title: poly IC Activated, MXD1 KO1, Biological Rep 3

city: St. Louis

first: David

middle: Alexander

last: Anderson III

state: Missouri

address: 660. S Euclid Ave., Campus Box 8118

department: Pathology and Immunology

institute: Washington University School of Medicine

description: Gene expression data from poly IC activated mice

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc). Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

source_name: FACS purified splenic cDC1

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: Spleens were minced and digested with stirring for 30 min at 37ºC in 5ml of IMDM plus 10% FBS with 30U/ml DNaseI (Sigma-Aldrich) and 250ug/ml collagenase B (Roche). For removal of debris, cells were passed through a 70-µm filter before red blood cells were lysed with ammonium chloride–potassium bicarbonate lysis buffer. For experiments with poly IC activation mice were injected intraperitoneally with PBS or PBS containing 100 micrograms of poly IC. For experiments with MYCL defieicnt mice, poly IC treatment lasted 5 hours prior to euthanization. For experiments with MXD1 defieicnt mice, poly IC treatment lasted 18 hours prior to euthanization.

tag: tissue

value: spleen

tag: genotype


title: high primed 5

status: Public on Dec 05 2019

type: SRA

city: Jena

first: Marco

last: Groth

address: Beutenbergstraße 11

department: Core Facility - Next Generation Sequencing

country: Germany

institute: Leibniz Institute on Aging - FLI

description: BV2_RNA5_100 ng/mL

library_source: transcriptomic

data_processing:
Reads were extracted in FastQ format using Illumina’s bcl2fastq v1.8.4
The reads were mapped to the mouse reference genome (GRCm38) with the Ensembl gene annotation (release 85) with TopHat2 v2.1.0 (parameters: -x 1 --no-coverage-search –no-novel-juncs --no-novel-indels -T)
All reads mapped to an Ensembl gene were counted using FeatureCounts v1.5.0.
Genome_build: GRCm38
Supplementary_files_format_and_content: xls file containing reads counts, RPMs and RPKMs per gene over all samples

molecule: total RNA

organism: Mus musculus

extract_protocol:
Total RNA was extracted from microglial cells using QIAzol Lysis Reagent (#79306) purchased from Qiagen (Hilden, Germany). RNA concentration and quality were checked by using the Nanodrop ND-1000 machine (Peqlab, Erlangen, Germany).
Preparation of libraries was done using Illumina‘s TruSeq stranded mRNA Kit according the manufacturer‘s description

tag: cell type

value: immortalized murine microglial cell line

tag: cell line

tag: treatment agent

value: LPS

tag: no. of treatments

value: twice

tag: concentration treatment one

value: 1 fg/mL

tag: concentration treatment two

value: 100 ng/mL


title: Pax28 dKO_005

type: RNA

city: Ann Arbor

first: Greg

last: Dressler

state: MI

address: 109 Zina Pitcher Drive

department: Pathology

country: USA

institute: University of Michigan

hyb_protocol: Following labeling procedure, 2.76 ug of cDNA were hybridized at 48C on Mouse Gene 2.1 ST Arrays, and were washed and stained using the Affymetrix Gene Atlas system (software version 2.0.0.460).

scan_protocol: Peg Arrays were scanned using the Affymetrix Gene Atlas system (software version 2.0.0.460).

data_processing: The Oligo and Limma packages of bioconductor were used in R version 3.4.0 to fit log2 RMA expression values and perform linear models.

label: biotin

source_name: Pax28 dKO_adult kidney

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

growth_protocol: Mice were kept on a 5008 Bredeers chow from 3-12 weeks of age.

extract_protocol: 2 weeks post injection, mice were euthanized and kidney tissue isolated. RNA was purified by Trizol Extraction according to manufacturer (In Vitrogen, Inc.)

treatment_protocol: At 8 weeks of age, mice were injected 3 X with Tamoxifen on consecutive days. Tamoxifin was 50mg/kg in corn oil injected I.P.  Protocol was repeated at 10 weeks.

tag: genotype/variation

value: Pax28 dKO

tag: Sex

value: female

value: kidney


title: poly IC Activated, MXD1 KO1, Biological Rep 1


title: Primary Breast Tumor:Ctrl_34

type: genomic

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

hyb_protocol: Restored DNA was arrayed using the Illumina Infinium HumanMethylation450K BeadChip Kit (WG-314-1003) in the JHU DNA Microarray Core.

scan_protocol: Arrays were imaged using Illumina iScan with Illumina scanner settings for Infinium chip

data_processing: Raw array file data were imported into Illumina GenomeStudio v2011.1 Illumina, San Diego, CA) without normalization. Probe hybridization and quality control were assessed within GenomeStudio, as was the level of CpG locus methylation, calculated as a β-value, low to high ranging from 0 to 1, respectively. Distributions of methylation levels were visualized using histograms. Data were then imported into the Partek Genomics Suite (Partek, Inc, St. Louis, MO) and analyzed using standard Partek functions as well as GraphPad Prism 5.0 (GraphPad Software, La Jolla, CA) tools.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Primary Breast Tumor

label_protocol: The EZ DNA Methylation kit (D5001; ZymoResearch) was used for bisulfite conversion. Bisulfite treated genomic DNA was restored (375 ng in 10 µl; Infinium HD FFPE DNA Restore Kit; WG-321-1002, Illumina, Inc.).

extract_protocol: FFPE tumor tissue sections were deparaffinized with xylene, digested for 24 hours at 56o C with 10 mM Tris pH 8, 150 mM NaCl, 2 mM EDTA, 0.5% SDS containing 4 mg proteinase K, and heated to 90o C. for 10 min.

value: Hopkins

value: Chemo

tag: treatment

value: RC

tag: age

tag: relapse

tag: dfsmo

tag: er

tag: grade

tag: ajcc

value: IA


title: high primed 4

description: BV2_RNA4_100 ng/mL


title: Control_006

source_name: Control_adult kidney

value: Control

tag: tissue


title: Primary Breast Tumor:Ctrl_33

value: IIB


title: Primary Breast Tumor:Ctrl_35

value: C

value: IIA


title: Control_004

value: male


title: poly IC Activated, MXD1 KO1, Biological Rep 2

value: spleen

tag: genotype


title: unprimed 6

tag: cell type

value: immortalized murine microglial cell line

value: LPS

value: once

value: no first treatment


title: Pax28 dKO_003

value: Pax28 dKO


title: Primary Breast Tumor:Ctrl_31


title: Primary Breast Tumor:Ctrl_32


title: U1AMO_62.5pmol

city: Philadelphia

first: Gideon

last: Dreyfuss

state: PA

address: 415 curie blvd

institute: University of Pennsylvania

description: nascent polyA mRNA

data_processing:
Illumina Casava1.9 software used for basecalling.
Reads were trimmed of adapter sequences using TrimGalore, and thenwere aligned to the reference genome (UCSC, hg38) using STAR by default parameters.
Reads with multiple alignments were filtered for downstream analysis.
FPKMs for RNA-seq were generated using GFold with default parameters.
3'UTR shortening was calculated using the new LECDS method where 3’UTR signals were compared to that from the last exon’s coding sequence. The significance of this read change was detected using a Fisher’s Exact test followed by Benjamini–Hochberg multiple testing with an adjusted P-value ≤ 0.01
Genome_build: hg38
Supplementary_files_format_and_content: Alignment data for the RNA-seq are given in bigwig format.

molecule: polyA RNA

source_name: Human Carcinoma Cells

growth_protocol: Cells grown in DMEM supplemented with 10% FBS and 1% antibiotics.

extract_protocol:
Total RNA extracted using trizol, total mRNA extracted using Oligotext poly(dT) beads from Qiagen, nascent RNA linked to Biotin and etracted on magnetic streptavidin beads
Libraries were prepared according to instructions accompanying the Ovation RNA-Seq System V2 and the Encore NGS Library System, both from NuGEN.

treatment_protocol: Cells transfected with antisense morpholino to control or U1 or U1 snRNA containing plasmid using Neon system for 8 hours or 24 hours.

tag: cell line

value: HeLa

tag: strain

value: PV


title: poly IC Activated, MXD1 WT1, Biological Rep 1


title: Primary Breast Tumor:Ctrl_36

value: Hopkins

value: DSRC


title: poly IC Activated, LMYC KO3, Biological Rep 5

value: MyclGFP/GFP


title: unprimed 5

tag: treatment agent

tag: no. of treatments

value: 100 ng/mL


title: Control_002

value: Control

value: female

value: kidney


title: poly IC Activated, MXD1 WT1, Biological Rep 2


title: Pax28 dKO_001


title: poly IC Activated, LMYC KO3, Biological Rep 4


title: U1AMO_12.5pmol

description: nascent polyA mRNA


title: Primary Breast Tumor:Ctrl_30

value: Chemo

value: RC

value: IA


title: unprimed 4

value: immortalized murine microglial cell line

tag: concentration treatment one

tag: concentration treatment two


title: cAMO_for_U1AMO

description: nascent polyA mRNA

tag: genotype/variation

value: cAMO


title: Primary Breast Tumor:Ctrl_29

tag: treatment

value: C

value: IIA


title: Primary Breast Tumor:Ctrl_26

tag: age


title: preclinical_MHCIImonocytes rep2

city: New York

first: Dan

last: Littman

state: NY

address: 430 East 29th St Room 403

institute: New York University School of Medicine

data_processing:
Fastq quality checked with fastqc from Subread package
Fastq files were aligned to mouse Ensembl genome GRCm38 with STAR v 2.6.1d.  Quantmode was used to count read pairs.
Normalization and differential expression analysis were conducted using DESeq2
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: microglia_normalizedcounts.txt, normalized counts from deseq2

source_name: ex vivo microglia cells

growth_protocol: not applicable

extract_protocol:
We performed Trizol-based extractions in accordance to the manufacturer's protocol with several modifications. 2ul of linear acrylamide (Cat No AM1354) was added before addition of 100% isopropanol. After the 75% ETOH wash, the samples were resuspended in 87.5ul of water and a mixture of 10ul of buffer RDD and 2.5ul of DNase I from Qiagen. Samples were left at room temp for 15min to allow the DNAse digestion to proceed. The samples were then processed and passed through Qiagen MinElute columns in accordance tro the manufacturer's protocol.
RNA was sent to Hudsonalpha for library prep with their low-input RNAseq protocol
Illumina HiSeq v3

treatment_protocol: not applicable

value: spinal cord

value: ex vivo microglia cells

tag: disease state

value: EAE onset


title: MCF7_siGATA3_aTRPS1

city: Amsterdam

first: Lisette

last: Cornelissen

address: Plesmanlaan 121

country: Netherlands

institute: The Netherlands Cancer Institute

library_source: genomic

data_processing:
Sequences were generated by the Illumina Hiseq 2500 (using 65bp reads) and were processed by the Illumina pipeline.
Reads were aligned to the Mouse Reference Genome (mm9) or Human Reference Genome (hg19) using BWA9. Reads with a BWA alignment quality score less than 20 were removed.
Peaks were called using DFilter (v1.5) and MACS (v1.4) peak caller. Only peaks called by both algorithms were used for further analysis.
Genome_build: mm9 (MTC), hg19 (MCF7)
Supplementary_files_format_and_content: filtered.intersect.bed files contain peaks called by both peak calling algorithms in bed format

source_name: Breast cancer cell line

extract_protocol:
Chromatin immunoprecipitations were performed as described previously, with adaptations (Schmidt et al., 2009). In short, cells were crosslinked in solution A (pH 7.4, 50mM Hepes, 100mM NaCl, 1mM EDTA, 0.5M EGTA) containing 2mM DSG for 35 minutes, then formaldehyde was added to a final concentration of 1% and incubated for another 10 minutes. After addition of Glycine to a final concentration of 125mM to quench the crosslinking reaction and washing with PBS, cells were collected. The Bioruptor Pico (Diagenode) was used for sonication. For ChIP, antibodies were used to detect TRPS1 (10ug, sc-26974, Santa Cruz; 5ug, AF4838, R&D) and GATA3 (10ug, sc-268, Santa Cruz) with 100 ml Protein A or G magnetic beads (Thermo Scientific).
Immunoprecipitated DNA was processed for library preparation (Part# 0801-0303, KAPA biosystems kit).

tag: cell-type

tag: chip antibody

value: aTRPS1 (sc-26974, Santa Cruz)

tag: sgrna/sirna

value: siGATA3 (pool)


title: poly IC Activated, LMYC KO3, Biological Rep 3

value: spleen

value: MyclGFP/GFP


title: ultra-low primed 4

description: BV2_RNA4_1 fg/mL

value: LPS

value: twice

value: 100 ng/mL


title: MCF7_siNT_aTRPS1

value: siNT


title: preclinical_microglia rep1


title: preclinical_MHCIImonocytes rep1

source_name: ex vivo infiltrating monocytes (MHC II+)


title: Primary Breast Tumor:Ctrl_28

value: Hopkins

value: Chemo

value: RC

tag: relapse

tag: dfsmo

tag: er

tag: grade

tag: ajcc


title: Primary Breast Tumor:Ctrl_27


title: MCF7_sgTRPS1#1_aGATA3

value: aGATA3 (sc-268, Santa Cruz)


title: naive_microglia rep2

tag: tissue

tag: cell type

value: MOCK mice


title: naive_microglia rep1


title: MCF7_sgScr#1_aGATA3

value: sgScr


title: MCF7_aGATA3_repl2


title: poly IC Activated, LMYC KO3, Biological Rep 2

tag: genotype


title: chronic_microglia rep2

value: spinal cord

value: EAE chronic


title: poly IC Activated, LMYC WT3, Biological Rep 5

value: Mycl+/+


title: Primary Breast Tumor:Ctrl_25

value: IIA


title: poly IC Activated, LMYC WT3, Biological Rep 3


title: poly IC Activated, LMYC KO3, Biological Rep 1


title: MCF7_aGATA3_repl1


title: poly IC Activated, MXD1 WT1, Biological Rep 3


title: chronic_microglia rep1

value: ex vivo microglia cells


title: MCF7_aTRPS1_repl2

value: aTRPS1 (AF4838 R&D)


title: chronic_MHCIImonocytes rep2

value: ex vivo infiltrating monocytes (MHC II+)


title: MCF7_aTRPS1_repl1

value: aTRPS1 (AF4838, R&D)


title: poly IC Activated, LMYC WT3, Biological Rep 4

value: spleen


title: chronic_MHCIImonocytes rep1


title: MDA-MB-231 Serum Deprived RNA-seq

city: Birmingham

first: Christos

last: Vaklavas

state: Alabama

address: NP2540M 1720 2nd Ave S

department: Medicine

institute: University of Alabama at Birmingham

data_processing:
Fastq files provided by the Heflin Center for Genomic Sciences were imported using the CLC Bio software (Qiagen Bioinformatics, Denmark); failed reads were removed.
Total RNA: reads that aligned to rRNA (using the following parameters: mismatch cost = 2, insertion/deletion cost = 3, non-strand specific, similarity and length fraction = 0.8, maximum number of hits for a read = 30) were discarded and the unmapped reads were aligned to the human genome and assembled using the GRCh37 build as a reference (parameters used: mismatch cost = 2, insertion/deletion cost =3, non-strand specific, similarity and length fraction = 0.8, maximum number of hits for a read = 10).
Ribosome protected fragments:  The ribosome footprints were trimmed of the 3ʹ linker sequence (ATTGATGGTGCCTACAG) and the 5ʹ end nucleotide. Reads that aligned to the rRNA, mtRNA, tRNA (downloaded from http://gtrnadb.ucsc.edu/), small nuclear RNA (downloaded from ensembl.org), PhiX sequences (mismatch cost = 2, insertion/deletion cost = 3, non-strand specific, similarity and length fraction = 0.8, maximum number of hits for a read = 30) were removed. The unmapped reads were aligned to the human genome and assembled using the GRCh37 build as a reference (parameters used: mismatch cost = 2, insertion/deletion cost =3, non-strand specific, similarity and length fraction = 0.8, maximum number of hits for a read = 10).
Genome_build: Homo_sapiens.GRCh37.75 (hg19)
Supplementary_files_format_and_content:
gene_expression_merged_table: csv file where the *_gene files for each  individual cell line and replicate have been merged.
transcript_expression_merged_table: csv file where the *_transcript.csv files for each  individual cell line and replicate have been merged.
PCA_transcription_protein_encoding_genes: merged csv file containing the unique reads for protein encoding genes from RNA sequencing of all cell lines analyzed and their replicates. File used for principle component analysis using the DESeq2 package in R.
PCA_transcription_all_genes: merged csv file containing the unique reads for all genes from RNA sequencing of all cell lines analyzed and their replicates. File used for principle component analysis using the DESeq2 package in R.
PCA_translation_protein_encoding_genes: merged csv file containing the unique reads for protein encoding genes from sequencing of the ribosome protected fragments of all cell lines analyzed and their replicates. File used for principle component analysis using the DESeq2 package in R.
PCA_translation_all_genes: merged csv file containing the unique reads for all genes from sequencing of the ribosome protected fragments of all cell lines analyzed and their replicates. File used for principle component analysis using the DESeq2 package in R.
translational_efficiency_ratio_transcripts: merged csv file with the translational efficiency (ratio of ribosome protected fragment RPKM: RNA RPKM) ratio of each malignant (T47D, ZR75-1, SUM159PT, MDA-MB-231) or nontransformed (MCF10A) cell line vs. nonmalignant counterpart (human mammary epithelial cells, HMEC). Each value indicates how many fold the translational efficiency of each transcript is up (>1) or down (<1) as compared to HMECs.
MCF10A_transcripts: Excel file of the gene ontology analysis of the transcripts commonly transcribed in MCF10A and HMEC cells and preferentially translated in MCF10A cells by a 3-fold or greater efficiency. Analyses done using the default parameters of the DAVID bioinformatics resource (https://david.ncifcrf.gov/)
T47D_transcripts: Excel file of the gene ontology analysis of the transcripts commonly transcribed in T47D and HMEC cells and preferentially translated in T47D cells by a 3-fold or greater efficiency. Analyses done using the default parameters of the DAVID bioinformatics resource (https://david.ncifcrf.gov/).
ZR75-1_transcripts: Excel file of the gene ontology analysis of the transcripts commonly transcribed in ZR75-1 and HMEC cells and preferentially translated in ZR75-1 cells by a 3-fold or greater efficiency. Analyses done using the default parameters of the DAVID bioinformatics resource (https://david.ncifcrf.gov/).
SUM159PT_transcripts: Excel file of the gene ontology analysis of the transcripts commonly transcribed in SUM159PT and HMEC cells and preferentially translated in SUM159PT cells by a 3-fold or greater efficiency. Analyses done using the default parameters of the DAVID bioinformatics resource (https://david.ncifcrf.gov/).
MDA-MB-231_transcripts: Excel file of the gene ontology analysis of the transcripts commonly transcribed in MDA-MB-231 and HMEC cells and preferentially translated in MDA-MB-231 cells by a 3-fold or greater efficiency. Analyses done using the default parameters of the DAVID bioinformatics resource (https://david.ncifcrf.gov/).
csv files: The csv files contain the RPKM values, unique and total number of gene (suffix _gene in the name of the file) of transcript (suffix _transcript in the name of the file) reads from sequencing the RNA (_RNA_ in the name of the file) or the ribosome protected fragments (_RPF_ in the name of the file) of each cell line (HMEC_, MCF10A_, T47D_, ZR75-1_,  SUM159PT_, MDA-MB-231_ in the prefix of the respective file) under normal growth (_FS_ in the name of the file) or serum deprived conditions for 1 hour (_SD1h_ in the name of the file) or growth with media supplemented with charcoal stripped serum (_CCS1h_ in the name of the file)
dds_HMEC_MDA-MB-231_transcription: csv file of differentially expressed genes at the level of transcription (unique gene reads from RNA sequencing) between MDA-MB-231 triple negative breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_MDA-MB-231_translation: csv file of differentially expressed genes at the level of translation (unique gene reads from sequencing of the ribosome protected fragments) between MDA-MB-231 triple negative breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_SUM159PT_transcription: csv file of differentially expressed genes at the level of transcription (unique gene reads from RNA sequencing) between SUM159PT triple negative breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_SUM159PT_translation: csv file of differentially expressed genes at the level of translation (unique gene reads from sequencing of the ribosome protected fragments) between SUM159PT triple negative breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_T47D_transcription: csv file of differentially expressed genes at the level of transcription (unique gene reads from RNA sequencing) between T47D estrogen receptor positive breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_T47D_translation: csv file of differentially expressed genes at the level of translation (unique gene reads from sequencing of the ribosome protected fragments) between T47D estrogen receptor positive breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_ZR75-1_transcription: csv file of differentially expressed genes at the level of transcription (unique gene reads from RNA sequencing) between ZR75-1 estrogen receptor positive breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.
dds_HMEC_ZR75-1_translation: csv file of differentially expressed genes at the level of translation (unique gene reads from sequencing of the ribosome protected fragments) between ZR75-1  estrogen receptor positive breast cancer and human mammary epithelial cells (HMECs). Table generated using DESeq2 package in R and the rld function.

source_name: Human triple negative breast cancer

growth_protocol:
Human mammary epithelial cells (HMECs): were obtained from Lonza and cultured in the medium recommended by the manufacturer.
MCF10A cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and were propagated using standard techniques in DMEM/F12 media supplemented with 5% horse serum (Invitrogen, cat# 16050-122), recombinant human EGF 20 ng/mL (Peprotech, cat# AF-100-15), hydrocortisone 0.5 mg/mL (Sigma Aldrich, cat# H-0888), cholera toxin 100 ng/mL (Sigma Aldrich, cat# C8052), insulin (ThermoFisher Scientific, cat#12585014), penicillin/streptomycin 1%.
T47D cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and propagated using standard techniques in RPMI-1640 medium containing 10% fetal calf serum (FCS, HyClone, cat# SH30071.03), 10 μg/ml insulin, and 10 mM HEPES.
ZR75-1 cells were obtained from the American Type Culture Collection (ATCC, Manassas, VA, USA) and propagated in RPMI-1640 with 20% FCS and 10 mM HEPES.
SUM159PT cells were obtained from Asterand Bioscience (Detroit, MI, USA) and propagated in Ham’s F-12 media supplemented with 5% FCS, 10 mM HEPES, 5 μg/ml insulin, 1 μg/ml hydrocortisone, and penicillin/streptomycin 1%.

extract_protocol:
Experiments were designed so as cells were ~80% confluent at the time of harvesting and lysis and at least 3 days after plating. Media was changed to fresh media in all flasks 24 hours prior to harvesting and to serum deprived media or media supplemented with charcoal stripped serum (T47D and ZR75-1 cells) 1 hour prior to harvesting as indicated. We used cycloheximide (final concentration 100 µg/mL, incubation for 10 minutes prior to collection) to halt the translating ribosomes. Ribosome profiling was conducted following the protocol from Ingolia, et al (Ingolia, N. T., Brar, G. A., Rouskin, S., McGeachy, A. M. & Weissman, J. S. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc 7, 1534-1550, doi:10.1038/nprot.2012.086 (2012).) with the following modifications: (1) rRNA depletion was performed upfront using the Ribo-zero Gold rRNA removal kit (Illumina, cat# MRZG126) following manufacturer’s instructions and (2) the linker-ligated ribosome protected fragments were retrieved using the RNA Clean and Concentrator Kit (Zymo Research, cat# R1015) following manufacturer’s instructions. Total RNA (after digestion with Turbo DNase, Invitrogen cat# AM2238) and digested ribosome protected RNA was isolated using the Qiagen miRNeasy kit (Qiagen, cat# 217004) following manufacturer’s protocol. Total RNA was rRNA depleted using the Ribo-zero Gold rRNA removal kit (Illumina, cat# MRZG126).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
HMECs: Serum deprived media consisted of MEBM supplemented with amphotericin/gentamicin and hydrocortisone (as provided by the manufacturer) admixed with full serum media in a combination ratio of 9:1. Essentially the serum deprived conditions contained 10% of the full concentration of recombinant human EGF, bovine pituitary extract (BPE), and insulin.  MCF10A: Serum deprived conditions consisted of DMEM/F12 media plus full serum media as described previously in a combination ratio of 9:1. The concentration of cholera toxin was kept at 100 ng/mL because it regulates formation of mammary epithelial acini in vitro which is a feature of differentiation.  T47D: Charcoal stripped serum conditions consisted of RPMI-1640 plus 10% charcoal stripped FCS and 10 mM HEPES (no insulin). Fetal calf serum was charcoal stripped according to the following protocol: fetal calf serum was stirred very slowly on a hot plate at 37ºC with 1% charcoal and 0.1% dextran (Sigma Aldrich, cat#D1662, molecular weight 35,000 – 45,000) for 4 hours and then collected into 50 mL tubes. The tubes were then spun to precipitate the charcoal, the supernatants were collected and sterile filtered. All experiments were conducted with the same aliquot.  Serum deprived conditions (immunofluorescence microscopy studies) consisted of RPMI-1640 plus FCS 0.5% (no insulin).   ZR75-1: Charcoal stripped serum conditions consisted of RPMI-1640 supplemented with 20% charcoal stripped serum and 10 mM HEPES.  SUM159PT: Serum deprived conditions consisted of Ham’s F12 media supplemented with 0.5% FCS and 10 mM HEPES (no insulin and hydrocortisone).   MDA-MB-231: Serum deprived conditions consisted of DMEM high glucose (4.5 gr/L) pyruvate L-glutamate supplemented with FCS 1% and penicillin/streptomycin 1%.
HMECs: Serum deprived media consisted of MEBM supplemented with amphotericin/gentamicin and hydrocortisone (as provided by the manufacturer) admixed with full serum media in a combination ratio of 9:1. Essentially the serum deprived conditions contained 10% of the full concentration of recombinant human EGF, bovine pituitary extract (BPE), and insulin.
MCF10A: Serum deprived conditions consisted of DMEM/F12 media plus full serum media as described previously in a combination ratio of 9:1. The concentration of cholera toxin was kept at 100 ng/mL because it regulates formation of mammary epithelial acini in vitro which is a feature of differentiation.
T47D: Charcoal stripped serum conditions consisted of RPMI-1640 plus 10% charcoal stripped FCS and 10 mM HEPES (no insulin). Fetal calf serum was charcoal stripped according to the following protocol: fetal calf serum was stirred very slowly on a hot plate at 37ºC with 1% charcoal and 0.1% dextran (Sigma Aldrich, cat#D1662, molecular weight 35,000 – 45,000) for 4 hours and then collected into 50 mL tubes. The tubes were then spun to precipitate the charcoal, the supernatants were collected and sterile filtered. All experiments were conducted with the same aliquot.  Serum deprived conditions (immunofluorescence microscopy studies) consisted of RPMI-1640 plus FCS 0.5% (no insulin).
ZR75-1: Charcoal stripped serum conditions consisted of RPMI-1640 supplemented with 20% charcoal stripped serum and 10 mM HEPES.
SUM159PT: Serum deprived conditions consisted of Ham’s F12 media supplemented with 0.5% FCS and 10 mM HEPES (no insulin and hydrocortisone).
MDA-MB-231: Serum deprived conditions consisted of DMEM high glucose (4.5 gr/L) pyruvate L-glutamate supplemented with FCS 1% and penicillin/streptomycin 1%.

tag: cell line/type

tag: tissue source

value: breast

tag: developmental stage

value: adult

tag: tumor stage

value: metastatic


title: poly IC Activated, LMYC WT3, Biological Rep 2


title: acute_microglia rep2

value: EAE peak


title: Primary Breast Tumor:Ctrl_24

value: Hopkins

value: Chemo

tag: treatment

value: C

tag: age


title: acute_microglia rep1

tag: disease state


title: poly IC Activated, LMYC WT3, Biological Rep 1


title: MDA-MB-231 Full Serum RNA-seq


title: acute_MHCIImonocytes rep2


title: MDA-MB-231 Serum Deprived ribosome protected fragments

tag: molecule subtype

value: ribosome protected fragments


title: Steady State, LMYC WT2, Biological Rep 5

description: Gene expression data at steady state in vivo


title: acute_MHCIImonocytes rep1

value: spinal cord


title: Primary Breast Tumor:Ctrl_21

value: IIB


title: Steady State, LMYC WT2, Biological Rep 4

value: Mycl+/+


title: Primary Breast Tumor:Ctrl_20

value: RHC

value: IIA


title: Steady State, LMYC WT2, Biological Rep 1


title: Steady State, LMYC WT2, Biological Rep 3


title: MDA-MB-231 Full Serum ribosome protected fragments


title: SUM159PT Serum Deprived 24 hours RNA-seq

value: primary tumor


title: Cdh1F/F;Trps1F/F day28 repl2

description:
Organoids_log2_norm_counts.txt
Organoids_Cdh1FF Trps1FF_vs_Cdh1FF Trps1wt_day28_diff_expr_analysis.txt

data_processing:
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.) and sequenced on a HiSeq 2500 (using 65bp reads)
Sequencing data was aligned to or GRCm38 using TopHat and number of reads per gene were measured with HTSeq count.
Read counts were corrected for differences in sequencing depth by using DESeqs median-of-ratios and the normalized counts were log2-transformed.
Genome_build: GRCm38
Supplementary_files_format_and_content: Log2_norm_counts files contain expression tables of samples (columns) by transcript (rows) reporting normalized counts. Diff_expr_analysis files contain differential gene expression analysis per transcript (rows)

source_name: Primary mammary organoids

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA universal kit (Qiagen) according to the manufacturer’s instruction with Qiagen’s QIAcube robot. Samples with a RIN>8 were considered for library preparation.
Libraries were generated with the Illumina TruSeq RNA Library Preparation kit (RS-122-2001/2, Illumina Inc.).

tag: cell-type

value: Mammary organoids

tag: genotype/strain

value: AdCre transduction, harvested after 28 days


title: Steady State, LMYC KO2, Biological Rep 5

value: spleen

value: MyclGFP/GFP


title: Primary Breast Tumor:Ctrl_19

value: HC

tag: relapse

tag: dfsmo

value: IA


title: Primary Breast Tumor:Ctrl_17

value: RC

tag: er

tag: grade


title: Primary Breast Tumor:Ctrl_23

value: Hopkins

tag: ajcc


title: Steady State, LMYC KO2, Biological Rep 4

tag: tissue

tag: cell type


title: Primary Breast Tumor:Ctrl_14

value: Chemo

value: DSRC


title: Steady State, LMYC WT2, Biological Rep 2

tag: genotype


title: Cdh1F/F;Trps1F/F day28 repl1


title: SUM159PT Serum Deprived 1 hour RNA-seq

tag: cell line/type

tag: tissue source

value: breast

value: adult


title: Steady State, LMYC KO2, Biological Rep 3


title: Primary Breast Tumor:Ctrl_15

value: C


title: Cdh1+/F;Trps1F/F day28 repl2


title: Cdh1+/F;Trps1F/F day28 repl1


title: Primary Breast Tumor:Ctrl_13


title: SUM159PT Full Serum RNA-seq

tag: developmental stage

tag: tumor stage


title: Primary Breast Tumor:Ctrl_12

tag: treatment

tag: age


title: Steady State, LMYC KO2, Biological Rep 2


title: SUM159PT Serum Deprived 24 hours ribosome protected fragments

tag: molecule subtype

value: ribosome protected fragments


title: Steady State, LMYC KO2, Biological Rep 1


title: Primary Breast Tumor:Ctrl_11


title: Cdh1F/F;Trps1+/+ day28 repl2

tag: cell-type


title: Cdh1F/F;Trps1+/+ day28 repl1

tag: genotype/strain


title: SUM159PT Serum Deprived 1 hour ribosome protected fragments


title: SUM159PT Full Serum 5 hours ribosome protected fragments


title: Steady State, LMYC HET1, Biological Rep 5

value: MyclGFP/+


title: Cdh1F/F;Trps1F/F day14 repl2

description:
Organoids_log2_norm_counts.txt
Organoids_Cdh1FF Trps1FF_vs_Cdh1FF Trps1wt_day14_diff_expr_analysis.txt

value: AdCre transduction, harvested after 14 days


title: Primary Breast Tumor:Ctrl_09

tag: relapse


title: SUM159PT Full Serum ribosome protected fragments

value: primary tumor


title: Steady State, LMYC HET1, Biological Rep 4


title: Primary Breast Tumor:Ctrl_06

value: RHC

tag: dfsmo

value: IIIA


title: Cdh1F/F;Trps1F/F day14 repl1

value: Mammary organoids


title: Primary Breast Tumor:Ctrl_05

tag: er


title: Primary Breast Tumor:Ctrl_04

tag: grade


title: Steady State, LMYC HET1, Biological Rep 3

value: spleen


title: ZR75-1 Charcoal Stripped Serum RNA-seq

source_name: Human ER(+) breast cancer

value: metastatic


title: Primary Breast Tumor:Ctrl_03

tag: ajcc

value: IIA


title: Primary Breast Tumor:Ctrl_01


title: Cdh1+/F;Trps1F/F day14 repl1


title: ZR75-1 Full Serum RNA-seq


title: Cdh1+/F;Trps1F/F day14 repl2


title: Cdh1F/F;Trps1+/+ day14 repl2


title: Primary Breast Tumor:Ctrl_02


title: ZR75-1 Charcoal Stripped Serum ribosome protected fragments


title: Cdh1F/F;Trps1+/+ day14 repl1


title: ZR75-1 Full Serum ribosome protected fragments


title: Obese ASCs [3998998011_R03C01]

city: Tarragona

first: Miriam

last: Ejarque

address: c/Mallafré Guasch 4

country: Spain

institute: Institut d'Investigacions Sanitaries Pere Virgili

description: Final Integration of 6 obese samples

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: DNA methylation data were processed using GenomeStudio software (Illumina) by applying the default settings

data_processing: All computations and statistical analyses were performed using R 3.0.2 and Bioconductor 2.13. Analysis of the beadchip was performed using BiSeq 1.8.0 package (20), which involved the following stages: creation of an object of the Bssraw class (container of the raw data), CpG cluster identification, methylation ratio smoothing in each CpG cluster identified, test and model group effect for each CpG site inside of CpG clusters, test CpG clusters for differential methylation and identification of DMSs. Smoothing criteria was performed using 90% quantiles, and CpG clusters considered for DMS identification were filtered using a false discovery rate <10% and with at least 1 differentially-methylated position. The β value, which represents the percentage of methylation at each CpG site, was calculated from the normalized intensity value. The Δβ or log 2-fold change values at all CpGs sites from the different comparisons (undifferentiated minus differentiated state or lean minus obese condition) were analyzed using an unpaired Student t-test and results with P-values <0.0001 were further investigated.

label: Cy3 and Cy5

source_name: obese

label_protocol: Standard Illumina protocol for Human Methylation450k DNA Analysis bead chip (Cy3, Cy5)

growth_protocol: DMEM media with 10% FBS and 1% ab/am

extract_protocol: NucleoSpin® Tissue Kit (Macherery-Nagal GmbH) gDNA extraction

treatment_protocol: No treatemnt, just ASCs from different origins, patients lean (BMI 20-24-9) vs obese (BMI <30)

tag: group

value: obese

value: Adipose derived stem cells


title: CAC_C9_D100

city: Nanjing

first: TINGTING

last: WANG

address: 22 Hankou Road

country: China

institute: Nanjing University

description: CARD9 knockout mice with C57BL/6 background treated with AOM/DSS for 100days

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Clean Reads mapped to GRCm38  genome using Mapsplice v2.1.8 with  parameters -s 22 -p 15 --ins 6 --del 6 --non-canonical --bam -o
count counting
Genome_build: mm10
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: colon tissues

growth_protocol: colons were separated and colon tissues were acquired

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen).
RNA library using standard Ion proton RNA-Seq Kit v2.0 protocol

treatment_protocol: WT and Card9-/- mice  were injected intraperitoneally with AOM (10 mg/kg) on day 1. After 5 days, 2% DSS (molecular weight, 36-50 kDa) was added to the drinking water for 7 consecutive days. Three cycles of DSS treatment were used, and mice were euthanized on day 100. Colon tissues were collected from mice. mRNA of the colon tissues were isolated with TRIZOL and subject to RNA-seq

tag: strain background

tag: genotype/variation

tag: treated with

value: AOM/DSS for 100days

tag: tissue

value: colon tissues


title: Steady State, LMYC KO1, Biological Rep 2

tag: cell type

tag: genotype

value: MyclGFP/GFP


title: T47D Charcoal Stripped Serum RNA-seq

tag: cell line/type

tag: tissue source

value: breast

tag: developmental stage

value: adult

tag: tumor stage


title: HC11_sgTrps1_repl1

description:
HC11_sgScr_sgTrps1_log2_norm_counts.txt
HC11_sgScr_vs_sgTrps1_diff_expr_analysis.txt

source_name: Mammary epithelial cell line

tag: cell-type

tag: sgrna

value: sgTrps1 #1


title: T47D Full Serum RNA-seq


title: Steady State, LMYC HET1, Biological Rep 2

value: MyclGFP/+


title: HC11_sgTrps1_repl2


title: Steady State, LMYC KO1, Biological Rep 1


title: T47D Charcoal Stripped Serum ribosome protected fragments

tag: molecule subtype

value: ribosome protected fragments


title: CAC_WT_D100

description: Wild type mice with C57BL/6 background treated with AOM/DSS for 100days

value: wild type


title: Obese ASCs [3998998011_R05C02]

description: Final Integration of 6 obese samples


title: Steady State, LMYC KO1, Biological Rep 3


title: HC11_sgScr_repl2

value: sgScr #1


title: Obese ASCs [3999002143_R01C02]

description: Final Integration of 6 obese samples


title: DMCPD24hrR2

city: Chapel Hill

first: Yanyan

last: Yang

state: NC

address: 120 Mason Farm Road

department: Biochemistry & Biophysics

institute: University of North Carolina  at Chapel Hill

description: replicate 2

data_processing:
Library strategy: XR-seq
adaptor trimming
filtering reads based on length
random sampling
alignment
read filtering based on nucleotide composition
strand separation
gene coverage count
Genome_build: dm6 and hg38
Supplementary_files_format_and_content: bigWig

organism: Drosophila melanogaster

source_name: S2-DGRC cells

extract_protocol:
S2-DGRC cells were obtained from the Drosophila Genetic Resources Center. Cells were cultured in Schneider’s medium at 27 degrees with heat inactivated FBS at 10% (v/v).  For UV treatments, cells were inoculated into R-150 plates and grown to about 25 to 80 percent confluence.  Media was gently removed from the semi-adherent monolayer, cells were irradiated with UV-C, and then fresh media containing sterilized, conditioned media was added to cells, and cells were incubated at 27 degrees.  XR-seq assays employed 20 Jm-2.    Following predetermined repair times, plates were placed on ice and cooled cells were harvested by scraping and rinsing with ice-cold PBS. Cells were pelleted, transferred to Eppendorf tubes, washed with cold PBS, and resuspended in 320 to 340 ul of cold TE.  Samples were processed using 5 ul RNase A and proteinase K.
Samples were immunoprecipitated with anti-CPD antibody, and then ligated to adapters and processed for sequencing (XR-seq).  One plate of S2 cells per repair time point was sufficient for XR-seq assay.  Drosophila possesses photolyases, so cells were kept in the dark or under dim yellow illumination from the time of irradiation to the time of addition of NaCl to cell lysates. After PCR amplification, libraries wrere sequencing on HS4000.

tag: cell line

tag: treatment

value: UV

tag: repair time


title: SUM159PT Full Serum 5 hours RNA-seq

value: primary tumor


title: Steady State, LMYC KO1, Biological Rep 4

value: spleen


title: T47D Full Serum ribosome protected fragments

value: metastatic


title: NON_C9_D0

description: CARD9 knockout mice with C57BL/6 background without any treatment


title: HC11_sgScr_repl1


title: Steady State, LMYC HET1, Biological Rep 1


title: Obese ASCs [3999002143_R03C01]

description: Final Integration of 6 obese samples

tag: group


title: MTC_with TRPS1 insertions_aTRPS1

source_name: Tumor derived primary cells

value: MTC (mouse tumor-derived cells)

tag: chip antibody

value: aTRPS1 (sc-26974, Santa Cruz)


title: NON_WT_D0

description: Wild type mice with C57BL/6 background without any treatment

tag: strain background

tag: genotype/variation


title: Obese ASCs [3999002143_R05C02]

description: Final Integration of 6 obese samples

value: obese

value: Adipose derived stem cells


title: Obese ASCs [3998998011_R01C02]

description: Final Integration of 6 obese samples


title: MCF10A Serum Deprived RNA-seq

source_name: adult human female breast, fibrocystic disease

value: fibrocystic disease


title: DMCPD16hrR2

description: replicate 2


title: DMCPD30mR2

description: replicate 2


title: MTC_no TRPS1 insertions_aTRPS1


title: MCF10A Full Serum RNA-seq


title: 4C-rDNA-old primers hs+ rep1

city: Moscow

first: Nickolai

last: Tchurikov

address: 32, Vavilova str.

department: Department of Epigenetic Mechanisms of Gene Expression Regulation

country: Russia

institute: Engelhardt Institute of Molecular Biology

description: Replica 1

data_processing:
Base calling and quality control were performed in real time with standard Illumina analysis pipeline using a phiX control.
Sequenced reads were trimmed for adaptor sequences and low quality sequences by cutadapt v. 1.16 using the following options: --trim-n --times=6 --minimum-length 20 -q 26 --untrimmed-output=4C_notail.fastq.gz -g CTAAGCCTGCTGAGAACTTTC -g GCATTCTGTAGGGAGATCAAATC -a GAAAGTTCTCAGCAGGCTTAG -a GATTTGATCTCCCTACAGAATGC -a GATCTCCCTACAGAATGCTG
Untrimmed sequences from the file 4C_notail.fastq.gz were trimmed for the following adaptor sequences by cutatapt v. 1.16 using the following options --trim-n --times=6 --trimmed-only --minimum-length 20 -q 26 -g GAAAAAAATCCCAGAAGTGGT -g TCCAGAAATCAACTCGCCAGT -a ACTGGCGAGTTGATTTCTG -a ACCACTTCTGGGATTTTTTTC. Then outputs of previous and current adaptor removal steps were concatenated in one file 4C_trimmed.fastq.gz for furher processing
Trimmed reads were mapped to hg19p13 by bwa 0.7.12-r1039 using the mem algorithm. All non-aligned reads were removed from resulting alignment file by samtools 1.6: -b -S -F 4 -@ 10 allalign.sam > aligned.bam
Mapping and alignment results were converted to resulting tables using samtools 1.6 and ad hoc Perl scripts.
Each replica results table was converted to bedGraph file for further processing using reads amount as data value. Intersection file was built by bedtools v. 2.27.1 with the following command line: bedtools intersect -a 4C_hg19_old_hs+_rep1.bedGraph -b 4C_hg19_old_hs+_rep2.bedGraph -wb. Ad hoc Perl script was used to convert bedtools output file back to bedGraph file with summing up in the overlapped regions.
Genome_build: Homo Sapiens hg19/GRCh37.p13 genome with included to chr14 from address 1 Human ribosomal DNA U13369
Supplementary_files_format_and_content: Tab-delimited text file include the following features of each mapping: begin, end, length, coverage, number of reads, sequence. bedGraph files for each replica and intersection are supplied too.

growth_protocol: HEK293T cells were grown in DMEM with 10% FBS in a humidified incubator at 37°C and 5% CO2 to 80% confluency.

extract_protocol: DNA samples were prepared as described before (Dekker et al., 2002; Osborne et al., 2004; http://www.protocol-online.org/cgi-bin/prot/view_cache.cgi?ID=3978).  Cross-linking  To suspension containing about 20x106 HEK293T cells in 40 ml of DMEM formaldehyde solution was added to final concentration 1.5%. After mixing incubation of cell suspension was performed for 10 min at room temperature with mixing. The quenching with 2.75 ml of 2M glycin (final concentration 0.125M) was performed. After incubation at room temperature for 5 min the suspension was cooled for 15 min in ice bath and then cells were collected by centrifugation for 15 min at 3500 rpm at +2°C.  Lysis   The pellet of cells was resuspended at °C in 1ml of buffer containing 10 mM tris-HCl buffer, pH 8, 10 mM NaCl, 0.2% NP-40 and freshly added protease inhibitors – 0.1 mM PMSF and 1:500 protease inhibitor cocktail (Sigma). After incubation for 15 min cells were homogenized by passing through insulin syringe about 50 times into Eppendorf. Then nuclei were spin down by centrifugation for 5 min at 5000 rpm in Eppendorf centrifuge 5415 R at +2°C.  Digestion with EcoRI  The nuclei pellet was resuspended in 756 l of solution containing 40 mM tris-HCl buffer, pH 7.4, 50 mM NaCl, 10 mM MgCl2 and 10 mM 2-mercaptoethanol. Then 20% SDS was added to final concentration 0.3% and incubation with shaking was performed for 1 h at +37°C. To sequester SDS 180 l of 10% Triton X-100 was added and the incubation for 1 h at +37°C was performed. Before digestion 1 l of BSA (5 mg/ml) was added with mixing. Then 50 l of EcoRI (10 u/l) was added and after mixing digestion was performed overnight at +37°C.   Ligation  To inactivate the restriction enzyme, 35l of 20% SDS was added (final concentration 0.7%) and the probe was heated to 65°C for 30 min. Then the mixture was transferred into 15 ml Nunc tube and consequently 375 l of 20% Triton X-100 (to final concentration 1%), 750 l of 10x ligase buffer, 7,5l of BSA (5 mg/ml), 80l of 100 mM ATP, and 5241l of milliQ water  were added and the final 7.5 ml solution was well mixed. Then 10 l of T4 DNA ligase (200 u/l) was added and after mixing incubation was performed for 5 h at +16°C and then for 30 min at room temperature. Usually during ligation DNA concentration was equal to 2 ng/l.    DNA purification  For isolation of DNA 50l of proteinase K (10 mg/ml) was added (final concentration 50 g/ml) and after mixing incubation was performed at 55°C B1overnight. For RNA digestion 40l of RNase A (10 mg/ml) was added (final concentration 0.5 g/ml) and after mixing incubation was performed for 30 min at +37°C. After extensive extraction with phenol-chloroform extraction (three times with 7 ml each) DNA was precipitated by 2.5 vol. of ethanol after addition of 40 l 10 mg/ml glycogen and 175 l 4M NaCl. The final DNA pellet was washed twice with 70% ethanol and then dissolved in 0.1xTE.   Digestion with FaeI  About 15 g of DNA was digested in 250l solution with 75 u of FaeI overnight at +37°C. Then the enzyme was inactivated by heating at 65°C for 30 min. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 100l of 0.1xTE.   Ligation  For circularization 15g of DNA was incubated in 8 ml of T4 DNA ligase buffer containing 400 u of T4 DNA ligase for 5 h at +16°C. DNA was isolated after phenol-chloroform extraction, precipitated by ethanol and dissolved in 50l of 0.1xTE.   PCR and library preparation  One or two rounds of PCR were used as described below. There are about 300-400 copies of rDNA. That is why a single round of PCR (with up to 35 cycles) was found to be sufficient. DNA concentration was titrated and finally about 30 ng of DNA was used for PCR with primers   5’ TCTTTGAAAAAAATCCCAGAAGTGGT 3’ and 5’ AAGTCCAGAAATCAACTCGCCAGT 3’ (for PCR-1), and 5’ GCCTAAGCCTGCTGAGAACTTTC 3’ and 5’ CAGCATTCTGTAGGGAGATCAAATC 3’ (for PCR-2). After separation in 2% agarose gels two DNA fractions (200-400 bp and higher 400 bp) were eluted using QIAqiuck gel extraction kit (Quigen). The libraries were prepared using TruSeq RNA Sample Preparation Kit v2 (Illumina) using adapter AR006 for 200-400 bp DNA fraction and adapter R007 for DNA fraction higher 400 bp. The samples were sequenced using MiSeq (Illumina).

treatment_protocol: Heat shock treatment was performed for 30 min at +43°C followed by recovery for 2.5 h at +37°C.

tag: strain

tag: tissue

value: kidney

tag: stress

value: heatshock


title: MCF10A Serum Deprived ribosome protected fragments

tag: cell line/type

value: breast

value: adult


title: U3056_DMSO_6h_3

city: Uppsala

first: Fredrik

middle: Johansson

last: Swartling

address: Dag Hammarskjölds väg 20

department: Immunology, Genetics and Pathology

country: Sweden

institute: Uppsala University

data_processing:
Base calling was performed using standard parameters in build-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2).
Sequenced reads were mapped to hg19_AmpliSeq_Transcriptome_ERCC_v1 using standard parameters and build-in software provided with the Ion Torrent Proton sequencer  (Torrent suite ver.5.2.2).
RPM were calculated using internal built-in software provided with the Ion Torrent Proton sequencer (Torrent suite ver.5.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes gene symbol and gene expression in RPM for each sample.

source_name: tumor cell line

extract_protocol:
RNA from fresh-frozen tumor biospy, alternatively from 10^6 cells, was extracted according to QUIAGEN RNEasy extraction protocol
Library was prepared according to Thermo Fisher Scientific protocol for AmpliSeq next generation sequencing application

value: brain tumor derived cell line U3056

value: DMSO


title: mOPC_CAGE_n3

city: Yokohama

first: Kosuke

last: Hashimoto

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: nuclear RNA

data_processing:
Basecalls performed using CASAVA version 1.8.
Ribosomal RNAs were identified and removed using RNAdust (ver. 1.0.2) with a ribosomal DNA repeating unit (GenBank: BK000964.2).
CAGE tags were aligned to the mouse genome using BWA (ver.0.5.9) with aln and samse functions.
Genome_build: mm10
Supplementary_files_format_and_content: Transcription start sites with read counts in the bed format

source_name: Oli-neu

growth_protocol: Oli-neu cells were grown on poly-L-lysine coated dishes and expanded in proliferation media consisting of DMEM (lifetech 41965062), N2 supplement, Pen/Strep Glu (lifetech 10378016), T3 (Sigma-Aldrich T6397) 340ng/ml, L-thyroxine (Sigma-Aldrich 89430) 400 ng/ml, bFGF 10ng/ml and PDGF-BB 1ng/ml. Culture media was changed on alternate days and the cells were passaged every 5-6 days.

extract_protocol:
RNA from nuclear fractions of mESCs and mOPCs were extracted as previously published (Fort et al, Nat Genet 2014).
CAGE libraries were prepared according to (Takahashi et al, Nat Protocol 2012).  Briefly, 3ug of nuclear RNA was used for reverse transcription with random primer. 5’ end of cDNA-RNA hybrids was biotinylated and captured using magnetic streptavidin-coated beads. After capture, cDNAs from cap-trapped RNA were released, ligated to 5’ barcoded linkers and digested with EcoP15I. The cDNA tags were then ligated with a 3’linker and amplified with 9 cycles. Libraries were sequenced on Illumina HiSeq 2500, 50bp single-end reads.

tag: cell type

value: mOPC


title: MCF10A Full Serum ribosome protected fragments

tag: tissue source

tag: developmental stage

value: ribosome protected fragments


title: mOPC_CAGE_n1

description: nuclear RNA


title: HMECs Serum Deprived 24 hours RNA-seq

source_name: adult human female breast

value: Human mammary epithelial cells (HMECs)

tag: tumor stage

value: no apparent disease


title: Lean ASCs [3998998011_R04C02]

description: Final Integration of 6 lean samples

source_name: lean

value: lean


title: Lean ASCs [3998998011_R01C01]

description: Final Integration of 6 lean samples


title: Lean ASCs [3998998011_R05C01]

description: Final Integration of 6 lean samples


title: mOPC_CAGE_n2

description: nuclear RNA


title: mESC_CAGE_n3

description: nuclear RNA

source_name: mESC R08

growth_protocol: mES R08 cells were grown under feeder-free conditions in mouse ESC medium containing DMEM (Wako), 1,000 U/ml leukemia inhibitory factor (LIF; Millipore), 15% FBS (Gibco), 2.4 mM l-glutamine (Invitrogen), 0.1 mM non-essential amino acids (NEAA; Invitrogen), 0.1 mM 2-mercaptoethanol (Gibco), 50 U/ml penicillin and 50 μg/ml streptomycin (Gibco). Culture media were changed daily, and cells were passaged every 2–3 days.

value: mESC


title: U3056_JQ1_6h_3


title: U3056_DMSO_6h_2


title: U3056_DMSO_6h_1


title: Lean ASCs [3999002143_R01C01]

description: Final Integration of 6 lean samples


title: 4C-rDNA-old primers hs+ rep2

description: Replica 2

tag: genotype

value: wild type


title: U3056_JQ1_6h_2


title: mESC_CAGE_n1

description: nuclear RNA


title: mESC_CAGE_n2

description: nuclear RNA


title: HMECs Full Serum RNA-seq


title: AC16 cells treated with PM2.5, biological rep3

city: Beijing

first: 唐

last: 伟评

address: 2 Anzhen Rd, Chaoyang District,

institute: Beijing Institute of Heart Lung and Blood Vessel Diseases

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Human myocardial cells AC16 were exposed to PM2.5 for 24h

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

value: myocardial cell line AC16

value: PM2.5 for 24h


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_48hrs 48-S-3

data_processing:
Fastq quality checked with fastqc from Subread package
Fastq files were aligned to mouse Ensembl genome GRCm38 with STAR v 2.6.1d
Read pairs were counts using featurecounts from the Subread package v 1.6.2
Normalization and differential expression analysis were conducted using DESeq2
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: text, raw count file

source_name: in vitro cultured CD4+ T cells

growth_protocol: Naïve, (CD25NegCD44LoCD62Lhi) CD4+ T cells were isolated from the spleens and lymph nodes of C57BL/6 mice using a FACS ARIA II. Cells were resuspended in complete IMDM media supplemented with 10% FCS (Atlanta) and containing 0.25ug/ml of anti-hamster CD3 (clone 145-2E11, BioXcell) and 1ug/ml of anti-hamster CD28 (clone 37.51, BioXcell) at a density of 1e6/ml. Contents were added to PBS-washed wells of flat-bottom plates coated over-night with goat, anti-hamster IgG (Cat No. 56984, MP Biomedicals) diluted 1:20 in PBS and stimulated for 24hrs.

extract_protocol:
We performed Trizol-based extractions in accordance to the manufacturer's protocol with several modifications. 2ul of linear acrylamide (Cat No AM1354) was added before addition of 100% isopropanol. After the 75% ETOH wash, the samples were resuspended in 87.5ul of water and a mixture of 10ul of buffer RDD and 2.5ul of DNase I from Qiagen. Samples were left at room temp for 15min to allow the DNAse digestion to proceed. The samples were then processed and passed through Qiagen MinElute columns in accordance tro the manufacturer's protocol.
RNA quantity and quality were determined using Agilent's RNA 6000 Pico Chip
RNA-seq libraries were prepared with the TruSeq Stranded
Total RNA Library Prep Gold Kit (Illumina, 20020598). The sequencing was performed using the
Illumina NovaSeq. RNA-seq libraries were prepared and sequenced by the Genome
Technology Core at New York University School of Medicine.

treatment_protocol: For samples 1, 2, and 3, supernatant was aspirated and replaced with a cocktail containing 20ng/ml of IL6 + a vehicle control resulting in a final NaCl concentration of 10mM in place of SAA1 + 2.5ug/ml of anti-IL-4 (Clone 11B11, BioXcell) + 2.5ug/ml of anti-IFN-g (Clone XMG.2, BioXcell). Samples 1, 2, and 3 were stimulated for 3, 12, and 48 hrs, respectively. For samples 4, 5, and 6, supernatant was aspirated and replaced with a cocktail containing 20ng/ml of IL6 + 0.3ng/ml of TGF-b + 2.5ug/ml of anti-IL-4 (Clone 11B11, BioXcell) + 2.5ug/ml of anti-IFN-g (Clone XMG.2, BioXcell). Samples 4, 5, and 6 were stimulated for 3, 12, and 48 hrs, respectively. For samples 7, 8, and 9, supernatant was aspirated and replaced with a cocktail containing 20ng/ml of IL6 + 10ug/ml of rmSAA1 (Cat No 2948-SA, R&D Systems) + 2.5ug/ml of anti-IL-4 (Clone 11B11, BioXcell) + 2.5ug/ml of anti-IFN-g (Clone XMG.2, BioXcell). Samples 7, 8, and 9 were stimulated for 3, 12, and 48 hrs, respectively.

tag: cell typ

value: CD4+ T cell

tag: time (h)


title: HMECs Serum Deprived 24 hours ribosome protected fragments

tag: molecule subtype


title: mOPC_NPM_n2 DNA

description:
total RNA and genomic DNA
mOPC_NPM_n2_significant.txt.gz

data_processing:
Basecalls performed using CASAVA version 1.8.
RNA and DNA tags at both ends of the adapter were extracted from raw sequencing reads using TagDust2 (ver. 2.31).
PCR duplicates were removed from paired RNA-DNA tags using FastUniq.
Ribosomal RNAs were identified and removed from the extracted RNA tags using RNAdust (ver. 1.0.6) with a ribosomal DNA repeating unit (GenBank: BK000964.2).
RNA and DNA tags were aligned to the mouse genome using BWA (ver. 0.7.15-r1140) with aln and samse functions.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file

extract_protocol:
Around 2 million mouse cells were crosslinked with 1% or 2% formaldehyde. Nuclei were isolated, washed and genomic DNA was sheared by controlled DNase I digestion. After binding of nuclei to Ampure beads, genomic DNA was end-repaired and dA-tailed. During dA-tailing, RNA is treated with RNase H. After washes, nuclei were mixed with RADICL-seq adapter and T4 RNA Ligase 2-truncated KQ for ssRNA ligation. Subsequently, excess of adapter was washed away and nuclei were resuspended in T4 DNA ligase solution for ligation of RADICL-seq adapter to genomic DNA. RNA- and DNA-ligated RADICL-seq adapter molecules were first reverse-crosslinked by Proteinase K digestion at 65°C, then precipitated and used for library preparation.
The RNA ligated to the RADICL-seq adapter was first reverse transcribed with SuperScript IV and then converted into double stranded DNA by second strand synthesis. RADICL-seq adapters ligated only with RNA were neutralised by ligation with hairpin molecule with overhang A. Newly formed dsDNA molecules containing RADICL-seq adapter were first digested with EcoP15I fro generate paired-end tags, ligated with sequencing linkers and then affinity-purified by Streptavidin-conjugated beads. Recovered dsDNA was PCR amplified to generate libraries for Illumina sequencing and size-selected using a 6% native polyacrylamide gel.

treatment_protocol: For the ActD-treated RADICL-seq libraries, mES R08 were treated with Actinomycin D (Sigma) at a final concentration of 5 µg/ml for 4 h before crosslinking, as described below.

tag: sample type

value: chimeric RNA-DNA molecule linked by an adapter


title: U3056_JQ1_6h_1

tag: cell line

tag: treatment


title: AC16 cells treated with PM2.5, biological rep2


title: AC16 cells as control, biological rep3

source_name: AC16, control

value: control


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_48hrs 48-S-2


title: AC16 cells treated with PM2.5, biological rep1


title: AC16 cells as control, biological rep2


title: HMECs Full Serum ribosome protected fragments


title: U3054_DMSO_6h_3

value: brain tumor derived cell line U3054


title: mOPC_NPM_n2 RNA


title: Lean ASCs [3999002143_R03C02]

description: Final Integration of 6 lean samples

tag: group

value: Adipose derived stem cells


title: Lean ASCs [3999002143_R05C01]

description: Final Integration of 6 lean samples


title: U3054_DMSO_6h_2


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_12hrs 12-S-3


title: IR+ Dox- 3R

city: West Lafayette

first: Chang-Deng

last: Hu

state: IN

address: 201 S. University St, Hansen Life Sciences Building, Room 401A

department: Department of Medicinal Chemistry and Molecular Pharmacology

institute: Purdue University

description:
irradiation.counts
Sample 11

data_processing:
Base calling and quality scoreing were performed in Illumina HiSeq (sample 7 to sample 10)/Illumina MiSeq (sample 1 to sample 6).
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to Gencode 25 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: GENCODE 25 GRCh38
Supplementary_files_format_and_content: Raw counts

source_name: Prostate cancer

growth_protocol: LNCaP-shPRMT5 cells were cultured in RPMI1640 medium with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated using Trizol Reagent (Ambion, Carlsbad, CA, USA). Total RNA was reverse transcribed into cDNA and cDNA was used as template for RNA-seq analysis.
Library Construction RNA polyA+

treatment_protocol: LNCaP-shPRMT5 cells were seeded on 10 cm dishes and Doxycyline (Dox) was applied at the final concentration of 1 µg/mL every 48 hours to establish and maintain PRMT5 knockdown. For the IR+ group, cells were then subjected to 2 Gy IR and cells were harvested 24 h following IR treatment.

value: Dox-

tag: genotype/variation

value: No knockdown

value: 2 Gy radiation


title: U3054_DMSO_6h_1

value: DMSO


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_12hrs 12-S-2

tag: strain


title: mOPC_NPM_n1 RNA

description:
total RNA and genomic DNA
mOPC_NPM_n1_significant.txt.gz

value: mOPC


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_12hrs 12-S-1


title: mOPC_1FA_n3 DNA

description:
total RNA and genomic DNA
mOPC_1FA_n3_significant.txt.gz


title: U3054_JQ1_6h_3


title: U3054_JQ1_6h_2


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_3hrs 3-S-3


title: mOPC_1FA_n3 RNA


title: IR+ Dox+ 1R

description:
irradiation.counts
Sample 8

value: Dox+

value: PRMT5 knockdown


title: HMECs Serum Deprived 1 hour ribosome protected fragments

value: Human mammary epithelial cells (HMECs)

value: breast

value: adult

value: no apparent disease

value: ribosome protected fragments


title: U3054_JQ1_6h_1


title: mOPC_1FA_n2 DNA

description:
total RNA and genomic DNA
mOPC_1FA_n2_significant.txt.gz


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_3hrs 3-S-2

value: CD4+ T cell


title: IR+ Dox- 1R

description:
irradiation.counts
Sample 7


title: HMECs Serum Deprived 1 hour RNA-seq


title: IR+ Dox+ 3R

description:
irradiation.counts
Sample 12


title: mOPC_NPM_n1 DNA

value: chimeric RNA-DNA molecule linked by an adapter


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_3hrs 3-S-1


title: mOPC_1FA_n2 RNA


title: U3024_DMSO_6h_2

value: brain tumor derived cell line U3024


title: mOPC_1FA_n1 DNA

description:
total RNA and genomic DNA
mOPC_1FA_n1_significant.txt.gz


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_48hrs 48-T-3


title: IR+ Dox+ 2R

description:
irradiation.counts
Sample 10


title: IR+ Dox- 2R

description:
irradiation.counts
Sample 9


title: U3024_DMSO_6h_1


title: mOPC_1FA_n1 RNA


title: D23580_MAC_dRNAseq-1

city: Hinxton

first: Alexander

last: Predeus

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

data_processing:
The remaining reads of each library were aligned to the corresponding genomes using Bowtie2 v2.2.9 and alignments were filtered with Samtools v1.3.1 using a MAPQ cut-off of 15. Reads were assigned to genomic features using featureCounts v1.5.1.
TPMs were calculated using raw read counts obtained in featureCounts, with effective gene length equal to gene length in annotation.
Genome_build: D23580 experiments were aligned to D23580 genome and quantified using D23580 annotation.
Supplementary_files_format_and_content: TPM values in tab-separated text columns

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. D23580

source_name: in vitro culture

growth_protocol: Growth conditions and treatment for 16 in vitro conditions are described previously (PMID 24331466). Growth conditions for intra-macrophage transcriptome are described in PMID 26561851.

extract_protocol:
Transcription and RNA turnover were stopped using 2/5 volumes of the cell suspension using ice-cold ‘‘stop solution’’ (19% ethanol, 1% acidic phenol [pH 4.3]) and incubated on ice for 30 min to prevent RNA degradation. RNA was isolated using TRIzol (Invitrogen) and digested with DNase I.
RNA samples were first fragmented with ultrasound (4 pulses of 30 sec at 4°C) and then treated with polynucleotide kinase (PNK). This was followed by treatment with Terminator exonuclease and then the RNA samples were poly(A)-tailed using poly(A) polymerase. The 5'PPP structures were removed using a 5' Polyphosphatase. Afterwards, a RNA adapter was ligated to the 5'-phosphate of the RNA. First-strand cDNA synthesis was performed using an oligo(dT)-adapter primer and the MMLV reverse transcriptase. The resulting cDNAs were PCR-amplified to about 20-30 ng/μl using a high fidelity DNA polymerase (cycle numbers and barcode sequences which are part of the 3' TruSeq sequencing adaptor are indicated in the pool 1 description below). The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis.

value: wildtype


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_48hrs 48-T-2


title: mESC_NPM_n2 DNA

description:
total RNA and genomic DNA
mESC_NPM_n2_significant.txt.gz

value: mESC


title: U3024_JQ1_6h_3


title: BaumsDatabaseID_12814

city: University Park

first: Iliana

middle: B

last: Baums

address: 212 Mueller Laboratory, Penn State University

department: Biology

institute: The Pennsylvania State University

data_processing:
Library strategy: MethylRAD
Raws reads were converted from Illumin 1.8+ to FastQSanger quality scores using FastQ Groomer (Blankenberg et al. 2010).
Illumina adaptors were removed with Trim Galore! (The Babraham Institute by @FelixKrueger) and Trim (Galaxy Version 0.0.1) was used to clip 2 base pairs off both ends.
A reference-based approach was used by extracting FspE1 methyl sites from an Acropora palmata genome assembly (version 1.0) using a custom Perl script (provided by Shi Wang) and reads were mapped against these reference sites using Bowtie2 (default settings,(Langmead & Salzberg 2012)).
Samtools IdxStats (Li et al. 2009) was used to tabulate mapping stats into counts of mapped reads per reference sites for each sample.
Differential DNA methylation analysis was performed in EdgeR. Within the EdgeR vignette, data is converted to reads per million and filtered for only those methylation sites that have at least 10 reads per million in at least 6 samples. Then normalization factors were calculated to correct for the different compositions of the samples. The effective library sizes are then the product of the actual library sizes and these factors. After library size normalization the data was subjected to non-parametric batch normalization with the ComBat package for R software (http://http://www.bu.edu/jlab/wp-assets/ComBat/Abstract.html).
Genome_build: Acropora palmata genome assembly (version 1.0) https://usegalaxy.org/u/skitch/p/acropora-genomes
Supplementary_files_format_and_content: Excel file containing counts normalized for library size and batch effects.
Supplementary_files_format_and_content: Segkk0_pilon-14044 and etc are the scaffold identifiers in the genome.

organism: Acropora palmata

source_name: Whole tissue extract

extract_protocol:
Coral tissue samples were snap frozen in liquid nitrogen and kept at -80° C before extraction using the DNeasy Blood & Tissue Kit (QIAGEN) with the following modifications.  Time of incubation in extraction buffer was increased to 16-20 hours. Further, only the second elution was retained for library production as this fraction contained the high molecular weight (HMW) DNA .
A total of 100ng of HMW genomic DNA was digested with FspEI (NEB) at 37°C for 4 hours. Five µL of digested DNA was run on a 1% agarose gel to verify digestion. Ligation was performed in a 30 µL reaction with 20 µL of digested DNA, 0.2 µM each of two adaptors, 1 mM ATP and 800 U of T4 DNA ligase (NEB). Ligation was carried out at 4° C overnight. Adaptor and primer sequences are provided in the supplementary material (Table S3). Ligation products were amplified in 40 µL reactions containing 15 µL of ligated product, 0.2 mM of each primer (p1 and p2), 0.3 mM dNTP, 1X Phusion HF buffer and 0.4 U Phusion high-fidelity DNA polymerase (NEB). PCR was performed in an Eppendorf Mastercycler with 22 cycles of 98°C for 5 s, 60°C for 20 s, 72°C for 10 s, and a final extension of 5 min at 72°C. The target DNA band (approx. 100 bp) was excised from a 10% TBE polyacrylamide gel, and the DNA was diffused from the gel in 50 µL of nuclease-free water for 12 h at 4°C. Barcodes were added in a second PCR amplification (total volume =20 µL), which contained 7 µL of gel-extracted PCR product, 0.2 mM of each primer (p3 and index primer), 0.3 mM dNTP, 1X Phusion HF buffer and 0.4 U Phusion high-fidelity DNA polymerase (NEB). Seven PCR cycles with the same profile outlined above were performed. PCR products were purified using QIAquick minElute PCR purification kit (Qiagen) and then with Ampure XP beads (Agencourt). Libraries were run on an Illumina HiSeq 2500 sequencer using 50 nt single read sequencing.

tag: peak bleaching status

value: Normal Color

tag: reef

value: Sand Island

tag: location of within colony sampling

value: Branch

tag: coral genet id


title: U3024_JQ1_6h_1


title: U3024_DMSO_6h_3

value: DMSO


title: mESC_NPM_n2 RNA

tag: cell type


title: D23580_MAC_dRNAseq-2


title: mESC_NPM_n1_reseq DNA

description:
total RNA and genomic DNA
N/A


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_12hrs 12-T-2


title: mESC_NPM_n1_reseq RNA

description:
total RNA and genomic DNA
N/A


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_12hrs 12-T-1


title: U3009_DMSO_6h_3

value: brain tumor derived cell line U3009


title: BaumsDatabaseID_12810


title: BaumsDatabaseID_12811

value: Very Pale

value: Not a Branch


title: U3009_DMSO_6h_2


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_3hrs 3-T-3


title: mESC_NPM_n1 DNA

description:
total RNA and genomic DNA
mESC_NPM_n1_significant.txt.gz


title: BaumsDatabaseID_12808

value: Bleached


title: U3009_DMSO_6h_1


title: mESC_NPM_n1 RNA


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_3hrs 3-T-2


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_48hrs 48-T-1


title: U3024_JQ1_6h_2


title: BaumsDatabaseID_12793

value: Molasses


title: BaumsDatabaseID_12813


title: U3009_JQ1_6h_3


title: BaumsDatabaseID_12789


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_12hrs 12-T-3


title: BaumsDatabaseID_12812


title: mESC_ActD4_n2 DNA

description:
total RNA and genomic DNA
mESC_ActD4_n2_significant.txt.gz


title: IL6 (20ng/ml) + TGF-b (0.3ng/ml) treated_3hrs 3-T-1


title: U3009_JQ1_6h_2


title: U3009_JQ1_6h_1


title: mESC_ActD4_n2 RNA


title: IL6 (20ng/ml) + rmSAA1 (10ug/ml) treated_48hrs 48-S-1


title: BaumsDatabaseID_12787


title: BaumsDatabaseID_12785


title: IL6 (20ng/ml) treated_48hrs 48-V-2

description:
IL6 (20ng/ml) treated_48hrs
48-V-2


title: RNAPII_ChIA-PET_Control

city: FARMINGTON

first: Yijun

last: Ruan

state: CT

address: 10 DISCOVERY DR

department: Ruan

institute: The Jackson Laboratory

data_processing:
Library strategy: ChIA-PET
Filtering linker sequence using in-house script
Mapping to reference genome using BWA MEM
Deduplicating reads using Picard (MarkDuplicates)
Peak-calling using MACS (v1.4)
2D contact map using Juicer tool
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited txt format for peak (bed), loop (bedpe), binary data format for Juicebox (hic)

growth_protocol: Both U937-PR9 and NB4 cells were cultured in RPMI 1640 (ThermoFisher, A10491), supplemented with 10% fetal bovine serum (ThermoFisher, 10082147). These cells were cultured at 37 ℃ , 5% CO2, and ambient oxygen levels.

extract_protocol:
When performing ChIA-PET library, the same precedures were used as those in previous paper. (Li et al., 2012; Tang et al., 2015)
Paired-end sequencing (2 ×150bp) was used for ChIA-PET libraries  with Illumina Hiseq 2500 or Illumina Nextseq 500.

treatment_protocol: The U937-PR9 cells were treated with 100 μM ZnSO4 (Sigma, Z0251) for 4 hours for ChIA-PET and ChIP-Seq experiment. The U937-PR9 cells were treated with 100 μM ZnSO4  and then collected these cells at 4, 6, 12, 24 hours for RNA-Seq experiment. These cells was preincubated with 100 μM ZnSO4 for 4 hours and then treated with ATRA (Sigma, R2625) for 24 and 48 hours used for RNA-Seq experiment. NB4 cells were treated with ATRA for 24 and 48 hours used for RNA-Seq experiment.

tag: method

value: ChIA-PET

tag: factor

value: RNAPII (Biolegend, catalog# 920102)

value: nuclear chromatin


title: mESC_ActD4_n1 RNA

description:
total RNA and genomic DNA
mESC_ActD4_n1_significant.txt.gz


title: BaumsDatabaseID_12784


title: IL6 (20ng/ml) treated_48hrs 48-V-1

description:
IL6 (20ng/ml) treated_48hrs
48-V-1

value: CD4+ T cell


title: mESC_2FA_n3 DNA

description:
total RNA and genomic DNA
mESC_2FA_n3_significant.txt.gz

value: chimeric RNA-DNA molecule linked by an adapter


title: PML_ChIA-PET_ZnSO4 Treatment

description: PML_ChIA-PET_ZnSO4 Treatment

value: PML (Santa Cruz, catalog# sc-996X)


title: IL6 (20ng/ml) treated_12hrs 12-V-3

description:
IL6 (20ng/ml) treated_12hrs
12-V-3


title: IL6 (20ng/ml) treated_12hrs 12-V-2

description:
IL6 (20ng/ml) treated_12hrs
12-V-2


title: mESC_2FA_n3 RNA


title: BaumsDatabaseID_12782


title: mESC_2FA_n2 DNA

description:
total RNA and genomic DNA
mESC_2FA_n2_significant.txt.gz


title: BaumsDatabaseID_12721

value: Key Largo


title: IL6 (20ng/ml) treated_12hrs 12-V-1

description:
IL6 (20ng/ml) treated_12hrs
12-V-1


title: PML_ChIA-PET_Control


title: IL6 (20ng/ml) treated_48hrs 48-V-3

description:
IL6 (20ng/ml) treated_48hrs
48-V-3


title: mESC_ActD4_n1 DNA

value: mESC


title: mESC_2FA_n2 RNA


title: BaumsDatabaseID_12719

value: Normal Color


title: IR- Dox+ 2

description:
non_irradiation.counts
Sample 4

value: Dox+

value: PRMT5 knockdown

tag: stress

value: 0 Gy radiation


title: BaumsDatabaseID_12720

value: Branch


title: mESC_2FA_n1 DNA

description:
total RNA and genomic DNA
mESC_2FA_n1_significant.txt.gz


title: IL6 (20ng/ml) treated_3hrs 3-V-2

description:
IL6 (20ng/ml) treated_3hrs
3-V-2

tag: cell typ


title: IR- Dox- 3

description:
non_irradiation.counts
Sample 5

value: Dox-

value: No knockdown


title: BaumsDatabaseID_12718


title: IL6 (20ng/ml) treated_3hrs 3-V-3

description:
IL6 (20ng/ml) treated_3hrs
3-V-3

tag: time (h)


title: IL6 (20ng/ml) treated_3hrs 3-V-1

description:
IL6 (20ng/ml) treated_3hrs
3-V-1


title: IR- Dox- 2

description:
non_irradiation.counts
Sample 3


title: BaumsDatabaseID_12717

value: Very Pale


title: IR- Dox+ 1

description:
non_irradiation.counts
Sample 2


title: mESC_1FA_n3 DNA

description:
total RNA and genomic DNA
mESC_1FA_n3_significant.txt.gz


title: IR- Dox- 1

description:
non_irradiation.counts
Sample 1


title: BaumsDatabaseID_12715


title: IR- Dox+ 3

description:
non_irradiation.counts
Sample 6


title: mESC_1FA_n3 RNA


title: BaumsDatabaseID_12724


title: mESC_1FA_n2 DNA

description:
total RNA and genomic DNA
mESC_1FA_n2_significant.txt.gz


title: Fgf20aHOM_3

city: London

first: David

last: Wilkinson

address: 1 Midland Road

institute: The Francis Crick Institute

data_processing:
Reads were and aligned against zebrafish genome GRCz10 and Ensembl release 86 transcript annotations using STAR v2.5.1b via the transcript quantification software RSEM v1.2.31
RSEM estimated gene level counts were rounded to integers
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited counts matrix with row representing genes and columns representing samples.

organism: Danio rerio

source_name: Dissected hindbrain and surrounding tissues

extract_protocol:
Embryos were decorionated and deyolked in DMEM with high Glucose, no Glutamine, no Calcium (11530556, Gibco); hindbrains were micro-dissected using 0.33mm micro-fine sterile needles; RNA was isolated using Quick-RNA Microprep kit (Zymo Research)
Samples were prepared with the Ovation® RNA-Seq System V2 (7102, NuGEN) for cDNA amplification, followed by NexteraXT (Illumina) for library preparation.

tag: tissue

tag: Stage

value: Fgf20a HOM

tag: genotype

tag: growth


title: BaumsDatabaseID_12723

value: Bleached


title: mESC_2FA_n1 RNA

tag: sample type


title: Fgf20aHOM_1

value: Dissected hindbrain and surrounding tissues


title: mESC_1FA_n2 RNA


title: mESC_1FA_n1 RNA

description:
total RNA and genomic DNA
mESC_1FA_n1_significant.txt.gz


title: BaumsDatabaseID_12711


title: mESC_1FA_n1 DNA


title: Cnt 4

value: LondonAB

value: wt


title: BaumsDatabaseID_12712


title: AC16 cells as control, biological rep1

tag: cell line

value: myocardial cell line AC16

tag: treatment

value: control


title: BaumsDatabaseID_12709

tag: peak bleaching status

value: Key Largo


title: Cnt 2

tag: strain


title: v134_exvivo_vSMC_input

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

institute: MRC Laboratory of Molecular Biology

description:
Input
processed data file: Processed_H3K9me2_ChIP.txt

data_processing:
Raw sequencing reads were trimmed using Trim Galore v0.4.2 and Cutadapt v1.9.1.
Reads were aligned to the GRCm38 mouse genome using Bowtie2 v 2.2.7.
Reads within +/- 1kb of transcription start site were quantitated using Seqmonk v1.4.
Genes with fewer than 20 read counts in input samples were excluded from analysis.
The ratio of H3K9me2 ChIP signal / input signal was calculated for each gene passing the filtering criteria.
Genome_build: GRCm38
Supplementary_files_format_and_content: Processed_H3K9me2_ChIP.txt: The processed data file is a tab-separated text file containing the read counts within +/- 1kb region around the transcription start site of genes. Columns 1-4 list values for individual samples, columns 5-6 list combined values for H3K9me2 ChIP replicates and input replicates and the final column shows the H3K9me2 ChIP / input ratio.

source_name: Aortic vascular smooth muscle cells (medial cell layer)

growth_protocol: Medial aortic cells were isolated directly from tissue. Aortas were dissected from C57Bl/6J male animals, dissected free of adipose tissue and then adventitial and endothelial cell layers were manually removed.

extract_protocol:
Fixed ex vivo tissue samples were snap frozen and homogenised using a metal mortar. The homogenised tissue was resuspended in nuclear lysis buffer (50 mM Tris-HCl pH 8.1, 10 mM EDTA pH 8.0, 1% SDS) supplemented with protease inhibitors (Roche) and incubated on ice for a minimum of 5 minutes.
The DNA SMART ChIP-seq kit (Clontech, 634865) was used to generate Illumina-compatible sequencing libraries from 100pg to 2ng of DNA from two independent H3K9me2 ChIP experiments and associated input.

treatment_protocol: The isolated medial layer was fixed in 1% formaldehyde in PBS for 10 minutes at room temperature before quenching with 0.125 mM glycine for 5 minutes. Subsequently, the cells/tissue were washed three times in PBS.

tag: strain/background

tag: Sex

value: Male

value: ex vivo aortic vascular smooth muscle cells

tag: chip antibody


title: Cnt 3


title: v102_exvivo_vSMC_input

tag: cell type


title: BaumsDatabaseID_12681

tag: reef

value: Grecian Rocks

tag: location of within colony sampling

tag: coral genet id


title: Cnt 1


title: Fgf20aHOM_2


title: v134_exvivo_vSMC_H3K9me2

description:
H3K9me2 ChIP
processed data file: Processed_H3K9me2_ChIP.txt


title: 44hpf_Hindbrain_scRNA-seq

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library
Three 10X libraries representing the 16hpf, 24hpf and 44hpf stages of embryonic development were aggregated using the 10X software “cellranger aggr” function, which sub-samples reads such that all libraries have the same effective sequencing depth.
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text file containing aggregated Cell Ranger counts

extract_protocol:
Embryos were decorionated and deyolked in DMEM with high Glucose, no Glutamine, no Calcium (11530556, Gibco); hindbrains were micro-dissected using 0.33mm micro-fine sterile needles; 40 tissues per stage were polled together and immediately processed for cell dissociation; samples were incubated with FACS max cell dissociation solution (T200100, Amsbio) supplemented with 1mg/ml Papain (10108014001, Sigma) for 25min at 37°C and resuspended one-time during incubation; cells were then transferred to HBSS (no calcium, no magnesium, no phenol red; 11140035, ThermoFisher Scientific) supplemented with 5%FBS, rock inhibitor (Y-27632, Stem Cell Technologies), and 1X non-essential amino acids (11140035, ThermoFisher Scientific); cells were further disaggregated by pipetting and filtered several times using 20µm strainers (130-101-812, Miltenyi Biotech GmbH)
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v2 protocol (PN-120233, 10X Genomics); cDNA amplification involved 12 PCR cycles


title: X02 MLT

city: Seoul

first: Hyemin

last: Lee

address: Kyunghee-dae-ro 26

country: South Korea

institute: Kyunghee Univ

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Glioblastoma stem like cell

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: A549 and H1299 were grown in RPMI with 10% FBS and antibiotics. XO1 and XO2 were grown in DMEM-F12 with B27 and antibiotics supplemented with growth factors (EGF and bFGF).

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.

treatment_protocol: CNOT2 gene was knocked down for 48 hr and melatonin 1mM was treated for 24 hr.

value: glioblastoma stem like cancer cell

value: brain

tag: agent

value: melatonin


title: X02 C

tag: tissue


title: BaumsDatabaseID_12676

value: Slightly Pale

value: Branch


title: X01 C


title: X01 MLT


title: BaumsDatabaseID_12710

value: Normal Color


title: A549-shCNOT2

description: 2. A549-shCNOT2

source_name: non small lung cancer cell

value: non small lung cancer cell

value: lung

tag: genotype/variation

value: CNOT knockdown


title: H1299-con sh

description: 3. H1299-con sh


title: v102_exvivo_vSMC_H3K9me2


title: A549-con sh

description: 1. A549-con sh


title: 24hpf_Hindbrain_scRNA-seq

value: Dissected hindbrain and surrounding tissues

tag: Stage

value: LondonAB

tag: genotype


title: 16hpf_Hindbrain_scRNA-seq

value: wt

tag: growth


title: BaumsDatabaseID_12670

value: Bleached


title: Full_2nd

city: Chengdu

first: Rui

last: Chen

address: 20 Temple RD.Jingjiang District,Chengdu

institute: Horticulture Institute, Sichuan Academy of Agricultural Science

description: samples collected in the full-blooming flowering stage of second flowering round

data_processing:
Basecalls performed using CASAVA version 1.7
Raw reads of fastq format were cleaned by trimming low quality ends, discarding reads of overall minor quality, and removal of adaptor sequence using scripts of the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/)
De novo assembly was implemented by trinity software (Grabherr et al, 2011). The left files (read1 files) from all libraries/samples were pooled into one big left.fq file, and right files (read2 files) into one big right.fq file. Transcriptome assembly was accomplished based on the left.fq and right.fq using Trinity software with min_kmer_cov set to 2 by default and all other parameters set default.
Following contig generation, the transcriptome assemblies for Trinity were referenced to the NR (NCBI non-redundant protein sequences), GO (Gene Ontology,http://www.geneontology.org/), KO (KEGG ORTHOLOGY, http://www.genome.jp/kegg/), SwissProt (A manually annotated and reviewed protein sequence database, http://www.ebi.ac.uk/uniprot/), PFAM (Protein family, http://pfam.sanger.ac.uk/), String (http://string-db.org/), as BLASTx queries using the Blast2GO® software suite. In order to be used in downstream analyses, BLASTx hits had to be below an E-value of 1 × 10-6. Annotation analyses were performed at levels 2 and 3. The Blast2GO® software suite was also used to predict Gene Ontology (GO) terms to the contigs.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Osmanthus fragrans

source_name: plant cell

growth_protocol: Flower petal growing in the tree under natural condition, and colleted in September.

extract_protocol:
Isolation of total RNA from petal tissue of O. fragrans was performed using TRIzol® Reagent (Invitrogen) according to the protocol described by the manufacture. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity and concentration was checked using the Nanodrop® spectrophotometer (Thermo Fisher Scientific Inc,, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using Illumina TruseqTM RNA sample 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. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 4000 platform and paired-end reads were generated.

treatment_protocol: None. Collected at different dates according to the stages of the flowering

value: Osmanthus fragrans var. semperflorens


title: BaumsDatabaseID_12669

value: Not a Branch


title: BaumsDatabaseID_12667


title: CA_fgfr1_4

extract_protocol:
Embryos were decorionated and deyolked in DMEM with high Glucose, no Glutamine, no Calcium (11530556, Gibco); hindbrains were micro-dissected using 0.33mm micro-fine sterile needles; RNA was isolated using Quick-RNA Microprep kit (Zymo Research).
Samples were prepared with the Clontech SMARTer kit (634926, TaKaRa) for cDNA amplification, followed by NexteraXT (Illumina) for library preparation.

value: constitutively active fgfr1

value: 28.5°C until 22hpf, 30min at 38.5°C, 2hr 28.5°C


title: CA_fgfr1_3


title: Int_2nd

description: samples collected in the initial flowering stage of second flowering round


title: Abs_1st

description: samples collected in the abscission flowering stage of fhe first flowering round


title: H1299-shCNOT2

description: 4. H1299-shCNOT2

tag: cell line


title: BaumsDatabaseID_12664

value: Grecian Rocks


title: CA_fgfr1_2


title: Late_1st

description: samples collected in the late full-blooming flowering stage of the first flowering round


title: BaumsDatabaseID_12659


title: S2_Term_1

first: Lei

last: Yue

address: NO.1 Beichen West Road, Chaoyang District

department: Institute if Microbiology

institute: Chinese academy of science

data_processing:
For RNA-seq raw reads of fastq format were firstly processed through in-house perl scripts to remove low quality reads and those containing adapter or ploy-N. The clean reads were mapped against predicted transcripts of the M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/) by using Bowtie2-2.2.3. HTSeq v0.6.1 was used to count the read numbers mapped to each gene, and then the FPKM was calculated based on the gene length and mapped read counts.
Genome_build: M. maripaludis S2 genome (https://www.ncbi.nlm.nih.gov/nuccore/NC_005791.1/)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample of RNA_seq. The TESs for each stain identified in duplicate and the average head reads (reads number of -1 site minus +1 site) and ratio1_1 (ratio of -1 site to +1 site) are listed in tab-delimited text files.

organism: Methanococcus maripaludis

source_name: Neural strain cells

growth_protocol: The Methanococcus maripaludis strains were grew until mid-log phase and harvested

extract_protocol:
RNA was harvested using Trizol reagent. 3 ug of total RNA was used for RNA-seq and 5 ug of total RNA was used for Term-seq .
RNA libraries were prepared for sequencing using standard Illumina protocols

value: wild type

tag: growth period

value: mid-log phase


title: S2_Term_2


title: CPSF1_Term_1

value: aCPSF1 depletion


title: CPSF1_RNAseq_3

description:
aCPSF1_3
FPKM of RNA_seq.txt


title: CA_fgfr1_1


title: BaumsDatabaseID_12653

tag: peak bleaching status

value: Branch


title: Cnt4

tag: strain


title: CPSF1_RNAseq_1

description:
aCPSF1_1
FPKM of RNA_seq.txt


title: BaumsDatabaseID_12650

value: Normal Color


title: Int_1st

description: samples collected in the initial flowering stage of first flowering round


title: CPSF1_RNAseq_2

description:
aCPSF1_2
FPKM of RNA_seq.txt


title: BaumsDatabaseID_12652

value: Slightly Pale


title: Cnt3


title: S2_RNAseq_3

description:
S2_3
FPKM of RNA_seq.txt


title: BaumsDatabaseID_12649


title: Cnt2


title: S2_RNAseq_2

description:
S2_2
FPKM of RNA_seq.txt


title: BaumsDatabaseID_12648


title: S2_RNAseq_1

description:
S2_1
FPKM of RNA_seq.txt


title: MiRNA-Seq liver TSC1 mutant, replicate 4

status: Public on Dec 04 2019

city: Zurich

first: Andrzej

middle: Jerzy

last: Rzepiela

address: John-von-Neumann-Weg 9

department: ScopeM

country: Switzerland

institute: ETH

data_processing:
The raw miRNA sequencing data was uploaded to the ClipZ server (M. Khorshid et al. Nucleic Acids Res 39, D245-252,2011) for adapter removal and annotation.
Differentially expressed miRNAs were extracted using DESeq implemented as a Bioconductor package. A cutoff at 0.05 for the adjusted p-value provided by DESeq was used to filter the hits.
Supplementary_files_format_and_content: The file "normalised_expression_control_mutant.csv" contains normalised (DESeq) miRNA reads for each condition and replicate. In each column normalised miRNA expression values for the control (C) and mutant (M) samples are provided.

source_name: Liver

growth_protocol: Mice were maintained under temperature and humidity-controlled conditions with 12-hour light and 12-hour dark cycle with free access to food and water.

extract_protocol:
Total RNA was isolated from 50mg of mouse liver and was homogenized in 1ml TRIzol (Sigma) using lysing matrix D tubes (Q-Biogene) and a bead beater. Subsequent steps were performed as per TRIzol manufacturer’s instructions.
1ug of total RNA was used to generate small RNA libraries for sequencing as described in R. Gumienny et al.,Nucleic Acids Res 45, 2341-2353 (2017). Libraries were sequenced on an Illumina HiSeq-2500 deep sequencer.

treatment_protocol: Small-RNA sequencing on livers of L-Tsc1KO animals and littermate controls, at 14 weeks of age

value: Liver

value: TSC1 mutant

tag: age

value: 14 weeks


title: MiRNA-Seq liver TSC1 mutant, replicate 5


title: MiRNA-Seq liver TSC1 mutant, replicate 2


title: MiRNA-Seq liver TSC1 mutant, replicate 1


title: MiRNA-Seq liver control, replicate 4

value: control


title: MiRNA-Seq liver control, replicate 5


title: MiRNA-Seq liver TSC1 mutant, replicate 3


title: MiRNA-Seq liver control, replicate 2


title: MiRNA-Seq liver control, replicate 3


title: MiRNA-Seq liver control, replicate 1


title: Full_1st

description: samples collected in the full-blooming flowering stage of the first flowering round


title: Cbln1-EGFP-Rpl10a-NIDA030 cortex IP Rep4

city: New York

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description: 921_Cbln1_TRAP_NIDA030_cortex_IP4_CTTGTA_L001

data_processing:
FASTX Toolkit 0.0.13 was used to assess the quality of reads and trim trailing adaptors.
Trimmed reads were aligned to annotated exons using the mm10 genome using STAR v2.0.0e_r291 using default settings.
Raw counts of mapped reads were generated with HTSeq framework v0.6.0 using the htseq-count module with the "union" mode and default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Text files of counts

source_name: Cbln1-EGFP-Rpl10a-NIDA030 cortex IP

extract_protocol:
The cerebral cortex was dissected and homogenized and tagged polysomes were immunopurified with monoclonal anti-EGFP antibodies bound to biotinylated-Protein L (Thermo Fisher) coated streptavidin-conjugated magnetic beads (Life Technologies). Total RNA from IPs was purified with the Agilent Nanoprep kit following manufacturer's protocol.
Ribosomal-bound RNA was extracted and treated as described in PMID 24810037, Heiman M, Kulicke R, Fenster RJ, Greengard P, Heintz N. (2014) Cell type-specific mRNA purification by translating ribosome affinity purification (TRAP). Nat Protoc. 9:1282-1291

value: Cbln1-TRAP NIDA030

value: adult

value: Cerebral cortex

tag: sample type

value: Immunopurified (IP); Ribosomal-bound RNA


title: Cbln1-EGFP-Rpl10a-NIDA030 cortex IP Rep2

description: 920_Cbln1_TRAP_NIDA030_cortex_IP2_GCCAAT_L001


title: Cbln1-EGFP-Rpl10a-NIDA030 cortex INPUT Rep4

description: 923_Cbln1_TRAP_NIDA030_cortex_Input4_CTTGTA_L002

source_name: Cbln1-EGFP-Rpl10a-NIDA030 cortex INPUT

value: Input; total RNA


title: Cbln1-EGFP-Rpl10a-NIDA030 cortex INPUT Rep2

description: 922_Cbln1_TRAP_NIDA030_cortex_Input2_GCCAAT_L002


title: Cnt1

value: Dissected hindbrain and surrounding tissues

value: wt

value: 28.5°C until 22hpf, 30min at 38.5°C, 2hr 28.5°C


title: 5XFAD_6mo_3

city: Memphis

first: Timothy

middle: Isham

last: Shaw

state: TN

address: 262 Danny Thomas Pl

department: Computational Biology

institute: St Jude Children's Research Hospital

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058776_G1

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using an internal perl script and converted to FPKM using mm9
Genome_build: mm9

source_name: 5XFAD transgenic mice

extract_protocol:
RNAs were extracted by Trizol (Invitrogen) from about 20 mg aliquots of the same tumor samples for proteomics analyses.
For RNAseq, libraries were generated from ~1 µg total RNA using the Illumina Stranded Total RNA kit with the Human/Mouse/Rat Ribo-Zero Gold ribosomal reduction kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry

value: 6 months

value: Cortex

value: amyloid deposition expresses five familial AD (FAD) mutations


title: 5XFAD_6mo_2

description:
Total RNA was extracted from cortex 6 months of age.
SJMMALZ058775_G1