title: DF1_0_6_Run_2

city: La Joll

first: Gene

last: Tan

address: 4120 Capricorn Lane

institute: J. Craig Venter Institute

description: Avian (chicken) origin

data_processing:
Cell Ranger v2.2.0 mkfastq
Genome_build: The chicken genome uses the GRCg6a (Gallus_gallus.GRCg6a.dna.toplevel.fa.gz) genome assembly; the dog genome uses the CanFam3.1 (Canis_familiaris.CanFam3.1.dna.toplevel.fa.gz) genome assembly.
Supplementary_files_format_and_content: *tsv, *mtx: Tab-delimited files that either have each barcode on one 'axis' of the table or read counts for each gene on the other 'axis' of the table.
Supplementary_files_format_and_content: *fa, *gtf: Fasta and gtf files for reference genomes.

organism: Gallus gallus

source_name: DF1 cells

growth_protocol: DF-1 and MDCK cells were cultured in DMEM with 10% FBS and 1% pen/strep on 6-well culture plates at 5 x 10e5 cells per well and incubated at 5% CO2 and 37°C.

extract_protocol:
Single-cell gel beads in emulsion (GEMs) generated by the 10x Genomics chromium controller were reverse transcribed followed by 14 cycles of cDNA amplification. After cDNA cleanup, quantity and quality control of the amplified cDNA were analyzed using Bioanalyzer. Libraries were constructed by fragmentation, end-repair and A-tailing followed by adaptor and sample index ligation according to the manufacturer’s instructions. Finally, library constructs were qualitatively analyzed by Bioanalyzer and quantified by q-PCR before sequencing.
Preparation for single-cell transcriptomic sequencing followed the protocol for 10x Genomics Chromium Single Cell platform.
10X Genomics 3` RNA-seq

treatment_protocol: In the first experiment, MDCK and DF-1 cells were infected with wildtype A/Guinea Fow/Hong Kong/WF10/99 (wtWF10) at a multiplicity of infection of 0.067, 0.2, 0.6 or 1.8. In the second experiment, MDCK and DF-1 cells were infected with the wtWF10 and a barcoded version of wtWF10 (mVar) at a 1:1 ratio that equated to a multiplicity of infection (MOI) of 0.02, 0.067, 0.2 and 0.6. A helper virus, another version of WF10, was added to cells at a final MOI of 1 for MDCK cells or 0.1 for DF-1 cells. Virus stocks were serially diluted in cold 1X PBS and incubated on ice until use. Viruses were titered using flow cytometry (using anti-NP antibody). Before infection, cells were washed three times with cold 1X PBS and placed on ice. To infect, cells were inoculated with a 200 µL volume inoculum (with respective MOIs) and placed on ice for 45 minutes. Plates were rocked back and forth every 10 minutes to evenly spread the inoculum and prevent the monolayers from drying. After 45 minutes, the inoculum was aspirated and 2 mL of pre-warmed (at 37ºC) infection media was added. Plates were incubated at 37ºC for 3 hours. Afterwards, the infection media was replaced with 2 mL of pre-warmed infection media supplemented with 1M NH4Cl. Plates were placed back into incubator for an additional 5 hours. Subsequently, culture media was aspirated and cells washed once with 1X PBS. Cells were then trypsinized with 200 µL of 0.25% Trypsin EDTA until all cells came off the plate and un-clumped. To each well, 0.5 mL of virus infection media was added and replicates were pooled (2 wells per MOI). Cells for each sample were counted. Samples were spun at 150 rcf for 3 minutes and washed with 0.5 mL of 1X PBS/0.04% BSA. Washings were performed two more times. Finally, cells were resuspended with 1X PBS/0.04% BSA to get a final cell count of 7 x 10e5 cells/mL for each sample.

tag: cell line

tag: virus

value: wtWF10, barcoded WF10 (mVar) and helper WF10

tag: multiplicity of infection


title: DF1_0_02_Run_2

status: Public on Jun 16 2020

type: SRA

country: USA

description: Avian (chicken) origin

library_source: transcriptomic

molecule: total RNA


title: DF1_0_2_Run_2

description: Avian (chicken) origin


title: DF1_1_8_Run_1

description: Avian (chicken) origin

value: Wildtype A/Guinea Fowl/Hong Kong/WF10/99 (wtWF10)


title: DF1_0_067_Run_2

description: Avian (chicken) origin


title: mESCs.Zbtb7a.ChIP

city: GuangZhou

first: Jiangping

last: He

address: Kai yuan avenue 190

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH), CAS

library_source: genomic

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the genome(mm10) with bowtie2
ChIP-seq reads were aligned to the mouse mm10 genome using bowtie247 with the options ‘-p 20– very-sensitive–end-to-end–no-unal–no-mixed -X 2000’. The multimapped reads were kept for TE analysis, but only the best alignment is reported for those reads, if more than one equivalent best alignment was found, then one random alignment was reported. Whereas the reads mapping to mitochondrial DNA or unassigned sequences were discarded
Genome_build: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: PNT reprogramjing cells D3

growth_protocol: Male mouse embryonic stem cells (mESCs) were derived from 3.5 d.p.c inner cell mass (ICM) from female 129 mice (Stock No.: 217, Beijing Vital River Laboratory Animal Technology Co., Ltd.). Animal care and experimental protocols were approved by the animal ethics committee of the Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences. ESCs with genetic engineering, including Ythdc1-conditional knockout (cKO), MERVL::tdTomato reporter, and Halo- Ythdc1 knockin (KI) , and TurboID overexpression (OE) were constructed and cultured in feeder- free condition, using serum/LIF medium containing high-glucose Dulbecco’s modified Eagle’s medium (DMEM, HyClone, #SH30022.01), 15% fetal bovine serum (FBS, Front Biomedical, # OPT500), 1× GlutaMAX, 1× nonessential amino acids (NEAA, Gibco, #11140076), 1× Penicillin- Streptomycin (Hyclone, #SV30010), 1× Sodium Pyruvate (Gibco, #11360070), 1 mM 2- Mercaptoethanol (Gibco, # 21985023), and 1000 U/ml LIF. HEK293T (ATCC, # CRL-1126) and NIH3T3 (ATCC, #CRL-1658) cells were maintained in high-glucose DMEM supplemented with 10% FBS (Natocor, #SFBE), 1× GlutaMAX (Gibco, #35050079), and 1× NEAA. All the cell lines were cultivated at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol: Native ChIP-seq was performed as described44. In brief, 1 × 107 cells were harvested and resuspended in 500 μl Buffer 1 (0.32 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 EDTA-free protease inhibitor cocktail [Roche, #4693132001]) supplemented with 0.1% IGEPAL CA-630 (Sigma, # I8896) on ice for 10 min. The lysates was carefully layered on the top of 1 ml Buffer 3 (1.2 M sucrose, 15 mM Tris-HCl pH 7.5, 60 mM KCl, 15 mM NaCl, 5 mM MgCl2, 0.5 mM DTT, 0.1 mM EGTA, 0.1 mM PMSF, 1:1000 PIC). After centrifugation (10,000 ×g for 20 min at 4°C), the nuclei were resuspended in 500 μl Buffer A (0.34 M sucrose, 60 mM KCl, 15 mM HEPES pH7.4, 15 mM NaCl, 4 mM MgCl2, 1 mM DTT, 0.1 mM PMSF, 1:1000 PIC) supplemented with 3 mM CaCl2 and 2 U/μl MNase (NEB, # M0247S) and digested for 15 min at 37°C. Then 5 mM EGTA was added to stop the reaction. After centrifuged at 13,500 ×g for 10 min at 4°C, chromatin was resuspended in 10 mM EDTA (pH 8.0) supplemented with 1 mM PMSF and 1:1000 PIC, followed by rotation at 4 °C for 2-4 h. The mixture was adjusted to 500 mM NaCl and rotated for additional 45 min. After centrifugation, the supernatant containing chromatin was diluted to 100 ng/μl with buffer B (20 mM Tris-HCl pH8.0, 5 mM EDTA, 500 mM NaCl, 0.2% Tween 20) and the fragmentation of chromatin was detected by agarose electrophoresis. A total of 2.5 μg fragmented chromatin was kept as the input. For immunoprecipitation, the reaction mixture, including 20 μg fragmented chromatin, 2 μg anti-H3K9me3 antibody (Abcam, #ab8898), and 50 μl protein A/G dynabeads (GE Healthcare) was incubated overnight with gentle rotation at 4°C. The beads were washed three times with Buffer B, and once with Buffer B without Tween 20 at 4°C for 5 min. The DNA was eluted with 300 μl elution buffer (20 mM Tris-HCl pH8.0, 20 mM EDTA, 0.5% SDS), digested with PK enzyme (NEB, #P8107S), and purified using a MinElute kit (Qiagen, #28006). The ChIP DNA library was constructed by a KAPA HTP/LTP Library Preparation Kit according to the manufacturer’s instructions.

tag: cell type

value: embryonic stem cells

tag: gender

value: male

tag: background strain


title: mESCs.ChIP.Input


title: DF1_0_2_Run_1

description: Avian (chicken) origin


title: Cut-and-Run-EZH2-AB2-brain-mNPC-Ybx1wt-S2

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
library strategy: CUT&RUN
Basecalls performed using CASAVA
For ChIP-seq, Single-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data. For peak calling of H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
For Cut-and-Run, Paired-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated properly paired reads have been kept by samtools (parameter “-q  1 -F 1804” version 1.2). To generate the bigwig tracks, we count the reads number mapped for dm6 and normalized tracks to 10 million dm6 reads(i.e. double the height if the sample have 5 million dm6 reads).
Genome_build: mm10(GRCm38.p5)
Supplementary_files_format_and_content: bigwig

source_name: Neural Tube

growth_protocol: Cells were grown in NeuroCult™Proliferation Media (STEMCELL Technologies 05702) supplemented with 10 μg/mL rhEGF (STEMCELL Technologies 78006) to a final concentration of 20 ng/mL. For routine passaging, cells were grown to 75–80% confluency and then dissociated using Accutase for 5 min in the incubator. Cells were then diluted with an equal volume of growth medium and dissociated by trituration. Cells were pelleted as described above and resuspended in fresh culture medium to plate at recommended densities. For differentiation, cells were plated at recommended densities on poly-D-lysine/laminin–coated 6-well plates or Matrigel (ThermoFisher 354240)–coated 8-well chamber slides (EMD Millipore PEZGS0816) and left O/N. Cells were washed once in Neurocult™Proliferation Media without EGF and incubated in Neurocult™. Differentiation media (STEMCELL Technologies 05704) for indicated times are detailed in figure legends.

extract_protocol:
Ultra-low input native ChIP (ULI-nChIP) was performed as described in Brind’Amour et.al. 2015.  Briefly, mNPCs from Sox2-GFP positive embryos were isolated and sorted as described above.  Using an equal number of cells as input, nuclei were isolated using Nuclear Isolation Buffer  (MilliporeSigma NUC101) and diluted MNase enzyme added to digest DNA. The MNase  reaction was carried out for 7.5 min at 37°C and stopped by addition of EDTA. A 1% Triton/1%  deoxycholate solution was added to lyse nuclei and complete immunoprecipitation buffer added  to allow for ~200 μl lysate/immunoprecipitation. Antibodies were bound to Protein A/G magnetic  beads (ThermoFisher) and after pre-clearing on washed magnetic beads with no antibody,  antibody-bead complexes were added to chromatin O/N at 4°C. After successive washes in low  salt and high salt wash buffers, chromatin was eluted in ChIP elution buffer for 1.5 h at 65°C.  DNA was extracted using phenol-chloroform-isoamyl alcohol extraction and MaXtract phaselock  tubes (QIAGEN) to retain maximal DNA. DNA was further purified using Ampure XP beads  (Agencourt) and libraries constructed through the following processes: 1) End repair with T4  PNK, Klenow DNA polymerase, and T4 DNA polymerase; 2) A-tailing with dATP and Klenow  (3’-5’ exo-) polymerase; 3) Adapter ligation with annealed Illumina adapters and Quick DNA  ligase; and 4) Library amplification with Illumina paired-end indexed primers and 2X Phusion HF  Master Mix. Library amplification was performed for 12 cycles and DNA purified by Ampure XP  beads and library yield and quality evaluated using a D1000 High Sensitivity screentape on an  Agilent TapeStation.
CUT&RUN was performed as described in Skene and Henikoff (2018), with minor variations.  Briefly, mNPCs from Sox2-eGFP–positive embryos were isolated and sorted as described  above. Cells were pelleted and resuspended in wash buffer. Bio-Mag Plus Concanavalin-A  coated beads (Bangs Laboratories BP531) were added to cells (diluted in binding buffer) to bind  nuclei to beads. Supernatant was removed and samples were blocked for 5 min at RT with  digitonin block buffer. Antibody diluted in digitonin block buffer was added and samples were  rotated for 3 h, 5 h, or O/N in the cold. Beads were collected and washed 3× with digitonin block  buffer before adding pA-MNase to beads. After a 1-h incubation, beads were washed 3× and  resuspended in wash buffer. After equilibration on ice, 100 mM CaCl2 was added to tubes and  samples were incubated for 25 min with agitation at the 15-min mark. The reaction was stopped  by adding the stop buffer. Samples were incubated at 37°C for 30 min to release chromatin.  DNA was isolated by phenol–chloroform–isoamyl alcohol extraction and MaXtract phase-lock  tubes (QIAGEN) to maximally retain chromatin. Chromatin was resuspended in low EDTA TE  buffer and analyzed by TapeStation using the HS DNA Kit (Agilent). Libraries were made using  the Accel-NGS® 1S Plus DNA Library Kit (Swift Biosciences) and submitted for sequencing. In  all cases, ~15% input was removed and IgG was used as a negative control.

tag: strain background

tag: genotype/variation

value: wild type

value: Mouse Neural Progenitor Cell

tag: chip antibody

value: EZH2 (ActiveMotif,39875)


title: Cut-and-Run-H3K27me3-AB1-brain-mNPC-Ybx1wt-S2-Rep2-5hrs

value: H3K27me3 (Millipore,07-449)


title: Cut-and-Run-EZH2-AB2-brain-mNPC-Ybx1ko-S2


title: DF1_0_07_Run_1

description: Avian (chicken) origin


title: DF1_0_6_Run_1

description: Avian (chicken) origin


title: Cut-and-Run-H3K27me3-AB1-brain-mNPC-Ybx1ko-S2-Rep1-3hrs


title: Cut-and-Run-H3K27me3-AB1-brain-mNPC-Ybx1ko-S2-Rep2-5hrs


title: Cut-and-Run-H3K27me3-AB1-brain-mNPC-Ybx1wt-S2-Rep1-3hrs


title: Cut-and-Run-YBX1-KO

data_processing:
Library strategy: CUT&RUN
Basecalls performed using CASAVA
For ChIP-seq, Single-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data. For peak calling of H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
For Cut-and-Run, Paired-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated properly paired reads have been kept by samtools (parameter “-q  1 -F 1804” version 1.2). To generate the bigwig tracks, we count the reads number mapped for dm6 and normalized tracks to 10 million dm6 reads(i.e. double the height if the sample have 5 million dm6 reads).
Genome_build: mm10(GRCm38.p5)
Supplementary_files_format_and_content: bigwig

tag: strain

value: YBX1 KO


title: Cut-and-Run-YBX1-WT


title: H3K4me3-AB2-YBX1WT replicate 2

data_processing:
Basecalls performed using CASAVA
For ChIP-seq, Single-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated reads have been kept by samtools (parameter “-q  1 -F 1024” version 1.2). We followed ENCODE guideline for quality control of our data. For peak calling of H3K4me3, we used MACS2(version 2.1.1.20160309). To assure the  replicability, we first finalized reproducible peaks for each group as only retained a peak if it called with stringent cutoff(macs2 -q 0.05) in one sample and at least called with lower  cutoff(macs2 -q 0.5) in the other sample. Peaks for H3K27me3 were called by reproducible peaks between SICER(V1.1) and MACS2. Correlation plots indicated the libraries are  reproducible between biological replicates.
For Cut-and-Run, Paired-end reads of 50bp were mapped to combined genome of mm10(Gencode GRCm38.p5) and dm6(UCSC BDGP6) by BWA (version  0.7.12-r1039, default parameter), duplicated reads were then marked with biobambam2 (v2.0.87) and only non-duplicated properly paired reads have been kept by samtools (parameter “-q  1 -F 1804” version 1.2). To generate the bigwig tracks, we count the reads number mapped for dm6 and normalized tracks to 10 million dm6 reads(i.e. double the height if the sample have 5 million dm6 reads).
Genome_build: mm10(GRCm38.p5)
Supplementary_files_format_and_content: bigwig


title: H3K4me3-AB2-YBX1KO replicate 2


title: INPUT-YBX1WT


title: RNAseq_c2c12_diff_hnrnpa2b1_wt3_S24

city: Boulder

first: Joshua

middle: Riley

last: Wheeler

state: CO

address: 3415 Colorado Ave

department: Biochemistry

institute: University of Colorado

data_processing:
RNA-sequencing processing was performed using nextflow/rnaseq pipeline (nf-core/rnaseq, v1.4.2)
Reads were trimmed (FASTQC, Trim Galore!), filtered for repetitive elements, and aligned to the mm9 genomic sequence using STAR.
Counts relative to genes or transcripts were generated using featureCounts, StringTie and Salmon respectively
Genome_build: mm9
Supplementary_files_format_and_content: Txt files for count tables containing raw reads generated by featureCounts, FPKM txt files from stringtie

source_name: Differentiated C2C12 cells

growth_protocol: C2C12 Hnrnpa2b1-WT and KO myoblasts were seeded at 6 x 106 cells per 15 cm plate, grown for 24hrs at 37C, 5% CO2 and differentiated via serum withdrawal and ITS supplementation for two days.

extract_protocol:
Differentiated C2C12 myoblasts and myotubes were washed with PBS in a laminar flow hood and scraped from the tissue culture plate. Total RNA was extracted using a Qiagen RNeasy Plus Mini Kit, following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols and run on NovaSEQ 6000 (Paired End 150 cycle 2x150)

tag: genotype

value: WT


title: H3K4me3-AB2-YBX1KO replicate 1


title: INPUT-YBX1KO


title: RNAseq_c2c12_diff_hnrnpa2b1_ko2_S20

value: hnrnpa2b1 KO


title: RNAseq_c2c12_diff_hnrnpa2b1_ko3_S21


title: RNAseq_c2c12_diff_hnrnpa2b1_ko1_S19


title: RNAseq_c2c12_diff_hnrnpa2b1_wt1_S22


title: RNAseq_c2c12_diff_hnrnpa2b1_wt2_S23


title: MDCK_0_6_Run_2

description: Mammalian (dog) origin

organism: Canis lupus familiaris

source_name: MDCK cells

value: MDCK


title: MDCK_0_06_Run_2

description: Mammalian (dog) origin


title: MDCK_1_8_Run_1

description: Mammalian (dog) origin


title: MDCK_0_07_Run_1

description: Mammalian (dog) origin


title: MDCK_0_02_Run_2

description: Mammalian (dog) origin


title: MDCK_0_6_Run_1

description: Mammalian (dog) origin


title: MDCK_0_2_Run_2

description: Mammalian (dog) origin


title: MDCK_0_2_Run_1

description: Mammalian (dog) origin


title: T24-TET1CD-2

city: Shanghai

first: Yilin

last: Yan

address: 100 Haining Road

institute: Shanghai General Hospital

data_processing:
Base calling were conducted by the HiSeq Control Software (HCS) + OLB + GAPipeline-1.6 (Illumina) on the HiSeq X Ten instrument.
Data filtering steps:In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.0.1)
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Homo sapiens

growth_protocol: RPMI + 10% FCS

extract_protocol:
total RNA was extracted using Trizol following the manufacturing protocol
Library preparations were constructed according to the manufacturer’s protocol. Briefly, The poly(A)mRNA isolation was performed using Poly(A) mRNA Magnetic Isolation Module or rRNA removal Kit.The mRNA fragmentation and priming was performed using First Strand Synthesis Reaction Buffer andRandom Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified doublestranded cDNA by beads was then treated with End Prep Enzyme Mix to repair both ends and add a dAtailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptorligated DNA was then performed using beads, and fragments of ~420 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 13 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using beads, validated using an Qsep100 (Bioptic， Taiwan， China), and quantified by Qubit3.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).Then libraries with different indices were multiplexed and loaded on a HiSeq X Ten instrument according to manufacturer’s instructions (Illumina, San Diego, CA, USA).

value: bladder cancer cells

value: expressing TET1-CD


title: T24-control-1

value: control


title: T24-control-2


title: endometrium 1

city: Jinan

first: Tao

last: Su

state: Shandong

address: 440 Jiyan Rd

institute: Shandong Cancer Hospital and Institute

data_processing:
Quality assessment of sequencing data
Reference sequence alignment analysis
Transcript splicing
Supplementary_files_format_and_content: txt files include RPKM values for each samples

organism: Sus scrofa

source_name: endometrium

extract_protocol:
Total RNA was extracted from the endometrium using the Trizol reagent
RNA libraries were prepared for sequencing using standard protocols

tag: tissue

value: tissue

tag: gestation

value: day 18 of pregnancy

tag: breed

value: Yorkshire


title: T24-TET1CD-1


title: endometrium 2


title: Liver_mouse_Sham_4

type: RNA

city: Jette

first: Eva

middle: Anne D

last: Gijbels

state: Brussels

address: Laarbeeklaan 103, Building G, 2th floor, Department IVTD

country: Belgium

institute: VUB

description: Gene expression of mouse 6 weeks post sham surgery, wherein the common bile duct was isolated but not ligated

hyb_protocol: 12.5 μg of fragmented amplified RNA was hybridized to Affymetrix Human genome U133 plus 2.0 GeneChip and Affymetrix Mouse Genome 430 2.0 GeneChip. Subsequently, the chips were placed in a GeneChip Hybridization Oven 645 (Affymetrix, Germany). After incubation, the arrays were washed with GeneChip Fluidics Station 450 (Affymetrix, Germany) and stained with Affymetrix HWS kit.

scan_protocol: Stained arrays were scanned via an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
Robust Multichip Average (RMA) Express was utilized for normalization and summarization.
Background adjustment, quantile normalization and summarization using median polish was executed via RMA Expression Software.

label: Biotin

source_name: Liver samples of sham (control) mice

label_protocol: 100 ng total RNA per sample was amplified using a GeneChip 3′IVT Express Kit following manufacturer’s instructions (Affymetrix, Germany). Amplified RNA was purified with magnetic beads and 15 mg biotin-amplified RNA was treated with fragmentation reagent.

growth_protocol: Sv129 were housed in the animal facility of the Faculty of Medicine and Health Sciences at Ghent University, Belgium, and allowed to acclimatize at least 1 week prior to the experiments under controlled conditions. Cryopreserved differentiated HepaRG cells (Biopredic International, France) were thawed and seeded following manufacturer’s instructions with basal hepatic cell medium (Williams’ E basal medium with GlutaMAX containing phenol red, Biopredic International, France) supplemented with thaw seed and general purpose medium (Biopredic International, France). Hereafter, HepaRG cells were maintained in basal hepatic cell medium supplemented with maintenance and metabolism medium (Biopredic International, France) and refreshed every 2–3 days. Cells were treated from day 7 after seeding.

extract_protocol: Total RNA was extracted using the Rneasy mini kit (Qiagen, Belgium)

treatment_protocol: Sv129 mice were subjected to common bile duct ligation surgery and HepaRG cells were treated with cholestatic drugs atazanavir, cyclosporin A and nefazodone in absence or presence of a 50 times concentrated bile acid mixture.

value: liver

tag: treatment

value: sham surgery


title: Liver_mouse_Sham_5


title: Liver_mouse_Sham_2


title: Liver_mouse_CBLD_5

description: Gene expression of mouse 6 weeks post common bile duct ligation surgery

source_name: Liver samples of bile duct ligated mice

value: common bile duct ligation surgery


title: Liver_mouse_Sham_1


title: Liver_mouse_CBLD_2


title: Liver_mouse_CBLD_4


title: Liver_mouse_CBLD_1


title: Liver_mouse_CBLD_6


title: Liver_mouse_CBLD_3


title: 3B3-3l mESCs in serum_replicate1

city: Newcastle upon Tyne

first: Ruchi

last: Shukla

address: Ellison A Building

department: Applied Biosciences

country: United Kingdom

institute: Northumbria University

hyb_protocol: 600 ng of Cy3-labelled aRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 mouse GE 8x60k Microarrays (G4852A) for 17 hours at 65°C in a rotating hybridization oven (Shel Lab).  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on NimbleGen MS 200 (Roche) in single mode.

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1 (Agilent) using default parameters (protocol GE1-1105_Oct12 and Grid: 028005_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: 3B3-3l mESCs in serum

label_protocol: Cyanine-3 (Cy3) labeled aRNA was prepared from 1 ug RNA using Amino Allyl MessageAmp II aRNA kit (Ambion) following manufacturers protocol. One-Color RNA Spike-in (Agilent) was included as internal control. Dye incorporation and aRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Serum culture conditions are: Dulbecco's Modified Eagle's medium (DMEM) high-glucose supplemented with 15% FCS, 1x Non-essential amino acids, 1mM Sodium Pyruvate, 50mg/ml Penicillin/Streptomycin, 0.1% beta-mercaptoethanol and 500U/ml ESGRO LIF (Millipore).

extract_protocol: Total RNA was extracted using an RNeasy kit (Qiagen), following the manufacturer’s protocol and using qiashredder columns (Qiagen) to homogenise the samples and an Rnase free DNase kit (Qiagen) to perform on column DNA digestion. RNA integrity (RIN) was assessed using an Agilent 2100 Bioanalyzer (samples used had RIN score of ≥9.5).

treatment_protocol: Two weeks of 2i culture is in : N2B27 medium (DMEM F-12:  GIBCO,  Neurobasal: GIBCO, N2: GIBCO, B27: GIBCO,  50ug/ml Penicillin/streptomycin, 3.3% BSA (GIBCO), 0.15 mM monothioglycerol and MEK inhibitor PD0325901 [1uM] and Gsk3 beta inhibitor CHIR99021 (3uM) with 1000U/ml ESGRO LIF (Millipore).

value: mouse embryonic stem cells (mESCs)


title: 3B3-3l mESCs in 2i_replicate1

description: Expression array after 2 weeks in 2i culture conditions

source_name: 3B3-3l mESCs in 2i


title: Liver_mouse_Sham_3


title: 3B3-3l mESCs in serum_replicate2


title: TKO mESCs in 2i_replicate3

source_name: TKO mESCs in 2i


title: TKO mESCs in 2i_replicate1


title: Liver_mouse_Sham_6


title: TKO mESCs in 2i_replicate2


title: TKO mESCs in serum_replicate1

source_name: TKO mESCs in serum


title: 3B3-3l mESCs in 2i_replicate2


title: J1 WT mESCs in 2i_replicate2

source_name: J1 WT mESCs in 2i


title: J1 WT mESCs in serum_replicate3

source_name: J1 WT mESCs in serum


title: J1 WT mESCs in 2i_replicate3


title: TKO mESCs in serum_replicate2


title: J1 WT mESCs in serum_replicate1


title: J1 WT mESCs in serum_replicate4


title: J1 WT mESCs in 2i_replicate1


title: J1 WT mESCs in serum_replicate2


title: setd1

city: Boston

first: Khalid

last: Shah

state: Massachusetts

address: 60 Fenwood Road

institute: Harvard Medical School

description: brain tumor tissue from SetD

data_processing:
Pseudoalignment with salmon, version ,0.9.1
Import and summarize salmon generated counts with tximport, version 1.6.0
Analyze differential expression with DESeq2 BioConductor package, version 1.18.1
mm10
comma separated format, tpm matrix contains transcripts per million normalized counts as calculated by tximport
Supplementary_files_format_and_content: comma separated format, rawCounts matrix file contains raw counts as generated by Salmon and imported by tximport (these counts were used for the DESeq2 analysis)
Supplementary_files_format_and_content: comma separated format, tpm matrix contains transcripts per million normalized counts as calculated by tximport

source_name: brain tumor Mut3

growth_protocol: 6-8-week-old C57BL/6 (Charles river laboratories) were anaesthetized and immobilized on a stereotactic frame. 1X105 cells for CT2A, GL261 and 005 GFP-Fluc lines and 5X105  Mut3 tumor cells in 4 µl PBS were implanted 2 mm deep, 2.5 mm lateral from bregma and 2.5 mm ventral from dura in the right hemisphere. On reaching endpoint, mice were perfused with 30ml of PBS by cardiac puncture. Tumor tissue was isolatated.

extract_protocol:
Tumor tissue was isolated from mice that have reached humane end-point and stored in RNAlater (Qiagen) at 4 degrees overnight followed by -80 degree storage until all samples were collected. RNA was isolated using RNeasy mini kit (Qiagen) followed by on-column DNase treatment with RNase-free DNase set (Qiagen). The concentration for RNA samples were checked using Qubit RNA HS assay kit (ThermoFisher).
whole transcriptome sequencing was performed on Illumina at the Broad Technology Labs from 50ng RNA. Reads were aligned using STAR v2.4.2a with GENCODE mouse genome. Duplicate reads were marked and summary metrics were gathered using Picard tools and RNA-SeQC.

treatment_protocol: not applicable

tag: tumor status

value: tumor

tag: tumortype

value: D

tag: replicate


title: setd2

description: brain tumor tissue from SetD


title: setd3

description: brain tumor tissue from SetD


title: setc3

description: brain tumor tissue from SetC

source_name: brain tumor 005

value: C


title: setb3

description: brain tumor tissue from SetB

source_name: brain tumor GL261

value: B


title: setc2

description: brain tumor tissue from SetC


title: setb2

description: brain tumor tissue from SetB


title: setb1

description: brain tumor tissue from SetB


title: control3

description: control brain tissue

source_name: naïve brain


title: seta2

description: brain tumor tissue from SetA

source_name: brain tumor CT2A

value: A


title: seta1

description: brain tumor tissue from SetA


title: setc1

description: brain tumor tissue from SetC


title: control2

description: control brain tissue


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D19.1] reanalysis

city: Barcelona

first: Montse

last: BARRAGAN

state: Select One

address: Baldiri Reixac, 15

country: Spain

institute: Clinica EUGIN

hyb_protocol: Affymetrix's standard protocol

scan_protocol: AGCC Standard Protocol / GCS 3000

data_processing: Samples were processed using Affymetrix Power Tools (APT) utilizing GCCN-SST RMA with gain lock percent set to 0.75

label: biotin

label_protocol: 8 µg cDNA (3.2 µg from the first round and 4.8 µg from the second) were subsequently fragmented by DNAseI and biotinylated by terminal transferase (GeneChip Mapping 250K Nsp assy kit; Affymetrix, CA, USA).

extract_protocol: The zona pellucida was removed by Pronase (Roche Diagnostics, Spain) and oocytes were immediately and individually placed in 45 µl of a Proteinase K-based lysis buffer (20 mM DTT, 0.5% SDS, 1 μg/μl proteinase K, 10 mM Tris.HCl, pH 7.4), incubated at 65ºC for 15 minutes, and stored at -80ºC until use (González-Roca, 2010). Total RNA extraction and amplification were based on the Pico-Profiling protocol and successive improvements for single oocyte use (Gonzalez-Roca et al, 2010; Vassena et al, 2011). Pico-profiling faithfully amplifies the total RNA from as little as 10 somatic cells, or 1 MII oocyte, with a level of false positive signal in downstream analysis that is equivalent to that obtained without an amplification step. Briefly, RNA was purified individual oocytes using RNA Clean XP bead suspension (Agencourt Bioscience, La Jolla, CA, USA) and eluted in 20 µl water. The RNA preparation was used for library preparation and amplification by Whole Transcriptome Amplification (WTA2, Sigma-Aldrich, Spain). SYBRGreen (Sigma-Aldrich, Spain) was added to the amplification reaction, which was performed in a CFX Real-time instrument (Bio-Rad, CA, USA) to monitor amplification yield. The first amplification reaction was stopped when the SYBRGreen signal reached a plateau, and cDNA was purified and quantified on a Nanodrop ND-1000 spectrophotometer (Thermo-Fischer, MA, USA). A second round of amplification was performed from 10 ng of cDNA.

treatment_protocol: Oocytes were denuded 60 minutes after pick-up by exposure to 80 IU/ml hyaluronidase (Hyase-10x, Vitrolife, Sweden) in G-MOPS medium (Vitrolife, Sweden), followed by gentle pipetting. Once denuded, oocytes were scored for polar body presence. Immature GV oocytes were collected freshly and group-cultured in 100μl of G-2TM PLUS (Vitrolife, Sweden) medium in a humidified atmosphere of 6%CO2/94% at 37ºC for 2 hours after denudation.

tag: age

value: 20-22 at donation

tag: ovarian reserve

value: high ovarian reserve


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D6.1] reanalysis

value: 33-35 at donation

value: low ovarian reserve


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D26.2] reanalysis


title: Fail to mature oocyte after ovarian stimulation_Sample 4

description: CELs transformed using GCCN-SST with gain_lock=0.75, then processed using RMA-Sketch. These analysis capabilities are available in Affymetrix Power Tools 1.18.3

source_name: Human immature oocyte (GV) at oocyte pick-up after ovarian stimulation

tag: sample type

value: immature oocyte


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D12.1] reanalysis


title: Age 20-22 at donation + high ovarian reserve Sample 1 [D17.2] reanalysis


title: Age 20-22 at donation + low ovarian reserve Sample 1 [D13.2] reanalysis


title: Age 33-35 at donation + low ovarian reserve Sample 1 [D1.1] reanalysis


title: Fail to mature oocyte after ovarian stimulation_Sample 1

description: CELs transformed using GCCN-SST with gain_lock=0.75, then processed using RMA-Sketch. These analysis capabilities are available in Affymetrix Power Tools 1.18.0

source_name: immature GV oocyte at oocyte pick-up after ovarian stimulation


title: Fail to mature oocyte after ovarian stimulation_Sample 3

description: CELs transformed using GCCN-SST with gain_lock=0.75, then processed using RMA-Sketch. These analysis capabilities are available in Affymetrix Power Tools 1.18.2


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D25.1] reanalysis


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D27.1] reanalysis


title: control1

description: control brain tissue

value: control


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D24.1] reanalysis


title: H3K27me3-AB3-YBX1WT replicate 1

source_name: Neural Tube

value: wild type

tag: cell type

value: Mouse Neural Progenitor Cell


title: H3K4me3-AB2-YBX1WT replicate 1


title: H3K27me3-AB3-YBX1KO replicate 1

value: YBX1 KO


title: single cell RNA sequencing of dissected mouse posterior foreguts at embryonic day 9.5

city: Cincinnati

first: Aaron

last: Zorn

state: OH

address: 240 Albert Sabin Way, Bld S

department: Developmental Biology

institute: Cincinnati Children's Hospital and Medical Center

description: epithelial and mesenchymal progenitors of upper digestive organs (including the stomach, liver, pancreatobiliary system and small  intestine)

data_processing:
Raw scRNA-Seq data was processed using cellranger (v2.0.0 10xGenomics) (https://github.com/10XGenomics/cellranger). Reads were aligned to mouse genome [mm10] to produce counts of genes across barcodes. Barcodes with less than ~5k UMI counts were not included in downstream analysis. Percentage of reads mapped to transcriptome was ~70% each sample. QC, Filtering, Normalization and Clustering was carried out using Seurat [v2.3.4]
Genome_build: mm10
Supplementary_files_format_and_content: Processed Data files consists of counts matrixs of counts of genes across all cells and metadata providing information of each cells cluster definition.

growth_protocol: Mice were maintained in specified pathogen free condition in accordance with institutional guidance.

extract_protocol:
Single cell dissociation by cold active protease protocol was performed as described previously23. Rapidly dissected C57BL/6J mouse embryo tissues were transferred in ice-cold PBS with 5 mM CaCl2, 10 mg/ml of Bacillus Licheniformis protease (Sigma) and 125 U/ml DNAse (Qiagen), and incubated on ice with mixing by pipet. After 7 min, single cell dissociation was confirmed with microscope. Cells were then transferred to a 15 ml conical tube, and 3ml ice cold PBS with 10 % FBS (FBS/PBS) was added. Cells were pelleted (1200 G for 5 min), and resuspended in 2 ml PBS/FBS. Three washes in 5 ml PBS/0.01%BSA (PBS/BSA) followed with pelleting (1200 G, 5 min) were performed. Cells were resuspended in PBS/BSA and cell concentration was determined with a hemocytometer. Cell concentration was adjusted to 100,000 cells/ml for scRNAseq.
RNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: Timed mating between C57BL6 mice were performed and the date when a plug was detected was considered embryonic day 0.5.

tag: source

value: micro-dissected foregut

tag: developmental stage

value: embryonic day 9.5


title: single cell RNA sequencing of dissected mouse anterior foreguts at embryonic day 9.5

description: epithelial and mesenchymal progenitors of pharyngeal, respiratory and upper digestive organs (including the esophagus, stomach)


title: Fail to mature oocyte after ovarian stimulation_Sample 2

description: CELs transformed using GCCN-SST with gain_lock=0.75, then processed using RMA-Sketch. These analysis capabilities are available in Affymetrix Power Tools 1.18.1


title: single cell RNA sequencing of dissected mouse foreguts at embryonic day 8.5

description: epithelial and mesenchymal progenitors of pharyngeal, respiratory and upper digestive organs (including the esophagus, stomach, liver, pancreatobiliary system and small  intestine)

value: embryonic day 8.5


title: single cell RNA sequencing of dissected mouse foreguts at embryonic day 9.0

value: embryonic day 9.0

value: epithelial and mesenchymal progenitors of pharyngeal, respiratory and upper digestive organs (including the esophagus, stomach, liver, pancreatobiliary system and small  intestine)


title: 394.4

data_processing:
CSBB [v3.0] (https://github.com/csbbcompbio/CSBB-v3.0) pipeline was used to align raw reads to mouse genome [mm10] and quantify gene expression. Differentially expressed transcripts between the two genotypes were obtained using RUVSeq [Rpackage] (LogFC ><= |1| and FDR <= 0.1)
Genome_build: mm10
Supplementary_files_format_and_content: Processed files consist of TPM matrix of genes TPM across all samples

source_name: Gli2--, Gli3-- foregut 2

extract_protocol:
RNeasy Mini Kit manufacture protocol
Our Core Facility used the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara), for the initial amplification step for samples with low amounts of RNA (< 500 picograms of total RNA). This assay is designed to select and sequence polyadenylated transcripts. Specifically the Takara protocol, the SMART-Seq v4 Ultra Low Input RNA Kit, amplifies RNA samples with less than 500 picograms, to create 3 -17 nanograms of cDNA. The Illumina protocol, the Nextera XT DNA Library Preparation Kit, is then used to create DNA library templates from the cDNA.

value: micro-dissected mouse foregut

tag: embryonic somite stage

tag: mouse genetic background

value: mixed strain

value: Gli2 mutant and Gli3 mutant


title: 376.2

source_name: Gli2+-, Gli3+- foregut 3

value: Gli2 and Gli3 heterozygous control


title: 297.9

source_name: Gli2+-, Gli3+- foregut 1


title: 297.7

source_name: Gli2--, Gli3-- foregut 1


title: 397.5

source_name: Gli2--, Gli3-- foregut 3


title: seta3

description: brain tumor tissue from SetA

tag: strain

value: tumor

value: A


title: Input_T23_R172H/wt

city: Cold Spring Harbor

first: David

middle: A.

last: Tuveson

state: NY

address: 1 Bungtown Rd.

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
Sequencing reads were mapped to the reference mouse genome mm10 using Bowtie2 version 2.2.3 using --very-sensitive settings.
Peaks were identified using MACS2 software version 2.1.1.20160309 using 5% FDR cut off and broad peak option.
Off-chromosome locations were removed from BedGraph files using bedclip and bedtools slope with default parameters.
BedGraph files were converted to BigWig files using bedGraphToBigWig (UCSC Kent Utilities) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Primary pancreatic ductal adenocarcinoma tumor from KPC mouse

growth_protocol: Organoids were cultured inside Matrigel domes overlaid with mouse complete organoid medium as described in Boj et al. 2015 (PMCID: PMC4334572).

extract_protocol:
Whole cell extracts were sonicated to solubilize the chromatin. The chromatin extracts containing DNA fragments with an average size of 250 bp were immunoprecipitated using  H3K27ac (Abcam, ab4729) antibody.
Libraries were prepared for Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers.

tag: genotype

tag: chip antibody

value: input


title: Input_T6_R172H/wt

tag: tissue

value: Primary pancreatic ductal adenocarcinoma tumor


title: ChIP_T23_R172H/LOH

value: H3K27ac (Abcam, ab4729)


title: ChIP_T6_R172H/LOH


title: 396.6

source_name: Gli2+-, Gli3+- foregut 2


title: ChIP_T23_R172H/wt


title: Input_T6_R172H/LOH


title: ChIP_T6_R172H/wt


title: Input_T23_R172H/LOH


title: M10

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.8 (Babraham Bioinformatics).
Reads were then mapped to transcripts from GENCODE M22 on mouse GRCm38.p6  genome using STAR alignment software version 2.6.0c.
RSEM version 1.3.1 was used to calculate expression estimates per gene and per isoform.
Genome_build: Genome Reference Consortium Mouse Build 38 patch release 6 (GRCm38.p6)
Supplementary_files_format_and_content: The gene.results.txt files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM. The isoforms.results.txt files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.

source_name: pancreatic ductal adenocarcinoma organoid

growth_protocol: Mouse organoids were grown to 70-90% confluency in a 50 uL dome of 100% Matrigel overlaid with 500 uL of mouse complete media [DMEM F12 Advanced (Invitrogen), 10 mM HEPES pH 7.2-7.5 (Invitrogen), 1X GlutaMax (Invitrogen),  1X Penicillin/Streptomycin (Invitrogen), 0.5 uM A83-01 (TOCRIS), 0.05 ug/mL mEGF (Invitrogen), 0.1 ug/mL FGF-10 (Peprotech), 0.01 uM Gastrin I (Sigma), 0.1 ug/mL mNoggin (Peprotech), 1.25 mM N-aceylcysteine (Sigma), 10 mM Nicotinamide (Sigma), 1X B27 Supplement (Invitrogen), 10% R-spondin-conditioned media], in 4-6 wells of a 24-well plate.

extract_protocol:
Media was removed from Matrigel domes, and 4-6 wells of organoids were harvested in 1 mL total of Trizol (15596-018; Thermo Fisher Scientific). RNA was extracted using the PureLink RNA Mini Kit (12183018A; Thermo Fisher Scientific)  per manufacturer’s instructions. RNA quality was assessed on a 2100 Bioanalyzer Instrument (Agilent) using the RNA 6000 Nano Kit (5067-1511; Agilent). Only RNAs with RIN values >9 were used for RNA-sequencing.
Sequencing libraries were generated from 1 ug of total RNA using a TruSeq Stranded Total RNA Kit with Ribo-zero human/mouse/rat (RS-122-2201 and RS-122-2202; Illumina) per manufacturer’s instructions. Libraries were quality checked and quantified using a Bioanalyzer 2100 (Agilent) with a DNA 1000 Kit (5067-4626; Agilent).

value: Mouse 4

tag: metastatic site

value: peritoneum

tag: tumor stage

value: metastasis


title: M30

value: pancreatic ductal adenocarcinoma organoid

value: Mouse 6

value: ovary


title: T23


title: M3P

value: Mouse 2


title: M28

value: liver


title: T6


title: M15

value: Mouse 5

value: diaphragm


title: T34


title: M16

value: lung


title: T69b


title: T19

value: Mouse 3


title: M6


title: T3

value: Mouse 1

value: tumor


title: TO_16_S16

data_processing:
Each library was mapped to GENCODE GRCm38 primary asssembly genome using STAR (v2.7.3).
Gene expression values, including raw count, TPM and FPKM were estimated using RSEM (v1.2.19).
Differential expression analysis was conducted using DESeq2 (v1.22.2) with default parameters using a table of raw counts generated by a customized shell script. Adjusted-pvalue of 0.05 was used to select significant genes.
Genome_build: GRCm38
Supplementary_files_format_and_content: Raw, TPM and FPKM tables of gene expression values. Differential expressed test results from DESeq.

source_name: organoids derived from murine pancreatic ductal adenocarcinoma liver metastasis

growth_protocol: M3L organoids were cultured in murine complete media (as previously described in Boj et al. 2015, Cell PMCID: PMC4334572) or in cholesterol media (murine complete media supplemented with 50mM cholesterol) for 24 hours.

extract_protocol:
RNA was extracted using TRIzol following manufacture’s protocol. 0.5-2ug total RNA was used for constructing RNA-seq library
RNA-seq libraries were constructed using the Illumina TruSeq sample prep kit v2 following manufacture’s protocol. Briefly, RNA was polyA selected and enzymatically fragmented. cDNA was synthesized using Super Script II master mix, followed by end repair, A-tailing and PCR amplification.

value: Kras-LSLG12D/+; Trp53-LSLR172H/+; Pdx1-Cre; Cas9; sg-Soat1

value: M3L PDAC organoids

value: Cholesterol Media


title: TO_08_S8

value: Complete Media


title: TO_15_S15


title: TO_13_S13

value: Kras-LSLG12D/+; Trp53-LSLR172H/+; Pdx1-Cre; Cas9; sg-Rosa26

value: ROSA26 locus (negative control)


title: TO_14_S14


title: M1

value: pancreatic ductal adenocarcinoma organoid

value: metastasis


title: TO_05_S5


title: TO_06_S6


title: T69a

value: Mouse 6


title: Control_5 [Sample6]

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

data_processing:
Illumina bcl2fastq 2.17 software was used for base calling.
Adapter sequences and low quality ends were removed with cutadapt, v1.4.2, trimming for TrueSeq and polyA sequences. Reads were aligned to mouse genome build mm10 using HISAT2 aligner.
Raw counts per gene were calculated with featureCounts, v1.4.4.
Raw counts were normalized with EdgeR TMM method.
Genome_build: mm10
Supplementary_files_format_and_content: tab separated raw counts from featureCounts with Ensembl gene ID, tab separated log2 normalized counts with Ensembl gene ID

molecule: polyA RNA

source_name: Mouse lung tumour

growth_protocol: Ad5SPC-Cre at 2.10^8 PFU/mouse were intratracheallly delivered into the lungs of C57BL6/J background, K-rasLSL-G12D/WT; p53Fl/Fl (KP) or K-rasLSL-G12D/WT; p53Fl/Fl; Glut1Fl/Fl (KPG1). Tumour-bearing KP and KPG1 mice were sacrified at 18 weeks and 6 days post-tumour initiation and lung tumours were macrodissected. Single cell suspensions from macrodissected tumours were obtained using a gentleMACS Octo Dissociator (Miltenyi Biotec). Magnetic cell sorting to remove immune cells was performed using anti-CD45 MicroBeads (Miltenyi Biotec). RNA from the CD45 negative fractions was extracted using TRIzol (15596018, ThermoFisher Scientific).

extract_protocol:
RNA from the CD45 negative fractions was extracted using TRIzol (15596018, ThermoFisher Scientific). TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500 ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: M

value: Lung tumour

value: heterozygous fl/wt

tag: group

value: Control


title: M29

value: diaphragm


title: Glut1KO_4 [Sample5]

value: homozygous fl/fl

value: KO

tag: replicate


title: Glut1KO_3 [Sample4]


title: Glut1KO_2 [Sample1]


title: Control_3 [Sample15]


title: Control_2 [Sample12]


title: Control_1 [Sample11]


title: Glut1KO_1 [Sample10]


title: TO_07_S7


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D30.1] reanalysis

tag: age

value: 33-35 at donation

value: high ovarian reserve


title: Age 33-35 at donation + high ovarian reserve Sample 1 [D29.1] reanalysis

tag: ovarian reserve


title: KPG1_3

growth_protocol: Lenti.TRE-PPARaD13_PGK-Cre at 6000 viral units/mouse were intratracheallly delivered into the lungs of C57BL6/J background, K-rasLSL-G12D/WT; p53Fl/Fl; CCSP-rtTA (KP-rtTa) or K-rasLSL-G12D/WT; p53Fl/Fl; Glut1Fl/Fl; CCSP-rtTA (KPG1-rtTa). Tumour-bearing KP-rtTa and KPG1-rtTa mice were fed on a doxycycline-containing diet (625 mg kg-1; Kliba) for 15 days, to enable doxycycline-mediated PPARaD13 transgene expression, or on a regular diet as control. Mice were then sacrified at 26 weeks post-tumour initiation and lung tumours were macrodissected. Single cell suspensions from macrodissected tumours were obtained using a gentleMACS Octo Dissociator (Miltenyi Biotec). Magnetic cell sorting to remove immune cells was performed using anti-CD45 MicroBeads (Miltenyi Biotec). RNA from the CD45 negative fractions was extracted using TRIzol (15596018, ThermoFisher Scientific).

treatment_protocol: Mice were fed on doxycycline-containing pellets (625 mg kg-1; Kliba) for 15 days, or on a regular diet as control.

tag: treatment

value: No treatment

value: fl/fl rrTA+


title: KP_PPARaDN_1

value: Doxycyclin

value: wt/wt rtTA+


title: KPG1_1


title: KPG1_2


title: KPG1_PPARaDN_2


title: KP_2

value: F

value: KP


title: KP_PPARaDN_3


title: Control_4 [CC-6]

growth_protocol: 1500 lenti.PGK-Cre viral units per mouse were intratracheallly delivered into the lungs of C57BL6/J background, K-rasLSL-G12D/WT; p53Fl/Fl (KP). Tumour-bearing KP mice were sacrified at 22 weeks and 5 days post-tumour initiation and lung tumours were macrodissected. Single cell suspensions from macrodissected tumours were obtained using a gentleMACS Octo Dissociator (Miltenyi Biotec). RNA from the single cell suspensions was extracted using TRIzol (15596018, ThermoFisher Scientific).

extract_protocol:
Single cell suspensions from macrodissected tumours were obtained using a gentleMACS Octo Dissociator (Miltenyi Biotec). RNA from the single cell suspensions was extracted using TRIzol (15596018, ThermoFisher Scientific). TruSeq stranded mRNA kit (Illumina) was used to prepare sequencing libraries, starting from 500 ng total RNA.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: KP_PPARaDN_2


title: KP_1


title: Control_1 [CC-27]


title: Glut1KO_3

growth_protocol: Ad5CC10-Cre at 2.10^8 PFU/mouse were intratracheallly delivered into the lungs of C57BL6/J background, K-rasLSL-G12D/WT; p53Fl/Fl (KP) or K-rasLSL-G12D/WT; p53Fl/Fl; Glut1Fl/Fl (KPG1). Tumour-bearing KP and KPG1 mice were sacrified at 20 weeks and 1 day post-tumour initiation and lung tumours were macrodissected. Single cell suspensions from macrodissected tumours were obtained using a gentleMACS Octo Dissociator (Miltenyi Biotec). Magnetic cell sorting to remove immune cells was performed using anti-CD45 MicroBeads (Miltenyi Biotec). RNA from the CD45 negative fractions was extracted using TRIzol (15596018, ThermoFisher Scientific).


title: Glut1KO_1


title: KP_3


title: Glut1KO_2


title: KPG1_PPARaDN_1


title: KPG1_PPARaDN_3


title: Control_3 [CC-34]


title: Control_3


title: Glut1KO_4


title: Glut1KO_5 [Sample9]


title: Control_5


title: Glut1KO_5


title: Control_1


title: Control_4 [Sample16]


title: Control_2 [CC-32]


title: Control_2


title: Ad-CMV-GL rep2

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

country: Germany

institute: TUM

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
DESeq2 v1.14.1 R package was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab delimited text file include sequence read counts of each sample

extract_protocol:
Isolation of RNA from liver was performed using NucleoSpin RNA Kit from Macherey-Nagel.
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

tag: strain background

value: 7 weeks

value: Ad-CMV-GL

value: liver


title: Ad-CMV-GL rep3


title: Control_4

value: M

value: Lung tumour


title: Ad-CMV-GL rep1


title: uninfected rep4

source_name: uninfected _liver

value: uninfected


title: uninfected rep3


title: uninfected rep1


title: uninfected rep2


title: 5c-KO2_H3K4me3

city: Ann Arbor

first: Christina

middle: N

last: Vallianatos

state: MI

address: 1241 East Catherine

department: Human Genetics

institute: University of Michigan

description:
5c-KO_H3K4me3_merged.bw
5c-KO_H3K4me3_MACS2_peaks.bed

data_processing:
Reads were mapped to mm10 and to a custom genome containing the barcodes from our synthetic nucleosome spike-in using bowtie-1.
The enrichment of mapped synthetic nucleosomes compared to input was calculated and used as a normalization coefficient for read depth each ChIP-seq replicate, as described in PMID: 26004229.
BAM files were deduplicated (samtools) and converted to BigWig files incorporating the normalization coefficient described above.
Peaks were called using MACS2 software (version 2.1.0.20140616) using input bam files for normalization, with filters for a q-value < 0.1 and a fold enrichment greater than 1.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files represent genome coverage by reads after normalization using our synthetic nucleosome spike-in approach. Bed files are the locations of peaks, as called by MACS2.

source_name: mouse adult male amygdala tissue

extract_protocol:
Mouse amygdala tissue was dissected from adult males. Nuclei were isolated using Nuclei EZ prep Kit (Sigma, NUC-101), and counted. 20,000 nuclei were used as input.
ChIP-Seq library preparation was performed as described in PMID 25607992 with two exceptions. 1) We used a kit to generate sequencing library in one-tube reactions (NEB, E7103S). 2) We spiked in the panel of synthetic nucleosomes carrying major histone methylations (EpiCypher, SKU: 19-1001). We used the rabbit monoclonal H3K4me3 antibody (Thermo, clone #RM340).

tag: strain/background

value: F1 generation 129xB6

tag: genotype/variation

value: Male

value: Adult

value: Amygdala


title: WT_H3K4me3_input

value: WT


title: DM1_H3K4me3

description:
DM_H3K4me3_merged.bw
DM_H3K4me3_MACS2_peaks.bed

value: Kmt2a-Kdm5c double mutant

value: rabbit monoclonal H3K4me3 antibody (Thermo, clone #RM340)


title: 2a-HET_H3K4me3_input


title: 5c-KO_H3K4me3_input


title: DM3_H3K4me3


title: 5c-KO3_H3K4me3


title: DM_H3K4me3_input


title: WT2_H3K4me3

description:
WT_H3K4me3_merged.bw
WT_H3K4me3_MACS2_peaks.bed


title: 2a-HET3_H3K4me3

description:
2a-HET_H3K4me3_merged.bw
2a-HET_H3K4me3_MACS2_peaks.bed


title: 2a-HET1_H3K4me3


title: DM2_H3K4me3


title: RNA-seq.rESC

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the gencode (mm10 vM13) transcriptome using Bowtie2 (v2.2.5) and RSEM (v1.3.0)
Gene expression level was calculated using EDASeq (v2.4.1) GC-normalized method
Genome_build: mm10

source_name: mouse stem cells during primed convert to naïve state

growth_protocol: Mouse EpiSCs were derived from E5.5 mouse embryos generated by mating homozygous Oct4-GFP transgenic allele-carrying mice (CBA/CaJ X C57BL/6J) with 129/Sv female mice, following the protocol as described in (Brons et al., 2007; Guo et al., 2009;Greber et al., 2010). In short, epiblasts were dissected from the uterus and plated on mitomycin C-treated mouse embryonic fibroblast (MEF) feeder cells in N2B27+FA medium containing 50% DMEM/F12 (GIBCO), 50% Neurobasal (GIBCO), 0.5X N2 (GIBCO), 0.5 X B27 (GIBCO), 1% GlutMax (GIBCO), 1% nonessential amino acids (GIBCO), 0.1mM 2-mercaptoethanol (GIBCO)) supplemented with 20 ng/ml Activin A (PeproTech) and 12 ng/ml bFGF (Wuhan Healthgen Biotechnology Corp). Mouse ESCs and rESCs were maintained feeder-free on 0.1% gelatin in N2B27-2iL medium (Ying et al., 2008), including 50% DMEM/F12 (GIBCO), 50% Neurobasal (GIBCO), 0.5X N2 (GIBCO), 0.5 X B27 (GIBCO), 1% GlutMax (GIBCO), 1% nonessential amino acids (GIBCO), 0.1mM 2-mercaptoethanol (GIBCO)) supplemented with LIF (1000 U/ml), 1µM PD0325901 and 3µM CHIR99021. Mouse ESCs and rESCs were passaged by 0.05%Trypsin-EDTA dissociation every 3 days.

extract_protocol:
TRIzol, according to the manufacturers instructions
VAHTS mRNA-seq V2 Library Prep Kit for Illumina was used according to the manufacturer's instruction. Briefly, 1ug total RNA was used and mRNA was enriched using olig-dT dynabeads, followed by fragmentation by divalent cation at elevated temperature. First-strand cDNA synthesis by random hexamers and reverse transcriptase was followed by the second-strand cDNA synthesis. Then the reverse product was purified using AMPure XP beads. The cDNA was end repaired and a dA was added, followed by ligation, two round purification using AMPure XP beads, PCR amplification and PCR product purification. The library was quantified with an Invitrogen Qubit.

treatment_protocol: iCD1 medium (Chen et al., 2011) which contains Vitamin C (50μg/ml), bFGF (10 ng/ml), LiCl (5mM), LIF (1000U/ml) and CHIR99021(3μM) supplemented with BMP4 (10ng/ml), EPZ5676 (1μM) and EPZ6438 (2.5μM)

tag: cell type

value: mouse stem cells during primed convert to naive state


title: RNA-seq.d5

value: mouse stem cells during primed convert to naive state at day5


title: RNA-seq.d8

value: mouse stem cells during primed convert to naive state at day8


title: WT1_H3K4me3


title: RNA-seq.EpiSC

value: mouse primed epiblast stem cells


title: RNA-seq.d3-BMP4

value: mouse stem cells during primed convert to naive state at day3

value: without BMP4


title: RNA-seq.d3


title: ATAC-seq.mESC.rep2

data_processing:
bcl2fastq conversion software v2.17 used for basecalling.
Reads were aligned to the mouse (mm10) genome using bowtie2
Peaks were called using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: Processed peak (BED) files and bigWig trakcs

source_name: mouse embryonic stem cell

extract_protocol: ATAC-seq was performed as previously described (Buenrostro et al., 2013; Buenrostro et al., 2015a). Briefly, a total of 50,000 cells were washed once with 50 μL of cold PBS, then centrifuged for 5min at 500 g at 4oC, then resuspended in 50 μL lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.2% (v/v) IGEPAL CA-630) and incubated on ice for 10 minutes. The suspension of nuclei was then centrifuged for 5min at 500 g at 4oC, followed by the addition of 50 μL transposition reaction mix (10 μL 5X TTBL, 5 μL TTE Mix V50 and 35 μL nuclease-free H2O) of TruePrepTM DNA Library Prep Kit V2 for Illumina® (TD501-TD503, Vazyme) and incubated at 37oC for 30min. DNA fragments were isolated using a MinElute Kit (QIAGEN). ATAC-seq libraries were subjected to 13 cycles of amplification according to the TruePrepTM DNA Library Prep Kit V2 for Illumina® (TD501-TD503, Vazyme), then the libraries were purified with a Qiaquick PCR (QIAGEN) column. Library concentration was measured using a VAHTSTM Human Genomic DNA Quantification and QC Kit (NQ201, Vazyme) according to the manufacturer’s instructions. The concentration of ATAC library peaks was checked with Real-Time Quantitative PCR detecting the differential expression of housekeeping gene(GAPDH) and negative genes. Finally, the ATAC library was sequenced on a NextSeq 500 using a NextSeq 500 High Output Kit v2 (150 cycles) (FC-404-2002, Illumina) according to the manufacturer’s instructions.

value: mouse naive embryonic stem cell


title: ATAC-seq.rESC.rep1


title: 2a-HET2_H3K4me3


title: 5c-KO1_H3K4me3


title: ATAC-seq.d3


title: ATAC-seq.d3-BMP4


title: ATAC-seq.d5


title: ATAC-seq.d8


title: NC

city: Kyoto

first: Makoto

last: Ryosaka

address: 53 Kawahara-cho, Shogoin,

country: Japan

institute: Center for iPS Cell Research and Application (CiRA), Kyoto University

data_processing:
FPKM values were calculated from mapped reads by normalizing to total counts and transcripts.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and DESeq2 output

source_name: UB

growth_protocol: hiPSCs were plated at a density of 2.5 × 104 cells/cm2  in Stem Fit AK02N medium with 10 mM Y-27632 and 0.125 mg/cm2 iMatrix-511 silk. After 24 h, the cells were washed with PBS and treated with Essential 6 medium containing 100 ng/mL Activin A and 3 mM CHIR99021. After 16 - 24 h, the cells were washed with PBS and treated with Essential 6 medium containing 0.1 mM LDN193189, 1 mM A83-01 (WAKO), 0.1 mM 4-[(E)-2-(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl]-benzoic acid (TTNPB) and 200 ng/mL fibroblast growth factor (FGF) 8 for 2 days. Then the cells were replated at a density of 1 × 105 cells/cm2 in Matrigel- or Geltrex -coated 24-well culture plates in Essential 6 medium containing the same 4 factors and 10 mM Y-27632 and incubated for an additional 24 h to induce anterior intermediate mesoderm (AIM). AIM cells were treated with Essential 6 medium containing 1 M CHIR99021, 0.1 M LDN193189, 200 ng/mL FGF8, 100 ng/mL glial cell line-derived neurotrophic factor (GDNF) and 0.1 M TTNPB for 2 days to induce nephric duct (ND) leader cells. ND leader cells were dissociated into single cells by pipetting after treatment with Accutase for 3 min at 37C, seeded onto low-attachment 96-well plates at a density of 1 × 104 cells/well, and treated with the same medium and factors plus 10 M Y-27632 to induce epithelialized ND aggregates for 2 days. Unwanted cells were separated from ND aggregates by pipetting (Mae et al., 2018). The ND aggregates were treated with Essential 6 medium containing 1 M CHIR99021, 0.1 M LDN193189, 200 ng/mL FGF8, 100 ng/mL GDNF, 0.1 M TTNPB and 2% Matrigel for 6 days.

extract_protocol:
Day 6 iUB organoids were treated with DiI-VLDL for 2 h and dissociated into single cells by pipetting after treatment with Accutase for 3 min at 37C. Then flow cytometry analysis was performed to sort DiI-VLDL+ and DiI-VLDL- cells. The total RNA of sorted DiI-VLDL+ and DiI-VLDL- cells was isolated using a NucleoSpin RNA XS (TaKaRa).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: iUB organoids, tip colonies and ND aggregates were treated with 10 mg/mL DiI-VLDL for 2 h at 37C. Flow cytometry analysis of tip cells using DiI-VLDL iUB organoids and tip colonies treated with DiI-VLDL were dissociated into single cells by pipetting after Accutase treatment for 5 min at 37C. After washing with DMEM/10% FBS, the cells were re-suspended with PBS/2% FBS. Dead cells stained with 4’, 6-Diamidino-2-phenylindole, dihydrochloride (DAPI; 0.1 ng/ml) were excluded from the analysis. Single cells were analyzed and sorted using FACS Aria II. Cells derived from iUB organoids and tip colonies without DiI-VLDL treatment were used as negative controls for gating.

tag: cell tipe

value: iPSC-derived UB cells

tag: derived from cell line

tag: dil-vldl status

value: DiI-VLDL negative


title: DiI.VLDL

value: DiI-VLDL positive


title: TIP

data_processing:
FPKM values were calculated from mapped reads by normalizing to total counts and transcripts.
Differentially expressed genes were detected using the DESeq2 package (version 1.20.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include DeSEq for each Sample ...
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample …

growth_protocol: hiPSCs were plated at a density of 2.5 × 104 cells/cm2  in Stem Fit AK02N medium with 10 mM Y-27632 and 0.125 mg/cm2 iMatrix-511 silk. After 24 h, the cells were washed with PBS and treated with Essential 6 medium containing 100 ng/mL Activin A and 3 mM CHIR99021. After 16 - 24 h, the cells were washed with PBS and treated with Essential 6 medium containing 0.1 mM LDN193189, 1 mM A83-01 (WAKO), 0.1 mM 4-[(E)-2-(5,6,7,8-Tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1-propenyl]-benzoic acid (TTNPB) and 200 ng/mL fibroblast growth factor (FGF) 8 for 2 days. Then the cells were replated at a density of 1 × 105 cells/cm2 in Matrigel- or Geltrex -coated 24-well culture plates in Essential 6 medium containing the same 4 factors and 10 mM Y-27632 and incubated for an additional 24 h to induce anterior intermediate mesoderm (AIM). AIM cells were treated with Essential 6 medium containing 1 M CHIR99021, 0.1 M LDN193189, 200 ng/mL FGF8, 100 ng/mL glial cell line-derived neurotrophic factor (GDNF) and 0.1 M TTNPB for 2 days to induce nephric duct (ND) leader cells. ND leader cells were dissociated into single cells by pipetting after treatment with Accutase for 3 min at 37C, seeded onto low-attachment 96-well plates at a density of 1 × 104 cells/well, and treated with the same medium and factors plus 10 M Y-27632 to induce epithelialized ND aggregates for 2 days. Unwanted cells were separated from ND aggregates by pipetting (Mae et al., 2018). The ND aggregates were treated with Essential 6 medium containing 1 M CHIR99021, 0.1 M LDN193189, 200 ng/mL FGF8, 100 ng/mL GDNF, 0.1 M TTNPB and 2% Matrigel for 6 days. iUB organoids were treated with Accutase for 5 min at 37C and subsequently dissociated into single cells by pipetting. The cells were resuspended with DMEM/F12, GlutaMAX medium containing B-27 Supplement, minus vitamin A, 100 ng/mL GDNF, 200 ng/mL FGF1, 0.1 M TTNPB, 3 M CHIR99021 and 10 M Thiazovivin. The single cells obtained from 10 iUB organoids were seeded onto one well of 48-well plates coated with 150 L hydrogel, which is composed of DMEM/F12 medium containing 50% Matrigel and was solidified for 1 h at 37C before use. The single cells constructed tip colonies (TIP) after 6-7 days. For CDP cells, day 7 tip colonies detached from hydrogel were dissociated into single cells by pipetting after treatment with Accutase for 3 min at 37C. The single cells were resuspended with Essential 6 medium containing 1 M IWR-1 and 0.25 g/cm2 iMatrix-511 silk with or without 1 M A83-01 and seeded at a density of 4 × 104 cells/well in 96-well plates.

extract_protocol:
Day 10 CDPs and day 6 TIP cells dissociated into single cells by pipetting after treatment with Accutase for 3 min at 37C.The total RNA of each single cell was isolated using an RNeasy Mini Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell subtype

value: tip colonies (TIP)


title: CDP

value: collecting duct progenitor (CDP)


title: ATAC-seq.mESC.rep1

tag: strain


title: ATAC-seq.rESC.rep2


title: CO_Unt_2

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Homo sapiens genome reference (GRCh38/hg38) using the TopHat component of Tuxedo Suite software, then cuffquant and cuffdiff were used for gene-level read counting and differentially expression analysis.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text file includes  REFSEQ isoform id,  raw counts and fpkm values for each transcript, in each sample

source_name: COPD smoker_HBEC_Untreated

growth_protocol: Primary human bronchial epithelial cells (HBECs) from nonsmokers and COPD smokers cultured on air-liquid interface (ALI) for 28 days. Briefly, 1 x 10^5 cells in 100 µl of BronchiaLifeTM epithelial airway medium (BLEAM) (Cat# LL-0023, Lifeline® Cell Technology, Oceanside, CA, USA) were seeded in the apical chamber of a 0.4 µm pore-sized Transwell® insert (Cat# 3470, Corning®, Corning, NY, USA) pre-coated with human type IV collagen (Cat# C7521, Sigma Aldrich, St. Louis, MO, USA) with 1 ml of BLEAM in the basolateral chamber (ALI day -2). The following day, fresh BLEAM media was replaced in the apical and basolateral chambers (100 µl and 1 ml, respectively). Following two days of submerged culture, media from the apical chamber was removed to expose the cells to air (ALI day 0), and 1 ml of HBTEC ALI differentiation medium (Cat# LM-0050, Lifeline® Cell Technology) supplemented with Penicillin (100 I.U./ml) - Streptomycin (100 µg/ml) was added to the basolateral chamber. The media was replaced every other day and the cells allowed to differentiate for up to 28 days.

extract_protocol:
Total RNA was extracted via direct lysis of cells in the ALI well using the PureLinkTM RNA mini kit (Cat# 12183018A, Thermo Scientific, Waltham, MA, USA) and included DNase treatment (Cat# 12185-010, Thermo Scientific) on the column to remove contaminating genomic DNA. RNA concentrations were measured with a NanoPhotometer® N60 (Implen, Westlake Village, CA, USA)
RNA-sequencing was performed on a NextSeq 500 Flowcell, High SR75 (Illumina, San Diego, CA, USA) following library preparation using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen, Vienna, Austria). The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: ALI day 28 cells were treated with non-toxic concentrations of CSE (up to 2.5%) via the basolateral chamber for 7 days ( ALI day 28-35) with freshly thawed CSE added at each media change.

tag: source patient group

value: COPD smoker

tag: source patient gender

value: Female

tag: source patient age

value: 62 years old

tag: source patient race

value: Black

value: HBEC (Primary human bronchial epithelial cells )

value: Untreated


title: NS_CSE_4

source_name: nonsmoker_HBEC_2.5% CSE treated

value: nonsmoker

value: Male

value: 69 years old

value: 2.5% CSE treated


title: CO_CSE_1

source_name: COPD smoker_HBEC_2.5% CSE treated

value: 59 years old

value: Caucasian


title: CO_CSE_2


title: NS_CSE_1

value: 57 years old


title: NS_Unt_1


title: NS_Unt_2

value: 67 years old


title: CO_CSE_4

value: 66 years old


title: NS_CSE_2


title: NS_CSE_3

value: Hispanic


title: CO_Unt_3

value: 63 years old


title: CO_CSE_3

value: COPD smoker


title: CO_Unt_1


title: ATAC-seq.EpiSC

value: mouse primed epiblast stem cell


title: NS_Unt_3

value: Female


title: UCLA_UGS_repl2

first: Matthew

last: Freedman

address: 450 Brookline Avenue

institute: Dana Faber Cancer Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads were aligned to hg19 using BWA.
For peak calling MACS2 was used.
Genome_build: hg19
Supplementary_files_format_and_content: bw files were generated using MACS2 using the chilin pipeline

source_name: Cell line derived from urogenital sinus tissue

extract_protocol:
One (histone ChIP) or three (transcription factor ChIP) 2 mm2 frozen cores were pulverized using the Covaris CryoPrep system. Tissue was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

tag: tissue

value: Fetal prostate

tag: chip antibody

tag: chip antibody vendor

value: Diagenode

tag: chip antibody cat.#

tag: chip antibody lot/batch#


title: UCLA_UGS_repl1


title: DF_met_69

source_name: Patient liver met mCRPC biopsy

value: CRPC met


title: CO_Unt_4

value: HBEC (Primary human bronchial epithelial cells )

tag: treatment

value: Untreated


title: ATAC_DF_2480_T

source_name: Patient localized prostate tissue

value: localized prostate tissue

value: ATAC


title: DF_met_60


title: ATAC_DF_2114_T


title: ATAC_DF_2137_T


title: NS_Unt_4

value: nonsmoker

value: Male

value: 69 years old

value: Black


title: ATAC_DF_2025_T


title: ATAC_DF_2137_N


title: ATAC_DF_2485_N


title: ATAC_DF_2484_N


title: ATAC_DF_2038_T


title: ATAC_DF_2485_T


title: H3K27me3_DF_1820_T

value: Cell Signaling Technology


title: ATAC_DF_2114_N


title: H3K27me3_DF_2228_T


title: H3K27me3_DF_1944_T


title: H3K27me3_DF_1726_T


title: H3K27me3_DF_2319_N


title: H3K27me3_DF_2208_T


title: H3K27me3_DF_1752_T


title: H3K27me3_DF_2319_T


title: H3K27me3_DF_Anon_N


title: H3K4me3_DF_2208_T

value: diagenode


title: H3K4me3_DF_2342_T


title: H3K4me3_DF_2319_T


title: H3K4me3_DF_1734_T


title: H3K27me3_DF_2208_N


title: H3K27me3_DF_2228_N


title: H3K4me3_DF_1820_T


title: H3K4me3_DF_2228_T


title: H3K4me3_DF_2208_N


title: H3K4me3_DF_1820_N


title: K4me2_DF_2208_T

value: Millipore


title: H3K4me3_DF_1880_T


title: K4me2_DF_2342_N


title: K4me2_DF_2342_T


title: K4me2_DF_2228_N


title: K27ac_UW_PDX_189-4

source_name: CRPC PDX

value: CRPC pdx


title: H3K4me3_DF_2319_N


title: K4me2_DF_2208_N


title: K4me2_DF_2078_N


title: K4me2_DF_2228_T


title: K27ac_UW_PDX_170-3


title: K27ac_UW_PDX_189-3


title: K4me2_DF_2078_T


title: K27ac_UW_PDX_78


title: K27ac_UW_PDX_58


title: K27ac_UW_PDX_77


title: K27ac_UW_PDX_70


title: K27ac_UW_PDX_141


title: K27ac_UW_PDX_35


title: H3K27AC_NKI_29_T

value: Patient localized prostate tissue

value: Active Motif


title: K27ac_UW_PDX_167


title: K27ac_UW_PDX_136


title: K27ac_UW_PDX_92


title: K27ac_UW_PDX_170-2


title: H3K27AC_NKI_23_T


title: K27ac_UW_PDX_86-2


title: H3K27AC_NKI_27_T


title: H3K27AC_NKI_13_T


title: H3K27AC_NKI_5_T


title: H3K27AC_NKI_7_T


title: H3K27AC_NKI_1_T


title: K27ac_UW_PDX_81


title: H3k27ac_DF_2484_T


title: H3K27ac_DF_2480_T


title: H3K27ac_DF_2478_T


title: H3K27ac_DF_2482_T


title: H3K27ac_DF_2479_T


title: H3k27ac_DF_2137_T


title: H3K27ac_DF_2477_T


title: H3K27AC_NKI_19_T


title: H3k27ac_DF_1962_T


title: H3k27ac_DF_2088_T


title: H3k27ac_DF_2173_T


title: H3k27ac_DF_2185_T


title: H3k27ac_DF_2101_T


title: H3k27ac_DF_2114_T


title: H3k27ac_DF_2025_T


title: H3k27ac_DF_2192_T


title: H3K27ac_DF_2228_T


title: H3K27ac_DF_2030_T


title: H3K27ac_DF_2078_T


title: H3K27ac_DF_2076_T


title: H3k27ac_DF_2060_T


title: H3K27ac_DF_2319_T


title: H3k27ac_DF_2087_T


title: H3K27AC_NKI_27_N


title: H3K27AC_NKI_7_N


title: H3K27AC_NKI_29_N


title: H3K27AC_NKI_5_N


title: H3K27AC_NKI_25_N


title: H3K27AC_NKI_13_N


title: H3K27AC_NKI_1_N


title: H3K27ac_DF_2484_N


title: H3k27ac_DF_2038_T


title: H3k27ac_DF_2113_T


title: H3K27ac_DF_2101_N


title: H3K27ac_DF_2088_N


title: H3K27ac_DF_2114_N


title: H3K27ac_DF_1962_N


title: H3K27ac_DF_2185_N


title: H3K27ac_DF_2173_N


title: H3K27ac_DF_2038_N


title: H3K27ac_DF_2137_N


title: H3K27ac_DF_2192_N


title: H3K27ac_DF_2113_N


title: H3K27ac_DF_2087_N


title: H3K27ac_DF_2342_N


title: H3K27ac_DF_2030_N


title: H3K27ac_DF_2079_N


title: H3K27ac_DF_2025_N


title: H3K27ac_DF_2319_N


title: H3K27ac_DF_2228_N


title: H3K27ac_DF_2078_N


title: H3K27ac_DF_2060_N


title: H3K27ac_DF_2007_N


title: H3K27ac_DF_2076_N


title: H3K27AC_NKI_19_N


title: H3K27ac_DF_2480_N


title: H3K27ac_DF_2477_N


title: H3K27ac_DF_2482_N


title: H3K27ac_DF_2483_N


title: H3K27ac_DF_2478_N


title: H3K27ac_DF_2479_N


title: HOXB13_UW_PDX_167

value: Santa Cruz Biotechnology


title: HOXB13_UW_PDX_189-3


title: HOXB13_UW_PDX_189-4


title: HOXB13_UW_PDX_170-2


title: HOXB13_UW_PDX_141


title: DM4_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIPNT4

data_processing:
For RNA-Seq, libraries were sequenced on the Illumina Novaseq 6000 platform, with paired-end 150 base pair reads (24-35 million reads/library), according to standard procedures. Reads were mapped to the mm10 mouse genome (Gencode) using STAR (v2.5.3a).
For RNA-Seq, duplicates were removed by STAR, a counts file was generated using FeatureCounts (Subread v1.5.0), and BAM files were converted to bigwigs using deeptools (v3.1.3).
For RNA-Seq,DESeq2 (v1.14.1) was used to call differential gene expression between genotypes, and calculate FPKM.
Genome_build: mm10
Supplementary_files_format_and_content: For RNA-Seq, Bigwig files represent genome coverage. DESeq2 files represent differential gene expression between genotypes.

source_name: mouse adult male hippocampus tissue

extract_protocol:
For RNA-Seq, amygdala or hippocampal issue was homogenized in Tri Reagent (Sigma). Samples were subjected to total RNA isolation, and RNA was purified using RNEasy Mini Kit (Qiagen). ERCC spike-in RNA was added at this stage, according to manufacturer’s instructions (Life Technologies).
For RNA-Seq, libraries were prepared using the NEBNext® Ultra™ II Directional RNA Library Prep Kit with oligo-dT priming. Multiplexed libraries were pooled in approximately equimolar ratios and purified using Agencourt RNAClean XP beads (Beckman Coulter).

tag: generation

tag: genotype

value: DM

value: hippocampus


title: HOXB13_UW_PDX_92


title: HOXB13_UW_PDX_86-2


title: HOXB13_UW_PDX_35


title: HOXB13_UW_PDX_58


title: DM1_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2664


title: HOXB13_UW_PDX_81


title: 5c-KO1_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2622


title: 5c-KO2_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2816


title: 5c-KO4_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIPNT3


title: HOXB13_UW_PDX_78


title: 2a-HET4_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2882


title: 5c-KO3_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2818


title: DM2_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2889


title: DM3_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP3082


title: HOXB13_UW_PDX_70


title: 2a-HET3_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2880


title: HOXB13_UW_PDX_170-3


title: HOXB13_NKI_29_T


title: HOXB13_UW_PDX_77


title: HOXB13_NKI_27_T


title: HOXB13_NKI_23_T


title: 2a-HET2_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2821


title: HOXB13_UW_PDX_136


title: HOXB13_NKI_19_T


title: 2a-HET1_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2644


title: WT3_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2881

value: WT


title: HOXB13_NKI_5_T


title: HOXB13_NKI_7_T


title: HOXB13_NKI_13_T


title: WT4_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2886


title: HOXB13_NKI_1_T


title: WT1_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2572


title: DM3_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_3082

value: amygdala


title: HOXB13_DF_2484_T

value: localized prostate tissue


title: HOXB13_DF_2483_T


title: DM1_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2664


title: DM2_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2889


title: 5c-KO2_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2816


title: 5c-KO4_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_NT3


title: HOXB13_NKI_29_N


title: 5c-KO3_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2818


title: WT2_HIP

description:
Hippocampus_gene_expected_count.txt
Hippocampus_isoform_expected_count.txt
SampleHIP2879


title: 5c-KO1_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2622


title: HOXB13_DF_2078_T


title: HOXB13_NKI_25_N


title: HOXB13_NKI_27_N


title: HOXB13_NKI_23_N


title: HOXB13_DF_2480_T


title: HOXB13_NKI_13_N


title: HOXB13_NKI_5_N


title: DM4_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_NT4


title: HOXB13_NKI_19_N


title: HOXB13_NKI_7_N


title: WT3_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2881


title: 2a-HET3_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2880


title: 2a-HET4_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2882


title: WT2_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2879


title: 2a-HET1_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2644


title: HOXB13_DF_2484_N


title: WT4_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2886


title: HOXB13_NKI_1_N


title: HOXB13_DF_2030_T


title: WT1_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2572


title: HOXB13_DF_2483_N


title: HOXB13_DF_2480_N


title: HOXB13_DF_2078_N


title: RNA-YBX1-null

data_processing:
Basecalls performed using CASAVA
Paired-end 100-cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers (Illumina). RNA-sequencing was mapped as described previously (Downing et al., 2012), and HTSeq (version 0.6.1p1) (Anders et al., 2015) was used to obtain gene-level counts and estimated CPM based on GENCODE (v24lift37) (Harrow et al., 2012).
Genome_build: mm10(GRCm38.p5)
Supplementary_files_format_and_content: raw reads count by HTSEQ

source_name: Neural tubes

growth_protocol: Tissue culture plates for adherent culture were prepared by coating them with 10 μg/mL poly-Dlysine (MilliporeSigma P7280) for either 2 h at room temperature (RT) or at 4°C O/N (overnight). Plates were rinsed twice with 1× PBS and replaced with 10 μg/mL laminin (MilliporeSigma L2020) for 2 h at RT. As laminin is highly sensitive to drying, it was removed well-by-well and immediately replaced with sufficient culture medium to cover the surface of the well.

extract_protocol:
Total RNA was isolated from cultured cells and mouse neural tubes (after SOX2-positive FACS sorting from E13.5 embryos) using Ribozol (VWR) and purified using the Direct-zol RNA  Purification Kit (Zymo Research). DNA digestion with DNase I was performed as suggested and RNA concentration and purity was measured by NanoDrop (ThermoFisher).
total RNA with the TruSeq Stranded Total RNA Library Prep Kit were used according to the manufacturer’s directions (Illumina, San Diego, Ca.) Paired end 100 cycle sequencing was performed on HiSeq 2000 or HiSeq 4000 sequencers according to the manufacturer’s directions (Illumina.)

treatment_protocol: Cultures of mouse neural progenitor cells (mNPCs) were derived from E12.5–E13.5 mice as follows. Neural tubes were dissected from embryos in ice-cold Advanced DMEM culture media (ThermoFisher 2491015) and dissociated with 1/3 volume of Type II collagenase (10 mg/mL, Worthington LS004176) for 10 min at 37°C. The tissue was washed once in 1× PBS and incubated in 500 μL 0.25% Trypsin-EDTA (ThermoFisher 25200056) for 5 min at 37°C. Trypsinization was halted using 500 μL DMEM+10% fetal bovine serum, and cells were  mechanically dissociated by trituration and then pelleted by centrifugation at 1000 g for 3 min. Cells were resuspended in 1 mL of PBS and filtered through a 40 μm filter (ThermoFisher 22363547) to obtain single cells. NPCs were isolated by fluorescence-activated cell sorting (FACS) using Sox2-eGFP or NeuroFluor CDr3 (STEMCELL Technologies, #01800), resuspended in complete culture medium, and grown on ultra-low attachment 6-well plates. After sphere formation, spheres were dissociated with Accutase (STEMCELL Technologies 07920) for 5 min in the incubator and single cells plated on coated plates. Cells were grown in NeuroCult™Proliferation Media (STEMCELL Technologies 05702)  supplemented with 10 μg/mL rhEGF (STEMCELL Technologies 78006) to a final concentration of 20 ng/mL. For routine passaging, cells were grown to 75–80% confluency and then  dissociated using Accutase for 5 min in the incubator. Cells were then diluted with an equal volume of growth medium and dissociated by trituration. Cells were pelleted as described above and resuspended in fresh culture medium to plate at recommended densities. For differentiation, cells were plated at recommended densities on poly-D-lysine/laminin–coated 6-well plates or Matrigel (ThermoFisher 354240)–coated 8-well chamber slides (EMD Millipore PEZGS0816) and left O/N. Cells were washed once in Neurocult™Proliferation Media without EGF and incubated in Neurocult™. Differentiation media (STEMCELL Technologies 05704) for indicated times are detailed in figure legends.

tag: cell type

value: Mouse Neural Progenitor Cell

tag: genotype/variation


title: 2a-HET2_AMY

description:
Amygdala_gene_expected_count.txt
Amygdala_isoform_expected_count.txt
AMY_2821


title: RNA-YBX1-null-175-1


title: RNA-YBX1-WT-93-1

value: wildtype


title: FOXA1_UW_PDX_86-2

value: Abcam


title: FOXA1_UW_PDX_189-4


title: RNA-YBX1-WT-116-3


title: FOXA1_UW_PDX_189-3


title: RNA-YBX1-WT-116-1


title: FOXA1_UW_PDX_170-3


title: FOXA1_UW_PDX_170-2


title: HOXB13_DF_2030_N


title: low mPTP opening cells

city: guangzhou

first: zhongfu

last: ying

state: guangdong

address: kaiyuan

department: stem cell research

institute: chinese academy of sciences

data_processing:
Illumina Miseq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence. Bowtie2 v2.2.3 was used for building the genome index and then mapped to mm10  using TopHat v2.0.12.
Genome_build: mm10
Supplementary_files_format_and_content: text files include FPKM values for two Samples ...

source_name: MEF

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: MEF


title: high mPTP opening cells


title: FOXA1_UW_PDX_141


title: FOXA1_UW_PDX_167


title: FOXA1_UW_PDX_92


title: FOXA1_UW_PDX_136


title: RNA-YBX1-null-175-6

first: Beisi

last: Xu

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hosipital


title: FOXA1_UW_PDX_81


title: FOXA1_UW_PDX_78


title: FOXA1_UW_PDX_77


title: adult_testis_RNA

city: Beijing

first: Qiang

last: Tu

address: No.1 West Beichen Road,Chaoyang District

institute: Institute of Genetics and Developmental Biology

description:
Illumina TruSeq stranded  RNA-seq
gonad_expression_TPM.tab

data_processing:
for TPM.tab file: genome mapping using hisat2(2.1.0), default parameters
for TPM.tab file: gene expression quantification using stringtie(v1.3.3b), default parameters
for fasta file: gene model built from pacbio data and generate transcript sequance
Genome_build: medaka ASM223467v1
Supplementary_files_format_and_content: Two TPM.tab files are plain text(quantification count matrix  by TPM, rows are genes and columns  are samples), fasta file is transcript sequence use for quantification.
Supplementary_files_format_and_content: gff file: IGDB gene model generated of this study
Supplementary_files_format_and_content: plain text: lncRNA and TF genes predicted from the IGDB gene model

organism: Oryzias latipes

source_name: testis

extract_protocol:
RNA extraction using both TRIzol and Qiagen RNeasy Micro Kit
Illumina TruSeq stranded mRNA library preparation protocol for RNA-seq samples

value: d-rR,Qurt

value: testis

tag: developmental stages

value: adult(3 months)


title: adult_ovary_RNA

source_name: ovary

value: ovary


title: st41_RNA

description:
Illumina TruSeq stranded  RNA-seq
timecourse_expression_TPM.tab

source_name: whole embryo

value: Hd-rR

value: embryo


title: FOXA1_UW_PDX_70

value: CRPC pdx


title: st40_RNA


title: FOXA1_UW_PDX_58


title: FOXA1_UW_PDX_35


title: InVitro_24hr_PD-1_WT_2 [HBCL-002]

city: Nagoya

first: Akinobu

last: Ota

state: Aichi

address: 1-1 Yazakokarimata

department: Food and Nutritional Environment

institute: Kinjo Gakuin University

description: Gene expression of PD-1 wildtype VAL cells

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes according to the manufacturers instructions. After the fragmentation reaction, equal amount of Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Human Gene Expression v3 8x60K Microarray (G) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed for 1 minute at room temperature with GE Wash Buffer 1 (Agilent), for 1 minute with 37Â°C GE Wash buffer 2 (Agilent), and then dried for 1 minute at room temperature with acetonitrile.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 11.0.1.1 (Agilent) using default parameters (protocol GE1_1100_Jul11 and Grid: 072363_D_F_20150612) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: VAL PD-1/wildtype_24hr

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the Low Input Quick Amp Labeling Kit  (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: VAL cells were cultivated in RPMI1640 medium containing 10% FBS with penicillin-streptomycin. The cells were typically passaged at a split ratio 1:4 twice a week

extract_protocol: RNA was prepared using  NucleoSpin RNA kit (TaKaRa Bio Inc., Shiga, Japan) following the manufacturer's recommendations.  RNA concentration was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: VAL cells were incubated for 24 hours at 37 ºC in a humidified incubator with 5% CO2.

tag: cell line

value: VAL

value: human B cell lymphoma cell line

tag: source gender

value: female

tag: age


title: st36_RNA

tag: strain


title: st32_RNA


title: st29_RNA


title: FOXA1_DF_2484_T


title: FOXA1_DF_2483_T


title: st25_RNA


title: FOXA1_DF_2030_T


title: InVitro_24hr_PD-1_KO_2  [HBCL-004]

description: Gene expression of PD-1-depleted VAL cells

source_name: VAL PD-1/knockout_24hr


title: InVitro_24hr_PD-1_KO_1 [HBCL-003]


title: FOXA1_DF_2078_T


title: st15_RNA


title: FOXA1_NKI_29_T

value: Patient localized prostate tissue


title: st11_RNA


title: FOXA1_NKI_27_T


title: st06_RNA


title: FOXA1_NKI_23_T


title: RBFOX2 RNA input replicate 2

city: Cambridge

first: Bridget

middle: E

last: Begg

state: MA

address: 31 Ames St

department: Biology

institute: Massachusetts Institute of Technology

description: 3' UTR 110-nt synthetic oligonucleotides

data_processing:
Reads were aligned to the designed library.
Perfectly-mapping reads only were assigned to each oligonucleotide.
Only oligonucleotides with 100 or more attributable reads in the input RNA library were considered for further analyses.
Genome_build: 3' UTR nsRBNS library: hg19, mm9
Supplementary_files_format_and_content: Each processed data file contains the perfectly mapping reads attributable to each oligonucleotide in that sample.

organism: synthetic construct

source_name: predesigned sequence library using 3' UTRs from H. sapiens/M. musculus

extract_protocol:
RBP:RNA:bead complexes were pulled down with a magnet and washed gently 2X. RNA was eluted by two incubations with biotin for 30m at RT. RNA eluate was purified with Ampure beads.
RNA was reverse transcribed. The cDNA was amplified for 6-16 cycles and gel-purified to produce the final library.

treatment_protocol: Recombinantly-expressed, tagged RBFOX2 RRM was incubated at varied concentrations with 250nM synthetic RNA oligonucleotide library to equilibrium (1h 4C).

tag: protein concentration

value: RBFOX2 RNA input

tag: replicate

value: replicate 2


title: FOXA1_NKI_19_T

tag: tissue


title: RBFOX2 RNA input replicate 1

value: replicate 1


title: st38_RNA


title: RBFOX2 0nM replicate 2

value: RBFOX2 0nM


title: RBFOX2 0nM replicate 1


title: FOXA1_DF_2480_T

value: localized prostate tissue

tag: chip antibody

value: Abcam


title: FOXA1_NKI_5_T

tag: chip antibody vendor


title: InVitro_24hr_PD-1_WT_1 [HBCL-001]


title: FOXA1_NKI_7_T

tag: chip antibody cat.#


title: RBFOX2 4nM

value: RBFOX2 4nM


title: FOXA1_NKI_1_T

tag: chip antibody lot/batch#


title: FOXA1_NKI_29_N


title: RBFOX 121nM replicate 2

value: RBFOX 121nM


title: RBFOX2 43nM

value: RBFOX2 43nM


title: st19_RNA


title: FOXA1_NKI_27_N


title: RBFOX2 121nM replicate 1

value: RBFOX2 121nM


title: FOXA1_NKI_19_N


title: RBFOX2 365nM

value: RBFOX2 365nM


title: FOXA1_NKI_25_N


title: RBFOX2 14nM

value: RBFOX2 14nM