description:
WT6 Rep2
GRO-seq of 6h LPS-stimulated macrophages


title: RKO_PIPP_NCD38_day30_H3K4me3

value: Histone H3K4me3 antibody [pAb] (#ab7766, Abcam, Lot#GR160184-2)


title: DF_ab1566_F_d3_id1171

description: DF_ab1566_F_d3_id1171 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 522 Pixel Size : 10 Laser on time : 199065 Laser Power : 3.07 Scan Date : 2013-01-25 Scan Temperature : 33.99 Scan Time : 16:49:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-8

source_name: DF_ab1566_F_d3_id1171 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_NCD38_day30_H3K4me3


title: WT_LPS_1h_GROseq_rep2

description:
WT1 Rep2
GRO-seq of 1h LPS-stimulated macrophages


title: RKO_P4_NCD38_day30_H3K4me3


title: RKO_PIPP_NCD38_day30_H3K4me2


title: WT_LPS_6h_GROseq_rep1

description:
WT6 Rep1
GRO-seq of 6h LPS-stimulated macrophages


title: WT_unstimulated_GROseq_rep1

description:
WT0 Rep1
GRO-seq of unstimulated macrophages


title: DF_ab253_M_d3_id1150

description: DF_ab253_M_d3_id1150 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 485 Pixel Size : 10 Laser on time : 204327 Laser Power : 3.10 Scan Date : 2013-04-27 Scan Temperature : 35.24 Scan Time : 00:33:53 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-31

source_name: DF_ab253_M_d3_id1150 paxgene RNA aa-aRNA Cy5 labeled


title: RKO_NCD38_day30_H3K4me2


title: WT_unstimulated_GROseq_rep2

description:
WT0 Rep2
GRO-seq of unstimulated macrophages


title: WT_LPS_6h_Rad21_input_rep2

description:
WT6 Input Rep2
Input DNA for ChIP-seq of 6h LPS-stimulated macrophages

extract_protocol:
For RAD21 ChIP cells were crosslinked (1% formaldehyde), lysed and sonicated a Bioruptor for 25 cycles at power H in RAD21 sonication buffer (1% Triton, 0.1% Sodium Deoxycholate, 0.1% SDS, 0.8M NaCl, 10mM Tris, 1mM EDTA). Then they were imunoprecipitated over-night using a-Rad21 (ab992, Abcam), incubated with Dynabeads Protein G, washed, decrosslinked and purified.
Libraries were prepared using a NEBNext Ultra DNA LIbrary Prep kit (New England Biolabs E7370) and assessed for quality and quantity with Bioanalyzer and Qubit.


title: JEV CLIP-seq (ZAP-S)

city: Taipei

first: Hsin-Ping

last: Chiu

address: No.1 Jen Ai road section 1

department: Microbiology

country: Taiwan

institute: National Taiwan University

data_processing:
library strategy: CLIP-seq
Basecalls performed using Torrent Suite v5.0
The trimmed reads were mapped to the JEV RP-9 genome using CLC Genomics Workbench 11.0.1 with the following parameters.
Parameter: match score = 1; mismatch cost = 2; insertion/deletion cost = 3; length fraction = 0.9; similarity fraction = 0.9; Non-specific match handling = ignore
Genome_build: JEV RP-9 strain (GenBank accession: AF014161)
Supplementary_files_format_and_content: Excel file shows the read number of each postion

source_name: A549 cell

growth_protocol: A549 cells were cultured in F-12 medium containing 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin.

extract_protocol:
A549-ZAP-S-V5 cells infected with JEV (MOI = 5) for 24 h were UV-crosslinked. Cells lysates were treated with RQ1 DNase and RNase A/T1, then immunoprecipitated with anti-V5 antibody. After washed by lysis buffer and protease K digestion, the bound RNA was purified by Direct-zol™ RNA kit (Zymo Research).
The sequence library was constructed using Ion Total RNA-seq Kit v.2 (Thermo Fisher Scientific).

value: Human lung carcinoma cell line

tag: genotype/variation

value: JEV-infected ZAP-S overexpressing cells

tag: clip antibody

value: Mouse anti-V5 (R960-25, Invitrogen)


title: WT_LPS_1h_Rad21_input_rep2

description:
WT1 Input Rep2
Input DNA for ChIP-seq of 1h LPS-stimulated macrophages


title: RKO_DMSO_day30_H3K4me3

source_name: RKO


title: WT_unstimulated_Rad21_input_rep2

description:
WT0 Input Rep2
Input DNA for ChIP-seq of unstimulated macrophages

value: unstimulated


title: Huh7_DDB_treated_test

city: Seongnam

first: Young Min

last: Park

state: Gyeonggi

address: 20, Seohyeon Road 180th street, Bundang-gu

department: Biomedical Research Center

country: South Korea

institute: Bundang Jesaeng General Hospital

hyb_protocol: 600ng of each labeled cRNA was fragmented by adding five μl 10 x blocking agent and one μl of 25 x fragmentation buffer and then heated at 60°C for 30 min. Finally, 25 μl 2 x GE hybridization buffer was added to dilute the labeled cRNA. 40μl of hybridization solution was dispensed into the gasket slide and assembled to the Agilent SurePrint G3 Human GE 8X60K, V3 Microarrays (Agilent®). The slides were incubated for 17 h at 65°C in an Agilent hybridization oven.

scan_protocol: Then washed at room temperature by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). The hybridized array was immediately scanned with an Agilent Microarray Scanner D (Agilent Technologies, Inc.)

data_processing: Raw data were extracted using the software provided by Agilent Feature Extraction Software(v11.0.1.1). The raw data for the same gene was then summarized automatically in Agilent feature extraction protocol to generate raw data text file, providing expression data for each gene probed on the array. The ID column represents the Agilent Feature Extraction feature number.

source_name: Huh7, DDB-treated, Test

label_protocol: RNA labeling and hybridization were performed by using the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology, V 6.5, 2010). Briefly, 100ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP. The labeled cRNAs were purified by RNAeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000(NanoDrop, Wilmington, USA).

growth_protocol: Three human hepatoma cell lines, HepG2, Hep3B and Huh7, were utilized in this study. Cells were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 100 U/ml penicillin, 100 µg/mL streptomycin (Gibco-BRL; Grand Island, NY, USA) and 100 mL/L heat-inactivated fetal bovine serum (FBS; HyClone, Logan, UT, USA). Cells were allowed to grow to confluence at 37 °C in a humidified incubator supplied with 50 mL/L CO2.

extract_protocol:
Total RNA of the cells was isolated using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s recommendations. Complementary DNA (cDNA) was synthesized from 1 µg of total RNA with an iScript cDNA synthesis kit (Bio-Rad, Hercules, CA, USA) using the recommended protocol [25 °C (5 min), 42 °C (30 min), 85 °C (5 sec), 4 °C].
RNA purity and integrity were evaluated by ND-1000 Spectrophotometer (NanoDrop, Wilmington, USA), Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, USA).

treatment_protocol: Dimethyl dicarboxylate biphenyl (DDB, dimethyl-4,4'-dimethoxy-S ,6,5 ',6' ,-dimemethylenedioxy-biphenyl-2,2'-dicarboxylate; Celltrion Inc., Chungcheongbuk-do, Korea) 0.1 mmol/L was used as a test reagent. Dimethyl sulfoxide (DMSO) 7.6 g/L (Sigma-Aldrich, St.Louis, MO, USA) was used as a control reagent. Cells were treated with the reagent, then refreshed every 24 h, and harvested after 48 h of culture.

tag: hepatoma cell line

tag: origin

value: Hepatocellular carcinoma (HCC) assciated with hepatitis C virus (HCV) infection

value: p53-point mutation

value: 48 h of culture with test reaget (DDB 0.1 mmol/L)


title: Huh7_DDB_untreated_control

source_name: Huh7, DDB-untreated, Control

value: 48 h of culture with control reaget (DMSO 7.6 g/L)


title: DHF_ab4729_M_d2_id1224

description: DHF_ab4729_M_d2_id1224 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 204247 Laser Power : 3.06 Scan Date : 2013-04-26 Scan Temperature : 34.63 Scan Time : 23:13:23 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-28

source_name: DHF_ab4729_M_d2_id1224 paxgene RNA aa-aRNA Cy5 labeled

label_protocol:
Type of label : Cy5
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-1

value: Dengue Hemorrhagic Fever

tag: tissue


title: DF_ab392_M_d1_id1122

description: DF_ab392_M_d1_id1122 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 541 Pixel Size : 10 Laser on time : 205456 Laser Power : 3.12 Scan Date : 2013-05-16 Scan Temperature : 36.43 Scan Time : 13:26:18 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-35

source_name: DF_ab392_M_d1_id1122 paxgene RNA aa-aRNA Cy5 labeled

value: Dengue Fever


title: DF_ab1032_F_d2_id1185

description: DF_ab1032_F_d2_id1185 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 474 Pixel Size : 10 Laser on time : 203596 Laser Power : 3.11 Scan Date : 2013-04-25 Scan Temperature : 35.91 Scan Time : 15:31:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-19

value: Human Universal Reference RNA (Stratagene)

source_name: DF_ab1032_F_d2_id1185 paxgene RNA aa-aRNA Cy5 labeled


title: WT_LPS_1h_GROseq_rep1

description:
WT1 Rep1
GRO-seq of 1h LPS-stimulated macrophages

tag: cell type

value: 1 hour of LPS stimulation

value: wild-type


title: DF_ab2082_F_d2_id1076

description: DF_ab2082_F_d2_id1076 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 466 Pixel Size : 10 Laser on time : 203433 Laser Power : 3.09 Scan Date : 2013-04-25 Scan Temperature : 35.09 Scan Time : 12:47:50 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-15

source_name: DF_ab2082_F_d2_id1076 paxgene RNA aa-aRNA Cy5 labeled

value: Whole Blood


title: SK-CO-1-derived iPC_OSKM-transduced_Clone1_rep1

city: Sg. Long

first: Kong Bung

last: Choo

state: Selangor

address: Jalan Sungai Long

department: Preclinical Sciences

country: Malaysia

institute: Universiti Tunku Abdul Rahman

description: miRNA expression of OSKM-transduced SK-CO-1 C1

hyb_protocol: The dried samples were re-suspended with nuclease-free water before adding in the hybridization mix. For the hybridization mix, spike-in solution was also added in. Samples are then hybridized on SurePrint Human MiRNA Microarray Release 21.0 (Agilent), G4872A-070156 at 55oC for 20 hours. After incubation, slides are washed using Agilent Wash Buffer 1 and 2; and placed in a slide holder before proceed for scanning.

scan_protocol: The slides are scanned using scan protocol Agilent G3_miRNA on Agilent SureScan Microarray Scanner, G4900DA. The scan image which is in .tiff format are then extracted using Agilent Feature Extraction Software version 11.5.1.1.

data_processing: The data (.txt) extracted out from Agilent Feature Extraction Software were analysed using GeneSpring GX software version 13.0.

source_name: SK-CO-1-derived, OSKM transduced, Clone 1, replicate 1

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 100 ng of total RNA using miRNA Complete Labeling and Hybridization Kit (Agilent) according to the manufacturer's instruction. Spike-in solutions were also included in the experiment to help distinguish significant biological data from processing issues. During the labelling step, phosphatase treatment was performed on the total RNA samples and then the dephosphorylated RNA was denatured before proceed for labelling with Cy-3. The labelled RNA was then desalted by drying the samples with vacuum concentrator for around 30 minutes until fully dried.

growth_protocol: CRC cell lines were maintained in basal medium, supplemented with 10% FBS, 1% penicilin-streptomycin. CRC-iPC clones were maintained in standard hESC medium, on irradiated MEF feeder layer.

extract_protocol: Total RNA was isolated using the miRNeasy Mini kit (Qiagen, California, USA) following manufacturer's instruction

treatment_protocol: CRC cell lines were transduced with retrovirus supernatant of OSKM. The OSKM-transduced cells were supplemented with 5 µg/ml polybrene. Upon confluency, the OSKM-transduced cells were passaged to inactivated MEF and cultured using the hESC protocol.

value: SK

tag: transduction

value: OSKM

tag: morphology

value: adherent colony

tag: disease

value: ascites of colorectal adenocarcinoma-derived


title: SK-CO-1-derived iPC_OSKM-transduced_Clone2_rep1

description: miRNA expression of OSKM-transduced SK-CO-1 C2

source_name: SK-CO-1-derived, OSKM transduced, Clone 2, replicate 1

tag: cell line


title: WT_LPS_6h_Rad21_input_rep1

description:
WT6 Input Rep1
Input DNA for ChIP-seq of 6h LPS-stimulated macrophages

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages

tag: stimulation

value: 6 hours of LPS stimulation

tag: genotype

tag: chip antibody


title: WT_LPS_1h_Rad21_input_rep1

description:
WT1 Input Rep1
Input DNA for ChIP-seq of 1h LPS-stimulated macrophages


title: WT_unstimulated_Rad21_input_rep1

description:
WT0 Input Rep1
Input DNA for ChIP-seq of unstimulated macrophages

value: unstimulated


title: WT_LPS_6h_Rad21_ChIP_rep2

description:
WT6 Rad21 Rep2
Rad21 ChIP-seq of 6h LPS-stimulated macrophages

value: Rad21 (Abcam ab992)


title: HCT-15-derived iPC_OSKM-transduced_Clone5_rep1

description: miRNA expression of OSKM-transduced HCT-15 C5

source_name: HCT-15-derived, OSKM transduced, Clone 5, replicate 1

value: colorectal adenocarcinoma-derived


title: HCT-15-derived iPC_OSKM-transduced_Clone1_rep1

description: miRNA expression of OSKM-transduced HCT-15 C1

source_name: HCT-15-derived, OSKM transduced, Clone 1, replicate 1


title: WT_LPS_1h_Rad21_ChIP_rep2

description:
WT1 Rad21 Rep2
Rad21 ChIP-seq of 1h LPS-stimulated macrophages


title: HepG2_DDB_treated_test

source_name: HepG2, DDB-treated, Test

value: Hepatoblastoma

tag: treatment

value: 48 h of culture with test reaget (DDB 0.1 mmol/L)


title: Hep3B_DDB_untreated_control

source_name: Hep3B, DDB-untreated, Control

value: Hepatocellular carcinoma (HCC) assciated with hepatitis B virus (HBV) infection

value: p53-deleted mutation

value: 48 h of culture with control reaget (DMSO 7.6 g/L)


title: Hep3B_DDB_treated_test

source_name: Hep3B, DDB-treated, Test


title: WT_LPS_6h_Rad21_ChIP_rep1

description:
WT6 Rad21 Rep1
Rad21 ChIP-seq of 6h LPS-stimulated macrophages


title: HepG2_DDB_untreated_control

source_name: HepG2, DDB-untreated, Control


title: HCT-15_non-OSKM-transduced_rep1

description: miRNA expression of non-OSKM-transduced

source_name: CRC, non-OSKM transduced, control, replicate 1

value: non-OSKM

value: adherent monolayer

value: colorectal adenocarcinoma


title: SK_non-OSKM-transduced_rep1

description: miRNA expression of non-OSKM-transduced

value: SK

value: ascites of colorectal adenocarcinoma


title: Liver Tumor HCC 058

city: Heidelberg

first: Sven

last: Diederichs

address: Im Neuenheimer Feld 280

department: RNA Biology & Cancer

country: Germany

institute: German Cancer Research Center (DKFZ)

hyb_protocol: Agilent gene expression hybridization kit

scan_protocol: Agilent scanner

data_processing: Agilent Feature Extraction Software (FE) 10.7.3.1.

source_name: HCC Tumor

label_protocol: Invitrogen SuperScript Indirect cDNA labeling system

extract_protocol: Qiagen RNeasy Midi

value: Tumor


title: Liver Tumor HCC 074


title: WT_LPS_1h_Rad21_ChIP_rep1

description:
WT1 Rad21 Rep1
Rad21 ChIP-seq of 1h LPS-stimulated macrophages

value: 1 hour of LPS stimulation

value: wild-type


title: Liver Tumor HCC 057


title: Liver Tumor HCC 053


title: DF_ab1142_F_d5_id1091

description: DF_ab1142_F_d5_id1091 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 497 Pixel Size : 10 Laser on time : 204211 Laser Power : 3.07 Scan Date : 2013-04-26 Scan Temperature : 34.23 Scan Time : 22:37:16 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

source_name: Strat UHR and v4 MJ doping control aa-aRNA labeled Winter 2012

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-26

tag: sample name

value: Human Universal Reference RNA (Stratagene)

source_name: DF_ab1142_F_d5_id1091 paxgene RNA aa-aRNA Cy5 labeled

value: Dengue Fever

value: Whole Blood


title: DF_ab1785_F_d4_id1190

description: DF_ab1785_F_d4_id1190 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 512 Pixel Size : 10 Laser on time : 199397 Laser Power : 3.07 Scan Date : 2013-01-30 Scan Temperature : 34.08 Scan Time : 18:01:08 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-11

source_name: DF_ab1785_F_d4_id1190 paxgene RNA aa-aRNA Cy5 labeled

tag: disease state


title: Rad21tev+etOH_liver_mac_unstimulated_RNAseq_rep3

description:
TEV_Etoh_3
RNA-seq of ethanol-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread.
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

source_name: Fetal liver derived macrophages

growth_protocol: Macrophages were isolated from fetal liver. On embryonic day 14 fetal liver was removed from the embryo and dissociated in PBS with 10% FCS. Cells were then resuspended and plated in IMDM (Sodium Pyruvate 1mM, beta-mercapto ethanol 50uM, l-glutamine 2mM, PenStrep 1%) containing 20% L929-conditioned media. Cells were transduced with retrovirus on DIV2 by resuspending 4x10^6 cells in 2ml of retroviral supernatant supplemented with 4ug of polybrene, in a single well of a 6 well plate, and centrifuged at 1250g for 90 minutes at 37ºC. Following centrifugation, cells were returned to incubator and left for 2 hours in viral supernatant. Viral supernatant was then replaced with IMDM (as above) with 20% L929-conditioned media. Cells were sorted using a FACSAria Fusion instrument on DIV10 for GFP. Top 20% of GFP expressing cells were sorted for analysis.

extract_protocol:
Cells were sorted into PBS with 10% BSA and 5mM EDTA and spun down at 3000g for 5 minutes. RNA was purified using the PicoPure RNA isolation kit (ThermoFisher) following the manufacturer's instructions.
100ng of total RNA was used to prepare libraries using the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina following the manufacturer recommendations. Library quality and quantity were assessed on a Bionalyser and Qubit respectively.

treatment_protocol: On DIV10 500nM 4-hydroxy tamoxifen or ethanol (as indicated in each individual sample) was added to the cells for 8 hours. LPS-stimulated samples were treated for two more hours with 10ng/ml LPS.

value: Fetal liver derived macrophages

tag: oht induction

value: ethanol

value: Unstimulated


title: Liver Tumor HCC 048


title: Liver Tumor HCC 051


title: Liver Tumor HCC 044


title: WT_unstimulated_Rad21_ChIP_rep2

description:
WT0 Rad21 Rep2
Rad21 ChIP-seq of unstimulated macrophages

value: Bone marrow-derived macrophages

value: unstimulated

value: Rad21 (Abcam ab992)


title: Liver Tumor HCC 050


title: Liver Tumor HCC 063


title: Rad21tev+etOH_liver_mac_unstimulated_RNAseq_rep1

description:
TEV_Etoh_1
RNA-seq of ethanol-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: WT_liver_mac_LPS_2h_RNAseq_rep3

description:
WT_4OHT_LPS_3
RNA-seq of tamoxifen-treated LPS-stimulated WT macrophages transduced with ERT2-TEV

value: 4-hydroxy tamoxifen

value: 2 hours of LPS


title: S_063

city: Singapore

first: Vivien

last: Koh

address: 1E Kent Ridge Road

country: Singapore

institute: National University Health System

description: Gene expression data of human gastric tumor

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were processed by the Robust Multi-array Average (RMA) algorithm using Affymetrix Expression Console software.

label: Biotin

source_name: Human stomach

label_protocol: Standard Affymetrix labeling protocol

extract_protocol: Total RNA was isolated using QIAGEN RNeasy Mini Kit following manufacturer's instructions

value: Gastric tumor


title: S_065


title: WT_unstimulated_Rad21_ChIP_rep1

description:
WT0 Rad21 Rep1
Rad21 ChIP-seq of unstimulated macrophages


title: S_078


title: WT_liver_mac_LPS_2h_RNAseq_rep2

description:
WT_4OHT_LPS_2
RNA-seq of tamoxifen-treated LPS-stimulated WT macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 043


title: Liver Tumor HCC 041


title: Liver Tumor HCC 040


title: WT_liver_mac_LPS_2h_RNAseq_rep1

description:
WT_4OHT_LPS_1
RNA-seq of tamoxifen-treated LPS-stimulated WT macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 039


title: S_048


title: S_050


title: S_047


title: Liver Tumor HCC 038


title: S_045


title: Liver Tumor HCC 042


title: WT_liver_mac_unstimulated_RNAseq_rep3

description:
WT_4OHT_3
RNA-seq of tamoxifen-treated unstimulated WT macrophages transduced with ERT2-TEV


title: S_046


title: WT_liver_mac_unstimulated_RNAseq_rep2

description:
WT_4OHT_2
RNA-seq of tamoxifen-treated unstimulated WT macrophages transduced with ERT2-TEV


title: WT_liver_mac_unstimulated_RNAseq_rep1

description:
WT_4OHT_1
RNA-seq of tamoxifen-treated unstimulated WT macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 037


title: Rad21tev+OHT_liver_mac_LPS_2h_RNAseq_rep3

description:
TEV_4OHT_LPS_3
RNA-seq of tamoxifen-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Rad21tev+OHT_liver_mac_LPS_2h_RNAseq_rep2

description:
TEV_4OHT_LPS_2
RNA-seq of tamoxifen-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: S_044


title: S_042


title: Rad21tev+OHT_liver_mac_LPS_2h_RNAseq_rep1

description:
TEV_4OHT_LPS_1
RNA-seq of tamoxifen-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 028


title: Liver Tumor HCC 027


title: Rad21tev+etOH_liver_mac_LPS_2h_RNAseq_rep2

description:
TEV_Etoh_LPS_2
RNA-seq of ethanol-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: S_037


title: Liver Tumor HCC 029


title: Liver Tumor HCC 022


title: Rad21tev+etOH_liver_mac_LPS_2h_RNAseq_rep1

description:
TEV_Etoh_LPS_1
RNA-seq of ethanol-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: S_041


title: Liver Tumor HCC 025


title: S_038


title: Rad21tev+OHT_liver_mac_unstimulated_RNAseq_rep3

description:
TEV_4OHT_3
RNA-seq of tamoxifen-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 023


title: S_036


title: Liver Tumor HCC 015


title: Liver Tumor HCC 018


title: DF_ab1562_M_d3_id1071

description: DF_ab1562_M_d3_id1071 paxgene RNA aa-aRNA Cy5 labelled vs Stratagene UHR aa-aRNA Cy3 labeled

scan_protocol: Scan Power : 100 PMT Volts : 484 Pixel Size : 10 Laser on time : 204308 Laser Power : 3.10 Scan Date : 2013-04-27 Scan Temperature : 35.18 Scan Time : 00:15:27 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.3.2 Focus Position : 0

label_protocol:
Type of label : Cy3
reference URL : http://www.gelifesciences.com/webapp/wcs/stores/servlet/ProductDisplay?categoryId=11158&catalogId=10101&productId=16547&storeId=11787&langId=-30

source_name: DF_ab1562_M_d3_id1071 paxgene RNA aa-aRNA Cy5 labeled


title: S_035


title: Rad21tev+etOH_liver_mac_LPS_2h_RNAseq_rep3

description:
TEV_Etoh_LPS_3
RNA-seq of ethanol-treated LPS-stimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Rad21tev+OHT_liver_mac_unstimulated_RNAseq_rep2

description:
TEV_4OHT_2
RNA-seq of tamoxifen-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Rad21tev+OHT_liver_mac_unstimulated_RNAseq_rep1

description:
TEV_4OHT_1
RNA-seq of tamoxifen-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV


title: Liver Tumor HCC 019


title: Liver Tumor HCC 011


title: Liver Tumor HCC 010


title: Rad21-/-_IfnLPS_8h_RNAseq_rep3

description:
KOi8_3
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg

data_processing:
The reads were aligned to mouse genome mm9 using Tophat2 with arguments  “--library-type fr-firststrand --b2-very-sensitive --b2-L 25” with gene annotation from Ensembl version 67
Number of reads counts on exons were summarised using Rsubread
Genome_build: mm9
Supplementary_files_format_and_content: reads counts on genes

extract_protocol:
RNA was extracted from 2 millon cells per condition with RNeasy minikit and using Qiashredder disruption following the manufacturer's instructions (Qiagen). Quality of RNA was assessed using a Bioanalyzer instrument (Agilent) and quantified with Qubit (Invitrogen). ERCC RNA Spike-Ins (Ambion) were added to each purified RNA solution.
750ng of total RNA were used to prepare libraries using the TruSeq stranded total RNA Kit for Illumina following the manufacturer's recommendations. Library quality and quantity were assessed on a Bionalyser and Qubit respectively.

treatment_protocol: Macrophages were subjected to LPS treatment (10ng/ml) and Interferon-gamma treatment (10ng/ml) at the indicated time points (see individual samples).

value: primed for 24h with IFNg and 8 hours of LPS stimulation


title: S_027

description: Gene expression data of human gastric tumor


title: S_024


title: S_030


title: S_031


title: S_034


title: Liver Tumor HCC 008


title: S_021


title: Liver Tumor HCC 006


title: Rad21-/-_IfnLPS_8h_RNAseq_rep1

description:
KOi8_1
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg


title: Rad21-/-_IfnLPS_2h_RNAseq_rep2

description:
KOi2_2
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg

value: primed for 24h with IFNg and 2 hours of LPS stimulation


title: Rad21-/-_IfnLPS_2h_RNAseq_rep3

description:
KOi2_3
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg


title: Liver Tumor HCC 005

value: Tumor


title: S_018


title: S_015


title: Rad21-/-_IfnLPS_8h_RNAseq_rep2

description:
KOi8_2
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg


title: WT_IfnLPS_8h_RNAseq_rep3

description:
WTi8_3
RNA-seq of 8h LPS-stimulated macrophages primed for 24h with IFNg


title: WT_IfnLPS_8h_RNAseq_rep2

description:
WTi8_2
RNA-seq of 8h LPS-stimulated macrophages primed for 24h with IFNg


title: WT_IfnLPS_8h_RNAseq_rep1

description:
WTi8_1
RNA-seq of 8h LPS-stimulated macrophages primed for 24h with IFNg


title: Liver Tumor HCC 003


title: Liver Tumor HCC 001


title: Rad21-/-_IfnLPS_2h_RNAseq_rep1

description:
KOi2_1
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages primed for 24h with IFNg


title: S_014


title: WT_IfnLPS_2h_RNAseq_rep3

description:
WTi2_3
RNA-seq of 2h LPS-stimulated macrophages primed for 24h with IFNg


title: S_008


title: S_011


title: WT_IfnLPS_2h_RNAseq_rep2

description:
WTi2_2
RNA-seq of 2h LPS-stimulated macrophages primed for 24h with IFNg


title: Normal Liver 012

source_name: Normal Liver

value: Normal


title: S_012


title: Normal Liver 011


title: Normal Liver 014


title: Normal Liver 015


title: Normal Liver 013


title: S_007


title: S_005


title: WT_IfnLPS_2h_RNAseq_rep1

description:
WTi2_1
RNA-seq of 2h LPS-stimulated macrophages primed for 24h with IFNg

value: wild-type


title: Normal Liver 001


title: Normal Liver 010


title: S_006


title: S_004


title: Rad21-/-_LPS_8h_RNAseq_rep3

description:
KO8_3
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages

value: 8 hours of LPS stimulation


title: cell line H12.1D, replicate 1

city: Halle (Saale)

first: Martin

middle: Sebastian

last: Staege

state: Sachsen-Anhalt

address: Ernst-Grube-Str. 40

department: Universitätsklinik u. Poliklinik für Kinder- u. Jugendmedizin

description: Gene expression data from established cell line

hyb_protocol: Following fragmentation, biotinylated cDNA was hybridized on HG_U133A Microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 7G

data_processing: The data were analyzed using the RMA algorithm with Affymetrix Expression Console

label: biotin

source_name: cell line H12.1D, replicate 1

label_protocol: Biotinylated cDNA was prepared according to the standard Affymetrix protocol

growth_protocol: Cell lines were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum, 100U/mL penicillin, and 100µg/mL streptomycin

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

value: germ cell tumour cell line


title: S-077


title: Rad21-/-_LPS_8h_RNAseq_rep2

description:
KO8_2
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages

source_name: Bone marrow-derived macrophages


title: Rad21-/-_LPS_8h_RNAseq_rep1

description:
KO8_1
RNA-seq of 8h LPS-stimulated Rad21-/- macrophages


title: cell line H12.1D, replicate 2

source_name: cell line H12.1D, replicate 2


title: S-075


title: Rad21-/-_LPS_2h_RNAseq_rep2

description:
KO2_2
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages

value: 2 hours of LPS stimulation


title: Rad21-/-_LPS_2h_RNAseq_rep3

description:
KO2_3
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages


title: Rad21-/-_LPS_2h_RNAseq_rep1

description:
KO2_1
RNA-seq of 2h LPS-stimulated Rad21-/- macrophages


title: Rad21-/-_unstimulated_RNAseq_rep3

description:
KOUT_3
RNA-seq of unstimulated Rad21-/- macrophages


title: cell line GCT72, replicate 2

source_name: cell line GCT72, replicate 2


title: cell line GCT72, replicate 1

source_name: cell line GCT72, replicate 1


title: S-074

description: Gene expression data of human gastric tumor


title: NUH_R021


title: S-071


title: Rad21-/-_unstimulated_RNAseq_rep2

description:
KOUT_2
RNA-seq of unstimulated Rad21-/- macrophages


title: Rad21-/-_unstimulated_RNAseq_rep1

description:
KOUT_1
RNA-seq of unstimulated Rad21-/- macrophages


title: cell line H12.5, replicate 1

source_name: cell line H12.5, replicate 1


title: cell line H12.5, replicate 2

source_name: cell line H12.5, replicate 2


title: S_003


title: cell line 1411HP, replicate 1

source_name: cell line 1411HP, replicate 1


title: NUH_R019


title: NUH_R020


title: WT_LPS_8h_RNAseq_rep1

description:
WT8_1
RNA-seq of 8h LPS-stimulated macrophages


title: S-072


title: WT_LPS_2h_RNAseq_rep3

description:
WT2_3
RNA-seq of 2h LPS-stimulated macrophages


title: cell line 1411HP, replicate 2

source_name: cell line 1411HP, replicate 2


title: NUH_R018


title: NUH_R017


title: cell line 1777NRpmet, replicate 1

source_name: cell line 1777NRpmet, replicate 1


title: Huh7_UV_48h_a_51

city: New York

first: Angela

last: Rasmussen

state: NY

department: Center for Infection and Immunity

institute: Columbia University

hyb_protocol: Individual cRNA samples were hybridized to Agilent human whole-genome oligonucleotide 4X44K microarrays according to the manufacturer's instructions.

scan_protocol: Slides were scanned with an Agilent DNA microarray scanner, and the resulting images were analyzed using Agilent Feature Extractor version 8.1.1.1. This software was used to perform image analysis, including significance of signal and spatial detrending and to apply a universal error model. For these hybridizations, the most conservative error model was applied.

data_processing:
Raw data from Agilent Feature Extractor was normalized using the Quantile Normalization method in GeneData Analyst.  The GeneData Analyst-generated normalized signals are not available.
Matrix shows log2 ratio data (relative to mock-infected values) for DENV-infected and UV DENV-treated Huh7 cells. Probe list was selected after applying a cutoff of p<0.05 in GeneData Analyst.  The Matrix of log2 ratios forms the basis of conclusions in the manuscript and is linked as supplementary file on Series record.

source_name: Huh7_UV_48h, human hepatoma continuous cell line

label_protocol: cRNA probes were generated from each sample by the use of an Agilent one-color LowInput Quick Amp labeling kit (Agilent Technologies, Santa Clara, CA).

growth_protocol: Cells were propagated in complete Dulbecco's minimal essential medium with 10% fetal bovine serum, 100 IU/mL penicillin, and 2.5 ug/mL Plasmocin

extract_protocol: Cells were washed and lysed using TRIzol reagent and total RNA was extracted according the manufacturer's instructions

treatment_protocol: Cells were infected with DENV2/NGC at MOI=10, treated with UV-irradiated DENV2, or mock-infected

value: hepatoma

value: treated with UV-irradiated DENV2

tag: time post-infection

value: 48 hr


title: Huh7_UV_24h_b_40

source_name: Huh7_UV_24h, human hepatoma continuous cell line

value: 24 hr


title: cell line 1777NRpmet, replicate 2

source_name: cell line 1777NRpmet, replicate 2


title: cell line H12.1, replicate 1

source_name: cell line H12.1, replicate 1


title: WT_LPS_2h_RNAseq_rep2

description:
WT2_2
RNA-seq of 2h LPS-stimulated macrophages

value: Bone marrow-derived macrophages


title: WT_LPS_2h_RNAseq_rep1

description:
WT2_1
RNA-seq of 2h LPS-stimulated macrophages


title: Huh7_UV_24h_a_39


title: NUH_R015

source_name: Human stomach


title: NUH_R014


title: cell line H12.1, replicate 2

source_name: cell line H12.1, replicate 2


title: Huh7_mock_48h_b_50

source_name: Huh7_mock_48h, human hepatoma continuous cell line

value: Mock-infected


title: Huh7_mock_48h_a_49


title: WT_unstimulated_RNAseq_rep2

description:
WTUT_2
RNA-seq of unstimulated macrophages

value: unstimulated


title: Huh7_mock_24h_b_38

source_name: Huh7_mock_24h, human hepatoma continuous cell line


title: NUH_R010


title: Huh7_mock_24h_a_37


title: WT_unstimulated_RNAseq_rep1

description:
WTUT_1
RNA-seq of unstimulated macrophages

source_name: Bone marrow-derived macrophages


title: Huh7_DV-2_48h_b_54

source_name: Huh7_DV-2_48h, human hepatoma continuous cell line


title: NUH_R006


title: WT_unstimulated_RNAseq_rep3

description:
WTUT_3
RNA-seq of unstimulated macrophages


title: NUH_R008


title: NUH_R009


title: NUH_R012


title: Huh7_DV-2_24h_a_41

source_name: Huh7_DV-2_24h, human hepatoma continuous cell line


title: Huh7_DV-2_24h_b_42


title: Huh7_DV-2_48h_a_53


title: NUH_R005


title: NUH_R002


title: Rad21tev+etOH_liver_mac_unstimulated_RNAseq_rep2

description:
TEV_Etoh_2
RNA-seq of ethanol-treated unstimulated Rad21-Tev macrophages transduced with ERT2-TEV

source_name: Fetal liver derived macrophages

value: Fetal liver derived macrophages

value: ethanol

value: Unstimulated


title: NUH_R004

value: Gastric tumor


title: NUHR_027


title: NCC_R021


title: NCC_R025


title: NUH_R003


title: NCC_R026