title: Leaf_ET_drought_rep3

city: Jena

first: Klaus

last: Gase

address: Hans-Knoell-Strasse 8

department: Molecular Ecology

institute: Max-Planck-Institute for Chemical Ecology

description: Gene expression in leaves and roots

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent platform GPL21138 for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed at room temperature with GE Wash Buffer 1 (Agilent) and at 37°C with GE Wash buffer 2 (Agilent) as outlined in the One-Color Microarray-Based Gene Expression Analysis manual (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 95 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

organism: Nicotiana attenuata

source_name: leaf from EV/irTOC1 graft 7 pm drought

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the Quick Amp labeling kit (Agilent, Santa Clara, CA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, Germany).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: N. attenuata wild type were grown in glasshouse conditions 18-35C under 16:8 h of light:dark regime.

extract_protocol: Total RNA was extracted from leaves and roots using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

treatment_protocol: 13 day-old rosette stage EE, ET and TT plants were treated by withholding water for 7 days (drought) or maintaining normal watering regime (control). Leaves and roots from 20 day-old rosette stage control and drought EE, ET, and TT plants were collected at around 7 pm (TOC1 peaking time).

tag: genotype

value: ET

value: drought

value: leaf


title: Root_TT_control_rep3

status: Public on Jan 08 2019

type: RNA

country: Germany

description: Gene expression in leaves and roots

molecule: total RNA

source_name: root from irTOC1/irTOC1 graft 7 pm control watering

value: TT

tag: treatment

value: control

tag: tissue

value: root


title: Infection_ChIPseq_input

type: SRA

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description: Agambiae_genes_and_promoters_ChIP_rpkm_counts.txt

library_source: transcriptomic

data_processing:
We mapped reads for various histone modifications and the input to A.gambiae PEST strain genome version 4.3 using Bowtie v2.2.9 with default parameters except for --no-mixed
Reads were trimmed 5 bases from each read 5’ end (--trim5 5). Mapped reads were sorted and deduplicated using SAMtools v.1.6. We applied a quality threshold of 10 in MAPQ score. All libraries were downsampled (SAMtools) to the same number of reads (9M) for further downstream analysis
We conducted peak calling using MACS2 (v.2.1.1) [61] “callpeak” module with -t and -c options and default parameters, except for -g 2.73e8 --keep-dup all -B --SPMR -q 0.01 –nomodel
To quantitative compare histone modification profiles between infected and control mosquito tissues, we used diffReps software. ChIP-seq data for infected and control and the corresponding inputs were provided with -tr, -co, --btr and --bco options. Due to the lack of biological replicates, the statistical test used was G-test (-me gt). Rest of parameters were set as default except for --window 1000
We performed annotation of MACS2 peaks and diffReps regions to genomic features (TSSs, exons, introns, and intergenic regions) using the annotatePeaks.pl module in HOMER (v.3.12)
We mapped RNA paired directional reads to A.gambiae PEST strain genome version 4.3 using TopHat v2.0.13. We aligned reads using the option of library type set as first-strand for directional RNA-seq
Quantification and differential gene expression analysis was conducted using HTSeq/DESeq2 packages
Genome_build: AgamP4.3 (VectorBase)
Supplementary_files_format_and_content: Tracks of ChIP-seq signal, normalized and input corrected, per histone and condition (bw). The bedGraph files were built with MACS2 “bdgcmp" module (-m ppois) and bigwig files using bedGraphToBigWig tool
Supplementary_files_format_and_content: RNA-seq mapped reads coverage was obtained in bigwig format (_coverage.bw) using bamCoverage tool
Supplementary_files_format_and_content: Counts of normalized (RPKM) and input corrected ChIP-seq reads per histone and condition (txt). The counts were obtained using bedtools intersect -c

organism: Anopheles gambiae

source_name: mosquito midgut

growth_protocol: Three- to five-day-old female A.gambiae mosquitoes were sourced from an outbred colony established in 2008 and repeatedly replenished with F1 from wild-caught mosquito females collected in Kou Valley (11°23'14"N, 4°24'42"W), 30 km from Bobo-Dioulasso, south-western Burkina Faso (West Africa). Mosquitoes were maintained under standard insectary conditions (27 ± 2°C, 70 ± 5% relative humidity, 12:12 LD)

extract_protocol:
Dissection of mosquito midguts and salivary glands was performed in situ on adult females at 7 days post-blood meal. To determine infection levels, mosquito guts were dissected 7 days after blood feeding and were stained with 2% Mercurochrome before microscopic examination. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) and fresh tissues were immediately processed for chromatin and RNA analyses
Chromatin immunoprecipitation was performed in mosquito as previously described by us in Gomez-Diaz et al. Antibodies to histone modifications used in this study were anti-H3K9ac (Millipore #07-352), antiH3K4me3 (Abcam ab8580), anti-H3K27ac (Abcam ab4729), and anti-H3K9me3 (Abcam ab8898).ChIP-seq libraries were prepared following the procedure in Bowman et al., and using the HiFi Kapa Sybr library preparation kit (KapaBiosystems). To obtain the quantity needed to perform ChIP-seq, the samples were pooled, resulting in one biological replicate for infected mosquito midguts and one biological replicate of uninfected tissues. ChIP-seq libraries were sequenced at the HudsonAlpha Institute for Biotechnology using an Illumina HiSeq2000 sequencer.

treatment_protocol: Females were fed through membranes on gametocyte-infected blood from malaria patients. To eliminate transmission-blocking factors, venous blood was collected and the serum was replaced by a non-immune AB serum to avoid transmission of human blocking factors

value: midgut and salivary gland

tag: Sex

value: female

tag: time

value: 7 days post-blood meal

tag: infection status

value: Infected

tag: replicate


title: Infection_ChIPseq_H3K9me3


title: Infection_ChIPseq_H3K4me3


title: Root_ET_drought_rep4

description: Gene expression in leaves and roots

source_name: root from EV/irTOC1 graft 7 pm drought


title: Root_EE_control_rep3

description: Gene expression in leaves and roots

source_name: root from EV/EV graft 7 pm control watering

value: EE


title: Root_TT_drought_rep3

description: Gene expression in leaves and roots

source_name: root from irTOC1/irTOC1 graft 7 pm drought


title: glp-4_NGM_A

city: Houston

first: Natalia

middle: V

last: Kirienko

state: TX

address: 6100 Main St. MS140

department: BioSciences

country: USA

institute: Rice University

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: Data were analyzed with GC-RMA in the R programming language, using the Bioconductor package gcrma. Analysis was performed using default settings.

label: biotin

organism: Caenorhabditis elegans

source_name: glp-4, NGM (agar), 8h

label_protocol: Affymetrix standard protocol

growth_protocol: glp-4 worms were synchronized by hypochlorite treatment. Arrested L1s were plated on 10 cm NGM plates seeded with E. coli OP50 and grown at 15°C overnight then shifted to 25°C for 44h until they reached sterile young adult stage.

extract_protocol: RNA was extracted using TRI Reagent (Molecular Research Center) according to manufacturer's instructions and purified using an RNeasy column (Qiagen).

treatment_protocol: Animals were grown until young adult stage. Afterward, worms were incubated for 12 hours at 25°C in 6-well plates with liquid S basal media + E. coli with media control or pyoverdine (PVD). A cohort of glp-4 worms that remaind on 10 cm NGM plates served as an additional control

tag: media

value: NGM, E. coli OP50

value: Whole organism


title: Leaf_EE_drought_rep3

description: Gene expression in leaves and roots

source_name: leaf from EV/EV graft 7 pm drought


title: Root_ET_drought_rep3

description: Gene expression in leaves and roots


title: Root_TT_drought_rep4

description: Gene expression in leaves and roots


title: Leaf_TT_drought_rep3

description: Gene expression in leaves and roots

source_name: leaf from irTOC1/irTOC1 graft 7 pm drought


title: Root_ET_control_rep3

description: Gene expression in leaves and roots

source_name: root from EV/irTOC1 graft 7 pm control watering


title: Leaf_ET_drought_rep4

description: Gene expression in leaves and roots


title: Leaf_TT_drought_rep4

description: Gene expression in leaves and roots


title: Root_EE_drought_rep3

description: Gene expression in leaves and roots

source_name: root from EV/EV graft 7 pm drought


title: POOL2__pMPRA1__input_DNA

city: Boston

first: Martha

middle: L.

last: Bulyk

state: MA

address: 77 Avenue Louis Pasteur, Rm 468

department: Division of Genetics

institute: Brigham and Women's Hospital

library_source: genomic

data_processing:
We used cutadapt to remove adapters from the raw reads and trim bases with a Phred score < 20.
We then counted barcodes if they exactly matched an 11-bp barcode in the design index as well as the constant upstream 6 bp.
All scripts used for subsequent data analysis of processed files can be found at https://github.com/kmattioli/2018__lncRNA_promoter_MPRA
Genome_build: hg19
Supplementary_files_format_and_content: Barcode sequence and count per replicate

molecule: genomic DNA

organism: synthetic construct

source_name: plasmid DNA

extract_protocol:
RNA from transiently transfected K562, HeLa, and HepG2 was precipitated by phenol-chloroform extraction according to standard protocols. DNase treatment (Worthington) was followed by cDNA synthesis with SuperScript III First-Strand Synthesis System (Invitrogen).
cDNA was subject to library amplification and libraries were cleaned up with AMPure beads (0.6x, 1.6x, 1.0x).
plasmid sequencing and RNA-seq

treatment_protocol: K562 cells were transiently transfected for 48 hours with a ratio of 1:1 with Xtreme Gene HP (Roche), HeLa and HepG2 both with 3:1 Xtreme Gene HP according to the manufacturer protocol. 4x10e6 K562 cells in 6 cm dish, 1.6x10e6 HeLa or HepG2 cells in 10 cm dish were seeded 12-16 hours prior to the transfection. Cells were counted before the transfection and per 1 x 10e6 cells, 5 µg oligopool were transfected. Media was not changed and transfection efficiency was microscopically determined by GFP expression 48 hours post transfection.

tag: sample type

value: plasmid DNA


title: Leaf_ET_control_rep3

description: Gene expression in leaves and roots

source_name: leaf from EV/irTOC1 graft 7 pm control watering


title: Infection_ChIPseq_H3K9ac


title: Shah_029 Nik(delta)IE

city: Ann Arbor

first: XIANG

last: XUE

state: Michigan

address: 1301 E. Catherine Street

institute: Umich

description: Gene expression data from colons.

hyb_protocol: Following fragmentation, 3.7 ug of cDNA were hybridized at 48C on a Mouse Gene 2.1 ST Array strip using the Affymetrix Gene Atlas system (software version 1.0.4.267)

scan_protocol: Arrays were scanned using the Affymetrix Gene Atlas system.

data_processing: Data was analyzed using the oligo Bioconductor package implemented in the R-statistical environment version 3.0.0. RMA was used to fit log2 transformed expression values.

organism: Mus musculus

source_name: Inflamed Colon

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix Plus WT kit protocol from 400 ng total RNA (GeneChip® WT Plus Reagent Kit Manual P/N 703174 Rev. 2).

growth_protocol: All mice were C57BL/6 background and maintained in standard cages in a light and temperature-controlled room and were allowed standard chow and water ad libitum.

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

treatment_protocol: Normal and inflamed colon tissues were got from 3 months old mice

tag: genotype/variation

value: Nik(delta)IE

tag: colon phenotype

value: inflamed

tag: age

value: 3 months old


title: Infection_ChIPseq_H3K27ac


title: POOL1__pNoCMVMPRA1__input_DNA


title: Control_RNAseq_replicate2

extract_protocol:
Dissection of mosquito midguts and salivary glands was performed in situ on adult females at 7 days post-blood meal. To determine infection levels, mosquito guts were dissected 7 days after blood feeding and were stained with 2% Mercurochrome before microscopic examination. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) and fresh tissues were immediately processed for chromatin and RNA analyses
Total RNA was extracted from fresh mosquito tissues (~25 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer protocol and used for mRNA library preparation.

value: Control


title: POOL1__pMPRA1__input_DNA


title: Leaf_TT_control_rep3

description: Gene expression in leaves and roots

source_name: leaf from irTOC1/irTOC1 graft 7 pm control watering


title: Control_RNAseq_replicate1


title: Leaf_EE_drought_rep4

description: Gene expression in leaves and roots

value: drought


title: Infection_RNAseq_replicate2


title: Shah_028 Nik+/+

description: Gene expression data from colons.

value: Nik+/+


title: Shah_027 Nik(delta)IE

description: Gene expression data from colons.

source_name: Normal Colon

value: normal


title: 48h_siPOU3F2_24h_UVB_R1

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Raw fastq files were then trimmed of poly-A using  cutadapt {Martin, 2011 }
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is  count-per-million prior to glmQLFTest.

organism: Homo sapiens

growth_protocol: All cell lines were grown at 37°C with 10% CO2 in RPMI-1640 (Gibco BRL, Invitrogen) supplemented with penicillin and streptomycin, 10% fetal bovine serum (FBS, Biosera).

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

treatment_protocol: Cells were treated with the indicated siRNA prior to UVB treatment as describe in the paper

tag: disease state

value: melanoma

tag: cell line

tag: transfection

value: 48h siPOU3F2 24h UVB


title: 48h_siPOU3F2_24h_UVB_R2


title: Infection_RNAseq_replicate1

extract_protocol:
Dissection of mosquito midguts and salivary glands was performed in situ on adult females at 7 days post-blood meal. To determine infection levels, mosquito guts were dissected 7 days after blood feeding and were stained with 2% Mercurochrome before microscopic examination. Tissues were maintained in ice-cold Schneider’s insect culture medium (Sigma-Aldrich) and fresh tissues were immediately processed for chromatin and RNA analyses
Total RNA was extracted from fresh mosquito tissues (~25 midguts and ~ 50 salivary glands) using the mirVana™ RNA Isolation Kit (Ambion®) according to the manufacturer protocol and used for mRNA library preparation. RNA concentration was quantified using a Qubit® 2.0 Fluorometer, and RNA integrity was determined with an Agilent 2100 Bioanalyzer. Illumina libraries were prepared and sequenced at the HudsonAlpha Institute for Biotechnology, using an Illumina HiSeq2000 sequencer, standard directional RNA-seq library construction, 50 bp paired end reads with ribosomal reduction (RiboMinus™ Eukaryote Kit, Ambion®)

value: midgut and salivary gland


title: 48h_siPOU3F2_24h_UVB_R3


title: Leaf_EE_control_rep3

description: Gene expression in leaves and roots

source_name: leaf from EV/EV graft 7 pm control watering

value: control

value: leaf


title: Shah_026 Nik+/+

description: Gene expression data from colons.


title: 48h_siPOU3F2_12h_UVB_R2

value: 48h siPOU3F2 12h UVB


title: Root_ET_drought_rep2

description: Gene expression in leaves and roots

value: ET

value: root


title: 48h_siPOU3F2_12h_UVB_R1


title: 48h_siPOU3F2_12h_UVB_R3


title: Root_ET_drought_rep1

description: Gene expression in leaves and roots


title: Root_ET_control_rep2

description: Gene expression in leaves and roots


title: LAS61 input OP37 DPY-27 RNAi emb ChIP-seq

city: New York City

first: Lena

middle: Annika

last: Street

state: NY

address: 100 Washington Square East

department: Biology

institute: New York University

data_processing:
Basecalls were performed using CASAVA version 1.8.
ChIP-seq reads were aligned to the WS220 genome assembly using bowtie version 1.2.0 using default parameters for allowing mismatches in the seed (-n option) and suppressing alignments for reads with more than 4 reportable alignments.
Peaks were called using MACS version 1.4.3 with the following setting: input, genome size (-g ce), format (-f BAM), p-value (-p 1e-10 and -p 1e-5)
Genome coverage was estimated using MACS version 1.4.3 with the following setting: genome size (-g ce), format (-f BAM), output in wiggle format (-w), whole genome output (-S), resolution (--space=1)
Coverage per base was normalized to the genome-wide median coverage (excluding the mitochondrial chromosome). Final ChIP enrichment score per base was obtained by subtracting matching input coverage.
Replicates were merged by averaging coverage at each base position. To determine a set of final peaks, reads from the replicates were combined using the BEDTools utility mergeBam version 2.13.442, and MACS was used to call peaks (see above, p-value -p 1e-10). Only those peaks present in the majority of the individual replicates identified below p-value 1e-5 were included in the final peak set.
RNA-seq reads were aligned to the WS220 genome assembly using tophat version 2.1.1 using default parameters, specifying first strand alignment.
Resultant RNA-seq bam files were converted to sam files using samtools version 1.6. Sam files were used to generate count data using htseq-cout version 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: BigWig files were generated by converting wiggle files using the UCSC wigToBigWig utility. Wiggle files were generated using MACS version 1.4.3, normalized according to the genome-wide mean coverage and then input subtracted. Scores represent the average coverage of each replicate at each base position.
Supplementary_files_format_and_content: Bed files were generated by combining replicate reads and using MACS version 1.4.3 at two different p-values. Only peaks at the more stringend cut-off were inlcuded in the final set that were overlapping with the majority of peaks of each of the replicates at the less stringend p-value.
Supplementary_files_format_and_content: Counts files were generated using Htseq-counts version 0.6.1.

source_name: whole worms

growth_protocol: Embryos were isolated by bleaching gravid adults grown on plates at 20C.

extract_protocol:
Embryos were washed and dounced in FA buffer (50 mM HEPES/KOH pH 7.5, 1 mM EDTA, 1% Triton X-100, 0.1 % sodium deoxycholate; 150 mM NaCl). 0.1 sarkosyl was added before sonicating to obtain chromatin fragments of majority between 200-800 bp. 1-2 mg of embryo extract and 3-5 ug of antibody was used per ChIP.
Half of the ChIP DNA were ligated to Illumina or home-made multiplexed adapters and amplified by PCR. Library DNA between 250-500 bp in size was gel purified.

treatment_protocol: Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.

tag: strain

tag: developmental stage

value: mixed embryo

tag: antibody target

value: INPUT

tag: chip antibody (vendor, cat#, lot#)


title: LAS60 input OP37 Control RNAi emb ChIP-seq


title: Leaf_ET_control_rep4

description: Gene expression in leaves and roots

tag: genotype

tag: treatment

tag: tissue


title: 48h_siPOU3F2_6h_UVB_R1

value: 48h siPOU3F2 6h UVB


title: 48h_siPOU3F2_6h_UVB_R3


title: 48h_siPOU3F2_6h_UVB_R2


title: Root_ET_control_rep1

description: Gene expression in leaves and roots


title: 48h_siPOU3F2_0h_UVB_R3

value: 48h siPOU3F2 0h UVB


title: LAS70 input N2 emb ChIP-seq


title: LAS59  input OP37 DPY-27 RNAi emb ChIP-seq


title: LAS58 input OP37 Control RNAi emb ChIP-seq


title: 48h_siPOU3F2_0h_UVB_R2


title: 48h_siPOU3F2_0h_UVB_R1


title: 48h_siCTR_24h_UVB_R3

value: siCTR

value: 48h siCTR 24h UVB


title: SK-MEL-1_IFN-b_treated_vs_non-treated

city: Minato-ku

first: Yoshinori

last: Watanabe

state: Tokyo

address: 3-19-18, Nishi-shimbashi

country: Japan

institute: Jikei Hospital

hyb_protocol: standard Agilent protocol

scan_protocol: standard Agilent protocol

data_processing: Raw data were normalized with a locally weighted scatterplot smoothing linear algorithm using Feature Extraction 10.7.3.1 software (Agilent Technologies)

source_name: SK-MEL-1 melanoma cell line, IFN-beta,  0 IU/ml

label_protocol: standard Agilent protocol

growth_protocol: All cell lines were grown in each medium +10% FBS

extract_protocol: mRNA was isolated with QIAGEN RNeasy Plus mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyzer.

treatment_protocol: total RNA was extracted from melanoma cells after treatment with or without IFN-β at a concentration of 1,000 IU/ml for 48 h

value: Melanoma

source_name: SK-MEL-1 melanoma cell line, IFN-beta,  1000 IU/ml


title: LAS52 input GW638 emb ChIP-seq


title: SDC3 GW638 emb rep2 ChIP-seq

description:
SDC3_GW638_Emb_LAS66_LAS67_average.bw
SDC3_GW638_Emb_LAS66_LAS67_final_peaks.bed

value: Covance Research Products Inc, JL00002_SDC3

tag: antibody antigen

tag: antibody (host, clone)

value: Rabbit, polyclonal

tag: matching input


title: Leaf_EE_control_rep4

description: Gene expression in leaves and roots

value: EE


title: Root_EE_drought_rep4

description: Gene expression in leaves and roots

value: drought


title: Leaf_TT_control_rep4

description: Gene expression in leaves and roots

value: TT


title: 48h_siCTR_24h_UVB_R2

value: melanoma


title: RPMI-7951_IFN-b_treated_vs_non-treated

source_name: RPMI-7951 melanoma cell line, IFN-beta, 0 IU/ml

source_name: RPMI-7951 melanoma cell line, IFN-beta, 1000 IU/ml


title: SK-MEL-5_IFN-b_treated_vs_non-treated

source_name: SK-MEL-5 melanoma cell line, IFN-beta,  0 IU/ml

source_name: SK-MEL-5 melanoma cell line, IFN-beta,  1000 IU/ml


title: Root_TT_control_rep4

description: Gene expression in leaves and roots

source_name: root from irTOC1/irTOC1 graft 7 pm control watering

value: control


title: A375_IFN-b_treated_vs_non-treated

source_name: A375 melanoma cell line, IFN-beta, 0 IU/ml

source_name: A375 melanoma cell line, IFN-beta, 1000 IU/ml


title: Leaf_ET_drought_rep2

description: Gene expression in leaves and roots

source_name: leaf from EV/irTOC1 graft 7 pm drought

value: leaf


title: Leaf_ET_control_rep2

description: Gene expression in leaves and roots

value: ET


title: H4panAc N2 emb rep3 ChIP-seq

description:
H4panAc_N2_Emb_SE205_SE206_LAS63_average.bw
H4panAc_N2_Emb_SE205_SE206_LAS63_final_peaks.bed

value: Active Motif, 39243

value: amino terminal region of Tetrahymena histone H2A acetylated at multiple lysines


title: Root_EE_control_rep4

description: Gene expression in leaves and roots

source_name: root from EV/EV graft 7 pm control watering

value: root


title: Root_TT_drought_rep2

description: Gene expression in leaves and roots

source_name: root from irTOC1/irTOC1 graft 7 pm drought


title: Root_TT_control_rep2

description: Gene expression in leaves and roots


title: Leaf_ET_control_rep1

description: Gene expression in leaves and roots

source_name: leaf from EV/irTOC1 graft 7 pm control watering


title: Leaf_ET_drought_rep1

description: Gene expression in leaves and roots


title: Leaf_TT_drought_rep2

description: Gene expression in leaves and roots

source_name: leaf from irTOC1/irTOC1 graft 7 pm drought


title: 48h_siCTR_12h_UVB_R3

value: 48h siCTR 12h UVB


title: H3K4me1 N2 emb rep2 ChIP-seq

description:
H3K4me1_N2_Emb_LW166_LAS53_average.bw
H3K4me1_N2_Emb_LW166_LAS53_final_peaks.bed

value: mixed embryo

value: Abcam, ab8895

value: Human Histone H3 aa 1-100 (mono methyl K4) conjugated to Keyhole Limpet Haemocyanin (KLH)


title: 48h_siCTR_12h_UVB_R2

value: siCTR


title: Root_ET_control_rep4

description: Gene expression in leaves and roots

source_name: root from EV/irTOC1 graft 7 pm control watering


title: 48h_siCTR_6h_UVB_R3

value: 48h siCTR 6h UVB


title: 48h_siCTR_12h_UVB_R1


title: SDC3 GW638 emb rep1 ChIP-seq

value: Covance Research Products Inc, JL00002_SDC3

value: Rabbit, polyclonal


title: wild type DMSO (rep 3)

city: La Jolla

first: Emily

last: Troemel

state: CA

department: Cell and Developmental Biology

institute: University of California, San Diego

description:
Nematocida.counts.matrix (column 14)
022_f-N2-DMSO_S20_L004

data_processing:
Reads were aligned to WS235 using Bowtie 2.
Transcript abundance was estimated using RSEM.
Genome_build: WormBase Release WS235
Supplementary_files_format_and_content: comma-delimited file containing raw counts

source_name: L4 stage whole animal

growth_protocol: For all strains and treatments, synchronized L1 animals were grown at 20°C until the L4 stage. For N2, ERT415, and ERT451, animals were then shifted to 25°C for 4 hours before  harvesting for RNA extraction. For DMSO and Bortezomib treated N2 animals, treatment was administered and animals were incubated at 20°C for 4 hours before harvesting for RNA extraction.

extract_protocol:
Total RNA was extracted using TriReagent (Sigma-Aldrich) and cleaned using RNAeasy (Qiagen) column purification. RNA quality was assesed using Tapestation analysis.
Paired-end sequencing libraries were constructed using TruSeq Stranded mRNA (Illumina) prep kit.

treatment_protocol: Bortezomib was added to plates to a final concentration of 20uM and animals were incubated at 20°C for 4 hours. For mock treatment control samples, an equivalent amount of DMSO was added.

value: wt

value: whole animals

value: DMSO

value: L4 stage


title: pals-22(-) pals-25(-) untreated (rep 3)

description:
Nematocida.counts.matrix (column 13)
022_c-jy3-jy9_S17_L004

value: pals-22(jy3) pals-25(jy9)


title: wild type Bortezomib (rep 3)

description:
Nematocida.counts.matrix (column 15)
022_g-N2-BTZ_S21_L004

value: Bortezomib


title: pals-22(-) untreated (rep 3)

description:
Nematocida.counts.matrix (column 12)
022_b-jy3_S16_L004


title: 48h_siCTR_24h_UVB_R1

value: melanoma

value: 48h siCTR 24h UVB


title: 48h_siCTR_0h_UVB_R3

value: 48h siCTR 0h UVB


title: Leaf_TT_control_rep2

description: Gene expression in leaves and roots

source_name: leaf from irTOC1/irTOC1 graft 7 pm control watering

value: TT

value: control

value: leaf


title: wild type Bortezomib (rep 2)

description:
Nematocida.counts.matrix (column 10)
020_g-N2-BTZ_S14_L004


title: 48h_siCTR_6h_UVB_R2


title: Root_TT_drought_rep1

description: Gene expression in leaves and roots

value: drought

value: root


title: 48h_siCTR_0h_UVB_R2

value: siCTR


title: 48h_siCTR_0h_UVB_R1


title: wild type Bortezomib (rep 1)

description:
Nematocida.counts.matrix (column 8)
019_g-N2-BTZ_S12_L004


title: wild type DMSO (rep 2)

description:
Nematocida.counts.matrix (column 9)
020_f-N2-DMSO_S13_L004


title: wild type DMSO (rep 1)

description:
Nematocida.counts.matrix (column 7)
019_f-N2-DMSO_S11_L004


title: PC3-TRIB1-rep2

city: Guangzhou

first: Yifeng

last: Luo

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Institute of Respiratory Diseases of Sun Yat-sen University

country: China

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

description:
Gene expression of prostate cancer
PC3yong.pre.TRIB1.2

data_processing:
Sequenced reads were aligned to hg38-ref-mRNA using tophat/2.0.14-gcc-4.8.5
Transcripts Per Kilobase of exon model per Million mapped reads (TPM) were calculated using Htseq
Different expression genes were calculated by DESeq (Anders et al,2010) edgeR package, |log2(FoldChange)| > 1 ,Pvalue < 0.05,"https://bioconductor.org/biocLite.R"
Genome_build: hg38

source_name: PC3 Cell Line

growth_protocol: All cells were incubated at 37°C in 5% CO2

extract_protocol:
Total RNA from prostate cancer cells (including PC3-NC, PC3-OE-TRIB1; DU145-NC, DU145-OE-TRIB1) were isolated by TRIzol (No.:15596026, Thermo Fisher Scientific, USA) and extracted by chloroform. RNA degradation and contamination were monitored on 1% agarose gels and purity was checked by the NanoPhotometer spectrophotometer (IMPLEN, CA USA). RNA concentration was measured using Qubit RNA Assay Kit in Qubit 2.0 Flurometer(Life Technologies, CA, USA) and integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzeer 2100 system (Agilent Technologies, CA, USA ).
Sequencing libraries were generated using NEBNest UltraTM RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: DU145 and PC3 cell line were transfected with TRIB1-overexpression lentivirus or blank ventor lentivirus as control group

value: Overexpression

tag: cancer type

value: Prostate cancer


title: PC3-TRIB1-rep1

description:
Gene expression of prostate cancer
PC3yong.pre.TRIB1.1


title: PC3-control-rep2

description:
Gene expression of prostate cancer
PC3yong.pre.000.2

value: negative control


title: mouse LSEC RNA-seq NASH-3

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

description:
CD11b+ cells were depleted with CD11b microbead (Miltenyi Biotec, cat. No. 130-092-634) according to the manufactures’ instruction after NPCs cell extraction. Continually, LSECs were purified from CD11b- cells by magnetic separation with CD146 microbead (Miltenyi Biotec, cat. No. 130-092-007)).
DESeq2_LSEC_RNA_seq.csv

data_processing:
FastQC was used to assess the sequencing quality on fastq files.
STAR was used for alignment to generate bam files.
The reads aligned to each gene feature were counted by HTSeq.
R package DESeq2 was used for differential expression analysis.
Single-cell RNA seq data was processed by Seurat package.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain DESeq2-normalized read counts from bulk RNA-seq, UMI count matrices from single cell RNA-seq.

source_name: liver

extract_protocol:
please see samples description
RNA libraries were prepared for sequencing using standard Illumina and 10X genomics Chromium single cell protocols

treatment_protocol: mice were fed on NASH diet (D09100301, Research Diets) for 36 weeks

value: liver sinusoid endothelial cells

tag: phenotype

value: NASH


title: pals-22(-) pals-25(-) untreated (rep 2)

description:
Nematocida.counts.matrix (column 6)
019_c-jy3-jy9_S8_L004

value: whole animals

value: L4 stage


title: pals-22(-) untreated (rep 2)

description:
Nematocida.counts.matrix (column 5)
019_b-jy3_S7_L004


title: Leaf_TT_control_rep1

description: Gene expression in leaves and roots


title: Leaf_EE_drought_rep2

description: Gene expression in leaves and roots

source_name: leaf from EV/EV graft 7 pm drought

value: EE


title: Root_EE_control_rep2

description: Gene expression in leaves and roots


title: wild type untreated (rep 3)

description:
Nematocida.counts.matrix (column 11)
022_a-N2-_S15_L004

value: wt


title: Leaf_EE_control_rep2

description: Gene expression in leaves and roots

source_name: leaf from EV/EV graft 7 pm control watering


title: Root_TT_control_rep1

description: Gene expression in leaves and roots


title: pals-22(-) pals-25(-) untreated (rep 1)

description:
Nematocida.counts.matrix (column 3)
018_c-jy3-jy9_S3_L004

value: pals-22(jy3) pals-25(jy9)


title: mouse LSEC RNA-seq NASH-1


title: Leaf_TT_drought_rep1

description: Gene expression in leaves and roots


title: Root_EE_control_rep1

description: Gene expression in leaves and roots


title: DU145-TRIB1-rep1

description:
Gene expression of prostate cancer
DU145.PRE.TRIB1.1

source_name: DU145 Cell Line


title: Root_EE_drought_rep1

description: Gene expression in leaves and roots

source_name: root from EV/EV graft 7 pm drought


title: pals-22(-) untreated (rep 1)

description:
Nematocida.counts.matrix (column 2)
018_b-jy3_S2_L004


title: DU145-TRIB1-rep2

description:
Gene expression of prostate cancer
DU145.PRE.TRIB1.2


title: mouse LSEC RNA-seq chow-3

value: chow


title: Leaf_EE_drought_rep1

description: Gene expression in leaves and roots


title: wild type untreated (rep 2)

description:
Nematocida.counts.matrix (column 4)
019_a-N2-_S6_L004


title: mouse LSEC RNA-seq chow-2


title: wild type untreated (rep 1)

description:
Nematocida.counts.matrix (column 1)
018_a-N2-_S1_L004


title: PC3-control-rep1

description:
Gene expression of prostate cancer
PC3yong.pre.000.1


title: DU145-control-rep1

description:
Gene expression of prostate cancer
DU145.PRE.000.1


title: mouse LSEC RNA-seq chow-1


title: mouse LSEC RNA-seq NASH-2


title: PBS_P4_1

status: Public on Jan 07 2019

city: Athens

first: Christian

last: Andersen

state: Georgia

address: 501 D.W. Brooks Dr., Physiology and Pharmacology

department: Physiology and Pharmacology

institute: University of Georgia

data_processing:
Reads were trimmed and clipped for quality control in Trimmomatic (v0.36)
Read quality was checked for each sample using FastQC (v0.11.5)
HISAT2 (v2.1.0) was used for alignment to reference genome
SAM files were converted to BAM files and sorted using SAMtools (v1.6)
BAM files are passed to StringTie (v1.3.4d) for transcript assembly, then merged into a unifying transcript list, and final passed through StringTie again for new abundance estimates.
Estimated counts of sequencing reads were generated using Stringtie function prepde.py
Differential expression analysis is performed on gene count data by Deseq2 (v1.18.1) in an R Studio (v1.1.456) environment running R version 3.4.4.
Genome_build: GRCm38
Supplementary_files_format_and_content: CSV file with un-normalized  estimated read counts

source_name: Uterus

extract_protocol:
Total RNA from whole uterus homogenate was extracted and purified using the Trizol protocol.
TruSeq Total RNA-Seq Library Prep kit

tag: hormone treatment

tag: dox treatment

value: PBS


title: DOX_P4_2

value: DOX


title: PBS_P4_2


title: DOX_P4_3


title: PBS_P4_3


title: DU145-control-rep2

description:
Gene expression of prostate cancer
DU145.PRE.000.2


title: DOX_E2_2


title: PBS_E2_3


title: DOX_E2_1


title: DOX_OIL_3

value: OIL


title: PBS_E2_2


title: DOX_OIL_1


title: PBS_E2_1


title: DOX_P4_1


title: PBS_OIL_2


title: PBS_OIL_3


title: DOX_OIL_2


title: PBS_OIL_1


title: DOX_E2_3


title: PWS_iPSC_1-Input

city: Farmington

first: Justin

last: Cotney

state: CT

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
4C-seq: r3Cseq:
demultiplex biological replicates by viewpoint using Cutadapt 1.10: cutadapt -g ^<viewpoint adapter sequence> --discard-untrimmed -e 0.20 -m 20 -O 12 -f fastq -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.fastq ~/4C/AS_<cell>_<rep>_<sample>_<read>_<lane>.fastq.gz >> anchored_AS_<cell>_<rep>_<viewpoint>_trimming_report.txt
Align to genome using Bowtie 2.2.8: ~/TOOLS/bcbio/bin/bowtie2 -p 8 -x ~/TOOLS/bcbio/genomes/Hsapiens/hg19/bowtie2/hg19 -U anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.fastq  -S anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.sam
Generate bam format with samtools 1.3.1: samtools view -bS anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.sam > anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bam
Sort bam using samtools 1.3.1: samtools sort -T TEMP -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam  anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bam
Make bedGraph of the raw interaction data using bedtools 2.24.0: bedtools genomecov -ibam anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam -bga > anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bg
Convert bedGraph to bigWig: bedGraphToBigWig anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bg http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes anchored_AS_<cell>_<rep>_<viewpoint>.bigWig
Split bam into two bams, one containing the region 1.5kb upstream and 1.5kb downstream of viewpoint and the other all reads outside of that window: samtools view -b -h -@ 8 -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_reads_1.5k_near_vp.bam -U anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_omit_1.5k_near_vp.bam -L ~/ANALYSIS/4C/<viewpoint>_remove_1.5kb.bed  ~/ANALYSIS/4C/anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam
Add back 0.01% of reads to the region 1.5kb upstream and 1.5kb downstream of the viewpoint: samtools view anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_reads_1.5k_near_vp.bam -b -h -s 10.0001 -o anchored_AS_<cell>_<rep>_<viewpoint>_near_vp_downsampled.bam
Normalize to sample across all reads at level that both tissue replicates at that viewpoint contain: samtools view anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged.bam -b -h -s $value -o anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged_bfnorm.bam # where value=$subsample/$total_reads+10
Make bedGraph of the normalized reads with minimal reads near the viewpoint: samtools view -b anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged_bfnorm.bam | bedtools genomecov -bg -ibam stdin > ~/4C/anchored_AS_<cell>_<rep>_<viewpoint>_bfnormalized.bg
Identify significant long-distance interactions using modified version of R package r3Cseq (found at https://github.com/cotneylab/r3Cseq):
Create a file of significant (p<=0.05) interactions on same chromosome as viewpoint: cat Batch.experiment.interaction.txt|awk '$6<=0.05'|awk '/chr6/{print $2" "$3}'>anchored_AS_<cell>_<rep>_<viewpoint>_mid_10kb_2frag_4plot.txt
Convert file of significant interactions to bigBed format: bedToBigBed sorted_anchored_AS_<cell>_<rep>_<viewpoint>_dumbell_interactions_bed12.bed -type=bed12 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes anchored_AS_<cell>_<rep>_<viewpoint>_hg19_interactions.bigBed
fastq files of reads from individual tissue replicates by viewpoint: bigBed file of significant (p<=0.01 & q<=0.05) interactions between viewpoint and locations on same chromosome
ChIP-seq analysis::
Align to genome using bowtie 2.2.5: bowtie2 -p 6 -N 1 -X 2000 -t -x ~/GENOME/hg19/dna/hg19_nh -U ~/DATA/ChIP/BASESPACE/<sample>_<CTCF>.fastq.gz -S <sample>_<CTCF>.sam
Generate bam format and normalize with samtools 1.3: samtools view -@ 6 -b -F 4 -q 10 -o <sample>_<CTCF>_norm.bam <sample>_<CTCF>.sam
Sort bam with samtools 1.3: samtools sort -@ 6 -T aln.sorted.<sample>_<CTCF> -o <sample>_<CTCF>_norm_sorted.bam <sample>_<CTCF>_norm.bam
Index bam with samtools 1.3: samtools index <sample>_<CTCF>_norm_sorted.bam
Convert to tagAlign format for size estimation: samtools view -F 0x0204 -o - <sample>_<CTCF>_norm_sorted.bam  | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c >  <sample>_<CTCF>_norm_sorted.tagAlign.gz
Estimate fragment size using phantompeakqualtools: Rscript ~/TOOLS/phantompeakqualtools/run_spp.R -c=../align/<sample>_<CTCF>_norm_sorted.tagAlign.gz -i=../align/<sample>_<CTCF>-Input_norm_sorted.tagAlign.gz -savp -rf -s=-500:5:500 -p=16 -out=<sample>_<CTCF>_fragment.txt -tmpdir=~ANALYSIS/ChIP/Human/macs/tmp -filtchr=M -filtchr=Y
Call peaks with MACS2 2.1.1.20160309:
Generate p-value signals versus input with MACS2 2.1.1.20160309: macs2 bdgcmp -t <sample>_<CTCF>_treat_pileup.bdg -c <sample>_<CTCF>_control_lambda.bdg -o <sample>_<CTCF>_ppois.bdg -m ppois -S $sval
Convert to bedGraph to bigWig for display on UCSC genome browser: bedGraphToBigWig <sample>_<CTCF>.pval.signal.bedGraph ~/GENOME/hg19/dna/hg19_nh.chrom.sizes  <sample>_<CTCF>.pval.signal.bigWig
Convert to peak call beds to bigBeds for display on UCSC genome browser: bedToBigBed -type=bed6+3 -as=<sample>_<CTCF>_peaks.broadPeak.as  -extraIndex=name <sample>_<CTCF>_peaks.broadPeak ~/GENOME/hg19/dna/hg19_nh.chrom.sizes <sample>_<CTCF>_peaks.broadPeak.bigBed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of 4C interaction data: bigBed of significant interactions
Supplementary_files_format_and_content: bigBed for peak calls: bigWig for p-value ChIP-Seq Signals

source_name: Prader-Willi Syndrome iPSC, rep 1

growth_protocol: AS iPSC (AS del 1-0) were generated and maintained by mechanical passaging on mouse embryonic fibroblasts as previously described (Chamberlain SJ, et al. (2010), Proc Natl Acad Sci U S A 107(41):17668-17673. )

extract_protocol:
ChIP-seq extraction performed with Millipore EZ-Magna ChIP G – Chromatin Immunoprecipitation Kit (17-409) from 6-10 million cells, 4C-seq extraction from ~2 million formaldehyde-fixed cells according to Cotney JL & Noonan JP  ((2015) Cold Spring Harb Protoc 2015(4):419.)
ChIP-seq library preparation performed by the Yale Stem Cell Center Genomics Core; 4C-seq library prepared according to van de Werken HJ, et al. ((2012) Nat Methods 9(10):969-972.) using NlaIII for the first restriction digestion and DpnII for the second restriction digestion.

treatment_protocol: AS iPSCs were edited with CRISPR gRNAs or ssODNs

tag: cell type

value: Prader-Willi Syndrome iPSC


title: PWS_iPSC_2_ChIP-seq

source_name: Prader-Willi Syndrome iPSC, rep 2

tag: ctcf antibody


title: PWS_iPSC_1_ChIP-seq


title: AS_iPSC_1_Input

source_name: Angelman Syndrome iPSC, rep 1

value: Angelman Syndrome iPSC


title: AS_iPSC_1_ChIP-seq


title: AS_iPSC_2_ChIP-seq

source_name: Angelman Syndrome iPSC, rep 2


title: AS_iPSC_2_Input


title: PWS_iPSC_2-Input


title: AS_iPSC_2_4C-seq

data_processing:
library strategy: 4C-seq
4C-seq: r3Cseq:
demultiplex biological replicates by viewpoint using Cutadapt 1.10: cutadapt -g ^<viewpoint adapter sequence> --discard-untrimmed -e 0.20 -m 20 -O 12 -f fastq -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.fastq ~/4C/AS_<cell>_<rep>_<sample>_<read>_<lane>.fastq.gz >> anchored_AS_<cell>_<rep>_<viewpoint>_trimming_report.txt
Align to genome using Bowtie 2.2.8: ~/TOOLS/bcbio/bin/bowtie2 -p 8 -x ~/TOOLS/bcbio/genomes/Hsapiens/hg19/bowtie2/hg19 -U anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.fastq  -S anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.sam
Generate bam format with samtools 1.3.1: samtools view -bS anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.sam > anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bam
Sort bam using samtools 1.3.1: samtools sort -T TEMP -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam  anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bam
Make bedGraph of the raw interaction data using bedtools 2.24.0: bedtools genomecov -ibam anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam -bga > anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bg
Convert bedGraph to bigWig: bedGraphToBigWig anchored_AS_<cell>_<rep>_<viewpoint>_trimmed.bg http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes anchored_AS_<cell>_<rep>_<viewpoint>.bigWig
Split bam into two bams, one containing the region 1.5kb upstream and 1.5kb downstream of viewpoint and the other all reads outside of that window: samtools view -b -h -@ 8 -o anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_reads_1.5k_near_vp.bam -U anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_omit_1.5k_near_vp.bam -L ~/ANALYSIS/4C/<viewpoint>_remove_1.5kb.bed  ~/ANALYSIS/4C/anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam
Add back 0.01% of reads to the region 1.5kb upstream and 1.5kb downstream of the viewpoint: samtools view anchored_AS_<cell>_<rep>_<viewpoint>_trimmed_sorted.bam_reads_1.5k_near_vp.bam -b -h -s 10.0001 -o anchored_AS_<cell>_<rep>_<viewpoint>_near_vp_downsampled.bam
Normalize to sample across all reads at level that both tissue replicates at that viewpoint contain: samtools view anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged.bam -b -h -s $value -o anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged_bfnorm.bam # where value=$subsample/$total_reads+10
Make bedGraph of the normalized reads with minimal reads near the viewpoint: samtools view -b anchored_AS_<cell>_<rep>_<viewpoint>_ts_merged_bfnorm.bam | bedtools genomecov -bg -ibam stdin > ~/4C/anchored_AS_<cell>_<rep>_<viewpoint>_bfnormalized.bg
Identify significant long-distance interactions using modified version of R package r3Cseq (found at https://github.com/cotneylab/r3Cseq):
Create a file of significant (p<=0.05) interactions on same chromosome as viewpoint: cat Batch.experiment.interaction.txt|awk '$6<=0.05'|awk '/chr6/{print $2" "$3}'>anchored_AS_<cell>_<rep>_<viewpoint>_mid_10kb_2frag_4plot.txt
Convert file of significant interactions to bigBed format: bedToBigBed sorted_anchored_AS_<cell>_<rep>_<viewpoint>_dumbell_interactions_bed12.bed -type=bed12 http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/hg19.chrom.sizes anchored_AS_<cell>_<rep>_<viewpoint>_hg19_interactions.bigBed
fastq files of reads from individual tissue replicates by viewpoint: bigBed file of significant (p<=0.01 & q<=0.05) interactions between viewpoint and locations on same chromosome
ChIP-seq analysis::
Align to genome using bowtie 2.2.5: bowtie2 -p 6 -N 1 -X 2000 -t -x ~/GENOME/hg19/dna/hg19_nh -U ~/DATA/ChIP/BASESPACE/<sample>_<CTCF>.fastq.gz -S <sample>_<CTCF>.sam
Generate bam format and normalize with samtools 1.3: samtools view -@ 6 -b -F 4 -q 10 -o <sample>_<CTCF>_norm.bam <sample>_<CTCF>.sam
Sort bam with samtools 1.3: samtools sort -@ 6 -T aln.sorted.<sample>_<CTCF> -o <sample>_<CTCF>_norm_sorted.bam <sample>_<CTCF>_norm.bam
Index bam with samtools 1.3: samtools index <sample>_<CTCF>_norm_sorted.bam
Convert to tagAlign format for size estimation: samtools view -F 0x0204 -o - <sample>_<CTCF>_norm_sorted.bam  | awk 'BEGIN{OFS="\t"}{if (and($2,16) > 0) {print $3,($4-1),($4-1+length($10)),"N","1000","-"} else {print $3,($4-1),($4-1+length($10)),"N","1000","+"} }' | gzip -c >  <sample>_<CTCF>_norm_sorted.tagAlign.gz
Estimate fragment size using phantompeakqualtools: Rscript ~/TOOLS/phantompeakqualtools/run_spp.R -c=../align/<sample>_<CTCF>_norm_sorted.tagAlign.gz -i=../align/<sample>_<CTCF>-Input_norm_sorted.tagAlign.gz -savp -rf -s=-500:5:500 -p=16 -out=<sample>_<CTCF>_fragment.txt -tmpdir=~ANALYSIS/ChIP/Human/macs/tmp -filtchr=M -filtchr=Y
Call peaks with MACS2 2.1.1.20160309:
Generate p-value signals versus input with MACS2 2.1.1.20160309: macs2 bdgcmp -t <sample>_<CTCF>_treat_pileup.bdg -c <sample>_<CTCF>_control_lambda.bdg -o <sample>_<CTCF>_ppois.bdg -m ppois -S $sval
Convert to bedGraph to bigWig for display on UCSC genome browser: bedGraphToBigWig <sample>_<CTCF>.pval.signal.bedGraph ~/GENOME/hg19/dna/hg19_nh.chrom.sizes  <sample>_<CTCF>.pval.signal.bigWig
Convert to peak call beds to bigBeds for display on UCSC genome browser: bedToBigBed -type=bed6+3 -as=<sample>_<CTCF>_peaks.broadPeak.as  -extraIndex=name <sample>_<CTCF>_peaks.broadPeak ~/GENOME/hg19/dna/hg19_nh.chrom.sizes <sample>_<CTCF>_peaks.broadPeak.bigBed
Genome_build: hg19
Supplementary_files_format_and_content: bigWig of 4C interaction data: bigBed of significant interactions
Supplementary_files_format_and_content: bigBed for peak calls: bigWig for p-value ChIP-Seq Signals

tag: ipw viewpoint adapter sequence

value: GCTTTCTGGGAGAAGCCATG

tag: par1-3 (pwar1) viewpoint adapter sequence

value: ATATGCCCACATTCCACATG


title: AS_iPSC_1_4C-seq


title: AS_Neu_1_4C-seq

source_name: Neurons from Angelman Syndrome iPSC, rep 1

value: Neurons from Angelman Syndrome iPSC


title: AS_Neu_2_4C-seq

source_name: Neurons from Angelman Syndrome iPSC, rep 2


title: X6_HoxB8tdTom_Cx3Cr1-GFP

city: Salt Lake City

first: Chris

last: Stubben

state: Utah

address: 2000 Cir of Hope Dr

department: University of Utah

institute: Huntsman Cancer Institute

data_processing:
Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome.
The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file.
Read counts at the gene level were generated using featureCounts from the SubRead package.
Deseq2 analyses were conducted independently on all count data sets to compare relative transcript levels between the green (non-Hoxb8, control) and yellow (Hoxb8, experimental) microglia data sets. Deseq2 was run using default parameters and differentially expressed genes determined based upon a padj cutoff value <0.1.
Genome_build: Gencode GRCm38
Supplementary_files_format_and_content: Raw counts in Excel file

source_name: 12 week old mouse Brain

growth_protocol: Typical Husbandry

extract_protocol:
Cortical microglia were isolated from four independent ∼12-week-old two- color animals (Cx3Cr1GFP/+; Hoxb8IRES-Cre/+; ROSA26CAG-LSL-tdTomato/+).  Animals were humanely euthanized by isoflurane, cortical tissue dissected and meninges removed, minced and trypsin digested (1% trypsin, 37°C, 30min in HBSS). Cortical single-cell suspensions were generated by mechanical trituration and successive filtration (70 and 30 μm mesh) and glia enriched via capture with anti-Cd11b (Itgam) magnetic beads (Miltenyi Biotec). Bead-associated cortical microglia were then sorted on a BD FACSAriaII gating on tdTomato and GFP with collection into RNAlater solution, flash frozen and stored at −80°C
Total RNA was isolated and cloned by the University of Utah High-throughput Genomics Core using a Clontech UltraLow RNA isolation kit, and barcoded libraries sequenced on an Illumina HiSeq platform (50 bp nonstranded single-end reads), resulting in ∼25-30  million sequences per biological replicate. Sequence quality was confirmed by FastQC. Raw fastq reads were mapped using STAR (2.4.1c) (Dobin et al., 2013). Indices for STAR were built based upon the Gencode GRCm38v3 release M5 of the mouse genome. The index for STAR was constructed based upon the primary assembly and included splice junction information from the GTF file.

tag: ID

tag: strain

tag: age

value: 12 week old

value: brain

value: Microglia

tag: cell type sorted


title: X25_Cx3Cr1-GFPonly


title: X13_Cx3Cr1-GFPonly


title: X22_HoxB8tdTom_Cx3Cr1-GFP


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_IL-33_RNA-seq_rpt_2

city: Akita City

first: Takashi

last: Ebihara

address: 1-1-1 Hondo

department: Department of Medical Biology

institute: Akita University Graduate School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8.2.
RNA-seq and ChIP-seq sequences were aligned on mm9 using TopHat and bowtie2 (version 2.1.0) with default parameter, respectively.
Cufflinks to calculate RPKM values of RNA-seq data. Homer to call peaks of ChIP-seq and generate bedgraph files of ChIP-seq data.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each RNA-seq sample. Bedgraph files for read histograms normalized to 10,000,000 reads for ChIP-seq data.

source_name: Lung ILC2

growth_protocol: ILC2s were sorted from the lung for RNA-seq ex vivo. For RNA-seq of activated ILC2s, lung ILC2s were stimulated with IL-2 and IL-33 in vitro. For ChIP-seq, lung ILC2s were cultured with IL-2 and IL-7 in vitro for 2 weeks and stimulated together with IL-33 for 4 days.

extract_protocol:
RNA was purified by Trizol first and then by RNeasy micro kit for RNA-seq. Lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
RNA libraries were prepared for sequencing using standard Illumina protocols. ChIP-seq libraries were created from the DNA with NEBNext ChIP-seq Library Prep Master Mix set for Illumina Kit (NEB).

tag: genotype

value: Lung

value: Group 2 innate lymphoid cells (ILC2s)

tag: chip antibody


title: Lung_ILC2_Cbfb-het-PLZF-Cre_IL33_RNA-seq_rpt_3

tag: tissue


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_RNA-seq_rpt_3


title: Lung_ILC2_Cbfb-het-PLZF-Cre_IL33_RNA-seq_rpt_2


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_RNA-seq_rpt_1


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_IL-33_RNA-seq_rpt_1


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_IL-33_RNA-seq_rpt_3


title: Lung_ILC2_Cbfb-het-PLZF-Cre_IL33_RNA-seq_rpt_1


title: Lung_ILC2_Cbfb-het-PLZF-Cre_RNA-seq_rpt_3


title: hPSC-KCs_2

city: Singapore

first: Farah

last: Tasnim

address: 31 Biopolis Way

country: Singapore

institute: Institute of Bioengineering and Nanotechnology

hyb_protocol: Following fragmentation, cRNA was hybridized for 16 hr at 45°C on Human Gene 2.0 ST Array. GeneChips were washed and stained in the GeneChipTM Fluidics Station 400.

scan_protocol: GeneChips were scanned using GeneChipTM Scanner 3000 7G.

data_processing: Expression data was summarized and normalized using the sst-RMA (Robust Multi-array Average) method of the Affymetrix® Expression Console software. The normalized data obtained from Expression Console was analyzed using Affymetrix® Transcriptome Analysis Console.

source_name: hPSC-KCs

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1 ug total RNA (GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays).

growth_protocol: PHKCs (Life Technologies) were cultured as per manufacturer's instructions. hPSCs were cultured as described in Tasnim F, et al. (PMID: 26310107).

extract_protocol: Total RNA was isolated using RNeasy Micro-kit (Qiagen) according to manufacturer's instructions.

treatment_protocol: Protocol for differentiation of hPSC-KCs are available in the paper.

value: pluripotent stem cell-derived Kupffer cells


title: X21_Cx3Cr1-GFPonly


title: Lung_ILC2_Cbfb-het-PLZF-Cre_RNA-seq_rpt_2


title: NL-Mφ_2

source_name: NL-Mφ

value: non-liver macrophages


title: NL-Mφ_3


title: NL-Mφ_1


title: PHKCs_2

source_name: PHKCs

value: primary Kupffer cells


title: PHKCs_3


title: PHKCs_1


title: Leaf_EE_control_rep1

description: Gene expression in leaves and roots

data_processing: Data was acquired with the Agilent Scan Control software (version A.7.0.1 for the B scanner) and extracted using the Agilent Feature Extraction software (version 9.5). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. 95 percentile normalization was performed for each array of raw data (keeping the controls in the list). Log transformation was done. Controls were removed from the list. All replicated probes were averaged.

extract_protocol: Total RNA was extracted from leaves and roots using the Plant RNeasy kit (Qiagen, Hilden, Germany) and its quality checked by spectrophotometry (NanoDrop, Wilmington, DE). Genomic DNA was removed by DNAse treatment following commercial instructions (Turbo DNase; Ambion, Europe), RNA was cleaned up with RNeasy MinElute columns (Qiagen) and the RNA quality was checked with the RNA 6000 Nano kit (Agilent, Santa Clara, CA) using an Agilent 2100 Bioanalyzer (Agilent).

value: EE

tag: treatment

value: control

value: leaf


title: hPSC-KCs_1


title: Root_EE_drought_rep2

description: Gene expression in leaves and roots

value: drought

value: root


title: X14_HoxB8tdTom_Cx3Cr1-GFP


title: Lung_ILC2_Cbfb-homo-PLZF-Cre_RNA-seq_rpt_2


title: Lung_ILC2_Cbfb-het-PLZF-Cre_RNA-seq_rpt_1


title: Control 3

city: hangzhou

first: chengchao

last: zhang

address: Xuelin Street No.16

institute: Hangzhou Normal University

data_processing:
The paired-end sequencing was performed on an Illumina Hiseq 4000 platform
The reads containing adaptor, low quality bases and undetermined bases were  removed
The processed data (*txt) was generated using software Trinity 2.4.0
The TPM values were contained in the processed data (*txt).

organism: Dendrobium officinale

source_name: Dendrobium

growth_protocol: The growth conditions were set at 25 ± 1°C with a light/dark cycle of 12/12 h and a 60%–70% relative humidity

extract_protocol:
Total RNAs were isolated from the leaves using Total RNA Purification Kit, TRK1001 according to the manufacturer’s protocol (LC Science, Houston, TX) and quantified using Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The leaves of 6-month-old D. officinale sprayed with 100 μM of MeJA (in ethanol solvent) for 24 h were harvested as the treatment group, and the leaves of 6-month-old D. officinale seedlings sprayed with ethanol solvent without MeJA were harvested as the control group.

value: leaves

value: Control


title: Control 2


title: Control 1


title: MeJA treated 2

value: 100 uM of MeJA (in ethanol solvent) for 24 h


title: X5_Cx3Cr1-GFPonly


title: WSD24 (RRBS)

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

data_processing:
base calling
Sequencing reads were evaluated with FastQC (v0.11.5)
adapters and low quality bases trimmed with TrimGalore (v0.4.2) with parameter --rrbs
trimmed reads aligned to Mmul8 reference genome with Bismark (v0.16.1) using default parameters
acquire methylated and unmethylated counts per CpG as "cytosine report" file using bismark_methylation_extractor function
calculate methylation rate per CpG as number of methylated counts divided by total counts
DMC analysis: limited to CpGs with at least 10X coverage in at least 4 of the 6 replicates among all 4 groups (841,143 CpGs)
arcsin transform methylation rate values and use Limma to fit 4 group model and perform pariwise contrasts
DMR analysis: use same CpGs and pvalues obtained from limma DMC analysis as input into comb-p software to find DMRs
Genome_build: Mmul8
Supplementary_files_format_and_content: tab delimited text file of a filtered methylation rate table containing the methylation rate (methylated count / coverage) for CpGs used in DMC and DMR analysis
Supplementary_files_format_and_content: the first column "CpG_ID" contains the chr_start coordinates for the CpG using ensembl's Mmul8 reference genome and 1-based start coordinates. There is then a column for each sample.

organism: Macaca mulatta

source_name: white adipose tissue

growth_protocol: Young adult female rhesus macaques received testosterone (to mimic hyperandrogenemia) or control cholesterol implants for 3 years.  Animals were maintained either on monkey chow (control) or high-fat western-style diet.

extract_protocol:
DNA extracted using the AllPrep DNA/RNA purification kit (QIAGEN) according to the manufacturer’s instructions
RRBS libraries were generated starting with genomic DNA extracted from WAT.  Overnight digestion was performed on ~200ng DNA using the restriction enzyme MspI (New England Biolabs, Ipswich, MA). Reaction clean-up was performed with AMPure XP magnetic beads (Beckman Coulter, Brea, CA) before use with the NEXTflex Bisulfite-Seq Kit (Bioo Scientific Corporation, Austin, TX) for library preparation.  The digested DNA was quantified and then ~80ng was end-repaired, A-tailed, and ligated with the NEBNext Methylated Adaptor (New England Biolabs).  The ligated DNA was cleaned and then size-selected using AMPure XP magnetic beads to produce a final library size of 350 bp.  Bisulfite conversion was performed with the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA) before carrying out PCR amplification with NEBNext Multiplex Oligos for Illumina (New England Biolabs) to barcode each library. Two AMPure XP bead cleans were performed and the resulting libraries were quantified with the Qubit High Sensitivity dsDNA Assay (Life Technologies, Eugene, OR) and the Bioanalyzer High Sensitivity DNA Kit (Agilent, Santa Clara, CA).

treatment_protocol: Visceral (omental) adipose tissue biopsies were collected in year 3 of treatment.

tag: condition

value: western style diet

tag: Sex

value: female

value: 4 years old

value: white adipose tissue


title: WSD23 (RRBS)


title: hPSC-KCs_3


title: Indian Rhesus Macaque Tumor 3 Poly-A selected

city: New Orleans

first: Erik

middle: K

last: Flemington

state: LA

address: 1430 Tulane Ave., SL79

department: Pathology

institute: Tulane Health Sciences Center

description:
Poly-A selected
Tumor 3

data_processing:
Reads were aligned using STAR version 2.5
Backsplice junctions were called using find_circ version 1.2
Genome_build: MM10 + MHV68, HG38 + KSHV, MMUL8.01 +  rLCV
Supplementary_files_format_and_content: Backsplice coordinates and counts of RNAse R sequencing data in BED format

organism:
Macaca mulatta
Macacine gammaherpesvirus 4

source_name: lymphoma

extract_protocol:
RNA was harvested using Trizol.
1 ug of RNA was input into the Illumina TruSeq RNA Sample Prep Kit v2 (Cat# RS-122-2001) to construct the sequencing libraries.

tag: infection 1

value: rLCV+

tag: infection 2

value: SIV+


title: Indian Rhesus Macaque Tumor 3 RNase R treated

description:
RNase R treated
Tumor 3


title: Indian Rhesus Macaque Tumor 1 Poly-A selected

description:
Poly-A selected
Tumor 1


title: WSD22 (RRBS)


title: NIH3T12

description:
RNase R treated
Lytic

organism:
Mus musculus
Murid herpesvirus 68

source_name: fibroblast

value: MHV68 infected


title: WSD20 (RRBS)


title: WSD19 (RRBS)


title: Indian Rhesus Macaque Tumor 1 RNase R treated

description:
RNase R treated
Tumor 1


title: WSD21 (RRBS)


title: Indian Rhesus Macaque Tumor 2 RNase R treated

description:
RNase R treated
Tumor 2

source_name: lymphoma (adjacent to jejunum)


title: HE2.1

description:
RNase R treated
Latent

source_name: B-cell


title: T17 (RRBS)

value: testosterone


title: Lactating_Isthmus_Contra_3

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

data_processing:
Reads were converted to Fastq using the bcl2fastq (v.1.8.4) converter from Illumina.
Illumina adapters were clipped from the 3’-end of each read using a custom script.
Poly-A tails were removed from the 3’-/5’-end of each read with a seed length of 6 nt. Reads with length <25 after clipping were filtered out.
Reads were mapped against the reference genome (BosTau7) using Tophat2 (v.2.0.13) with default settings and the gene annotation obtained from Illumina’s iGenomes Project (UCSC: bosTau7).
Transcript abundance was counted using htseq-count (v. 0.6.1) with strand specificity (-s yes) intersection-strict mode (-m intersection-strict) and GFF attribute ‘gene’ (-i gene). The used gene annotation was obtained from Illumina’s iGenome Project (UCSC: bosTau7).
Genome_build: BosTau7
Supplementary_files_format_and_content: Tab-delimited text file containing the read counts per gene

organism: Bos taurus

source_name: Isthmus epithelial cells

extract_protocol:
Oviduct epithelial cells recovered from the ampulla and isthmus ipsilateral and contralateral to the CL were lysed with Trizol according to the manufacturer’s instructions. After precipitation, RNA quality and quantity was confirmed using the Agilent Bioanalyzer system and all RNA samples used for RNA. sequencing had an RNA Integrity Number (RIN) of 7.9 or greater.
Starting from total RNA, stranded RNA sequencing libraries were constructed with the Encore Complete RNA-Seq library system of NuGEN.

tag: sample type

value: lactating


title: Lactating_Isthmus_Contra_4


title: Indian Rhesus Macaque Tumor 2 Poly-A selected

description:
Poly-A selected
Tumor 2


title: MeJA treated 1


title: Lactating_Isthmus_Contra_2


title: T16 (RRBS)


title: T15 (RRBS)


title: T14 (RRBS)


title: Lactating_Isthmus_Ipsi_4


title: Lactating_Isthmus_Ipsi_1


title: Lactating_Isthmus_Ipsi_3


title: T+WSD12 (RRBS)

value: testosterone + western style diet


title: Lactating_Isthmus_Ipsi_2


title: T+WSD11 (RRBS)


title: T13 (RRBS)


title: T+WSD10 (RRBS)


title: Lactating_Ampulla_Contra_4

source_name: Ampulla epithelial cells


title: T18 (RRBS)


title: T+WSD9 (RRBS)


title: Lactating_Ampulla_Contra_2


title: Lactating_Ampulla_Contra_1


title: C6 (RRBS)

value: control


title: 48h_siCTR_6h_UVB_R1

data_processing:
Raw fastq files (with base-calling quality score) were obtained form Wellcome Trust Genomics service
Two technical replicates (same library sequence in two separate flow cells) which were stitched together using UNIX to generate a single fastq
Raw fastq files were then trimmed of poly-A using  cutadapt {Martin, 2011 }
Processed fastq files were mapped using STAR {Dobin, 2013 #5946} with custome hg38 build which contains ERCC as well as mouse-Mitf
Counts per gene from STAR were used as input for differential gene expression analysis using EdgeR {Robinson, 2010 }.
Reads for each sample set were first filtered for genes whose expression is  count-per-million prior to glmQLFTest.

extract_protocol:
RNA-samples were extracted using QIAGEN RNeasy kit
Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

tag: disease state

value: melanoma

tag: cell line

tag: transfection

value: siCTR

value: 48h siCTR 6h UVB


title: T+WSD7 (RRBS)


title: Lactating_Ampulla_Ipsi_4


title: Lactating_Ampulla_Ipsi_2


title: C5 (RRBS)


title: C4 (RRBS)


title: Lactating_Isthmus_Contra_1


title: C3 (RRBS)


title: Lactating_Ampulla_Ipsi_1


title: C2 (RRBS)


title: C1 (RRBS)


title: Heifer_Isthmus_Contra_4

value: heifer


title: Lactating_Ampulla_Contra_3


title: Heifer_Isthmus_Ipsi_5


title: Heifer_Isthmus_Contra_3


title: Heifer_Isthmus_Contra_2


title: T+WSD8 (RRBS)


title: WSD20 (RNA-seq)

data_processing:
base calling
Sequencing reads were evaluated with FastQC (v0.11.5)
adapters and low quality bases trimmed with Trimmomatic (v0.36)
trimmed reads aligned to Mmul8 reference genome with STAR (v2.5.2b) with default parameters
Gene counts were obtained via STAR with the “--quantMode GeneCounts” parameter and Ensembl annotation (Mmul8 version 92)
DESeq2 (v1.18.1) used for differential gene expression analysis
Genome_build: Mmul8
Supplementary_files_format_and_content: tab delimited text file containing the raw counts for each gene (Ensembl Gene ID) in each sample

extract_protocol:
RNA extracted using the AllPrep DNA/RNA purification kit (QIAGEN) according to the manufacturer’s instructions
High-quality RNA samples (RIN >8) were used for library construction using the TruSeq Rybo-zero method


title: Heifer_Isthmus_Ipsi_4


title: WSD22 (RNA-seq)


title: T18 (RNA-seq)


title: WSD19 (RNA-seq)


title: WSD21 (RNA-seq)


title: Lactating_Ampulla_Ipsi_3


title: T17 (RNA-seq)


title: Heifer_Isthmus_Ipsi_2


title: Heifer_Isthmus_Ipsi_1


title: Heifer_Ampulla_Contra_5


title: T15 (RNA-seq)


title: Heifer_Isthmus_Ipsi_3


title: Heifer_Ampulla_Contra_3


title: T14 (RNA-seq)


title: T13 (RNA-seq)


title: WSD23 (RNA-seq)


title: WSD24 (RNA-seq)


title: Heifer_Ampulla_Contra_2


title: T16 (RNA-seq)


title: T+WSD12 (RNA-seq)


title: Heifer_Ampulla_Ipsi_5


title: Heifer_Ampulla_Contra_4


title: T+WSD7 (RNA-seq)


title: T+WSD9 (RNA-seq)


title: T+WSD10 (RNA-seq)


title: Heifer_Ampulla_Ipsi_4


title: Heifer_Ampulla_Ipsi_3


title: Heifer_Ampulla_Ipsi_1


title: C6 (RNA-seq)


title: C4 (RNA-seq)


title: C5 (RNA-seq)


title: Heifer_Ampulla_Contra_1


title: Non-lactating_Isthmus_Contra_4

value: non-lactating


title: C3 (RNA-seq)


title: C2 (RNA-seq)


title: Non-lactating_Isthmus_Contra_1


title: T+WSD8 (RNA-seq)


title: Non-lactating_Isthmus_Ipsi_5


title: Non-lactating_Isthmus_Contra_2


title: C1 (RNA-seq)


title: Heifer_Isthmus_Contra_5


title: K27Rdouble-Rep2

city: New York

first: Christopher

middle: Mitsuo

last: Uyehara

address: 413 E 69th St

department: Meyer Cancer Center

institute: Weill Cornell Medicine

description: DJM93_6_K27RdoubleRep2_TTGGCA_S6_L001_R1_001_Aligned

data_processing:
Sample K27R-Rep1 was sequenced twice, once with a single-end MiSeq and a second time with a paired-end MiSeq. For the paired-end experiment, to make it equivalent to the single-end experiment, only the first read was used and a modified fastq file was made with the read length truncated to 50bp. The modified fastq file was then concatenated to the single-end fastq file prior to alignment.
Sequenced reads were aligned to a modified dm3 genome using STAR v2.5.2b using parameters --alignIntronMax 50000 --alignMatesGapMax 50000. Briefly, dm3 genome files were modified as follows: All sequences and annotations for His2A, His2B, His3 and His4 were removed. An additional sequence that contained a single, 5kb copy of His2A, His2B, His3, and His4 was appended as an additional chromosome. Each ERCC spike-in sequence was also appended as an individual chromosomes.
The bam file was indexed and sorted using samtools v1.3.1
Subread v1.28.1 was used to count reads mapping to genes. ERCC spike-in chromsomes were removed post-feature counting for seperate analysis.
RPKM values were calculated using a custom R script. Briefly, all exons from individual genes were merged to form a meta-gene. Reads mapping to each meta-gene were counted and then scaled by the number of reads in the sample and the length of each meta-gene.
DESeq2 (v1.18.1) was used to identify differentially expressed genes using the lfcShrink function to shrink log-fold changes
Genome_build: dm3
Supplementary_files_format_and_content: comma delimited table that contains DESeq2 results for each comparison for each gene.
Supplementary_files_format_and_content: comma delimited table that contains RPKM values for all genes in each sample

organism: Drosophila melanogaster

source_name: Whole male pharates

extract_protocol: RNA-seq libraries were prepared using Nugen Ovation RNA-seq System 1-16 for Model Organisms

tag: developmental stage

value: pharate (96-108APF)

value: Whole animal

value: K27R double mutant

value: Male


title: T+WSD11 (RNA-seq)

value: female

value: 4 years old

value: white adipose tissue


title: Non-lactating_Isthmus_Ipsi_4


title: K27Rdouble-Rep1

description: DJM93_5_K27RdoubleRep1_CACAGT_S5_L001_R1_001_Aligned


title: Non-lactating_Isthmus_Contra_3


title: K27R-Rep2

description: DJM93_4_K27Rrep2_TCAGAG_S4_L001_R1_001_Aligned

value: yw, H3.3BK27R

value: K27R mutant


title: yw-Rep2

description: DJM93_2_ywRep2_TGGTGA_S2_L001_R1_001_Aligned

value: yw

value: Wild-Type


title: K27R-Rep1

description: DJM93_3_K27Rrep1_techMerge_CGTAGA_S3_L001_R1_001_Aligned


title: Non-lactating_Ampulla_Contra_4


title: Non-lactating_Isthmus_Ipsi_2


title: Non-lactating_Ampulla_Contra_5


title: Non-lactating_Ampulla_Contra_3


title: Non-lactating_Isthmus_Ipsi_1


title: Papilloma- CWO 3

first: Ellen

middle: A

last: Lumpkin

address: 1150 St. Nicholas Avenue, room 302

department: Physiology and Cellular Biophysics

institute: Columbia University

data_processing:
RTA (Illumina) for base calling
bcl2fastq (version 1.8.4) for converting BCL to fastq format coupled with adaptor trimming
Reads were mapped to a reference genome (Mouse: UCSC/mm9) using Tophat (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10). To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
Relative abundance (aka expression level) of genes and splice isoforms was estimated using cufflinks (version 2.0.2) with default settings.
Differentially expressed genes are determined under various conditions using DEseq. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: comma-delimited files include FPKM gene values for each Sample and fold-change

molecule: polyA RNA

source_name: Papilloma- CWO

extract_protocol:
RNA isolation proceeded using the TRIzol Plus RNA Purification Kit (Thermo Fisher, Cat. #12183-555). Briefly, homogenized epidermis in TRizol was incubated at room temperature for five minutes. 0.2 mL chloroform (Sigma Aldrich, CAS 67-66-3, PN 360927) was added. Lysate was centrifuged in 5 PRIME, phase lock heavy 2 mL tubes (Cat. # 2303830). An equal volume of ethanol was added (Decon, CAS 64-17-5). DNAse treatment using RNAse-Free DNAse was performed (Qiagen Cat. #79254). RNA was eluted using DEPC Treated Water (Invitrogen, Part no. 46-2224). A series of washing steps was conducted following the directions provided in the TRIzol Plus RNA Purification Kit. The purity of RNA was confirmed using a Bioanalyzer (Instrument Name DE72901373, Firmware C.01.069, Type G2939A. Three samples from each treatment with the best RNA integrity were chosen for RNA sequencing.
Poly-A pull-down was used to enrich mRNAs from total RNA samples (200ng-1ug per sample, RIN>8 required). Library preparation was performed by using Illumina TruSeq RNA prep kit according to manufacturer protocols.

treatment_protocol: Mice were shaved at age 6-7 wks with electric clippers and telogen, the resting hair cycle stage, was confirmed after 2 d. One topical application of 400 nmol DMBA in 200 L acetone was administered, followed by one week of rest then twice-weekly applications 200 L of 10 nmol TPA in acetone. This TPA regimen ensured each mouse generated a high tumor burden by 15 wks with at least one malignant conversion before endpoint. Mice were treated for six weeks with 20% Camphor White OIl or Acetone Vehicle and then tumors were harvested. Four pre-malignant tumors of approximately the same size per mouse were pooled (N=3 mice per treatment). The pooled tumors were homogenized in 1 mL TRizol using an Omni International homogenizer with soft tissue disposable tips.

value: FVB/NJ

value: Papilloma

value: 20% Camphor White Oil 6 w


title: Papilloma- CWO 2


title: Non-lactating_Ampulla_Contra_2


title: Non-lactating_Ampulla_Contra_1


title: Non-lactating_Ampulla_Ipsi_4


title: Papilloma- Vehicle 1

source_name: Papilloma- Vehicle

value: Vehicle 6 w


title: Papilloma- Vehicle 2


title: Non-lactating_Ampulla_Ipsi_3


title: Papilloma- Vehicle 3


title: Non-lactating_Ampulla_Ipsi_5


title: Non-lactating_Ampulla_Ipsi_2


title: Non-lactating_Isthmus_Contra_5


title: Non-lactating_Isthmus_Ipsi_3


title: yw-Rep1

description: DJM93_1_ywRep1_AACCAG_S1_L001_R1_001_Aligned


title: Papilloma- CWO 1


title: Epidermis- CWO 2

source_name: Epidermis- CWO

treatment_protocol: FVB mice were shaved. One week later, five mice received 400 µL topical 20% camphor white oil or acetone vehicle. 24 h after treatment, mice were sacrificed and epidermis was isolated via 40-min incubation in 3.8% ammonium thiocyanate (Sigma-Aldrich, CAS 1762-95-4) in RNAse free PBS (Ambion, 10x PBS buffer pH 7.4, PN AM9625). The work area was kept RNAse free using RNaseZap (PN AM9780). The epidermis was homogenized in 1 mL TRizol (Thermo, Cat. #15596026) using Omni International homogenizer with soft tissue disposable tips (PN 32750).

value: Epidermis

value: 20% Camphor White Oil 24 h


title: Epidermis- CWO 1


title: Epidermis- Vehicle 3

source_name: Epidermis- Vehicle

value: Vehicle 24 h


title: Epidermis- Vehicle 1


title: Epidermis- Vehicle 2


title: Epidermis- CWO 3


title: MeJA treated 3

value: leaves

value: 100 uM of MeJA (in ethanol solvent) for 24 h


title: Non-lactating_Ampulla_Ipsi_1

value: non-lactating


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_K27me3_rp2

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP sequences were aligned on mm9 using TopHat and bowtie2 (version 2.1.0) with default parameter, respectively.
MACS to call peaks of ChIP-seq and generate wig files of ChIP-seq data.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS.

source_name: Lung ILC2

growth_protocol: For ChIP-seq, lung ILC2s were cultured with IL-2/IL-7/IL-33 in vitro for 4 weeks, and were cultured with or without IL-33 for a week.

extract_protocol:
Lysates were purified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were created from the DNA with NEBNext ChIP-seq Library Prep Master Mix set for Illumina Kit (NEB).

value: WT

value: Lung

tag: cell type

value: Group 2 innate lymphoid cells (ILC2s)

tag: antibody

value: Mouse anti H3K27 trimethylation mAb (Abcam ab6002)


title: Lung_ILC2_WT_IL2_7_33_input

tag: strain

value: Input


title: TA-Nuc-3

city: Padova

first: Gerolamo

last: Lanfranchi

address: Via U. Bassi, 58/B

department: CRIBI - Biotechnology Center and Biology Department

country: Italy

institute: University of Padova

description: RNA extraction from the nuclear fraction of a pool containing 5-10 TA myofibers from mouse identified as 3 (Nuclei-TA-3)

hyb_protocol: Labeled cDNA were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

scan_protocol: Microarrays were scanned using the Agilent Technologies Scanner G2505C US22502723 (ChipScan software version A.8.5.1), scan region 61 x 21.6 mm, scan resolution 3 micron single pass, Green PTM 100%, no extended dynamic range (NO XDR).

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Microarray probes were re-annotated according to their ability to match to transcripts in Ensembl 74 and probes identifying coding genes and non-coding genes were treated separately because their different expression. Non-coding RNAs are lesser expressed than coding RNAs and therefore corresponding signal intensity is smaller. Quantile inter-arrays normalization was performed in R statistic ambient considering only the gProcessedSignal column for probes identifying non-coding RNAs. Normalized values only for non-coding RNAs are indicated. Probes with gIsPosAndSignif value of zero were disregarded and labeled as “NA”. Mean values were calculated for multiple probes with the same ProbeName (Agilent Probe ID).

source_name: TA myofiber pool, nuclear fraction, biological replicate 3

label_protocol: Fluorescent cRNA to hybridize onto microarray was produced by Low Input Quick Amp Labeling Kit (Agilent) according to manufacturer instructions.

growth_protocol: CD1 female mice were housed in a normal environment provided with food and water and were killed by rapid cervical dislocation to minimize suffering.

extract_protocol: 1 ml of TRIzol Reagent (Thermo Fisher Scientific) was used to extract RNA from each purified fraction of nuclei or cytoplasm. 300 μl of aqueous phase were additioned with 300 μl of isopropanol, samples were stored o/n at -20°C and then centrifuged for 20 min at 12,000 x g, 4°C to precipitate RNA. Pellet was washed twice with 70% EtOH and resuspended in 20 μl of DNase/RNase free water.

treatment_protocol: Muscles were digested in type I collagenase (10mg/ml in DMEM) and single myofibers were dissociated. Intact (non contracted) single myofibers were picked under a sterereomicroscope and washed in PBS. Pools of 5-10 myofibers were lysed in RLN Buffer (Water, 50 mM TrisHCl pH 8.0, 140 mM NaCl, 1.5 mM MgCl2, 0.5% v/v Triton-X100, 0.36 units/µl RNase OUT) by repeatedly passing the solution through a 0.2 μm needle. Nuclei were then precipitated in a microcentrifuge for 5 min at 600 g, 4°C. Surnatant volume was reduced by 50% in a Savant SpeedVac. Total RNA was extracted from each fraction.

tag: gender

value: female

value: TA muscle

tag: age

value: 3 months


title: TA-Nuc-2

description: RNA extraction from the nuclear fraction of a pool containing 5-10 TA myofibers from mouse identified as 2 (Nuclei-TA-2)

source_name: TA myofiber pool, nuclear fraction, biological replicate 2


title: TA-Cyt-1

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 TA myofibers from mice identified as 5 and 1 (Cyto-TA-5.1)

source_name: TA myofiber pool, cytoplasmic fraction, biological replicate 1


title: SOL-Cyt-3

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 SOL myofibers from mice identified as 7 and 8 (Cyto-S-7.8)

source_name: SOL myofiber pool, cytoplasmic fraction, biological replicate 3

value: Soleus muscle


title: TA-Nuc-1

description: RNA extraction from the nuclear fraction of a pool containing 5-10 TA myofibers from mouse identified as 1 (Nuclei-TA-1)

source_name: TA myofiber pool, nuclear fraction, biological replicate 1


title: SOL-Nuc-2

description: RNA extraction from the nuclear fraction of a pool containing 5-10 SOL myofibers from mice identified as 5 and 6 (Nulcei-S-5.6)

source_name: SOL myofiber pool, nuclear fraction, biological replicate 2


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_K27me3_rp1

tag: genotype


title: TA-Cyt-2

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 TA myofibers from mice identified as 5 and 2 (Cyto-TA-5.2)

source_name: TA myofiber pool, cytoplasmic fraction, biological replicate 2

tag: tissue


title: EDL-Nuc-2

description: RNA extraction from the nuclear fraction of a pool containing 5-10 EDL myofibers from mice identified as 5 and 6 (Nuclei-E-5.6)

source_name: EDL myofiber pool, nuclear fraction, biological replicate 2

value: EDL muscle


title: SOL-Cyt-2

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 SOL myofibers from mice identified as 5 and 6 (Cyto-S-5.6)

source_name: SOL myofiber pool, cytoplasmic fraction, biological replicate 2


title: SOL-Nuc-3

description: RNA extraction from the nuclear fraction of a pool containing 5-10 SOL myofibers from mice identified as 7 and 8 (Nulcei-S-7.8)

source_name: SOL myofiber pool, nuclear fraction, biological replicate 3


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_K27ac_rp2

value: Rabbit anti-H3K27 acetylation mAb (Cell Signalling #8173)


title: SOL-Nuc-1

description: RNA extraction from the nuclear fraction of a pool containing 5-10 SOL myofibers from mice identified as 3 and 4 (Nulcei-S-3.4)

source_name: SOL myofiber pool, nuclear fraction, biological replicate 1


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_K27ac_rp1


title: SOL-Cyt-1

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 SOL myofibers from mice identified as 3 and 4 (Cyto-S-3.4)

source_name: SOL myofiber pool, cytoplasmic fraction, biological replicate 1


title: EDL-Nuc-1

description: RNA extraction from the nuclear fraction of a pool containing 5-10 EDL myofibers from mice identified as 3 and 4 (Nuclei-E-3.4)

source_name: EDL myofiber pool, nuclear fraction, biological replicate 1


title: EDL-Cyt-3

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 EDL myofibers from mice identified as 7 and 8 (Cyto-E-7.8)

source_name: EDL myofiber pool, cytoplasmic fraction, biological replicate 3


title: EDL-Nuc-3

description: RNA extraction from the nuclear fraction of a pool containing 5-10 EDL myofibers from mice identified as 7 and 8 (Nuclei-E-7.8)

source_name: EDL myofiber pool, nuclear fraction, biological replicate 3


title: TA-Cyt-3

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 TA myofibers from mouse identified as 9 (Cyto-TA-9)

source_name: TA myofiber pool, cytoplasmic fraction, biological replicate 3


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_R3_rp2

source_name: Lung ILC2

value: Rabbit anti-Runx3 mAb (CST D6E2)


title: EDL-Cyt-1

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 EDL myofibers from mice identified as 3 and 4 (Cyto-E-3.4)

source_name: EDL myofiber pool, cytoplasmic fraction, biological replicate 1


title: EDL-Cyt-2

description: RNA extraction from the cytoplasmic fraction of a pool containing 5-10 EDL myofibers from mice identified as 5 and 6 (Cyto-E-5.6)

source_name: EDL myofiber pool, cytoplasmic fraction, biological replicate 2


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_R3_rp1


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_R1_rp2

value: Rabbit anti-Runx1 pAb (Abcam ab23980)


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_R1_rp1


title: Quant-seq_Day 28_neuron_rep1

city: San Francisco

first: Ruilin

last: Tian

address: 675 Nelson Rising Lane, 3rd Floor

department: Institute for Neurodegenerative Diseases

institute: University of California, San Francisco

description: Quant-seq

data_processing:
For the Quant-seq data, raw reads were trimmed with Bbduk, aligned with STAR Aligner, and counted with HTSeq-count to yield gene counts. For the CROP-seq data, Cell Ranger (version 2.2.0) was used to align reads and generate digital expression matrices from single-cell sequencing data. To map sgRNA transcripts together with other mRNA transcripts to individual cells, a custom reference was generated by extending the human genome assembly (Ensembl GRCh38 release) with ‘pseudo-genes’ representing sgRNA-containing transcripts (one sgRNA sequence per pseudo-gene with 250bp upstream and 230bp downstream sequences).
Genome_build: hg38
Supplementary_files_format_and_content: For the Quant-seq data, files containing gene Ensembl IDs and counts are provided in Tab-delimited text (.txt) format. For the CROP-seq data, expression matrices output by cellranger are provided in Matrix Market (.mtx) format and the associcated gene ID and cell barcode files are provided as Tab Separated Values (.tsv) files. For the sgRNA enrichment data, cell barcodes and their mapped sgRNAs with UMI counts are provided as txt files.

source_name: Human iPSC-derived neuron

growth_protocol: Classic Neuronal Medium

extract_protocol:
RNA was extracted using the Quick-RNA Miniprep Kit (Zymo; Cat. No. R1054), and RNA concentrations were determined with the Qubit RNA HS Assay Kit (Invitrogen; Cat. No. Q32855) on a Qubit 2.0 Fluorometer (Invitrogen; Cat. No. Q32866)
Libraries were prepared according to protocol accompanying the Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit (Cat. No. 015)

value: Day 28 neuron


title: Quant-seq_Day 28_neuron_rep2

description: Quant-seq


title: Quant-seq_Day 21_neuron_rep2

description: Quant-seq

value: Day 21 neuron


title: Myofiber MyHC-2B_10(E15.3)

description: Gene expression of single mouse myofiber. Biological replicates of the same myofiber type were numbered from 1 to 11 for soleus (S) and from 1 to 10 for EDL (E) and the number of the animal. Therefore, the sample name is indicated as follow: Biological replicate number_Soleus(S)/EDL(E)Myofiber number_Mouse number

hyb_protocol: 800 ng of labeled cDNA were mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

source_name: Individual pure type 2B myofiber from EDL muscle.

label_protocol: RNA was exponentially amplified using the TransPlex WholeTranscriptome Amplification 2 Kit (Sigma-Aldrich) in accordance with the manufacturer’s instructions, for 18 cycles. Amplification product was purified with the GenElute PCR Clean-up columns (Sigma-Aldrich). Resulting cDNA was quantified with Nanodrop ND-1000 spectrophotometer (Thermo Scientific). 2 µg of amplified-purified cDNA were labeled using the Genomic DNA Enzymatic Labeling Kit (Agilent Technologies), as described by protocol, and purified using the Amicon 30kDa filters (Millipore). On average, cDNA yield was about 4 µg and the specific activity of 30 pmol Cy3 per µg cDNA.

growth_protocol: CD1 male mice were housed in a normal environment provided with food and water and were killed by rapid cervical dislocation to minimize suffering.

extract_protocol: A single myofiber was lysed in 250 µl of TRIzol Reagent (Life Technologies) and, following the manufacturer’s instructions, RNA was extracted in the aqueous phase. 70% ethanol was added before column purification with RNeasy Micro Kit (Qiagen). Total RNA quality was monitored using the RNA Pico LabChip on a 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: Muscles from both hind limbs of the same mouse were immediately removed by microdissection, taking care to handle them only by their tendons to minimize mechanical damage to the fibers. Digestion proceeded for 40 – 45 min. at 37°C in 1 ml high-glucose DMEM (Life Technologies) containing 10 mg type I collagenase (220 U mg-1, Sigma-Aldrich). The collagenase-treated muscles were sequentially rinsed for 2 min. in 3 ml of DMEM, 3 ml DMEM supplemented with 10% fetal bovine serum (FBS) and 3 ml of DMEM and finally transferred into 50 mm x 18 mm well containing 3 ml of DMEM with 10% FBS. Single myofibers were liberated by gentle physical trituration with a wide-mouth plastic Pasteur pipette (about 4 mm diameter). Quickly, intact and well-isolated fibers were picked under stereomicroscope and washed first in DMEM and then in phosphate buffered saline. About one-third of each fiber was clipped and placed in Laemmli buffer for fiber typing by SDS-PAGE; the remaining part of the fiber was dissolved in TRIzol Reagent (Life Technologies) for RNA extraction. All samples were collected within 45 min. from the last trituration step.

value: Male


title: Myofiber MyHC-2B_6(E9.6)


title: Quant-seq_Day 21_neuron_rep1

description: Quant-seq


title: Heifer_Ampulla_Ipsi_2

source_name: Ampulla epithelial cells

value: heifer


title: Myofiber MyHC-2B_8(E14.3)


title: Myofiber MyHC-2B_9(E12.5)


title: Human fetal ileum IBU_4

city: Sherbrooke

first: Jean-François

last: Beaulieu

state: Québec

address: 3001, 12ème avenue nord

department: Anatomie & biologie cellulaire

country: Canada

institute: Université de Sherbrooke

description: Biological replicate 4

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalisation with Illumina GenomeStudio software.

source_name: Human fetal ileum

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions and then purified on QIAgen RNeasy columns.

value: ileum

tag: gestional age

value: 18 weeks


title: Quant-seq_Day 14_neuron_rep2

description: Quant-seq

value: Day 14 neuron


title: Myofiber MyHC-2B_4(E8.3)


title: Myofiber MyHC-2B_2(E10.4)


title: Myofiber MyHC-2B_7(E7.7)


title: Myofiber MyHC-2B_5(E9.5)


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_gata3_rp1

value: WT

value: Lung

value: Group 2 innate lymphoid cells (ILC2s)

value: Mouse anti-GATA3 mAb (BD L50-823)


title: Human fetal ileum IBU_3

description: Biological replicate 3

value: 17 weeks


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_Cbfb_rp2

value: Rabbit anti-Cbfb pAb


title: Human fetal ileum IBU_1

description: Biological replicate 1


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_Cbfb_rp1


title: Lung_ILC2_WT_IL2_7_33_ChIP-seq_gata3_rp2


title: Quant-seq_Day 14_neuron_rep1

description: Quant-seq


title: Myofiber MyHC-1_11(S10.10)

source_name: Individual pure type 1 myofiber from soleus muscle.

value: Soleus muscle

value: 3 months


title: Human fetal ileum IBU_2

description: Biological replicate 2


title: Human fetal ileum control_4

description: Biological replicate 4


title: Myofiber MyHC-2B_1(E13.3)

value: EDL muscle


title: Lung_ILC2_WT_IL2_7_input

value: Input


title: Lung_ILC2_WT_IL2_7_ChIP-seq_gata3_rp2


title: Heifer_Isthmus_Contra_1

source_name: Isthmus epithelial cells


title: Lung_ILC2_WT_IL2_7_ChIP-seq_gata3_rp1


title: Myofiber MyHC-2B_3(E11.9)


title: CROP-seq_Day 7_neuron_10x_lane_2

description: CROP-seq

extract_protocol:
Single cells were lysed in droplets using the 10X Chromium instrument.
Libraries were prepared according to the Chromium Single Cell 3' Reagent Kits User Guide (v2 Chemistry) from 10X Genomics.

value: Day 7 neuron


title: CROP-seq_Day 7_neuron_10x_lane_1

description: CROP-seq


title: CROP-seq_iPSC_sgRNA_enrichment_for_lane2

source_name: Human iPSC

growth_protocol: Essential 8 Medium

value: iPSC


title: Myofiber MyHC-1_10(S5.9)

value: Male


title: Human fetal ileum control_2

description: Biological replicate 2


title: Lung_ILC2_WT_IL2_7_ChIP-seq_Cbfb_rp1

value: Rabbit anti-Cbfb polyclonal pAb


title: Human fetal ileum control_1

description: Biological replicate 1

value: ileum


title: CROP-seq_iPSC_sgRNA_enrichment_for_lane1


title: Myofiber MyHC-1_9(S9.4)


title: Myofiber MyHC-1_8(S10.8)


title: Human fetal ileum control_3

description: Biological replicate 3


title: BCBL1 (uninduced)

description:
RNase R treated
Induced with tetradecanoyl phorbol acetate

organism:
Homo sapiens
Human gammaherpesvirus 8

source_name: B-cell lymphoma

value: KSHV+


title: Lung_ILC2_WT_IL2_7_ChIP-seq_Cbfb_rp2


title: CROP-seq_Day 7_sgRNA_enrichment_for_lane1


title: C2C12-Gapmer-d0-3

description: RNA extraction from proliferating C2C12 with Pvt1 silencing

hyb_protocol: Labeled cDNA was mixed with 5 µl of 10X Blocking Agent (Agilent Technologies) and water to a final volume of 25 µl. Samples were denatured at 95°C for 2 min. and added to 25 µl of 2X GEx Hybridization Buffer HI-RPM (Agilent Technologies). 40 µl mix was dispensed onto one array of the SurePrint G3 Mouse Gene Expression V2 8x60K microarray. Slides were loaded into the Agilent SureHyb chambers and hybridization was performed in a hybridization oven at 65°C for 17 hours with 10 rpm rotation. Finally, slides were washed using Wash Buffer Kit (Agilent Technologies) and dried at room temperature.

data_processing: Data was extracted from the scanned image using the Agilent Feature Extraction Software version 10.7.3.1 (protocol GE1_107_Sep09). Probes identifying coding genes and non-coding genes were treated separately because of their different expression. Non-coding RNAs are lesser expressed than coding RNAs. Therefore, after eliminating probes for lncRNAs (those including in the description column at least one of the following words: ncRNA, long non-coding RNA, lincRNA, misc_RNA) quantile inter-arrays normalization was performed in R statistic ambient considering only the gProcessedSignal column for probes identifying coding RNAs. Normalized values only for coding RNAs are indicated. Probes with gIsPosAndSignif value of zero were disregarded and labeled as “NA” also for coding RNAs. Mean values were calculated for multiple probes with the same NAME (Agilent Probe ID).

source_name: C2C12, proliferating, Pvt1 silencing, biological replicate 3

growth_protocol: C2C12 myoblasts were cultured on Tissue Culture Dishes or Tissue Culture Multiwell Plates (Thermo Fisher Scientific). Myoblasts were maintained in proliferation medium (DMEM, 10% FBS, 1 unit/ml Penicillin, 100 µg/ml Streptomycin), detached when reaching ~80% confluence using Trypsin-EDTA (Thermo Fisher Scientific) and re-seeded at a lower density. Cell cultures were maintained in a humid environment with controlled temperature and carbon dioxide levels (37°C, 5% v/v CO2).

extract_protocol: 1 ml of TRIzol Reagent (Thermo Fisher Scientific) was used to extract RNA from each sample. 300 μl of aqueous phase were additioned with 300 μl of isopropanol, samples were stored over night at -20°C and then centrifuged for 20 min. at 12,000 X g, 4°C to precipitate RNA. Pellet was washed twice with 70% EtOH and resuspended in 20 μl of DNase/RNase free water.

treatment_protocol: In vitro Pvt1 silencing experiments were performed by transfecting proliferating C2C12 myoblasts with Lipofectamine 2000 Transfection Reagent (Termo Fisher Scientific) and antisense LNA GapmeRs (Exiqon) (Pvt1_1 ACCGTAGTAGAGTTAA; Pvt1_3 AGTCAACGCTTCACAT). Cells transfected with Lipofectamine 2000 and Antisense LNA GapmeR Negative Controls (Exiqon) were used as negative controls (Mock). Silencing efficiency was assessed by qRT-PCR analysis of Pvt1 expression.

tag: passage

tag: silencing


title: Myofiber MyHC-1_5(S14.2)


title: Myofiber MyHC-1_6(S7.3)


title: Myofiber MyHC-1_7(S15.2)


title: CROP-seq_iPSC_10x_lane_2

description: CROP-seq