title: ChIP-seq MAX COL0829

extract_protocol:
Lysates were prepared from sonicated cells and TF-DNA complexes were isolated with antibody.
An Illumina sequencing library was prepared from  DNA using the NEBNext ChIP-seq library prep reagent set for Illumina (New England Biolabs) as per manufacturer’s protocol with DNA purification using Qiaquick PCR purification or Minelute PCR purification kits and 2% agarose gel DNA size selection. The library was sequenced with an Illumina HiSeq 2500 (Rapid Run, single-end, 50 bp)

tag: sirna

tag: antibody

value: MAX


title: Mouse38.05 [RNA-Seq]

status: Public on Dec 14 2018

type: SRA

city: Bar Harbor

first: Catherine

middle: C

last: Kaczorowski

state: ME

address: 600 Main Street

country: USA

institute: The Jackson Laboratory

description: KD

library_source: transcriptomic

data_processing:
Raw fastq files (R1 an R2) were subjected to filtering and triming of poor quality reads and bases using a custom python script
We used rsem (v1.2.12) for alignment and expression estimation of trimmed reads were using Bowtie2 (v2.2.0). Depending of the sample's  strain background, we used either the  C57BL/6J (GRCm38.74) or DBA/2J (build-mm10) genomes, as deemed appropriate.
Genome_build: C57BL/6J (GRCm38.74) or DBA/2J (build-mm10) genomes
Supplementary_files_format_and_content: normalized counts_mrna.csv, normalized counts from DESeq2
Supplementary_files_format_and_content: genes_expected_counts_merge.csv, expected read counts (not normalized, used as DESeq2 input)

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus

growth_protocol: Male mice (3-5mo) received an injection of either AAV9-shRNA-Hp1bp3 or AAV9-scrmb-shRNA. A minimum of six weeks later, mice were sacrificied and brains harvested for electrophysiology and/or molecular characterization.

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy Mini kit.
Libraries were made with the KAPA Biosystems mRNA Hyper Prep Kit.

treatment_protocol: The hippocampus was freshly dissected from brain tissue and immediately snap-frozen in liquid nitrogen. Samples were kept at -80C until further use.

tag: strain

tag: treatment


title: Mouse36.04 [RNA-Seq]

description: CTRL

value: AAV-scrmb-shRNA


title: Mouse35.03 [RNA-Seq]

description: KD


title: Mouse49.08 [RNA-Seq]

description: KD


title: HEB_ChIP-seq-input

city: Shanghai

first: Chun-hui

last: Xu

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

country: China

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

description: ChIP-seq input

library_source: genomic

data_processing:
Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, ribosome RNA, Qual < 20 reads), clean sequenced reads were alignmented to hg38 by TopHat(2.0.9), allow 2 mismatches and multihits <=2 per read.(RNA-seq)
Aligned reads were extracted by Htseq(0.9.1) with default parameters and normalized with TMM(trimmed mean of M values) method, FPKM were calculated by perl script.(RNA-seq)
Raw reads were filtered by Seqtk(remove adapters, length less than 25 reads, Qual < 20 reads), clean reads were alignmented to hg19 by bowtie2(2.2.9) with parameters: -N 1 -p5.(ChIP-seq)
Peaks were called by macs2(2.1.1.20160309) callpeaks algorithm with default set. BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq)
Genome_build: hg19 for ChIP-seq, hg38 for RNA-seq
Supplementary_files_format_and_content: FPKM files were calculated by definition.(RNA-seq)
Supplementary_files_format_and_content: BigWig files were generated by macs2 bdgcmp algorithm with default set.(ChIP-seq)

molecule: genomic DNA

organism: Homo sapiens

source_name: Myeloblast

growth_protocol: Kasumi-1 cells were cultured in RPMI 1640 Medium (Gibco) supplemented with 10% fetal bovine serum (FBS), 50 U/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
At 4 days after retrovirus infection of MIGR1 and E-protein, GFP+ Kasumi-1 cells were harvested by flow sorting and RNA was extracted with TRIzol Reagent (Invitrogen). (RNA-seq)
At 3 days after retrovirus infection of E-protein, GFP+ Kasumi-1 cells were sorted by BD FACSARIA III through FITC channel. Then they were crosslinked with 1% formaldehyde for 10 mins and then stopped by 125 mM Glycine. After lysis and sonication, 3 μg of HA-Tag (C29F4) Rabbit mAb (CST #3724) was incubated with chromatin sample overnight at 4 ℃, and 20μl protein A/G beads (Smart lifesciences SA032005) were used for immunoprecipitation. Finally, DNA were purified with PCR recovery kit (QIAGEN #28006).(ChIP-seq)
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina #RS-122-2001) and sequenced with Illumina HiSeq2500.(RNA-seq)
Library preparation was according to the manufacture’s guidelines (KAPA Biosystems KK8503) and sequencing procedures were carried out according to Illumina protocols with minor modifications (Illumina, San Diego).(ChIP-seq)

tag: cell type

value: leukemic cell line with an 8;21 chromosome translocation

tag: passages

value: 4-5 passages

tag: chip antibody

tag: genotype/variation

value: overexpress HEB

tag: cell line


title: Mouse30.01 [miRNA-Seq]

description:
CTRL
Mouse30.01

data_processing:
Raw fastq files (R1 only) were subjected to QC using fastqc (v0.11.3), following which adapter sequences were trimmed using cutadapt (v1.14)
Trimmed reads were then alingned to the Mouse miRNA-precursor miRBase reference (miRBase release 21) using bowtie (v1.0.0)
Following alignment, counts were extracted using featureCounts function from the subread (v1.5.2)  package
Genome_build: mm10
Supplementary_files_format_and_content: miRNA_counts.csv - expected read counts for each miRNA sample
Supplementary_files_format_and_content: miRNAcounts_normalized_rlog.csv - normalized and log transformed count data exported from DESeq2

extract_protocol:
Total RNA was isolated using the Qiagen miRNeasy Mini kit.
miRNA libraries were made with the Illumina TruSeq Small RNA Library Prep Kit


title: Mouse32.02 [RNA-Seq]

description: KD


title: E2-2_ChIP-seq

value: HA-Tag (C29F4) Rabbit mAb (CST #3724)

value: overexpress E2-2


title: E2-2_ChIP-seq-input

description: ChIP-seq input


title: HEB_ChIP-seq


title: Myoblasts_si-Circ#2

city: Rome

first: Francesca

last: Rossi

state: RM

address: Piazzale Aldo Moro, 5

department: Dipartimento di Biologia e Biotecnologie "Charles Darwin"

country: Italy

institute: Sapienza University of Rome

description:
Processed data file: myoblast_rpkm.tsv
processed data file column header: SI_B

data_processing:
Illumina Casava1.8 software used for basecalling.
Adapter sequences and poor quality ends were removed using the Trimmomatic software; reads with length < 20 nt after trimming were filtered out.
Reads were mapped to human GRCh38 genome and Ensembl 90 transcriptome using STAR software. Htseq-count software was used to count reads mapping to Ensembl 90 human genes; the overlap resolution mode was set to intersection-strict.
Differential gene expression was performed using edgeR R package after filtering out genes with a CPM (Count Per Million) value less than 1 in at least two samples; TMM normalization was applied independently for myoblast and rhabdomyosarcoma samples. RPKM values were calculated using the edgeR rpkm function.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample. Genes are specified using their Ensembl Gene ID.

source_name: Primary myoblasts from skeletal muscle

growth_protocol: Human primary myoblasts and Rhabdomyosarcoma cell lines were maintained in growth conditions

extract_protocol:
Total RNA was extracted with Qiazol reagent (Qiagen) and Direct-zol RNA Miniprep kit (Zymo Research), according to the manufacturer’s protocol. Then RNA was treated with DNase I (New England Biolabs) to remove genomic DNA, according to the manufacturer's instructions.
Illumina TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero treatment

treatment_protocol: Cells were transfected with si-SCR or si-Circ 48 hours before being harvested for RNA extraction. 3 pmol siRNA (Dharmacon) and 0,15 μl Dharmafect transfection reagent 1 (Dharmacon) in 150 μl DMEM (Sigma-Aldrich) were added to each 100 μl of culture medium in the plate. Medium was replaced 24h after the transfection.

value: wild-type primary myoblast cells

value: si-Circ


title: Mouse30.01 [RNA-Seq]

description: CTRL


title: Mouse53.09 [RNA-Seq]

description: CTRL


title: BMM KO WNV 12h rep 1

city: Minneapolis

first: Michael

last: Gale

state: Minnesota

address: 689 23rd Ave SE

department: Microbiology and Immunology

institute: University of Minnesota

data_processing:
Constructed libraries were sequenced on an HiSeq 2500 Illumina platform, producing 50-nt single-end reads. Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using STAR (version 2.4.0)
We mapped reads to the mouse reference genome (mm10) from Illumina's igenomes using STAR. After mapping, we assigned aligned read counts from BAM files to exons and genes using the python package HT-Seq.  HT-Seq provided the most accurate way of aligning read counts to overlapping exons. Reads that mapped to multiple positions were removed. After counts were generated we normalized with voom from the limma package in R.
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: raw count matrix

source_name: BMM KO WNV 12h

growth_protocol: BMMs were cultured in complete DMEM supplemented with recombinant mouse M-CSF (40ng/ml, Peprotech) for 7 days, changing media on day 3. Cells were kept at 37°C with 5% CO2 .

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN) with on-column DNase treatment.
TruSeq RNA Library Prep Kit v2
Library quality was evaluated using the Qubit® 3.0 Fluorometer and the Agilent 2100 Bioanalyzer instrument. Constructed libraries were sequenced on an NextSeq 500 Illumina platform, producing 2x75nt stranded paired end reads (52 Gb). Image analysis, base calling, and error estimation were performed using Illumina Analysis Pipeline (version 2.8).

treatment_protocol: BMMs were resuspended in serum-free RPMI with 2.5 MOI of WNV for 1.5 hours with gentle rocking.

tag: time

tag: infection

value: WNV

tag: genotype

value: Bone marrow macrophages

tag: replicate


title: BMM KO WNV 12h rep 2


title: Mouse56.11 [RNA-Seq]

description: CTRL


title: E2A_ChIP-seq-input

description: ChIP-seq input

value: overexpress E2A


title: BMM KO WNV 6h rep 2

source_name: BMM KO WNV 6h


title: E2-2_RNA-seq


title: Input COL0829

city: Urbana

first: Miroslav

last: Hejna

state: Illinois

address: 1110 West Green Street

department: Department of Physics

institute: University of Illinois

data_processing:
Alignment to genome (hg19) using Bowtie2
Deduplication of aligned reads
Peak calling using Macs2 (narrow peak option for MITF, broad peak option for H3K4me3)
Cuffdiff used for RNA-seq differential expression
Genome_build: hg19
Supplementary_files_format_and_content: narrowPeak and broadPeak files of ChIP-seq peaks, CuffDiff differential expression output

growth_protocol: Primary human melanocytes were cultured in TIVA medium (Ham’s F-10 (Corning), 7.5% fetal bovine serum (Atlanta Biologicals), 50 ng/ml 12-O-tetradecanoylphorbol-13-acetate, 0.1 mM 3-isobutyl-1-methylxanthine, 1 mM sodium orthovanadate, 1 mM N6,2′-O-Dibutyryladenosine 3′,5′-cyclic monophosphate sodium salt (Sigma-Aldrich)).

treatment_protocol: Primary human melanocytes were transfected with control siRNA pool (siGENOME Non-Targeting siRNA #2 (Dharmacon)) or siRNA pool against MITF (siGENOME MITF siRNA (Dharmacon)) using lipidoid and incubated 72 hours.


title: BMM KO WNV 6h rep 1


title: Mouse40.06 [RNA-Seq]

description: CTRL


title: BMM KO mock 12h rep 2

source_name: BMM KO mock 12h

value: Mock


title: HEB_RNA-seq


title: BMM KO mock 12h rep 1


title: BMM KO mock 6h rep 2

source_name: BMM KO mock 6h


title: Mouse57.12 [RNA-Seq]

description: KD


title: E2A_ChIP-seq


title: λH1-hESC derived_β-like cells

city: Miami

first: Juan

last: Domínguez-Bendala

state: FL

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

description: λH1-hESC derived β-like cells treated with prodrugs Ganciclovir and CB1954

data_processing:
Real time image analysis and base calling were performed on the instrument using the HiSeq Sequencing Control Software version 2.2.58
The raw FASTQ files were split into files containing 4,000,000 reads and checked for quality using the FASTX-Toolkit. The reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed based on the quality results (5 nucleotides at the left end of both the R1 and R2 reads).
Sequence alignment was performed using TopHat v2.1.0 with the following settings: tophat2 -p 2 -o [OUTPUT FOLDER] --library-type fr-firststrand –r [Dx] –mate-std-dev [Ds] [hg38 BOWTIE2 GENOME INDEX] [FASTQ 1] [FASTQ 2]. Where Dx and Ds represent sample-specific values for the mean and standard deviation, respectively, of the inner distance between reads, as determined by non-gapped alignment to human mRNA. FASTQ1 and FASTQ2 represent two files containing matched pairs of reads. The hg38 genome, hg38.fa.gz, was downloaded from ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/  and the BOWTIE2 index generated using the following command: bowtie2-build hg38.fa hg38. In practice split FASTQs with 4 million reads each were aligned separately to the genome to accelerate processing. An example execution command of an alignment of a single FASTQ file is given here: tophat2 -p 2 -o SL253780_CB602ANXX_L006_000 --library-type fr-secondstrand -r 112 --mate-std-dev 108 bowtie2_index/hg38 SL253780_CB602ANXX_L006_R1_000.fastq.gz SL253780_CB602ANXX_L006_R2_000.fastq.gz. Following the alignment BAM files were merged on a per-sample basis.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
RPKM values were then normalised using the formula log2(x+1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes mRNA RPKM values for the sample.

growth_protocol: Differentiated λH1-hESC derived β-like cells were ultured ontop of oxygen permeable PFC dishes in DMEM-F12 media (Invitrogen) 1% insulin free B27 (Thermofischer Scientific) and 1μM ALK5 inhibitor (Axxora), for 7 days. Afterwards cells were cultured for a further 7 days in DMEM-F12 medium with 1% Insulin free B27

extract_protocol:
RNA harvested from ~150,000 cells using Trizol reagent. (RNA processing, cDNA library construction and NGS sequencing were all performed at Ocean Ridge biosciences FL. USA) Total RNA was isolated from the tissue samples using the TRI Reagent® (Molecular Research Center; Part #: TR118) method. Following isolation, RNA was pooled from 3 human samples, quantified by O.D. measurement, and then digested with RNase free DNase I (Epicentre; Part # D9905K) and re-purified using RNeasy MinElute columns (Qiagen; Part #: 74204). The newly digested RNA samples were then quantified by O.D. measurement and checked for quality by chip-based capillary electrophoresis using an Agilent 2100 Bioanalyzer.
Amplified cDNA libraries suitable for sequencing were prepared from 8 nanograms (ng) of DNA-free total RNA using the Clontech SMARTer Stranded Total RNA-Seq Kit v2 – Pico Input Mammalian (Clontech/Takara; Part # 634411). The quality and size distribution of the amplified libraries were determined by chip-based capillary electrophoresis (Agilent 2100 Bioanalyzer; Agilent Technologies). Libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Boston, MA).
The libraries were pooled at equimolar concentrations and diluted prior to loading onto the flow cell of the Illumina cBot cluster station. The libraries were extended and bridge amplified to create sequence clusters using the Illumina HiSeq PE Cluster Kit v4 and sequenced on an Illumina HiSeq Flow Cell v4 with 50 nt paired-end reads plus dual index reads using the Illumina HiSeq SBS Kit v4.

treatment_protocol: Cells treated with Ganciclovir (100μM) and CB1954 (10μM) for 14 days on PFC dishes, along with the media described in the growth protocol.

tag: donor samples

tag: tissue

value: Human embryonic stem cell

tag: patient type

value: Human


title: BMM WT WNV 12h rep 2

source_name: BMM WT WNV 12h

value: WT


title: Mig RNA-seq

value: overexpress MigR1 control vector


title: E2A_RNA-seq


title: WNV 12h IRF5-ip rep 2

description:
ChIP-exo
wnv_12hr_IRF5.GEM_events.bed

data_processing:
Next-generation sequencing was performed on the Illumina HiSeq 2500 instrument by the Genome Technology Access Center (Washington University).
Quality control of the primary sequencing data was performed using FastQC (version 0.11.3) and included adapter trimming using cutadapt (version 1.8.3).
Reads were aligned using Bowtie v1.1.1
Genome_build: mouse genome (mm10)
Supplementary_files_format_and_content: We mapped reads to the mouse reference genome (mm10) from Illumina's igenomes using Bowtie v1.1.1. After mapping, we called peaks using GEM v3.1 on replicates together with corresponding input-ip samples as controls.

source_name: Bone marrow dendritic cells

growth_protocol: BMDCs were cultured in complete RPMI supplemented with recombinant mouse IL-4 (40ng/ml, Invivogen) and GM-CSF (40ng/ml, Invivogen) for 7-9 days, changing media on day 3. Cells were kept at 37°C with 5% CO2.

extract_protocol:
Chromatin was isolated using a truChIP chromatin shearing kit (Covaris) and sheared using M220 focused-ultrasonicator (Covaris). Sheared chromatin was run on an agarose gel and band corresponding to size 200-700bp was extracted. Immunoprecipitation was performed with validated IRF5 antibodies (Bethyl A303-385 and 386).
Exonuclease processing of sheared chromatin and library construction was performed using ChIP-exo kit (Active Motif).
Library size and quality was assessed using High Sensitivity DNA kit (Agilent) on the 2100 Bioanalyzer (Agilent). Next-generation sequencing was performed on the Illumina HiSeq 2500 instrument by the Genome Technology Access Center (Washington University).

treatment_protocol: BMDCs were resuspended in serum-free RPMI with 2.5 MOI of WNV for 1.5 hours with gentle rocking.

value: WNV infection


title: BMM WT mock 6h rep 1

source_name: BMM WT mock 6h


title: BMM WT mock 12h rep 1

source_name: BMM WT mock 12h


title: WNV 6h IRF5-ip rep 3

description:
ChIP-exo
wnv_6hr_IRF5.GEM_events.bed


title: BMM WT WNV 6h rep 2

source_name: BMM WT WNV 6h


title: BMM WT WNV 12h rep 1


title: WNV 12h IRF5-ip rep 3

description:
ChIP-exo
wnv_12hr_IRF5.GEM_events.bed


title: BMM WT mock 6h rep 2


title: WNV 6h input

description: ChIP-exo


title: Mock 12h IRF5-ip rep 3

description:
ChIP-exo
mock_12hr_IRF5.GEM_events.bed


title: WNV 12h IRF5-ip rep 1

description:
ChIP-exo
wnv_12hr_IRF5.GEM_events.bed


title: WNV 12h input

description: ChIP-exo


title: BMM WT mock 12h rep 2


title: Mock 12h IRF5-ip rep 2

description:
ChIP-exo
mock_12hr_IRF5.GEM_events.bed


title: Mock 6h IRF5-ip rep 3

description:
ChIP-exo
mock_6hr_IRF5.GEM_events.bed


title: BMM KO mock 6h rep 1


title: Mock 6h IRF5-ip rep 2

description:
ChIP-exo
mock_6hr_IRF5.GEM_events.bed


title: IgG

description: ChIP-exo


title: WNV 6h IRF5-ip rep 2

description:
ChIP-exo
wnv_6hr_IRF5.GEM_events.bed


title: Mock 6h IRF5-ip rep 1

description:
ChIP-exo
mock_6hr_IRF5.GEM_events.bed


title: Mock 12h IRF5-ip rep 1

description:
ChIP-exo
mock_12hr_IRF5.GEM_events.bed


title: Mock 12h input

description: ChIP-exo


title: Mock 6h input

description: ChIP-exo


title: HeLa S_M si1

type: RNA

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

department: Pathology

institute: University of Virginia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
The data were normalized using quantile normalization
Series supplementary file .txt reports fold change of RNA expression in samples compared to control sample

label: biotin

source_name: HeLa cells with SLC2A11-MIF siRNA1

label_protocol: Standard Illumina labelling protocol

growth_protocol: The Hela cells are maintained in DMEM high glucose medium with 10% FBS, 1% Pen/Strep at 37 degree incubator with 5% CO2

extract_protocol: RNA was extracted using Trizol reagent. RNA was used for microarray analysis on Illumina Human HT-22 v4 platform. QC of all samples were analyzed by Agilenet Technologies 2100 Bioanalyzer with an RNA Integrity Number(RIN) value greater than or equal to 8.

treatment_protocol: siRNA target fusion RNA SLC2A11-MIF, MIF, SLC2A11 and negative control were transfected into Hela cells to knocking down the targets's RNA expression. The cells will be treated for 48hrs using siRNAs before havest RNAs.

value: HeLa

value: SLC2A11-MIF siRNA1


title: HeLa S_M CON

source_name: HeLa cells with control siRNA

value: control siRNA


title: WNV 6h IRF5-ip rep 1

description:
ChIP-exo
wnv_6hr_IRF5.GEM_events.bed


title: HeLa SLC2A11 si

source_name: HeLa cells with SLC2A11 siRNA

value: SLC2A11 siRNA


title: BMM WT WNV 6h rep 1


title: HeLa MIF si

source_name: HeLa cells with MIF siRNA

value: MIF siRNA


title: HeLa S_M si2

source_name: HeLa cells with SLC2A11-MIF siRNA2

value: SLC2A11-MIF siRNA2


title: LC47

city: Heidelberg

first: Ruprecht

last: Kuner

address: Im Neuenheimer Feld 460

department: Molecular Genetics

country: Germany

institute: German Cancer Research Center and National Center of Tumor Diseases

description:
replicate 1
LC47_7018852014_K.mean

data_processing: Processing of the Illumina microarray data was performed using open source Illumina microarray pipeline lumi (Du et al. Bioinformatics 2008)

source_name: Tumor tissue

label_protocol: 20ng of total RNA was amplified and Biotin-labeled using the MessageAmpTM Premier RNA Amplification Kit (Life Technologies) according to the manufacturer’s instructions.

extract_protocol: Total RNA from the 48 microdissected adenocarcinoma tissues was extracted using RNeasy protocol (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

value: lung tumor

tag: tumor type

value: adenocarcinoma

tag: adenocarcinoma architecture

value: lepidic


title: LC38

description:
replicate 1
LC38_7018852014_B.mean

value: papillary


title: LC43

description:
replicate 1
LC43_7018852014_G.mean


title: LC45

description:
replicate 1
LC45_7018852014_I.mean

value: micropapillary


title: LC34

description:
replicate 1
LC34_6991001077_J.mean


title: LC36

description:
replicate 1
LC36_6991001077_L.mean

value: acinar


title: LC40

description:
replicate 1
LC40_7018852014_D.mean


title: LC41

description:
replicate 1
LC41_7018852014_E.mean


title: LC37

description:
replicate 1
LC37_7018852014_A.mean


title: LC29

description:
replicate 1
LC29_6991001077_E.mean


title: LC48

description:
replicate 1
LC48_7018852014_L.mean

value: solid


title: LC46

description:
replicate 1
LC46_7018852014_J.mean


title: LC31

description:
replicate 1
LC31_6991001077_G.mean


title: LC39

description:
replicate 1
LC39_7018852014_C.mean


title: LC33

description:
replicate 1
LC33_6991001077_I.mean


title: LC35

description:
replicate 1
LC35_6991001077_K.mean


title: LC28

description:
replicate 1
LC28_6991001077_D.mean


title: LC32

description:
replicate 1
LC32_6991001077_H.mean


title: LC27

description:
replicate 1
LC27_6991001077_C.mean


title: LC25

description:
replicate 1
LC25_6991001077_A.mean


title: LC42

description:
replicate 1
LC42_7018852014_F.mean


title: LC30

description:
replicate 1
LC30_6991001077_F.mean


title: LC23

description:
replicate 1
LC23_6991001101_K.mean


title: LC44

description:
replicate 1
LC44_7018852014_H.mean


title: LC26

description:
replicate 1
LC26_6991001077_B.mean


title: LC24

description:
replicate 1
LC24_6991001101_L.mean


title: LC22

description:
replicate 1
LC22_6991001101_J.mean


title: RibosomeProfiling_Rep2_CHX_LPS

city: Boston

first: Lina

last: Kroehling

state: MA

address: 91 E Concord St

institute: Boston Unviersity

description:
Supplementary_Table_1.xlsx
CHX_LPS

data_processing:
Library strategy: Ribosome profiling
Ribosome Profiling Reads were trimmed for adaptor sequence using Fastx Toolkit version 0.0.14.
RNA-seq, RiboTag and Ribosome Profiling reads were aligned to the mm10 genome assembly using Tophat version 2.1.1
RiboTag and Ribosome Profiling aligned reads were filtered to include only high quality and unique reads using AS:i:0, AS:i:-1  and AS:i:-2, and NH:i:1
Tuxedo Suite v 2.2.1 was used for differential analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values and further analyses are compiled and reported in Supplementary_Table_1.xlsx

source_name: Bone Marrow Derived Macrophages

growth_protocol: Bone marrow was isolated from the tibia and femur mice hind legs. BM was flushed and RBC lysis conduct. BM cells were seeded in DMEM supplemented with 10% FBS and PSG. 50 ng/ml of MCSF was adminstered. Cells were grown for 7 days, with media replaced on day 3.

extract_protocol:
BMDM cells were lysed usiig the illumina mammalian Ribosome profiling kit
Libraries were prepared according to Illumina instructions

treatment_protocol: LPS stimulation for 6 or 24 hours

value: bone marrow

value: Macrophage

tag: background strain


title: LC21

description:
replicate 1
LC21_6991001101_I.mean


title: RibosomeProfiling_Rep2_CHX_NT

description:
Supplementary_Table_1.xlsx
CHX_NT

value: WT


title: RibosomeProfiling_Rep1_CHX_NT

description:
Supplementary_Table_1.xlsx
CHX_NT


title: RibosomeProfiling_Rep1_CHX_LPS

description:
Supplementary_Table_1.xlsx
CHX_LPS


title: LC20

description:
replicate 1
LC20_6991001101_H.mean


title: RiboTag_24hr_Rep2

description:
Supplementary_Table_1.xlsx
24hr

data_processing:
Library strategy: RiboTag
Ribosome Profiling Reads were trimmed for adaptor sequence using Fastx Toolkit version 0.0.14.
RNA-seq, RiboTag and Ribosome Profiling reads were aligned to the mm10 genome assembly using Tophat version 2.1.1
RiboTag and Ribosome Profiling aligned reads were filtered to include only high quality and unique reads using AS:i:0, AS:i:-1  and AS:i:-2, and NH:i:1
Tuxedo Suite v 2.2.1 was used for differential analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values and further analyses are compiled and reported in Supplementary_Table_1.xlsx

extract_protocol:
Cell lysed were immunoprecipated using anti-HA antibody. RNA was isoalted from HA tagged ribosomes using Qiagen RNAeasy microkit.
Libraries were prepared according to Illumina instructions

value: LysM-Cre x RiboTag


title: LC17

description:
replicate 1
LC17_6991001101_E.mean


title: LC19

description:
replicate 1
LC19_6991001101_G.mean


title: LC13

description:
replicate 1
LC13_6991001101_A.mean


title: LC16

description:
replicate 1
LC16_6991001101_D.mean


title: LC14

description:
replicate 1
LC14_6991001101_B.mean


title: LC15

description:
replicate 1
LC15_6991001101_C.mean


title: LC09

description:
replicate 1
LC09_6898376003_I.mean


title: LC18

description:
replicate 1
LC18_6991001101_F.mean


title: LC10

description:
replicate 1
LC10_6898376003_J.mean


title: LC11

description:
replicate 1
LC11_6898376003_K.mean


title: LC04

description:
replicate 1
LC04_6898376003_D.mean


title: LC07

description:
replicate 1
LC07_6898376003_G.mean


title: LC06

description:
replicate 1
LC06_6898376003_F.mean


title: BMDM_LPSrep3_RNA_seq

description:
Supplementary_Table_1.xlsx
LPS3

data_processing:
Ribosome Profiling Reads were trimmed for adaptor sequence using Fastx Toolkit version 0.0.14.
RNA-seq, RiboTag and Ribosome Profiling reads were aligned to the mm10 genome assembly using Tophat version 2.1.1
RiboTag and Ribosome Profiling aligned reads were filtered to include only high quality and unique reads using AS:i:0, AS:i:-1  and AS:i:-2, and NH:i:1
Tuxedo Suite v 2.2.1 was used for differential analysis.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values and further analyses are compiled and reported in Supplementary_Table_1.xlsx

extract_protocol:
RNA was extracted using RNAeasy microcoloumns from Qiagen
Libraries were prepared according to Illumina instructions


title: BMDM_LPSrep2_RNA_seq

description:
Supplementary_Table_1.xlsx
LPS2


title: RiboTag_NT_Rep1

description:
Supplementary_Table_1.xlsx
NT


title: BMDM_WTrep3_RNA_seq

description:
Supplementary_Table_1.xlsx
NT3


title: RiboTag_NT_Rep2

description:
Supplementary_Table_1.xlsx
NT


title: BMDM_WTrep1_RNA_seq

description:
Supplementary_Table_1.xlsx
NT1


title: BMDM_WTrep2_RNA_seq

description:
Supplementary_Table_1.xlsx
NT2


title: LC08

description:
replicate 1
LC08_6898376003_H.mean


title: BMDM_LPSrep1_RNA_seq

description:
Supplementary_Table_1.xlsx
LPS1


title: LC03

description:
replicate 1
LC03_6898376003_C.mean


title: LC12

description:
replicate 1
LC12_6898376003_L.mean


title: RiboTag_6hr_Rep1

description:
Supplementary_Table_1.xlsx
6hr


title: LC01

description:
replicate 1
LC01_6898376003_A.mean


title: Hltf-KO rep 3

city: Lubbock

first: Beverly

middle: S

last: Chilton

state: TX

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

description: bilsulfite conversion

data_processing:
Sequence reads from bisulfite-treated EpiQuest libraries were identified using standard Illumina base-calling software
analyzed using a Zymo Research proprietary analysis pipeline, which is written in Python and used Bismark to perform the alignment.
The --non_directional parameter was applied while running Bismark. All other parameters were set to default.
The library was constructed in a non strand specific manner, alignments to all four bisulfite strands are reported
Genome_build: mm10
Supplementary_files_format_and_content: bigbed

source_name: placenta

extract_protocol:
Individual samples [1 term placenta/sample x 3 biological replicates for null and control mice = 6 total samples] were flash frozen prior to DNA isolation and purity assessment
Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine
Adaptor-ligated size-selected fragments of 150–250 bp and 250–350 bp were bisulfite-treated and sequenced.

tag: strain

value: term placenta

tag: age

value: gestation day 18.5


title: Hltf-KO rep 1

description: bilsulfite conversion


title: Hltf-KO rep 2

description: bilsulfite conversion


title: LC02

description:
replicate 1
LC02_6898376003_B.mean


title: Wild type rep 3

description: bilsulfite conversion


title: Wild type rep 2

description: bilsulfite conversion


title: HltfKO10

description:
rRNA depleted
RMS5097

data_processing:
Paired-end 100 nucleotide reads were aligned (mapped) to genomic assembly mm10
FPKM (fragments per kilobase of transcript per million mapped reads) were mapped against mm10 with Tophat (V1.3.3) to obtain .bam mapping files that were input into Cufflinks for transcript assembly.
Cuffdiff (V 1.3.0), part of the Cufflinks package, uses the alignment reads for rigorous statistical comparison of two conditions (null, control) and five replicates for each condition.
Exon quantification was performed to show the relative expression of all known Hltf exons in the placenta
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files of RPKM values for each sample

extract_protocol:
Individual samples [1 placenta/sample x 5 biological replicates for test and control littermate female mice = 10 total samples] were flash frozen and sent to Otogenetics Corp. (Norcross, GA) for RNA-seq assays
Random-primed cDNA (rRNA-depleted) using standard Illumina protocols


title: HltfKO8

description:
rRNA depleted
RMS5095


title: HltfKO7

description:
rRNA depleted
RMS5094


title: Wild type rep 1

description: bilsulfite conversion


title: HltfKO9

description:
rRNA depleted
RMS5096


title: MCNT rep2

city: LA JOLLA

first: Kristin

last: Baldwin

state: CA

address: 10550 N. Torrey Pines

department: DNC

institute: TSRI

description: Sample 5

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Embryonic stem cell line

growth_protocol: iPSC and ESC were grown in knock-out DMEM supllemented with 15% KSR and LIF

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic stem cell line

tag: protocol

value: Generated by nuclear transfer


title: Wt5

description:
rRNA depleted
RMS5092


title: Wt3

description:
rRNA depleted
RMS5090


title: PBS treated mice, Replicate 3

city: Helsinki

first: Emmi

last: Joensuu

address: Haartmaninkatu 8

department: Research Programs Unit of the Faculty of Medicine

country: Finland

institute: University of Helsinki

description:
DEG_PFD-treated-without-rep2_vs_CTRL.txt
DEG_PFD-treated_vs_CTRL.txt

data_processing:
Chipster v3.12 software was used for processing and analyses. www.chipster.csc.fi
The quality of the reads was checked using FastQC and PRINSEQ. Library-type fr-firststrand.
Alignment with STAR aligner for single end reads and human genome GRCh38.9 with Chipster default parameters, after alignment RNA-seq quality metrics was read with RseQC, aligned reads per genes (exons) were counted with HTSeq with Chipster default parameters,
count files were combined, differential expression analyzed using edgeR (default FDR <0.05) and DESeq2 (default padj <0.1) both with Chipster default parameters (normalization is included)
Create a dataset where edgeR and DESeq2 results are ovelapping
Genome_build: GRCh38.9
Supplementary_files_format_and_content: tab-delimited text file including raw counts for each sample and differential expression results for both edgeR and DESeq2 for the whole dataset and a second file for the same set without PFD-rep2 which did not respond to treatment

growth_protocol: JP5 mesothelioma cells were rutinely cultured in uncoated T75 flasks with RMPI medium supplemented with 10% FBS, L-glutamine, penicillin and streptomycin. Replating once a week.

extract_protocol:
Tumor tissue was collected in RNAlater solution (Life Technologies). Total cellular RNA was isolated using QIAzol and Rneasy Mini Kit (Qiagen). RNA quality was verified using Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: JP5 cells (1000000) were injected mixed with Matrigel matrix (final concentration 7 mg/ml) into the flank region of mice. Daily treatment (PBS or 200mg/kg pirfenidone in PBS, oral gavage) was started one day after injection. Mice were sacrificed after 60 days.

tag: mouse strain

value: Balb/c nu/nu

value: human mesothelioma cell xenograft

tag: human cell line

tag: treatment time

value: 60 days


title: PBS treated mice, Replicate 2


title: Wt1

description:
rRNA depleted
RMS5088


title: PBS treated mice, Replicate 1


title: HltfKO6

description:
rRNA depleted
RMS5093


title: Wt2

description:
rRNA depleted
RMS5089


title: PFD treated mice, Replicate 5


title: PFD treated mice, Replicate 3


title: PFD treated mice, Replicate 4


title: PFD treated mice, Replicate 2


title: PFD treated mice, Replicate 1


title: HTBE_H5N1_mock_Input_2

city: La Jolla

first: Max

last: Chang

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Adapter sequences were trimmed with fastp 0.12.5
Reads were mapped to the human hg38 genome with Bowtie 2.3.4
Genomic coverage was calculated using deepTools 3.0.1, with binSize=1 and extendReads=150
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files normalized by BPM

growth_protocol: HTBE cells (Lonza) were maintained in PneumaCult-Ex Medium (Stemcell Technologies) according to the manufacturer’s recommendations.

extract_protocol:
Previously described protocols (see PMID: 17512414 and PMID: 17406303) with minor modifications were used: (i) Sonication: A refrigerated Bioruptor (Diagenode) was used . Sonication conditions were optimized to generate DNA fragments of approximately 200-500 bp. (ii) Antibodies (Ab) were coupled with Invitrogen Dynabeads anti-mouse M-280 #112-02, or Dynabeads anti-rabbit M-280 #112-04 for 6hours. Ab-beads and chromatin were then immunoprecipitated overnight. (iii) After the wash steps, reverse crosslinking was carried out at 65°C for 2 hours in a thermomixer programmed for mixing at 700 rpm 2 min on/ min off. ChIP DNA was then isolated, after RNase digestion and proteinase K digestion, using QIAGEN MinElute kit (28004).
For library preparation, 30 ul of ChIP DNA was used to generate blunt-ended DNA using the Epicenter DNA ENDRepair kit (Epicenter Biotechnologies, cat# ER0720), and purified end-repaired DNA using the QIAGEN PCR purification kit (28104). DNA END Repair was done using Klenow Fragment (NEB M0212L), and purified DNA was collected with QIAGEN MinElute kit. Ligation of Illlumina/Solexa adapters (#FC-102-1003) to DNA fragments overnight was achieved using T4 DNA ligase (NEB M0202L). Adaptor-ligated DNA fragments were purified with the QIAGEN MinElute kit. 18 cycles of PCR was performed with the Illumina/Solexa primers 1.0 and 2.0, and an aliquot of material was used to check the fragment size on agarose gel. The remaining DNA was column purified and bio-analyzed before sequencing.

treatment_protocol: 24 hours before infection, HTBE cells (Lonza, Donor 4F1289J) were plated at a density of 2 x 10^6 cells in a 10 cm dish. For infection, growth medium was replaced with virus diluted to the appropriate concentration in Pneumacult-Ex complete medium at a total volume of 2 mL. Dishes were incubated in a cell culture incubator with gentle rocking every 15 minutes. After 60 minutes, the inoculum was removed and cells were washed twice washed gently with 5 mL Pneumacult-Ex. 10 mL of Pneumacult-Ex was added and cells were incubated for the specified length of time.

tag: cell type

value: Human tracheobronchial epithelial (HTBE) cells

tag: infected with

value: H5N1 influenza virus

tag: time point

value: uninfected (mock control)

tag: chip antibody

value: none (input)

tag: biological replicate


title: HTBE_H5N1_mock_IgG_2

value: IgG


title: Wt4

description:
rRNA depleted
RMS5091


title: HTBE_H5N1_mock_IgG_1


title: B130_Normal Breast Tissue

city: Chicago

first: Yoo-Jeong

last: Han

state: IL

address: 900E. 57th street

department: Medicine

institute: University of Chicago

description: Gene expression from normal breast tissues or tumors

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) 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:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 045997_D_F_20121218) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
All Targets Value (Entities where at least 18 out of 30 samples have flags in [Present, Marginal])

source_name: Normal Breast Tissue

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

extract_protocol: Tumors/tissues were homogenized by TissueLyzer LT (Qiagen, Valencia, CA).  RNAs were extracted using the Qiagen AllPrep DNA/RNA/Protein mini kit protocol (Qiagen, Valencia, CA).

treatment_protocol: OCT-embeded frozen breast tissues/tumors

value: Normal Breast Tissue

tag: pam50 subtype

value: Normal


title: HTBE_H5N1_mock_H3K27ac_2


title: B360_Normal Breast Tissue

tag: tissue


title: B932_Normal Breast Tissue


title: B100_Normal Breast Tissue


title: B200_Normal Breast Tissue

value: LumA


title: B455_Normal Breast Tissue


title: A823_Breast Tumor

source_name: Breast Tumor

value: Breast Tumor

value: Basal


title: A890_Breast Tumor


title: B668_Normal Breast Tissue


title: B812_Normal Breast Tissue


title: B064_Normal Breast Tissue


title: A345_Breast Tumor


title: HTBE_H5N1_mock_H3K27ac_1


title: B306_Normal Breast Tissue


title: A407_Breast Tumor


title: RiboTag_6hr_Rep2

description:
Supplementary_Table_1.xlsx
6hr

value: bone marrow

value: Macrophage

tag: genotype

value: LysM-Cre x RiboTag


title: HTBE_H5N1_18h_Input_2

value: 18h post-infection


title: A030_Breast Tumor


title: A811_Breast Tumor


title: HTBE_H5N1_18h_H3K27ac_2


title: HTBE_H5N1_18h_Input_1


title: A348_Breast Tumor


title: HTBE_H5N1_18h_H3K27ac_1


title: A245_Breast Tumor

value: LumB


title: A128_Breast Tumor


title: 180036_MK198_6_Th17_D4_S85_L005_R1_001

city: Turku

first: Tommi

last: Välikangas

address: Huhkonmaantie 26 as.11

department: Turku Centre for Biotechnology

institute: University of Turku

data_processing:
The raw data was base called with CASAVA1.8
The RNA-seq raw reads were mapped to the Ensembl human reference genome GRCh38 (Genome Reference Consortium Human Build 38) using the STAR aligner version 2.5.2. The read counts were generated using the featureCounts tool in the Subread software package version 1.5.1. Gene counts for all samples were combined into a single file. The uniquely mapped reads were filtered for lowly expressed genes (genes with counts per million (cpm) >1 in at least 5 replicate samples were retained) and used for further analysis.
The gene counts were normalized using the trimmed mean of M-values (TMM) normalization from the Bioconductor package edgeR after which the data was transformed to counts per million (cpm), offsetted by 1 and log2-transformed.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited txt files include gene counts for each sample. The comma  separated values (csv) file includes the TMM normalized, cpm and log2 transformed gene count data for all samples.

source_name: Th17 cells

growth_protocol: To obtain naive CD4+ T cells, human peripheral blood mononuclear cells (PBMCs) were isolated from the umbilical cord blood of healthy neonates (Turku University Central Hospital, Turku, Finland) by the density gradient Ficoll- Paque method (Ficoll-Paque PLUS; GE Healthcare). Naive CD4+ cells were further purified using CD4+ Dynal positive selection beads (Dynal CD4 Positive Isolation Kit; Invitrogen), and after the isolation, cells from individual donors were either activated directly or pooled before activation. CD4+ T cells were stimulated with plate-bound αCD3 (3750 ng/6-well culture plate well; Immunotech) and soluble αCD28 (1 μg/mL; Immunotech) in a density of 2.5 × 106 cells/mL of X-vivo 20 serum-free medium (Lonza). The X-vivo 20 me dium was supplemented with L-glutamine (2 mM, Sigma-Aldrich), and antibiotics (50 U/mL penicillin and 50 μg/mL streptomycin; Sigma-Aldrich). Th17 cell polarization was initiated with a cytokine cocktail of IL-6 (20 ng/mL; Roche), IL-1β (10 ng/mL) and TGF-β (10 ng/mL) in the presence of neutralizing anti-IFNγ (1 μg/mL) and anti-IL-4 (1 μg/mL) to block Th1 and Th2 differentiation, respectively. For the control cells (Th0), CD4+ T cells were TCR stimulated with aCD3 and aCD28 in the presence of neutralizing antibodies without differentiating cytokines and cultured in parallel. All cytokines and neutralizing antibodies used in the study were purchased from R&D Systems unless otherwise stated. All cell cultures were maintained at 37°C in a humidified atmosphere of 5% (v/v) CO2/air.

extract_protocol:
RNA was isolated (RNeasy Mini Kit, QIAGEN) and DNase treated (RNase-Free Dnase Set; QIAGEN).
Library preparation was performed according to Illumina TruSeq® Stranded mRNA Sample Preparation Guide (part # 15031047).

tag: timepoint

tag: polarizing cytokines

value: IL-6 + IL1-β + TGF-β + anti-IFNγ + anti-IL4


title: 180036_MK198_6_Th17_D5_S85_L005_R1_001


title: 180036_MK198_6_Th17_D3_S85_L005_R1_001


title: HTBE_H5N1_12h_Input_1

value: 12h post-infection


title: 180036_MK198_6_Th17_D2_S85_L005_R1_001


title: A798_Breast Tumor


title: A202_Breast Tumor


title: small RNA in sperm

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

institute: Northwest A&F University

description: sperm from breeder cock

data_processing:
Data processing was followed the procedures described in a previous study (Li et al. 2010) by LC Sciences Service (Hangzhou, China). Raw sequencing reads, obtained with the Illumina pipeline filter (Solexa 0.3), were further filtered to obtain mappable sequencing with an in-house program (ACGT101-miR, LC Sciences, Houston, Texas, USA) (Wu et al. 2017a). In this step, rRNA, tRNA, snRNA, snoRNA, and repeat sequences, as well as the sequences containing the polyA tail, were removed from the small RNA sequences.
Unique sequences with lengths from 18 to 26 nt were mapped to specific species precursors in miRBase21.0 (ftp://mirbase.org/pub/mirbase/CURRENT/) by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. The unique sequences mapping to Gallus gallus mature miRNAs in hairpin arms and the remaining sequences mapping to other selected species precursors (with the exclusion of specific species, Table S1) in miRBase 21.0 were defined as known miRNAs. Moreover, mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The unmapped sequences were BLASTed against the specific genomes and the hairpin RNA structures were predicated using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi/) (Wu et al. 2017a).
Unique sequences with lengths in 25-37 nt were compared against noncoding RNAs deposited in the Rfam 11.0 database to remove any matched reads, except those matched to piRNAs. Then, the retained unique small RNAs were mapped onto the Gallus gallus genome (ftp://ftp.ensembl.org/pub/release-78/fasta/gallus gallus/dna). There are some overlaps in the size between miRNA and piRNA, so the miRNA related reads predicted by ACGT101-miR-v3.5 were discarded. Then we mapped the potential piRNAs reads on the piRNAs database and identified the reads which mapped to specific piRNAs in piRNA database as the known piRNAs. Moreover, as for other reads which have not mapped to specific piRNAs in piRNA database, we used two features to select candidates of piRNA-like RNA. The reads clustered in genome and had a “uridine base (U)” at the first position were considered as novel piRNA-like RNAs (Wei, Liu, and Zhang 2012; Xu et al. 2016; Capra et al. 2017).
Meanwhile, we normalized the expression abundances of miRNAs and piRNAs in the sperm samples; the formula was: Normalized Expression (NE) = Actual miRNA (or piRNA) count/Total count of clean reads.
Genome_build: Gallus gallus 4
Supplementary_files_format_and_content: all expressed miRNAs.xls and all expressed piRNA.xls

organism: Gallus gallus

source_name: sperm

extract_protocol:
Total RNA from sperm sample were extracted using Phenol Water (Solarbio, Beijing, China) according to the manufacturer’s procedure. The quantity and purity of total RNA were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip TM Kit (Agilent, CA, USA) with RIN number >7.0.
Equal quantities of the RNA extracted from the sperm of five cockerels were pooled into one sample. Approximately 1 μg of total RNAs were used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep TM Kits (Illumina, San Diego, USA), and then we performed the single-end sequencing (1*50bp) on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following the recommended protocol (Chen et al. 2015).

treatment_protocol: Five healthy Arbor Acres rooster at forty weeks of age were randomly selected. Sperm was gathered by the gloved hand technique into a 1 mL pre-warmed vacuum bottle and two ejaculates were respectively obtained and collected from each donor over three interrupted days. After collection, characteristics of sperm samples (total sperm numbers per ejaculate, subjective sperm motility, acrosome integrity and normal morphology) were microscopically assessed. Only ejaculate sperm samples with more than 90% motile spermatozoa and more than 90% morphologically normal spermatozoa were used.  All ten sperm samples were stored at – 196℃ until analyzed.

value: sperm


title: A518_Breast Tumor


title: A596_Breast Tumor


title: A929_Breast Tumor


title: A181_Breast Tumor


title: A221_Breast Tumor


title: A172_Breast Tumor


title: A378_Breast Tumor


title: HTBE_H5N1_12h_H3K27ac_1

value: Human tracheobronchial epithelial (HTBE) cells

value: H5N1 influenza virus


title: HTBE_H5N1_12h_H3K27ac_2


title: 180036_MK198_6_Th17_D1_S85_L005_R1_001


title: HTBE_H5N1_06h_Input_2

value: 06h post-infection

value: none (input)


title: HTBE_H5N1_mock_Input_1

value: uninfected (mock control)


title: HTBE_H5N1_06h_Input_1


title: 180036_MK198_1_Th0_D4_S81_L005_R1_001

source_name: CD3/CD28 activated T (Th0) cells

value: anti-IFNγ + anti-IL4


title: 180036_MK198_1_Th0_D3_S81_L005_R1_001


title: 180036_MK198_1_Th0_D2_S81_L005_R1_001


title: HTBE_H5N1_06h_H3K27ac_1


title: HTBE_H5N1_06h_H3K27ac_2


title: 180036_MK198_1_Th0_D1_S81_L005_R1_001


title: RiboTag_24hr_Rep1

description:
Supplementary_Table_1.xlsx
24hr


title: 180036_MK198_1_Th0_D5_S81_L005_R1_001


title: HTBE_H5N1_03h_Input_1

value: 03h post-infection


title: HTBE_H5N1_03h_Input_2


title: HTBE_H5N1_03h_H3K27ac_2


title: ΔCYC2 x ΔCYC2

city: taiyuan

first: jing

last: xu

state: shanxi

address: wuchen road

institute: shanxi university

description: KO

data_processing:
Basecalls performed using Illumine Hiseq XTen PE150
The adaptor sequences were trimmed with the software cutadapt, and low-quality reads (contianing over 10% of N, or the quality score of over 50% of base is lower than 5) were discarded to get clean reads for downstream analysis. At the same time, Q20, Q30 and GC content the clean data were calculated.
Tetrahymena macronuclear reference genome and gene model annotation files were downloaded from NCBI Genome Database (https://www.ncbi.nlm.nih.gov/genome/?term=txid5911) directly.
Index of the reference genome was built using Bowtie v2.1.0 and paired-end clean reads were aligned to the reference genome using TopHat v2.1.1 with the default parameters.
TopHat is selected as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
The Cufflinks v2.2.1 Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results for each sample.
Cuffmerge was used to merge together all Cufflinks assemblies
Combined.gtf file produced by Cuffmerge as input to along with gene model annotation file. The tracking file provided by Cuffcompare was used to infer splice isoforms unique to cancer by examining manually.
The transcripts with class code j were selected for novel isoforms evaluation.
RSEM v1.2.27 was used to count the reads numbers mapped to each transcript
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
FPKM, Fragments Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Genome_build: Tetrahymena macronuclear genome assembly (version:June2014; downloaded from Tetrahymena Genome Database)
Supplementary_files_format_and_content: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq R package (1.24.0)
Supplementary_files_format_and_content: Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the topGO R package (2.24.0), in which gene length bias was corrected.
Supplementary_files_format_and_content: KEGG is a database resource for understanding high-level functions and utilities of the biological system, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing andother high-through put experimental technologies (http://www.genome.jp/kegg/).

organism: Tetrahymena thermophila

source_name: Tetrahymena thermophila whole cell

growth_protocol: The Tetrahymena B2086 and CU428 wild-type (WT) strain (obtained from the Tetrahymena Stock Center at Cornell University) and mutant strains (ΔCYC2) were maintained in Super Proteose Peptone (SPP) medium (1% Proteose peptone, 0.2% Glucose, 0.1% Yeast extract, 0.003% Sequestrene) at 30°C on a rotary shaker at 170 rpm.

extract_protocol:
Samples were collected from 5ml of conjugational Tetrahymena WT and mutant cells (density: 2.5 x 105 cells/mL) and transferred into 2 ml RNase-free tube. 1ml RNAiso was added into the tubes to lyse cells. The tube placed 4 ℃ centrifuge, 12800 rpm for 1 minute，Absorb supernatant to a spin column，4℃，8800 rpm for 20 seconds. Absorb supernatant in collection tube to a 1.5ml RNase-free tube，add 0.5 volumes of ethanol, followed by all of the liquid was transferred to a spin column, 4℃，8800 rpm for 20 seconds. Now RNA adsorbed on a silicon membrane inside the spin column.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）. First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase（RNase H-）. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

tag: genetic background

tag: genotype/variation

value: Somatic CYC2 gene knockout

tag: gene accession number


title: HTBE_H5N1_12h_Input_2


title: HTBE_H5N1_03h_H3K27ac_1


title: WT x WT

description: WT

value: Wild type


title: A359_Breast Tumor

value: Breast Tumor


title: LC05

description:
replicate 1
LC05_6898376003_E.mean

value: lung tumor

tag: tumor type

value: adenocarcinoma

tag: adenocarcinoma architecture

value: solid


title: MLX population 2, male, rep 2

city: Lund

first: Jessica

middle: K.

last: Abbott

address: Sölvegatan 37

department: Dept. of Biology

country: Sweden

institute: Lund University

description: MLX population 2 males

hyb_protocol: Sample preparation and hybridisation was carried out at the Uppsala Array Platform (following the manufacturer's instructions for GeneChip Drosophila Genome 2.0 Affymetrix microarrays)

scan_protocol: Image acquisition was carried out at the Uppsala Array Platform

data_processing: Analysis was carried out in BioConductor, and data were pre-processed using Robust Multichip Average (RMA) in the “affy” package.

label: Biotin

organism: Drosophila melanogaster

source_name: Whole fly

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

growth_protocol: Standard fly culturing protocol for LHm population, described in Abbott et al. PLoS One 2013;8(7):e70493

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

tag: Sex

value: male

tag: population

value: MLX


title: MLX population 3, male, rep 1

description: MLX population 3 males


title: MLX population 3, female, rep 2

description: MLX population 3 females

value: female


title: MLX population 2, male, rep 1

description: MLX population 2 males


title: MLX population 1, male, rep 1

description: MLX population 1 males


title: MLX population 1, male, rep 2

description: MLX population 1 males


title: MLX population 2, female, rep 2

description: MLX population 2 females


title: MLX population 3, male, rep 2

description: MLX population 3 males


title: MLX population 3, female, rep 1

description: MLX population 3 females


title: Control population 3, male, rep 2

description: Control population 3 males

value: control


title: A889_Breast Tumor

value: Normal


title: Control population 2, male, rep 2

description: Control population 2 males


title: MLX population 1, female, rep 1

description: MLX population 1 females


title: T1

city: Pecs

first: Zsuzsanna

last: Helyes

address: Szigeti u. 12

department: Pharmacology and Pharmacotherapy

country: Hungary

institute: University of Pecs Medical School

description: lncRNA and mRNA expression after 7 days after CFA injection

hyb_protocol: The labeled cRNAs were hybridized onto the Rat LncRNA Array v1.0 (4 x 44K, Arraystar). Hybridization was performed in Agilent’s SureHyb Hybridization Chambers.

scan_protocol: After having washed the slides, the arrays were scanned by the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. The raw microarray data were analysed using R and Bioconductor.

organism: Rattus norvegicus

source_name: Trigeminal ganglia tissue

label_protocol: Sample labeling, array hybridization and primary data analysis was performed by ArrayStar Inc. (Rockville, MD, USA). Briefly, total RNA samples were amplified and labeled with Cy3-dCTP. Each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar).

extract_protocol: Total RNA were isolated from snap-frozen samples using RNeasy Mini Kit (Qiagen, Carlsbad, CA) and high quality samples (RIN>8.0) were used for subsequent expression analyses. The sample preparation and microarray hybridization were performed based on the manufacturer’s standard protocols with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre).

treatment_protocol: Orofacial inflammation was induced by unilateral s.c. injection of 50 µl complete Freund's adjuvant (CFA; Sigma-Aldrich, Saint Louis, USA; killed mycobacteria suspended in paraffin oil; 1 mg/ml) into the whisker pad of male rats, while under ketamine (72 mg/kg) and xylazine (8 mg/kg) anaesthesia.

value: Trigeminal ganglia tissue

tag: rat no.

tag: side

value: CFA-treated

tag: treatment

value: 7 days after CFA injection

tag: gender


title: T8


title: MLX population 2, female, rep 1

description: MLX population 2 females


title: Control population 3, male, rep 1

description: Control population 3 males


title: T6


title: T2


title: T3


title: MLX population 1, female, rep 2

description: MLX population 1 females


title: Control population 2, male, rep 1

description: Control population 2 males


title: T5


title: C5


title: Control population 1, male, rep 2

description: Control population 1 males


title: Control population 3, female, rep 2

description: Control population 3 females


title: C3


title: Control population 1, male, rep 1

description: Control population 1 males


title: Control population 2, female, rep 1

description: Control population 2 females


title: Rhizophore1

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description:
A rhizophore was defined as a 4-7 day-old ventral angle meristem outgrowth 2.5-3.5cm in length that lacked all of the following features: a root cap, root hairs, green pigmentation, and mature or presumptive microphylls.
processed data file: Table_S2.xlsx
processed data file: Table_S3.xlsx

data_processing:
Reads were aligned to the Selaginella moellendorffii v1.0 genome (including the full genome, i.e. both haplotypes) using bowtie2 (bowtie2 --local).
Gene models were obtained from Phytozome and 2,719 new ORFs were included from a list of 4,763 additional gene models from a recent transcriptomic characterization in Selagenella (Zhu et al., 2017), which were filtered for duplicates and gene fragments.
Gene read counts were obtained using ngsutils (bamutil count -library unstranded -multiple partial).
EdgeR was used to normalize the libraries using the trimmed mean method.
Genome_build: Selaginella moellendorffii v1.0
Supplementary_files_format_and_content: Table_S2.xlsx: Excel spreadsheet of raw counts.
Supplementary_files_format_and_content: Table_S2.xlsx: Excel spreadsheet of normalized counts.

organism: Selaginella moellendorffii

growth_protocol: Y-shaped cuttings of mature stems that included existing points of angle meristem outgrowths were applied to soil for general propagation. Explants were kept in high humidity (80%) and in a 16h ambient light/8h dark cycle.

extract_protocol:
For each sample, 40 excised tissues were pooled in 20µL of RLT Buffer (Qiagen RNeasy Micro Kit), flash frozen, and ground using methods described previously (Sena et al., 2009). RNA yields and quality were assessed by a Bioanalyzer 2100 (RNA Picochip).
Illumina libraries for two biological repeats of each tissue were generated using the Nugen Ovation Amp V2 DR kit, with modifications made for multiplexing.
Pooled libraries were sequenced using Illumina HiSeq 2500 to generate 50bp single-end reads.

treatment_protocol: No treatment. For growth characterizations, a root was defined as a 10-20 day-old ventral angle meristem outgrowth that was 5-10cm in length, as measured from the distal-most tip to the main shoot axis, and displayed a well-developed root cap and root hairs. A rhizophore was defined as a 4-7 day-old ventral angle meristem outgrowth 2.5-3.5cm in length that lacked all of the following features: a root cap, root hairs, green pigmentation, and mature or presumptive microphylls.

value: Rhizophore


title: Root2

description:
A root was defined as a 10-20 day-old ventral angle meristem outgrowth that was 5-10cm in length, as measured from the distal-most tip to the main shoot axis, and displayed a well-developed root cap and root hairs.
processed data file: Table_S2.xlsx
processed data file: Table_S3.xlsx

value: Root


title: Rhizophore2


title: Root1


title: Leaf2

description:
Leaf tissue was harvested from whole, 10-14 day-old microphylls.
processed data file: Table_S2.xlsx
processed data file: Table_S3.xlsx

value: Leaf


title: Leaf1


title: TPC-1 cells treated with si-Control, rep3

city: Columbus

first: Yanqiang

last: Wang

state: Ohio

address: 12th w street

institute: The Ohio State University

description: Gene expression data from TPC-1 cells treated with si-Control for 24h

hyb_protocol: Samples were hybridized using Herring sperm DNA, Acetylated BSA (50mg/mL), Eukaryotic Hybridization Controls (Affymetrix) •Heat 65°C  for 5 minutes, 99°C  for 5 minutes, 45°C  for 5 minutes centrifuge top speed for 5 minutes •Hybridize 16 hours at 45°C  at 60rpm• Fluidics washing is FS450_0001

scan_protocol: The arrays were  scanned with the Affymetrix Genen Chip Scannner 3000 7G system using Affymetrix GeneChip Command Console (AGCC) software.

data_processing: Signal intensities were processed by RMA method using Affymetrix Expression Console software

source_name: TPC-1 cells treated with control siRNA for 24h

label_protocol: 5.5 ug of single stranded cDNA were enzymatically fragmented and biotinylated using the WT Terminal Labeling Kit (Affymetrix)

growth_protocol: TPC-1 cells were seeded in 6-well-plate and grown to ~85% confluence at the time of transfection.

extract_protocol: Total RNA was extracted by using Trizol reagent (Thermo Fisher SCIENTIFIC) then treated by DNase-I (Ambion) to eliminate DNA contamination. RNA concentration was determined by using Qubit 2.0 Fluorometer (Agilent Technologies) with an RNA HS Assay Kit. The integrity of the RNA samples was assessed by BioAnalyzer (Agilent).  All RNA integrity numbers (RINs) were greater than 9.0.

treatment_protocol: 25pmol si-SMAD3 or si-Control were transfected into the cells using 4.5ul RNAiMAX lipofectamine (Thermo Fisher SCIENTIFIC). Cells were harvest after 24h treatment.

tag: cell line


title: C6


title: ve-1_1_FeFREE

city: Prague 2

first: Tereza

last: Ormsby

address: Hlavova 2030

country: Czech Republic

institute: Charles University in Prague

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and the public server at usegalaxy.org was used to analyze the data. Specifically, the read quality was checked using FastQC, trimmed the adaptors using Trim Galore, aligned the reads and obtain read count using RNA STAR with intron length set to max 1000 bp. Differential gene expression analysis done by DESeq2 examined pair-wise differences between WT and Δve-1 after 48 hour growth under standard or iron-free conditions. Genes with log2 ≥ 1.0 or ≤ −1.0 changed expression and adjusted P values ≤ 0.05 were used for further analysis.
Genome_build: Neurospora crassa assembly 12 Fixed (files: neurospora_crassa_or74a_12_genome_FIXED.fasta, and neurospora_crassa_or74a_12_transcripts_FIXED.gtf; files are found in GEO submission GSE71024)
Supplementary_files_format_and_content: The .txt files were generated by the program RNA STAR at Galaxy platform. These RNASTAR.txt files report read number counts per gene for each replicate sample (two replicates total) from wild-type and ve-1 under standard or iron-free conditions. The four dataset.xlsx files were produced using the replicate RNASTAR.txt files in the program DESeq2 to determine genes that were differentially expressed > two fold and were significant (p < 0.05). Comparisons of mutant strains (N7373/N7374) versus   WT (N3752/N3753) under standard (Dataset_1) and iron-free (Dataset_2) conditions as well as changes between standard and iron-free conditions in wt (Dataset_3) or ve-1 (Dataset-4) were created.

molecule: polyA RNA

organism: Neurospora crassa

source_name: germinated condia

growth_protocol: Cultures (2.5 x 10E6 conidia) were grown in standard Vogels medium and 1.5% sucrose (standard minimal medium) or in Iron-free Vogles and 1.5% sucrose, shaking for 48 hours at 32C.

extract_protocol:
Mycelia were harvested and added to a tube containing ~300uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 10 minutes at room temperature. Samples were cleared by centrifugation, and the aqueous (top) phase was added to 650uL cold 100% EtOH.  Samples were precipitated at -20C, pelleted by centrifugation, washed twice with 1 ml  70% EtOH, and resuspended in DEPC-treated dH2O.
10 ug RNA was treated with DNAse (DNA-free™ DNA Removal Kit, Thermo Fisher Scientific), cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter), and 4 ug DNAse-free RNA was used for RNA-seq libraries (KAPA Stranded mRNA-seq kit, KAPA Biosystems)

treatment_protocol: Iron-free cultures were grown in media without iron. All glassware including the one used to make the Vogel media was treated with 1 mM EDTA overnight, then with 5% HCl overnight, then rinsed well with Millipore water and baked

tag: growth protocol

value: iron-free condition

value: mycelia


title: ve-1_2_standcond

value: standard condition

tag: tissue


title: wt_2_FeFREE

tag: genotype

value: wt


title: wt_1_FeFREE


title: wt_2_standcond


title: ve-1_2_FeFREE


title: ve-1_1_standcond


title: Shoot1

description:
Shoot tissue was sampled from the distal-most region of young shoots that were 10-20 days post-branch from main shoot axis, green, and had given rise to microphylls.
processed data file: Table_S2.xlsx
processed data file: Table_S3.xlsx

value: Shoot


title: Shoot2


title: wt_1_standcond


title: Control population 2, female, rep 2

description: Control population 2 females


title: Control population 1, female, rep 2

description: Control population 1 females


title: C1


title: C2


title: C12

city: Daejeon

first: Yoonkang

last: Hur

address: 99 Daehak-ro, Yuseong-gu

department: Biological Sciences

country: South Korea

institute: Chungnam National University

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu. The plants grown in the growth chamber at 22℃ for about 3 weeks were exposed to 12 ° C for 2 days

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).

organism: Brassica rapa subsp. pekinensis

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Two Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu and Kenshin, plants seeds were sown in the thirty two-hole tray (6x6x6cm x 32 holes) and grown for approximately 3 weeks in a growth chamber at 22℃ under 16 h light/8 h dark photoperiod with a photon flux density of 140 μmol m-2 s-1. For warming treatment, plants were subjected to 12℃ for 2 days under same photoperiod, and transferred to 28℃ for 3 h. For extreme heat shock treatment, warming-exposed plants were further incubated at 45℃ growth chamber for 3h. Samplings were performed at the end of each treatment

extract_protocol: Total and polysomal RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen).

tag: phenotype

value: normal


title: Control population 1, female, rep 1

description: Control population 1 females


title: TPC-1 cells treated with si-SMAD3, rep3

description: Gene expression data from TPC-1 cells treated with si-SMAD3 for 24h

source_name: TPC-1 cells treated with SMAD3 siRNA for 24h


title: TPC-1 cells treated with si-SMAD3, rep2


title: CBMS1_Day7Diff_ESC_single_MidS_24

status: Public on Dec 13 2018

city: Kobe

first: Ichiro

last: Hiratani

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Developmental Biology

country: Japan

institute: RIKEN

data_processing:
BrdUIP, Population early-S, 100-cells, Single-cell data: sequence reads were trimmed to remove adapter sequences using the cutadapt program before mapping. For WGA samples, we performed a two-step adapter trimming, first removing the Illumina adapter based on the index of each NGS library and then removing the SEQXE adapter. As the SEQXE adapter sequence was not available, we empirically estimated it as the sequence that repeatedly appeared near the 5’ end.
BrdUIP, Population early-S, 100-cells, Single-cell data: trimmed reads were mapped into mm9, hg19, CBMS1-specific (CBA/MsM) diploid genome based on mm9 genome by using bwa (ver: 0.7.10-r789, command: bwa aln => bwa samse). CBMS1-specific diploid genome was constructed as described in Sakata et al. Development (2017) with minor modifications using CBA or MsM strain genomic reads. Duplicated reads mapped into mm9 or hg19 were removed by using picard tool and the reads overlapped with mm9, hg19 black list regions (https://sites.google.com/site/anshulkundaje/projects/blacklists) were filtered out. The mapped reads with MAQP>10 were used for the further analysis. For the diploid genome mapping, we defined MAPQ>16 as the allele specific reads and used the liftover tool (UCSC Genome Browser) to convert to the mm9 genome coordinates. After this, duplicate reads identified as an identical chromosome start position and strand information were filtered out.
BrdUIP data: we counted the reads of early and late S-phase BrdU-IP samples in sliding windows of 200 kb at 40-kb or 80-kb intervals (written in the processed data file as “w200sk40k” or “w200ks80k”, respectively) in non-overlapping 400-kb windows (“400k”) and performed rpm (reads per million) normalization. Then, the ratio of early-S to total read counts [(Early-S reads)/(Early-S reads + Late-S reads)] was calculated for each bin and their distribution converted to fit within a ± 1 scale, and this value was defined as the BrdU-IP RT score of each bin. We filtered out bins whose total read counts were within the bottom 5% of all bins.
Population early-S data: we counted the reads of early-S and G1 in sliding windows of 200 kb at 40-kb intervals, performed rpm normalization in a manner identical to BrdU-IP data processing, and defined Log2[(Early-S reads)/(G1 reads)] as the population early-S RT score.
100-cells data: we counted the reads of 100 mid-S and G1 cells in sliding windows of 200 kb at 40-kb intervals and used the correctMappability command in the R package AneuFinder (http://bioconductor.org/packages/release/bioc/html/AneuFinder.html) for normalizing mid-S data based on G1 data. From the mappability corrected mid-S read counts, the genome-wide median was obtained and used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the 100-cell mid-S RT score.
Single-cell data (hTERT-RPE1): For the analysis of single mid-S cells, we counted the reads in sliding windows of 200 kb at 40-kb intervals, and used the AneuFinder’s correctMappability command sfor normalizing mid-S data based on the merged G1 control. From the mappability corrected mid-S read counts, the genome-wide median was obtained and was used to generate Log2[(Mappability corrected Mid-S reads)/median] scores, which we defined as the single-cell mid-S RT score.
Single-cell data (CBMS1 un-resolved): first, we counted the reads in non-overlapping 80-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the merged G1 control. Binarization was performed using the Mappability corrected 25per-S (25% S-phase) , Mid-S (50% S-phase), 75per-S (75% S-phase) reads described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy"; options for Mid-S, 75per-S: method="HMM", max.iter=3000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy"; 1-somy, unreplicated; 2-somy, replicated]. In the processed data files, replicated bin was shown as 1, unrelicated bin was shown as -1, and no-data was shown as 0. “Repliscore” was calculated as a percentage of replicated bins in the total number of replicated and unreplicated bins.
Single-cell haplotype-resolved data: after the specific filtering steps for haplotype-resolved data, we counted the reads in non-overlapping 400-kb windows, and used the AneuFinder’s correctMappability command for normalizing mid-S data (Mappability corrected Mid-S reads) based on the filtered merged G1 control. Binarization was performed as described above by using the findCNVs command in AneuFinder [2-HMM; options for 25per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="1-somy" ; options for Mid-S, 75per-S: method="HMM", max.iter=5000, states=c("zero-inflation", "0-somy", "1-somy", "2-somy"), eps=0.01, most.frequent.state="2-somy" ].
Binarized unresolved data: Sample_Name_80k_100S_MAP_2HMM2_eps0.01.binary.bedGraph, Binarized CBA data: Sample_name_cba_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph, Binarized MsM data: Sample_name_msm_400k_100S_MAP_HMM2_eps0.01.binary.bedGraph
For paired-end reads, only "R1" (Fwd) reads were used for the analysis.
RNA-seq: allele-specific RNA-seq analysis was performed using CBA/MsM diploid genome as described in Sakata et al. Development 2017. We defined genes with allelic expression imbalance as those with the percentage of either MsM- or CBA-specific reads above 60% (or >70%) among genes that show ≥10 total reads (i.e. CBA+MsM read numbers combined) and >0.1 FPKM (fragments per kilobase of exon per million fragments mapped, in a non-allelic manner) in three biological replicates (CBMS1_allele_specific_genetable.txt).
Genome_build: hg19 / mm9 / CBMS1 diploid genome
Supplementary_files_format_and_content: bedGraph, bigWig

source_name: Day7 Differentiated CBMS1 ESC

growth_protocol: hTERT-RPE1 cells were grown in MEM-alpha supplemented with 10% FBS and penicillin/streptomycin. CBMS1 mESCs have been described (Murakami et al. Development, 2011) and were grown in 2i/LIF medium as described (Hayashi K et al., Nat. Protoc., 2013).

extract_protocol:
For BrdU-IP samples, we followed our routine protocol as described (Ryba et al., Nat. Protoc. 2011). A Sony SH800 cell sorter was used in the ultra-purity mode, fractionating early and late S-phase populations. The BrdU-IP protocol has been described in detail (Ryba et al., Nat. Protoc. 2011), except that we used a Bioruptor UCD-250 (Sonic Bio) for gDNA sonication in high output mode, with ON/OFF pulse times of 30 sec/30 sec for 6 minutes. After BrdU-IP, immunoprecipitated DNA samples were subject to WGA with a SeqPlex kit (Sigma, SEQXE).   For early S-phase population samples, 200,000 cells from the first half of S-phase were sorted by Sony SH800 cell sorter, and gDNA was isolated using a Qiagen kit (Qiagen #69504, DNeasy Blood & Tissue Kit) and fragmented to 200–300 bp with a Covaris ultrasonciator (model: S220, tube: microTUBE snap-cap) according to the manufacturer’s instructions (peak incident power: 175, duty factor: 10%, cycles per burst: 200, treatment time: 120), followed by cleanup and size selection via Agencourt AMPure XP SPRI beads (Beckman Coulter).  For single or 100 cells samples, cells were sorted with a Sony SH800 cell sorter using the single-cell mode. Sample preparations were based on the previous study (Baslan et al., Genome Res. 2015). Extracted gDNA samples were subjected to WGA with a SeqPlex kit (Sigma, SEQXE). Amplified gDNA was purified and size-selected with Agencourt AMPure XP SPRI beads and the SEQXE adapter sequence was removed by the primer removal enzyme Eco57I (Sigma, SEQXE). The DNA fragment size peak should be within 150–200 bp, which was confirmed by a capillary electrophoresis system, MultiNA (Shimadzu).  For RNA-seq samples, cells were lysed in TRI Reagent (Molecular Research Center, Inc. cat. TR 118) to extract total RNA.
NGS libraries were constructed with a NGS LTP Library Preparation Kit (KAPA, KK8232) according to the manufacturer’s instructions, with slight modifications based on the previous study (Kadota et al., Sci. Rep. 2017). For a multi-plex NGS run, a SeqCap adapter kit A/B (Roche, 07141530001/ 07141548001) and NEXTflex DNA barcode (Bio Scientific, NOVA) were used. The samples were subjected to NGS on an Illumina Hiseq 1500 system (80, 84, 127-bp length, single-read or paired-end read). For NGS on Ion Proton system, libraries were constructed using Ion Plus Core Module for AB Library Builder System (Thermo Fisher Scientific, #4477683) with Ion Xpress Barcode Adapters 1-16 Kit (Thermo Fisher Scientific, #4477683).  For RNA-seq, NGS library preparation was performed using 500ng of total RNA following the standard protocol of TruSeq Stranded mRNA Sample Prep Kit (Illumina).

treatment_protocol: For differentiation, CBMS1 mESCs were differentiated to EpiLCs for 2 days and then switched to aggregation culture (EB/embryoid body culture) in Nunclon Sphera 96U-well plates (ThermoFisher, #174925), starting from 2,000 EpiLCs per well exactly as described (Hayashi K et al. Nat. Protoc., 2013), except for the use of plain GK15 medium (Hayashi K et al. Nat. Protoc., 2013) without any additional factors added during the aggregation culture. This process is practically identical to the SFEBq neural method of mESC differentiation (serum-free floating culture of EB-like aggregates with quick reaggregation) (Eiraku et al. Nat. Protoc., 2012) except that we started from EpiLCs instead of mESCs. In our hands, this resulted in efficient formation of neurectoderm cells based on gene expression after 7 days of differentiation (2 days to EpiLCs and then 5 additional days of EB culture).

tag: strain

value: CBA/MsM

tag: cell type

value: day7 differentiated ESCs

tag: sample state

value: Single cell

tag: xx or xo chromosomes in single cell samples

value: XX

tag: xa allele (based on rt, only for cbms1 single-cell mids xx samples)

value: MsM

tag: xi allele (based on rt, only for cbms1 single-cell mids xx samples)

value: CBA

tag: repliscore of 40–70%

value: TRUE

tag: cell cycle phase

value: MidS


title: CBMS1_Day7Diff_ESC_single_MidS_33


title: CBMS1_Day7Diff_ESC_single_MidS_31


title: CBMS1_Day7Diff_ESC_single_MidS_19


title: CBMS1_Day7Diff_ESC_single_MidS_20


title: CBMS1_Day7Diff_ESC_single_MidS_39


title: CBMS1_Day7Diff_ESC_single_MidS_41


title: C28

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu.The plants grown in the growth chamber at 22℃ for about 3 weeks were exposed to 12 ° C for 2 days and then treated at 28℃ for 3 hours


title: CBMS1_Day7Diff_ESC_single_MidS_25


title: K12

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin. The plants grown in the growth chamber at 22 ℃ for about 3 weeks were exposed to 12 ° C for 2 days


title: CBMS1_Day7Diff_ESC_single_MidS_42


title: K28

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin.The plants grown in the growth chamber at 22℃ for about 3 weeks were exposed to 12 ° C for 2 days and then treated at 28℃ for 3 hours


title: CBMS1_Day7Diff_ESC_single_MidS_30


title: Chiffu

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu. grown for approximately 3 weeks in a growth chamber at 22℃

value: Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Chiifu.  grown for approximately 3 weeks in a growth chamber at 22C


title: Kenshim

description:
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin
Chinese cabbage (Brassica rapa ssp. pekinensis) inbred lines, Kenshin.grown for approximately 3 weeks in a growth chamber at 22℃


title: CBMS1_Day7Diff_ESC_single_MidS_15


title: TPC-1 cells treated with si-Control, rep1


title: TPC-1 cells treated with si-Control, rep2


title: TPC-1 cells treated with si-SMAD3, rep1


title: CBMS1_Day7Diff_ESC_single_MidS_10


title: Reh_PMA_rep2

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

data_processing:
Alignment: tophat2 (2.0.11), using tophat -G hg19_refFlat.gtf --library-type fr-firststrand hg19 <R1.fq> <R2.fq>
FPKM quantification: cuffnorm (2.2.1) using cuffnorm --library-type fr-firststrand -o <outdir> -L <labels> hg19_refFlat.gtf <bam1_rep1><bam1_rep2> […] <bamx_rep1><bamx_rep2>
Coverage track generation: bedtools genomecov (2.19), using bedtools genomecov -ibam <bam> -g hg19.chrom.sizes -bg -split -trackline -trackopts ‘name=<name> description=<description>’
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format representing read depth coverage, tsv format representing normalised FPKM values

source_name: Pro-B lymphoblastic leukemia cell line

growth_protocol: KM-H2, L1236 and L428 were cultured in IMDM, Namalwa and Reh cells in RPMI, both supplemented with 10% FCS, 2mM Glutamine, plus P/S. All cultures were incubated at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
RNA was isolated using a Nucleospin RNA extraction column with on-column DNase treatment (Machery Nagel, France).
RNA Sequencing libraries were produced in duplicate using the TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Human/Mouse/Rat (Illumina).

treatment_protocol: PMA treatment was at 2 ng/ml media at a cell density of 1x106 / ml.

tag: lymphoma type

value: Non-Hodgkin's lymphoma cell line

value: PMA


title: Reh_PMA_rep1


title: CBMS1_Day7Diff_ESC_single_MidS_28


title: L428_rep2

source_name: Hodgkin's lymphoma cell line

value: Hodgkin's lymphoma cell line


title: CBMS1_Day7Diff_ESC_single_G1_03

description: control


title: CBMS1_Day7Diff_ESC_single_MidS_05


title: CBMS1_Day7Diff_ESC_single_G1_02

description: control


title: CBMS1_Day7Diff_ESC_single_MidS_22


title: CBMS1_Day7Diff_ESC_single_G1_01

description: control


title: KM-H2_rep2


title: Reh_IKK_Dox_rep3 (RACE)

description: cDNA from THE1B 5’ RACE

data_processing:
Trimming: cutadapt (1.4). RACE adapter and generic THE1B primer trimming was performed using zcat <fq.gz> | cutadapt -g TCATACACATACGATTTAGGTGACACTATAGAGCGGCCGCCTGCAGGAAA - | cutadapt -g CATGGCTGGGAGGCCTC -
Alignment: bowtie2 (2.1.0). Alignment was performed in paired-end mode using bowtie2 -x hg19 -1 <fq1> -2 <fq2> --very-sensitive-local
Read filtering on uniquely aligned reads: samtools (1.1). samtools view -hbq 2 <in.bam> -o <out.bam>
Peak detection and coverage track generation: MACS (1.4.1). macs14 -t <bam> -n <name> -g hs –keep-dup=all -w -S
Genome_build: hg19
Supplementary_files_format_and_content: Variable step 10bp bin wig format representing depth coverage

extract_protocol:
RACE was performed using the specific primer CATGGCTGGGGAGGCCTCA to amplify cDNA products containing a conserved region of the THE1B LTR and the transcription start site. RACE was carried out based on the ExactSTART™ Eukaryotic mRNA 5’-& 3’-RACE Kit (Epicentre) using the supplied protocol. However, due to the discontinuation of supply of the Tobacco Acid Pyrophosphatase enzyme, a number of modifications were made. To perform 5’ RACE RNA was treated with Alkaline Phosphatase for 15 minutes at 37°C (10 µl Apex Buffer, 5 µl Apex Heat-liable Alkaline Phosphatase (Epicentre), 1 µg RNA, made up to 100 µl with H2O). An Ampure RNA-clean bead purification was then carried out prior to treatment with RNA 5’ Pyrophosphohydrolase (RppH) for 1 hour at 37 °C (Purified RNA (40 µl), 10 x Thermopol Buffer (NEB)(5 µl), RppH Enzyme (NEB)(5 µl)). The RppH reaction was stopped by addition of 1 µl of 500 mM EDTA solution and then purified with a further Ampure RNA-clean bead purification and eluted in 16 µl H20. The 5’ RACE acceptor oligonucleotide was ligated at 37 °C for 30 minutes after addition of 4 µl H2O, 2 µl RNA ligase buffer, 1 µl 5’ acceptor oligonucleotide, 1 µl 2mM ATP solution and 1 µl T4 RNA ligase (NEB). First strand cDNA synthesis was carried out by addition of 14 µl H2O, 1 µl cDNA synthesis primer, 2 µl dNTP PreMix, 2 µl MMLV RT Buffer and 1 µl MMLV RT, the reaction was incubated at 37°C for 1 hour followed by 85°C for 10 minutes. The reaction then had 1 µl of RNase added and was incubated at 55°C for 5 minutes. The second strand cDNA synthesis reaction components were added at 55°C. The consensus biotinylated THE1B LTR primer CATGGCTGGGGAGGCCTCA (20 µM, 2 µl ) was used along with a primer complementary to the previously ligated 5’ RACE adaptor (5 µl ), 21 µl  H2O, 30 µl PCR mix and 1 µl (2.5 U) PfuUltra II polymerase and incubated for 21 cycles (95°C 30 seconds, 21 x 95°C 20 seconds, 60 °C 20 seconds, 72°C 3 minutes). Following second strand synthesis the fragments incorporating a biotinylated primer were selected using T1 Dynabeads (Thermo Fisher Scientific) as follows. T1 dynabeads (20 µl) were washed in B&W buffer (10 mM Tris-HCL, 1 mM EDTA, 2 M NaCl) using magnetic separation and re-suspended in 50 µl of 2 x buffer B&W buffer. An equal volume of RACE product was added and samples were mixed on a slow rotating wheel at room temperature for 1 hour. The beads were then captured using a magnetic separator washed with B&W buffer and TE andwere re-suspended in 33.75 µl 1 x TE. The selected DNA was amplified off the beads by a 3 cycle PCR (95°C 2 minutes, 3 x 95°C 20 seconds, 56 °C 20 seconds, 72°C 30 seconds and 72°C 3 minutes) using a non-biotinylated THE1B LTR primer (1.25 µl, 20µM), the 5’ RACE adaptor primer (4 µl), 5 µl dNTPs (10mM), 5 µl PFU Ultra Buffer and 1 µl PFU Ultra polymerase. Finally purification was carried out using the Qiagen MiniElute PCR Cleanup Kit and the final product was eluted in 11 µl elution buffer.
Libraries for genome wide RACE-Seq were produced using the MicroPlex Library Preparation Kit v2 (Diagenode). Purified RACE material (10 µl) was added to 2 µl of template preparation buffer and 1 µl of Template Preparation Enzyme and incubated at 22°C for 25 minutes followed by 55°C for 20 minutes. The prepared template was then mixed with 1 µl Library synthesis buffer according to the manufacturer’s instructions and 1 µl Library synthesis enzyme and incubated at 22°C for 40 minutes. The libraries were then mixed with amplification buffer (25 µl), amplification enzyme (1 µl), H2O (4 µl) and a Barcoded Indexing Reagent (5 µl) to allow for the samples to be multiplexed for sequencing. The mix was split into 2 reactions of 25 µl which were amplified at 12 and 14 cycles to allow for selection of enough material to sequence without introducing clonal amplification (Extension and Cleavage: 72°C 3 minutes, 85°C 2 minutes, Denaturation: 98°C 2 minutes, Addition of Indexed oligonucleotides: 4 x 98°C 20 seconds, 67°C 20 seconds, 72°C 40 seconds, Library Amplification: 12 or 14 x 98°C 20 seconds, 72°C 50 seconds). Finally size selection and purification of the libraries was carried out by running products on a 1.2% TAE agarose gel (with 0.05% ethidium bromide) and excising fragments between 190 and 300 bp. These were then extracted using the Qiagen mini-elute gel extraction kit and eluted twice in 12 µl H2O. The libraries were run on a Bioanalyzer 2100 with a High Sensitivity DNA Assay chip (Agilent) to determine the average fragment size and quantified by PCR using the Kappa Illumina Library Quantification Kit on an Applied Biosystems StepOne Plus RT PCR system. The indexed libraries were pooled and sequenced on Illumina MiSeq using the 150-Cycle paired end kit or a NextSeq 500 as a fraction of a 150 cycle flow cell.
RACE-Seq

treatment_protocol: PMA treatment was at 2 ng/ml media at a cell density of 1x106 / ml. Induction with doxycycline (2 μg/ml) was performed for 48 hours followed by sorted by fluorescence-activated cell sorting for GFP labeling.

value: Tet-on IKK transfection + doxycycline

tag: specific primer

value: CATGGCTGGGGAGGCCTCA

tag: 5' race primer+adapter


title: Reh_PMA_rep2 (RACE)

description: cDNA from THE1B 5’ RACE

tag: treatment


title: CBMS1_Day7Diff_ESC_100cells_MidS_02_rep3


title: Reh_IKK_Dox_rep2 (RACE)

description: cDNA from THE1B 5’ RACE


title: CBMS1_Day7Diff_ESC_100cells_MidS_02_rep2


title: CBMS1_Day7Diff_ESC_100cells_G1_02_rep1

description: control


title: L1236_rep2


title: CBMS1_Day7Diff_ESC_100cells_MidS_01_rep3


title: CBMS1_Day7Diff_ESC_100cells_G1_01_rep1

description: control


title: CBMS1_Day7Diff_ESC_Population_G1_rep1

description:
Without whole genome amplifications
control

value: Population


title: CBMS1_Day7Diff_ESC_100cells_MidS_01_rep1


title: Reh_IKK_noDox_rep2 (RACE)

description: cDNA from THE1B 5’ RACE

value: Tet-on IKK transfection - doxycycline


title: CBMS1_Day7Diff_ESC_100cells_MidS_01_rep2


title: Reh_GFP_Dox_rep3 (RACE)

description: cDNA from THE1B 5’ RACE

value: Tet-on GFP transfection + doxycycline


title: Reh_IKK_noDox_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: Reh_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: Reh_PMA_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: Reh_GFP_Dox_rep2 (RACE)

description: cDNA from THE1B 5’ RACE


title: Reh_GFP_Dox_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: CBMS1_Day7Diff_ESC_Pupulation_EarlyS_rep1

description: Without whole genome amplifications

value: CBA/MsM

value: EarlyS


title: CBMS1_Day7Diff_ESC_BrdUIP_EarlyS_rep2

description:
P263_27_28_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph
P263_27_28_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph
P263_27_28_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph

value: day7 differentiated ESCs

value: BrdUIP


title: CBMS1_Day7Diff_ESC_BrdUIP_LateS_rep2

value: LateS


title: CBMS1_Day7Diff_ESC_100cells_MidS_02_rep1


title: CBMS1_Day7Diff_ESC_BrdUIP_LateS_rep1

description:
P259_23_24_rpm_w200ks80k_BrdUIP_Percent_q0.05.bedGraph
P259_23_24_rpm_cba_400k_BrdUIP_Percent_q0.05.bedGraph
P259_23_24_rpm_msm_400k_BrdUIP_Percent_q0.05.bedGraph


title: L428_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: L428_rep2 (RACE)

description: cDNA from THE1B 5’ RACE


title: Namalwa_rep3 (RACE)

description: cDNA from THE1B 5’ RACE

source_name: Burkitt’s lymphoma cell line


title: Reh_IKK_Dox_rep1 (RACE)

description: cDNA from THE1B 5’ RACE


title: Reh_IKK_noDox_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: L1236_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: KM-H2_rep3 (RACE)

description: cDNA from THE1B 5’ RACE


title: KM-H2_rep2 (RACE)

description: cDNA from THE1B 5’ RACE


title: CBMS1_ESC_single_MidS_31

source_name: CBMS1 ESC

value: embryonic stem cell

value: Single cell

value: XX


title: LCM5_TU

data_processing:
Alignment: hisat2 (2.1.0), using hisat2-align-s hg19 -1 <R1.fq> -2 <R2.fq>
Read count: featureCounts (1.5.0) using featureCounts --countSplitAlignmentsOnly -s 0 -p -a hg19_refFlat.gtf -o <outdir> <bam1> […] <bamx>
FPKM quantification: DESeq2 (1.10.1)
Coverage track generation: bedtools genomecov (2.19), using bedtools genomecov -ibam <bam> -g hg19.chrom.sizes -bg -split -trackline -trackopts ‘name=<name> description=<description>’
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph format representing read depth coverage, tsv format representing normalised FPKM values

source_name: Laser capture microdissected HL tissue

growth_protocol: Frozen tumor tissue was fixed for 10 minutes with 100% ethanol and air dried. Following fixation 200-400 HRS and bystander cells were excised using a Zeiss PALM LCM system and catapulted onto adhesive caps (415190-9191-000 - Zeiss).

extract_protocol:
Cell lysis, RNA extraction and purification were performed using the Absolutely RNA Nanoprep Kit (400753  Agilent).
RNA-Seq libraries were produced using the SMARTer Stranded Total RNA-Seq Kit v2  Pico input Mammalian (Takara Bio).

tag: tissue type

value: Tumour cells


title: CBMS1_ESC_single_MidS_33

value: TRUE

value: MidS


title: LCM4_TU


title: CBMS1_ESC_single_MidS_32


title: LCM5_NTC

value: Non tumour cells


title: LCM4_NTC


title: CBMS1_ESC_single_MidS_28


title: CBMS1_ESC_single_MidS_29


title: LCM3_TU


title: CBMS1_ESC_single_MidS_30


title: CBMS1_ESC_single_MidS_27


title: CBMS1_ESC_single_MidS_26


title: CBMS1_Day7Diff_ESC_BrdUIP_EarlyS_rep1


title: LCM3_NTC


title: CBMS1_ESC_single_MidS_34


title: L1236_rep2 (RACE)

description: cDNA from THE1B 5’ RACE

value: Hodgkin's lymphoma cell line


title: CBMS1_ESC_single_MidS_24


title: CBMS1_ESC_single_MidS_21


title: LCM2_NTC