title: LEF1cKO_Rep2

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample. File on series record (WT_LEF1cKO_LEF1TCF7dKO_TPM.txt) includes TPM for all samples.

source_name: Mouse back skin

extract_protocol:
Activated hair gem stem cells (by hair depilation) were purified from wild-type, LEF1 single knock out, and LEF1/TCF7 double knock out mice.
FACS-isolated cells were directly lysed into TRIzol LS (Invitrogen). Total RNA was purified using the Direct-zol RNA MiniPrep kit (Zymo Research) per manufacturer’s instructions. Quality of the RNA for sequencing was determined using an Agilent 2100 Bioanalyzer; all samples used had RNA integrity numbers >8. Library preparation using the Illumina TrueSeq mRNA sample preparation kit was performed at the Weill Cornell Medical College Genomic Core facility (New York), and RNAs were paired-end sequenced on Illumina HiSeq 4000 machines.

value: back skin

value: hair germ stem cells

tag: Sex

value: Mixed

tag: age

tag: sorting markers

value: YFP, integrin b1, CD34, Sca-1, Pcadherin, SCA1


title: LEF1_TCF7dKO_Rep1

status: Public on Jan 11 2018

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: cell type

tag: genotype


title: WT_Rep2


title: Cdx2-/- Villus H3K27me3 ChIP-seq 5+3d biological rep1

city: Boston

first: Ramesh

last: Shivdasani

state: MA

address: 450 Brookline Ave. Dana 720D

department: Medical Oncology

institute: Dana Farber Cancer Institute

description: Cdx2-/- Villus H3K27me3 X-linked ChIP-seq 5+3d biological rep1

library_source: genomic

data_processing:
Alignment: ATAC-seq and ChIP-seq: Bowtie2; RNA-seq: Tophat, version 2.0.6
ATAC-seq and ChIP-seq peak calling: MACS2, version 2.1.1
RNA-Seq - Read counts were obtained using HTSeq and normalized using DeSeq2 with default parameters. DeSeq2 was further used for calculating differntial gene expression (q<0.01).
Genome_build: mm9
Supplementary_files_format_and_content: ATAC-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: ChIP-Seq: bigwig file for visualizing aligned sequence tags
Supplementary_files_format_and_content: RNA-Seq: Table with counts from HTSeq for all genotypes

molecule: genomic DNA

source_name: Mouse intestinal villus epithelial cells

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 5 ug H3K27me3 antibody (EMD Millipore, 07-449) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Mice were injected i.p. with 1mg Tamoxifen for 5 consecutive days to activate tamoxifen-inducible Cre for recombination of conditional alleles, and were sacrificed 3 days after last injection.

tag: strain

value: B6;129 mixed background

value: Adult differentiated jejunal epithelial cells; middle 1/3 of intestine

value: Cdx2f/f; Villin-cre

tag: protocol

value: Villi from middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were cross-linked and immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.


title: LEF1_TCF7dKO_Rep2


title: Cdx2-/- Villus H3K27ac MNase ChIP-seq biological rep1

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ul H3K27ac antibody (Active Motif, 39135) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.

value: Villi from middle 1/3rd (jejunum) of mouse small intestine were isolated by incubating in 5mM EDTA in PBS for 45 minutes at 4°C. Cells were immediately snap-frozen in liquid nitrogen for subsequent ChIP analysis.


title: Cdx2-/- Villus H3K4me2 MNase ChIP-seq biological rep1

extract_protocol:
Villus chromatin digested with MNase was incubated overnight with 5 ul H3K4me2 antibody (EMD Millipore, 07-030) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K4me2 MNase ChIP-seq biological rep1

treatment_protocol: Mice were injected i.p. with sunflower oil (vehicle for tamoxifen) for 5 consecutive days and were sacrificed 3 days after last injection.


title: Wild-type Villus KDM6A ChIP-seq biological rep2

description: Wild-type Villus KDM6A X-linked ChIP-seq biological rep2

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with Dyna beads (Thermo Fisher Scientific) conjugated with 5 ug KDM6A antibody (Cell Signaling Technology, 33510) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus H3K27ac MNase ChIP-seq biological rep1


title: Wild-type Villus Input_Mnase

description: Wild-type Villus Input_Mnase

extract_protocol:
Fraction of villus chromatin digested with MNase was used as input.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: LEF1cKO_Rep1


title: Cdx2-/- Villus KDM6A ChIP-seq biological rep2

description: Cdx2-/- Villus KDM6A X-linked ChIP-seq biological rep2


title: WT_Rep1


title: Wild-type Villus KDM6A ChIP-seq biological rep3

description: Wild-type Villus KDM6A X-linked ChIP-seq biological rep3


title: Wild-type Villus Mediator1 ChIP-seq biological rep1

description: Wild-type Villus Mediator1 X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with Dyna beads (Thermo Fisher Scientific) conjugated with 5 ug MED1 antibody (Bethyl Laboratories, A300-793A) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus CTCF ChIP-seq biological rep1

description: Wild-type Villus CTCF X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 7 ul CTCF antibody (EMD Millipore, 07-729) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Cdx2-/- Villus RNA PolII ChIP-seq biological rep1

description: Cdx2-/- Villus RNA PolII X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 1% formaldehyde were sonicated and incubated overnight with 5 ug RNAPII antibody (Santa Cruz, sc-899) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Cdx2-/- Villus CDX2 ChIP-seq biological rep1

description: Cdx2-/- Villus CDX2 X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 2 mM DSG and 1% formaldehyde were sonicated and incubated overnight with Dyna beads (Thermo Fisher Scientific) conjugated with 0.5 ug CDX2 antibody (Cell Signaling Technology, 12306) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Cdx2-/- Villus PBRM1 ChIP-seq biological rep1

description: Cdx2-/- Villus PBRM1 X-linked ChIP-seq biological rep1

extract_protocol:
Whole cell extracts from villi fixed with 2 mM DSG and 1% formaldehyde were sonicated and incubated overnight with Dyna beads (Thermo Fisher Scientific) conjugated with 5 ug PBRM1/BAF180 antibody (Bethyl Laboratories, A301-591A) for immunoprecipitation.
ThruPLEX DNA-seq Kit (Rubicon Genomics) was used to prepare libraries, and 75 bp single-end reads were sequenced on an Illumina NextSeq 500 instrument.


title: Wild-type Villus PBRM1 ChIP-seq biological rep1

description: Wild-type Villus PBRM1 X-linked ChIP-seq biological rep1


title: Wild-type Villus RNA PolII ChIP-seq biological rep1

description: Wild-type Villus RNA PolII X-linked ChIP-seq biological rep1


title: sbTAC_Rep2_ATAC

description:
processed data file:
sbTAC_ATAC_mm10_peaks.txt

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
Duplicates were removed using Picard. ATAC-seq signal tracks were presented by Integrative Genomics Viewer (IGV) software
Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Text file containing peak calling resutls

extract_protocol:
Bulge hair follicle stem cells (GFP+/CD34+/Itga6+/Itgb1+) and hair germ cells (GFP+/CD34-/Itga6+/Itgb1+) at the second telogen and basal TACs e (GFP-/CD34-/Itgb1high/Pcad+/SCA1-) and suprabasal TACs (GFPlow/Itga6-/CD34-) are FACS-purified and immediately sujected to ATAC-seq library generation.
FACS-sorted cells were pelleted and incubated with cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). After removing lysis buffer by centrifugation, samples were  subjected to a transposition reaction at 37°C for 30 min with 10μL transposase enzyme (Illumina Nextera DNA Preparation Kit). Transposed DNA was purified using QIAGEN MiniElute PCR purification kit and PCR amplified with 10-15 cycles. Library concentration and quality was assayed by D1000 Tape Station (Agilent) prior to sequencing. The samples were sequenced on Illumina HiSeq 2000 using a 50bp paired-end-reads setting.

value: suprabasal TAC

value: GFP, SCA1, CD34, integrin α6


title: Cdx2-/- Villus KDM6A ChIP-seq biological rep1

description: Cdx2-/- Villus KDM6A X-linked ChIP-seq biological rep1


title: bTAC_Rep1_ATAC

description:
processed data file:
bTAC_ATAC_mm10_peaks.txt

value: basal TAC

value: GFP, PCAD, SCA1, integrinß1, CD34


title: Wild-type Villus CDX2 ChIP-seq biological rep2

description: Wild-type Villus CDX2 X-linked ChIP-seq biological rep2


title: BU_Rep2_ATAC

description:
processed data file:
BU_ATAC_mm10_peaks.txt

value: bulge hair follicle stem cell

value: GFP, CD34, integrin α6, integrinß1


title: HG_Rep2_ATAC

description:
processed data file:
HG_ATAC_mm10_peaks.txt

value: hair germ cells


title: bTAC_Rep2_ATAC


title: Wild-type Villus CDX2 ChIP-seq biological rep1

description: Wild-type Villus CDX2 X-linked ChIP-seq biological rep1


title: Ana-VI_sbTACs_LEF1_ChIP-seq

description: Chromatin IP against LEF1

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm9, build 37) using the Bowtie program (Version 0.1.2.7). Unique reads mapped to a single genomic location (allowing two mismatches) were kept for peak identification.
Peak detection was performed with the software MACS (Version 1.4.2) with input as controls.
wig files created using IGVtools with 25bp windows with no extension to reads.
Genome_build: mm9
Supplementary_files_format_and_content: wig files; enrichment values in 25bp windows

extract_protocol:
Mouse sbTACs were FACS-purified from K14-H2BGFP mice at P30.
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody (LEF1, Abcam, #ab12034).  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 25 cycles and library fragments of 150-300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: suprabasal TACs

tag: hair cycle stage

value: Anagen VI

value: Female

value: K14-H2BGFP (CD1)

value: GFP, integrin α6, CD34, Sca-1

tag: chip antibody


title: BU_Rep1_ATAC

value: back skin

value: Mixed


title: Wild-type Villus KDM6A ChIP-seq biological rep1

description: Wild-type Villus KDM6A X-linked ChIP-seq biological rep1

value: B6;129 mixed background

value: Adult differentiated jejunal epithelial cells; middle 1/3 of intestine


title: Ana-VI_sbTACs_Input_DNA

description: Input DNA


title: RNA-Seq from BCOR-R cells, day 2

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

data_processing:
Reads were trimmed with Trimmomatic Version 0.32, parameters:ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed reads were mapped to the GRCh38 build of the human genome with STAR (version STAR_2.4.2a_modified)
Mapped reads were indexed and sorted with samtools 1.0
Peaks in BCOR dataset were called with MACS2 (version  2.1.0.20150731 ) with the options --broad --broad-cutoff 0.1 -g hs.
Gene quantification and differential expression was performed using  Salmon (version 0.8.2) with Gencode (Version 27), tximport (1.4.0), and DESeq2  (1.16.1).
Genome_build: hg38

molecule: polyA RNA

organism: Homo sapiens

source_name: Cultured Human Embryonic Stem Cells

growth_protocol: H1 cells were maintained in mTeSR media (StemCell Technologies) on Matrigel-coated plates (BD Biosciences). Cultures were split every 5-6 days by adding 1 mg/ml Dispase (StemCell Technologies) for 5–10 min at 37°C, dissociation, and replating onto fresh plate at the ratio 1:4.

extract_protocol:
RNAeasy Micro Kit (Qiagen) was used to prepare RNA from the samples described above.
TruSeq (Illumina) RNA libraries were prepared from the recovered RNA.

treatment_protocol: 1 ug/ml Doxycyclin were applicable.

value: H1 hESC

value: BCOR-R

tag: media

value: mTeSR (StemCell Technolgies)

tag: media supplement

tag: antibody

tag: fixation strategy

tag: sonication strategy


title: RNA-Seq from BCOR-R cells, day 3


title: RNA-Seq from BCOR-R cells, day 4


title: RNA-Seq from BCOR-R cells, day 0

value: 1micro/ml Doxycyclin


title: RNA-Seq from BCOR-R cells, day 5


title: RNA-Seq from BCOR-R cells, day 1


title: GRC303_95

city: Research Triangle Park

first: Brian

middle: Norris

last: Chorley

state: NC

address: 109 TW Alexander Dr

department: ORD

institute: US Environmental Protection Agency

description: small RNA

data_processing:
Basecalling was performed using RTA v2
Fastq files generated using bcl2fastq  with the following options: --ignore-missing-bcls --ignore-missing-filter --ignore-missing-positions --ignore-missing-controls --auto-set-to-zero-barcode-mismatches --find-adapters-with-sliding-window --adapter-stringency 0.9 --mask-short-adapter-reads 35 --minimum-trimmed-read-length 35 -R "/data/scratch/workspace/RunFolder" --sample-sheet "/data/scratch/workspace/RunFolder/SampleSheet.csv" -o "/data/scratch/workspace/RunFolder/Analysis/Fastq" -i "/data/scratch/workspace/RunFolder/Data/Intensities/BaseCalls"
Illumina adapters were trimmed using the Illumina Basespace app FASTQ Toolkit version 2.0.0. keeping sequences 16 bp and greater. Reads were further trimmed on quality score in Partek Flow (Build version 6.0.17.0723) with default settings except Min read length was set to 15
Trimmed reads were aligned to the rat genome (rn5) in Partek Flow using Bowtie v 1.0.0 with default setting except Seed mismatch limit was set 1 and Seed length was set to 10.
Aligned reads were quantified to miRBase mature microRNAs (version 21) in Parek Flow using Partek E/M with default settings
Raw microRNA counts were normalized in Partek Flow using the trimmed mean of M-values (TMM) method, then adding 1.0E-4 to all counts
Genome_build: rn5
Supplementary_files_format_and_content: All_Samples_microRNA_Normalized_counts.txt is a tab-delimited text file containing normalized counts for all processed samples
Supplementary_files_format_and_content: All_Samples_Raw_microRNA_counts.txt is a tab-delimited text file containing raw microRNA counts for all samples

organism: Rattus norvegicus

source_name: serum

extract_protocol:
Serum and EDTA plasma samples were collected from the abdominal aorta. 100 µl of serum thawed on ice were centrifuged at 3000 X g for 5 min. Small RNA was isolated using miRCURY RNA Isolation Biofluids Kit following manufacturer's instructions, including an optional on-column DNase digestion (Exiqon, Woburn, MA).
Indexed small RNA sequencing libraries were prepared using CleanTag Small RNA Library Prep Kit (TriLink BioTechnologies, San Diego, CA) with 10 ng of purified input RNA following manufacturer's instructions. Libraries were quantified using Bioanalyzer High-Sensitivity DNA chip, pooled, and were sequenced using a NextSeq 500 sequencer on High Output mode (Illumina, San Diego, CA) using 50 cycles of single-end reads.

treatment_protocol: Male Wistar Kyoto (WKY) rats were purchased from Charles Rivers Laboratories (Raleigh, NC) and brought to our AAALAC-approved animal facility at 4 wks old.  Animals were housed two/cage in polycarbonate cages with beta chip bedding and kept on a 12h light/dark cycle.  All experimental protocols were approved by the U.S. EPA's Institutional Animal Care and Use Committee (IACUC). Animals were fed either our normal facility food (Rodent Chow 5001, Ralston Purina Laboratories, St. Louis, MO) or a diet enriched with 6% by weight fish oil (Teklad Custom Research Diets #TD.140729, Harlan Laboratories, Inc.).  Animals were given water and food ad libitum starting at 4 weeks old for 8 weeks until exposure.   Animals were exposed to either filtered air or 0.8 ppm ozone for 4h/day for 2 consecutive days. The average (mean ± SEM) air temperature (75.01 ± 0.21), relative humidity (49.84 ± 0.30), and ozone concentration (0.8045 ± 0.0027 ppm) were monitored continuously.

value: Wistar Kyoto rats

tag: diet

value: fish oil

tag: exposure

value: ozone


title: sbTAC_Rep1_ATAC

value: suprabasal TAC

tag: Sex

value: GFP, SCA1, CD34, integrin α6


title: GRC303_94

description: small RNA


title: RNA-Seq from RNF2-R cells, day 6


title: GRC303_93

description: small RNA


title: HG_Rep1_ATAC

value: hair germ cells

tag: age

value: GFP, CD34, integrin α6, integrinß1


title: GRC303_91

description: small RNA


title: GRC303_92

description: small RNA


title: RNA-Seq from RNF2-R cells, day 1


title: GRC303_77

description: small RNA

value: air


title: GRC303_90

description: small RNA


title: GRC303_79

description: small RNA


title: GRC303_75

description: small RNA


title: RNA-Seq from RNF2-R cells, day 3


title: RNA-Seq from RNF2-R cells, day 0


title: RNA-Seq from RNF2-R cells, day 4


title: RNA-Seq from BCOR-R cells, day 6


title: GRC303_73

description: small RNA


title: RNA-Seq from RNF2-R cells, day 2


title: GRC303_29

description: small RNA

value: normal


title: GRC303_74

description: small RNA


title: RNA-Seq from KDM2B KO rep 1

value: KDM2B KO clone 1


title: RNA-Seq from RNF2-R cells, day 5


title: GRC303_27

description: small RNA


title: GRC303_25

description: small RNA


title: GRC303_26

description: small RNA


title: GRC303_16

description: small RNA


title: GRC303_76

description: small RNA


title: GRC303_28

description: small RNA


title: GRC303_30

description: small RNA


title: RNA-Seq from WT H1 Cells

value: WT


title: GRC303_12

description: small RNA


title: RNA-Seq from Control2 shRNA treated cells rep 2

description: H1_shCntrl2 Rep2

value: shRNA Cntrl


title: GRC303_11

description: small RNA


title: GRC303_9

description: small RNA


title: FB1+FB2_ax_1

city: Cambridge

first: Clement

last: Pellegrin

address: Downing Site

department: Plant Sciences

country: United Kingdom

institute: University of Cambridge

description:
Sample 1
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt

data_processing:
Reads were quality-filtered (PhredScores lower 20), trimmed for the TruSeq adapters and statically trimmed 12 nucleotides at the 5’ end. Reads smaller than 50 nucleotides were discarded. When the paired-end reads did overlap with at least 10 nucleotides, they were merged to single reads. All analysis was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all reads were filtered against the maize genes (90% identity over 80% of the sequence) and only un-mapped reads were mapped against the U. maydis genes (80% identity over 60% of the sequence). Mapping was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the Z. mays analysis, all reads were filtered against the U. maydis genes (90% identity over 60% of the sequence) and only un-mapped reads were mapped against the Z. mays genes (90% identity over 80% of the sequence). Mapping was performed using the CLC Genomics Workbench v8.5 (CLC Bio-Qiagen).
For the U. maydis analysis, all unique exon read counts of the samples 1-24 were normalized using DESeq2 v1.10.
For the Z. mays analysis, all unique exon read counts of the samples 3-45 were normalized using DESeq2 v1.10.
Genome_build: The U. maydis reference genome was from NCBI (https://www.ncbi.nlm.nih.gov , accession numbers NC_026478.1 - NC_026500.1, NW_011929455.1 - NW_011929458.1, NC_008368.1).
Genome_build: The Z. mays reference genome was from Ensembl (http://plants.ensembl.org/info/website/ftp/index.html  Zea_mays.AGPv3.28.dna.toplevel).
Supplementary_files_format_and_content: *txt: Tab-delimited text files containing total number of unique exon counts for each U. maydis gene (Counts_Um.txt), DESeq2-normalized counts for each U. maydis gene (NormCounts_Um.txt), total number of unique exon counts for each Z. mays gene (Counts_Zm.txt), DESeq2-normalized counts for each Z. mays gene (NormCounts_Zm.txt).

organism: Mycosarcoma maydis

source_name: fungal axenic culture

growth_protocol: Ustilago maydis strains FB1 and FB2 were grown to OD600=1.0 in YEPSL, pelleted and resuspended in water. The compatible strains were mixed in equal quantities and injected into 7-day-old maize seedlings.

extract_protocol:
For each sample, leaf sections from 10 different plants infected with FB1 x FB2 U. maydis wild type strains were collected, pooled and frozen in liquid nitrogen. Samples were ground to a fine powder in liquid nitrogen and total RNAs were extracted using the TRIzol method (Invitrogen).
Sequencing libraries were prepared with the Illumina TruSeq stranded mRNA library Prep Kit starting from 2µg total RNA.

tag: fungal strain

value: FB1 plus FB2

tag: fungal cell type

value: yeast-like cells


title: FB1+FB2_ax_3

description:
Sample 3
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt


title: FB1+FB2_ax_2

description:
Sample 2
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt


title: RNA-Seq from Ring1/RNF2 shRNA treated cells rep 1

description: H1_shRAB Rep1

tag: cell type

value: H1 hESC

value: shRNA Ring1, shRNA RNF2


title: RNA-Seq from Ring1/RNF2 shRNA treated cells rep 2

description: H1_shRAB Rep2

tag: genotype

value: mTeSR (StemCell Technolgies)


title: GRC303_15

description: small RNA

tag: strain

value: Wistar Kyoto rats


title: ATF6+/+ hMSC vehicle-2 H3K4me3 ChIP-seq

city: Beijing

first: Boqiang

middle: John

last: Hu

address: 5th Yiheyuan Road

department: bio-dynamic imaging center

country: China

institute: Peking university

data_processing:
QC: For RNA Seq, the whole pipeline were availuable in https://github.com/huboqiang/RNA_v2 for details.
RNA-seq: Tophat(v2.0.9) mapping
RNA-seq: Cufflinks(v2.2.11) quantification
QC: For ChIP Seq, the whole pipeline were availuable in https://github.com/huboqiang/ChIP
ChIP-seq: bwa mapping(0.7.5a)
ChIP-seq: macs2(v2.1.0.20150731) calling peaks with IDR pipeline
Genome_build: hg19
Supplementary_files_format_and_content: processed data of RNA seq were  FPKM values in csv format. ChIP-Seq data were narrowPeaks results of MACSs2

source_name: MSC

growth_protocol: hESCs were maintained on Matrigel-coated plates with mTeSR medium. hMSCs were cultured in aMEM medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin, 0.1 mM non-essential amino acids, and 1 ng/ml bFGF. hWAPCs were cultured in DMEM medium with 7.5% KOSR, 7.5% BSA, 0.5% non-essential amino acids, 0.5% penicillin/streptomycin, 0.1 mM dexamethasone, 10 mg/ml insulin and 0.5 mM Rosiglitazone.

extract_protocol:
Total RNA was extracted  with Trizol reagent. To obtain the genomic DNA  fragments of interest, the cells were crosslinked and lysed, and then the chromatin was sheared into fragments using sonication. Then samples were incubated with anti-H3K4me3 antibody(Abcam, ab8580) or anti-FLAG(Sigma, F1804) antibody overnight. The DNA was de-crosslinked and extracted on the next day.
1.5 μg of total RNA was used to construct RNA sequencing libraries by TruSeq RNA Sample Preparation Kit (Illumina) following the manufacturer’s recommended protocol. After the DNA was de-crosslinked and extracted, the ChIP-sequencing library was constructed by TruSeq DNA Sample Preparation Kit (Illumina) or NEBNext® DNA Library Prep Reagent Set (NEB) according to the manufacturer’s instructions.

treatment_protocol: Cell were treated with vehicle or Tunicamycin for 12 hours.

value: MSC

tag: treatment

value: vehicle

tag: passages


title: ATF6+/+ hMSC tunicamycin-1 H3K4me3 ChIP-seq

value: tunicamycin

tag: chip antibody


title: ATF6+/+ hMSC vehicle-3 H3K4me3 ChIP-seq


title: RNA-Seq from Control shRNA treated cells rep 2

description: H1 shCntrl1 Rep2

tag: media


title: ATF6+/+ hMSC tunicamycin-2 H3K4me3 ChIP-seq


title: RNA-Seq from Control2 shRNA treated cells rep 1

description: H1_shCntrl2 Rep1

tag: media supplement


title: RNA-Seq from KDM2B KO rep 2

value: KDM2B KO clone 2

tag: antibody


title: RNA-Seq from BCOR shRNA treated cells rep 2

description: H1 shBCOR Rep2

value: shRNA BCOR

tag: fixation strategy


title: ATF6+/+ hMSC tunicamycin-3 H3K4me3 ChIP-seq


title: ATF6+/+ hMSC vehicle-1 H3K4me3 ChIP-seq


title: ATF6-/- hMSC tunicamycin-1 H3K4me3 ChIP-seq


title: ATF6-/- hMSC tunicamycin-2 H3K4me3 ChIP-seq


title: ATF6-/- hMSC vehicle-3 H3K4me3 ChIP-seq


title: ATF6-/- hMSC tunicamycin-3 H3K4me3 ChIP-seq


title: KDM2B ChIP from RNF2-R Cells (plus dox)

extract_protocol:
ChIP DNA samples for sequencing were prepared by reversing protein-DNA cross-links at 55°C to help maintain duplex fragments.   PCR cleanup with minElute PCR Purification kits yielded 20 ul  ChIP DNA which was used immediately in a 23.3 ul combined End-Repair, A-Tailing reaction (KAPA Hyperprep KK8502) for 30 min at 20°C followed by 30 minutes at 65°C.  Ten ul of ligase buffer, 3.7 ul of Y-Adapters diluted 1:50 (Illumina 5179206) and 3.3 ul ligase (KAPA KK8502) were added and incubated at 20°C for 4 hours.  Double stranded DNA fragments were purified from this reaction with bead cleanup (0.8X, Kapa Pure Beads KK8000) and eluted in 22 ul 10mM Tris ph 8.0.  The amplification cycle number was determined empirically by using 1 ul of the eluent in a 10 ul test reaction containing 1:10,000 dilution of SYBR Green (Thermo Scientific/Invitrogen #S7563), 2x KAPA HotStart ReadyMix (Kapa KM2618) and custom barcoding primers.   An appropriate number of cycles was used in a subsequent 50 ul reaction with the remaining eluent in the absence of SYBR Green.  Libraries were size selected on a 2% eGEL (Thermo Scientific /Invitrogen G402002) and fragments between 150 and 350 bp were extracted using a Qiagen Gel Extraction Kit performed at room temperature.  Libraries were quantitated with a high sensitivity DNA Qubit (Thermo Scientific / Invitrogen Q32854) and pooled prior to submission to the University of Minnesota Genomics Center for quality control analyses and next-generation sequencing.
TruSeq (Illumina) RNA libraries were prepared from the recovered RNA.

value: 1micro/ml Doxycyclin

value: KDM2B (rabbit A) (Beguelin et al, 2016, Gearhart et al, 2006)

value: ethylene glycol bis(succinimidyl succinate) + formaldehyde

tag: sonication strategy

value: Covaris S220


title: KDM2B ChIP from RNF2-R Cells (minus dox)


title: ATF6-/- hMSC vehicle-2 H3K4me3 ChIP-seq


title: GRC303_14

description: small RNA

tag: diet

value: normal

value: air


title: BCOR ChIP from RNF2-R Cells (plus dox)

description: BCOR_H1_rnf2rplus_081817_broad_peaks.broadPeak.gz

value: BCOR 185 (Beguelin et al, 2016)


title: RNA-Seq from BCOR shRNA treated cells rep 1

description: H1 shBCOR Rep1


title: Input DNA from RNF2-R Cells (minus dox)

description: BCOR_H1_rnf2rminus_081817_broad_peaks.broadPeak.gz


title: ATF6-/- hMSC vehicle-1 H3K4me3 ChIP-seq


title: ATF6+/+ hMSC tunicamycin-3 IgG ChIP-seq

value: IgG


title: RNA-Seq from Control shRNA treated cells rep 1

description: H1 shCntrl1 Rep1

value: H1 hESC

value: shRNA Cntrl


title: ATF6+/+ hMSC tunicamycin-2 IgG ChIP-seq


title: ATF6+/+ hMSC tunicamycin-1 IgG ChIP-seq


title: ATF6+/+ hMSC vehicle-1 IgG ChIP-seq


title: Input DNA from RNF2-R Cells (plus dox)

value: mTeSR (StemCell Technolgies)


title: Input DNA from Wild Type Cells (Bioruptor)

value: WT

value: Bioruptor


title: H3K36me2 ChIP Sample from Wild Type Cells (Bioruptor)

value: H3K36me2 Upstate 07-369


title: UbH2A ChIP Sample from Wild Type Cells

value: UbH2A Cell Signaling 8240S


title: BCOR ChIP from KDM2B Knockout Cells

description: BCOR_H1_k2bko_081817_broad_peaks.broadPeak.gz

value: KDM2B KO

value: formaldehyde


title: 24_H_FN10

city: St. Andrews

first: David

last: Shuker

address: Greenside Place

department: School of Biology

institute: University of St Andrews

description: ReadCountsPerGene.txt

data_processing:
Raw reads were filtered for quality (reads with a Phred quality score of 30 or higher were retained) and adapter contamination using cutadapt (v1.8.3).
Filtered, adapter-trimmed reads were subsequently aligned to the Nasonia vitripennis genome (Assembly Nvit 2.1: NCBI Accession: GCF_000002325.3) using tophat2 (version 2.0.14).
Read counts per gene were obtained using HTSeq (v6.0.1) “union” mode with “NCBI Nasonia vitripennis Annotation Release 101”.
Genome_build: Assembly Nvit 2.1: NCBI Accession: GCF_000002325.3
Supplementary_files_format_and_content: Matrix table of read counts per gene per sample in excel format. Read counts are raw, i.e. not normalised.

organism: Nasonia vitripennis

source_name: Nasonia vitripennis female heads

growth_protocol: The focal females used in this experiment were from the AsymC strain, originally isolated in 1986 by curing the wild-type strain LabII of Wolbachia and is known to be free of sex-ratio distorters [34,35]. Wasps have been maintained on Calliphora vomitoria or C. vicina hosts at 25 °C, 16L:8D light conditions ever since. Where co-foundresses were required, these were taken from the red-eye mutant STDR strain, allowing us to track the offspring of a single AsymC female using eye colour. The STDR strain is maintained under conditions identical to the AsymC strain.

extract_protocol:
RNA was isolated from 12 pooled heads using the TRIzol Plus RNA Purification Kit in conjunction with the PureLink RNA Mini Kit (Life Technologies, Paisley, UK) according to the manufacturer’s instructions. Additional steps for “On-Column PureLink DNase Treatment During RNA Purification” were followed.
mRNA library preparation for paired-end sequencing was carried out using the Illumina TruSeq RNA Sample Prep Kit (Illumina, San Diego, CA) following the Illumina TruSeq Sample Preparation v2 (Low Sample) protocol. Briefly, mRNA was purified from total RNA samples using oligo-dT attached magnetic beads and fragmented using divalent cations at 94 °C. First-strand cDNA synthesis was carried out using reverse transcriptase and random hexamer primers. Second-strand synthesis was carried out using RNA polymerase I and RNase H. Overhangs resulting from fragmentation were converted to blunt ends and 3’ ends were subsequently adenylated. Sanger indexing adapters were ligated to the fragments that were then purified and PCR-amplified to create the final cDNA libraries for sequencing.

treatment_protocol: Females were allocated to one of three “foundress number” groups: (i) single foundress, (ii) five foundress (i.e. one experimental female plus four STDR co-foundresses ovipositing simultaneously) or (iii) ten foundress (i.e. one experimental female plus nine STDR co-foundresses ovipositing simultaneously). Females were given access to three hosts and allowed to explore the hosts and oviposit for three hours. At the end of the three-hour period, focal females were identified by eye colour and their heads excised and placed into RNAlater (ThermoFisher Scientific, Waltham MA, USA).

value: AsymC

tag: experimental treatment

value: Ten foundress

tag: tissue

value: 12x adult female heads


title: 22_H_FN10

description: ReadCountsPerGene.txt


title: Input DNA from KDM2B Knockout Cells

value: Covaris S220


title: ATF6-/- hMSC tunicamycin-3 IgG ChIP-seq

value: MSC

value: tunicamycin


title: ATF6+/+ hMSC vehicle-3 IgG ChIP-seq

value: vehicle


title: 23_H_FN10

description: ReadCountsPerGene.txt


title: ATF6-/- hMSC tunicamycin-2 IgG ChIP-seq

value: IgG


title: 21_H_FN10

description: ReadCountsPerGene.txt


title: PCGF1 ChIP Sample from Wild Type Cells

value: H1 hESC

value: PCGF1 (Oliviero, 2015, Gearhart et al, 2006)

value: ethylene glycol bis(succinimidyl succinate) + formaldehyde


title: RYBP ChIP Sample from Wild Type Cells

value: WT

value: mTeSR (StemCell Technolgies)

value: RYBP Chemicon Ab3637


title: 18_H_FN10

description: ReadCountsPerGene.txt


title: ATF6-/- hMSC tunicamycin-1 IgG ChIP-seq


title: RNF2 ChIP Sample from Wild Type Cells

value: A302869A (Bethyl)


title: ATF6-/- hMSC vehicle-3 IgG ChIP-seq


title: ATF6+/+ hMSC vehicle-2 IgG ChIP-seq


title: KDM2B ChIP Sample from Wild Type cells

value: KDM2B (rabbit A) (Beguelin et al, 2016, Gearhart et al, 2006)


title: BCOR ChIP from RNF2-R Cells (minus dox)

value: BCOR 185 (Beguelin et al, 2016)


title: 14_H_FN5

description: ReadCountsPerGene.txt

value: AsymC

value: Five foundress


title: 15_H_FN5

description: ReadCountsPerGene.txt

value: 12x adult female heads


title: ATF6-/- hMSC vehicle-2 IgG ChIP-seq


title: 17_H_FN10

description: ReadCountsPerGene.txt

value: Ten foundress


title: BCOR ChIP Sample from Wild Type cells

value: Vivian Bardwell Lab; University of Minnesota, Cat# anti-BCOR, RRID:AB_2716801

value: formaldehyde

value: Covaris S220


title: 13_H_FN5

description: ReadCountsPerGene.txt


title: 11_H_FN5

description: ReadCountsPerGene.txt


title: 12_H_FN5

description: ReadCountsPerGene.txt


title: ATF6-/- hMSC vehicle-1 IgG ChIP-seq

value: MSC

value: vehicle

value: IgG


title: ATF6+/+ hMSC vehicle-2 RNA-seq


title: 8_H_FN1

description: ReadCountsPerGene.txt

value: Single foundress


title: ATF6+/+ hMSC vehicle-1 RNA-seq


title: 19_H_FN10

description: ReadCountsPerGene.txt


title: 10_H_FN5

description: ReadCountsPerGene.txt


title: ATF6+/+ hMSC tunicamycin-2 RNA-seq

value: tunicamycin


title: 6_H_FN1

description: ReadCountsPerGene.txt


title: 7_H_FN1

description: ReadCountsPerGene.txt


title: Input DNA from Wild Type cells

value: H1 hESC

value: WT

value: mTeSR (StemCell Technolgies)

value: ethylene glycol bis(succinimidyl succinate) + formaldehyde


title: 5_H_FN1

description: ReadCountsPerGene.txt


title: 20_H_FN10

description: ReadCountsPerGene.txt


title: 16_H_FN5

description: ReadCountsPerGene.txt


title: ATF6+/+ hMSC tunicamycin-1 RNA-seq


title: 4_H_FN1

description: ReadCountsPerGene.txt


title: ATF6-/- hMSC tunicamycin-2 RNA-seq


title: ATF6-/- hMSC tunicamycin-1 RNA-seq


title: PC9-GR3, late emerging T790M clone and treated with WZ4002 for 24 hrs [miRNA-seq]

first: Wen Cai

last: Zhang

state: MASSACHUSETTS

address: 330 BROOKLINE AVENUE, CLS417

department: Pathology

institute: Beth Israel Deaconess Medical Center

description:
processed data file:
comparison_3.xls

data_processing:
The 3' adaptor was trimmed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned to the human genome and miRbase using Bowtie.
Genome_build: GRCh37; miRbase v21;
Supplementary_files_format_and_content:
comparison_1.xls: miRNA expression profile of VEH_PC9_parental, GEF_PC9_G01, AZD_PC9_A01, VEH_HCC827, GEF_HCC827, AZD_HCC827
comparison_2.xls: miRNA expression profile of Veh_PC9_EL, Veh_PC9_GP2, Gef_PC9_GP2, Veh_PC9_GP2, WZ4002_PC9_WP2
comparison_3.xls: miRNA expression profile of Veh_PC9_EL, Gef_PC9_EL, WZ4002_PC9_EL, Veh_PC9B, WZ4002_PC9B, Veh_PC9C, WZ4002_PC9C, Veh_PC9_ET13, WZ4002_PC9_ET13, Veh_PC9_LT12, WZ4002_PC9_LT12

source_name: Lung cancer

growth_protocol: Human lung EGFR mutant cell lines H1975, HCC827, PC9 and PC9ER (provided by Dr. Susumu Kobayashi) were cultured in DMEM (high glucose) (GIBCO) with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin. For 3D organoid formation, single-cell suspensions (2000 cells/well/20 ul) were co-plated with geltrex (25 ul) in 96-well non-treated clear plate (Corning, cat# 08-772-53). The plate was incubated 20 minutes at 37c followed by adding 100 ul complete growth media. The comple growth media is advanced DMEM/F12 with glutamax (1x), HEPES (1x), 1.25 mM NAC (N-Acetylcysteine), 10 mM Nicotinamide (NTM), 10 uM Forskolin (FSK), B27 (1x), 5 ng/ml Noggin, 20 ng/ml FGF2, 50 ng/ml EGF, 10 uM Y-27632 and 1% penicillin-streptomycin.  For differentiation, 10 ng/ml PDGFa and 10 ng/ml FGF7 were supplemented into the above meida from day 7 to day 24. Y-27632 was used only for the initial three days. The media was changed every three days.

extract_protocol:
RNA was extracted with mirVana miRNA isolation Kit in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.
Illumina Truseq Small RNA Preparation

treatment_protocol: To establish gefitinib or osimertinib tolerant cells, EGFR mutated cells (HCC827 cells and PC9 cells) were treated with 40 nM gefitinib for 14 days, respectively. To establish gefitinib or WZ4002 persistent cells, PC9 cells were treated with 40 nM gefitinib and WZ4002 for 14 days, respectively. Gefitinib-resistant PC9-GR2 and PC9-GR3 cells were established by culturing parental cells in escalating concentrations of gefitinib (10 nM–1 μM). Early, drug-tolerant and late PC9 resistant clones were established by culturing in 300 nM gefitinib until resistant, at which point they were maintained in 1 μM gefitinib. During generation of resistance, medium and drug were replaced twice per week.

tag: cell line background

value: lung cancer cell line

tag: phenotype

value: resistant to gefitinib, partial sensitive to WZ4002


title: early emerging T790M clone and treated with WZ4002 [miRNA-seq]

description:
processed data file:
comparison_3.xls

value: resistant to gefitinib, sensitive to WZ4002


title: early emerging T790M clone [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: 3_H_FN1

description: ReadCountsPerGene.txt

value: AsymC

value: 12x adult female heads


title: late emerging T790M clone [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: PC9-GR3, late emerging T790M clone [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: late emerging T790M clone and treated with WZ4002 [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: 1_H_FN1

description: ReadCountsPerGene.txt


title: ATF6+/+ hWAPC vehicle-2 RNA-seq

source_name: WAPC

value: WAPC


title: PC9-GR2, early emerging T790M clone [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: PC9 treated with WZ4002 for 24 hrs [miRNA-seq]

description:
processed data file:
comparison_3.xls

value: sensitive to gefitinib


title: PC9 treated with gefitinib for 24 hrs [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: PC9 persisters after 2 weeks WZ4002 and treated with WZ4002 for 24 hrs [miRNA-seq]

description:
processed data file:
comparison_2.xls

value: persistent to WZ4002


title: ATF6+/+ hWAPC tunicamycin-2 RNA-seq


title: ATF6+/+ hWAPC vehicle-1 RNA-seq


title: ATF6+/+ hWAPC tunicamycin-1 RNA-seq


title: PC9 persisters after 2 weeks gefitinib and treated with gefitinib for 24 hrs [miRNA-seq]

description:
processed data file:
comparison_2.xls

value: persistent to gefitinib


title: PC9 persisters after 2 weeks WZ4002 [miRNA-seq]

description:
processed data file:
comparison_2.xls


title: ATF6-/- hMSC vehicle-2 RNA-seq

value: MSC

value: vehicle


title: ATF6-/- hWAPC tunicamycin-2 RNA-seq


title: ATF6-/- hWAPC tunicamycin-1 RNA-seq


title: ATF6-/- hWAPC vehicle-2 RNA-seq


title: HCC827OTR [miRNA-seq]

description:
processed data file:
comparison_1.xls

value: tolerance to osimiertinib


title: ATF6-/- hWAPC vehicle-1 RNA-seq


title: PC9-veh [miRNA-seq]

description:
processed data file:
comparison_2.xls; comparison_3.xls

value: sensitive to gefitinib and osimertinib


title: PC9-GR2, early emerging T790M clone and treated with WZ4002 for 24 hrs [miRNA-seq]

description:
processed data file:
comparison_3.xls


title: ATF6-/- hMSC vehicle-1 RNA-seq


title: 2_H_FN1

description: ReadCountsPerGene.txt

value: Single foundress


title: ATF6+/+ hESC vehicle-1 RNA-seq

source_name: ESC

value: ESC


title: HCC827 [miRNA-seq]

description:
processed data file:
comparison_1.xls


title: PC9OTR [miRNA-seq]

description:
processed data file:
comparison_1.xls


title: DT3017pDT16r3

city: York

first: Katherine

last: Newling

address: Wentworth Way

department: Biology

institute: University of York

description:
Normalised_counts.txt
Differential_expression_DT3017_DT3017pDT16.txt
Differential_expression_DT3017pDT16_J1929.txt

data_processing:
Reads were quality-trimmed using Sickle
Reads were aligned to the S. coelicolor genome using BWA-MEM
Read alignments were quantified using HTSeq-count
Abundances were normalised and differential expression analysis performed using DESeq2
Genome_build: NCBI reference NC_003888
Supplementary_files_format_and_content: Text files containing normalised counts and differential expression values (log2-fold change, p-values and Benjamini-Hochberg false-discovery rate corrected q-values) derived from DESeq2 analysis.

organism: Streptomyces coelicolor A3(2)

source_name: mycelium

growth_protocol: Cultivations for RNAseq analysis were performed in 7 litre fermentors (Applikon) containing 2.5 litres of DN broth and 2 ml antifoam C emulsion (Sigma-Aldrich) with a starting pH adjusted to 7 with NaOH. Temperature was maintained at 30 °C and pH maintained at 7 through the automatic addition of 2 M HCl.  Dissolved oxygen was maintained at a minimum of 30 % by automatic adjustment of the agitation speed, with a minimum and maximum rate of 300 and 1000 respectively, and a constant aeration pressure of 2.5 - 3.5 bar. For the inoculum approximately 109 CFU S. coelicolor spores were germinated for 10 hrs in 100 ml germination medium in 1 L baffled flasks at 30 °C following heat shock as described in Kieser et al. (2000) before being used to inoculate equilibrated fermentor culture medium to an OD450 of 0.05. Growth was measured using dry weight while dissolved oxygen, pH, agitation speed and temperature were logged online throughout.

extract_protocol:
RNA isolation was performed using a modified version of the modified Kirby mix protocol as follows: 14 g of glass beads were added to defrosted pellets along with 5 ml of 30 °C modified Kirby mix (in 50 mM TrisHCl ph8.3; 1% w/v sodium-triisopropylnaphthalene sulphonate, 6% w/v sodium 4-aminosalycilate, 6% phenol mixture) before being vigorously vortexed for 2 minutes. Acid phenol: chloroform 1:1 was then used to isolate nucleic acids before being precipitated with 4 M acetate and 100 % isopropanol. Nucleic acids were subject to an ethanol wash before final resuspension in water. Nucleic acids were repeatedly treated with DNase I using conditions described by the vendor (Roche) until DNA could no longer be amplified using polymerase chain reaction (PCR). RNA was then enriched for mRNA using MICROBExpressTM Bacteria beads, as described by the manufacturer (Ambion).
mRNAs were fragmented with ultrasound before antarctic phosphatase treatment and re-phosphorylation with polynucleotide kinase. RNA fragments were then poly(A)-tailed using poly(A) polymerase and an RNA adapter was ligated to mRNA 5’ phosphate. First strand cDNA synthesis was performed using an oligo(dT)-adapter primer and M-MLV reverse transcriptase before PCR amplification. The cDNA samples were pooled and size fractionated in the range of 250-500 bp and run on an Illumina HiSeq 2000 system with a 100 bp read length.

treatment_protocol: The equivalent of 40 OD600 units were sampled and immediately added to 1/8th volume stop solution (5% phenol in ethanol, stored at – 20 °C). Cultures were spun down at 12,000 rpm, 4 °C for 5 minutes before pellets were flash frozen in liquid nitrogen and stored at -80 °C

tag: hour post-inoculation


title: DT3017pDT16r2


title: ATF6+/+ hESC tunicamycin-2 RNA-seq

tag: cell type

value: tunicamycin


title: DT3017r3

description:
Normalised_counts.txt
Differential_expression_DT3017_DT3017pDT16.txt
Differential_expression_DT3017_J1929.txt

tag: genotype


title: DT3017pDT16r1


title: ATF6-/- hESC tunicamycin-2  RNA-seq


title: DT3017r2


title: PC9 [miRNA-seq]

description:
processed data file:
comparison_1.xls


title: DT3017r1


title: PC9 persisters after 2 weeks gefitinib [miRNA-seq]

description:
processed data file:
comparison_2.xls


title: ATF6-/- hESC vehicle-2 RNA-seq


title: PC9-147b

data_processing:
The 3' adaptor was trimmed from raw reads and reads with the length less than 10 were excluded to constitute the mappable reads.
The mappable reads were aligned to the human transcripts using Bowtie2 and gene abundance is estimated using RSEM.
Genome_build: GRCh37;
Supplementary_files_format_and_content: read_summary.xls: gene expression profile

growth_protocol: Human lung EGFR mutant cell lines H1975, HCC827, PC9 and PC9ER (provided by Dr. Susumu Kobayashi) were cultured in DMEM (high glucose) (GIBCO) with 10% FBS, 2 mM L-glutamine and 1% penicillin-streptomycin. Immortalized tracheobronchial epithelial (AALE) cells were derived as previously described (Lundberg et al., 2002) and maintained in SAGM media (Lonza). For 3D organoid formation, single-cell suspensions (2000 cells/well/20 ul) were co-plated with geltrex (25 ul) in 96-well non-treated clear plate (Corning, cat# 08-772-53). The plate was incubated 20 minutes at 37c followed by adding 100 ul complete growth media. The comple growth media is advanced DMEM/F12 with glutamax (1x), HEPES (1x), 1.25 mM NAC (N-Acetylcysteine), 10 mM Nicotinamide (NTM), 10 uM Forskolin (FSK), B27 (1x), 5 ng/ml Noggin, 20 ng/ml FGF2, 50 ng/ml EGF, 10 uM Y-27632 and 1% penicillin-streptomycin.  For differentiation, 10 ng/ml PDGFa and 10 ng/ml FGF7 were supplemented into the above meida from day 7 to day 24. Y-27632 was used only for the initial three days. The media was changed every three days.

extract_protocol:
RNA was extracted with mirVana miRNA isolation Kit in accordance with the prescribed protocol. Quality control was performed with Agilent Bioanalyser.
Illumina Truseq mRNA Library Preparation

treatment_protocol: To establish gefitinib or osimertinib tolerant cells, EGFR T790M negative cells (HCC827 cells and PC9 cells) as well as EGFR T790M positive cells (H1975 cells and PC9ER) were treated with 40 nM gefitinib and 20 nM osimertinib for 14 days, respectively. For lentivirla infection, live cells at 60% confluent were infected with the lentiviral particles  (ABM) in growth media containing 1:100 Viralplus transduction enhancer (ABM) and 8 ug/ml polybrene (Sigma). The cells were changed with fresh growth media on the 2nd day and cultured continuously until the cells were 80% confluent. Then the cells were passaged at 1:10 ratio and selected by 0.5 ug/ml puromycin (Sigma) until negative control cells were all dead in 3-5 days.

tag: genotype/variation

value: MIR147B overexpression


title: J1929r3

description:
Normalised_counts.txt
Differential_expression_DT3017pDT16_J1929.txt
Differential_expression_DT3017_J1929.txt

value: wild type


title: ATF6+/+ hMSC late passage-2 RNA-seq


title: ATF6+/+ hMSC late passage-1 RNA-seq


title: HCC827-21

value: lung cancer cell line

value: MIR21 overexpression


title: PC9-Scr

value: Scrambled overexpression


title: HCC827GTR [miRNA-seq]

description:
processed data file:
comparison_1.xls

value: tolerance to gefitinib


title: Mock_12dpi_3

description:
Sample 45
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

organism: Zea mays

source_name: plant material, 12 days post mock infection

tag: host plant variety

value: EGB

tag: host tissue

value: leaves

tag: time point

value: 12 days post mock infection


title: ATF6+/+ hESC tunicamycin-1 RNA-seq

tag: treatment

tag: passages


title: J1929r2


title: PC9GTR [miRNA-seq]

description:
processed data file:
comparison_1.xls


title: Mock_12dpi_2

description:
Sample 44
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: HCC827-147b


title: ATF6-/- hMSC late passage-2 RNA-seq


title: ATF6+/+ hESC vehicle-2 RNA-seq


title: J1929r1


title: FB1xFB2_12dpi_2

description:
Sample 23
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

organism:
Zea mays
Mycosarcoma maydis

source_name: infected plant material, 12 days post infection

tag: fungal strain

value: FB1 x FB2

value: 12 days post infection


title: ATF6-/- hMSC late passage-1 RNA-seq

value: MSC


title: HCC827-Scr


title: FB1xFB2_12dpi_3

description:
Sample 24
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_12dpi_1

description:
Sample 43
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: PC9ER-anti21

value: MIR21 knocking down


title: FB1xFB2_12dpi_1

description:
Sample 22
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_8dpi_3

description:
Sample 42
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 8 days post mock infection

value: 8 days post mock infection


title: PC9ER-anti147b

value: MIR147B knocking down


title: ATF6-/- hESC vehicle-1 RNA-seq

value: ESC

value: vehicle


title: Mock_8dpi_2

description:
Sample 41
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: FB1xFB2_8dpi_2

description:
Sample 20
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 8 days post infection

value: 8 days post infection


title: Mock_8dpi_1

description:
Sample 40
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_6dpi_3

description:
Sample 39
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 6 days post mock infection

value: 6 days post mock infection


title: FB1xFB2_8dpi_1

description:
Sample 19
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: H1975-anti21

value: non-small-cell lung cancer cell line


title: H1975-anti147b


title: FB1xFB2_6dpi_2

description:
Sample 17
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 6 days post infection

value: 6 days post infection


title: Mock_6dpi_1

description:
Sample 37
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_6dpi_2

description:
Sample 38
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: FB1xFB2_6dpi_3

description:
Sample 18
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: FB1xFB2_6dpi_1

description:
Sample 16
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: AALE-21

source_name: AALE

value: AALE

value: lung bronchial epithelial cell line

value: MIR21 overexpression


title: ATF6-/- hESC tunicamycin-1  RNA-seq

value: tunicamycin


title: PC9-21

value: lung cancer cell line


title: AALE-Scr

value: Scrambled overexpression


title: Mock_4dpi_1

description:
Sample 34
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 4 days post mock infection

value: EGB

value: leaves

value: 4 days post mock infection


title: Mock_4dpi_2

description:
Sample 35
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: FB1xFB2_4dpi_1

description:
Sample 13
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 4 days post infection

value: FB1 x FB2

value: 4 days post infection


title: FB1xFB2_4dpi_3

description:
Sample 15
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: AALE-147b

value: MIR147B overexpression


title: Mock_2dpi_3

description:
Sample 33
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 2 days post mock infection

value: 2 days post mock infection


title: HCC827OTR

tag: response to gefitinib or osimertinib

value: tolerant to osimiertinib


title: PC9ER-antictrl

value: control knocking down


title: FB1xFB2_2dpi_3

description:
Sample 12
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 2 days post infection

value: 2 days post infection


title: HCC827GTR

value: tolerant to gefitinib


title: Mock_2dpi_2

description:
Sample 32
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: H1975-antictrl

value: non-small-cell lung cancer cell line


title: FB1xFB2_8dpi_3

description:
Sample 21
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

value: 8 days post infection


title: FB1xFB2_2dpi_2

description:
Sample 11
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_4dpi_3

description:
Sample 36
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: HCC827

value: sensitive to gefitinib and osimertinib


title: FB1xFB2_2dpi_1

description:
Sample 10
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: Mock_24hpi_3

description:
Sample 30
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 24 hours post mock infection

value: 24 hours post mock infection


title: Mock_2dpi_1

description:
Sample 31
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: PC9GTR

value: lung cancer cell line


title: Mock_24hpi_2

description:
Sample 29
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: PC9OTR


title: Mock_12hpi_2

description:
Sample 26
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: plant material, 12 hours post mock infection

value: 12 hours post mock infection


title: Mock_12hpi_3

description:
Sample 27
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

value: EGB


title: FB1xFB2_4dpi_2

description:
Sample 14
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

value: leaves


title: FB1xFB2_24hpi_2

description:
Sample 8
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 24 hours post infection

value: 24 hours post infection


title: PC9


title: FB1xFB2_24hpi_3

description:
Sample 9
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

value: FB1 x FB2


title: srt1srt2 4 hour air RNAseq, rep1

city: Austin

first: FAN

last: ZHANG

address: 2506 speedway, NMS5.324

institute: The University of Texas at Austin

description: air treated for 4 hours

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to TAIR10 whole genome using TopHat version 2.0.9 with default parameters
Differential expressed genes were calculated by Cuffdiff version 2.2.1
Genome_build: tair10
Supplementary_files_format_and_content: srt1srt2_arivsC2H4.xlsx file include RPKM values for each Sample, generated by Cuffdiff version 2.2.1

organism: Arabidopsis thaliana

source_name: srt1srt2 4 hour air RNAseq

growth_protocol: Arabidopsis seeds were dark-grown and treated with air (hydrocarbon-free air (Zero grade air, AirGas)) at 24 ºC for 3 days

extract_protocol:
RNA was harvested using Trizol reagent from seedlings.
Libraries were prepared according to NEB instructions of the RNA Library Kit (NEB #E7420S/L)

treatment_protocol: Treated with air (hydrocarbon-free air (Zero grade air, AirGas)) or ethylene (hydrocarbon-free air with 10 parts per million (ppm) ethylene) for 4 hours

tag: ecotype background

value: Col

value: srt1srt2 mutant

tag: age

value: 3-day old etiolated seedlings

tag: treated with

value: air for 4 hours


title: srt1srt2 4 hour ethylene RNAseq, rep2

description: ethylene treated for 4 hours

source_name: srt1srt2 4 hour ethylene RNAseq

tag: tissue

value: ethylene for 4 hours


title: srt1srt2 4 hour ethylene RNAseq, rep1

description: ethylene treated for 4 hours


title: FB1xFB2_12hpi_2

description:
Sample 5
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

source_name: infected plant material, 12 hours post infection

value: 12 hours post infection


title: FB1xFB2_12hpi_1

description:
Sample 4
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: S11_210min

status: Public on Jan 10 2018

city: Auckland

first: Cameron

middle: J

last: Mitchell

address: 85 Park Road, Grafton

department: Liggins Institute

country: New Zealand

institute: University of Auckland

data_processing:
mirna_soft - 3’ adapter sequences removed, aligning the reads to miRBase (version18), reads are tallied to generate total counts for each miRNA, statistical significance (p-value) between 2 or more samples is calculated to generate differential expression profiles
Genome_build: miRBase (version18)
Supplementary_files_format_and_content: 73_samples.mir.expr - result of comparisons for statistical significance

source_name: vastus lateralis muscle

extract_protocol:
Total RNA was extracted from ~20mg of muscle tissue using the AllPrep® DNA/RNA/miRNA Universal Kit (QIAGEN GmbH, Hilden, Germany) following the manufacturer's instructions. RNA was quantified using a NanoDrop 1000 with quality determined using RNA 6000 NANO Chips (Agilent Technologies, California, USA) on a 2100 Bioanalyzer (Agilent Technologies) to derive the RNA integrity number (RIN). Samples with a RIN ≥ 8.0 were utilised for sequencing.
Truseq small RNA kit (Illumina Inc. San Diego, CA, USA) according to manufacturer's instructions

value: vastus lateralis muscle

tag: time


title: S21_90min


title: S21_baseline

value: Baseline

tag: age (y)

tag: knee extension strength (nm)

tag: mid thigh cross sectional area

tag: muscle attenuation (hu)

tag: myosin heavy chain gene expression ratio (type iia/type i )


title: S37_baseline


title: S04_baseline


title: S26_baseline


title: S27_210min


title: FB1xFB2_24hpi_1

description:
Sample 7
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

tag: host plant variety


title: S24_baseline


title: S16_baseline


title: S52_baseline


title: S32_210min


title: S26_210min


title: Mock_24hpi_1

description:
Sample 28
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

tag: host tissue


title: S11_baseline


title: srt1srt2 4 hour air RNAseq, rep2

description: air treated for 4 hours

tag: genotype/variation


title: Mock_12hpi_1

description:
Sample 25
Gene expression data
PolyA RNA
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt

tag: time point


title: S54_baseline


title: S30_210min


title: S21_210min


title: S47_baseline


title: S43_baseline


title: S53_baseline


title: S28_90min


title: S32_baseline


title: S24_210min


title: S39_210min


title: S35_210min


title: S32_90min


title: S23_210min


title: S13_baseline


title: S15_baseline


title: S56_baseline


title: S22_baseline


title: S28_baseline


title: S35_90min


title: FB1xFB2_12hpi_3

description:
Sample 6
Gene expression data
PolyA RNA
Processed data file: Counts_Um.txt
Processed data file: NormCounts_Um.txt
Processed data file: Counts_Zm.txt
Processed data file: NormCounts_Zm.txt


title: S31_210min


title: S46_baseline


title: S37_90min


title: S30_baseline


title: S49_baseline


title: S55_baseline


title: S09_baseline


title: S20_baseline


title: S39_baseline


title: S27_baseline


title: S07_baseline


title: S17_baseline


title: S03_baseline


title: S41_baseline


title: S37_210min


title: S50_baseline


title: S29_baseline


title: S29_210min


title: S08_baseline


title: S44_baseline


title: S29_90min


title: S31_baseline


title: S02_baseline


title: S33_baseline


title: S28_210min


title: S38_baseline


title: S03_90min


title: S05_baseline


title: S23_baseline


title: S11_90min


title: S19_baseline


title: S39_90min


title: S40_baseline


title: S48_baseline


title: S03_210min


title: S35_baseline


title: S51_baseline


title: S12_baseline


title: S06_baseline


title: S18_baseline


title: S10_baseline


title: HeLa_BR_6_TR_2_Total

first: John

last: Rinn

address: 7 Divinity Avenue

department: SCRB

institute: Harvard University

description:
Total6
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv

data_processing:
Library strategy: MPRA
Basecalls performed using CASAVA version 1.8.
The reads were analyzed using the oligoGames package. First, we use the mapReads function to map the reads back to the oligo pool. Next, we used normCounts to normalize the counts table. We use modelNucCounts to model nucleotide counts from oligo level counts. We use DRfinder to infer differential regions.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: normCounts.tsv: Tab-separated text file includes the normalized counts of all the oligos in the samples of the MPRA experiments.
Supplementary_files_format_and_content: oligoGames.DRs.tsv: Tab-separated text file includes the final nuclear enrichment regions discovered by the MPRA experiment.

source_name: HeLa, total

extract_protocol:
RNA was isolated by TRIzol (ThermoScientific) - chloroform extraction, followed by isopropanol precipitation, according to standard procedures. 2 µg of BioAnalyzer-validated RNA were digested with recombinant DNase-I (2.77 U/µl, Worthington #LS006353) at 37°C for 30 min, followed by heat-inactivation at 75°C for 10 min. Reverse transcription was performed with SuperScript III cDNA synthesis kit (ThermoScientific). Quantitative RT-PCR was performed using the FastStart Universal SYBR Green Master mix (Roche) on an ABI 7900. Primers were: NEAT1 forward TGATGCCACAACGCAGATTG, reverse GCAAACAGGTGGGTAGGTGA, and SNHG5 forward GTGGACGAGTAGCCAGTGAA, reverse GCCTCTATCAATGGGCAGACA. After processing the raw data by qPCR Miner (PMID 16241897), the efficiency of each primer set was used to calculate the relative initial concentration of each gene. The relative expression in the nuclear and cytoplasmic fractions was then calculated by normalization to that in the whole cell.
Sequencing libraries were prepared by PCR amplification using PfuUltra II Fusion DNA polymerase (Agilent #600672) and primers designed to anneal to the universal primer site flanking the oligos and to add sequencing index barcode for multiplexing: forward caagcagaagacggcatacgagatCGTGATgtgactggagttcagacgtgtgctcttccgatctACTGGCCGCTTCACTG, reverse AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT (capital letters indicate (1) the index for the library and (2) the region complementary to the universal primer site). PCR amplification (initial denaturation 95°C – 2 min; cycling 95°C – 30 secs, 55°C – 30 secs, 72°C – 30 sec; final extension 72°C – 10 min) was carried out for 30 cycles followed by triple 0.6x, 1.6x, and 1x SPRI beads (Agencourt AMPure XP, Beckman Coulter) cleanup. The quality and molarity of the libraries was evaluated by BioAnalyzer and the samples were sequenced in a pool of 6 on the Illumina HiSeq2500, full flow cell, single-read 100 bp.

tag: cell line

value: HeLa

tag: subcellular location

value: Total


title: HeLa_BR_6_TR_1_Total


title: 77_Young_CS

city: Mississauga

first: Iva

middle: Toronto

last: Zovkic

state: Ontario

address: 3359 Mississauga Road North, CCT Building Room 4071

country: Canada

institute: University of Toronto Mississauga

data_processing:
Both ChIP and RNA seq data were quality cheked using FastQC and adaptors were trimmed uing Trim Galore (v.0.4.) running Cutadapt.
For ChIP and RNAseq, reads were aligned using Bowtie2 (v2.2.1)
For ChIPseq, enrichment analysis (increased non-random genome coverage) was conducted using Repitools (v.1.12.1) with R (v3.1.0). For RNA seq, Tophat alignments were processed with HTSeq-count (v.0.6.1p2) to assign reads to genes in the “intersection_nonempty” mode.
For ChIPseq, peaks (regions enriched for reads) were identified using MACS2 (v.2.0.10) and consensus peaks for all samples were assembled using DiffBind (v.1.12.2) with R (v.3.1.0) based on peak presence in at least 2 samples.  For RNA seq, Two-condition differential expression for specific comparisons  was assessed using EdgeR R package (v.3.8.6) and genes that are not expressed were excluded by only including reads for which CPM (counts per million reads) was >0.25 in at least 2 samples. Reads for all samples were normalized using TMM implemented by the calcNormFactors(y) function.
For ChIP seq, Consensus peaks were annotated using Annovar for gene mapping and ChIPpeakAnno (v.2.16.4) for transcript mapping. Feature sets used for ChIPpeakAnno were: RefSeq coding and non-coding transcripts; Ref seq coding transcripts; blacklisted genomic regions; and ENCODE histone modification peaks for the whole mouse brain. Given that ENCODE peaks were only available in mm9, the coordinates were translated to mm10 with liftOver in Galaxy.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP seq, .txt file shows the H2A.Z consensus peaks and analyses for differential H2A.Z binding for all groups, carried out with DiffBind (v.1.12.2). For RNAseq, .txt file containsHTSeq counts

source_name: hippocampus

extract_protocol:
Brains were extracted and rapidly frozen in isopentane 30 min after training. Extracted hippocampi were processed for H2A.Z ChIP or RNA extraction.
Libraries were prepared using standard Illumina protocols

treatment_protocol: Fear conditioned C57BL/6J mice were exposed to a 5 minute training procedure. They were given 2 min to explore, followed by three 0.5 mA shocks (2 sec) administered 1 min apart. They were given 1 extra minute to explore before being removed.

value: hippocampus

tag: testing

value: fear conditioned

tag: sample

value: RNA

value: 2.5 months


title: 83_Young_Naive

value: naïve

tag: age


title: 81_Young_Naive


title: HeLa_BR_3_TR_2_Total

description:
Total3
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_3_TR_1_Total


title: HeLa_BR_5_TR_1_Total

description:
Total5
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: 71_Old_Naive

value: 15.5 months


title: 79_Young_Naive


title: HeLa_BR_2_TR_1_Total

description:
Total2
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_1_TR_2_Total

description:
Total1
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_4_TR_2_Total

description:
Total4
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_4_TR_1_Total


title: HeLa_BR_6_TR_2_Nuclei

description:
Nuclei6
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv

source_name: HeLa, nuclei

value: Nuclei


title: HeLa_BR_2_TR_2_Total


title: 75_Young_CS


title: 67_Old_Naive


title: HeLa_BR_1_TR_1_Total


title: 65_Old_CS


title: 63_Old_CS


title: 183_Young_Naive_IP

value: H2A.Z ChIP


title: HeLa_BR_5_TR_2_Nuclei

description:
Nuclei5
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_4_TR_2_Nuclei

description:
Nuclei4
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_6_TR_1_Nuclei


title: 183_Young_Naive_Input

value: input


title: 73_Young_CS


title: HeLa_BR_4_TR_1_Nuclei


title: 69_Old_Naive


title: HeLa_BR_3_TR_1_Nuclei

description:
Nuclei3
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_3_TR_2_Nuclei


title: 78_Young_Naive_Input


title: 74_Young_CS_IP


title: 76_Young_CS_IP


title: HeLa_BR_5_TR_1_Nuclei


title: 74_Young_CS_Input


title: 78_Young_Naive_IP


title: 76_Young_CS_Input


title: HeLa_BR_1_TR_2_Nuclei

description:
Nuclei1
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_2_TR_2_Nuclei

description:
Nuclei2
Processed data file: normalizedCounts.tsv
Processed data file: oligoGames.DRs.tsv


title: HeLa_BR_2_TR_1_Nuclei


title: 72_Young_CS_Input

value: Input


title: 70_Old_Naive_IP


title: 72_Young_CS_IP


title: 61_Old_CS


title: 68_Old_Naive_IP


title: 68_Old_Naive_Input


title: 70_Old_Naive_Input


title: 64_Old_CS_IP


title: 66_Old_Naive_Input


title: 82_Young_Naive_IP


title: 82_Young_Naive_Input


title: 64_Old_CS_Input


title: 62_Old_CS_IP


title: HeLa_BR_1_TR_1_Nuclei


title: 60_Old_CS_IP


title: 62_Old_CS_Input


title: 60_Old_CS_Input


title: 66_Old_Naive_IP


title: HeLa_BR_5_TR_2_Total


title: PolII-shSET1B

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: Cells treated with human SET1B dsRNA

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq output.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 using Bowtie version 0.12.9.  Only uniquely mapping reads with at most two mismatches were retained.
RNA-seq reads were aligned to UCSC hg19 using Tophat version 2.0.9.  Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
To create RNA-seq coverage plots, the mapped RNA-seq reads were split according to strand, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated using the genomicRanges R package.  Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.

growth_protocol: Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10%  serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life  Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C

extract_protocol:
RNA was extracted using QIAGEN RNeasy kit. DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit. RNA-sequencing  libraries were prepared using the Illumina TruSeq Stranded Total RNA Preparation Kit with  Ribo-Depletion. Input RNA quality was validated using the Agilent RNA 6000 Nano Kit. 200ng-1 µg  of total RNA was used as starting material. Libraries were validated using the Agilent DNA  1000 Kit

tag: passages

value: Low passages (6-10)

tag: shRNA

tag: chip antibody

value: Pol II (CST)


title: 2b-11-8

city: Göttingen

first: Melina

last: Schuh

address: Am Fassberg 11

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

data_processing:
Demultiplexing: bcl2fastq (v 2.19.1.403)
Illumina adaptor trimming: bcl2fastq (v 2.19.1.403)
Quality control: FastQC (v 0.11.5)
Read mapping: STAR (v 2.5.1b)
Read counting: HTSeq (v 0.6.0)
Count normalization: DESeq2 (v 1.6.3)
Differential expression analysis: DESeq2 (v 1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: counts-files, contain unnormalized gene counts

growth_protocol: NIH3T3 and NIH3T3-mCherry-mTRIM21 were cultured under standard conditions in DMEM medium (Gibco; 31966021) supplemented with 10% Calf Serum and penicillin-streptomycin.

extract_protocol:
After 16 h, cells were washed with PBS and lysed with Trizol (TRizol reagent, Thermo Fisher, 15596026). For phase separation, chloroform was added. Total RNA in the upper layer was precipitated with isopropanol and washed with 70% ethanol. The sample was DNase (Turbo DNase, Thermo Fisher, 40226) treated, and purified total RNA was phenol/chloroform extracted.
Strand specific Illumina TruSeq RNA library preparation kit v2 with polyA enrichment was used to construct libraries from total RNA

treatment_protocol: NIH3T3 and NIH3T3-mCherry-mTRIM21 cells were resuspended in Buffer R (ThermoFisher) at a concentration of 3 x 107 cells ml-1. For each electroporation reaction 3 x 106 cells (100 µl) were mixed with 7.5 µg of antibody (ab18447), BSA or PBS. The mixture was taken up into a 100 µl Neon® Pipette Tip (Thermo Fisher) and electroporated using the following settings: 1400V, 20 ms, 2 pulses. Electroporated cells were transferred to medium supplemented with 10% Calf Serum without antibiotics.

tag: tissue

value: embryonic fibroblasts

tag: genotype

value: wild-type

tag: treatment (electroporation)

value: PBS


title: 2a-11-8

value: IgG


title: 1b-14-8


title: 1b-11-8


title: 2a-10-8


title: 2c-14-8

value: BSA


title: 1a-14-8


title: 2a-14-8


title: 2c-10-8


title: 1a-11-8


title: 1c-10-8


title: 2b-14-8


title: 1a-10-8


title: 2b-10-8


title: 2c-11-8


title: 1c-11-8


title: 1b-10-8


title: Rap1-AA-full-length-Rap1_2h-rapa

city: Montpellier

first: Domenico

last: Libri

address: 1919 route de Mende

country: France

institute: IGMM - CNRS

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor is clipped with Cutadapt (-m 10) (martin M. embnet.journal, 2011) and the resulting insert is quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
RNAseq samples were demultiplex by the sequencing platform with bcl2fastq2 v2.15.0;  adaptor trimming of standard illumina trueseq adaptors was performed with cutadapt 1.9.1. Samples were subsequently quality trimmed with trimmomatic (see above) and mapped to the R64 genome with bowtie2 (default options).
Genome_build: R64
Supplementary_files_format_and_content: Wig files providing coverage for all samples. All wigs are normalized to 10,000,000 reads.

organism: Saccharomyces cerevisiae

source_name: S.cerevisiae culture

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For Anchor Away strains, rapamycin was added at OD600=0.4 for two hours to a final concentration of 1 µg/mL. For rna15 experiment, cells were grown at 25°C to OD600=0.6. 1 volume of media preheated at 30 or 37°C was added and cultures were incubated at 30 or 37°C for 1 hour and half.

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20 min at 20000 xg at 4°C. IgG and nickel purification steps were performed as previously described in the original protocol (Granneman et al., 2009) with minor changes: i) IgG purification steps were done using M-280 tosylactivated dynabeads (15 mg per sample) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol. RNA were reverse transcribed using the Reverse transcriptase IV (Invitrogen)
Between half to ¾ of the cDNA solution was used to performed multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of ech primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per milliliter of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

treatment_protocol: Cells were submitted to UV crosslink in a UV lamp system (Megatron) for 50 seconds. Cells were harvested by centrifugation, washed in cold PBS and resuspended in 2.4 volume / g of cells of TN150 buffer (50 mM Tris pH 7.8, 150 mM NaCl, 0.1% NP-40 and 5 mM beta mercaptoethanol) supplemented with protease inhibitors (cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail). This suspension was flash frozen in droplets and cells were mechanically broken using the Mixer Mill MM 400 by doing 5 cycles of 3 minutes at 20 Hrz. Resulting powder was kept at -80°C

tag: treatment

value: 2h Rapamycin

value: as w303, Rpb1-HTP::Ura, Rap1-FRB-Rap1::LEU tor1-1 fpr1::NAT, RPL13A-2xFKBP12::TRP1 rrp6-delta:His


title: Input-shCtrl-R2

description: Cells treated with non-targeting dsRNA


title: H3K4me1-shSET1B-R2

description: Cells treated with human SET1B dsRNA

value: H3K4me1 (homemade)


title: PolII-shCtrl

description: Cells treated with non-targeting dsRNA

source_name: PolII-shCtrl

value: shCtrl


title: Rap1-AA-full-length_1h-rapa

value: 1h Rapamycin


title: 1c-14-8


title: Rap1-AA-DBD_2h-rapa


title: Rap1-AA-empty-plasmid_2h-rapa


title: Input-shSET1B-R2

description: Cells treated with human SET1B dsRNA


title: Rap1-AA-empty-plasmid_1h-rapa


title: H3K4me1-shCtrl-R2

description: Cells treated with non-targeting dsRNA


title: H3K4me3-shSET1B-R2

description: Cells treated with human SET1B dsRNA

value: H3K4me3 (homemade)


title: Input-shCtrl-R1

description: Cells treated with non-targeting dsRNA


title: Rap1-AA-DBD_1h-rapa


title: H3K4me1-shCtrl-R1

description: Cells treated with non-targeting dsRNA


title: H3K4me1-shSET1B-R1

description: Cells treated with human SET1B dsRNA


title: H3K4me3-shCtrl-R2

description: Cells treated with non-targeting dsRNA


title: Input-shSET1B-R1

description: Cells treated with human SET1B dsRNA


title: Rap1-AARrp6delta+Rapa


title: Rap1-AA-full-length-Rap1_no-rapa


title: Reb1-AARrp6delta+Rapa

value: as w303, RPB1-HTP::TRP1 REB1-FRB::KAN tor1-1 fpr1::loxP RPL13A-2xFKBP12::loxP rrp6-delta:His


title: H3K4me3-shSET1B-R1

description: Cells treated with human SET1B dsRNA


title: Nrd1-AID+auxin

data_processing:
sequencing performed with NextSeq 500 High Output Kit 75 cycles V2.
Samples were demultiplexed using the pyBarcodeFilter script from the pyCRAC utility suite (webb et al). Subsequently, the 3' adaptor is clipped with Cutadapt (-a TGGAATTCTCGGGTGCCAAGGATCTCGTATGCCGTCTTCTGCTTG -m 10) (martin M. embnet.journal, 2011) and the resulting insert is quality trimmed from the 3' end using Trimmomatic rolling mean clipping (bolger et al, 2014) (window size = 5, minimum quality = 25). At this stage the pyCRAC script pyFastqDuplicateRemover is used to collapse PCR duplicates and ensure each insert is represented only once. Each unique insert in our library is associated with a 6 nucleotides random tag within the 5' adaptor. During demultiplexing, pyBarcodeFilter retains this information in the header of each sequence. This information is used at this stage to better discern between entical inserts and PCR duplicates of the same insert. The resulting sequences are reverse complemented with Fastx reverse complement (part of the fastx toolkit, http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the R64 genome (cherry et al, 2012, nar) with bowtie2 (-N 1 -f) (langmead et al, 2012).
Genome_build: R64
Supplementary_files_format_and_content: Wig files providing coverage for all samples. All wigs are normalized to 10,000,000 reads.

growth_protocol: For all datasets, 2L of yeast cells expressing Rpb1-HTP tag were grown at 30°C to OD600=0.6 in DO-Trp (drop out without tryptophan) . For Anchor Away strains, rapamycin was added at OD600=0.4 for two hours to a final concentration of 1µg/ml. For rna15 experiment, cells were grown at 25°C to OD600=0.6. 1 volume of media preheated at 30 or 37°C was added and cultures were incubated at 30 or 37°C for 1 hour and half.

extract_protocol:
Powders were defrozen and the resulting extracts were treated for one hour at 25°C with DNase I (165U/g of cells) to solubilize the chromatin and then clarified by centrifugating 20’ at 20000g at 4°C.IgG and nickel purification steps were performed as previously described in the original protocol (granneman et al., 2009) with minor changes: i) IgG purification steps has been realized using M-280 tosylactivated dynabeads (15mg per samples) coupled with rabbit IgG. ii) To increase the stringency, washes following both IgG and nickel purification steps were done at high salt concentration (1 M NaCl). After over-night binding on nickel columns, sequencing adaptors were added on the RNA as described in the original procedure. Because we work on nascent transcripts, some changes were required to fit with our purpose: For instance, since nascent transcripts contain a 3’ hydroxyl group that is protected inside the polymerase, we decided not to do the dephosphorylation step usually required because of the RNAse treatement that leads to 3’ phosphate transcripts. Also, we modified both 5’ and 3’ adaptors in order to sequence RNA molecules from the 3’ end so that we can determine the exact position of the polymerase. The 3’ ligation has been realized with T4 rnl 2 truncated K227Q enzyme (NEB) instead of classical T4 RNA ligase. RNA-protein complexes were eluted in 400 µl of elution buffer (50mM Tris pH 7.8, 50mM NaCl, 150mM Imidazole, 0.1% NP-40, 5mM beta mercaptoethanol). Eluates were concentrated in Vivacon® ultrafiltration spin columns 30 KDa MWCO to a final volume of 120 µl. A protein fractionation step was performed using the Gel Elution Liquid Fraction Entrapment Electrophoresis (Gelfree) system from Expedeon. RNA pol II containing fractions were treated with 100 µg of proteinase K in a buffer containing 0.5% SDS. RNA was purified by two phenol chloroform isoamyl and one chloroform steps and precipitated in ethanol. RNA were reverse transcribed using the Reverse transcriptase IV (Invitrogen)
Between half to ¾ of the cDNA solution was used to performed multiple PCR reactions in a final volume of 25 µl using the following conditions: 0.4 µM of ech primers, 0.2 mM dNTP, 2.5 U LA Taq DNA polymerase from Takara, 1X LA PCR Buffer II and 2 µl of cDNA per reaction with the programme: 95°C 2’, 95°C 30’’, 58°C 45’’, 72°C 1’, 72°C 5’. PCR were pooled and treated with 200 U of Exonuclease I (NEB) per milliliter of PCR reaction for 1 hour at 37°C. After Exonuclease I inactivation for 20’ at 80°C, DNA was purified on PCR clean up columns (NucleoSpin® Gel and PCR Clean-up, Macherey-Nagel) and sent to sequence using Illumina technology (NextSeq sequencing).

value: 1h Auxin

value: Rpb1-HTP::Trp1kl Nrd1-3Flag-mAID,  KAN::OsTIR1


title: Rap1-AA-DBD_no-rapa


title: MDA-MB-231-shBOD1-c1-R2

description: Cells treated with human BOD1 dsRNA


title: Nrd1-AID-auxin


title: WT 37C

value: 1.5h heatshock 37C

value: as BMA, RPB1-HTP::TRP1kl


title: MDA-MB-231-shBOD1-c2-R1

description: Cells treated with human BOD1 dsRNA

value: Low passages (6-10)


title: Rap1-AARrp6delta-Rapa


title: Rap1-AA-empty-plasmid_no-rapa


title: MDA-MB-231-shSET1B-c2-R1

description: Cells treated with human SET1B dsRNA


title: MDA-MB-231-shSET1B-c2-R2

description: Cells treated with human SET1B dsRNA


title: Rna15-1 30C

value: 1.5h heatshock 30C

value: as w303, Rpb1-HTTP::TRP1 rna15-2


title: WT 30C


title: Rna15-1 37C


title: H3K4me3-shCtrl-R1

description: Cells treated with non-targeting dsRNA


title: MDA-MB-231-shBOD1-c2-R2

description: Cells treated with human BOD1 dsRNA


title: MDA-MB-231-shSET1B-c1-R2

description: Cells treated with human SET1B dsRNA


title: Reb1-AARrp6delta-Rapa


title: Reb1-AA+rapa

value: as w303, RPB1-HTP::TRP1 REB1-FRB::KAN tor1-1 fpr1::loxP RPL13A-2xFKBP12::loxP


title: MDA-MB-231-shSET1B-c1-R1

description: Cells treated with human SET1B dsRNA


title: MDA-MB-231-shBOD1-c1-R1

description: Cells treated with human BOD1 dsRNA


title: MDA-MB-231-shCtrl-R2

description: Cells treated with non-targeting dsRNA


title: 2_E_TH_77

first: Emma

last: Erickson

state: TX

address: 2500 Speedway MBB 1.124

department: Neuroscience

institute: University of Texas at Austin

data_processing:
Base-calling was performed with BCL2fastq (version 2.17)
Samples were trimmed with FASTX Toolkit (version 0.0.14) and adapter sequences removed with Cutadapt (version 1.8)
Alignment was performed using Bowtie2 (version 2.2.5) against the mouse reference genome (UCSC, mm10)
Duplicate reads were filtered with Picard (version 1.141)
Raw counts were obtained with HTSeq (version 0.5.3p9)
Normalized counts and differential expression results were obtained with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: text files including raw read counts

source_name: brain

extract_protocol:
The medial prefrontal cortex was dissected, minced, and resuspended in HBSS. 5% of the suspension was taken as the total homogenate, spun at 1000 x g and flash frozen in liquid nitrogren.
RNA was harvested using Qiagen Rneasy Micro Kit (Cat No. 74004).
Samples were Poly(A) selected using the Poly(A) Purist Kit (Thermo Fisher Scientific Inc.) and prepared using NEBNext® Ultra™ Directional RNA Library Preparation Kit (New England BioLabs, Ipswich, MA). Samples went through 15 cycles of PCR. Samples were sequenced on the HiSeq 4000 (Illumina, San Diego, CA) using (150 bp; paired-end reads) to a minimum target depth of 20 million reads per sample.

treatment_protocol: Mice were allowed to voluntary drink 15% (v/v) ethanol every other day for 72 days. Only water was available on off days. Mice were sacrificed 24hrs after their last drinking day

tag: strain

value: brain

tag: brain region

value: prefrontal cortex

value: Ethanol

tag: cell type

value: total homogenate


title: anchor-away-parental+rapa

value: as w303, Rpb1-HTP::Ura, tor1-1 fpr1::NAT, RPL13A-2xFKBP12::TRP1


title: ∆comR_sComS_RNA-seq

city: Lausanne

first: Johann

last: Mignolet

address: Biophore Quartier UNIL-SORGE

department: DMF

country: Switzerland

institute: UNIL

description:
mRNAs
Table 2.xls

data_processing:
Sequenced mRNAs or sRNAs generated several million reads that were mapped on the WT S. salivarius chromosome and processed through both bowties V0.12.9 and samtools V0.1.18 algorithms to yield BAM files encompassing the read coordinates. In regard to RNAseq, we imported these files into SeqMonk V0.23.0 (www.bioinformatics.babraham.ac.uk/projects/) to assess the total number of reads for each coding sequence (CDS). The dataset was exported into an excel file for further analyses. First, the dataset was standardized to CDS-mapped reads per million overall reads count. Then, we estimated a normalized ratio of CDS-mapped reads in mutants vs WT. The implemented file was used to generate a regulatory network scheme from the Cytoscape software (www.cytoscape.org/). Concerning smRNAseq, the genome was subdivided into 50 bp-probes and, for every probe, we calculated a value that represents the number of reads which occur within the probe
Genome_build: Streptococcus salivarius HSISS4: CP013216
Supplementary_files_format_and_content: the xls files reporting RNAseq were generated by SeqMonk sofware.The sheet is organized in columns as follows:   column 1 : gene name  column 2 : genome unit   column 3 : probe start  column 4 : probe end   column 5 : gene function  column 6 : locus tag  column 7 : old locus tag assigned in the previous genome sequencing  column 8 : orientation of the probe in regard to the associated gene  column 9 : It is reported here the absolute value of reads per probe in the WT  column 10 : It is reported here the absolute value of reads per probe in the comR mutant  column 11 : It is reported here the absolute value of reads per probe in the comX mutant  column 12 : Ratio of Normalized abundance of reads per probe in comR mutant versus WT background  column 13 : Ratio of normalized abundance of reads per probe in comX mutant versus WT background  column 14 : log10 transformation of column 12  column 15 : log10 transformation of column 13
Supplementary_files_format_and_content: the xls files reporting smRNAseq were generated by SeqMonk sofware.The sheet is organized in columns as follows:   column 1: probe name  column 2 : genome unit   column 3 : probe start  column 4 : probe end   column 5 : closest gene   column 6 : probe location from the closest gene   column 7 : probe distance, the distance of the probe from ORF  column 8 : It is reported here the absolute value of reads per probe in the WT (+DMSO)  column 9 : It is reported here the absolute value of reads per probe in the WT activated with the pheromone  column 10 : normalized abundance of reads per probe in mock condition (DMSO)  column 11 : normalized abundance of reads per probe in pheromone-activated WT  column 12 : ratio of normalized abundance of reads per probe in pheromone-activated WT versus mock condition (DMSO)

organism: Streptococcus salivarius

growth_protocol: Streptococcus salivarius and derivatives were grown at 37°C in chemically defined medium supplemented with glucose (CDMG) without shaking

extract_protocol:
Total stranded mRNA libraries were prepped with the NEBNext Ultra Directional RNA Library Prep kit for Illumina (New England Biolabs). Library PCR was executed for 15 cycles. Quality of the libraries was evaluated with the use of a High sensitivity DNA chip (Agilent technologies) and concentrations were determined through qPCR according to Illumina protocol.
S. salivarius WT, ∆comR and ∆comX strains were overnight precultivated in CDMG at 37°C. They were resuspended in 50 ml of fresh pre-warmed CDMG at a final OD600=0.05 and grown for approximately 2h30 (OD600=0.2) at 37°C. We then supplemented the medium with either DMSO (negative control) or 1µM sComS and incubated for 30 min at 37°C. Cells were harvested by centrifugation (10 min; 4.000 rpm), the supernatant were discarded and the cell pellets were frozen with liquid nitrogen. Finally, RNAs were extract using the RiboPure bacteria kit (Ambion-Life Technologies) and follow the protocol as provided by the manufacturer, with exception of cell lysis and RNA precipitation. For Lysis, cells were resuspended in RNAwiz buffer supplemented with Zirconia beads and shaked for 40 sec (4 times) in a fastPrep homogenizer device (MP biomedicals). For RNA precipitation, a 1.25-ethanol volume (instead of 0.5) was added to partially purified RNAs. Total RNA was checked for quality on a RNA Nano chip (Agilent technologies) and concentration was measured using Ribogreen assay (Life technologies). rRNA depletion was performed on 2 µg total RNA with the Ribo-Zero rRNA removal kit for Gram Positive Bacteria (Illumina) according to manufacturer’s instructions

tag: medium supplemented with

value: sComS


title: Rap1-AA+rapa rep1

value: 1h Rapamycin

value: as w303, Rpb1-HTP::Ura, Rap1-FRB-Rap1::LEU tor1-1 fpr1::NAT, RPL13A-2xFKBP12::TRP1