title: SCC13_vivo_T1_Rep16

description:
sgRNA library
SCC13_vivo_gene_logFC.txt

data_processing:
Library strategy: CRISPR screen
Sequencing reads were first clipped using fastx clipper (from the FASTX-Toolkit package) for the sequence TCTTGTGGAAAGGACGAAACACCG. PCR duplicates were collapsed using the nine degenerate nucleotides added in PCR 1. Reads were then trimmed to the spacer sequence using fastx trimmer and mapped to the guide library using bowtie2. A read counts table was generated and used for downstream analysis.
The resulting matrix of read counts for each sgRNA (rows) and each sample (column) was then depth normalized so that each sample summed to ten million reads. These counts were log2-normalized, and the values for the time point 0 for each sgRNA were subtracted from time point 1 (three weeks of culture for in vitro and 8-10 weeks of xenograft growth for in vivo). Then for each sample, the median value of non-targeting sgRNAs was subtracted from all gene-targeting sgRNAs. These values are presented as “logFC” in the processed data tables.
Genome_build: NA
Supplementary_files_format_and_content: Processed data files contain the mean log2 fold-change of sgRNAs for each gene between the T1 time point (post-selection in vitro or xenograft tumor growth in vivo) and T0 time point (pre-selection).  Each column of data represents a replicate in ascending order (Rep1, Rep2, Rep3, etc).

growth_protocol: SCC-13, CAL27, and A-431 cells were transduced with pLEX_Cas9 (Addgene: 117987) lentivirus and selected with blasticidin HCl for three to four days to establish stably expressing Cas9 lines. Cas9 expression was confirmed by anti-FLAG (F3165, Millipore Sigma) western blotting. Pooled guide lentivirus was titrated in each of the Cas9 expressing cell lines to achieve an MOI of 0.3. Following selection with puromycin for two to three days, three million cells were frozen at -80°C for the initial screen timepoint. Cells were cultured for three weeks for the in vitro CRISPR screen. For the in vivo CRISPR screen, two to four million cells were mixed with Matrigel (Corning) and injected into the rear flanks of SHO mice (for A431 and CAL27 lines) or NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (Jackson Laboratory) for SCC-13 cells. Resulting tumors were dissected after approximately two months. Tumors were minced and homogenized in an MP Biomedicals Benchtop Homogenizer (MP Biomedicals, Burlingame, CA) using MP Biomedicals lysing matrix A tubes.

extract_protocol:
Genomic DNA was isolated from cells/tumors using the DNeasy Blood and Tissue Kit (Qiagen).
Two rounds of PCR were used to generate CRISPR screen sequencing libraries. To maintain guide library complexity, 36 100uL PCR 1 reactions were set up, each containing 500ng of genomic DNA, PrimeSTAR Max DNA Polymerase, and primers 3 and 4. PCR 1 reactions were heated at 98°C for 10 seconds, 56°C for 15 seconds, and 72°C for 15 seconds for a total of 5 cycles. Reactions were concentrated using the DNA Clean and Concentrator-100 kit (Zymo, Irvine, CA). PCR 1 primers were then removed using 1.1X AMPure XP beads (Beckman Coulter Life Sciences).
A single 100mL PCR 2 reaction was performed containing PrimeSTAR Max DNA  Polymerase (Takara), the product from PCR 1, primers containing Illumina indexes and adapter sequences, and SYBR green (Thermofisher Scientific). The same cycling conditions used in PCR 1 were followed in PCR 2. The reaction was monitored on a Stratagene MX3005P quantitative PCR (qPCR) machine and stopped in the linear phase of amplification, typically after 20-25 cycles. The PCR 2 product was gel purified on a 2% agarose gel. The resulting library was analyzed on a Bioanalyzer and quantitated by qPCR with the KAPA Library Quantification Kit (Roche) prior to library mixing and deep sequencing on an Illumina MiSeq.


title: P5_cSCC_WES

status: Public on Jun 22 2020

type: SRA

city: New York

first: Andrew

last: Ji

state: NY

address: 1428 Madison Ave.

country: USA

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Library strategy: DNA-seq
Raw reads were aligned to hg19 using BWA with default parameters and duplicate reads were removed, resulting in a mean sequencing depth of 158x for on-target regions. The resulting aligned reads were processed using GATK 4.1.0.0 and Mutect2 variant calling for tumor-normal matched pairs, mostly following parameters from the GATK 4 documentation (https://software.broadinstitute.org/gatk/documentation). Mutect2 was run using a panel of normals derived from our cohort and the HapMap 3.3 allele frequencies as a germline resource. The resulting VCF files were filtered using FilterMutectCalls and FilterByOrientationBias and finally annotated using Funcotator, all within GATK tools.
Genome_build: hg19
Supplementary_files_format_and_content: All mutations passing filter for tumor vs. normal comparison are listed as rows of the table, the following columns: gene name, mutation type, mutation code, original base, and mutated base.

molecule: genomic DNA

organism: Homo sapiens

source_name: Skin

growth_protocol: Cutaneous SCCs and patient-matched normal adjacent skin samples were collected under a protocol approved by the Institutional Review Board at Stanford University Medical Center (Protocol #21750). Individuals donating fresh surgical tissue provided informed consent. All diagnoses were verified by histological review. For tumors of adequate size, small fragments of each tumor were snap frozen in optical cutting tissue (OCT) compound (Fisher Healthcare) and/or fixed in 10% formalin (Sigma-Aldrich).

extract_protocol:
Approximately 10-12 8mm sections of fresh-frozen tissue in OCT were dissolved in PBS to remove OCT. The tissue was pelleted and used as input for the DNeasy Blood and Tissue Kit (Qiagen) to extract genomic DNA.
The Agilent V6 whole exome capture kit (60 Mbp) was used and the resulting libraries were sequenced on the BGISEQ-500 instrument using paired-end 100bp reads to achieve approximately 100x coverage for each tumor sample and 50x coverage for each normal skin sample.

tag: tissue

value: cSCC


title: SCC13_vivo_T1_Rep15

description:
sgRNA library
SCC13_vivo_gene_logFC.txt

tag: cell line


title: P3_normal_scRNA

library_source: transcriptomic

data_processing:
For patient tissue, raw sequencing data was processed with the cellranger pipeline (version 2.1.0, 10X Genomics) and mapped to the hg19 reference genome to generate matrices of gene counts by cell barcodes
For xenograft tumors, raw sequencing data was processed with the cellranger pipeline (version 2.1.0, 10X Genomics) and mapped to the combined hg19 and mm10 reference genomes to generate matrices of gene counts by cell barcodes
Genome_build: hg19 for patients, hg19/mm10 combined reference for xenograft tumors
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices

molecule: polyA RNA

growth_protocol: Cutaneous SCCs and patient-matched normal adjacent skin samples were collected under a protocol approved by the Institutional Review Board at Stanford University Medical Center (Protocol #21750). Individuals donating fresh surgical tissue provided informed consent. All diagnoses were verified by histological review.

extract_protocol:
Fresh tumor specimens (patient or xenograft) and normal skin (patient only) were minced with a scalpel in serum-free DMEM (Gibco) with DNAse I (0.2 mg/mL, Worthington, Inc., Columbus, OH) to pieces <1 mm3 and placed in 5mL of 0.25% trypsin-EDTA (Gibco) at 37C for 30 minutes with trituration with a wide-bore pipet tip every 10 minutes. For normal skin, subcutaneous fat was removed with surgical scissors prior to mincing and trypsin-EDTA incubation. After 30 minutes, trypsin-EDTA was quenched with DMEM supplemented with 10% FBS and cells were filtered through a 70mm filter (BD Falcon). Dissociated cells were pelleted and washed once with cold serum-free DMEM with DNase I and were immediately cryopreserved in 90% SCC-13 media with 10% DMSO (Sigma-Aldrich). All steps other than trypsin incubation were completed at 4°C or on ice. For patients 3 and 8, samples were incubated in 0.25% trypsin-EDTA and type I collagenase 5mg/mL (Gibco) for 30 minutes (instead of trypsin-EDTA 0.25% alone for other patients), which led to recovery of higher numbers of T cells in normal skin samples from these patients. We did not observe major differences in downstream processing of cells recovered from collagenase dissociation. On the day of scRNA-seq droplet capture, cells were thawed in at least 5X dilution volume of SCC-13 media to wash off residual DMSO in cryopreservation media. Cells were pelleted and resuspended in cold phosphate buffered saline (PBS) (Gibco) with 2% FBS and 2mM EDTA (Invitrogen, Carlsbad, CA). Cells were stained with propidium iodide (Sigma-Aldrich) prior to sorting on a BD FACS Aria II. For patients 1 and 8, cells were stained with anti-CD45 antibody conjugated to V450 (clone HI30, 560367, BD Biosciences) to separate immune cells from non-immune cells. For patient 1, only CD45-negative cells were sequenced while for patient 8, both CD45+ and CD45- fractions were sequenced, neither of which affected downstream data processing. Sorted cells were pelleted and resuspended in PBS with 2% FBS and 2mM EDTA prior to scRNA-seq droplet capture
10X Genomics Chromium 3' v2 kit according to manufacturer's protocol

value: Normal Skin

tag: strain


title: P9_normal_WES


title: P7_normal_WES


title: P6_cSCC_WES


title: P3_normal_WES


title: P4_cSCC_WES


title: P2_normal_scRNA


title: SCC13_vivo_T1_Rep10

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: P2_cSCC_WES


title: SCC13_vivo_T1_Rep11

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep14

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep7

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep8

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep13

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep12

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep9

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: P5_normal_WES


title: CAL27_vivo_T1_Rep10

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: P4_normal_WES


title: SCC13_vivo_T1_Rep1

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: P3_cSCC_WES


title: SCC13_vivo_T1_Rep6

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep4

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep4

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep3

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep1

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep2

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep3

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep5

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T0_Rep2

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: SCC13_vivo_T1_Rep2

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: CAL27_vitro_T1_Rep1

description:
sgRNA library
CAL27_vitro_gene_logFC.txt


title: CAL27_vitro_T0_Rep2


title: A431_vivo_T1_Rep8

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep5

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: A431_vivo_T1_Rep7

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: SCC13_vivo_T0_Rep1

description:
sgRNA library
SCC13_vivo_gene_logFC.txt


title: P4_ST_vis_rep1

description:
10X Visium platform
ST_Visium_counts.txt.gz

data_processing:
Library strategy: Spatial Transcriptomics
For Visium, libraries were sequenced on a NextSeq (Illumina), with 28 bases from read 1 and 120 from read 2, and at a depth of 84-116 million reads per sample. Following demultiplexing of bcl files, the read 2 fastq files were trimmed using Cutadapt (Martin, 2011) (Martin, 2011) to remove full-length or truncated template switch oligo (TSO) sequences from the 5’ end and polyA homopolymers from the 3’ end. The TSO sequence ( AAGCAGTGGTATCAACGCAGAGTACATGGG) was used as a non-internal 5’ adapter with a minimum overlap of 5, meaning that partial matches (up to 5 base pairs) or intact TSO sequences were removed from the 5’ end of read 2. The error tolerance was set to 0.1 for the TSO trimming to allow for a maximum of 3 errors. For the 3’ homopolymer trimming, a sequence of 10 As was used as a regular 3’ adapter to remove potential polyA tail products regardless of its position in the read, also with a minimum overlap of 5 base pairs. The trimmed data was processed with the spaceranger pipeline (version 1.0.0, 10X Genomics) and mapped to the GRCH38 v93 genome assembly.
Genome_build: GRCh38 v86
Supplementary_files_format_and_content: Tab-delimited text files containing genes by barcode counts matrices, JPEG/PNG of all replicate images, barcode file containing spot barcode position information (same file for all ST 2K patient replicates), and Visium tissue position lists per replicate

extract_protocol:
For Visium, two sections per patient were cut at 10 µm thickness and mounted onto Visium slide capture areas. Sequencing libraries were prepared following the manufacturer’s protocol, again with the Hematoxylin staining time adapted to 4 minutes. After tissue staining, bright-field images were taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 14 minutes, as established in the TO assay.
The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.

tag: patient number


title: A431_vivo_T1_Rep5

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: CAL27_vitro_T1_Rep2


title: A431_vivo_T1_Rep3

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep6

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: P2_normal_WES


title: CAL27_vitro_T0_Rep1


title: CAL27_vivo_T0_Rep2

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep7

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: CAL27_vivo_T1_Rep8

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: A431_vitro_T1_Rep1

description:
sgRNA library
A431_vitro_gene_logFC.txt


title: A431_vivo_T1_Rep6

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: A431_vitro_T1_Rep2

description:
sgRNA library
A431_vitro_gene_logFC.txt


title: P7_cSCC_WES


title: P6_ST_vis_rep2


title: CAL27_vivo_T1_Rep9

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: P6_ST_vis_rep1


title: P4_ST_vis_rep2


title: A431_vivo_T1_Rep4

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: A431_vivo_T1_Rep2

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: P10_ST_rep3

description:
P10_ST_rep3
ST 2K

data_processing:
Library strategy: Spatial Transcriptomics
Raw sequencing data was processed using the open source ST Pipeline v1.7.2 (Navarro et al., 2017) with the GRCh38 v86 genome assembly as reference and corresponding GENCODE annotation file (version 25). The ST pipeline was executed with two-pass mode enabled for alignment and discarding reads in which the UMI had at least 6 low quality bases. The count matrices were filtered to keep only protein-coding, long non-coding, and antisense genes, and Ensembl IDs were replaced by HGNC symbols
Genome_build: GRCh38 v86
Supplementary_files_format_and_content:
ST_all_counts matrix: Tab-delimited text files containing genes by barcode counts matrices. The first 4 rows contain: the patient, section replicate, and X and Y pixel coordinates for each section.
ST_barcode_id.txt includes cell barcode for X,Y coordinates.
In addition to counts matrix with all patients merged for the ST 2K samples, the processed ST Pipeline outputs are included.

extract_protocol:
The Spatial Transcriptomics (ST) protocol was optimized for cSCC tissue  according to recommendations (Salmén et al., 2018). Once optimal conditions had been established, three cryosections per patient were cut at 10μm thickness onto spatial slides and processed immediately. For pre-permeabilization, sections were incubated at 37°C for 20 min with 0.5 U/µl collagenase (ThermoFisher) and 0.2 µg/µl BSA (NEB, Ipswich, MA) in HBSS buffer (ThermoFisher), washed with 0.1× SSC (Sigma-Aldrich), after which permeabilization was conducted at 37°C for 7 min in 0.1% pepsin (Sigma-Aldrich) dissolved in 0.1M HCl (Sigma-Aldrich). After incubation, the pepsin solution was removed and wells washed with 0.1× SSC. Reverse transcription and steps thereafter proceeded according to the ST protocol (Salmen et al., 2018).
Second-strand cDNA synthesis was followed by in vitro transcription, adapter ligation, and a second RT. Sequencing handles and indexes were added in an indexing PCR and the finished libraries were purified and quantified as previously described (Ståhl et al., 2016)


title: CAL27_vivo_T0_Rep1

description:
sgRNA library
CAL27_vivo_gene_logFC.txt


title: P9_ST_rep3

description:
P9_ST_rep3
ST 2K


title: A431_vivo_T1_Rep1

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: A431_vitro_T0_Rep2

description:
sgRNA library
A431_vitro_gene_logFC.txt


title: A431_vivo_T0_Rep1

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: P10_ST_rep1

description:
P10_ST_rep1
ST 2K


title: A431_vitro_T0_Rep1

description:
sgRNA library
A431_vitro_gene_logFC.txt


title: A431_vivo_T0_Rep2

description:
sgRNA library
A431_vivo_gene_logFC.txt


title: P9_ST_rep2

description:
P9_ST_rep2
ST 2K


title: P9_ST_rep1

description:
P9_ST_rep1
ST 2K


title: P5_ST_rep2

description:
P5_ST_rep2
ST 2K


title: P10_ST_rep2

description:
P10_ST_rep2
ST 2K


title: P2_ST_rep3

description:
P2_ST_rep3
ST 2K


title: P2_ST_rep2

description:
P2_ST_rep2
ST 2K


title: P5_ST_rep1

description:
P5_ST_rep1
ST 2K


title: WT_42°C_Rep2

status: Public on Apr 30 2020

city: Dresden

first: Scientific Computing

last: Facility

address: Pfotenhauerstrasse 108

country: Germany

institute: MPI-CBG

description:
Ribosome Footprints
WT_42_2

data_processing:
Library strategy: Ribo-Seq
Basecalling was performed with bcl2fastq 2.17.1.14
Adapter trimming was done using cutadapt v1.17 (-a ATCGTAGATCGGAAGAGCACACGTCTGAA -q20 --discard-untrimmed -m20 -M45 -O6)
Removal of reads which could be mapped to RNA coding genes with bowtie2 v2.2.6 (--trim5 2 --trim3 5)
Mapping of remaining reads was performed with STAR 2.5.2b (--quantMode GeneCounts --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Genome_build: R64-2-1_20150113
Supplementary_files_format_and_content: Raw counts

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: Yeast liquid culture

growth_protocol: Cells from each strain were inoculated in duplicates in 50 ml pre-cultures, which were grown at 30°C overnight and subsequently diluted to an OD600 of 0.05 in a 1 L main culture. The main culture was grown at 30°C to an OD600 of 0.5.

extract_protocol:
RNA was extracted using the hot acid-phenol method (according to Becker et al. 2013)
DNA libraries were generated following previously published protocols (Shiber et al. 2018, McGlincy and Ingolia, 2017)

treatment_protocol: The main cultures were split into three 200 ml cultures that were incubated for 10 minutes at  30°C, 40°C or 42°C. The cultures were subsequently harvested by filtration and immediately flash frozen in liquid nitrogen and then stored at -80°C

value: W303 Ade+

tag: genotype

tag: incubation temperature

value: 42 degreeC


title: IDRm_42°C_Rep2

description:
Ribosome Footprints
IDR-mut_42_2


title: IDRm_40°C_Rep1

description:
Ribosome Footprints
IDR-mut_40_1

value: 40 degreeC


title: IDRm_30°C_Rep2

description:
Ribosome Footprints
IDR-mut_30_2

value: 30 degreeC


title: IDRm_42°C_Rep1

description:
Ribosome Footprints
IDR-mut_42_1


title: WT_40°C_Rep2

description:
Ribosome Footprints
WT_40_2


title: WT_42°C_Rep1

description:
Ribosome Footprints
WT_42_1


title: IDRm_30°C_Rep1

description:
Ribosome Footprints
IDR-mut_30_1


title: WT_30°C_Rep1

description:
Ribosome Footprints
WT_30_1


title: MM-rep3

status: Public on Mar 31 2020

city: Braunschweig

first: Jasper

last: Schierstaedt

address: Messeweg 11-12

department: EP

institute: Julius kühn-Institute

data_processing:
To reveal transcriptional differences in S. Typhimurium 14028s exposed to the different media Illumina HiSeq sequencing were performed at the ZIEL - Institute for Food & Health, Core Facility Microbiome/NGS, Technische Universität München, Freising, Germany.
The sequence analyses were mapped to NC_003197.2 whole genome using Bowtie2 v0.6 with parameters -s -p -x -U -s -o
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using cufflinks v2.2.1 with cufflinks parameters -I 1 -F 0.0 -j 0.0 -G, cuffmerge parameters -g cuffdiff parameters -FDR 0.05 -c 10 -library-norm-method geometric -dispersion-method pooled
Genome_build: NC_003197.2
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each treatment, fold change and significance levels

organism: Salmonella enterica

source_name: RNA from Salmonella grown in minimal medium

growth_protocol: Salmonella was grown overnight at 37°C in LB broth . The cells were pelleted at (1500 x g, 10 min), washed twice in 10 mM MgCl2 and OD600 = 1 was prepared. Two mL of this suspension were pipetted into dialysis tubes which were placed into 50 mL conical tubes containing 30 mL of minimal medium (MM). 2x 0.5 mL from each dialysis tube were mixed with RNAprotect then pelleted and the pellets used for RNA extraction.

extract_protocol:
The total RNA from the bacterial samples was extracted, the rRNA was removed and then the RNA was fragmented using the ultrasonicator.
The library preparation was done with the TruSeq Small RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

treatment_protocol: The minimal medium (MM) consisted of 20% M9 salts, 2 mM MgSO4 and 1.23 mM glucose in sterile deionized water. Tomato Medium (TM) and Lettuce medium (LM) contained 25% (v/v) plant extract and 20% M9 salts and 55% sterile deionized water. Plant root exudate media (LX, TX) consisted of lyophilized exudates (from about 25 plants, 4 h) resuspended in MgCl2. Soil suspensions consisted of 33% (v/v) soil in MgCl2.

tag: serovar

value: Typhimurium

tag: medium

value: minimal medium


title: P5_ST_rep3

description:
P5_ST_rep3
ST 2K


title: MM rep3


title: P2_ST_rep1

description:
P2_ST_rep1
ST 2K


title: IDRm_40°C_Rep2

description:
Ribosome Footprints
IDR-mut_40_2


title: MM rep2


title: MM-rep2


title: MM-rep1


title: Empty4

status: Public on Mar 27 2020

type: genomic

city: Chicago

first: Minoli

last: Perera

state: IL

address: 303 E Chicago Ave.

department: Pharmacology

institute: Northwestern Univeristy

description: novel eQTLs in African-Americans

hyb_protocol: Samples were processed for array hybridization using Illumina provided array reagents.

scan_protocol: Standard protocol.

data_processing: Genotyping outputs were created by Genome Studio using 0.15 GenCall score cutoff.

label: Cy3, Cy5

source_name: liver hepatocytes

label_protocol: SNPs were genotyped using Illumina Multi-Ethnic Genotyping array (MEGA) at the University of Chicago Functional Genomics Core using standard protocols.

growth_protocol: Cells were plated at a density of 0.6 x 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37° C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer's instructions. The media was replaced every 24 hours for three days.    For primary hepatocyte cultures, cell viability was determined by trypan blue (Lonza) exclusion using a hemocytometer (Fisher Scientific).78 If viability was low, Percoll gradient (Sigma-Aldrich) centrifugation of cell suspensions was carried out to improve the yield of viable cells. Cell were plated at a density of 0.6 × 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37 °C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer’s instructions. The media was replaced every 24 h for 3 days.

extract_protocol: DNA was extracted from each hepatocyte line using Gentra Puregene Blood kit (Qiagen).

tag: gender

value: Female

tag: age

tag: batch


title: Empty2

description: novel eQTLs in African-Americans


title: MP-89

description: novel eQTLs in African-Americans


title: Empty1

description: novel eQTLs in African-Americans


title: Empty3

description: novel eQTLs in African-Americans


title: MP-90

description: novel eQTLs in African-Americans

tag: ancestry

value: Male


title: MM rep1


title: GT_E13_5_WT_CnR_HoxA13

status: Public on Apr 25 2020

city: Lausanne

first: Ana Rita

middle: Amandio

last: Lhopitallier

address: SV2842, Station 19

department: SV-ISREC-EPFL

country: Switzerland

institute: EPFL

data_processing:
Library strategy: CUT & RUN
CUT&RUN reads processing was done on the Duboule local Galaxy server (Afgan et al., 2016). Adapters and bad-quality bases were removed with Cutadapt version 1.16 (Martin, 2011). Reads were mapped to the mouse genome (mm10) using Bowtie2 (v2.3.4.1) (Langmead and Salzberg, 2012), (-I 0 -X 1000 --fr --dovetail --very-sensitive). Reads with mapping quality below 30 or not properly paired were removed from the analysis. The output BAM file was converted to BED using bamtobed bedtools v2.18.2 (Quinlan, 2014). The coverage was obtained as the output of MACS2 (v2.1.1.20160309) (Zhang et al., 2008) (--format BED --keep-dup 1 --bdg --nomodel --extsize 200 --shift -100).
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph

organism: Mus musculus

source_name: genital tubercule

extract_protocol: CUT&RUN (Schmid et al., 2004; Skene and Henikoff, 2017) was performed as described in (Meers et al., 2019; Skene et al., 2018). Micro-dissected tissues were isolated in PBS supplemented with 10% fetal calf serum and dissociated to single cell by collagenase treatment. After isolation, 500’000 cells were washed and bound to concanavalin A-coated magnetic beads and permeabilized with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, and Roche Complete protein inhibitor) containing 0.02% digitonin. Bound cells were incubated with primary antibody (anti-HOXA13, AbCam ab106503; anti-CTCF, Active Motif, 6131) for 2h at room temperature. After washes the samples were incubated with Protein A-MNase (pA-MN) for 1 hour at 4oC, then washed twice more with Wash Buffer. Samples were resuspended in low-salt rinse buffer (20 mM HEPES, pH7.5, 0.5 mM spermidine, and 0.125% Digitonin) and chilled to 0°C and the liquid was removed on a magnet stand. Ice-cold calcium incubation buffer (3.5 mM HEPES pH 7.5, 10 mM CaCl2, 0.05% Digitonin) was added and samples were incubated on an ice-cold block for 30 min. STOP buffer (270 mM NaCl, 20 mM EDTA, 4 mM EGTA ,0.02% Digitonin, 50 µg glycogen, 50 µg RNase A) was added and samples were incubated at 37°C for 30 min, replaced on a magnet stand and the liquid was removed to a fresh tube. DNA was extracted by Phenol-Chloroform extraction and ethanol precipitation. Libraries were prepared as described in (Skene et al., 2018). Library quality was checked on a fragment analyzer, and paired-end sequencing was performed on an Illumina NextSeq 500 instrument (read length 2 × 37 base pairs).

value: wildtype

tag: developmental stage

value: CBA / C57BL/6 mix


title: WT_30°C_Rep2

description:
Ribosome Footprints
WT_30_2


title: MP-87

description: novel eQTLs in African-Americans


title: MP-88

description: novel eQTLs in African-Americans


title: MP-86

description: novel eQTLs in African-Americans


title: WT_40°C_Rep1

description:
Ribosome Footprints
WT_40_1


title: MP-84

description: novel eQTLs in African-Americans


title: MP-83

description: novel eQTLs in African-Americans


title: MP-85

description: novel eQTLs in African-Americans


title: MP-82

description: novel eQTLs in African-Americans


title: MP-75_rep

description: novel eQTLs in African-Americans


title: MP-79

description: novel eQTLs in African-Americans


title: MP-78

description: novel eQTLs in African-Americans


title: MP-81

description: novel eQTLs in African-Americans


title: MP-80

description: novel eQTLs in African-Americans


title: MP-77

description: novel eQTLs in African-Americans


title: MP-76_rep

description: novel eQTLs in African-Americans


title: MP-76

description: novel eQTLs in African-Americans


title: MP-75

description: novel eQTLs in African-Americans


title: MP-73

description: novel eQTLs in African-Americans


title: MP-71

description: novel eQTLs in African-Americans


title: MP-72

description: novel eQTLs in African-Americans


title: MP-68

description: novel eQTLs in African-Americans


title: MP-66

description: novel eQTLs in African-Americans


title: MP-65

description: novel eQTLs in African-Americans


title: MP-70

description: novel eQTLs in African-Americans


title: MP-64

description: novel eQTLs in African-Americans


title: MP-57

description: novel eQTLs in African-Americans


title: MP-62

description: novel eQTLs in African-Americans


title: MP-61

description: novel eQTLs in African-Americans


title: MP-67

description: novel eQTLs in African-Americans


title: MP-69

description: novel eQTLs in African-Americans


title: MP-60

description: novel eQTLs in African-Americans


title: MP-48

description: novel eQTLs in African-Americans


title: MP-47

description: novel eQTLs in African-Americans


title: MP-33

description: novel eQTLs in African-Americans


title: MP-63

description: novel eQTLs in African-Americans


title: MP-13

description: novel eQTLs in African-Americans


title: MP-17

description: novel eQTLs in African-Americans


title: MP-22

description: novel eQTLs in African-Americans


title: MP-10

description: novel eQTLs in African-Americans


title: MP-55

description: novel eQTLs in African-Americans


title: MP-56

description: novel eQTLs in African-Americans


title: MP-59

description: novel eQTLs in African-Americans


title: MP-19

description: novel eQTLs in African-Americans


title: MP-51

description: novel eQTLs in African-Americans


title: MP-46

description: novel eQTLs in African-Americans


title: MP-58

description: novel eQTLs in African-Americans


title: MP-53

description: novel eQTLs in African-Americans


title: MP-45

description: novel eQTLs in African-Americans


title: MP-36

description: novel eQTLs in African-Americans


title: MP-43

description: novel eQTLs in African-Americans


title: MP-39

description: novel eQTLs in African-Americans


title: MP-49

description: novel eQTLs in African-Americans


title: MP-38

description: novel eQTLs in African-Americans


title: MP-11

description: novel eQTLs in African-Americans


title: MP-54

description: novel eQTLs in African-Americans


title: MP-52

description: novel eQTLs in African-Americans


title: MP-40

description: novel eQTLs in African-Americans


title: MP-29

description: novel eQTLs in African-Americans


title: MP-41

description: novel eQTLs in African-Americans


title: MP-31

description: novel eQTLs in African-Americans


title: MP-34

description: novel eQTLs in African-Americans


title: MP-44

description: novel eQTLs in African-Americans


title: MP-37

description: novel eQTLs in African-Americans


title: MP-42

description: novel eQTLs in African-Americans


title: MP-35

description: novel eQTLs in African-Americans


title: MP-50

description: novel eQTLs in African-Americans


title: MP-24

description: novel eQTLs in African-Americans


title: MP-30

description: novel eQTLs in African-Americans


title: MP-32

description: novel eQTLs in African-Americans


title: MP-28

description: novel eQTLs in African-Americans


title: MP-25

description: novel eQTLs in African-Americans


title: MP-4_rep

description: novel eQTLs in African-Americans


title: MP-15

description: novel eQTLs in African-Americans


title: MP-16

description: novel eQTLs in African-Americans


title: MP-20

description: novel eQTLs in African-Americans


title: MP-27

description: novel eQTLs in African-Americans


title: MP-8

description: novel eQTLs in African-Americans


title: MP-18

description: novel eQTLs in African-Americans


title: MP-9

description: novel eQTLs in African-Americans


title: MP-12

description: novel eQTLs in African-Americans


title: MP-7

description: novel eQTLs in African-Americans


title: MP-6

description: novel eQTLs in African-Americans


title: MP-4

description: novel eQTLs in African-Americans


title: MP-1

description: novel eQTLs in African-Americans


title: MP-0

description: novel eQTLs in African-Americans


title: MP-5

description: novel eQTLs in African-Americans


title: MP-2

description: novel eQTLs in African-Americans


title: MP-21

description: novel eQTLs in African-Americans


title: MP-3

description: novel eQTLs in African-Americans


title: MP-14

description: novel eQTLs in African-Americans


title: Sox9_2

description: Sox9 - biological replicate 2

data_processing:
Basecalling was performed with bcl2fastq 2.17.1.14
Reads were mapped using STAR v2.5.2b (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed with STAR (--quantMode GeneCounts)
Genome_build: GRCm38, Ensembl v70
Supplementary_files_format_and_content: Raw counts and FPKM normalized expression values

source_name: Dissociated, FAC-sorted primary embryonic neural progenitors_Sox9

growth_protocol: Embryonic neocortex of E13.5, Tis21-CreERT2 embryos were in utero electroporated with either control or Sox9 constructs. The embryos were collected after 48 hours (at E15.5).

extract_protocol:
Total RNA from sorted cells was extracted using the QIAGEN RNeasy Micro kit according to the manufacturer’s protocol. cDNA synthesis was performed with SmartScribe reverse transcriptase (Clontech), universal poly-dT primers and template switching oligos. Purified cDNA was amplified with Advantage 2 DNA Polymerase in 12 cycles, and subjected to ultrasonic shearing with Covaris S2.
Standard Illumina fragment libraries were prepared using NEBnext chemistries (New England Biolabs). Library preparation consisted of fragment end-repair, A-tailing and ligation to indexed Illumina TruSeq adapters, followed by a universally primed PCR amplification of 15 cycles. Then, libraries were purified using XP beads (Beckman Coulter) and quantified by qPCR.

treatment_protocol: Embryonic noecortices were dissected and dissociated. RFP expressing cells were sorted by FACS.

value: Tis21-CreERT2 mouse line

tag: genotype/variation

value: Sox9 constructs

value: Embryonic day 15.5

value: Brain

tag: cell type

value: dissociated, FAC-sorted primary embryonic neural progenitors


title: Sox9_3

description: Sox9 - biological replicate 3


title: Sox9_1

description: Sox9 - biological replicate 1


title: Control_2

description: Control - biological replicate 2

source_name: Dissociated, FAC-sorted primary embryonic neural progenitors_control

value: control


title: MP-26

description: novel eQTLs in African-Americans


title: Control_1

description: Control - biological replicate 1


title: Control_4

description: Control - biological replicate 3


title: Microglia from Toxoplasma gondii-infected mice 2

status: Public on Mar 10 2020

city: Charlottesville

first: Tajie

last: Harris

address: 409 Lane Rd

institute: University of Virginia

data_processing:
Read Filtering and Trimming: Trimmomatic v0.39 in paired-end mode, phred33 scoring, a 4 bp sliding window, and minimum average, leading, and trailing quality scores of 15, 3, and 3 respectively. Minimum Fragment length was 36 bp.
Read QC Analysis: Performed before filtering and trimming and after filtering and trimming with FastQC v0.11.5
Transcript Quantification: Pseudo-alignment quantification was done with Salmon v0.8.2 with the GENCODE M13 reference genome.
Transcript Conversion: Conversion from ENSEMBL transcripts to ENSEMBL gene abundances accomplished with Tximport v1.4.0
Genome_build: GENCODE M13
Supplementary_files_format_and_content: Processed data in quant.sf file format and contain ENSEMBL transcript abundances

source_name: Immune

growth_protocol: Mice were age- and sex-matched for all experiments, T. gondii was maintained in chronically infected CBA/J (4-8 weeks) mice before being homogenized and isolated for infections.

extract_protocol:
Immediately after sacrifice mice were perfused with 30 mL of cold 1X PBS. Brains were harvested and put into cold complete RPMI media. For serum, blood from the heart was collected and allowed to clot at 4°C overnight. Brains were minced and homogenized, digested with 0.227 mg/mL collagenase/dispase and 50 U/mL DNase (Roche) at 37°C for 45 minutes. Homogenate was passed through a 70 µm filter (Corning) and washed with cRPMI. Filtered brain homogenate was then resuspended with 20 mL of 40% Percoll and spun at 650 x g for 25 minutes. Myelin was aspirated, samples were washed with cRPMI, and then resuspended in cRPMI.
Single cell suspensions from tissue samples were plated in a 96-well U-bottom plate. Cells were initially incubated with 50 µL Fc block (1 µg/mL 2.4G2 Ab (BioXCell), 0.1% rat g globulin) for 10 min at room temperature. Cells were then surface stained with antibodies and a Live/Dead stain for 30 minutes at 4°C. Cells were then washed with FACS buffer (0.2% BSA and 2 mM EDTA in 1X PBS) and fixed at 4°C for 30 minutes with either 2% paraformaldehyde (PFA) or a fixation/permeabilization kit (eBioscience). Cells were then permeabilized and stained with any intracellular markers for 30 minutes at 4°C. Samples were then washed, resuspended in FACS buffer, and run on a Gallios flow cytometry (Beckman Coulter). Analysis was done using FlowJo software v.10. Antibody clones used include: CD31 (390), CD45 (30-F11), MHC-II (M5/114.15.2), NK1.1 (PK136), CD19 (1D3), CD3 (17A2), CD4 (GK1.5), CD11c (N418), CD11b (M1/70), Foxp3 (FJK-16s), Ly6G (1A8), Ly6C (HK1.4), CD8a (53-6.7), IFN-g (XMG1.2), NOS2 (CXNFT), IL-1a (ALF-161), and pro-IL-1b (NJTEN3). For cell sorting, CX3CR1creERT2 x ZsGreen 492 fl/stop/fl mice were used. After surface staining, live cells were analyzed on a BD Aria in the UVA flow cytometry core facility. Cells were sorted based on ZsGreen expression into Trizol for RNA-sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Experimental mice were  injected  Intraperitoneally with 10 Me49 cysts. All procedures followed the regulations of the Institutional Animal Care and Use Committee at the University of Virginia

value: Microglia

tag: agent

value: Toxoplasma gondii type II strain Me49


title: Sox9_4

description: Sox9 - biological replicate 4


title: Macrophage from Toxoplasma gondii-infected mice 2

value: Macrophage


title: Microglia from Toxoplasma gondii-infected mice 3


title: Microglia from Toxoplasma gondii-infected mice 1


title: TCRd-Foxp3_Thymus_Treg_m3_beta

status: Public on Jan 10 2020

city: Baltimore

first: Nan-Ping

last: Weng

address: 251 Bayview Blvd

department: LMBI

institute: NIA

data_processing:
Library strategy: TCR-seq
The raw sequences were first separated by the sample barcode using a custom Python script. The sequences then were then filtered through a custom Python script in order to separate erroneous sequences under each UMI cluster. Sequences that had a successfully identified sample barcode and were successfully filtered were then processed via the MIGEC (v.1.2.7) program, which assembles consensus sequences for each UMI cluster and identifies the V, J, and CDR3 sequences via BLAST. Post MIGEC analysis included removal of contaminated TCR sequences using a custom Python script. A successful TCR had to meet the following criteria: each UMI ≥ 3 sequence reads, a known V and J gene, and an intact and functional CDR3 amino acid sequence. TCR clonotypes were defined as a unique combination of V, J and CDR3 amino acid sequences. CDR3 length was based on the definition of IMGT.
Genome_build: mm10
Supplementary_files_format_and_content: Each processed data file is a tab-delineated .txt with 5 columns. The first 3 columns contains important TCR information: the first column contains the TCR V-Gene, the second column contains the CDR3 amino acid (AA) sequence, the third column contains the TCR J-Gene. The fourth column represents the UMI count associated with each TCR and the fifth column represents the number of reads associated with each TCR. Each line in a file represents a unique TCR clonotype based on the V Gene-CDR3 AA-J Gene combination.

source_name: Treg TCRb sequencing of mus musculus: young female thymus

growth_protocol: All mice were maintained under specific pathogen free conditions at the animal facility of National Cancer Institute and Duke University. Animal procedures were reviewed and approved by NIH or Duke Institutional Animal Care and Use Committee.

extract_protocol:
Thymic tTreg and Tconv cells were isolated from 4-8 week-old mice of three strains, all on a C57BL/6 background: 1) Rag-GFP-Foxp3-RFP: tTreg and Tconv cells were isolated from three individual mice based on GFP and Foxp3-RFP expression and were sequenced independently. 2) TcrdCreERZsGreen-Foxp3-RFP: TcrdCreER knockin with tamoxifen-induced ZsGreen reporter for TCRδ expression (three doses of 1 mg tamoxifen i.p. every other day, cells isolated 2 weeks after last injection): tTreg and Tconv T cells were isolated from 9 mice based on expressions of ZsGreen, FoxP3-RFP and CD25, and sequencing was performed on 3 pools (three mice pooled in one sample). 3) Foxp3-GFP TCRα+/- TCRβ-transgenic mice carrying the DO11.10 TCRβ: tTreg and Tconv samples from three individual mice were sorted based on Foxp3 reporter + and -, respectively, and individual samples were sequenced independently. Total RNA was isolated from tTreg and Tconv cells using a Qiagen RNeasy Micro kit.
Isolated total RNA (50-500 ng) was used for cDNA synthesis using TCRα and TCRβ constant region specific primers ac1R and bc1R, SMARTScribe reverse transcriptase (CloneTech), and SmartN oligos for template switching at the 5’ end in order to incorporate a unique molecular identifier (UMI) and MISS sequence for PCR. The cDNA products were treated with uracil-DNA glycosylase (NEN biolab) at 37 oC for 30 min to remove SmartN oligos. Three rounds of PCR using Super fidelity Platinum® Taq DNA Polymerase (ThermoFisher Scientific) were performed to prepare libraries for sequencing. The first PCR (18-24 cycles) was used to enrich TCRs using M1SS (part of SmartN used as a 5’ PCR primer) and TCR constant region primers (mTRAC1 and mTRBC1), and primers were removed by the QIAquick PCR purification kit (Qiagen). The second PCR (20-32 cycles) was used to add an 8 bp sample barcode to each sample at 5’ end and internal constant region primers. PCR products were separated by 2% agarose (UltraPure, ThermoFisher Scientific) gel electrophoresis and DNA fragments (400–800 bp) were further purified by a QIAquick Gel Extraction kit (Qiagen). Purified DNAs of each sample were quantitated by a BioAnalyser (Agilent) and combined for the third round of PCR (10 cycles) which incorporates the Illumina adaptor. Amplified DNA was separated by 2% agarose gel electrophoresis and further purified by QIAquick Gel Extraction and followed by the PCR purification kits. The amount of purified DNA was measured using a Qubit fluorometer (ThermoFisher). Fifty picomoles of DNA were used for sequencing on an Illumina HiSeq 2500 system. A modified paired end sequencing protocol was used: TCR-specific sequencing primers TRA and TRB were used for first round sequencing of 150 bps. Illumina RD2 primer was used for second round sequencing of 50 bps covering the sample barcode and UMI.

value: TCRdCreER ZsGreen Foxp3 RAF

value: Thymus

value: CD4+ Regulatory T-cells

tag: tcr chain

value: beta

tag: development stage

value: young

tag: Sex

value: female

tag: isolate

value: mouse #3


title: TCRd-Foxp3_Thymus_Treg_m3_alpha

source_name: Treg TCRa sequencing of mus musculus: young female thymus

tag: tissue

value: alpha


title: Macrophage from Toxoplasma gondii-infected mice 3

tag: strain


title: TCRd-Foxp3_Thymus_Treg_m2_alpha

tag: genotype

value: mouse #2


title: TCRd-Foxp3_Thymus_Treg_m2_beta


title: TCRd-Foxp3_Thymus_Treg_m1_beta

value: mouse #1


title: TCRd-Foxp3_Thymus_Tconv_m3_beta

source_name: Tconv TCRb sequencing of mus musculus: young female thymus

value: CD4+ Conventional T-cells


title: TCRd-Foxp3_Thymus_Treg_m1_alpha


title: Macrophage from Toxoplasma gondii-infected mice 1


title: TCRd-Foxp3_Thymus_Tconv_m2_beta


title: Macrophage from Toxoplasma gondii-infected mice 4


title: TCRd-Foxp3_Thymus_Tconv_m1_alpha

source_name: Tconv TCRa sequencing of mus musculus: young female thymus


title: TCRd-Foxp3_Thymus_Tconv_m1_beta


title: RAG-Foxp3_Thymus_Treg_m2_beta


title: RAG-Foxp3_Thymus_Treg_m2_alpha


title: RAG-Foxp3_Thymus_Treg_m3_beta


title: RAG-Foxp3_Thymus_Treg_m3_alpha


title: Microglia from Toxoplasma gondii-infected mice 4


title: RAG-Foxp3_Thymus_Treg_m1_alpha


title: RAG-Foxp3_Thymus_Tconv_m3_alpha


title: RAG-Foxp3_Thymus_Tconv_m2_beta


title: RAG-Foxp3_Thymus_Tconv_m3_beta


title: RAG-Foxp3_Thymus_Tconv_m2_alpha


title: RAG-Foxp3_Thymus_Tconv_m1_beta


title: TCRd-Foxp3_Thymus_Tconv_m3_alpha


title: TCRB-Tg_Thymus_Tconv_m2_alpha

value: TCRalpha +/- TCRbeta Tg


title: TCRB-Tg_Thymus_Treg_m3_alpha


title: RAG-Foxp3_Thymus_Tconv_m1_alpha


title: TCRB-Tg_Thymus_Treg_m2_alpha


title: TCRB-Tg_Thymus_Tconv_m3_alpha


title: Relapse sedentary gap-matched rep4

status: Public on Dec 10 2019

city: Oklahoma City

first: Michael

middle: C.

last: Rudolph

state: OK

address: 975 NE 10th St. BRC North rm 364

department: Biochemistry and Physiology

institute: OUHSC

description:
relgm29
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx

data_processing:
Trimmomatic to remove sequencing adaptors.
gSNAP for sequence alignments.
Cufflinks to generate FPKM counts.
Genome_build: Rattus_norvegicus.Rnor_5.0.74
Supplementary_files_format_and_content: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx: Excel file includes FPKM counts.

organism: Rattus norvegicus

source_name: Liver

extract_protocol:
Livers were removed after 24 hours of refeeding and immediately flash frozen. RNA was isolated using RNeasy kit from Qiagen according to instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Wistar

value: Liver

tag: exercise during weight loss and maintenance

value: Sedentary

tag: diet after wlm

value: Energy gap-matched

tag: time point

value: First day of weight regain


title: Relapse sedentary gap-matched rep5

description:
relgm30
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: TCRd-Foxp3_Thymus_Tconv_m2_alpha

value: TCRdCreER ZsGreen Foxp3 RAF


title: TCRB-Tg_Thymus_Tconv_m1_alpha

value: Thymus


title: Relapse exercise rep3

description:
relx23
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx

value: Treadmill exercise

value: ad libitum


title: Relapse exercise rep2

description:
relx22
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse exercise rep1

description:
relx21
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse sedentary rep3

description:
rels18
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse sedentary rep2

description:
rels17
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse sedentary rep4

description:
rels19
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse exercise rep4

description:
relx24
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse sedentary rep5

description:
rels20
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: Relapse sedentary gap-matched rep2

description:
relgm27
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: IDRm_40°C_SN_Rep1

status: Public on Nov 26 2019

data_processing:
Basecalling was performed with bcl2fastq 2.19.1
Mapping of remaining reads was performed with STAR 2.5.2b (--quantMode GeneCounts --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Genome_build: R64-2-1_20150113
Supplementary_files_format_and_content: Raw counts

extract_protocol:
RNA was extracted using the hot acid-phenol method (according to Becker et al. 2013)
Ribosomal RNA was depleted using illumina ribominus, RNA libraries were prepared for sequencing using standard  protocols

value: W303 Ade+

tag: incubation temperature

tag: fraction

value: soluble fraction yeast RNA


title: IDRm_42°C_SN_Rep2


title: RAG-Foxp3_Thymus_Treg_m1_beta

value: CD4+ Regulatory T-cells

value: beta

value: young

value: female


title: Relapse sedentary gap-matched rep1

description:
relgm26
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx


title: TCRB-Tg_Thymus_Treg_m1_alpha

value: alpha

value: mouse #1


title: IDRm_40°C_SN_Rep2


title: IDRm_30°C_SN_Rep1


title: Relapse exercise rep5

description:
relx25
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx

value: Wistar


title: IDRm_42°C_SN_Rep1


title: WT_30°C_SN_Rep1


title: WT_40°C_SN_Rep1


title: Relapse sedentary rep1

description:
rels16
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx

value: Liver


title: IDRm_42°C_pellet_Rep1

value: insoluble fraction yeast RNA


title: Relapse sedentary gap-matched rep3

description:
relgm28
processed data file: 2019_8_9__Processed_liver_RNAseq_FPKM.xlsx

value: Sedentary

value: Energy gap-matched


title: IDRm_30°C_SN_Rep2


title: WT_42°C_SN_Rep2


title: IDRm_30°C_pellet_Rep1


title: WT_42°C_pellet_Rep1


title: IDRm_40°C_pellet_Rep1


title: WT_42°C_pellet_Rep2


title: WT_40°C_pellet_Rep1


title: WT_42°C_SN_Rep1


title: WT_30°C_pellet_Rep1


title: IDRm_42°C_pellet_Rep2


title: IDRm_42°C_total_Rep2

value: total yeast RNA


title: IDRm_40°C_total_Rep2


title: WT_30°C_SN_Rep2


title: WT_42°C_total_Rep2


title: IDRm_40°C_pellet_Rep2


title: WT_40°C_pellet_Rep2


title: IDRm_30°C_pellet_Rep2


title: WT_40°C_total_Rep2


title: WT_42°C_total_Rep1


title: WT_30°C_total_Rep2


title: WT_30°C_pellet_Rep2


title: WT_30°C_total_Rep1


title: MP-8

status: Public on Oct 31 2019

description:
ancestry health disparity
condition1_expression_tmm_normalization.txt

data_processing:
RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits and sequenced on an Illumina HiSEQ2500 or 4000 according to Illumina provided protocols.
Post alignment and QC, reads were mapped to genes referenced with comprehensive gene annotation (GENCODE version 25) by HTSeq (version 0.6.1p1) with union mode and minaqual = 20
HTSeq raw counts were supplied for gene expression analysis and were normalized using regularized log transformation and principal component analysis (PCA) using Bioconductor package DESeq2 (version1.20.0)
We calculated TPM (transcript per million) by first normalizing the counts by gene length and then normalizing by read depth (Wagner, Kin, & Lynch, 2012). Gene expression values were filtered based on the expression thresholds > 0.1 TPM in at least 20% of samples and ≥ 6 reads in at least 20% of samples as done in the GTEx consortium (gtexportal.org, Analysis Methods, V7, updated 09/05/2017).
We normalized expression values across samples by TMM (trimmed mean of M-values) implemented in edgeR (Robinson & Oshlack, 2010) and then normalized for each gene by inverse normal transformation.
Genome_build: hg37
Supplementary_files_format_and_content: MP-xxxcount.txt data contain raw counts data from Htseq
Supplementary_files_format_and_content: condition1_expression_tmm_normalization.txt contain TMM normalized expression values across samples

growth_protocol: Cell were plated at a density of 0.6 x 106 cells/well in 500 µL InVitroGro-CP media (BioIVT, Baltimore, MD) in collagen-coated plates with matrigel (Corning, Bedford, MA) overlay and incubated overnight at 37° C. Cultures were maintained in InVitroGro-HI media (BioIVT) supplemented with Torpedo antibiotic mix (BioIVT) per the manufacturer's instructions. The media was replaced every 24 hours for three days.

extract_protocol:
RNA was extracted after three days using the RNeasy Plus mini-kit (Qiagen) per manufacturer's instructions.
RNA-QC was performed using an Agilent Bio-analyzer. RNA-SEQ libraries were generated using Illumina mRNA TruSeq kits.

tag: ancestry

tag: gender

value: Male

tag: age

tag: platform

tag: batch


title: MP-90


title: IDRm_40°C_total_Rep1


title: IDRm_42°C_total_Rep1


title: IDRm_30°C_total_Rep2


title: MP-70

value: Female


title: MP-78


title: MP-76


title: IDRm_30°C_total_Rep1


title: MP-77


title: MP-7


title: MP-63


title: WT_40°C_total_Rep1


title: MP-9


title: MP-75


title: MP-61


title: MP-59


title: MP-67


title: MP-66


title: MP-65


title: MP-69


title: MP-58


title: MP-57


title: MP-62


title: MP-68


title: MP-53


title: MP-64


title: MP-60


title: MP-6


title: MP-54


title: MP-55


title: WT_40°C_SN_Rep2


title: MP-90

description: ancestry health disparity

scan_protocol: Arrays were stained with Illumina provided reagnets and scanned using an Illumina HiSCAN.

data_processing: ChAMP v2.10.1

label: Cy5 and Cy3

label_protocol: CT-conversion was performed using Zymo-Research EZ DNA Methylation kits.

extract_protocol: DNA was extracted from each hepatocyte line using Gentra Puregene Blood kit (Qiagen) as per manufacturer’s instructions from 1-2 million cells.


title: MP-78

description: ancestry health disparity


title: MP-66

description: ancestry health disparity


title: MP-76

description: ancestry health disparity


title: MP-73

description: ancestry health disparity


title: MP-60

description: ancestry health disparity


title: MP-67

description: ancestry health disparity


title: MP-77

description: ancestry health disparity


title: MP-62

description: ancestry health disparity


title: MP-70

description: ancestry health disparity


title: MP-55

description: ancestry health disparity


title: MP-53

description: ancestry health disparity


title: MP-61

description: ancestry health disparity


title: MP-63

description: ancestry health disparity


title: MP-58

description: ancestry health disparity


title: MP-65

description: ancestry health disparity


title: MP-64

description: ancestry health disparity


title: MP-57

description: ancestry health disparity


title: MP-68

description: ancestry health disparity


title: MP-44

description: ancestry health disparity


title: MP-59

description: ancestry health disparity


title: MP-75

description: ancestry health disparity


title: MP-52

description: ancestry health disparity


title: MP-69

description: ancestry health disparity


title: MP-46

description: ancestry health disparity


title: MP-49

description: ancestry health disparity


title: MP-50

description: ancestry health disparity


title: MP-43

description: ancestry health disparity


title: MP-45

description: ancestry health disparity


title: MP-51

description: ancestry health disparity


title: MP-51


title: MP-40

description: ancestry health disparity


title: MP-52


title: MP-37

description: ancestry health disparity


title: MP-49


title: MP-50


title: MP-39

description: ancestry health disparity


title: MP-42

description: ancestry health disparity


title: MP-44


title: MP-43


title: MP-42


title: MP-34

description: ancestry health disparity


title: MP-41


title: MP-31

description: ancestry health disparity


title: MP-32

description: ancestry health disparity


title: MP-39


title: MP-35


title: MP-34


title: MP-29

description: ancestry health disparity


title: MP-28

description: ancestry health disparity


title: MP-31


title: MP-9

description: ancestry health disparity


title: MP-37


title: MP-30


title: MP-18

description: ancestry health disparity


title: MP-45


title: MP-14

description: ancestry health disparity


title: MP-7

description: ancestry health disparity


title: MP-40


title: MP-1

description: ancestry health disparity


title: MP-15

description: ancestry health disparity


title: MP-24

description: ancestry health disparity


title: MP-3


title: MP-25


title: MP-27

description: ancestry health disparity


title: MP-35

description: ancestry health disparity


title: MP-8

description: ancestry health disparity


title: MP-3

description: ancestry health disparity


title: MP-30

description: ancestry health disparity


title: MP-21

description: ancestry health disparity


title: MP-16


title: MP-15


title: MP-16

description: ancestry health disparity


title: MP-6

description: ancestry health disparity


title: MP-27


title: MP-32


title: MP-26

description: ancestry health disparity


title: MP-28


title: MP-26


title: MP-1


title: MP-24


title: MP-2


title: MP-21


title: MP-18


title: MP-0

description: ancestry health disparity


title: MP-20


title: ChIP_Calibrated_Nz_Thiolutin_Smc1-6HA Spt16-AID_Biological replica 2

status: Public on Oct 11 2019

city: London

first: Jonay

last: Garcia-Luis

state: London

address: Du Cane Road

department: London Institute of Medical Sciences

country: United Kingdom

institute: UKRI

data_processing:
The quality of the raw sequence data was assessed using FastQC (version 0.11.5). The reads were mapped to the S. cerevisiae genome (sacCer3) as the experimental genome or C. glabrata genome (CBS138) as calibration genome using Bowtie2 (version 2.3.4) with the default parameters. To generate an alignment in which all the sequences exclusively map to the sacCer3 genome, the whole reads were first mapped to CBS138 genome and the unmapped reads were retrieved as a separate Fastq file. Subsequently, these unmapped reads were re-aligned to sacCer3 genome and the generated aligned BAM file therefore contained reads that were unique to sacCer3. A same method was used to generate alignments unique to CBS138.
Genome_build: SaCer3

organism:
Saccharomyces cerevisiae
Nakaseomyces glabratus

source_name: ChIP Calibrated Nz Thiolutin Smc1-6HA Spt16-AID Biological

growth_protocol: Cells were arrested in G2/M by adding Nocodazole (1.5 mg/ml stock in DMSO 100%) to exponentially growing cultures (OD600=0.5) to a final concentration of 0.015 mg/ml. Once the cells were arrested in Nocodazole they were spun and resuspended in YPD containing fresh nocodazole (0.015 mg/ml) and IAA at a final concentration of 6mM for 2 hours. To inhibit transcription a stock of thiolutin at  1mg/ml in DMSO was added for 30 minutes to the culture at a final concentration of 10ug/ml. 87 OD600 units of S. cerevisiae were mixed with 43 OD600 units of asynchronous C. glabrata.

extract_protocol: Cells were fixed for 15 minutes at 25 °C, and quenched with glycine (final concentration 125 mM) for 7 minutes before cells were harvested by centrifugation at 4,000 r.p.m. for 1 minute. The cell pellets were washed in PBS and transferred to a screw cap tube and frozen on dry ice. The pellets were stored at -80 °C. Pellets were resuspended in 300 μl of IP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, NP-40 (0.05% v/v), Triton® X-100 (1% v/v)) containing phenylmethanesulfonyl fluoride (PMSF, final concentration 1 mM) and Complete protease inhibitor cocktail (without EDTA, from Roche). 500 μl of glass beads were added to the tubes. Cells were broken in a FastPrep® FP120 (BIO101) by 3 repetitions of a 20 seconds cycle, power setting 5.5. Cells were maintained on ice for 2 minutes after each cycle. The tubes were pierced with a hot needle and placed into new eppendorf and spun at 2000 r.p.m. for 2 minutes to collect the lysate. 100 μl of IP buffer containing PMSF and protease inhibitors were then added and tubes spun again at 2000 r.p.m. for 1 minute. The cell lysate was spun down for 10 minutes at 15,000 r.p.m at 4 °C. This pellet was resuspended in 1ml of IP buffer containing PMSF and protease inhibitors, and sonicated for 1 hour (30 seconds on, 30 seconds off) at high power at 4 °C in a Diagenode Bioruptor. After sonication samples were spun down for 10 minutes at 15,000 r.p.m. and the supernatant taken. 200 μl of the sonicated chromatin were taken as “input” and 400 μl was incubated with 40 μg of HA antibody (anti-HA 12CA5 from Roche) in a sonicator at low power for 30 minutes (30 seconds on, 30 seconds off). The “input” DNA was precipitated with 0.3 M sodium acetate and 2.5 volumes of cold ethanol and spun down at 15,000 r.p.m. for 30 minutes, and the supernatant removed. The pellet was washed with 70 % ethanol and air dried. After antibody binding the IP sample was spun down at 13,000 r.p.m for 5 minutes and the supernatant added to 60 μl of Dynabeads protein G (Invitrogen) previously    equilibrated with IP buffer. Then the samples were incubated for 2 hours at 4 °C in a rotating wheel and washed 5 times with IP buffer using a magnetic separator rack. Finally “input” samples and IP samples were resuspended in de-crosslinking buffer (TE 1X, 1 % SDS, 10 μg/ml RNase A , 1 mg/ml proteinase K) and incubated at 65 °C overnight. Samples were purified using ChIP DNA Clean & Concentrator kit (Zymoresearch) according to the manufacturer instructions

tag: chip antibody

value: Anti-HA antibody. Supplier name:Sigma-Aldrich. Catalog number 11666606001 Lot number 21900900 Clon 12CA5


title: ChIP_Calibrated_Nz_Smc1-6HA_Biological Replica 2

source_name: ChIP Calibrated Nz Smc1-6HA Biological

growth_protocol: Cells were arrested in G2/M by adding Nocodazole (1.5 mg/ml stock in DMSO 100%) to exponentially growing cultures (OD600=0.5) to a final concentration of 0.015 mg/ml. Once the cells were arrested in Nocodazole they were spun and resuspended in YPD containing fresh nocodazole (0.015 mg/ml) and IAA at a final concentration of 6mM for 2 hours. 87 OD600 units of S. cerevisiae were mixed with 43 OD600 units of asynchronous C. glabrata.


title: ChIP_Calibrated_Nz_Smc1-6HA WPL1D

source_name: ChIP Calibrated Nz Smc1-6HA WPL1D


title: ChIP_Calibrated_G1_Smc1-6HA Spt16-AID_Biological Replica 2

source_name: ChIP Calibrated G1 Smc1-6HA Spt16-AID Biological

growth_protocol: Cells were arrested in G1 by adding alpha factor to exponentially growing cultures (OD600=0.5) to a final concentration of 3 x 10-8 M. Once the cells were arrested in G1 IAA at a final concentration of 6mM was added for 3 hours. Finally Galactose was added to the culture to a final concentration of 2%. 87 OD600 units of S. cerevisiae were mixed with 43 OD600 units of asynchronous C. glabrata.


title: ChIP_Calibrated_Nz_Thiolutin_Smc1-6HA

growth_protocol: Cells were arrested in G2/M by adding Nocodazole (1.5 mg/ml stock in DMSO 100%) to exponentially growing cultures (OD600=0.5) to a final concentration of 0.015 mg/ml. Once the cells were arrested in Nocodazole they were spun and resuspended in YPD containing fresh nocodazole (0.015 mg/ml) and IAA at a final concentration of 6mM for 2 hours. During the las 30 minutes Thiolutin was added at a final concentration of 10ug/ml. 87 OD600 units of S. cerevisiae were mixed with 43 OD600 units of asynchronous C. glabrata.

tag: antibody


title: ChIP_Calibrated_Nz_Smc1-6HA Spt16-AID_Biological Replica 2

source_name: ChIP Calibrated Nz Smc1-6HA Spt16-AID Biological


title: ChIP_Calibrated_Nz_Thiolutin_Smc1-6HA Spt16-AID

source_name: Thiolutin_Smc1-6HA Spt16-AID


title: ChIP_Calibrated_G1_Untagged

source_name: Untagged


title: MP-14

source_name: liver hepatocytes


title: ChIP_Calibrated_Nz_Smc1-6HA Sth1-AID_Biological replica 2

source_name: ChIP Calibrated Nz Smc1-6HA Sth1-AID Biological


title: MP-0


title: MP-12


title: ChIP_Calibrated_Nz_Smc1-6HA Spt16-AID WPL1D

source_name: ChIP Calibrated Nz Smc1-6HA Spt16-AID WPL1D


title: ChIP_Calibrated_G1_Untagged_Biological Replica 2

source_name: ChIP Calibrated G1 Untagged Biological


title: ChIP_Calibrated_Nz_Untagged 2


title: ChIP_Calibrated_Nz_Smc1-6HA Sth1-AID

source_name: Smc1-6HA Sth1-AID


title: ChIP_Calibrated_Nz_Thiolutin_Smc1-6HA_Biological replica 2

source_name: ChIP Calibrated Nz Thiolutin Smc1-6HA Biological


title: ChIP_Calibrated_G1_Smc1-6HA


title: ChIP_Calibrated_G1_Smc1-6HA_Biological Replica 2

source_name: ChIP Calibrated G1 Smc1-6HA Biological


title: ChIP_Calibrated_Nz_Smc1-6HA Spt16-AID

source_name: Smc1-6HA Spt16-AID


title: ChIP_Calibrated_Nz_Untagged 1


title: ChIP_Calibrated_G1_Smc1-6HA Spt16-AID


title: RNA-Seq_Smc1-6HA Spt16-AID_Biological replica 2

data_processing:
Sequencing reads were aligned to the S.cerevisiae (SacCer3) genome using Bowtie. Aligned reads were sorted based on chromosomal position using samtools version 0.1.18, and RNA-seq read counts were computed for exonic regions of sacCer3-Ensembl genes using featurecounts function in Rsubread R package, where we removed all multiple aligned reads. Genome wide coverage of the RNASeq datasets were generated as bedGraph files using BEDTools and converted to Bigwig files. The differentially expressed genes were identified applying DESeq2 with padj < 0.001 and fold-change > 2.
Supplementary_files_format_and_content: .bw
Genome_build: SacCer3

growth_protocol: Cells were arrested in G2/M by adding Nocodazole (1.5 mg/ml stock in DMSO 100%) to exponentially growing cultures (OD600=0.5) to a final concentration of 0.015 mg/ml. Once the cells were arrested in Nocodazole they were spun and resuspended in YPD containing fresh nocodazole (0.015 mg/ml) and IAA at a final concentration of 6mM to degrade Spt16-AID for 2 hours.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Protect Kit. Total RNA was depleted for ribosomal RNA using Ribo-Zero Magnetic Kit (Illumina)
Libraries of mononucleosomal and ChIP DNA were constructed following the Illumina compatible NEXTflexTM ChIP-Seq kit protocol and sequenced in an Illumina NextSeq500 platform using the paired-end protocol. Reads were aligned to the S.cerevisiae (SacCer3) genome using Bowtie. Nucleosome occupancy maps were generated using the NUCwave algorithm.  Nucleosome fuzziness was analyzed using the dpos utility of DANPOS2 application. To make it compatible with NUCwave maps, we used the following parameters: a span of 1 bp and a read extension of 50 bp. ChIP-seq data representation was performed using the Model-based Analysis of ChIP-Seq (MACS) with a read extension of 147 bp.

value: Smc1-6HA Spt16-AID


title: RNA-Seq_Smc1-6HA Spt16-AID_Biological replica 1


title: RNA-Seq_Smc1-6HA_Biological replica 2


title: MNase-seq_G2

data_processing:
Paired-end Sequencing reads were aligned to Yeast genome sacCer3 using bowtie version 2.2.9 with default parameters. DANPOS2 was applied for two separate pair-wise comparisons at each nucleosome between G1 arrest and G2/M arrest, and G2/M arrest and G2/M +IAA. DANPOS output for pair-wise comparison contains a set of reference positions (with fixed length of 200bp) for nucleosomes defined by integrating all the nucleosomal positions called in each of the two conditions under study. The DANPOS-generated reference positions in two pair-wise comparisons were very similar but there was a small fraction of positions that did not overlap well in two comparisons. DANPOS also calculated Fuzziness scores for each condition and FDR and log10 p-value for each pair-wise comparison. We reported the nucleosomes with significant fuzziness change as reference nucleosomes in each comparison with FDR < 0.01 and p-value<-2, recommended in DANPOS manual. The fuzziness of these nucleosomes may be increased or decreased from one condition to the other. We also used DNAPOS-generated wig files for visualization of Fuzziness on IGV genome browser.
Supplementary_files_format_and_content:  .wig
Genome_build: SacCer3

growth_protocol: Exponentially growing cultures (OD600=0.5) were arrested in G1 in minimal media by adding α-factor to a final concentration of 3 x 10-8 M for 3 hours at 25 Celsius degrees. Cells were released from G1 by pelleting them (4,000 r.p.m, 1 min) and washing in YPD 3 times. The pellet was then resuspended in YPD containing 0.1 mg/ml pronase and to arrest cells in G2/M, Nocodazole (1.5 mg/ml stock in DMSO 100%) was added to a final concentration of 0.015 mg/ml for 2 hours

extract_protocol:
For MNase digestions 160 ml of cells (OD600=1) where fixed with 1 % formaldehyde for 30 minutes at 25 °C with 100 r.p.m. agitation and quenched with 125 mM glycine for 10 minutes at 25 °C with 100 r.p.m. agitation. Cells were spun and washed twice with PBS. Pellet was resuspended in 20 ml sorbitol/ tris buffer (1M sorbitol, 50 mM Tris-HCl pH 7.5, 10 mM β-mercaptoethanol) containing 10 mg of Zymolyase 20T and incubated at 30 °C for 5 minutes or until spheroplast were formed. Spheroplasts were spun at 3,000 r.p.m. for 5 minutes and washed with sorbitol/tris buffer without b-mercaptoethanol. Spheroplasts were resuspended in NP buffer (1 M sorbitol, 50 mM NaCl, 10mM Tris pH 7.5, 5 mM MgCl2, 1mM CaCl2, 1mM b-mercaptoethanol, 500 μM spermidine, 0.075 % NP40) and digested with 600, 1200 or 1800 U/ ml of MNase (NEB) for 20 minutes at 37 °C. MNase digestion was stopped adding 200 μl of STOP solution ( 5% SDS, 50 mM EDTA). DNA was decrosslinked by adding 1 mg/ml proteinase K and incubating at 65 °C overnight. DNA was purified by adding 0.6M potassium acetate pH 5.5 and incubating on ice 5 minutes and centrifuging 10 minutes at 3,500 r.p.m followed by a phenol chloroform extraction. Finally DNA was precipitated by adding 25 μg/ml glycogen, 1/25 columes NaCl, 0.7 volumes Isopropanol, incubating 30 minutes at -20 °C and centrifuging 30 minutes at 13,200 r.p.m. The pellet was washed in 70 % ethanol and resuspended in TE 1X. Samples were run in parallel in a 1.5 % agarose gel and the mononucleosomes of a digestion with a ratio of 80:20 mononucleosomes to dinucleosomes were purified and used in Next Generation Sequencing
Libraries of mononucleosomal and ChIP DNA were constructed following the Illumina compatible NEXTflexTM ChIP-Seq kit protocol and sequenced in an Illumina NextSeq500 platform using the paired-end protocol. Reads were aligned to the S.cerevisiae (SacCer3) genome using Bowtie. Nucleosome occupancy maps were generated using the NUCwave algorithm.  Nucleosome fuzziness was analyzed using the dpos utility of DANPOS2 application. To make it compatible with NUCwave maps, we used the following parameters: a span of 1 bp and a read extension of 50 bp. ChIP-seq data representation was performed using the Model-based Analysis of ChIP-Seq (MACS) with a read extension of 147 bp.

tag: treatment


title: B6.CAST_E6.5_ExE_H3K4me3_2

status: Public on Sep 19 2019

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

institute: Altos Labs

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_ExE_H3K4me3.txt
Allelic_H3K4me3_dedupH3K4me3peaks_ExE_Readcount.txt

data_processing:
Reads were trimmed using Trim Galore v0.4.4 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. Mapping of ChIP-Seq data was performed using Bowtie 2 v2.3.2 against N-masked genomes of the mouse GRCm38 assembly (Black6/CAST). The resulting hits were filtered to remove mappings with a MAPQ scores of < 20. Following alignment, reads were split allele-specifically using SNPsplit (v0.3.4, https://github.com/FelixKrueger/SNPsplit).
Peak calling for each histone mark in epiblast and ExE for B6/CAST and CAST/B6 reciprocal hybrids was done using chromstaR, using a bins size of 1kb and step size of 500bp
ChIP-seq relicates were quantitated as RPKM per 1kb running window
Allelic histone enrichment was calculated for each allelically mapped replicate over peaks (merging and deduplicating peaks from reciprocal hybrids for a given mark in a given tissue) as raw read counts
Genome_build: GRCm38
Supplementary_files_format_and_content: [ChIP RPKM report] Annotated SeqMonk report for 1kb running windows annotated to the nearest gene within 10kb. The report is tab-delimited probe coordinates and their log2(RPKM) values as follows: col 1: <ID>, col2: <Chromosome>, col 3: <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.
Supplementary_files_format_and_content: [Allelic peak report] Annotated SeqMonk report for peaks for the relevant mark and tissue, annotated to the nearest gene within 10kb. The report is tab-delimited probe coordinates and their log2(RPKM) values as follows: col 1: <ID>, col2: <Chromosome>, col 3: <Start>, col 4: <End>, col 5: <Probe strand> and then listed samples <columns 12-end>.
Supplementary_files_format_and_content: [Peak calling file] The peak calling files are tab delimited, and contain the following relevant information in columns 1-4: <chromosome>,<start>, <end>, <histone mark>

source_name: Extra-embryonic ectoderm

extract_protocol:
Reciprocal natural timed matings were set up between C57BL6/Babr and CAST animals (denoted as B6/CAST and CAST/B6), and embryos were collected on embryonic day 6.5 (E6.5).  Natural timed matings were set up between Dnmt3a floxed/floxed, Dnmt3b floxed/floxed, Zp3 +ve B6/129 females (resulting in ablation of DNA methylation in the oocyte) and CAST males (denoted as DKO.CAST). The epiblast (Epi) and extra-embryonic ectoderm (ExE) for each embryo were manually separated.  E6.5 epiblast (N=4) and ExE (N=8) samples were pooled (an estimated ~2500 cells), washed in PBS, and then flash frozen in 10µL of nuclear lysis buffer (Sigma).  Samples were thawed on ice and permeabilised with 0.1% Triton-X/0.1% deoxycholate in PBS on ice.  MNase digestion was completed using 200U of micrococcal nuclease (New England Biolabs) in prepared digestion buffer, as previously described (Brind'Amour et al. 2015 Nat Comm).  Samples were digested at 21°C for 7.5 minutes and the reaction was stopped with 100mM EDTA.  Chromatin samples were precleared with Protein A/G beads rotating at 4°C for 2 hours and antibodies were bound to beads rotating at 4°C for 3 hours.  Prior to the immunoprecipitation with antibody-bound beads, each chromatin sample was divided into 5 aliquots: one for each antibody, one 10% input and one 10% input for bisulphite sequencing.  For each immunoprecipitation, 250ng of anti-H3K4me3 (Diagenode K02921004), 125ng of anti-H3K27me3 (Millipore 07-449) and 250ng of anti-H3K36me3 (C15410192) was used.  Chromatin was added to the antibody-bound beads and rotated overnight at 4°C.  This was proceeded by two low-salt washes, one high-salt wash, and the DNA was then eluted from the beads at 65°C for 1.5 hours.  DNA from immunoprecipitated chromatin or input was purified using solid phase reversible immobilization (SPRI) purification using Sera-Mag carboxylate-modified Magnetic SpeedBeads (Fisher Scientific) at a 1.8:1 ratio.
Library preparation was completed using the MicroPlex Library Preparation kit v2 (Diagenode) using Sanger 8-base indices for multiplexing, as per the manufacturers recommendations, and all libraries were amplified using 15 amplification cycles.  Libraries were purified with SPRI beads at a 1:1 ratio, and size and quality were assessed using a 2100 Bioanalyzer Instrument (Agilent) and Kapa library qPCR quantitation (Illumina).  Samples were multiplexed using 75bp paired-end sequencing on Illumina NextSeq500.

value: Extra-embryonic ectoderm

value: Wildtype

tag: hybrid strain

value: C57BL6/Babr x CAST/Ei

value: anti-H3K4me3 (Diagenode K02921004)


title: B6.CAST_E6.5_ExE_H3K4me3_1

tag: tissue


title: MNase-seq_G1

growth_protocol: Exponentially growing culture (OD600=0.5) were arrested in G1 in minimal media by adding α-factor to a final concentration of 3 x 10-8 M for 3 hours at 25 Celsius degrees.

tag: strain


title: MEFs, Normoxia 3

status: Public on Aug 28 2019

city: Cologne

first: Thomas

last: MacVicar

address: Joseph-Stelzmann Str 9B

institute: Max Planck Institute for Biology of Ageing

data_processing:
raw reads were mapped using HISAT version 2.1.0
transcripts were assembled using StringTie version 1.3.4d
differential gene expression was analyzed using cufflinks/cuffdiff version 2.2.1
Genome_build: BUILD_GRCm38_RELEASE_91
Supplementary_files_format_and_content: Tab-separated differential gene expression results

source_name: WT MEF

growth_protocol: 1x10e6 cells were incubated in normoxia or hypoxia for 16 h.

extract_protocol:
Cell pellets were frozen in LN2 prior to extraction. Total RNA was extracted from cells using NucleoSpin RNA (Macherey-Nagel)
Libraries were prepared using the Illumina® TruSeq® mRNA stranded sample preparation Kit. Library preparation started with 1µg  total RNA. After poly-A selection (using poly-T oligo-attached magnetic beads), mRNA was purified and fragmented using divalent cations under elevated temperature. The RNA fragments underwent reverse transcription using random primers. This is followed by second strand cDNA synthesis with DNA Polymerase I and Rnase H. After end repair and A-tailing, indexing adapters were ligated. The products were then purified and amplified (14 PCR cycles) to create the final cDNA libraries. After library validation and quantification (Agilent tape station), equimolar amounts of library were pooled. The pool was quantified by using the Peqlab KAPA Library Quantification Kit and the Applied Biosystems 7900HT Sequence Detection System.

tag: cell type

value: SV40 immortalized mouse embryonic fibroblast

tag: genotype

value: WT

value: 21% oxygen


title: MNase-seq_G2_IAA

growth_protocol: Exponentially growing cultures (OD600=0.5) were arrested in G1 in minimal media by adding α-factor to a final concentration of 3 x 10-8 M for 3 hours at 25 Celsius degrees. Cells were released from G1 by pelleting them (4,000 r.p.m, 1 min) and washing in YPD 3 times. The pellet was then resuspended in YPD containing 0.1 mg/ml pronase and to arrest cells in G2/M, Nocodazole (1.5 mg/ml stock in DMSO 100%) was added to a final concentration of 0.015 mg/ml for 2 hours. Then IAA (Stock at 800mM in DMSO) was added for 2 hours at a final concentration of 8mM to deplete the cells in Scc1-AID.


title: MEFs, Normoxia 2


title: ChIP_Calibrated_Nz_Smc1-6HA


title: RNA-Seq_Smc1-6HA_Biological replica 1


title: B6.CAST_E6.5_ExE_H3K36me3_1

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_ExE_H3K36me3.txt
Allelic_H3K36me3_dedupH3K36me3peaks_ExE_Readcount.txt


title: B6.CAST_E6.5_ExE_H3K27me3_1

description:
ChIP_Epi_ExE_RPKM.txt
B6.CAST_ExE_H3K27me3.txt
Allelic_H3K27me3_dedupH3K27me3peaks_ExE_Readcount.txt

value: anti-H3K27me3 (Millipore 07-449)


title: B6.CAST_E6.5_ExE_H3K27me3_2


title: LV1433_explant_input

status: Public on Apr 02 2019

city: Berkeley

first: Axel

last: Visel

state: CA

address: 1 Cyclotron Road

institute: Lawrence Berkeley National Laboratory

description: input chromatin

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline)
Genome_build: hg38
Supplementary_files_format_and_content: *replicated.broadPeak, peaks called by MACS2 with a q-value <= 0.05

source_name: adult left ventricle, input ChIP

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen left ventricle tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp.  Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated  with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2500 or 4000.

value: left ventricle

tag: developmental stage

value: adult

tag: disease

value: idiopathic dilated cardiomyopathy (DCM)


title: 12569_PCW10_input

description: input chromatin

source_name: fetal heart, input ChIP

value: heart


title: 11963_CS22_input

description: input chromatin

source_name: embryonic heart, input ChIP


title: 12434_PCW10_input

description: input chromatin


title: LV1532_explant_input

description: input chromatin


title: LV1392_explant_input

description: input chromatin


title: LV1437_explant_input

description: input chromatin


title: LV1342_explant_input

description: input chromatin


title: LV1371_explant_input

description: input chromatin


title: LV1304_explant_input

description: input chromatin


title: B6.CAST_E6.5_ExE_H3K36me3_2


title: LV1072_explant_input

description: input chromatin


title: LV1275_explant_input

description: input chromatin


title: LV1223_explant_input

description: input chromatin


title: MEFs, Normoxia 1


title: LV1300_explant_input

description: input chromatin


title: LV1535_explant_input

description: input chromatin


title: LV1290_explant_input

description: input chromatin


title: LV1264_explant_input

description: input chromatin


title: 12522_PCW10_input

description: input chromatin


title: LV1033_explant_input

description: input chromatin


title: LV1452_donor_input

description: input chromatin


title: MP-29


title: LV1009_explant_input

description: input chromatin


title: LV1400_donor_input

description: input chromatin


title: LV1558_donor_input

description: input chromatin


title: LV1028_explant_input

description: input chromatin


title: LV1471_donor_input

description: input chromatin


title: LV1262_explant_input

description: input chromatin


title: LV1273_donor_input

description: input chromatin


title: LV1259_donor_input

description: input chromatin


title: LV1356_donor_input

description: input chromatin


title: LV1200_donor_input

description: input chromatin


title: LV1325_donor_input

description: input chromatin


title: LV1226_donor_input

description: input chromatin


title: LV1248_donor_input

description: input chromatin


title: LV1277_donor_input

description: input chromatin


title: LV1202_donor_input

description: input chromatin


title: LV1160_donor_input

description: input chromatin


title: LV1294_donor_input

description: input chromatin


title: LV1215_donor_input

description: input chromatin


title: LV1183_donor_input

description: input chromatin


title: LV1121_donor_input

description: input chromatin


title: HH19_HL_WT_input

status: Public on Nov 27 2018

city: Yokohama

first: Nayuta

last: Yakushiji-Kaminatsui

state: Kanagawa

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

country: Japan

institute: RIKEN Center for Integrative Medical Sciences

description: chick HH19 WT whole hindlimb bud input

data_processing:
Demultiplexed ChIP-seq reads were mapped onto the galGal5 or mm10 using Bowtie (Version 0.12.7) (Langmead et al., 2009), with parameters “-m1 –strata –best” according to the conditions described previously (Riising et al. 2014), and PCR duplicates were removed from mapped reads using samtools (Version 0.1.18) (Li et al., 2009)
By using bamCompare (Version 2.5.0), The ChIP data from H3K27ac, H3K27me3 and H3K4me1 and the input data were normalized and compared to compute the log2 of the number of reads ratio.
The CTCF ChIP data was normalized to obtain 1x depth of coverage by using bamCoverage (Version 2.5.0) (Ramirez et al. 2014, 2016). Peaks of CTCF were called by using MACS2 (Version 2.1.0.20151222) with q-value (0.01) and used for the CTCF motif orientation analysis as previously described (Rodríguez-Carballo et al. 2017)
All analysis was done with our Galaxy server (the Bioteam Appliance Galaxy Edition, https://bioteam.net, https://bioteam.net/products/galaxy-appliance) (Afgan et al. 2016).
Genome_build: mm10 or galGal5
Supplementary_files_format_and_content: bedgraph of log2 of the normalized number of reads ratio histone marks ChIP versus Input; bedgraph of the normalized 1x depth of CTCF coverage; bed of CTCF narrow peaks with q-value=0.01

organism: Gallus gallus

source_name: Hindlimb

extract_protocol:
Chromatin immunoprecipitated experiment was performed as previously described (Beccari et al. 2016). Micro-dissected limb tissues from mouse and chick embryos were cross-linked with 1% formaldehyde/PBS for 15 min at room temperature. Chromatin was sheared and used for each immunoprecipitation with anti-H3K27ac (ab4729, Abcam), anti-H3K27me3 (07-449, Merck Millipore), anti-H3K4me1 (ab8895, Abcam) and anti-CTCF (61311, Active Motif), respectively.
Libraries were prepared with at least 5 ng of purified DNA following Illumina TruSeq ChIP library preparation guide. Sequencing was performed with 100-bp single-end.

tag: breed

value: White Leghorn

tag: tissues

value: Whole hindlimb bud

value: wild type


title: Mmu_mbRG_DiI_rep3

status: Public on Oct 10 2018

data_processing:
Basecalling was performed with bcl2fastq v2.19.1
Reads were mapped using STAR v2.5.2b (--outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterType BySJout --outFilterMultimapNmax 1 --outSJfilterCountUniqueMin 8 3 3 3)
Abundance estimation was performed with STAR (--quantMode GeneCounts)
Genome_build: GRCm38, Ensembl v81
Supplementary_files_format_and_content: Raw counts and TPM normalized expression scores

source_name: medial basal radial glial cells

extract_protocol:
Total RNA was extracted using the RNAeasy Plus Mini kit (Qiagen) according to the manufacturer's instructions. Universally tailed poly-dT primer and template switching oligos were used to synthesize complete cDNA from half of the isolated mRNA.　Purified cDNA was amplified with the Advantage 2 DNA Polymerase, ultrasonically sheared and subjected to standard Illumina fragment library preparation using the NEBnext chemistries (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: Tubb-GFP/+

value: medial basal radial glial cells


title: Mmu_mbRG_DiI_rep1


title: F3273

status: Public on Mar 12 2018

city: Lund

first: Lao

middle: H

last: Saal

address: Scheelevägen 2, MV404B2

department: Department of Oncology and Pathology

country: Sweden

institute: Lund University

description:
ER/PgR/HER2/Ki67: 0 negative/normal/low, 1 positive/amplified/high
processed data file:
gene_expression_3273_samples_and_136_replicates_transformed.csv
transcript_expression_3273_samples_and_136_replicates.csv

data_processing:
Base-calling using manufacturer's on-instrument software.
Demultiplexing was done with Picard versions 1.120 or 1.128. IlluminaBasecallsToFastq parameters used were ADAPTERS_TO_CHECK=INDEXED, ADAPTERS_TO_CHECK=PAIRED_END, INCLUDE_NON_PF_READS=false
Filtering to remove reads that align (using Bowtie 2 with default parameters except -k 1 --phred33 --local) to ribosomal RNA/DNA (GenBank loci NR_023363.1, NR_003285.2, NR_003286.2, NR_003287.2, X12811.1, U13369.1), phiX174 Illumina control (NC_001422.1), and sequences contained in the UCSC RepeatMasker track (downloaded March 14, 2011).
Fragment size distribution (mean and width) for the alignment step was estimated for each sample using bowtie2 2.2.3 and 2.2.5. Parameter set during estimation were -fr, -k 1, --phred33, --local, and -u 100000, using human genome assembly GRCh38.
Remaining reads were aligned using TopHat2 2.0.12 or 2.0.13 (default parameters except for --mate-inner-dist X (estimated in previous step), --mate-std-dev Y (estimated in previous step), --library-type fr-firststrand, --no-coverage-search, --max-insertion-length 20, --max-deletion-length 20, --read-gap-length 20, --read-edit-dist 22) to the human genome reference GRCh38 together with 104,133 transcript annotations from the UCSC knownGenes table (downloaded September 22, 2014).
Gene expression data in FPKM were generated using cufflinks 2.2.1 (default parameters except –GTF, --frag-bias-correct GRCh38.fa, --multi-read-correct, --library-type fr-firststrand, --total-hits-norm, --max-bundle-frags 10000000). The resulting data was was post-processed by collapsing on 30,865 unique gene symbols (sum of FPKM values of each matching transcript), adding to each expression measurement 0.1 FPKM, and performing a log2 transformation.
PAM50 subtyping was performed using an implementation of the Parker method (Parker et al., J.Clin Oncol 2009). In short, to avoid context dependency when assigning PAM50 subtype by nearest-centroid, a fixed reference was selected to match the original cohort used by Parker et al. with respect to available clinical characteristics. Before subtyping tumors in this study, gene expression of the PAM50 genes for each tumor was centered to the reference set separately using custom R scripts.
Single-gene classifiers (SGCs) and multi-gene classifiers (MGCs) were trained for ER, PgR, HER2, Ki67 (SGC and MGC) and NHG (MGC only) on the expression of the single underlying gene (ESR1, PGR, ERBB2 or MKI67) or multiple genes (5000 most varying genes across all samples) of a 405 sample cohort using consensus pathology scores as labels. Classifier training was performed by selecting expression thresholds that maximize prediction concordance to the consensus scores (SGCs) and nearest shrunken centroids using the pamr R package (MGCs). The classifiers were used to predict the biomarker status in a validation cohort of 3273 samples from patients enrolled in the SCAN-B study.
Genome_build: Human genome reference GRCh38/hg38.
Supplementary_files_format_and_content: Gene expression in FPKM in CSV format.

source_name: Primary breast tumor

extract_protocol:
QIAGEN AllPrep
Poly(A) mRNA is isolated from the total RNA in up to 96-well microtiter plate format by two rounds of purification with Dynabeads Oligo (dT)25 (Invitrogen) using a KingFisher Flex magnetic particle processor (ThermoScientific). Zinc-mediated fragmentation (Ambion) is performed and the fragmented mRNA retrieved using column purification (Zymo-Spin I-96 plates; Zymo). The sequencing library generation protocol is a modification of the dUTP method, which importantly retains the directionality (stranded-ness) of the sequenced RNA molecules. First strand cDNA synthesis is performed using random hexamers and standard dNTP mix followed by cleanup using Sephadex gel filtration (Illustra AutoScreen-96A plates; GE Healthcare), and second strand cDNA synthesis is performed using dUTP in place of dTTP in the dNTP-mix and cleanup using Zymo-Spin I-96 plates. The cDNA is end-repaired and A-tailed, and diluted TruSeq adapters with barcodes are ligated using a modified protocol (Illumina). Adapter-ligated cDNA is then size-selected to remove short oligonucleotides using carboxylic acid (CA) paramagnetic beads (Invitrogen) and polyethylene glycol (PEG), similar to the previously described methods, and automated on the KingFisher Flex. The second cDNA strand is digested using uracil-DNA glycosylase and the product is enriched by 12 PCR cycles (Illumina). The PCR product undergoes two cycles of size selection using CA-beads and varying concentrations of PEG, first to exclude DNA fragments >700 bp and then to exclude fragments <200 bp. Quality control is performed on control libraries using Qubit fluorometric measurement (Life Technologies) and Caliper LabChip XT microcapillary gel electrophoresis. Typically, 10-24 barcoded libraries are included in a pool and each pool is sequenced in at least one lane across dual flowcells. Paired-end sequencing of 50 bp read-length is performed on an Illumina HiSeq 2000 or NextSeq 500 instrument.

tag: scan-b external id

tag: instrument model

value: NextSeq 500

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

value: NodePositive

tag: er status

tag: pgr status

tag: her2 status

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

tag: her2 prediction sgc

tag: ki67 prediction sgc

tag: pam50 subtype

value: LumA

tag: overall survival days

tag: overall survival event

tag: endocrine treated

tag: chemo treated


title: F3266

tag: scan-b external id

tag: instrument model

tag: age at diagnosis

tag: tumor size

tag: lymph node group

tag: lymph node status

tag: er status

tag: pgr status

tag: her2 status


title: F3245

value: NodeNegative

tag: ki67 status

tag: nhg

tag: er prediction mgc

tag: pgr prediction mgc

tag: her2 prediction mgc

tag: ki67 prediction mgc

tag: nhg prediction mgc

tag: er prediction sgc

tag: pgr prediction sgc

value: LumB


title: HH19_HL_WT_H3K27ac

description: chick HH19 WT whole hindlimb bud H3K27ac

tag: breed

tag: age

tag: tissues

tag: genotype

tag: antibody


title: Mmu_mbRG_DiI_rep4

tag: strain

tag: Stage

tag: tissue


title: WT P14 B: Pregnant day 14, rep 2

status: Public on Mar 05 2019

type: RNA

description: Gene expression data from MECs following secretory differentiation.

hyb_protocol: Array Strips Hybridization for the GeneAtlas® Instrument was carried out according to the Affymetrix protocol hybridizing array strips on the GeneAtlas® System.

scan_protocol: Array strips were scanned using the GeneAtlas™ Imaging Station according to the Affymetrix protocol.

data_processing: Raw data were GC-RMA (robust multiarray averaging) normalized, log2 transformed, and statistics performed using the Partek Genomic Suite (Partek, St. Louis, MO).

label: Biotin

source_name: Mammary Epithelial Cells, depleted of mammary adipocytes, at pregnant day 14

label_protocol: Biotinylated sense-strand DNA targets from total RNA were generated according to the Affymetrix WT PLUS Reagent Kit for GeneChip® Whole Transcript (WT) Expression Arrays

growth_protocol: FVB mothers were staged for pregnancy by post coital plug and sacrificed at either day 14 of pregnancy or day 4 of lactation (day 1 is the first morning litters are born).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was cleaned up and DNA was digested on column according to the Qiagen Rneasy mini kit.

treatment_protocol: Mammary Epithelial Cells (MEC) at pregnant day 14 and lactation day 4 were depleted of the mammary adipocytes by rapid enzymatic tissue digestion (PMID: 20739508), washed with PBS, pelleted, and snap frozen for total RNA expraction.

value: FVB

tag: Sex

value: female

value: Mammary Epithelial Cells depleted of mammary adipocytes

tag: parity

tag: stage of mammary development

value: Secretory Differentiation


title: WT L4 A: Lactation day 4, rep 1

description: Gene expression data from MECs following secretory activation.

source_name: Mammary Epithelial Cells, depleted of mammary adipocytes, at lactation day 4

value: Secretory Activation


title: WT P14 C: Pregnant day 14, rep 3


title: Mmu_mbRG_DiI_rep2


title: WT P14 F: Pregnant day 14, rep 4


title: WT L4 B: Lactation day 4, rep 2


title: L-428

status: Public on Jan 22 2019

first: Claudia

last: Pommerenke

address: Inhoffenstraße 7B

institute: Leibniz Institute DSMZ

hyb_protocol: Samples were prepared for and measured on Affymetrix HGU133plus2 Chip (Santa Clara/CA).

scan_protocol: GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).

data_processing: After RMA-background correction, quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.

label: biotin

source_name: Hodgkin lymphoma cell line

label_protocol: Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.

extract_protocol: Total RNA was extracted using Trizol reagent.

tag: cell line

tag: cell type

value: Hodgkin lymphoma cell line


title: KM-H2


title: WT L4 C: Lactation day 4, rep 3


title: WT L4 E: Lactation day 4, rep 4


title: L-540


title: SUP-HD1


title: HDLM-2