title: 10m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 34


title: H21b_4.23.13

status: Public on Mar 16 2018

type: genomic

city: Berkeley

first: Yvette

middle: M

last: Piceno

state: CA

address: 1 Cyclotron Rd., MS 70A-3317

department: Ecology

country: USA

institute: LBNL

hyb_protocol: Arrays were hybridized overnight at 48degC and 60 rpm and then washed and stained using standard Affymetrix buffers/reagents.

scan_protocol: Images were captured on an Affymetrix GeneChip Scanner 3000 7G.

data_processing:
CEL files were converted to CELa files and then processed using proprietary software (PhyCA). Data processing performed by Second Genome (http://www.secondgenome.com/platform/services/).
Data are provided as binary or intensity values scaled to internal standards. See README_PhyloChip_FMF-probiotics_Pepoyan.txt on series record. The data file GSE111835_MIAME_Phylochip_data_FMF-probiotics_Pepoyan.txt includes species taxonmy, OTU_ID, GenBank accession ID (GB_ACC) and gg_ID.

label: biotin

molecule: genomic DNA

organism: human gut metagenome

source_name: Healthy volunteer

label_protocol: TDT enzyme (P/N PM1875; Promega; Madison, WI) and GeneChip Labeling Reagent (P/N 90042; Affymetrix; Santa Clara, CA) were used to label fragmented amplicons.

extract_protocol: The ZR Fecal DNA MiniPrep (ZYMO RESEARCH) and the UltraClean® Tissue & Cells DNA Isolation Kit (MoBIO) both were used for total genomic DNA isolation from each sample following the manufacturers’ recommendations. An equal amount of genomic DNA from each extract was combined for a given stool sample prior to 16S rRNA gene amplification for microarrays.

treatment_protocol: see publication

tag: subject id

tag: human donor diagnosis

value: Healthy volunteer

tag: tissue source of metagenome

value: human feces

tag: Sex

value: Female

tag: treatment

value: Placebo

tag: timepoint

value: post-treatment

tag: replicate

value: yes


title: H21a_4.23.13

value: pre-treatment


title: 10m, rep 2, veh, Pol2

type: SRA

city: Boston

first: Kelsey

last: Tyssowski

state: MA

address: 77 Ave Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 33

library_source: genomic

data_processing:
Base-calling with Illumina RTA v2 (default NextSeq settings)
Alignment was done using bowtie2.
Resulting SAM files were converted to BAM files then to BED files using samtools and bedtools, with reads extended to 300 base pairs
BED files were then converted to bedgraphs using bedtools and then to bigWigs using UCSC-tools, reads were assigned to individual enhancers or promoters using bedtools map
Data was normalized as specificed (either by input, control region, or read depth).
Genome_build: mm9
Supplementary_files_format_and_content: Excel files with input-normalized and control-region-normalized values for regions of interest.
BigWig files normalized for read-depth (H3K27ac) or to control regions (Pol2)

organism: Mus musculus

source_name: Primary Culture Mouse Neurons

extract_protocol:
Neurons were fixed in 1% formaldehyde and lysed in 10 mM Tris pH 8.0, 1mM EDTA, 1 mM EGTA, 1X Roche complete EDTA-free protease inhibitors, 0.15% SDS. Chromatin was sonicated and immunoprecipitaed, as described in the methods section of  the accompanying publication (Tyssowski et al., 2018).
Libraries were prepared using 5ug of immunoprecipitated DNA or input DNA with the NuGen Ultralow V2 1-96 library prep kit.

tag: mouse strain

tag: time point

tag: drug

value: DMSO

tag: chip antibody

value: anti-RNAPol2, abcam, ab817


title: 10m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 32


title: H20b_4.23.13


title: 1m, rep 2, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 31


title: H20a_dc_4.24.13


title: 30m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 38


title: H20a_comb_4.24.13


title: 1m, rep 1, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 30


title: 10m, rep 2, U0126, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 35


title: 1m, rep 2, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 29


title: 1m, rep 1, veh, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 28


title: H1a_4.23.13

value: Narine


title: H1b_4.23.13


title: unstim, rep 2, U0126 6h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 27


title: H19b_5.09.13


title: unstim, rep 2, U0126 1h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 26


title: S14_Pre

type: RNA

city: Stockholm

first: Eric

last: Rullman

address: C1:82 Karolinska University Hospital, Huddinge

department: Laboratory Medicine

country: Sweden

institute: Karolinska Institutet

description: Subject 14, Pre

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix HuGene-2_1-st array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: Affymetrix protocol

data_processing: The probe-set level intensities of the arrays were normalized using the Robust Multi-array Analysis method (RMA) implemented within Affymetrix Expression Console version 1.4.1.

molecule: total RNA

organism: Homo sapiens

source_name: Human skeletal muscle, Vastus lateralis

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

extract_protocol: Biopsies were obtained from the vastus lateralis muscle using the Bergström needle technique. The biopsies were immediately stored in liquid nitrogen until processing. Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: tissue

value: Vastus lateralis

tag: gender

value: Male

tag: subject

tag: time

value: Pre


title: S12_Post

description: Subject 12, Post

value: Post


title: S11_Post

description: Subject 11, Post


title: S14_Post

description: Subject 14, Post


title: S11_Pre

description: Subject 11, Pre


title: S9_Pre

description: Subject 9, Pre


title: unstim, rep 1, U0126 6h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 25


title: S12_Pre

description: Subject 12, Pre


title: S13_Pre

description: Subject 13, Pre


title: H18b_4.23.13


title: S7_Pre

description: Subject 7, Pre


title: S13_Post

description: Subject 13, Post


title: unstim, rep 1, U0126 1h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 24


title: H18a_4.23.13


title: S6_Pre

description: Subject 6, Pre


title: S7_Post

description: Subject 7, Post


title: S9_Post

description: Subject 9, Post


title: S5_Post

description: Subject 5, Post


title: S5_Pre

description: Subject 5, Pre


title: unstim, rep 2, veh 6h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 23


title: S4_Post

description: Subject 4, Post


title: H19a_4.24.13


title: S4_Pre

description: Subject 4, Pre


title: H17b_4.23.13


title: H17a_4.23.13


title: S6_Post

description: Subject 6, Post


title: unstim, rep 2, veh 1h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 22


title: S3_Post

description: Subject 3, Post


title: S2_Pre

description: Subject 2, Pre


title: S3_Pre

description: Subject 3, Pre


title: S2_Post

description: Subject 2, Post


title: H16a_4.23.13


title: H15b_4.23.13


title: S1_Pre

description: Subject 1, Pre


title: input, rep 2, veh (H3K27ac)

description: Sample 19


title: H14b_4.19.13


title: H15a_4.23.13


title: S1_Post

description: Subject 1, Post


title: input, rep 1, U0126 (H3K27ac)

description: Sample 18


title: H14a_4.19.13


title: unstim, rep 1, veh 1h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 20


title: 60m, rep 2, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 16

value: anti-H3K27ac, abcam, ab4729


title: 60m, rep1, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 15


title: 60m, rep 2, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 14


title: H13a_4.23.13


title: H13b_4.23.13


title: H12b_4.23.13


title: H12a_4.23.13


title: 60m, rep1, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 13


title: H16b_4.23.13


title: unstim, rep 1, veh 6h, Pol2

description:
Pol2_ChIPseq_processed_data.xlsx
Sample 21


title: 30m, rep 2, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 12


title: H11a_4.23.13


title: 30m, rep 1, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 11


title: 30m, rep 2, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 10


title: H11b_4.23.13


title: 30m, rep1, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 9


title: 10m, rep 2, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 8


title: 10m, rep 1, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 7


title: input, rep 1, veh (H3K27ac)

description: Sample 17


title: 10m, rep 2, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 6


title: 10m rep 1, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 5


title: unstim rep 2, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 4


title: SALK_059379 smallRNAseq

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

library_source: transcriptomic

data_processing:
RNA-seq:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.3.0
smallRNA-seq:
base-calling using RTA 2.7.7
Adapter trimmed using fastqc
alignment using Bowtie2 2.3.0
bisulfite-seq:
base-calling using RTA 2.7.7
alignment using methpip_se map w/ Bowtie 0.12.7
mC calling using methpipe_se_post_map
Genome_build: pBIN_ROK2_pCSA110_sequences.txt

organism: Arabidopsis thaliana

growth_protocol: grown in peat based, fertilized soil, controlled conditions, 21dC, 16h day, 8h dark

extract_protocol:
Vandivier et al. 2015 doi:10.1007/978-1-4939-2444-8_3
standard Illumina multiplexed library construction

tag: t-dna mutant

value: leave, whole rosette

tag: molecule subtype

value: small RNA


title: SAIL_232 bisulfite seq

extract_protocol:
DNeasy Plant Mini Kit
standard Illumina multiplexed library construction

value: bisulfite converted DNA


title: unstim, rep 2, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 2


title: SALK_059379 RNAseq

extract_protocol:
Qiagen Rneasy Plant Mini kit
standard Illumina multiplexed library construction

value: total RNA


title: unstim, rep 1, U0126, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 3


title: SAIL_232 RNAseq


title: unstim, rep 1, veh, H3K27ac

description:
H3K27ac_processed_by_enhancer.xlsx
Sample 1


title: SAIL_232 smallRNAseq


title: H10a_4.23.13

tag: subject id

value: Healthy volunteer

value: human feces

value: Female


title: H10b_4.23.13

tag: human donor diagnosis

value: post-treatment

value: yes


title: SALK_059379 bisulfite seq


title: Pax9 knockout Mouse esophagus, replicate 3

city: Camden

first: Xiaoxin

middle: Luke

last: Chen

state: NJ

address: 403 Haddon Ave

institute: Coriell Institute for Medical Research

description:
E42H3
Biological replicate 3 of 3 Pax9 knockout mouse esophagus.

hyb_protocol: Cy3 or Cy5 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit (Agilent p/n 5188-5242) according to the user guide.

scan_protocol: Scanned on an Agilent Microarray Scanner p/n G2565BA.

data_processing: Agilent Feature Extraction Software 9.1.

source_name: Esophageal epithelium of K5Cre;Pax9 loxp/loxp mouse

label_protocol: 1 µg of total RNA were labeled with Agilent Low RNA Input Linear Amplification Kit, PLUS, Two-Color (Agilent p/n 5188-5340) according to the provided protocol.

growth_protocol: The mice were bred in-house to generate offsprings of proper genotypes.

extract_protocol: Total RNA was extracted from mouse esophageal tissue using RNeasy Fibrous Tissue Mini Kit (Qiagen; Valencia, CA).

treatment_protocol: Mice were PCR-genotyped according to protocols provided by the original developers.

tag: strain/background

tag: genotype/variation

value: K5Cre;Pax9 loxp/loxp

tag: age

value: Adult

value: esophagus

source_name: Agilent's Universal Mouse Reference RNA

tag: cell line

value: 11 mouse cell lines

tag: cell type

value: Cultured cells

tag: sample type

value: reference


title: Pax9 knockout Mouse esophagus, replicate 2

description:
E42H2
Biological replicate 2 of 3 Pax9 knockout mouse esophagus.


title: WGBS_hESC_KO3A_dCas9PAX6ARX_D6_R1

status: Public on Mar 15 2018

city: Munich

first: Michael

middle: Johannes

last: Ziller

address: Kraepelinstrasse 2-10

department: Translational Psychiatry

country: Germany

institute: Max Planck Institute of Psychiatry

data_processing:
library strategy: WGBS
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.

growth_protocol: Stem cell cultures were maintained on Matrigel (BD Biosciences) with mTeSR1 media (Stem Cell Technologies and passaged on a weekly basis using 1mM EDTA or Accutase (Sigma). All cell cultures were maintained at 370C, 5% CO2.

extract_protocol:
RNA was purified using the Direct-zol™ RNA MiniPrep (Zymo Research Inc).
RNA-seq libraries generated using the Illumina TruSeq RNA Library Preparation Kits. Pools were sequenced on the Illumina HiSeq 2500 sequencer as 100bp paired-end reads.   WGBS:100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research per the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research) followed the instructions, eluting to 15 µl low TE buffer. To minimize continually loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) followed the manufacturer’s protocol. The libraries were sequenced on an Illumina HiSeq 2500 sequencer as 100-bp paired-end reads. scRNA-Seq libraries: WT and 3A-KO cells were dissociated on days 6 and 14 of differentiation with Accutase for 10 min. Cells were collected in DMEM:F12 (day 6) or Neurobasal (day 14) + 2% FBS, and centrifuged in order to quench and remove the Accutase. Cell pellets were re-suspended in PBS + 0.04% Bovine Serum Albumin (Millipore) and filtered through a 40µm Nylon Mesh-Cell strainer (Fisher Scientific). Next, we quantified cell number and cell viability using the Nexcelom Cell Counter (Nexcelom Bioscience). To generate Cell 3’ Libraries we used a Single Cell 3’ Reagent Kit v2 (10xGenomics, Chromium). In brief, 10K cells/sample with the RT master mix were loaded in a Single Cell 3’ Chip along with the RT Single Cell 3’ Gel Beads and the Partitioning oil, and run in a Chromium Controller to generate Single Cell Gel Bead-In-Emulsions (GEMs). RT reaction of the resulting single cell-beads suspension was run in order to obtain 10x Barcoded cDNA. Silane magnetic beads were used to clean the barcoded cDNA, which was amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation, End Repair and A-tailing Double Sided Size Selection were used to incorporate R2, P5, P7, 10bp randomer as well as i7 index read sequences that results in Illumina-ready sequencing libraries. To QC post cDNA Amplification reaction and libraries, we loaded 1-2 µl on Us d5000 and d1000 tapes, respectively, and run in a Tapestation 4200 (Agilent Technologies). To quantify DNA concentrations in the libraries we utilized a Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen). For sequencing of Single Cell 3’ libraries, we used standard Illumina sequencing primers and were run using paired-end sequencing with dual indexing following manufacturer’s recommendations. Subsequently each library was sequenced on a HiSeq4000 lane. Amplicon sequencing:  Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-Gold kit (Zymo Research) following manufacturer’s instructions. Individual amplicons were PCR amplified using TaKaRa EpiTaq™ HS (Clontech). The PAX6 and ARX amplicons were amplified using the primer pairs listed in Table S7. Amplicons were sequenced on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (300-cycles). The genomic coordinates for each amplicon are: PAX6 Amplicon 1: chr11: 31,821,416-31,821,910;  PAX6 Amplicon 2: chr11: 31,840,497-31,840,800; ARX Amplicon 1: chrX: 25,011,817-25,012,198; ARX Amplicon 2: chrX: 25,017,310-25,017,775.

treatment_protocol: hESC colonies were dissociated using Accutase and plated at a density of 74,000 cells/cm2 with 10µM ROCK inhibitor (Y-27632, DNSK International) in mTeSR1 for 48 hours. Media was replaced on day 0 with N2B27 medium (50% DMEM:F12, 50% Neurobasal, supplemented with  NEAA, Glutamax, N2 and B27; Gibco, Life Technologies) containing 10µM SB431542 (DNSK International), 100nM LDN-193189 (DNSK International), 1 µM Retinoic Acid (RA, Sigma) and 1µM of Smoothened-Agonist (SAG, DNSK International). Culture medium was changed daily for 6 days and then was switched to N2B27 medium supplemented with 1µM RA, 1µM SAG, 5µM DAPT (DNSK International) and 4µM SU5402 (DNSK International). Cells were fed daily until day 14 of differentiation. On day 14 MNs were dissociated using TrypLE Express (Gibco, Life Technologies) supplemented with DNase I (Worthington) and plated onto pre-coated Poly-D-Lysine/Laminin surfaces (BD Biosciences) and cultured in Neurobasal medium supplemented with NEAA, Glutamax, N2, B27, Ascorbic acid (0.2 µg/ml) and BDNF, CNTF and GDNF (10ng/mL, R&D systems).

value: human embryonic stem cells

tag: stage/time point

tag: modification


title: WGBS_hESC_WT_D6_R1

value: WT


title: WGBS_hESC_WT_D14_R2


title: Wild type Mouse (Negative control) esophagus, replicate 2

description:
E42A2
Biological replicate 2 of 3 wild type esophagus.

source_name: Esophageal epithelium of C57BL/6J mouse


title: WGBS_hESC_KO3B_D0_R1


title: WGBS_hESC_KO3B_D14_R2


title: Wild type Mouse (Negative control) esophagus, replicate 3

description:
E42A3
Biological replicate 3 of 3 wild type esophagus.


title: WGBS_hESC_KO3B_D14_R1


title: WGBS_hESC_KO3A_dCas9PAX6ARX_D14_R1


title: WGBS_hESC_KO3B_D0_R2


title: WGBS_hESC_KO3B_D6_R1


title: WGBS_hESC_KO3A_D0_R2


title: WGBS_hESC_KO3A_D14_R1


title: WGBS_hESC_KO3A_D6_R1


title: scRNASeq_hESC_HUES-64-D14

data_processing:
library strategy: scRNA-Seq
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.


title: WGBS_hESC_WT_D14_R1


title: scRNASeq_hESC_3A-KO-139-D6


title: WGBS_hESC_KO3B_D6_R2


title: RNASeq_hESC_KO3B_D6_R2

description: processed data file: genes_fpkm.txt

data_processing:
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.


title: scRNASeq_hESC_3A-KO-139-D14


title: scRNASeq_hESC_HUES-64-D6


title: RNASeq_hESC_KO3B_D14_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3B_D0_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3B_D6_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3B_D14_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3B_D0_R1

description: processed data file: genes_fpkm.txt


title: Pax9 knockout Mouse esophagus, replicate 1

description:
E42H1
Biological replicate 1 of 3 Pax9 knockout mouse esophagus.


title: RNASeq_hESC_WT_D6_R9

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R10

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D14_R7

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D6_R7

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R6

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R5

description: processed data file: genes_fpkm.txt


title: Wild type Mouse (Negative control) esophagus, replicate 1

description:
E42A1
Biological replicate 1 of 3 wild type esophagus.


title: RNA-sequencing of control N.T.

city: Parma

first: Guidantonio

last: Malagoli Tagliazucchi

address: Via Gramsci 14

department: Division of Research and Innovation

country: Italy

institute: Hospital of Parma

description: processed data file: KD_vs_NT_cuffdiff_gene_exp.txt

data_processing:
RNA-seq analysis was performed by aligning the reads to a reference genome (Mus musculus mm9) using Tophat (Trapnell C 2009 Bioinformatics). Then, we performed a differential expression analysis using Cufflinks (Trapnell C 2010 Nature Biotechnology) that is able is to calculate transcripts abundance and abundance of different gene isoforms using the "cuffdiff" module.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: KD_vs_NT_cuffdiff_gene_exp.txt: Tab-delimited text file (format gene_exp.diff of cuffdiff) with the results of gene-level differential expression (KD vs. NT) obtained from cufflinks and cuffdiff. The results for the three KD samples are combined.

source_name: ESC

growth_protocol: NT and T-UCstem1 KD ESCs were cultured in serum/LIF, as previously described (Bedzhov et al. 2014).

extract_protocol:
RNA was extracted from NT and KD ESCs by using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryonic stem cells (ESCs)

value: control


title: RNASeq_hESC_WT_D0_R3

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D14_R3

description: processed data file: genes_fpkm.txt


title: RNA-sequencing of clone 2 KD.uc.170

value: T-UCstem1 KD


title: RNA-sequencing of clone 1 KD.uc.170


title: RNASeq_hESC_KO3A_D14_R6

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D14_R3

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D0_R3

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D6_R3

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R3

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D6_R4

description: processed data file: genes_fpkm.txt


title: RNA-sequencing of clone 3 KD.uc.170


title: K1

city: Indianapolis

first: Xinxin

last: Huang

state: IN

address: 950 W. Walnut St R2 304

department: Microbiology and Immunology

institute: Indiana University School of Medicine

description: Analysis.xlsx

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina HiSeq 4000.
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the human genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned tohg19 refGene genes using featureCounts (from subread v1.5.1) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: human cord blood CD34+ HSPC

growth_protocol: CD34+ cells were isolated from human cord blood and culture in RPMI-1640 medium with 10% fetal bovine serum, 100 ng/mLSCF, TPO and Flt3L for 16 hours

extract_protocol:
RNA was extracted using the RNeasy Mini Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD34+ cells were treated with vehicle control (DMSO) or LMK235 for 16 hours

value: hematopoietic stem and progenitor cells

tag: treatment

value: LMK235 for 16 hours


title: K3

description: Analysis.xlsx


title: D3

description: Analysis.xlsx

value: DMSO for 16 hours


title: D2

description: Analysis.xlsx


title: RNASeq_hESC_WT_D6_R4

description: processed data file: genes_fpkm.txt


title: D1

description: Analysis.xlsx


title: B2-1-siCse1l-MeDIP

city: Beijing

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

country: China

institute: Institute of Biophysics, CAS

data_processing:
Basecalls performed by BGI, Shenzhen.
Data were filtered using samtools to remove potential PCR duplicates
MeDIP sequencing reads were mapped to the Human genome (hg19) using Bowtie2.
Sequencing qualities were evaluated with FASTQC software and then the reads were aligned to hg19 genome sequences with a maximum of 2 mismatches allowed. Only the uniquely mapped reads were kept, and duplicate reads were removed. Mapped reads were extended to the average fragment sizes. Genome profile files were generated with IGV tools and linearly normalized to the same depth of 10 million reads.
RNA-Seq data were mapped by TopHat and quantitified by Crosslinks.
Genome_build: hg19
Supplementary_files_format_and_content: The transcription levels (RPKM) were quantified with Cufflinks (v2.0.2) software. Bigwig files were generated with IGV tools followed by UCSC utilities.

source_name: siCse1l treated B2-1 cells

extract_protocol:
Genomic DNA was isolated by conventional phenol extraction and proteinase K treatment. For sperm samples, 40 mM DTT were added during cell lysis.
According to standard protocols provided by Illumina Kits.

tag: parental cell line

value: somatic cell line

value: B2-1 treated with siCse1l

tag: tissue

value: embryonic kidney

tag: developmental stage

value: fetus


title: B2-1-siCse1l-DIP-input


title: RNASeq_hESC_WT_D14_R6

description: processed data file: genes_fpkm.txt


title: B2-1-siCtrl-MeDIP

source_name: B2-1 ctrl cells

value: B2-1 treated with siCtrl


title: EV treated Microglia C

city: Clemson

first: David

middle: Matthew

last: Feliciano

state: South Carolina

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

description: EVs are derived from primary SVZ NSC Monolayer Culture.

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The reads were then mapped to the Mus musculus GRCm38 reference genome available on ENSEMBL using the STAR aligner. The RNA-seq aligner is executed using a splice aligner which detects splice junctions and incorporating them to help align the entire read sequences. BAM files were generated as a result of this step. Unique exon hit counts were calculated using Feature counts from the Subread package. After mapping and unique exon hit count calculations, downstream differential expression analysis was performed using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: *.counts.txt: Tab-delimited text files include number of mapped reads.

source_name: Microglia

extract_protocol:
Trizol Extraction RNA library preparation with polyA selection.
NEBNext Ultra RNA Library Preparation

treatment_protocol: EVs were isolated by serial centrifugation from primary NSCs cultured from the subventricular zone of CD1 mice. Cultured microglia were then subjected to control or EV treatments.

value: Microglia

value: Extracellular vesicles (EVs)


title: K2

description: Analysis.xlsx


title: EV treated Microglia A


title: B2-1-siCtrl-DIP-input


title: EV treated Microglia B


title: Control Microglia C

value: Control


title: Control Microglia B


title: WGBS_hESC_WT_D14_R4

description: This is re-accessioned GSM2406772 record, cited in the PMID 29531288


title: WGBS_hESC_KO3A_D6_R3


title: Control Microglia A


title: RNASeq_hESC_WT_D6_R8

description: processed data file: genes_fpkm.txt


title: WGBS_hESC_KO3A_D14_R2


title: RNASeq_hESC_KO3A_D6_R5

description: processed data file: genes_fpkm.txt


title: WGBS_hESC_WT_D6_R3


title: WGBS_hESC_WT_D6_R4

description: This is re-accessioned GSM2406773 record, cited in the PMID 29531288


title: WGBS_hESC_WT_D14_R3


title: WGBS_hESC_KO3A_D14_R3


title: WGBS_hESC_KO3A_D6_R2


title: RNASeq_hESC_WT_D14_R4

description: processed data file: genes_fpkm.txt


title: WGBS_hESC_WT_D6_R2


title: RNASeq_hESC_KO3A_D6_R6

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D14_R4

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R7

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D14_R5

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D0_R4

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D0_R4

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D0_R5

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D0_R5

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D6_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D14_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D14_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D14_R5

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D6_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D6_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D14_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D14_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D0_R2

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_KO3A_D0_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D0_R1

description: processed data file: genes_fpkm.txt


title: RNASeq_hESC_WT_D0_R2

description: processed data file: genes_fpkm.txt


title: QKI_techrep3_dim

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

description:
Technical replicate #3: RT enzyme: AffinityScript; SDS page gel size range: large (dimer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz

data_processing:
Trimming adapters: Raw reads were adapter-trimmed and filtered for short sequences using cutadapt v1.3 (Martin, 2011) in single-end mode (parameters: minimum read length: 18 nt, maximum error-rate: 0.2, minimum adapter overlap: 5 nt).
Trimming molecular barcodes (UMIDs): UMIDs were present in the first 10 bp of the read. For each read, these sequences were trimmed and incorporated in to the read ID line.
Mapping: Reads were mapped against the human reference genome (build GRChr37/hg19) using the iGenomes UCSC hg19 gene annotations with TopHat2 v2.0.10 (Kim, Pertea et al., 2013) using mate inner distance and standard deviation values estimated from a random subsample of 500,000 reads (optional parameters: -p 4 --GTF <gene annotation gtf file> --library-type=fr-firststrand --mate-inner-dist=<mate inner distance> --mate-std-dev=<mate standard deviation>).
Removal of PCR duplicates using UMIDs: UMIDs of reads which had both a) 5’ ends mapping to the same genomic position and b) identical alignment CIGAR strings, were analysed using python code and reads with UMID sequences ≤1 edit distance apart were classified as duplicates and collapsed to a single read.
Filtering low quality alignments: Low-quality alignments were discarded using samtools (Li, Handsaker et al., 2009) (view parameter: -bq 10)
Pooling samples: alignments from all 7 QKI technical replicates were pooled, likewise alignments from the 2 control technical replicates.
Peak calling: Peak calling was performed separately for each strand using MACS2 2.1.1.20160309 (Zhang, Liu et al., 2008) (callpeak program parameters: -t <experimental bam file> -c <control bam file> -f BAM -g hs --keep-dup all --nomodel --shift -15 --extsize 50 -B --call-summits --llocal 0 --slocal 0 --fe-cutoff 3 -q 0.05). The resulting peak files from each strand were merged.
Coverage track: Coverage tracks were produced using bedtools (bedtools genomecov -bg -strand + -trackline -ibam <bam>)
Genome_build: hg19
Supplementary_files_format_and_content: A BED file is provided of peaks called from comparing the pooled 8 QKI IP vs 2 control samples. Scores represent coverage (as per MACS2 “NarrowPeak” output file, MACS manual: https://github.com/taoliu/MACS). A coverage track file is provided of the alignments used for peak calling.

source_name: TGF-beta-treated HMLE cells

growth_protocol: Human breast cancer cell lines were cultured as described previously (Gregory et al., 2008).

extract_protocol:
The QKI-CLIP method was adapted from published methods (Jensen & Darnell, 2008), incorporating modifications from eCLIP (Van Nostrand, Pratt et al., 2016) and iCLIP (Sutandy, Hildebrandt et al., 2016).  UV crosslinking and preparation of lysates: MesHMLE cells were grown in 100mm plates to ~90% confluency, rinsed once with ice-cold PBS, and irradiated with 600 mJ/cm2 in ice-cold PBS using a UV Stratalinker-1800 (Agilent). Cells were collected by scraping, washed in PBS, and stored at -80°C as one pellet per plate. Each pellet was resuspended using 200 µl of 1 X QLB (1 X PBS, 0.3% SDS, 0.5% deoxycholate, 0.5% Igepal, EDTA-free Complete protease inhibitor cocktail (PIC; Roche, 11873580001) for 15 min on ice to liberate QKI from high molecular weight complexes, followed by addition of 400 µl of 1 X QDB (1 X PBS, 0.5% deoxycholate, 0.5% Igepal, PIC) and trituration by passing through a 21G needle and syringe 5 times. DNA was digested with 20 µl RQ1 DNAse (Promega, M6101) at 37°C for 10 min on a Thermomixer (750 rpm, Eppendorf). RNA was partially digested with RNase 1 (ThermoFisher, AM2295) by adding 6 µl of 1:50 diluted RNase 1 in 1 X PBS at 37°C for 5 min on a Thermomixer (750 rpm), then returned to ice. Lysates were centrifuged at 21,000 x g for 20 min at 4°C and supernatant transferred to a fresh tube.    Immunoprecipitation: QKI-RNA complexes were immunoprecipitated using a QKI5 specific antibody (Bethyl, A300-183A) with a rabbit IgG antibody (Santa Cruz sc-2027) used as a control (Appendix Supplementary Methods Figure S1B,C). Antibodies (5 µg) were conjugated to 100 µl protein A Dynabeads (ThermoFisher, 10002D) in PBS-Tw (1 X PBS, 0.05% Tween-20) for 45 min and washed three times with 1 X PXL (1 X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% Igepal) before resuspending the beads with 500 µl of prepared lysate and rotating for 2 hr at 4°C. A further 2% of IP input lysate was set aside to be used as a size-matched input (SMin) as in van Nostrand et al 2016 (Van Nostrand, Pratt et al., 2016).  Bound QKI-5-RNA complexes were washed twice each consecutively with ice cold 1 X PXL, 5 X PXL (5 X PBS, 0.1% SDS, 0.5% sodium deoxycholate, 0.5% Igepal), and 1 X PNK (50 mM Tris-Cl pH 7.5, 10 mM MgCl2, and 0.5% Igepal).  3’ end dephosphorylation and 3’ linker ligation: Beads were first treated with T4 PNK (NEB, M0201L; 20 U in 80 µl reaction volume) in the absence of ATP at 37°C, 850 rpm for 20 min, to dephosphorylate 3’ RNA ends followed by washes with 1 X PNK, 5 X PXL, and two washes with 1 X PNK at 4°C. The 3’ preadenylated linker (NEBNext 3’SR adaptor for Illumina) was ligated to the RNA fragments on bead using RNA ligase I (NEB M0437M; 75 U in a 30 µl reaction volume, 15% PEG8000, 2.5% DMSO, 0.25 µM adaptor) in the absence of ATP at 22°C, 75 min with periodic mixing. Beads were washed with 1 X PNK, 1 X PNK + EGTA (50 mM Tris-Cl pH 7.5, 20 mM EGTA, and 0.5% Igepal), 5 X PXL, and two washes with 1X PNK at 4°C. Twenty percent of beads were removed and labelled with P32 -ATP using T4 PNK (according to Sutandy et al 2016 (Sutandy, Hildebrandt et al., 2016)), washed then recombined with the unlabelled fraction to track the RNA in subsequent steps.   SDS PAGE, nitrocellulose transfer, and RNA extraction and size purification: QKI-5-RNA complexes were eluted with 40 µl 1 X Bolt LDS sample buffer (ThermoFisher) without reducing agent at 70°C for 10 min on a Thermomixer (1200 rpm). Samples were separated through Bolt 10% Bis-tris Plus gels (ThermoFisher) using Bolt MOPS SDS running buffer at 165 V for 47 min. Complexes were then transferred to nitrocellulose (Schleicher&Schuell, BA-85) by wet transfer using 1 X Bolt transfer buffer with 10% methanol (Appendix Supplementary Methods Figure S1D).Filters were placed on a phosphor screen and exposed using a Typhoon imager (GE). Nitrocellulose was cut as marked in Appendix Supplementary Methods Figure S1E and the RNA extracted by proteinase K digestion (2 mg/mL proteinase K, 100 mM Tris-HCl pH 7.5, 50 mM NaCl, 10 mM EDTA, 0.2% SDS) at 50°C for 60 min on a Thermomixer (1200 rpm) followed by extraction with acid phenol (ThermoFisher, AM9712) and precipitation with 1:1 isopropanol:ethanol. RNA was pelleted by centrifugation then separated on a 15% denaturing polyacrylamide gel (1:19 acrylamide, 1 X TBE, 7 M urea). The wet gel was wrapped in plastic wrap and exposed to a phosphor screen and imaged using a Typhoon. Gel slices were cut as marked in Appendix Supplementary Methods Figure S1F and the RNA eluted by the “crush and soak” method as previously described (Jensen & Darnell, 2008). Size match input controls (SMin) were prepared essentially as preciously described (Van Nostrand et al., 2016) with the addition of RNA size selection alongside the QKI-associated RNA fragments.
Reverse transcription, 5’ linker ligation and amplification were performed essentially as previously described (Van Nostrand et al., 2016)  but using a custom synthesized 5’ linker (IDT, 5’SRdeg /5Phos/NN NNN NNN NNG ATC GTC GGA CTG TAG AAC TCT GAA C/3SpC3/), and SR-RT primer for reverse transcription (IDT, AGACGTGTGCTCTTCCGATCT). Products were amplified for 17 (CLIP) or 9 (SMin) cycles using a common forward primer (NEBNext SR primer for Illumina) and barcoded reverse primers for each sample (NEBNext Index primers for Illumina). PCR products were purified using Qiagen Qiaquick PCR purification kit, separated on a 10% acrylamide (29:1) TBE non-denaturing gel, stained with SYBR Gold nucleic acid gel stain (ThermoFisher) and imaged on a ChemiDoc (BioRad). Products corresponding to an insert size of ~30 – 70 nt were excised from the gel as shown in Appendix Supplementary Methods Figure S1G and extracted by the “crush and soak” method as previously described (Jensen & Darnell, 2008). Library quality and quantity was assessed by Bioanalyzer (Agilent), Qubit (ThermoFisher) and qPCR, pooled and sequenced on an Illumina NextSeq 500 (1 x 75bp).
RNA-seq of UV cross-linked Immuno-precipitated RNA (HITS-CLIP)

treatment_protocol: HMLE cells (Mani, Guo et al., 2008) were cultured in HuMEC ready media (ThermoFisher) and induced to undergo EMT by transferring to DMEM: F12 media (1:1) supplemented with 10 μg/ml insulin, 20 ng/ml EGF, 0.5 μg/ml hydrocortisone, 5% fetal calf serum (FCS) and treating with 2.5 ng/ml of TGF-β1 (R&D) for at least 14 days. MesHMLE cells, which are derived from HMLE from prolonged treatment with TGF-β1 (Mani et al., 2008), were maintained in EMT-inducing media without additional TGF-β1.

value: Mesenchymal-like HMLE cells

value: Breast cancer

tag: immunoprecipitation antibody


title: SizeMatchedInput_techrep2

description:
Control Technical replicate #1; RT enzyme: AffinityScript; SDS page gel size range: large and small
QKI_HITSCLIP_peaks.bed.gz
SM_input_plusStrand.bedGraph.gz
SM_input_minusStrand.bedGraph.gz


title: QKI_techrep3_mon

description:
Technical replicate #3; RT enzyme: AffinityScript; SDS page gel size range: small (monomer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz

value: QKI5 specific antibody (Bethyl, A300-183A)


title: QKI_techrep1_dim

description:
Technical replicate #1; RT enzyme: AffinityScript; SDS page gel size range: large (dimer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz


title: QKI_techrep1_mon

description:
Technical replicate #1; RT enzyme: AffinityScript; SDS page gel size range: small (monomer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz


title: QKI_techrep2_dim

description:
Technical replicate #2: RT enzyme: AffinityScript; SDS page gel size range: large (dimer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz


title: QKI_techrep2_dim_SSIV

description:
Technical replicate #2: RT enzyme: SuperScriptIV; SDS page gel size range: large (dimer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz


title: SizeMatchedInput_techrep1


title: QKI_techrep2_mon

description:
Technical replicate #2; RT enzyme: AffinityScript; SDS page gel size range: small (monomer)
QKI_HITSCLIP_peaks.bed.gz
QKI_HITSCLIP_plusStrand.bedGraph.gz
QKI_HITSCLIP_minusStrand.bedGraph.gz


title: [D15] Ind+GSK-treated Replicate 4 6h

city: Calgary

first: Mark

last: Giembycz

state: Alberta

address: 3280 Hospital Drive NW

department: Physiology & Pharmacology

country: Canada

institute: University of Calgary

hyb_protocol: Standard Affymetrix procedures were used using U133plus2.0 human GeneChips.

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G

data_processing:
Data were processed (PLIER normalization) implemented in Transcriptome Analysis Console (v4, Affymetrix).
affymetrix-algorithm-name = plier
affymetrix-algorithm-version = 2.0

source_name: BEAS-2B cells following Ind+GSK 6h

label_protocol: Standard procedures were used where each RNA sample was converted into a biotinylated cRNA target using a 3' in vitro tranbscription express kit (Affymetrix).

growth_protocol: BEAS-2B cells were grown for three days in keratinocyte-containing, serum-free medium (KSFM) supplemented with epidermal growth factor, bovine piutuitary extract and antibiotics and for a further 24h in KSFM.

extract_protocol: BEAS-2B cells stored at -80° C were processed for RNA according to the RNeasy protocol (Qiagen).

treatment_protocol: BEAS-2B cells were treated with vehicle or indacaterol (10nM), GSK 256066 (10nM) or Indacaterol + GSK 256066 (both 10nM) for 1h, 2h, 6h and 18h.

value: human airway epithelial cell line

value: Ind+GSK 6h


title: [D11] Ind+GSK-treated Replicate 3 6h


title: [D9] Ind+GSK-treated Replicate 3 1h

source_name: BEAS-2B cells following Ind+GSK 1h

value: Ind+GSK 1h


title: [D16] Ind+GSK-treated Replicate 4 18h

source_name: BEAS-2B cells following Ind+GSK 18h

value: Ind+GSK 18h


title: [D10] Ind+GSK-treated Replicate 3 2h

source_name: BEAS-2B cells following Ind+GSK 2h

value: Ind+GSK 2h


title: HCCC-9810_si-MBD5_rep3

first: Yuanfeng

last: Li

address: No.38 shengmingyuan Road

institute: Beijing Institute of Radiation Medicine

description: HCCC-9810 with si-MBD5

hyb_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA

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

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

source_name: HCCC-9810 cell lines, transfected with MBD5 siRNAs

growth_protocol: Cells were cultured according to manufacturer's instruction.

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

treatment_protocol: Cells were treated according to manufacturer's instruction.

value: transfected with MBD5 siRNAs


title: Human esophageal squamous epithelial cells treated with 100mM ethanol, replicate 4

description: Biological replicate 4 of 4 human esophageal squamous epithelial cells treated with 100mM ethanol.

hyb_protocol: Cy3 labeled, linearly amplified cRNA samples were hybridized with Gene Expression Hybridization Kit according to the user guide.

data_processing: Agilent Feature Extraction Software 9.1 was used for background subtraction and LOWESS normalization.

source_name: Human esophageal squamous epithelial cells (KYSE510), ethanol

label_protocol: 1 µg of total RNA were labeled with Agilent Low RNA Input Linear Amplification Kit, PLUS, One-Color according to the provided protocol.

growth_protocol: The cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in 5% CO2/95% air.

extract_protocol: Total RNA was extracted from mouse esophageal tissue using RNeasy Kit (Qiagen; Valencia, CA).

treatment_protocol: The cells were treated with 100mM ethanol for 72 h.

value: esophageal squamous epithelial cells

value: 100mM ethanol


title: [D8] Ind+GSK-treated Replicate 2 18h


title: [D7] Ind+GSK-treated Replicate 2 6h


title: [D13] Ind+GSK-treated Replicate 4 1h


title: HCCC-9810_si-MBD5_rep1

description: HCCC-9810 with si-MBD5


title: [D14] Ind+GSK-treated Replicate 4 2h


title: [D12] Ind+GSK-treated Replicate 3 18h


title: HCCC-9810_si-BAP1_rep2

description: HCCC-9810 with si-BAP1

source_name: HCCC-9810 cell lines, transfected with BAP1 siRNAs

value: transfected with BAP1 siRNAs


title: [D2] Ind+GSK-treated Replicate 1 2h


title: Human esophageal squamous epithelial cells treated with 100mM ethanol, replicate 1

description: Biological replicate 1 of 4 human esophageal squamous epithelial cells treated with 100mM ethanol.


title: Human esophageal squamous epithelial cells treated with 100mM ethanol, replicate 3

description: Biological replicate 3 of 4 human esophageal squamous epithelial cells treated with 100mM ethanol.


title: [D4] Ind+GSK-treated Replicate 1 18h


title: [D3] Ind+GSK-treated Replicate 1 6h


title: Human esophageal squamous epithelial cells treated with 100mM ethanol, replicate 2

description: Biological replicate 2 of 4 human esophageal squamous epithelial cells treated with 100mM ethanol.


title: HCCC-9810_si-Control_rep3

description: HCCC-9810 with si-Control

source_name: HCCC-9810 cell lines, transfected with control shRNA

value: transfected with control shRNA


title: HCCC-9810_si-Control_rep1

description: HCCC-9810 with si-Control


title: HCCC-9810_si-Control_rep2

description: HCCC-9810 with si-Control


title: [D5] Ind+GSK-treated Replicate 2 1h


title: HCCC-9810_si-MBD5_rep2

description: HCCC-9810 with si-MBD5


title: [D6] Ind+GSK-treated Replicate 2 2h


title: [D1] Ind+GSK-treated Replicate 1 1h


title: Human esophageal squamous epithelial cells without treatment, replicate 4

description: Biological replicate 4 of 4 human esophageal squamous epithelial cells without treatment.

source_name: Human esophageal squamous epithelial cells (KYSE510), untreated


title: HCCC-9810_si-BAP1_rep1

description: HCCC-9810 with si-BAP1


title: HCCC-9810_si-BAP1_rep3

description: HCCC-9810 with si-BAP1


title: Human esophageal squamous epithelial cells without treatment, replicate 2

description: Biological replicate 2 of 4 human esophageal squamous epithelial cells without treatment.


title: Non treatment 1

city: Cleveland

first: Manoj

last: Veleeparambil

state: OH

address: 9500 Euclid Avenue

department: Immunology

institute: Lerner Research Institute Cleveland Clinic

description:
replicate 1
Non treatment 1

hyb_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic

data_processing: Analyzed by GenomeStudio software V2010.2 with quantile normalization.

source_name: RAW264.7 cells

growth_protocol: Cells were cultured in DMEM supplement with 10% FBS and Pen/Strep

extract_protocol: total RNA

treatment_protocol: RAW264.7 cells (in biological triplicate) were untreated or pretreated with gefitinib (10 µM) for 1h, and untreated or stimulated with CpG (10µg/ml) for 6 hours. Total RNA was extracted.

tag: agent

value: Non treatment


title: [C16] GSK 256066-treated Replicate 4 18h

source_name: BEAS-2B cells following GSK 256066 18h


title: Z3

city: Castanet Tolosan

first: Elodie

last: Gaulin

address: Pole de Biotechnologie Végétale, BP42617 Auzeville

department: Plant Pathology

country: France

institute: UMR5546 CNRS-Univ Paul Sabatier

data_processing:
Quality check with FastQC
RNAseq reads were aligned to the A. euteiches ATCC201684 genome (http://www.polebio.lrsv.ups-tlse.fr/aphanoDB/) using CLC Genomics Workbench 10.1.1
Properly paired reads aligned on A. euteiches genome were conserved
Statistical analysis was done using R package edgeR
Genome_build: A. euteiches ATCC201684 genome (http://www.polebio.lrsv.ups-tlse.fr/aphanoDB/). There is a FASTA file with the transcript sequences available on the series record.
Supplementary_files_format_and_content: Excel file with read counts and RPKM

organism: Aphanomyces euteiches

source_name: Zoospore

growth_protocol:
Aphanomyces euteiches zoopore suspension preparation: For zoospore preparation, mycelium explants from 10- to 15-day-old CMA plates (8,5g/L Corn Meal Agar, Sigma) were inoculated into 50 ml of 2% Bacto peptone and 0.5% glucose and incubated 3 days in the dark at 23°C, then the medium was washed once with 30 ml of source water (Volvic) and resuspended in 30 ml of source water. After 2 h of incubation in the dark, at 23°C, the water was drained and replaced by fresh source water. This procedure was repeated 2 h later, and the mycelium was incubated overnight in source water in the dark at 23°C. The released zoospores were counted using a hemocytometer and diluted with distilled water to the concentration required for the various experiment. See Badreddine et al., 2008, Eukaryotic Cell
Aphanomyces euteiches in vitro growth: A. euteiches is grown on CMA medium (8,5g/L Corn Meal Agar, Sigma), in the dark at 23°C
Infection of Medicago trunctaula roots with a suspension of Aphanomyces euteiches zoopore: Scarified and sterilized seeds of Medicago truncatula (H2SO4 for 7 min, followed by four washings in sterile deionized water and a 1-hour imbibition step in sterile deionized water) were plated on water-agar and stored 24H at 4°C in the dark for germination. One day later germinated seeds are transferred to M-agar medium (5 seeds /plate) and placed at 22°C.The primary root of 2-week-old seedlings was then inoculated by drops o f5 µl of zoosporesuspension along the root (10e5 cell·ml−1 zoospore). Samples are collected at 1, 3 or 9 days after incoluation. See Badreddine et al., 2008, Eukaryotic Cell

extract_protocol:
Total RNAs were extracted using the RNeasy Mini kit (Qiagen, Venlo, The Netherlands)  according to manufacturers recommandations.
Illumina TruSeq Stranded mRNA kit

value: Zoospore

tag: strain

tag: replicate number

value: Biological replicate 3


title: Z2

value: Biological replicate 2


title: Z1

value: Biological replicate 1


title: [C14] GSK 256066-treated Replicate 4 2h

source_name: BEAS-2B cells following GSK 256066 2h


title: Non treatment 2

description:
replicate 2
Non treatment 2

scan_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic


title: Human esophageal squamous epithelial cells without treatment, replicate 3

description: Biological replicate 3 of 4 human esophageal squamous epithelial cells without treatment.


title: F8

description: A. euteiches reads exclusively

source_name: Infected M. truncatula roots (9 DPI)

value: Infected M. truncatula roots (9 DPI)

tag: host

value: Medicago truncatula

tag: host strain


title: Gf treatment 3

description:
replicate 3
Gf treatment 3

label_protocol: Performed by the Lerner Research Institute Genomics Core at the Cleveland Clinic

value: Gf


title: CpG Gf treatment 3

description:
replicate 3
CpG Gf treatment 3

value: CpG Gf


title: Gf treatment 2

description:
replicate 2
Gf treatment 2


title: Non treatment 3

description:
replicate 3
Non treatment 3


title: Gf treatment 1

description:
replicate 1
Gf treatment 1


title: [C11] GSK 256066-treated Replicate 3 6h

source_name: BEAS-2B cells following GSK 256066 6h

value: human airway epithelial cell line


title: [C15] GSK 256066-treated Replicate 4 6h


title: F9

description: A. euteiches reads exclusively


title: CpG Gf treatment 2

description:
replicate 2
CpG Gf treatment 2


title: CpG treatment 1

description:
replicate 1
CpG treatment 1

value: CpG


title: [C13] GSK 256066-treated Replicate 4 1h

source_name: BEAS-2B cells following GSK 256066 1h


title: [C7] GSK 256066-treated Replicate 2 6h


title: CpG treatment 3

description:
replicate 3
CpG treatment 3


title: [C12] GSK 256066-treated Replicate 3 18h


title: Human esophageal squamous epithelial cells without treatment, replicate 1

description: Biological replicate 1 of 4 human esophageal squamous epithelial cells without treatment.


title: F7

description: A. euteiches reads exclusively


title: [C8] GSK 256066-treated Replicate 2 18h


title: CpG treatment 2

description:
replicate 2
CpG treatment 2


title: CpG Gf treatment 1

description:
replicate 1
CpG Gf treatment 1


title: [C10] GSK 256066-treated Replicate 3 2h


title: F5

description: A. euteiches reads exclusively

source_name: Infected M. truncatula roots (3 DPI)

value: Infected M. truncatula roots (3 DPI)


title: F6

description: A. euteiches reads exclusively


title: F4

description: A. euteiches reads exclusively


title: F3

description: A. euteiches reads exclusively

source_name: Infected M. truncatula roots (1 DPI)

value: Infected M. truncatula roots (1 DPI)


title: F2

description: A. euteiches reads exclusively


title: [C9] GSK 256066-treated Replicate 3 1h


title: [C6] GSK 256066-treated Replicate 2 2h


title: F1

description: A. euteiches reads exclusively


title: [C4] GSK 256066-treated Replicate 1 18h


title: IgG_ChIP: ectopic Sox2 expression and Nkx2-1 deletion

city: West Haven

first: Ryan

middle: D

last: Chow

state: CT

address: 850 West Campus Drive

institute: Yale University

data_processing:
Raw fastq reads were aligned to the mm10 genome using Bowtie v2.2.9, allowing for one mismatch in the seed region (-N 1), and converted to bam files using Samtools v1.4. Peaks and summits were then called using the callpeak function in MACS2 v2.1.1, with an extension size of 200 and using the goat-IgG samples as controsl. Differential binding between experimental conditions was performed using the bdgdiff function in MACS2 following recommended settings. Normalized fold enrichment tracks were generated by using the callpeak function with the -SPMR flag, then passing the bedgraph outputs into the bdgcmp function with the setting -m FE (fold enrichment). ChIP-seq average signal plots and clustered heatmaps were generated using ngs.plot v2.61.
Motif analysis was performed using HOMER v4.8.3. The differentially bound regions identified by MACS2 were used to perform motif enrichment compared to a normalized background using a window size of 200 bp and repeat regions masked. In addition, comparative motif analysis was performed by alternatively setting each of the two treatment conditions as the background control.
Genome_build: mm10
Supplementary_files_format_and_content: Fold enrichment bigwigs (Sox2 ChIP vs. goat IgG); peak calls in BED format from MACS2

source_name: lung epithelial cells

extract_protocol:
Chromatin immunoprecipitation was carried out as described previously with minor modifications (Saladi et al., 2017). Briefly, cells were cross-linked with 2 mM EGS (Ethylene Glycol-bis (Succinimidylsuccinate)) in PBS for 30 minutes at room temperature followed by cross-linking with 1% (v/v) formaldehyde at room temperature for 15 minutes. 125 mM glycine was added to stop cross-linking. Cells were then lysed in RIPA buffer for 1-2 hr at 40C. Nuclear lysates were sonicated 5 min for 8 times in a Bioruptor (Diagenode). Sonicated chromatin was precleared with Protein G Sepharose beads (GE Healthcare) pre-blocked with BSA and sonicated salmon sperm DNA (15632-011, Invitrogen). Samples were incubated with 2μg antibody (SOX2, IgG) for overnight at 40C followed by incubation with beads for additional 4 hrs. Immunoprecipitated beads were washed in wash buffer 1 (containing 150 mM NaCl), wash buffer 2 (containing 500 mM NaCl), wash buffer 3 (containing 250 mM LiCl). After the wash, beads were incubated for 3 hrs at 550C, then overnight at 650C in TE buffer containing, SDS, RNase A, and Proteinase K. DNA was purified via Qiaquick PCR purification kit (28106, Qiagen) as per manufacturer’s instructions. PCR was performed using IQ SYBR Green Supermix reagent (Bio-Rad) in a MX300P machine (Stratagene). Percentage of input from the IPs was calculated by using 10% as standard.
Libraries were preparation using the NEBNext Ultra DNA Library Prep Kit with manufacturer’s instructions. 11 cycles were used for the library amplification.
Compatible barcodes #1-12 from Illumina were used. Single end 50bp sequencing was done on HiSeq 2000 using TruSeq V3 High-output kits.

value: 8 week

tag: chip antibody

value: R&D normal goat IgG control (AB-108-C)


title: IgG_ChIP: Wildtype

tag: age


title: 28

source_name: Mycelium

value: Mycelium


title: 29


title: Gene expression in ventral prostate of PhIP-treated rats 1

city: Nagoya

first: Shugo

last: Suzuki

state: Aichi

address: 1 Kawasumi, Mizuho-Cho, Mizuho-Ku

department: Experimental Pathology and Tumor Biology

country: Japan

institute: Nagoya City University Graduate School of Medical Sciences

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Rat Genome 230 2.0 Array.

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000 (Affymetrix) and the image files were obtained.

organism: Rattus norvegicus

source_name: PhIP 1

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA using GeneChip IVT Labeling Kit (Affymetrix) following the manufacturer's protocol.

extract_protocol: Total RNA extracted using RNeasy mini kit (Qiagen, Hilden, Germany) following manufacturer's instructions.

treatment_protocol: Six-week-old male F344 rats were treated with/without PhIP 300 mg/kg, and sacrificed after 2 days.

value: Ventral prostate lobe


title: 30


title: Gene expression in ventral prostate of control rats 2

source_name: Control 2


title: ppGpp0/wt [G3_S15]

city: Bethesda

first: Jennifer

middle: Patterson

last: West

state: Md

address: 8 Center Drive

department: Laboratory of Cell and Molecular Biology

institute: NIDDK

data_processing:
Read data in fastq format was demultiplexed and aligned to E. coli B str. DE3 (NC_012971.2) reference genome using STAR v2.5.2, retaining unmapped reads.
Unmapped reads were then mapped in a second step to T4 reference (NC_000866.4)
In both cases, default alignment behavior was altered with the following arguments: --outFilterScoreMinOverLread 0 --outFilterMatchNmin 30 --outFilterMatchNminOverLread 0 --clip3pAdapterSeq AGATCGGAAGAGCGTCGTGTA --alignIntronMax 1.
RNA gene counts in both reference genomes were then quantified using the same NCBI gene definitions utilized in mapping index construction using the subread featureCounts v1.4.6-p3 package
Count data was normalize using Deseq2, which utilizes a normalization of means method for sample normalization and comparison.
Differential expression between samples fchanges in gene expression was predetermined to entail a fold change ≥ 2 and P value ≤ 0.05.
Genome_build: NC_000866.4
Supplementary_files_format_and_content: Comma seperated value text files include: 1) the fold change of each gene in two different samples determined using subread featureCounts v1.4.6-p3 package; 2) Benjamini-Hochberg p-value.
T4_BWvsBM_DifferentialExpression.csv = wt/wt vs. wt/motAam
T4_BWvsDM_DifferentialExpression.csv = wt/wt vs. DdksA/motAam
T4_BWvsDW_DifferentialExpression.csv = wt/wt vs. DdksA/wt
T4_BWvsGW_DifferentialExpression.csv = wt/wt vs. ppGpp0/wt
T4_BMvsDM_DifferentialExpression.csv = wt/motAam vs. DdksA/motAam

organism: Tequatrovirus T4

growth_protocol: B606, B606 DdksA, and B606 ppGpp0 were grown at 37C to early/mid log phase (OD600 ~ 0.4) then infected with moi of 10 of either wt T4 or T4motAam for 5 minutes

extract_protocol:
RNA was isolated  using method II of (Hinton 1989)
2.5 µg total RNA from each sample was treated with a Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria; Illumina San Diego, CA) to deplete rRNA. The enriched mRNA was fragmented, reverse-transcribed, ligated with dual indexes, and amplified using a TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA).

tag: host e. coli strain

value: B606 ppGpp0

tag: bacteriophage genotype

value: wt


title: Sox2_ChIP: ectopic Sox2 expression and Nkx2-1 deletion

value: R&D goat anti-Sox2 (AF2018)


title: ppGpp0/motAam [G4_S16]

value: motAam


title: ppGpp0/wt [G5_S17]


title: [B16] Indacaterol-treated Replicate 4 18h

source_name: BEAS-2B cells following Indacaterol 18h

tag: cell line

tag: cell type

value: Indacaterol 18h


title: Sox2_ChIP: Wildtype


title: IgG_ChIP: ectopic Sox2 expression


title: [C3] GSK 256066-treated Replicate 1 6h


title: ppGpp0/motAam [G6_S18]


title: ppGpp0/motAam [G2_S14]


title: Input DNA: ectopic Sox2 expression

value: input


title: Gene expression in ventral prostate of control rats 1

source_name: Control 1


title: ppGpp0/wt [G1_S13]


title: Sox2_ChIP: ectopic Sox2 expression


title: Input DNA: ectopic Sox2 expression and Nkx2-1 deletion


title: ΔdksA/motAam [D6_S12]

source_name: ΔdksA/motAam

value: B606 {delta}dksA


title: Input DNA: Wildtype


title: [B13] Indacaterol-treated Replicate 4 1h

source_name: BEAS-2B cells following Indacaterol 1h

value: Indacaterol 1h


title: [B14] Indacaterol-treated Replicate 4 2h

source_name: BEAS-2B cells following Indacaterol 2h

value: Indacaterol 2h


title: ΔdksA/motAam [D4_S10]


title: ΔdksA/wt [D5_S11]

source_name: ΔdksA/wt


title: [C1] GSK 256066-treated Replicate 1 1h

value: human airway epithelial cell line


title: ΔdksA/wt [D3_S9]


title: [B11] Indacaterol-treated Replicate 3 6h

source_name: BEAS-2B cells following Indacaterol 6h

value: Indacaterol 6h


title: [B10] Indacaterol-treated Replicate 3 2h


title: ΔdksA/wt [D1_S7]


title: [B8] Indacaterol-treated Replicate 2 18h


title: [B15] Indacaterol-treated Replicate 4 6h


title: [B12] Indacaterol-treated Replicate 3 18h

source_name: BEAS-2B cells following Indacaterol18h


title: [C5] GSK 256066-treated Replicate 2 1h


title: [B9] Indacaterol-treated Replicate 3 1h


title: [C2] GSK 256066-treated Replicate 1 2h

source_name: BEAS-2B cells following GSK 256066 2h


title: [B7] Indacaterol-treated Replicate 2 6h


title: [B6] Indacaterol-treated Replicate 2 2h


title: [B4] Indacaterol-treated Replicate 1 18h


title: ΔdksA/motAam [D2_S8]


title: wt/wt [B5_S5]

source_name: wt/wt

value: B606 wt


title: wt/motAam [B4_S4]

source_name: wt/motAam


title: wt/motAam [B6_S6]


title: [B5] Indacaterol-treated Replicate 2 1h


title: wt/wt [B3_S3]


title: [B2] Indacaterol-treated Replicate 1 2h


title: wt/motAam [B2_S2]


title: [B3] Indacaterol-treated Replicate 1 6h


title: IFN-b KO macrophages infected 6hrs; biological replicate 2

city: Baltimore

first: Darren

last: Perkins

state: MD

address: 685 W Baltimore st suite 380

institute: University of Maryland Baltimore

description: beta KO infected 2

hyb_protocol: following fragmentation cRNA (10ug) were hybrized to Mousee Genechip 2.0 for 16hr at 45 degrees

scan_protocol: Mouse Gene Chips were scanned with a Roche Array scanner

data_processing:
gene chips were analyzed using Array Suite with Affymetrix default settings
affymetrix-algorithm-name = rma-gene-full
affymetrix-algorithm-version = 1.0
affymetrix-array-type = MTA-1_0
program-name = Expression Console
program-version = 1.4.1.46
program-company = Affymetrix

source_name: IFN-beta KO 6hr ST infected macrophage

label_protocol: Biotinylated cRNA was generated according to Affymeterix reccomended protocol

growth_protocol: Elicited primary macrophages were maintained in RPMI with 2%  FBS at 37 deprees and 5% CO2

extract_protocol: Trizol extraction of total RNA was performed according to manufacturers instruction

treatment_protocol: Infetions were carried out at an moi=4 for 30 minutes at 37 degrees

tag: strain background

tag: genotype/variation

value: IFN-beta null

value: Thioglycollate elicited peritoneal macrophages

tag: infected with

value: S. typhimurium for 6 hrs


title: wt/wt [B1_S1]


title: [B1] Indacaterol-treated Replicate 1 1h

tag: treatment


title: [A14] Vehicle-treated Replicate 4 2h

source_name: BEAS-2B cells following vehicle 2h

value: Vehicle 2h


title: Wildtype macropgaes infected 6hrs; biological replicate 2

description: WT infected 2

source_name: Wild type 6hr ST infected macrophages

value: wild type


title: Wildtype macropgaes infected 6hrs; biological replicate 1

description: WT infected 1


title: [A12] Vehicle-treated Replicate 3 18h

source_name: BEAS-2B cells following vehicle 18h

value: Vehicle 18h


title: [A15] Vehicle-treated Replicate 4 6h

source_name: BEAS-2B cells following vehicle 6h

value: Vehicle 6h


title: IFN-b KO macrophages uninfected; biological replicate 2

description: beta KO mock 2

source_name: IFN-beta KO resting macrophages

value: none (mock-infected)


title: [A16] Vehicle-treated Replicate 4 18h


title: [A13] Vehicle-treated Replicate 4 1h

source_name: BEAS-2B cells following vehicle 1h

value: Vehicle 1h


title: Wildtype macropgaes unifected; biological replicate 1

description: WT Mock 1

source_name: Wild type resting macrophages


title: IFN-b KO macrophages uninfected; biological replicate 1

description: beta KO mock 1


title: [A11] Vehicle-treated Replicate 3 6h


title: [A10] Vehicle-treated Replicate 3 2h


title: DigestiveGland_100µg/L4NP_39day_Male_rep3

city: Boston

first: Bonnie

last: Blalock

address: 100 Morrissey Blvd

department: School for the Environment

institute: University of Massachusetts Boston

description: Gene expression after 39 day exposure

hyb_protocol: 600 ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 uL containing 5uL 10x blocking agent and 1 uL 25x Agilent fragmentation buffer following the manufacturers instructions.  On completion of the fragmentation reaction, 25uL of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to our custom 60,000 sequence Mytilus edulis microarray  for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent), 1 minute with 37°C GE Wash buffer 2 (Agilent), Acetonitrile for 10 seconds at room temperature, and stabilization and drying solution for 30 seconds.

scan_protocol: Microarray slides were scanned at five micron resolution using an Agilent DNA Microarray Scanner G2565CA (Agilent Technologies) at the University of Massachusetts Medical School in Worchester, MA.  Feature extraction was performed using Feature Extraction Software 11.5 (Agilent Technologies).

data_processing: Microarray intensity values were normalized by quantile normalization with median polish in Arraystar (DNAstar, Madison, Wisconsin).  Each treatment was compared to the unexposed control of the corresponding sex and DEG were selected with a 99% confidence interval and 2-fold change.

organism: Mytilus edulis

source_name: DigestiveGland, 100µg/L4NP, Male, 39 days

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200ng RNA using Quick Amp One Color Labeling kit and One Color RNA Spike-in kit following the manufactures protocols (Agilent Technology).  Dye incorporation and cRNA yield were checked with the NanoDrop  Spectrophotometer and met Agilents recommendation of a yield of at least 825 ng and a specific activity of 6pmol prior to hybridization.

growth_protocol: Mussels (M. edulis) were kept in glass aquarium kept at 11.24 +/- 0.3 °C, 8.4 +/- 0.2 mg/L dissolved oxygen, 32.9 +/- 2.1 PSU and a 10:14-h light dark cycle.  Water was changed and treatment (control, 5ng/L EE2, 50ng/L EE2, 1ug/L 4NP, 100ug/L 4NP) was renewed twice a week.  Mussels were fed a daily mixture of Isochrysis galbana and Thalassosira weissflogii for a total of 3.0*10^7cells/mussel.

extract_protocol: Total RNA was isolated using TriReagent (Molecular Research Center, Cincinnati, OH) to each tissue sample and homogenized for 10 min at 50 vibrations/s using a Tissue Lyser bead mill (Qiagen Inc., Valencia, CA) with 3.2 mm stainless steel beads (Biospec Products, Bartlesville, OK).  Total RNA was purified and Dnase I treatment was performed using the RNeasy kit (Qiagen).  RNA concentrations were examined using a NanoDrop Spectrophotometer (Thermo Scientific, Wilmington, DE) and RNA quality was checked using 1.5% agarose gel using NorthernMax-Gly buffer (Applied Biosystems/Ambion, Austin, TX).

treatment_protocol: Treatment tanks were dosed with 100uL of the appropriate concentration of EE2 and 4NP dissolved in ethanol or 100uL of ethanol only for the control.  The amount of ethanol added represented 0.004%.  Water was changed and treatment (control, 5ng/L EE2, 50ng/L EE2, 1ug/L 4NP, 100ug/L 4NP) was renewed twice a week.  At the end of the 39 day exposure digestive gland was dissected and stored in RNA later for future analysis.

tag: gender

value: Male

tag: tissue

value: digestive gland

tag: life stage

value: adult


title: DigestiveGland_100µg/L4NP_39day_Male_rep4

description: Gene expression after 39 day exposure


title: Ovarian_normal_2

city: San Giovanni Rotondo (FG)

first: Fabrizio

last: Bianchi

state: Outside U.S. & Canada

address: Viale Padre Pio 7

institute: Fondazione IRCCS Casa Sollievo della Sofferenza

hyb_protocol: Hybridization was performed using the Affymetrix GeneAtlas Hybridization, Wash and Stain Kit for WT Array Strips.   It contains mix for target dilution, DMSO at a final concentration of 10% and pre-mixed biotin-labeled control oligo B2 and bioB, bioC, bioD and cre controls (Affymetrix cat# 900299) at a final concentration of 50 pM, 1.5 pM, 5 pM, 25 pM and 100 pM respectively. Targets were diluted in hybridization buffer at a concentration of 23 ng/ul, denatured at 99 °C for 5 minutes, incubated at 45 °C for 5 minutes  and centrifuged at maximum speed for 1 minute prior to introduction into the Array Strip PEG. A single Human Gene ST 2.1 PEG Array Strip is hybridized with four  different biotin-labeled target. Hybridizations were performed for 20 hours at 48°C in the GeneAtlas™ Hybridization Station.  The Array Strips were washed and stained in the GeneAtlas™ Personal Fluidics Station . At the end of this procedure the array strip was placed by the fluidic station into the imaging tray, which contains the Array Holding buffer.

scan_protocol: The array strips were imaged using the GeneAtlas™ Imaging Station. Affymetrix GeneAtlas™ Command Console software was used to acquire the Array Strip images and generate .DAT and .CEL files, which were used for subsequent analysis with proprietary software.  Partek Genomics Suite v 6.4 was used for analysis of microarray data.

data_processing: Affymetrix Expression Console, RMA-sketch

source_name: Ovarian Normal Fimbriae

label_protocol: The quality of total RNA was first assessed using an Agilent Bioanalyzer 2100 (Agilent Technologies, Palo Alto, CA).   Bioin-labeled cDNA targets were synthesized starting from 5 ng of total RNA. Double stranded cDNA synthesis and related cRNA was performed with Nugen® Pico WTA Systems V2 (NuGEN Technologies, Inc). With the Encore® Biotin Module (NuGEN Technologies, Inc) was synthesized the fragmented and labeled cDNA. All steps of the labeling protocol were performed according to the manufacturer's recommended protocols.

growth_protocol: All primary cells were cultured in adherent conditions for a maximum of three passages after tissue digestion in order to preserve the biological features and the heterogeneity of original tissue. To perform the Affymetrix analysis, these cells were grown under non-adherent conditions for two rounds to form spheres. RNA was then extracted from second-generation spheres.

extract_protocol: Total RNA was isolated from second-generation spheres using the miRNeasy Micro kit (Qiagen) according to manufacturer’s protocol. After RNA extraction, samples derived from OC or from FTE were grouped in two independent pools for each tissue type, which were then used to perform gene expression analysis. Total RNA was quantified using a NanoDrop 2000 (Thermo Scientific).

value: ovarian fimbriae


title: Ovarian_tumor_2

source_name: Ovarian Cancer Ascite

value: high-grade serous ovarian cancer

tag: tumor type

value: High-Grade Serous Carcinoma

tag: tumor stage

value: FIGO Stage IIIC


title: [A9] Vehicle-treated Replicate 3 1h

value: human airway epithelial cell line


title: [A8] Vehicle-treated Replicate 2 18h


title: Ovarian_tumor_1


title: DigestiveGland_100µg/L4NP_39day_Male_rep1

description: Gene expression after 39 day exposure


title: DigestiveGland_1µg/L4NP_39day_Male_rep4

description: Gene expression after 39 day exposure

source_name: DigestiveGland, 1µg/L4NP, Male, 39 days


title: control-rep4

city: Seoul

first: Chong-Su

last: Kim

address: Gwanak-ro 1, Gwanak-gu

department: Food and nutrition

country: South Korea

institute: Seoul national university

hyb_protocol: Chips were prehybridized in a sealed chamber immersed in a 42°C waterbath using established procedures.Chips were then washed twice for 2 min with agitation, first in ultra-pure water, then in isopropyl alcohol. After the last isopropyl alcohol wash, samples were quickly placed in a room-temperature centrifuge and spun dry (3000 rmp, 5 min). The chips were hybridized overnight in a sealed humidified slide chamber immersed in a light-protected 42°C waterbath, then washed, dried, and stored in the dark until scanned.

scan_protocol: Chips were scanned using an Axon 4000B scanner and GenePix 4.0 software. Photomultiplier tube voltage settings were adjusted to allow 1% saturation of signal in both channels.

data_processing: Image data were extracted, and extracted data were normalized with lowess smoothing function.

source_name: control

label_protocol: Labeling RNA,(one for Cy3 and one for Cy5) using dUTP-Cy3 OR dUTP Cy5 by incubating reverse transcription reaction mixture at 42°C for 90 min, followed by degrading RNA and cleaning up labeled cDNA.

growth_protocol: Mice were bred and maintained at the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH).

extract_protocol: Isolate RNA using Trizol Reagent and clean up RNAs with Qiagen Rnase kit

treatment_protocol: Mice with conditional expression of the most common RVCL mutation, V235fs, and another mice expressing a conditional C-terminal mutation, D272fs, associated with a case of human SLE, were generated. All mice used in this study were maintained under specific pathogen free conditions

value: control

value: spleen

source_name: Reference RNA

tag: sample type

value: Universal reference RNA


title: [A7] Vehicle-treated Replicate 2 6h


title: IFN-b KO macrophages infected 6hrs; biological replicate 1

description: beta KO infected 1

source_name: IFN-beta KO 6hr ST infected macrophages

value: IFN-beta null

value: Thioglycollate elicited peritoneal macrophages

value: S. typhimurium for 6 hrs


title: [A6] Vehicle-treated Replicate 2 2h

value: Vehicle 2h


title: [A5] Vehicle-treated Replicate 2 1h


title: DigestiveGland_1µg/L4NP_39day_Male_rep2

description: Gene expression after 39 day exposure


title: control-rep3


title: control-rep2


title: [A4] Vehicle-treated Replicate 1 18h

value: Vehicle 18h


title: Wildtype macropgaes unifected; biological replicate 2

description: WT Mock  2

value: wild type

value: none (mock-infected)


title: DigestiveGland_50ng/LEE2_39day_Male_rep4

description: Gene expression after 39 day exposure

source_name: DigestiveGland, 50ng/LEE2, Male, 39 days

value: Male

value: digestive gland


title: Gene expression in ventral prostate of PhIP-treated rats 2

source_name: PhIP 2

value: Ventral prostate lobe


title: DigestiveGland_1µg/L4NP_39day_Male_rep3

description: Gene expression after 39 day exposure

value: adult


title: DigestiveGland_1µg/L4NP_39day_Male_rep1

description: Gene expression after 39 day exposure


title: [A3] Vehicle-treated Replicate 1 6h

value: Vehicle 6h


title: control-rep1


title: DigestiveGland_100µg/L4NP_39day_Male_rep2

description: Gene expression after 39 day exposure


title: control

city: Saitama

first: Taro

last: Fukui

address: 1-847 Amanuma-cho Omiya-ku

department: Surgery

institute: Jichi Medical University, Saitama Medical Center

description: SAMPLE 1

hyb_protocol: After enzymatically fragmentation and precipitation with isopropanol, the precipitates were re-suspended in hybridization buffer. After thermal denaturation, re-suspended DNA was applied to a MethylationEPIC BeadChip (Illumina Inc., CA, USA) and hybridization performed for about 23 h in hybridization oven.

scan_protocol: After washing, coating and drying the stained BeadChip, fluorescent images were obtained by iScan (Ver. 3.3.45)(Illumina).

data_processing:
Data was processed with GenomeStudio(Ver.V2011.1)(Illumina)/ Methylation Module(Ver. 1.9.0)
The signal_intensities.txt contains unmethylated and methylated signal intensities

label: Cy3 and Cy5

source_name: Jurkat

label_protocol: Hybridized genomic DNA was stained with a fluorophore-labeled antibody to label collected nucleotides.

growth_protocol: Jurkat cells were adjusted to a cell density of 1.0×106 cells/mL and incubated in RPMI-1640 culture medium (Sigma-Aldrich, St. Louis, MO, USA) containing 10% human inactivated serum (Cosmo Bio Co., Tokyo, Japan) for 72 h

extract_protocol: Genomic DNA was extracted from Jurkat cells with EZ1  DNA Investigator Kit (QIAGEN). DNA (500 ng) extracted from cells was processed with bisulfite using an EZ DNA Methylation Kit (Zymo Research Corp., Irvine, CA, USA).

treatment_protocol: RPMI-1640 culture medium containing 10% human inactivated serum (Cosmo Bio Co., Tokyo, Japan) for 72 h

value: Jurkat cells (E6-1, ATCC Number:TIB-152)

value: none (control)


title: [A1] Vehicle-treated Replicate 1 1h

value: human airway epithelial cell line

value: Vehicle 1h


title: [A2] Vehicle-treated Replicate 1 2h

source_name: BEAS-2B cells following vehicle 2h


title: Trex1 D272fs KI-rep3

description: human Trex1 D272fs KI

source_name: human Trex1 D272fs KI

value: Trex1 D272fs KI

value: spleen

value: Universal reference RNA


title: Trex1 D272fs KI-rep4

description: human Trex1 D272fs KI


title: Ovarian_normal_1

value: ovarian fimbriae


title: SPM(+)

description: SAMPLE 3

value: SPM(+)


title: DigestiveGland_50ng/LEE2_39day_Male_rep2

description: Gene expression after 39 day exposure


title: DigestiveGland_50ng/LEE2_39day_Male_rep3

description: Gene expression after 39 day exposure


title: DigestiveGland_50ng/LEE2_39day_Male_rep1

description: Gene expression after 39 day exposure


title: DFMO(+)

description: SAMPLE 2

value: DFMO(+)


title: SPM(+), DFMO(+)

description: SAMPLE 4

value: SPM(+), DFMO(+)


title: Trex1 D272fs KI-rep1

description: human Trex1 D272fs KI


title: Trex1 D272fs KI-rep2

description: human Trex1 D272fs KI


title: DigestiveGland_5ng/LEE2_39day_Male_rep2

description: Gene expression after 39 day exposure

source_name: DigestiveGland, 5ng/LEE2, Male, 39 days


title: DigestiveGland_5ng/LEE2_39day_Male_rep3

description: Gene expression after 39 day exposure


title: Liver_SoyEnrichedDiet_rep3

city: Cluj-Napoca

first: Simona

last: Visan

state: Cluj

address: 34-36 Republicii

department: Functional Genomics, Proteomics and Experimental Pathology

country: Romania

institute: The Oncology Institute “Prof Dr. Ion Chiricuta”,

hyb_protocol: The probes were hybridized on Agilent G3 Mouse Gene Expression v.2 arrays. Hybridization was carried out for 17 hours at 65°C, then slides were washed and dried acording to the manufacturer's protocol. In addition, to avoid the ozone effects on Cy-3 signal, a supplementary organic solvent containing an ozone scavenging compound dissolved in acetonitrile was used after washing step.

scan_protocol: Slides were scanned on Agilent G2505C Microarray Scanner at 3 µm resolution.

data_processing: Microarray images were processed with Agilent Feature Extraction (FE) software v. 11.5.1.1, using protocol GE1_1105_Oct12 and design 074809_D_F_20150624. Data processing was done in R/Bioconductor using as input the raw median signals generated by FE. Data were filtered by removing control and flagged (saturated, non-uniform) featues, background corrected (method=normexp, offset=50) and quantile normalized between arrays.  The intensities were summarized at the transcript level.

source_name: Liver tissue, mice fed soy-enriched food, replicate 3

label_protocol: The cRNA-Cy3 microarray probes were synthesized from 100 ng of total RNA using Agilent Low Input Quick Amp Labeling Kit. The quality of synthesized cRNAs was checked with Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies) considering a minimal yield of 1.65 μg and a specific activity of more than 6 pmol/μl Cy3/μg cRNA.

extract_protocol: Total RNA containing miRNA was extracted with TriReagent (Sigma-Aldrich), purified with RNeasy Mini Kit (Qiagen) and assessed for quality with Agilent 2100 Bioanalyzer (Agilent Technologies). All samples had the RNA Integrity Number (RIN) greater than 8.

treatment_protocol: Approximately 0,5 g of liver tissue was collected from the right hepatic lobe, taking care to spare the neighboring major blood vessels. All liver samples were immediately immersed in RNAlater (Qiagen) and stored at -80 °C until further use

value: liver

tag: diet

value: 75% granulated regular food, 25% soy bean powder


title: Input_2

city: Hamilton

first: Sonam

last: Bhatia

state: ON

address: 1280 Main Street West

institute: McMaster University

description: input genomic DNA

data_processing:
Sequencing reads were quality controlled using fastQC, and the adaptors were removed using cutadapt software using the illumina universal primer sequence AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC.
The reads were aligned to human genome assembly GRCh38 using hisat2 aligner (version hisat2-2.0.4) and duplicates were removed using samtools
Peak Calling for PLAG1 ChIP: macs2 callpeak -t FlagPlagChIP_file1.bam -c Input_merged.bam -f BAM -g hs –n ChIP_file1_peaks -B -s 50 --bw 150 -q 0.01 --outdir
Peak Calling for USF2 ChIP: macs2 callpeak –t USF2_ChIP_file1.bam -c Input_merged.bam -f BAM -g hs -n ChIP_file1_peaks -B -s 50 --bw 150 -q 0.05 –m 2 50 --outdir
Bedtools intersect was used to identify peaks common to the two replicates and were used for all downstream analysis. Peak files were annotated using HOMER annotatepeaks.pl script using hg38 as the background.
Genome_build: GRCh38
Supplementary_files_format_and_content: narrowPeak files are peaks files that are the output of Macs2 peak calling; bedgraph files are signal files build using macs2 bdgcmp

source_name: Input

growth_protocol: Iscove's Modified Dulbecco's Media (IMDM), 10% Fetal Bovine Serum, 1x Antibiotic-Antimycotic solution. 37ºC, 5% CO2

extract_protocol:
For ChIP-seq, 1x10^8 cells K562 cells co-overexpressing Flag-PLAG1-S and USF2 were cross-linked in 1% PFA and excess PFA was washed with glycine, cells were lysed in RIPA buffer (50mM Tris-Cl pH7.45, 150mM NaCl, 0.1% SDS, 2% NP-40, 1% Sodium deoxycholate) containing protease inhibitors and nuclei were subjected to probe sonication. Two percent of each sample was used for Input sequencing. Chromatin was diluted in dilution buffer (50mM Tris-Cl pH7.45, 150mM NaCl) to get a final SDS concentration of 0.025% to assist in immunoprecipitation (IP). Twenty μg anti-USF2 (SantaCruz, #sc-293443) or anti-Flag (Sigma, F1804) and Protein G dynabeads were used for IP. The precipitated complex was washed in low (50mM Tris-Cl, pH 7.45, 250mM NaCl, 2mM EDTA, 0.1%SDS w/v, 1% Triton X-100 v/v) and high salt buffer (same as low salt buffer except use 500mM NaCl) and chromatin was eluted in TE buffer at 65°C before reverse cross-linking with Proteinase K (NEB, P8107S).
Sequencing libraries were prepared using NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, E7645S) and sequencing as 50 bps single ended reads was performed on Illumina HiSeq 1500 at a depth of 55 million reads per input and 42.5 million reads per IP.

value: K562 cells

value: K562 cells co-overexpressing Flag-PLAG1-S and USF2 Clone# 5

tag: chip-antibody


title: Input_1

description: input genomic DNA

value: K562 cells co-overexpressing Flag-PLAG1-S and USF2 Clone# 4


title: USF2_ChIPSeq_1

description: chromatin immunoprecipitation genomic DNA

value: anti-USF2 (SantaCruz, #sc-293443, lot# C2217)


title: USF2_ChIPSeq_2


title: DigestiveGland_5ng/LEE2_39day_Male_rep1

description: Gene expression after 39 day exposure

value: Male

value: digestive gland

value: adult


title: Trex1 V235fs KI-rep2

description: human Trex1 V235fs KI

source_name: human Trex1 V235fs KI

value: Trex1 V235fs KI


title: FlagPLAG1_ChIPSeq_2

value: anti-Flag (Sigma, F1804, lot# SLBT7654)


title: Trex1 V235fs KI-rep3

description: human Trex1 V235fs KI

value: spleen


title: Liver_SoyEnrichedDiet_rep2

source_name: Liver tissue, mice fed soy-enriched food, replicate 2


title: Trex1 V235fs KI-rep4

description: human Trex1 V235fs KI

value: Universal reference RNA


title: Liver_RegularDiet_rep2

source_name: Liver tissue, mice fed regular food, replicate 2

value: 100% granulated regular food


title: Trex1 V235fs KI-rep1

description: human Trex1 V235fs KITrex1 V235fs KI


title: Liver_RegularDiet_rep3

source_name: Liver tissue, mice fed regular food, replicate 3


title: DigestiveGland_control_39day_Male_rep4

description: Gene expression after 39 day exposure

source_name: Digestive Gland, control, Male, 39 days


title: Liver_SoyEnrichedDiet_rep1

source_name: Liver tissue, mice fed soy-enriched food, replicate 1


title: Liver_RegularDiet_rep1

source_name: Liver tissue, mice fed regular food, replicate 1


title: FlagPLAG1_ChIPSeq_1


title: DigestiveGland_control_39day_Male_rep2

description: Gene expression after 39 day exposure


title: DigestiveGland_100µg/L4NP_39day_Female_rep3

description: Gene expression after 39 day exposure

source_name: Digestive Gland, 100µg/L4NP, Female, 39 days

value: Female


title: DigestiveGland_100µg/L4NP_39day_Female_rep4

description: Gene expression after 39 day exposure


title: DigestiveGland_control_39day_Male_rep3

description: Gene expression after 39 day exposure


title: DigestiveGland_5ng/LEE2_39day_Male_rep4

description: Gene expression after 39 day exposure


title: DigestiveGland_control_39day_Male_rep1

description: Gene expression after 39 day exposure


title: BiSeq_KO3A_Pax6gArxg_Arx_2_D6

city: Munich

first: Michael

last: Ziller

address: Kraepelinstrasse 2-10

institute: Max Planck Institute of Psychiatry

data_processing:
library strategy: Amplicon_BiSeq
RNA-Seq: Raw RNA-Seq reads were trimmed to a total length of 45 bp, removing 5bp from the 5’ end and removing all bases beyond bp 50 at the 3’ end using trimmomatic version 0.33 (Bolger et al., 2014). Subsequently, gene expression levels were quantified using Salmon (Patro et al., 2017) against the cDNA sequences of all ENSEMBL transcripts release 89 of genome assembly GRCh37 using default parameters.
Amplicon-BiSeq:Whole genome bisulfite sequencing and amplicon sequencing raw reads and amplicon sequencing data were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
single cell RNA-Seq: Raw reads were then processed using the 10X Genomics cell ranger pipeline (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest) with standard settings.
WGBS: Whole genome bisulfite sequencing raw reads were aligned using bsMap version 2.7  (Xi and Li, 2009) with default parameters against the human genome build GRCh37. Next, we used the Picard suite to remove all duplicate reads. Subsequently, we carried out methylation using the mcall module implemented in the MOABS suite (Sun et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: RNA-Seq: FPKM format output from DESeq2 (genes.fpkm.txt), tag locations of all raw reads as .bed file
WGBS: standard MOABS mcall output format (bed-like format containing chrom, start, end, ratio, totalC, methC, strand, next,  Plus,  totalC, methC, Minus, totalC, methC, localSeq columns)
scRNA-Seq: standard output from 10x Genomics pipeline: .mtx sparse matrix with UMI counts for each cell and gene, .tsv files containing the row (gene names) and column (individual cell barcodes) headers.

extract_protocol:
RNA was purified using the Direct-zol™ RNA MiniPrep (Zymo Research Inc).
RNA-seq libraries generated using the Illumina TruSeq RNA Library Preparation Kits. Pools were sequenced on the Illumina HiSeq 2500 sequencer as 100bp paired-end reads.   WGBS:100-200 ng of genomic DNA was fragmented using a Covaris S2 for 6 min according to the following program: duty cycle 5%; intensity 10; cycle per burst 200. The sheared DNA was purified using the DNA Clean & Concentrator kit from Zymo Research per the manufacturer’s recommendations. Bisulfite conversion of DNA was then conducted using the EZ DNA Methylation-Gold kit (Zymo Research) followed the instructions, eluting to 15 µl low TE buffer. To minimize continually loss during storage, bisulfite-converted DNA was immediately processed for generating WGBS libraries using the Accel-NGS Methyl-Seq DNA library kit (Swift Biosciences) followed the manufacturer’s protocol. The libraries were sequenced on an Illumina HiSeq 2500 sequencer as 100-bp paired-end reads. scRNA-Seq libraries: WT and 3A-KO cells were dissociated on days 6 and 14 of differentiation with Accutase for 10 min. Cells were collected in DMEM:F12 (day 6) or Neurobasal (day 14) + 2% FBS, and centrifuged in order to quench and remove the Accutase. Cell pellets were re-suspended in PBS + 0.04% Bovine Serum Albumin (Millipore) and filtered through a 40µm Nylon Mesh-Cell strainer (Fisher Scientific). Next, we quantified cell number and cell viability using the Nexcelom Cell Counter (Nexcelom Bioscience). To generate Cell 3’ Libraries we used a Single Cell 3’ Reagent Kit v2 (10xGenomics, Chromium). In brief, 10K cells/sample with the RT master mix were loaded in a Single Cell 3’ Chip along with the RT Single Cell 3’ Gel Beads and the Partitioning oil, and run in a Chromium Controller to generate Single Cell Gel Bead-In-Emulsions (GEMs). RT reaction of the resulting single cell-beads suspension was run in order to obtain 10x Barcoded cDNA. Silane magnetic beads were used to clean the barcoded cDNA, which was amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation, End Repair and A-tailing Double Sided Size Selection were used to incorporate R2, P5, P7, 10bp randomer as well as i7 index read sequences that results in Illumina-ready sequencing libraries. To QC post cDNA Amplification reaction and libraries, we loaded 1-2 µl on Us d5000 and d1000 tapes, respectively, and run in a Tapestation 4200 (Agilent Technologies). To quantify DNA concentrations in the libraries we utilized a Qubit® dsDNA High Sensitivity Assay Kit (Invitrogen). For sequencing of Single Cell 3’ libraries, we used standard Illumina sequencing primers and were run using paired-end sequencing with dual indexing following manufacturer’s recommendations. Subsequently each library was sequenced on a HiSeq4000 lane. Amplicon sequencing:  Bisulfite conversion of DNA was conducted using the EZ DNA Methylation-Gold kit (Zymo Research) following manufacturer’s instructions. Individual amplicons were PCR amplified using TaKaRa EpiTaq™ HS (Clontech). The PAX6 and ARX amplicons were amplified using the primer pairs listed in Table S7. Amplicons were sequenced on the Illumina MiSeq platform using the MiSeq Reagent Kit v2 (300-cycles). The genomic coordinates for each amplicon are: PAX6 Amplicon 1: chr11: 31,821,416-31,821,910;  PAX6 Amplicon 2: chr11: 31,840,497-31,840,800; ARX Amplicon 1: chrX: 25,011,817-25,012,198; ARX Amplicon 2: chrX: 25,017,310-25,017,775.

value: human embryonic stem cells

tag: stage/time point

tag: modification


title: BiSeq_KO3A_Pax6gArxg_PAX6_1_D14


title: BiSeq_KO3A_Pax6gArxg_Arx_1_D6


title: BiSeq_KO3A_Pax6gArxg_PAX6_2_D14


title: BiSeq_KO3A_Pax6gArxg_PAX6_1_D6


title: DigestiveGland_100µg/L4NP_39day_Female_rep1

description: Gene expression after 39 day exposure


title: BiSeq_KO3A_Pax6gArxg_PAX6_2_D6


title: BiSeq_KO3A_Pax6gArxg_Arx_2_D14


title: DigestiveGland_100µg/L4NP_39day_Female_rep2

description: Gene expression after 39 day exposure


title: BiSeq_KO3A_Pax6gArxg_Arx_1_D14


title: BiSeq_WT_ng_Pax6_1_D6

value: WT


title: DigestiveGland_50ng/LEE2_39day_Female_rep4

description: Gene expression after 39 day exposure

source_name: Digestive Gland, 50ng/LEE2, Female, 39 days


title: BiSeq_WT_ng_Pax6_2_D6


title: DigestiveGland_1µg/L4NP_39day_Female_rep2

description: Gene expression after 39 day exposure

source_name: Digestive Gland, 1µg/L4NP, Female, 39 days