title: htdp_a315t_fp_17_04_2015

description:
Ribosome footprint
Replicate 1- CAGCAT


title: Protein_footprint_H2O2_Rep2_0hr

status: Public on Oct 08 2018

type: SRA

city: New York

first: Shuvadeep

last: Maity

state: NY

address: 12 waverly place

department: Center for Genomics and Systems Biology

country: USA

institute: New york University

description: Protein protected RNA

library_source: transcriptomic

data_processing:
Library strategy: Protein-bound RNA profiling
illumina output file to fastq file conversion by bcl2fastq version 2.16 and demultiplexing by flexbar version 2.5
Sequenced reads were trimmed for adapter sequence and quality using fastx-toolkit v0.0.14 with parameters -t 20 -l 20 and fastq files from the same sample were merged.
Reads were mapped to abundant sequences to remove ribosomal rDNA, adapter contaminants, PhiX, and polyA/C sequences with bowtie2 v2.2.9 with default settings.
Remaining reads were mapped to hg19 genome with tophat v2.1.1 with parameter --no-coverage-search -G gencode.v19.basic.gtf
Aligned reads were filtered for unique mapping and length: RNA >25, Ribosome footprints 28-30, Protein footprints >25.
Read ounts were generated using htseq v0.6.1p1 with gencode.v19.basic.gtf and parameters --stranded==yes intersection-nonempty.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts from Htseq

molecule: total RNA

organism: Homo sapiens

source_name: cervical cancer cells

growth_protocol: All samples for the total RNA, ribosome footprinting and protein occupancy / footprint profiling were derived from cells grown in parallel. We grew Hela cells under standard conditions, i.e  in DMEM (Sigma) with 10% fetal bovine serum (Atlanta biologicals) and 1X penicillin streptomycin solution (Corning cellgro) at 37℃ and 5% CO2.

extract_protocol:
For RNA seq and ribosome foot print experiment, confluent plates of HeLa cells were first aspirated of their growth media and washed with fresh media supplemented with 0.1 mg/ml cycloheximide. The media was then removed and the cells were washed with 10 ml chilled PBS containing 0.1 mg/ml cycloheximide. Following removal of the PBS, 800 ul of Lysis Buffer was added and the cells were extensively scraped off plate and transferred to a pre-chilled eppendorf tube, recovering ~1 ml of lysate per sample. To insure complete lysis, we passed the lysate through a 25 gauge needle and further incubated on ice for ~10 min. The lysate was then clarified by centrifugation for 10 min at 20,000, 4°C and ∼1 ml supernatant was recovered. For each treatment (tunicamycin and hydrogen peroxide), we aliquoted 100 ul of the cell lysate for total RNA extraction and 200ul for ribosome footprinting. For protein foot print, we scraped crosslinked cells off the plates with a rubber policeman, collected by centrifugation, washed with ice-cold PBS . We resuspended cell pellets in lysis/binding buffer (100 mM Tris-HCl pH 7.5 at 25 °C, 500 mM LiCl, 10 mM EDTA pH 8.0 at 25 °C, 1% LiDS, 5 mM DTT, Complete Mini EDTA-free protease inhibitor (Roche)), incubated them at room temperature for 15 minutes for lysis and passed cells through a 21 gauge needle 10 times for shearing of genomic DNA. Lysates were processed to recover RNA-protein complex as described previously (Munschauer, 2015).
RNA libraries for RNA seq, Ribosome foot print and protein foot print were prepared according to the TruSeq Ribo Profile (Mammalian) kit protocol.

treatment_protocol: At ~60% confluency, we treated the cells with 60 μM H2O2or 0.5 μg/ml tunicamycin  to induce oxidative and ER stress, respectively. We treated samples 8, 4, 1, and 0 hours prior to collection and therefore collected all samples at the same time with similar confluency. For protein occupancy profiling, we added 200 μM of 4-thiouridine (4-SU) at ten hours before the treatment to incorporate photoreactive ribonucleoside analog required for protein occupancy profiling. For ribosome footprinting, we added 0.1 mg/ml cycloheximide for 5 min at 37℃ before the harvesting the cells.

tag: treatment

value: No Hydrogen peroxide

tag: cell line

value: HeLa


title: htdp_a315t_fp_22_05_2015

city: Hamburg

first: Giorgio

last: Gonnella

address: Bundesstrasse 43

department: Zentrum für Bioinformatik

country: Germany

institute: Universität Hamburg

description:
Ribosome footprint
Replicate 2- CAGCAT

data_processing:
Library strategy: Ribo-Seq
adapter clipping; cutadapt 1.8.1; parameters: --trimmed-only -e 0
filtering of non-coding RNA; Bowtie2; parameters: seed length: 14, minimum alignment length: 14
splitting of footprint into buckets, according to length; RiboPip; http://github.com/stepf/RiboPip
alignment of footprints to genome; TopHat2; parameters: read mapper: Bowtie2
joining of alignments of each bucket; RiboPip; http://github.com/stepf/RiboPip
count hits per feature; FeatureCounts 1.4.4
differential expression analysis; DeSeq1
Genome_build: GCA_000001635.7
Supplementary_files_format_and_content: tab-delimited files; output of FeatureCounts

organism: Mus musculus

source_name: MN1 cells

growth_protocol: MN1 cells were grown in D-MEM high glucose GlutaMAX culture medium (Gibco), supplemented with 10% Fetal Bovine serum, 1% Penicillin/Streptomycin antibiotics and 2.4% HEPES. MN1 cells were transiently transfected with plasmids using  Effectene Transfection Reagent (Qiagen) following the manufacturer’s protocol.Neurons were grown on dishes or glass coverslips coated with poly-L-Lysine in Primary Neuro Basal Medium (Lonza) supplemented with NSF-1, 1% Penicillin/Streptomycin antibiotics and L- Glutamine.  0.5 µM Cytosine β-D-arabinofuranoside (Ara-C) was added to the culture on DIV4. Neurons were cultured for 14d at 37°C in a 5% CO2 environment.

extract_protocol: Libraries were generated following original protocol by Ingolia, N.T., et al. (2012) The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nat Protoc, 7, 1534-1550.

treatment_protocol: MN1 cells were treated with 100 µg/mL Cycloheximide (CHX) for 3 mins before lysis.

tag: cell type

value: MN1 cells

tag: source

value: Clonal hybrid cells of mouse spinal motor neurons and mouse neuroblastoma

tag: passage

value: 10-12 passages

tag: genotype/variation

value: hTDP-43 A315T transfected cells


title: control_total_22_05_2015

description:
Total mRNA
Replicate 2- ACAGTG

data_processing:
adapter clipping; cutadapt 1.8.1; parameters: --trimmed-only -e 0
filtering of non-coding RNA; Bowtie2; parameters: seed length: 14, minimum alignment length: 14
splitting of footprint into buckets, according to length; RiboPip; http://github.com/stepf/RiboPip
alignment of footprints to genome; TopHat2; parameters: read mapper: Bowtie2
joining of alignments of each bucket; RiboPip; http://github.com/stepf/RiboPip
count hits per feature; FeatureCounts 1.4.4
differential expression analysis; DeSeq1
Genome_build: GCA_000001635.7
Supplementary_files_format_and_content: tab-delimited files; output of FeatureCounts

value: GFP transfected control


title: hTDP_wt_neuron_FP_17062015

description:
Ribosome footprint
Replicate 1- GTGAAA

source_name: primary cortical neurons

value: primary cortical neurons

value: E16 mouse cortical neurons

tag: stage and strain

value: Harvested DIV14- C57BL/6J

value: hTDP-43 WT


title: Protein_footprint_H2O2_Rep1_4hr

description: Protein protected RNA

value: Hydrogen peroxide 4Hr


title: htdp_a315t_total_17_04_2015

description:
Total mRNA
Replicate 1- ATCAGT


title: Ribosome_footprint_H2O2_Rep3_1hr

description: Ribosome protected RNA

data_processing:
Library strategy: Ribosome profiling
illumina output file to fastq file conversion by bcl2fastq version 2.16 and demultiplexing by flexbar version 2.5
Sequenced reads were trimmed for adapter sequence and quality using fastx-toolkit v0.0.14 with parameters -t 20 -l 20 and fastq files from the same sample were merged.
Reads were mapped to abundant sequences to remove ribosomal rDNA, adapter contaminants, PhiX, and polyA/C sequences with bowtie2 v2.2.9 with default settings.
Remaining reads were mapped to hg19 genome with tophat v2.1.1 with parameter --no-coverage-search -G gencode.v19.basic.gtf
Aligned reads were filtered for unique mapping and length: RNA >25, Ribosome footprints 28-30, Protein footprints >25.
Read ounts were generated using htseq v0.6.1p1 with gencode.v19.basic.gtf and parameters --stranded==yes intersection-nonempty.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts from Htseq

value: Hydrogen peroxide 1Hr


title: Protein_footprint_H2O2_Rep1_1hr

description: Protein protected RNA


title: Ribosome_footprint_H2O2_Rep3_8hr

description: Ribosome protected RNA

value: Hydrogen peroxide 8Hr


title: Ribosome_footprint_H2O2_Rep3_4hr

description: Ribosome protected RNA


title: hTDP_A315T_neuron_total_17062015

description:
Total mRNA
Replicate 1- ATCAGT

value: hTDP-43 A315T


title: Protein_footprint_H2O2_Rep1_0hr

description: Protein protected RNA


title: htdp_wt_fp_17_04_2015

description:
Ribosome footprint
Replicate 1- GTGAAA

value: hTDP-43 WT transfected cells


title: Ribosome_footprint_H2O2_Rep2_1hr

description: Ribosome protected RNA


title: htdp_wt_total_17_04_2015

description:
Total mRNA
Replicate 1- CTTGTA


title: 5hmC_WT2_GCB_Input

city: Farmington

first: Sheng

last: Li

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory

library_source: genomic

data_processing:
Reads were mapped to the GRCm38.p3 reference genome using BWA (version 0.7.12-r1039) with the default parameters.
Peaks were called using MACS2 (version 2.1.0.20151222) with -q 0.01 and -B flags.
Genome_build: GRCm38
Supplementary_files_format_and_content: *narrowPeak files contain 5hmC peaks; bed files contain differentially hydroxymethylated peaks (DHMR).

molecule: genomic DNA

source_name: Germinal Center B-cells

growth_protocol: Cells were isolated from mouse spleens

extract_protocol:
DNA was extracted using Qiagen Gentra Puregene kit
hMedIP

treatment_protocol: Not applicable

tag: tissue

value: spleen

tag: genotype

value: TET2 Wild-Type

tag: strain

value: Germinal Center B-cells


title: Protein_footprint_H2O2_Rep2_4hr

description: Protein protected RNA

value: HeLa


title: Ribosome_footprint_H2O2_Rep1_4hr

description: Ribosome protected RNA


title: Ribosome_footprint_H2O2_Rep1_1hr

description: Ribosome protected RNA


title: control_fp_17_04_2016

description:
Ribosome footprint
Replicate 1-GCCAAT

value: MN1 cells

value: Clonal hybrid cells of mouse spinal motor neurons and mouse neuroblastoma


title: htdp_wt_total_22_05_2015

description:
Total mRNA
Replicate 2- CTTGTA

value: 10-12 passages


title: Ribosome_footprint_H2O2_Rep2_8hr

description: Ribosome protected RNA


title: control_total_17_04_2015

description:
Total mRNA
Replicate 1- ACAGTG

value: GFP transfected control


title: 5hmC_WT3_GCB_PD


title: 5hmC_WT2_GCB_PD


title: 5hmC_WT3_GCB_Input


title: Ribosome_footprint_H2O2_Rep2_0hr

description: Ribosome protected RNA

value: No Hydrogen peroxide


title: Ribosome_footprint_H2O2_Rep3_0hr

description: Ribosome protected RNA


title: Total_RNA_H2O2_Rep3_4hr

data_processing:
illumina output file to fastq file conversion by bcl2fastq version 2.16 and demultiplexing by flexbar version 2.5
Sequenced reads were trimmed for adapter sequence and quality using fastx-toolkit v0.0.14 with parameters -t 20 -l 20 and fastq files from the same sample were merged.
Reads were mapped to abundant sequences to remove ribosomal rDNA, adapter contaminants, PhiX, and polyA/C sequences with bowtie2 v2.2.9 with default settings.
Remaining reads were mapped to hg19 genome with tophat v2.1.1 with parameter --no-coverage-search -G gencode.v19.basic.gtf
Aligned reads were filtered for unique mapping and length: RNA >25, Ribosome footprints 28-30, Protein footprints >25.
Read ounts were generated using htseq v0.6.1p1 with gencode.v19.basic.gtf and parameters --stranded==yes intersection-nonempty.
Genome_build: hg19
Supplementary_files_format_and_content: text file with read counts from Htseq


title: Ribosome_footprint_H2O2_Rep1_8hr

description: Ribosome protected RNA


title: 5hmC_KO3_GCB_PD

value: TET2 Knock-Out


title: 5hmC_KO3_GCB_Input


title: errbs_KO_GCB3

data_processing:
Adaptor sequences were removed using FAR software.
Preprocessed reads were then aligned to human genome reference using the bismark alignment software.
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files contain methylated cytosines positions.

extract_protocol:
DNA was extracted using Qiagen Gentra Puregene kit
ERRBS


title: 5hmC_KO2_GCB_PD


title: errbs_KO_GCB1


title: 5hmC_KO2_GCB_Input


title: Ribosome_footprint_H2O2_Rep1_0hr

description: Ribosome protected RNA


title: Total_RNA_H2O2_Rep2_1hr


title: Total_RNA_H2O2_Rep2_4hr


title: RNAseq-TET2KD-CONTROL_514_Ren9_rep_4

data_processing:
Raw reads were trimmed for truseq R1 adapter sequences using Flexbar.
Trimmed reads were mapped to the GRCm38.p3 reference genome using STAR (version 2.3.0e_r291) with the default parameters.
Read Counts per gene were computed using featureCounts (v1.5.1) tool from Subread package with the following parameters: -t "exon", -g "gene_name". GRCm38 Gencode was used as a reference gene annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: *genecounts.txt files contain raw read counts per gene.

source_name: B-cells

extract_protocol:
RNA was extracted using Trizol and Qiagen Rneasy kit
Illumina's RNA-seq-TruSeq-stranded-mRNA

value: B-cells


title: RNAseq-TET2KD-CONTROL_513_Ren8_rep_3


title: Total_RNA_H2O2_Rep2_0hr


title: Ribosome_footprint_H2O2_Rep2_4hr

description: Ribosome protected RNA


title: Total_RNA_H2O2_Rep1_8hr


title: Total_RNA_H2O2_Rep1_4hr


title: Total_RNA_H2O2_Rep3_8hr


title: RNAseq-TET2KD-CONTROL_515_Ren10_rep_5


title: errbs_WT_GCB3


title: RNAseq-TET2KD_6854_9_rep_1

value: TET2 Knock-Down


title: errbs_WT_GCB2


title: Protein_footprint_Tm_Rep3_4hr

description: Protein protected RNA

value: Tunicamycin(Tm) 4Hr


title: Total_RNA_H2O2_Rep2_8hr


title: Total_RNA_H2O2_Rep1_1hr

value: Hydrogen peroxide 1Hr


title: Total_RNA_H2O2_Rep3_0hr


title: RNAseq-TET2KD-CONTROL_511_Ren6_rep_1


title: Protein_footprint_Tm_Rep3_8hr

description: Protein protected RNA

value: Tunicamycin(Tm) 8Hr


title: Total_RNA_H2O2_Rep3_1hr


title: Protein_footprint_Tm_Rep3_0hr

description: Protein protected RNA

value: No Tunicamycin(Tm)


title: RNAseq-TET2KO_GCB_TET2_KO5


title: Total_RNA_H2O2_Rep1_0hr


title: RNAseq-TET2KD_6854_10_rep_2


title: RNAseq-TET2KO_GCB_TET2_KO3


title: Protein_footprint_Tm_Rep2_4hr

description: Protein protected RNA


title: errbs_KO_GCB2


title: Protein_footprint_Tm_Rep1_4hr

description: Protein protected RNA


title: RNAseq-TET2KO-CONTROL_GCB_TET2_WT1


title: Protein_footprint_Tm_Rep3_1hr

description: Protein protected RNA

value: Tunicamycin(Tm) 1Hr


title: Protein_footprint_Tm_Rep2_8hr

description: Protein protected RNA


title: RNAseq-TET2KO-CONTROL_GCB_TET2_WT4

value: spleen


title: Protein_footprint_Tm_Rep2_1hr

description: Protein protected RNA


title: Protein_footprint_Tm_Rep2_0hr

description: Protein protected RNA


title: RNAseq-TET2KD-CONTROL_512_Ren7_rep_2

value: TET2 Wild-Type


title: RNAseq-TET2KO_GCB_TET2_KO4

value: Germinal Center B-cells


title: RNAseq-TET2KO-CONTROL_GCB_TET2_WT3


title: Ribosome_footprint_Tm_Rep2_8hr

description: Ribosome protected RNA

value: HeLa


title: Ribosome_footprint_Tm_Rep3_0hr

description: Ribosome protected RNA


title: Ribosome_footprint_Tm_Rep2_4hr

description: Ribosome protected RNA


title: Ribosome_footprint_Tm_Rep3_8hr

description: Ribosome protected RNA


title: Ribosome_footprint_Tm_Rep3_4hr

description: Ribosome protected RNA


title: Protein_footprint_Tm_Rep1_1hr

description: Protein protected RNA


title: Protein_footprint_Tm_Rep1_8hr

description: Protein protected RNA


title: Protein_footprint_Tm_Rep1_0hr

description: Protein protected RNA


title: Ribosome_footprint_Tm_Rep3_1hr

description: Ribosome protected RNA


title: errbs_WT_GCB1


title: Ribosome_footprint_Tm_Rep2_0hr

description: Ribosome protected RNA


title: RNAseq-TET2KO_GCB_TET2_KO2


title: Ribosome_footprint_Tm_Rep1_0hr

description: Ribosome protected RNA


title: Ribosome_footprint_Tm_Rep1_4hr

description: Ribosome protected RNA


title: Total_RNA_Tm_Rep3_4hr


title: Ribosome_footprint_Tm_Rep2_1hr

description: Ribosome protected RNA


title: Ribosome_footprint_Tm_Rep1_8hr

description: Ribosome protected RNA


title: Total_RNA_Tm_Rep3_8hr


title: Total_RNA_Tm_Rep3_1hr


title: Total_RNA_Tm_Rep3_0hr


title: Ribosome_footprint_Tm_Rep1_1hr

description: Ribosome protected RNA


title: Total_RNA_Tm_Rep2_8hr


title: Total_RNA_Tm_Rep2_1hr


title: Total_RNA_Tm_Rep2_4hr


title: Total_RNA_Tm_Rep1_8hr


title: Pten;Sav1 dKO_2

type: RNA

city: Daejeon

first: Sun-Hye

last: Jeong

address: 291 Daehak-ro

department: Biological science

country: South Korea

institute: KAIST

description: SAMPLE 8

hyb_protocol: Illumina standard hybridization protocol.

scan_protocol: Illumina standard scanning protocol.

data_processing: The data were normalised using quantile normalisation with IlluminaGUI in R.

label: biotin

source_name: Mouse liver, Pten;Sav1 dKO

label_protocol: Biotinylated cDNA was obtained by Illumina TotalPrep RNA Amplification Kit.

extract_protocol: Total RNA was isolated by Ribo-EX (GeneAll, Korea) according to manufacturer's protocol.

tag: strain/background

value: B6;129 mixed

value: Pten;Sav1 dKO

tag: gender

value: Male

tag: age

value: 3 months

value: Liver


title: Sav1 KO_1

description: SAMPLE 5

source_name: Mouse liver, Sav1 KO

value: Sav1 KO


title: HREC

city: New Orleans

first: Shusheng

last: Wang

state: LA

address: 2000 Percival Stern Hall, 6400 Freret Street

department: Cell and Molecular Biology

institute: Tulane University

description: Gene expression

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (part number G2505C) using  one color scan setting.

data_processing: Quantile normalization and subsequent data processing were performed using the GeneSpring GX v12.0 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs that at least 1 out of 5 samples have flags in Present or Marginal (“All Targets Value”) were chosen for differentially expressed LncRNAs screening (All these LncRNAs can be found from the spread sheet “All Targets Value - LncRNAs” in LncRNA Expression Profiling Data.xls file).

source_name: cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA. The specific activity (pmol dyes per ug cRNA) of the labeled RNA was obtained by the following formula: specific activity= (pmol per ul dye)/(ug per ul cRNA)

growth_protocol: HUVEC (ATCC) cells were grown in EC growth medium EGM-2 (Lonza). HCEC and HREC cells were kindly provided by Dr. Ashwath Jayagapol from Vanderbilt University and grown in EGM2 media (Lonza). ARPE-19 (ATCC) cells were growth in DMEM/F12 (HyClone) media with 10% FBS. HDEF (ATCC) cells were grown in DMEM (HyClone) with 10% FBS.

extract_protocol: Total RNA was isolated from human  cell lines using TRIzol reagent (Invitrogen).

treatment_protocol: No treatment

value: HREC


title: HDEF

description: Gene expression

value: HDEF


title: Total_RNA_Tm_Rep2_0hr


title: Total_RNA_Tm_Rep1_4hr

value: Tunicamycin(Tm) 4Hr


title: Pten KO_2

description: SAMPLE 4

source_name: Mouse liver, Pten KO

value: Pten KO


title: HUVEC

description: Gene expression

value: HCEC


title: WT_2

description: SAMPLE 2

source_name: Mouse liver, WT

value: WT


title: Sav1 KO_2

description: SAMPLE 6


title: ARPE

description: Gene expression


title: Pten KO_1

description: SAMPLE 3


title: Pten;Sav1 dKO_1

description: SAMPLE 7


title: Sir3_dot1_pGPD-SIR3_yAT3183_Expo_NAM_Release_r1

type: genomic

city: Paris

first: Angela

last: Taddei

address: 26 rue d'Ulm

country: France

institute: Institut Curie

description: ChIP anti-Sir3 in exponentially S.cerevisiae  dot1 mutants overepressing SIR3 (pGPD promoter) 8 hours after release from YPD 5mM NAM to fresh YPD

hyb_protocol: 16 hours at 65°C in the 1X hybridization buffer supplied by Agilent

scan_protocol: Agilent G2565BA microarray scanner. GenePix6.0 software

data_processing: Normalized Ratio corresponds to raw ratio normalized by the lower decile of the whole array. Z-score corresponds to the standardized raw ratio, i.e z-score, that were computed using R function Scale with default parameters

organism: Saccharomyces cerevisiae

source_name: IP anti-Sir3

label_protocol: 4/5 of the immunoprecipitated DNA and 3/5 of the DNA from the whole cell extract were amplified by random primer extension followed by PCR amplification, incorporating amino-allyl dUTP for subsequent dye coupling

extract_protocol: A total of 20 660nm O.D equivalent of cells were fixed in 20 mL with 0.9 % formaldehyde for 15 min at 30°C, quenched with 0.125 M glycine and washed twice in cold TBS 1x pH 7.6. Pellets were suspended in 1mL TBS 1X, centrifuged and frozen in liquid nitrogen for -80°C storage. All following steps were done at 4°C unless indicated. Pellets were re-suspended in 500 µL of lysis buffer (0.01% SDS, 1.1% TritonX-100, 1.2 mM EDTA pH 8, 16.7 mM Tris pH8, 167 mM NaCl, 0.5 % BSA, 0.02 g.L-1 tRNA and 2.5 µL of protease inhibitor from SIGMA P1860) and mechanically lysed by three cycles of 30 s with 710-1.180 µm glass beads followed by two cycles of 30 s with 500 µm zirconium/silica beads (Biospec Products) using a Fastprep instrument (MP Biomedicals). Each bead beating cycle was followed by 5 min incubation on ice. The chromatin was fragmented to a mean size of 500 bp by sonication in the Bioruptor XL (Diagenode) for 14 min at high power with 30 s on / 30 s off and centrifuged 5 min at 13 000 rpm. 10 µL were kept to be used as Input DNA. Cleared lysate was incubated overnight with 1 µL of polyclonal antibody anti-Sir3 (Agro-bio). 50 µL of magnetic beads protein A (NEB) were added to the mixture and incubated for 4h at 4°C. Magnetic beads were washed sequentially with lysis buffer, twice with RIPA buffer (0.1% SDS, 10mM Tris pH7.6, 1mM EDTA pH8, 0,1% sodium deoxycholate and 1% TritonX-100), twice with RIPA buffer supplemented with 300 mM NaCl, twice in LiCl buffer (250 mM LiCl, 0.5% NP40, 0.5 % sodium deoxycholate), with TE 0.2% TritonX-100 and with TE. Input were diluted 10x with elution buffer (50mM Tris, 10mM EDTA pH8, 1%SDS) and beads were re-suspended in 100 µL elution buffer. A reversal cross-linking was performed by heating samples overnight at 65°C. Proteins were digested with proteinase K in presence of glycogen and the remaining DNA was purified on QIAquick PCR purification columns. Finally, samples were treated with 29 µg.mL-1 RNAse A 30 min at 37°C.

tag: growth protocol

value: 3 ml YPD culture were inoculated and allowed to grow in YPD for 12 hours. Those cultures were used to inoculate 50 mL of YPD culture at a O.D of 0.2. Cultures were allowed to grow until O.D reached ~1, at which time cells were fixed.

value: ade2-1::ADE2   adh4::URA3-4xUASG-(C1-3A)n   ppr1[delta]::HIS3 dot1::KANMx    rap1::GFP-RAP1(LEU2)   sir3::GPD-SIR3(NAT)

source_name: Whole cell extract

value: For exponentially growing cells, cells were precultured overnight in YPD, and grown from 0.2 to 1 O.D in rich medium (YPD) at 30°C.


title: Sir3_pGPD-SIR3_yAT1254_Expo_NAM_Release_r2

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR3 (pGPD promoter) 8 hours after release from YPD 5mM NAM to fresh YPD

value: ade2-1::ADE2   adh4::URA3-4xUASG-(C1-3A)n   ppr1[delta]::HIS3     rap1::GFP-RAP1(LEU2)   sir3::GPD-SIR3(NAT)


title: HCEC

description: Gene expression


title: Sir3_pGPD-SIR3_yAT1254_Expo_NAM_Release_r1


title: Sir3_pGPD_SIR2_pGPD_SIR3_yAT1668_r2

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR2 and SIR3 (both have a pGPD promoter)

value: rap1::RAP1-GFP(LEU2)   RDN1::ADE2   sir2::GPD-SIR2(KanMX)sir3::GPD-SIR3(NAT)


title: Total_RNA_Tm_Rep1_0hr

value: No Tunicamycin(Tm)

value: HeLa


title: Total_RNA_Tm_Rep1_1hr

value: Tunicamycin(Tm) 1Hr


title: Sir3_dot1_pGPD-SIR3_yAT3183_Expo_NAM_Release_r2

value: ade2-1::ADE2   adh4::URA3-4xUASG-(C1-3A)n   ppr1[delta]::HIS3 dot1::KanMx    rap1::GFP-RAP1(LEU2)   sir3::GPD-SIR3(NAT)


title: Sir3_pTEF-SIR3_yAT2629_Expo_Glu_r2

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR3 (pTEF promoter)

value: ade2-1::ADE2   hml[delta]::HPH  rap1::RAP1-GFP(LEU2)  sir3::pTEF-SIR3(NAT)


title: WT_1

description: SAMPLE 1

value: B6;129 mixed

value: Male

value: 3 months

value: Liver


title: Sir3_pGPD_SIR3-A2Q_yAT1256_Expo_Glu_r2

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR3-A2Q (pGPD promoter)

growth_protocol: 3 ml YPD culture were inoculated and allowed to grow in YPD for 12 hours. Those cultures were used to inoculate 50 mL of YPD culture at a O.D of 0.2. Cultures were allowed to grow until O.D reached ~1, at which time cells were fixed.

value: ade2-1::ADE2 adh4::URA3-4xUASG-(C1-3A)n ppr1{delta}::HIS3 rap1::GFP-RAP1(LEU2) sir3::GPD-sir3-A2Q(NAT)

growth_protocol: For exponentially growing cells, cells were precultured overnight in YPD, and grown from 0.2 to 1 O.D in rich medium (YPD) at 30°C.


title: WT-Neuron-rep2

city: Philadelphia

first: Hao

last: Wu

state: PA

address: 415 Curie Boulevard

department: Genetics

institute: University of Pennsylvania

data_processing:
Library strategy: ACE-Seq
Raw sequencing reads were trimmed for low-quality bases and adaptor sequences using Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), and the data quality was examined with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). The trimmed reads were mapped against the reference genomes with Bismark (v0.14.3)42. PCR duplicates were removed using the Picard program (http://picard.sourceforge.net/). To eliminate reads from strands not deaminated by A3A, reads with three or more consecutive non-converted cytosines in the CH context were removed. Raw signals were calculated as % of C/(C+T) at each site.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and ACE-Seq analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in mouse genome.

source_name: whole cortex

growth_protocol: WT or Tet TKO ESCs were cultured in feeder-free gelatin-coated plates in Dulbecco's Modified Eagle Medium (DMEM) (GIBCO) supplemented with 15% FBS (GIBCO), 2 mM L-glutamine (GIBCO), 0.1 mM 2-mercaptoethanol (Sigma), nonessential amino acids (GIBCO), and 1,000 units/mL LIF (Millipore, ESG1107), 3 µM of CHIR99021 (Stemgent) and 1 µM of PD032591 (Stemgent). The culture was passaged every 2–3 d using 0.05% Trypsin (GIBCO). Mice were group-housed in cages of three to five in a 12-h light/dark cycle with food and water provided ad libitum. All mice used for experiments were naive to behavioral assays and other procedures. Cortical excitatory neuronal nuclei (NeuroD6/NEX+) were purified from mouse brain using sucrose gradient ultracentrifugation.

extract_protocol:
Genomic DNA was extracted from mouse ESCs or neuronal nuclei using the DNeasy Blood & Tissue Kit (Qiagen 69504).
For all mammalian DNA samples, a total of 2 or 20 ng of sheared gDNA (~300 bp) was analyzed, containing the sheared methylated λ phage and T4-hmC spike-in controls (0.5% total by mass). In a total volume of 5 µL, 1–20 ng of the gDNA mixture was glucosylated using UDP-glucose and T4 β-glucosyltransferase (βGT, NEB) at 37 ºC for 1 hr. 1 µL of DMSO was added and the sample was denatured at 95 ºC for 5 min and snap cooled by transfer to a PCR tube rack pre-incubated at -80 ºC. Before thawing, reaction buffer was overlaid to a final concentration of 20 mM MES pH 6.0 + 0.1 % Tween, and A3A was added to a final concentration of 5 μM in a total volume of 10 µL. The deamination reactions were incubated under linear ramping temperature conditions from 4–50 ºC over 2 hrs. After deamination, the samples were prepared for Illumina sequencing using the Accel Methyl-NGS kit (Swift Biosciences). The resulting ACE-Seq libraries were sequenced at 1.9 pM with single-end mode on a NextSeq 500 sequencer (Illumina) using the NextSeq 500/500 High Output kit v2 (150 cycles).

value: neuron

tag: age (approx)

value: 6 weeks

tag: Sex


title: WT-Neuron-rep1

value: WT


title: TetTKO-mESC-rep1

source_name: mouse embryonic stem cells

value: mouse embryonic stem cells

value: TetTKO


title: WT Treg unstimulated

city: Dalian

first: Jinsong

last: Yan

address: 9 west section, Lvshun south road, Dalian, Liaoning Province, China

department: Institute of Cancer Stem Cell

country: China

institute: Dalian Medical University

data_processing:
Sequencing was performed on Illumina Hiseq2000 at Beijing Genomics Institute with the type of paired-end, 100bp.
The quality of sequencing data were assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
The mapping to mouse reference genome of mm10 was conducted by TopHat.
Differentially-Expressed genes were called by Cuffdiff, and the normalized FPKM values were called by Cuffnorm.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes normalized FPKM values for all Samples.

extract_protocol:
Total RNA was isolated by TRIZOL from naive CD4+ T cells, or natural Treg cells with or without the stimulation anti-CD3/CD28 for 48hr from wild type or YAP cKO mice.
Strand-specific RNA-seq libraries were prepared using TruSeq Stranded Total RNA LT Sample Prep Kit (with Ribo-Zero Gold, RS-122-2301, Illumina) from 322 ng of total RNA by following manufacturer protocols. Briefly, ribosomal RNA (rRNA) in both cytoplasm and mitochondria were depleted using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. After purification, the RNA was fragmented into small pieces using divalent cations under elevated temperature, which were transcribed into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. A single 'A' base was added to these cDNA fragments that were subsequently ligated with the adapter. The products were enriched with 12-cycle PCR. The concentration of final cDNA libraries in 30 ul ddH2O reached 24-27 ng/ul as determined on Qubit 2.0.

treatment_protocol: Naïve CD4+ (CD62L+ CD25-) T cells and natural Treg (nTreg, CD4+ CD62L+/- CD25HIGH) cells were flow sorted from WT (wild type) and YAP cKO (YAP flox/flox,CD4-Cre+) mice. Freshly sorted naïve and nTreg cells (2×10^6 per sample) were washed with 1X PBS twice and immediately snap-frozen. Some nTregs were activated with 2µg/ml of plate-coated αCD3 and 2µg/ml of soluble αCD28 and IL-2 (100U/ml) for 24hrs before harvest, freezing, and eventual RNA extraction.

tag: tissue source

value: Lymph nodes and spleens

value: Treg

tag: cell markers

value: wildtype

value: Freshly isolated by FACS


title: WT Treg stimulated

tag: treatment

value: Isolated by FACS, stimulated 24 hr with  alphaCD3/alphaCD28 and IL-2


title: YAP cKO Treg stimulated

tag: cell type

value: YAP cKO


title: YAP cKO Treg unstimulated


title: YAP cKO Naïve CD4+ T cells

value: CD4+ T cells


title: Sir3_pGPD-SIR3_yAT1254_Strain2_Expo_Glu_r2

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR3 (pGPD promoter)

value: ade2-1::ADE2 adh4::URA3-4xUASG-(C1-3A)n ppr1{delta}::HIS3 rap1::GFP-RAP1(LEU2) sir3::GPD-SIR3(NAT)


title: Sir3_pGPD-SIR3_yAT1254_Strain2_Expo_Glu_r1


title: Sir3_WT_Expo_yAT191_Glu_r2

description: ChIP anti-Sir3 in WT exponentially S.cerevisiae cells

value: ade2-1::ADE2 adh4::URA3-4xUASG-(C1-3A)n ppr1{delta}::HIS3 rap1::GFP-RAP1(LEU2)


title: Sir3_pGPD_SIR3_yAT2476


title: WT-mESC-rep1


title: Sir3_WT_Expo_yAT191_Glu_r1


title: Sir3_pADH-SIR3_yAT2627_Expo_Glu

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR3 (pADH promoter)

value: ade2-1::ADE2 hml{delta}::HPH rap1::RAP1-GFP(LEU2) sir3::pADH-SIR3(NAT)


title: Sir3_pTEF-SIR3_yAT2629_Expo_Glu

value: ade2-1::ADE2 hml{delta}::HPH rap1::RAP1-GFP(LEU2) sir3::pTEF-SIR3(NAT)


title: Sir3_pGPD_SIR2_pGPD_SIR3_yAT1668


title: Sir3_pADH-SIR3_yAT2627_Expo_Glu_r2

value: 3 ml YPD culture were inoculated and allowed to grow in YPD for 12 hours. Those cultures were used to inoculate 50 mL of YPD culture at a O.D of 0.2. Cultures were allowed to grow until O.D reached ~1, at which time cells were fixed.

value: ade2-1::ADE2   hml[delta]::HPH  rap1::RAP1-GFP(LEU2)  sir3::pADH-SIR3(NAT)

value: For exponentially growing cells, cells were precultured overnight in YPD, and grown from 0.2 to 1 O.D in rich medium (YPD) at 30°C.


title: Sir3_pGPD-SIR3_yAT2554_Strain1_Expo_Glu

value: ade2-1::ADE2 hml{delta}::HPH rap1::RAP1-GFP(LEU2) sir3::GPD-Sir3(NAT)


title: WT Naïve CD4+ T cells


title: TetTKO-mESC-rep2

value: mouse embryonic stem cells


title: Med3 ChEC-seq

city: Bloomington

first: Gabriel

middle: E

last: Zentner

state: IN

address: 915 E 3rd St

department: Biology

institute: Indiana University

data_processing:
library strategy: Chromatin endogenous cleavage (ChEC)-seq
Paired-end FASTQ files were aligned to the sacCer3 genome building using Bowtie2 with default parameters plus `-I 10 -X 700 --no-unal --no-discordant --no-mixed --dovetail`.
Alignment SAM files were used to make tag directories with HOMER.
Genome_build: sacCer3
Supplementary_files_format_and_content: RPM-normalized bigWig files for each experiment were generated using HOMER makeUCSCfile.

source_name: Yeast cells

growth_protocol: Yeast was grown in YPD at 30C with shaking.

extract_protocol: ChEC-seq was performed as described (PMID 26490019) except for the size selection step. RNase-treated ChEC DNA was brought up to 200 µL with 10 mM Tris pH 8 and 160 µL SPRI beads were added (0.8:1 beads:sample ratio versus the 2.5:1 ratio used in the original protocol). The sample was pipetted up and down ten times to mix and incubated at RT for 5 min. Beads were collected on a magnetic rack for 2 min and the supernatant was collected for DNA isolation. Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics.

value: W303 MED3-3FLAG-MNase-HIS3MX6


title: Sir3_pGPD_SIR2_yAT1667

description: ChIP anti-Sir3 in exponentially S.cerevisiae cells overepressing SIR2 (pGPD promoter)


title: Med14 ChEC-seq

value: W303 MED14-3FLAG-MNase-HIS3MX6


title: Med8 ChEC-seq

value: W303 MED8-3FLAG-MNase-HIS3MX6


title: genomic DNA from tumor biopsy [4177856]

city: Ulm

first: Rabea

last: Wagener

address: Albert-Einstein-Allee 11

department: Ulm University and Ulm University Medical Center

institute: Institute of Human Genetics

description: tumor sample

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium HumanMethylationEPIC BeadChip

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: GenomeStudio software v2011.1; methylation module 1.9.0

label: Cy5 and Cy3

source_name: Cryo-preserved tumor

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from tumor FFPE-biopsies using truXTRAC FFPE DNA micro Tube Kit (Covaris) and tumor from cryo-preserved biopsies using PUREGENE DNA Isolation Kit (Qiagen)

value: Male

tag: sample type

value: tumor

tag: disease state

value: Burkitt lymphoma


title: CTL_1

city: University Park

first: Curtis

middle: J.

last: Omiecinski

address: 101 Life Sciences Bldg

department: Veterinary & Biomedical Science

institute: Penn State University

data_processing:
Library strategy: ChIP-exo
Reads were mapped to mouse genome mm10 using BWA-MEM
Duplicate reads were removed using samtools rmdup feature
Samples bam files with the same treatment were merged into one file for peak calling and bigwig generation.
Peak calling were performed using macs14 default settings.
Bam files were converted to bedgraph files, then converted to bigwig files. Three samples from hCAR (hCAR_PB_1, hCAR_PB_2, hCAR_CIT_2) and three samples from mCAR (mCAR_PB_1, mCAR_PB_3, mCAR_TCP_1) were chosen to represent overall hCAR and mCAR.
Genome_build: mm10
Supplementary_files_format_and_content: BED files contains macs14 peak-calling results; bigWig files shows reads coverage on genome

source_name: CTL

extract_protocol:
The mice were maintained under a standard 12h light, 12h dark cycle at constant temperature (23±1°C) with 45-65% humidity. A total of 6 8-week-old male CAR (-/-) knockout mice were infected with YFP-hCAR AV (virus particle 1x10^12 per ml, approximately 100ul diluted injection volume per mouse) through tail-vein injection. At 72 and 94h, the mice were administrated with two successive doses of PB (75mg/kg, in saline) (n=3) or CITCO (5mg/kg, in DMSO) (n=3) through IP injection. Another 6 8-week-old male CAR (-/-) knockout mice were infected with YFP-mCAR AV constructs (virus particle 1x10^12 per ml) through tail-vein injection. At 72 and 94h, two successive doses of PB (75mg/kg, in saline) (n=3) or TCPOBOP (2mg/kg, in DMSO) (n=3) were administrated. After 96h, all AV-infected mice were harvested for liver tissues after CO2 asphyxiation induced euthanasia. Fresh YFP-hCAR or YFP-mCAR AV infected CAR (-/-) knockout mouse liver (~1.0g) was immediately minced and cross-linked with 1% formaldehyde (diluted from 16% formaldehyde solution methanol-free 1 ml ampules from Thermo Scientific) for 10 min followed by quenching with 0.125M Glycine for 5 min. Liver tissues then went through ice-cold PBS washing for three times, homogenized by Dounce homogenization followed by 100nm filtration. Nuclei lysates of liver tissues were prepared by incubating homogenized cells for 15 min in cell lysis buffer (10mM Tris pH 8.0, 10mM NaCl, 0.2% IGEPAL) on ice, and then incubating precipitation from previous step with nuclear lysis buffer (50mM Tris, pH8.0, 10mM EDTA, 0.5% SDS) for 20 min on ice. Nuclei lysates were aliquoted to 700ul per each 10ml sonication tubes (Diagenode, Denville, NJ) and sonicated on Bioruptor 300 (Diagenode, Denville, NJ) for 36 cycles of 30s on, 30s off cycles, to achieve an average chromatin fragmentation size 100bp to 200bp. Subsequent ChIP-exo procedures and sequencing were performed following previously published protocols (Rhee and Pugh 2012). Chromatin was immunoprecipitated using sepharose antibody-conjugated magnetic beads (All YFP-empty, YFP-hCAR and YFP-mCAR constructs infected samples utilize anti-YFP antibody Ab290 from Abcam), followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and later digestion on beads using lambda and recJ exonuclease. Following single-stranded DNA elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. Exonuclease treated ends were then ligated with a second Illumina sequencing adaptor; the products PCR-amplified and gel-purified.
ChIP-exo library constructions were performed following previously published protocols (Rhee and Pugh 2012)

value: liver

value: post natal 8 weeks

value: CAR -/-

tag: constructs

value: YFP-empty

value: PB (75mg/kg, in saline)

tag: chip antibody

value: Anti-GFP (Abcam Ab290, Lot:GR135929-1)


title: CTL_2

tag: tissue


title: Sir3_pGPD_SIR3-A2Q_yAT1256_Expo_Glu_r1

tag: genotype

value: ade2-1::ADE2 adh4::URA3-4xUASG-(C1-3A)n ppr1{delta}::HIS3 rap1::GFP-RAP1(LEU2) sir3::GPD-sir3-A2Q(NAT)


title: mCAR_TCP_3

description:
mCAR_TCP_peaks.bed
mCAR_TCP.bw

tag: strain

value: YFP-mCAR

value: TCPOBOP (2mg/kg, in DMSO)

value: Anti-GFP (Abcam Ab290, Lot:GR158277-1)


title: Med14-AID + 3-IAA TFIIB ChIP-seq replicate 2

data_processing:
Paired-end FASTQ files were aligned to the sacCer3 genome building using Bowtie2 with default parameters plus `-I 10 -X 700 --no-unal --no-discordant --no-mixed --dovetail`.
Alignment SAM files were used to make tag directories with HOMER.
Genome_build: sacCer3
Supplementary_files_format_and_content: RPM-normalized bigWig files for each experiment were generated using HOMER makeUCSCfile.

extract_protocol: After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C.  All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m.  Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice.  Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight.  Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics.

treatment_protocol: For depletion of Med14, a 50 mL culture at an OD600 > 0.8 was split in two. One culture was treated with DMSO and the other was treated with 500 uM 3-IAA for 30 min.

value: BY4705 pGPD1-OsTIR1-HIS3 MED14-3V5-IAA7-kanMX6 SUA7-6GLY-3FLAG-hphMX4

value: 500 uM 3-IAA for 30 min

value: Sigma anti-FLAG M2 magnetic agarose (M8823)


title: ΔHAC1-DTT-3

city: Dublin

first: Geraldine

last: Butler

address: Belfield, Dublin 4

department: School of Biomolecular and Biomedical Science

country: Ireland

institute: UCD Conway Institute

description: Δhac1/Δhac1 YPD + 5mM DTT sample 3

data_processing:
Raw Illumina reads for samples 1-12 were provided by BGI (http://www.genomics.cn/en/index)
Quality control of the data was verified using FastQC v0.11.2
Pair-end sequenced reads were trimmed for low-quality sequence or length using Skewer v0.1.120 with parameters -m pe -l 50 -q 15 -Q 15
Trimmed sequenced reads were mapped to the Candida parapsilosis CDC317 genome using Tophat v2.0.12 with parameters -g 1 --b2-very-sensitive --library-type fr-firststrand
Mapped reads were indexed and sorted for counting using Samtools v0.1.19
Raw number of mapped reads per gene was obtained using htseq-count from HTSeq (v0.6.1) with parameters -m union -s reverse -t exon -i Name
Differentially expressed genes from read count data were identified using the Bioconductor package DESeq2
Genome_build: Candida parapsilosis CDC 317
Supplementary_files_format_and_content: tab-delimited text files include raw counts of sequencing reads per gene for each SAMPLE

organism: Candida parapsilosis

growth_protocol: Strain was grown overnight at 30°C in YPD, diluted to an A600= 0.2 in 60 ml of YPD media and grown up to A600= 0.6 at 30°C.  DTT was added to a final concentration of 5 mM, and  cells were incubated for one additional hour at 30°C.

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19271
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

tag: growth phase

value: log phase


title: mCAR_PB_2

description:
mCAR_PB_peaks.bed
mCAR_PB.bw


title: genomic DNA from tumor biopsy [4133511]

description: tumor sample

tag: gender

value: Male


title: Med14-AID + DMSO TFIIB ChIP-seq replicate 2

value: DMSO


title: ΔHAC1-DTT-1

description: Δhac1/Δhac1 YPD + 5mM DTT sample 1

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19269
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: mCAR_TCP_1

description:
mCAR_TCP_peaks.bed
mCAR.bw

tag: age


title: ΔHAC1-DTT-2

description: Δhac1/Δhac1 YPD + 5mM DTT sample 2

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19270
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: WT-mESC-rep2

value: mouse embryonic stem cells

value: WT


title: mCAR_PB_3

description:
mCAR_PB_peaks.bed
mCAR.bw

value: liver

value: post natal 8 weeks


title: genomic DNA from tumor biopsy [Case6-ID]

description: tumor sample

source_name: FFPE tumor

value: Female

value: tumor

value: preBL


title: Med14-AID + 3-IAA TFIIB ChIP-seq

data_processing:
Paired-end FASTQ files were aligned to the sacCer3 genome build using Bowtie2 with default parameters plus `-I 10 -X 700 --no-unal --no-discordant --no-mixed --dovetail`.
Alignment SAM files were used to make tag directories with HOMER.
Genome_build: sacCer3 (R64)
Supplementary_files_format_and_content: RPM-normalized bigWig files for each experiment were generated using HOMER makeUCSCfile.

extract_protocol: After DMSO or 3-IAA treatment, cultures were fixed with formaldehyde (1% final) for 10 minutes at room temperature (RT), then quenched with glycine (125 mM final) for 5 minutes. After washing with PBS, fixed cell pellets were preserved at -80°C. Thawed pellets were later spheroplasted by resuspension in PBS along with 100 μl of 2 mg/mL zymolyase for 5 m at 37°C. All ChIP solutions henceforth were supplemented with a protease inhibitor cocktail. After washing with PBS, spheroplasts were lysed in 150 μL lysis buffer (50 mM Tris pH 8.0, 150 mM NaCl, 10 mM EDTA, 1% SDS) at RT for 5 m. Lysates were then adjusted to 1.5 mL with 1350 μL of dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA, 1% Triton X-100) and transferred to a Covaris milliTube on ice. Sonication of diluted ChIP lysate was performed in a Covaris S220 sonicator, with parameters of 150 W Peak Power, 40% Duty Cycle, and 200 Cycles/burst, for a time of 180 s. After sonication, samples were centrifuged for 10 m at 21,000 x g and 4°C. The soluble lysate was then transferred to a new tube along with 20 μL of Sigma FLAG beads (M8823) pre-blocked with BSA, and the IP was performed for 1 h at RT. Beads were then washed 3 x 1 mL cold wash buffer (20 mM Tris pH 8.0, 250 mM LiCl, 1 mM EDTA, 1% Triton, 0.1% Nonidet-P40) at RT, with each wash lasting 3 m. For extraction and de-crosslinking, washed beads were resuspended in 250 μL elution buffer (50 mM Tris pH 8.0, 250 mM NaCl, 10 mM EDTA, 1% SDS) with 60 μg proteinase K incubated overnight at 1,000 RPM and 65°C in an Eppendorf ThermoMixer. The next morning, ChIP DNA was extracted with 200 μL phenol/chloroform/isoamyl alcohol, treated with 10 μg RNase A for 20 m at 37C, re-extracted with phenol/chloroform, and precipitated with linear acrylamide in >80% EtOH at -80C overnight. Precipitated DNA was pelleted for 20 m at 4°C and 21,000 x g, washed with RT 75% ethanol, re-spun for 5 m, dried at RT, and finally resuspended in 20 μL low-TE (50 mM Tris, 0.1 mM EDTA). Libraries were constructed using the NEBNext Ultra II Library Prep Kit for Illumina at the Indiana University Center for Genomics and Bioinformatics.


title: mCAR_TCP_2

description:
mCAR_TCP_peaks.bed
mCAR_TCP.bw

value: CAR -/-


title: Med14-AID + DMSO TFIIB ChIP-seq


title: genomic DNA from tumor biopsy [4182393]

description: tumor sample

value: Burkitt lymphoma


title: genomic DNA from tumor biopsy [4194218]

description: tumor sample


title: ΔHAC1-YPD-2

description: Δhac1/Δhac1 YPD sample 2

growth_protocol: Strain was grown overnight at 30°C in YPD, diluted to an A600= 0.2 in YPD and grown up to A600= 0.6 at 30°C. 75 µl of water was added and cells were grown for one additional hour.

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19267
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: genomic DNA from tumor biopsy [4194891]

description: tumor sample


title: ΔHAC1-YPD-1

description: Δhac1/Δhac1 YPD sample 1

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19266
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: RNA-Seq POMIFNG2

city: Aurora

first: Yuwen

last: Zhu

state: CO

address: 12800 E 19th Avenue

department: Surgery

institute: University of Colorado Anschutz Medical Campus

description: IFN-gamma and POM

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC human reference genome assembly hg19 using STAR2.0. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC hg19 was used for gene annotation. Differential expression test was performed using Cuffdiff module.
Genome_build: hg19
Supplementary_files_format_and_content: DEG statistics tables for RNA-Seq data

extract_protocol:
Total RNA was extracted using RNAqueous® Micro Kit (Invitrogen, Waltham MA) as the manufacturer instruction
cDNA library was constructed using Illumina TruSeq kit.
The 151bp single-end fastq files generated from Illumina NextSeq500 platform were aligned to the UCSC human hg19 reference genome using the STAR 2.4.0 RNA-seq aligner

value: IFN-gamma and POM

tag: cell line


title: RNA-Seq IFNG1

description: IFN-gamma

value: IFN-gamma


title: RNA-Seq IFNG2

description: IFN-gamma


title: WT-CLIB214-DTT-2

description: Wild type YPD + 5mM DTT sample 2

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19264
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

value: wild type


title: genomic DNA from tumor biopsy [Case4-ID]

description: tumor sample


title: WT-CLIB214-DTT-3

description: Wild type YPD + 5mM DTT sample 3

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19265
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: hCAR_CIT_1

description:
hCAR_CIT_peaks.bed
hCAR_CIT.bw

value: YFP-hCAR

value: CITCO (5mg/kg, in DMSO)

value: Anti-GFP (Abcam Ab290, Lot:GR158277-1)


title: RNA-Seq POMIFNG1

description: IFN-gamma and POM


title: hCAR_CIT_2

description:
hCAR_CIT_peaks.bed
hCAR.bw


title: hCAR_PB_2

description:
hCAR_PB_peaks.bed
hCAR.bw

value: PB (75mg/kg, in saline)


title: WT-CLIB214-DTT-1

description: Wild type YPD + 5mM DTT sample 1

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19263
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

value: log phase


title: hCAR_PB_3

description:
hCAR_PB_peaks.bed
hCAR_PB.bw


title: RNA-Seq CTRL1


title: WT-CLIB214-YPD-3

description: Wild type YPD sample 3

growth_protocol: Strain was grown overnight at 30°C in YPD, diluted to an A600= 0.2 in 60 ml of YPD media and grown up to A600= 0.6 at 30°C. 75 µl of water was added and cells were grown for one additional hour.

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19262
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: mCAR_PB_1

description:
mCAR_PB_peaks.bed
mCAR.bw

value: YFP-mCAR


title: RNA-Seq CTRL2


title: RNA-seq of Escherichia coli strain 3

data_processing:
Sequencing was performed on Illumina Hiseq2500 with  paired-end of 150bp.
The quality of sequencing data were assessed by the software FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Mapping to the reference of Escherichia coli ATCC8739 (NC_010468.1) was conducted by TopHat2.
Gene expressed value (FPKM) was called and normalized by EdgeR.
Genome_build: Escherichia coli ATCC8739 (NC_010468.1)
Supplementary_files_format_and_content: tab-delimited text file include FPKM values of E3C_RNA

organism: Escherichia coli ATCC 8739

source_name: RNA-seq of Escherichia coli strain 3

growth_protocol: The strain was streaked on nutrient broth (NB) agar plate from freezer stocks and grown at 37 °C for 24 h. Bacteria from a single colony were inoculated in 20 ml NB broth in 100 ml Erlenmeyer flask. The culture was grown in a 37 °C shaker for 16 h.

extract_protocol:
The extraction of total RNA from bacteria liquid culture was followed the invitrogen™ TRIzol reagent method (Thermo Fisher Scientific, 15596018). To determine the yield and quality of total RNA, Ultraviolet spectrophotometry (VASTECH, NV3000) method was used, followed by electrophoresis under an agarose EtBr gel. rRNA was removed from total RNA using Ribo-Zero rRNA Removal Kit (Illumina, MRZB12424) to purify mRNA
Strand Specific mRNA-seq library was generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, E7530L) following the manufacturer’s instructions. Index was added to each sample by NEBNext Multiplex Oligos for Illumina (Index Primers Set 2) (New England Biolabs, E7500L).

value: ATCC 8739


title: RNA-Seq POMALYST2

description: POM

value: POM


title: WT-CLIB214-YPD-1

description: Wild type YPD sample 1

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19260
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq


title: hCAR_CIT_3

description:
hCAR_CIT_peaks.bed
hCAR_CIT.bw

value: liver

value: post natal 8 weeks


title: Pax5-/- Pax5:ER pro-B cells, 6hr b-estradiol treated 1

status: Public on Oct 07 2018

city: Parkville

first: Rhys

last: Allan

state: Victoria

address: 1G Royal Parade

department: Molecular Immunology

country: Australia

institute: The Walter and Eliza Hall Institute of Medical Research

data_processing:
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.6.0.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.

source_name: pro-B cells

extract_protocol:
In situ Hi-C was performed as described by Rao et al (Cell, 2014, PMID 25497547)
Libraries were prepared for sequencing on an Illumina NextSeq 500 using standard Illumina protocols.

value: male

value: bone marrow

value: pro-B cells

tag: genotype/variation

value: Pax5-/- Pax5:ER

value: 6 hour b-estradiol


title: Pax5-/- Pax5:ER pro-B cells, 6hr b-estradiol and 8hr a-amanitin treated 2

value: 6 hour b-estradiol and 8hr a-amanitin


title: Pax5-/- Pax5:ER pro-B cells, 6hr b-estradiol treated 2


title: RNA-Seq POMALYST1

description: POM


title: liver_smallRNA_LKO_flox_repB

city: Seattle

first: Paul

last: Valdmanis

state: WA

address: 1705 NE Pacific St, HSB J-309

department: Medicine

institute: University of Washington

description:
processed data file: microRNA_miR122_RPM.txt
LKO_flox_repB

data_processing:
RNAseq reads were aligned to the mouse mm9 genome
FPKM values were calculated by use of Cufflinks v2.2.1 with the following parameters: “--library-norm-method quartile” and removing ribosomal, snoRNA and mitochondrial sequences.
small RNA sequencing reads were sorted by barcode, barcode removed (4nt), linker-1 clipped and aligned to mouse hairpins from mirBase release 15 using bowtie (version 0.12.7) with 2 mismatches and command -- best
Genome_build: mm9, mirBase release 15
Supplementary_files_format_and_content: File of FPKM values for RNAseq samples,  of reads per million (RPM) mapped microRNA hits for mouse small RNA sequencing samples, all in tab delimited text format

extract_protocol:
Liver samples were snap frozen in liquid nitrogen and ground into powder.  Samples were homogenized and RNA was extracted by Trizol
RNAseq library samples  were prepared using an Illumina TruSeq kit
3ug of RNA per sample was ligated to Linker-1 (IDT) in the absence of ATP with T4 RNA ligase 1 (New England Biolabs). Ligated RNA was size selected (based on an 18-36nt small RNA fraction) on 15% PAGE. The 5’ ends RNA were ligated to 4nt barcoded adapters. Dual-ligated RNA was reverse transcribed, PCR amplified and size selected on 4% NuSieve (Lonza) agarose.  Small RNA sequencing was performed on the Illumina miSeq platform.

tag: strain background

tag: molecule subtype

value: small RNA


title: WT-CLIB214-YPD-2

description: Wild type YPD sample 2

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19261
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

value: wild type


title: liver_smallRNA_LKO_floxCre_repB

description:
processed data file: microRNA_miR122_RPM.txt
LKO_floxCre_repB


title: hCAR_PB_1

description:
hCAR_PB_peaks.bed
hCAR.bw

extract_protocol:
The mice were maintained under a standard 12h light, 12h dark cycle at constant temperature (23±1°C) with 45-65% humidity. A total of 6 8-week-old male CAR (-/-) knockout mice were infected with YFP-hCAR AV (virus particle 1x10^12 per ml, approximately 100ul diluted injection volume per mouse) through tail-vein injection. At 72 and 94h, the mice were administrated with two successive doses of PB (75mg/kg, in saline) (n=3) or CITCO (5mg/kg, in DMSO) (n=3) through IP injection. Another 6 8-week-old male CAR (-/-) knockout mice were infected with YFP-mCAR AV constructs (virus particle 1x10^12 per ml) through tail-vein injection. At 72 and 94h, two successive doses of PB (75mg/kg, in saline) (n=3) or TCPOBOP (2mg/kg, in DMSO) (n=3) were administrated. After 96h, all AV-infected mice were harvested for liver tissues after CO2 asphyxiation induced euthanasia. Fresh YFP-hCAR or YFP-mCAR AV infected CAR (-/-) knockout mouse liver (~1.0g) was immediately minced and cross-linked with 1% formaldehyde (diluted from 16% formaldehyde solution methanol-free 1 ml ampules from Thermo Scientific) for 10 min followed by quenching with 0.125M Glycine for 5 min. Liver tissues then went through ice-cold PBS washing for three times, homogenized by Dounce homogenization followed by 100nm filtration. Nuclei lysates of liver tissues were prepared by incubating homogenized cells for 15 min in cell lysis buffer (10mM Tris pH 8.0, 10mM NaCl, 0.2% IGEPAL) on ice, and then incubating precipitation from previous step with nuclear lysis buffer (50mM Tris, pH8.0, 10mM EDTA, 0.5% SDS) for 20 min on ice. Nuclei lysates were aliquoted to 700ul per each 10ml sonication tubes (Diagenode, Denville, NJ) and sonicated on Bioruptor 300 (Diagenode, Denville, NJ) for 36 cycles of 30s on, 30s off cycles, to achieve an average chromatin fragmentation size 100bp to 200bp. Subsequent ChIP-exo procedures and sequencing were performed following previously published protocols (Rhee and Pugh 2012). Chromatin was immunoprecipitated using sepharose antibody-conjugated magnetic beads (All YFP-empty, YFP-hCAR and YFP-mCAR constructs infected samples utilize anti-YFP antibody Ab290 from Abcam), followed by DNA polishing, A-tailing, Illumina adaptor ligation (ExA2), and later digestion on beads using lambda and recJ exonuclease. Following single-stranded DNA elution, a primer was annealed to EXA2 and extended with phi29 DNA polymerase, then A-tailed. Exonuclease treated ends were then ligated with a second Illumina sequencing adaptor; the products PCR-amplified and gel-purified.
ChIP-exo library constructions were performed following previously published protocols (Rhee and Pugh 2012)

value: CAR -/-

value: YFP-hCAR


title: liver_smallRNA_P270_repB

description:
processed data file: microRNA_miR122_RPM.txt
P270_repB

tag: developmental stage


title: liver_smallRNA_LKO_floxCre_repA

description:
processed data file: microRNA_miR122_RPM.txt
LKO_floxCre_repA


title: liver_smallRNA_P17

description:
processed data file: microRNA_miR122_RPM.txt
P17


title: liver_smallRNA_P28

description:
processed data file: microRNA_miR122_RPM.txt
P28


title: liver_smallRNA_P8_repB

description:
processed data file: microRNA_miR122_RPM.txt
P8_repB


title: liver_smallRNA_P270_repA

description:
processed data file: microRNA_miR122_RPM.txt
P270_repA


title: liver_smallRNA_P21

description:
processed data file: microRNA_miR122_RPM.txt
P21


title: liver_smallRNA_E18_repA

description:
processed data file: microRNA_miR122_RPM.txt
E18_repA


title: liver_smallRNA_P1_repB

description:
processed data file: microRNA_miR122_RPM.txt
P1_repB


title: Pax5-/- Pax5:ER pro-B cells, 6hr b-estradiol and 8hr a-amanitin treated 1

tag: treatment


title: liver_smallRNA_P12

description:
processed data file: microRNA_miR122_RPM.txt
P12


title: liver_smallRNA_miR122_floxCre_d36

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d36

tag: time point

value: 36 days after Cre removal of miR-122


title: liver_smallRNA_E14_repA

description:
processed data file: microRNA_miR122_RPM.txt
E14_repA


title: liver_smallRNA_P1_repA

description:
processed data file: microRNA_miR122_RPM.txt
P1_repA


title: liver_smallRNA_P8_repA

description:
processed data file: microRNA_miR122_RPM.txt
P8_repA


title: liver_smallRNA_miR122_floxCre_d25

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d25

value: 25 days after Cre removal of miR-122


title: liver_smallRNA_E18_repB

description:
processed data file: microRNA_miR122_RPM.txt
E18_repB


title: liver_smallRNA_LKO_flox_repA

description:
processed data file: microRNA_miR122_RPM.txt
LKO_flox_repA


title: liver_RNAseq_122ko_repA

description:
processed data file: RNAseq_miR122_FPKM.txt
122ko_repA

molecule: polyA RNA

value: miR-122 knockout


title: liver_RNAseq_122ko_repB

description:
processed data file: RNAseq_miR122_FPKM.txt
122ko_repB


title: liver_smallRNA_miR122_floxCre_d10

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d10

value: 10 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d14_repC

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d14_repC

value: 14 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d17

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d17

value: liver

value: 17 days after Cre removal of miR-122


title: liver_smallRNA_E14_repB

description:
processed data file: microRNA_miR122_RPM.txt
E14_repB


title: liver_smallRNA_miR122_floxCre_d3

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d3

value: 3 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d2

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d2

value: 2 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d7_repA

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d7_repA

value: 7 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d1

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d1

value: 1 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d7_repC

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d7_repC


title: liver_smallRNA_miR122_floxCre_d200

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d200

value: 200 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d14_repB

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d14_repB


title: liver_smallRNA_miR122_floxCre_d21_repC

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d21_repC

value: 21 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d7_repB

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d7_repB

value: small RNA


title: liver_smallRNA_miR122_floxCre_d45_repB

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d45_repB

value: 45 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d14_repA

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d14_repA


title: liver_smallRNA_miR122_floxCre_d21_repA

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d21_repA


title: liver_smallRNA_miR122_floxCre_d100

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d100

value: 100 days after Cre removal of miR-122


title: liver_smallRNA_miR122_floxCre_d21_repB

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d21_repB


title: liver_smallRNA_miR122_flox_d0_repC

description:
processed data file: microRNA_miR122_RPM.txt
miR122_flox_d0_repC


title: liver_smallRNA_miR122_floxCre_d45_repA

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d45_repA


title: liver_smallRNA_miR122_floxCre_d45_repC

description:
processed data file: microRNA_miR122_RPM.txt
miR122_floxCre_d45_repC


title: liver_smallRNA_miR122_flox_d0_repB

description:
processed data file: microRNA_miR122_RPM.txt
miR122_flox_d0_repB


title: liver_smallRNA_miR122_flox_d0_repA

description:
processed data file: microRNA_miR122_RPM.txt
miR122_flox_d0_repA


title: liver_RNAseq_122ko_repC

description:
processed data file: RNAseq_miR122_FPKM.txt
122ko_repC


title: liver_RNAseq_miR122_floxCre_d45_repA

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d45_repA

value: 45 days after receiving AAV-Cre


title: liver_RNAseq_miR122_floxCre_d45_repB

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d45_repB


title: liver_RNAseq_miR122_floxCre_d200

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d200

value: 200 days after receiving AAV-Cre


title: liver_RNAseq_miR122_floxCre_d100

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d100

value: 100 days after receiving AAV-Cre


title: RNA_seq_ES_dI4_day8_rep2

first: Phuong

middle: Thi

last: Hoang

address: 630 West 168th St

department: Pathology

institute: Columbia University Medical Center

description: RNA-seq

data_processing:
RTA (Illumina) was used for base-calling and CASAVA or bcl2fastq for converting BCL to fastq format, coupled with adaptor trimming. RNA-seq sequencing reads were aligned to the mouse UCSC/mm9 genome using TopHat with 4 mismatches and 10 maximum multiple hits.
The relative abundance (aka expression level) of genes was estimated using cufflinks (version 2.0.2) with default settings.
The FPKM (Fragments Per Kilobase of exon per Million fragments mapped) was calculated per individual gene.
Genome_build: mm9
Supplementary_files_format_and_content: Comma separated values files include: FPKM values for RNA-seq samples

source_name: Postmitotic dI4 interneurons day 8

growth_protocol: Motor neuron differentiation of mouse ESCs was performed as described previously (Wichterle et al., 2002). Briefly, ESCs were trypsinized and seeded at 2.5 x 10^5 cells/10 cm adherent cell culture dish (day 0). On Day 2, EBs were collected, spun down and split 1:4 into 10 cm non-adherent dishes and supplemented with 1 uM RA and 500 nM SAG. ESC-to-V1 IN differentiation was performed largely as described for MN differentiation, with the following modifications: En1-tdTomato or En1-GFP ESCs were plated at density of 7.0x10^5 cells/10 cm dish. On Day 2, EBs were split 1:6 into 10 cm dishes and supplemented with 1 µM RA and 5 nM smoothened agonist. Media was exchanged on Day 4 and 6 of differentiation with RA and SAG replacement. ESC-to-dI4 IN differentiation was performed as above, with the following modifications: Ptf1a-tdTomato ESCs were plated at density of 8.0x10^5 cells/10 cm dish. On Day 2 of differentiation, EBs were split 1:4 into 10 cm dishes and supplemented with 1 µM RA. Media was exchanged on Day 4 and 6 of differentiation with RA replacement.

extract_protocol:
For RNA-seq, EBs were collected and spun down, dissociated for FACS, followed by RNA extraction. TRIzol or TRIzol LS Reagent (Life Technologies) was used for RNA extraction, followed by flash freezing in liquid nitrogen and storage at -80°C until further processing. RNA as separated from DNA and protein fractions using chloroform (Sigma-Aldrich) with Phase Lock Gel columns (5 Prime). RNA supernatant was further purified using RNeasy (Qiagen) spin column mini kits. RNA concentration and quality was determined by Nanodrop spectrophotometer and stored at -80°C. RNA concentration and quality was screened using Bioanalyzer (200ng-1µg per sample, RIN>8 required, Agilent) and then submitted to JP Sulzberger Genome Center (Columbia University Medical Center) for Illumina TruSeq RNA prep with poly-A pull-down to enrich mRNA.
RNA-seq libraries were prepared using Illumina HiSeq 2000 at Columbia Genome Center. Samples were multiplexed in each lane, which yields targeted number (30 million) of single-end/paired-end 100bp reads for each sample, as a fraction of 180 million reads for the whole lane.

treatment_protocol: To inhibit Notch signaling, the gamma-secretase inhibitor DAPT (Selleck Chemicals) was added to some samples on early Day 4 for p1 progenitors at concentration 5 µg/mL in DMSO.

tag: cell type

value: ESC-derived spinal dI4 interneurons

value: Ptf1a-cre x ROSA-tdTomato

tag: cell culture

value: RA on day 2; dissociated for FACS

value: Day 8 postmitotic neurons


title: liver_RNAseq_miR122_floxCre_d45_repC

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d45_repC

value: liver


title: FOXP3-transduced CD4+ T cells treated with MS023, rep 1

city: Tokyo

first: Yuki

last: Kagoya

address: 35 Shinanomachi, Shinjuku

department: School of Medicine

country: Japan

institute: Keio University

description: FOXP3-transduced CD4+ T cells were cultured in the presence of the type I PRMT inhibitor MS023, rep 1

hyb_protocol: Samples were hybridized with Affymetrix PrimeView™ Human Gene Expression Array for 16 hours at 45°C.

scan_protocol: Affymetrix GeneChip Scanner 3000 (Scanner #4)

data_processing: Raw intensity files were processed using Affymetrix Expression Console (version 1.4.1)

source_name: FOXP3-transduced CD4+ T cells treated with MS023, biological replicate #1

label_protocol: Samples were labeled with Biotin.

growth_protocol: Human CD4+ T cells were stimulated with artificial antigen presenting cells (aAPC/mOKT3) that express a membranous form of an anti-CD3 mAb (clone OKT3), CD80 and CD83, and cultured in vitro (RPMI supplemented with 10% human AB serum, 100 IU/ml IL-2 and 10 ng/ml IL-15).

extract_protocol: RNA was collected from the DNGFR+ T cells seven days after the initial stimulation by using the RNeasy Micro Kit (Qiagen) according to the manufacturer’s instructions.

treatment_protocol: CD4+ T cells were transduced with control DNGFR, or FOXP3 and DNGFR linked with a P2A sequence two days after stimulation.  The T cells were then cultured in the presence of MS023 or DMSO.

tag: transduced gene

tag: chemical probe

tag: donor


title: FOXP3-transduced CD4+ T cells treated with MS023, rep 2

description: FOXP3-transduced CD4+ T cells were cultured in the presence of the type I PRMT inhibitor MS023, rep 2

source_name: FOXP3-transduced CD4+ T cells treated with MS023, biological replicate #2


title: RNA_seq_ES_dI4_day8_rep3

description: RNA-seq


title: FOXP3-transduced CD4+ T cells treated with DMSO, rep 2

description: FOXP3-transduced CD4+ T cells were cultured in the presence of DMSO, rep 2

source_name: FOXP3-transduced CD4+ T cells treated with DMSO, biological replicate #2

value: DMSO


title: Control DNGFR-transduced CD4+ T cells, rep 1

description: Control DNGFR-transduced CD4+ T cells were cultured in the presence of DMSO, rep 1

source_name: Control DNGFR-transduced CD4+ T cells, biological replicate #1

value: Control DNGFR


title: FOXP3-transduced CD4+ T cells treated with MS023, rep 3

description: FOXP3-transduced CD4+ T cells were cultured in the presence of the type I PRMT inhibitor MS023, rep 3

source_name: FOXP3-transduced CD4+ T cells treated with MS023, biological replicate #3


title: RNA_seq_ES_V1_DAPT_day8_rep2

description: RNA-seq

source_name: Postmitotic V1 interneurons day 8

value: ESC-derived spinal V1 interneurons

value: En1-cre x ROSA-tdTomato

value: RA, SAG on day 2; DAPT on day 4; dissociated for FACS


title: RNA_seq_ES_V1_day8_rep2

description: RNA-seq

value: RA, SAG on day 2; dissociated for FACS


title: RNA_seq_ES_dI4_day8_rep1

description: RNA-seq


title: RNA_seq_ES_V1_DAPT_day8_rep3

description: RNA-seq


title: RNA_seq_ES_V1_DAPT_day8_rep1

description: RNA-seq


title: Control DNGFR-transduced CD4+ T cells, rep 3

description: Control DNGFR-transduced CD4+ T cells were cultured in the presence of DMSO, rep 3

source_name: Control DNGFR-transduced CD4+ T cells, biological replicate #3


title: Control DNGFR-transduced CD4+ T cells, rep 2

description: Control DNGFR-transduced CD4+ T cells were cultured in the presence of DMSO, rep 2

source_name: Control DNGFR-transduced CD4+ T cells, biological replicate #2


title: FOXP3-transduced CD4+ T cells treated with DMSO, rep 1

description: FOXP3-transduced CD4+ T cells were cultured in the presence of DMSO, rep 1

source_name: FOXP3-transduced CD4+ T cells treated with DMSO, biological replicate #1


title: FOXP3-transduced CD4+ T cells treated with DMSO, rep 3

description: FOXP3-transduced CD4+ T cells were cultured in the presence of DMSO, rep 3

source_name: FOXP3-transduced CD4+ T cells treated with DMSO, biological replicate #3


title: shNC-2

city: Beijing

first: Lingfei

last: Jia

address: 22 zhongguancun nandajie

department: Central lab

institute: Peking University of stomatology school and hospital

description: hASCs transfected with control vectors

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

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: hASCs transfected with control vectors

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

growth_protocol: hASCs were grown in aMEM supplemented with 10% FBS.

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

treatment_protocol: hASCs were transfected with lentivirus containing the shMIR31HG or shNC.

value: hASCs

tag: transfection

value: control


title: RNA_seq_ES_V1_day8_rep3

city: New York

description: RNA-seq

tag: strain


title: shMIR31HG-KD-2

description: hASCs transfected with shMIR31HG

source_name: hASCs transfected with shMIR31HG

value: lentivirus containing the shMIR31HG


title: shNC-1

description: hASCs transfected with control vectors


title: liver_RNAseq_miR122_floxCre_d21_repB

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d21_repB

tag: tissue

value: 21 days after receiving AAV-Cre


title: shMIR31HG-KD-1

description: hASCs transfected with shMIR31HG


title: liver_RNAseq_miR122_floxCre_d21_repA

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d21_repA


title: liver_RNAseq_miR122_floxCre_d21_repC

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_floxCre_d21_repC


title: RNA_seq_ES_V1_day5_rep3

description: RNA-seq

source_name: Postmitotic V1 interneurons day 5

value: Day 5 postmitotic neurons


title: RNA_seq_ES_V1_day8_rep1

description: RNA-seq


title: ΔHAC1-YPD-3

description: Δhac1/Δhac1 YPD sample 3

extract_protocol:
Cells were collected, resuspended in RNA later and snap frozen in liquid nitrogen. RNA was extracted using RiboPure RNA purification kit (Ambion AM19268
Illumina HiSeq stranded RNA-seq mRNA (polyA) prepared by Beijing Genomics Institute (http://www.genomics.cn/en/index)
Strand-specific 100bp paired-end RNA-Seq

tag: growth phase

value: log phase

tag: genotype


title: RNA_seq_ES_V1_day5_rep2

description: RNA-seq


title: liver_RNAseq_miR122_flox_d0_repB

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_flox_d0_repB

value: uninjected


title: MesoT FCS p4 rep1

status: Public on Oct 06 2018

city: Athens

first: Stephen

last: Dalton

state: GA

address: 325 Riverbend Rd

department: Biochemistry & Molecular Biology

institute: University of Georgia

description: Dalton_MesoT_FCS counts_rep1

data_processing:
Basecalls were performed on the illumina Hiseq 2500 v4 platform
Processed reads were mapped to hg19 using tophat 2.0.13, HIAST2 2.1.0 and Bowtie 2.2.9 using default parameters
Reads over ENSEMBL genes were counted using Subread 1.4.2 with the following parameters featureCounts -p -t exon -g gene_id
Differential gene expression was performed using R studio (v 0.6.1p1)
ChIP-seq peaks were called using MACS2 2.1.1
Genome_build: hg19

source_name: Human Embryonic Stem Cells

growth_protocol: WA09 hESCs were maintained in chemically-defined media (CDM) consisting of DMEM/F12 w/o glutamine supplemented with 1x nonessential amino acids, 1x antimycotic/antibiotic, 1x trace elements A, B and C, 2 mM L-alanyl-L-glutamine, 10 mg/ml transferrin (HOLO), human plasma, tissue culture grade, 2% Probumin® bovine serum albumin life science grade, 0.1 mM b-mercaptoethanol, 50 μg/mL ascorbic acid, 10 ng/ml rhHeregulin b-1, 200 ng/ml LONG® R3 IGF-I human, 10 ng/ml rhActivin A and 8 ng/ml rhFGF basic on 1:200 Geltrex coated plates. For splanchnic mesoderm (SplM) induction, hPSCs were seeded at 50,000 cells/cm2 onto Geltrex coated plates into CDM supplemented with 25 ng/ml rhWNT3a and 100 ng/ml rhBMP4 for 4 days with media changed daily. For MesoT induction, CDM is supplemented with 25 ng/ml rhWNT3a, 50 ng/ml rhBMP4 and 4 μM all-trans retinoic acid for an additional 14 – 18 days. To self-renew MesoT (FCS), cells were passaged with collagenase type IV (800 units/ml) followed by 1x TrypLE Select and cultured with 10% fetal bovine serum, Minimal Essential Media, Alpha, 1x antibiotic/antimycotic, 2 mM L-alanyl-L-glutamine and 8 ng/ml FGF2 at an initial seeding density of 50,000 cells/cm2 on plastic then 10,000 cells/cm2 for subsequent passages using 1x TrypLE Select. Media was changed every day. For generation of mesothelium-like cells (MLCs), SplM is passed with 1x TrypLE select then replated at 150,000 cells/cm2 in CDM -FGF2 -Activin A +20 μM SB431542 +4 μM retinoic acid for 18 days total with media changed daily. SplM-derived smooth muscle was left in culture for 16-18 days. MesoT-derived MLCs were generated by replating MesT cells at 150,000 cell/cm2 using MLC media above.

extract_protocol:
Cells were collected using collagenase type IV (MesoT) and/or TrypLE Select (MesoT, MesoT FCS, MLC, smooth muscle). The outer mesothelial layer of mouse organs were digested by exposing intact organs to a dissociation buffer containing 1 mg/ml collagenase IV and 0.05% trypsin. All cells were homogenized with Omega Homogenizer Columns (HCR003). Total RNA were extracted using Trizol and purified with RNeasy mini kit (Qiagen) according to manufacture's protocol.
Samples with an RNA integrity number (RIN) above 0.9 were selected and sent out for standard RNA-Seq application, including poly A enrichment, adaptor ligation, bar-coding, library amplification, etc (Hudsonalpha, AL, US) and Georgia Genomics Facility (University of Georiga, US).
RNA-Seq, 50bp and 75bp pair-end, at least 25 million reads per sample; ChIP-seq, 50bp single-end, 25 millioms reads per sample

treatment_protocol: Wt1creERT2/+ Rosa26tdT/+ embryonic mice were generated by crossing Wt1creERT2/+ mice8 with a knock-in of tamoxifen inducible cre-recombinase in the Wt1 locus (Jackson Laboratory Stock #010912) and Rosa26tdT/tdT (Jackson Laboratory Stock #007914) mice with a loxP-flanked STOP cassette preventing transcription of a CAG promoter-driven red fluorescent protein variant, tdTomato{Madisen:2010fi}. At E12.5, pregnant dams were injected with 300 l of 10 mg/ml tamoxifen/corn oil solution intra-peritoneally at 24 hour intervals for three consecutive days. Embryos were harvested at E15.5 and the heart, lung, liver and gut were carefully isolated using sterile technique. The outer mesothelial layer was digested by exposing intact organs to a dissociation buffer containing 1 mg/ml collagenase IV and 0.05% trypsin and tdTomato+ fractions were sorted.

tag: cell line

tag: passages


title: RNA_seq_ES_V1_day5_rep1

description: RNA-seq


title: MesoT Day 18 rep2

description:
Dalton_MesoT_day18_counts_rep2
hPSC.MesoT_Rep3 - Sample 2 Dalton_HumanCounts.txt


title: MesoT-derived MLC rep1

description: hPSC.MLCs_Rep1 - Sample 7 Dalton_HumanCounts.txt


title: MesoT Day 18 rep1

description:
Dalton_MesoT_day18_counts_rep1
hPSC.MesoT_Rep1 - Sample 1 Dalton_HumanCounts.txt


title: MesoT FCS p4 rep2

description: Dalton_MesoT_FCS counts_rep2


title: MesoT Day 22 rep2

description: hPSC.MesoT_Rep4 - Sample 4 Dalton_HumanCounts.txt


title: liver_RNAseq_miR122_flox_d0_repC

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_flox_d0_repC

tag: strain background


title: invitro_rep8_UN

city: Montreal

first: Alain

last: Pacis

state: QC

address: 740 Dr Penfield Ave

country: Canada

institute: Canadian Centre for Computational Genomics (C3G)

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence.
Read count estimates per gene were obtained using Tophat2 software package.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files include count values for each sample

source_name: Intestinal intraepithelial cytotoxic T cells

growth_protocol: Small intestinal epithelial compartment was isolated from human duodenal biopsies via mechanical disruption. Briefly, 4 to 6 biopsies from each subject were collected in cell culture medium and suspended in 7 mL of 1640 RPMI containing 1% dialyzed fetal bovine serum (Biowest), 2 mM EDTA (Corning), and 1.5 mM MgCl2 (Thermo Fisher Scientific) and shaken at 250rpm for 30 minutes at 37°C. The procedure was repeated twice with fresh medium to enhance cell recovery. Cells were harvested from biopsy-free media via centrifugation and pooled for subsequent use. Single cell suspension was used for ex-vivo experiments. Ex vivo samples from both control subjects and CeD patients (color coded in each figure) have been obtained.  To generate short-term CD8+ lines, the single cell suspension obtained as described above was stained with fluorochrome-labeled anti-human CD45 (BD Biosciences, cat#564357), CD3 (Biolegend, cat#300426) TCRαβ (Biolegend, cat#306722) and CD8 (BD Biosciences, cat#564804) antibodies, CD45+CD3+CD8+TCRαβ+ positive cells were purified via fluorescence activated cell sorting (FACS). Sorted CD8+ T cells were subsequently expanded in vitro with 1μg/mL phytohaemagglutinin (PHA, Calbiochem) and a mixture of irradiated heterologous peripheral blood leukocytes and Epstein Barr Virus (EBV)-transformed cell lines in 1640 RPMI with 10% human serum AB (Atlanta Biologicals) and maintained in culture for ten to twelve days with 100U/mL of IL-2 (NIH AIDS Reagent Program cat#136). Prior to IL-15 and IL-21 stimulation, cells were deprived of IL-2 for 24 (prior to western blot or phospho-flow cytometry) or 48 (prior to RNA sequencing) hours and plated at a concentration of 1*106 cells/mL for stimulation and downstream experiments. Cell lines were generated from both controls and CeD patients, no differences in survival, cytolytic properties or response to cytokines were observed between the two groups.

extract_protocol:
To isolate RNA from whole duodenal biopsies, a single bioptic fragment was stored in RNA-later (QIAGEN) at the time of endoscopy, kept at 4°C for 24 hours and then frozen at -80°C upon RNA later removal until processing. Defrost tissues were homogenized using magnetic beads and a Cell Tissue Homogenizer (Bullet blender by Next Advance) and RNA was extracted using RNeasy columns (QIAGEN). RNA integrity was assessed by Bioanalyzer (Agilent). 500ng of high-quality RNA was reverse-transcribed into cDNA using the qScript cDNA SuperMix (Quanta Biosciences). TaqMan Gene Expression Assay (Applied BioSystems, final concentration 1X) using Taqman Fast Advanced Master Mix and Taqman specific probes were used to measure the expression levels of IL-15Ra (Hs00542604) and IL-21 (Hs00222327) genes. As housekeeping genes, we used: GAPDH(Hs02758991), GUSB (Hs99999908), HPRT1 (Hs99999909), and POLR2A(Hs00172187). PCR was performed using the following thermal protocol: 50 °C, 2 min; 95 °C, 2 min, PCR Cycle of 40 cycles of (95 °C, 1 sec; 60 °C, 20 sec). After the indicated treatments, cells were collected and homogenized in RLT plus buffer, RNA isolation was carried out using the RNeasy Plus Mini Kit (Qiagen cat#74134) or RNeasy Plus Micro Kit (Qiagen cat#74034) for cell lines and ex vivo samples respectively, according to manufacturer’s instructions.
RNA quantity was evaluated spectrophotometrically and the quality was assessed with the Agilent 2100 Bioanalyzer (Agilent Technologies); all tested samples showed RNA integrity number (RIN) above 8. RNA-sequencing libraries were prepared using the SMARTer® Stranded Total RNA Sample Prep Kit-HI Mammalian by Clontech Laboratories (Takara) for cell lines and the Illumina TruSeq Total RNA stranded kit (including Ribo-Zero depletion) for ex vivo samples, according to manufacturer’s instructions. Libraries quality was checked by Bioanalyzer (Agilent) prior to pooling and sequencing. Indexed cDNA libraries were pooled in equimolar amounts and sequenced with single-end 50bp reads with a high output Flow Cell (8 lane flow cell) on an Illumina HiSeq4000 at the University of Chicago Genomic Facility. In vitro and ex vivo samples were run separately. Number of reads sequenced per sample are in Table S1  .

treatment_protocol: CD8+ T cell lines or ex vivo single cell suspension from the epithelial compartment were stimulated with human recombinant IL-15 (Biolegend cat#570304), IL-21 (Biolegend cat#571202) or IL-2 (NIH AIDS Reagent Program cat#136) at the indicated concentrations for 20 minutes for signaling experiments (WB and phospho flow cytometry) or 2 hours for RNA-seq experiments. BNZ-2 (sequence in Fig. 1B), or a control peptide (scrambled sequence of BNZ-2), was added at the indicated concentrations ten minutes prior to cytokine stimulation.

tag: experiment type

value: in vitro

tag: replicate id

value: Replicate 8

value: UN


title: invitro_rep8_IL21_BNZ

tag: treatment

value: IL21 + BNZ


title: MesoT ChIP K27ac

description: MesoT ChIP K27ac


title: invitro_rep7_IL21_BNZ

value: Replicate 7


title: Splanchnic mesoderm-derived smooth muscle


title: MesoT ChIP Input


title: invitro_rep8_IL21_CP

value: IL21 + CP


title: invitro_rep7_IL21_CP


title: liver_RNAseq_miR122_flox_d0_repA

description:
processed data file: RNAseq_miR122_FPKM.txt
miR122_flox_d0_repA

value: liver

tag: time point


title: MesoT ChIP K4me1

description: MesoT ChIP K4me1


title: MesoT Day 22 rep1

description: hPSC.MesoT_Rep2 - Sample 3 Dalton_HumanCounts.txt


title: MesoT-derived MLC rep2

description: hPSC.MLCs_Rep2 - Sample 8 Dalton_HumanCounts.txt


title: invitro_rep6_UN

value: Replicate 6


title: invitro_rep8_IL21


title: invitro_rep6_IL21_BNZ


title: invitro_rep7_IL21


title: invitro_rep6_IL21


title: invitro_rep6_IL21_CP


title: invitro_rep7_UN


title: invitro_rep5_IL21_CP

value: Replicate 5


title: invitro_rep5_IL21_BNZ


title: invitro_rep5_IL21


title: invitro_rep5_IL15_IL21_CP

value: IL15 + IL21 + CP


title: invitro_rep5_UN


title: invitro_rep5_IL15_IL21_BNZ

value: IL15 + IL21 + BNZ


title: invitro_rep5_IL15_CP

value: IL15 + CP


title: invitro_rep5_IL15_BNZ

value: IL15 + BNZ


title: invitro_rep5_IL15_IL21


title: invitro_rep3_IL21_CP

value: Replicate 3


title: invitro_rep3_IL21


title: invitro_rep5_IL15


title: invitro_rep3_IL21_BNZ


title: invitro_rep3_UN


title: invitro_rep3_IL15_IL21_CP


title: invitro_rep3_IL15_IL21


title: invitro_rep3_IL15_BNZ


title: invitro_rep3_IL15


title: invitro_rep3_IL15_CP


title: invitro_rep2_UN

value: Replicate 2


title: invitro_rep3_IL15_IL21_BNZ


title: invitro_rep2_IL21_BNZ


title: invitro_rep2_IL21


title: invitro_rep2_IL15_IL21_CP


title: invitro_rep2_IL15_BNZ


title: invitro_rep1_IL21

value: Replicate 1


title: invitro_rep1_IL21_CP


title: invitro_rep2_IL15_CP


title: invitro_rep2_IL15_IL21


title: invitro_rep2_IL15


title: invitro_rep2_IL21_CP


title: invitro_rep2_IL15_IL21_BNZ


title: invitro_rep1_IL15_IL21_CP


title: invitro_rep1_IL15_IL21


title: exvivo_rep5_IL21_BNZ

source_name: Intestinal epithelial cells

value: ex vivo


title: exvivo_rep5_UN


title: invitro_rep1_IL15_BNZ

value: in vitro


title: invitro_rep1_IL15_IL21_BNZ


title: invitro_rep1_IL15


title: invitro_rep1_UN


title: invitro_rep1_IL21_BNZ


title: exvivo_rep5_IL15_IL21_BNZ


title: exvivo_rep5_IL21


title: exvivo_rep5_IL15_IL21


title: invitro_rep1_IL15_CP


title: exvivo_rep5_IL15_BNZ


title: exvivo_rep5_IL15


title: exvivo_rep4_UN

value: Replicate 4


title: exvivo_rep4_IL21_BNZ


title: exvivo_rep4_IL21


title: exvivo_rep4_IL15_IL21_BNZ


title: exvivo_rep4_IL15_IL21


title: exvivo_rep4_IL15_BNZ


title: exvivo_rep3_IL21


title: exvivo_rep3_UN

value: UN


title: LPS/LPS-24h (PD02M022)

city: Indianapolis

first: Takashi

last: Hato

address: 950 W. Walnut St. R2 202

hyb_protocol: Individual labeled samples were hybridized to the Mouse Gene 2.0 ST GeneChips® for 17 hours then washed and  stained.

scan_protocol: Chips were scanned with the standard protocol using Affymetrix GeneChip® Command Console Software (AGCC) to generate data (CEL files)

data_processing: CEL files were imported into Partek Genomics Suite 6.6 (Partek, Inc., St. Louis, Mo) for analysis. RMA  (Robust multichip average, Bolstad, 2003) expression levels were generated for all probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

source_name: LPS/LPS-24h, Kidney S2/S3

label_protocol: 1 ng of total RNA for each sample was labeled using the standard protocol for the Affymetrix WT Pico kit (Affymetrix, Santa Clara, CA).

extract_protocol: Mouse kidneys were sliced and tubular microdissection was performed in ice-cold dissection solution (135 mM NaCl, 1 mM Na2HPO4, 1.2 mM Na2SO4, 1.2 mM MgSO4, 5 mM KCl, 2 mM CaCl2, 5.5 mM glucose, 5 mM HEPES, 0.1% BSA; pH 7.4) using a Leica MZ 12.5 stereomicroscope equipped with Leica MC 170 HD digital microscope camera and ThermaZone cooling device. RNA was extracted using PicoPure RNA kit (Life Technologies).

treatment_protocol: Non-preconditioned mice were subjected to single-dose 5 mg/kg LPS (0111:B4) i.p. for 4 hrs or 24 hrs. Preconditioned mice were subjected to 0.25 mg/kg LPS followed 24 hrs later by 5 mg/kg LPS for 4 hrs or 24 hrs.

value: WT

tag: timepoint (post-treatment in hours)

value: LPS 0.25mg/kg/LPS5mg/kg

tag: gender

value: male

value: S2/S3 proximal tubular segments


title: LPS/LPS-24h (PD02M020)


title: LPS-24h (PD02M015)

source_name: LPS-24h, Kidney S2/S3

value: LPS 5mg/kg


title: LPS-24h (PD02M018)


title: LPS/LPS-4h (PD02M012)

source_name: LPS/LPS-4h, Kidney S2/S3


title: LPS-24h (PD02M016)


title: LPS/LPS-24h (PD02M021)


title: LPS/LPS-4h (PD02M011)


title: LPS-24h (PD02M013)


title: LPS-24h (PD02M017)


title: LPS-24h (PD02M014)


title: LPS/LPS-4h (PD02M009)


title: LPS/LPS-24h (PD02M019)


title: LPS/LPS-4h (PD02M010)


title: exvivo_rep3_IL15_IL21


title: LPS-4h (PD02M008)

source_name: LPS-4h, Kidney S2/S3


title: exvivo_rep3_IL21_BNZ

value: IL21 + BNZ


title: exvivo_rep3_IL15


title: control (PD02M004)

source_name: control, Kidney S2/S3

value: control


title: LPS-4h (PD02M007)


title: exvivo_rep3_IL15_IL21_BNZ

value: IL15 + IL21 + BNZ


title: exvivo_rep3_IL15_BNZ


title: LPS-4h (PD02M006)


title: LPS-4h (PD02M005)


title: exvivo_rep4_IL15


title: exvivo_rep2_IL15_IL21


title: control (PD02M003)


title: exvivo_rep2_IL15_IL21_BNZ


title: exvivo_rep2_UN


title: exvivo_rep2_IL21_BNZ


title: exvivo_rep2_IL15_BNZ


title: exvivo_rep1_IL15_IL21_BNZ


title: exvivo_rep1_UN


title: exvivo_rep1_IL15_IL21


title: exvivo_rep1_IL21


title: exvivo_rep2_IL15


title: exvivo_rep2_IL21


title: exvivo_rep1_IL15_BNZ


title: HepG2_16hrs 0.5% O2_NA_Rep 2

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3)
Reads were aligned to GRCh37 using Tophat 2.0.8b (http://ccb.jhu.edu/software/tophat/index.shtml) and bowtie 1.0.0 (http://bowtie-bio.sourceforge.net/index.shtml) and non-uniquely mapping fragments excluded using SAMtools (0.1.19)
Total read counts for each UCSC defined gene were extracted using HTSeq (0.5.4p3) with ‘intersection-strict’ mode
Significantly regulated genes were identified using DESeq2
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: tab-delimited text files from htseq

source_name: hepatocellular cancer cell line

growth_protocol: Cell lines were grown in Dulbecco’s modified Eagle’s Medium, 100 U/ml penicillin, 100 μg/ml streptomycin and 10% fetal bovine serum (Sigma Aldrich) and regularly tested for mycoplasma infection.

extract_protocol:
Total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion; Life Technologies Ltd, Paisley, UK) and treated with DNaseI (TURBO DNA‐free, Ambion).
PolyA+ RNA libraries were then prepared using the ScriptSeq v2 RNA‐Seq kit (Epicentre, Madison, WI, USA).
All RNA-seq experiments were performed in triplicate in accordance with ENCODE consortium guidelines

treatment_protocol: Hypoxic incubations were performed for the specified duration and ambient oxygen concentration in an In Vivo2 400 Hypoxia Work Station (Ruskinn Technology).

value: hepatocellular cancer cell line

tag: degree of hypoxia

tag: duration of hypoxia

value: 16 hours


title: HepG2_16hrs 0.5% O2_NA_Rep 3


title: HepG2_Normoxia_NA_Rep 3

value: normoxia


title: HepG2_16hrs 0.5% O2_NA_Rep 1


title: HepG2_Normoxia_NA_Rep 1


title: HepG2_Normoxia_NA_Rep 2


title: control (PD02M002)


title: RCC4_VHL_Hx_3_Replacement

source_name: kidney cancer cell line

value: kidney cancer cell line

value: 24 hours


title: control (PD02M001)


title: exvivo_rep1_IL21_BNZ

value: ex vivo

value: Replicate 1


title: exvivo_rep1_IL15


title: RCC4_VHL_Hx_2_Replacement


title: RCC4_VHL_Nx_3_Replacement


title: HKC8Hypoxia0.1O2rep3

description: sample split over two lanes

source_name: kidney proximal tubule cell line

value: kidney proximal tubule cell line


title: RCC4_VHL_Nx_1_Replacement


title: RCC4_VHL_Nx_2_Replacement


title: RCC4_VHL_Hx_1_Replacement


title: Mouse E15.5 gut mesothelium

source_name: Mouse Embryo

value: gut mesothelium