title: PFC-WT21-14-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107386


title: PFC-SERT-KO70-5-3

status: Public on Oct 01 2020

type: SRA

city: Nijmegen

first: Jo Huiqing

last: Zhou

address: Geert Grooteplein 26/28

country: Netherlands

institute: Radboud University

library_source: transcriptomic

data_processing:
42bp reads were mapped to the rat genome build rn4 using bwa version 0.6.1
BedGraph tracks were generated from BAM files using 'bedtools genomecov', normalized using the '-scale' option
Genome_build: rn4
Supplementary_files_format_and_content: Gzip-compressed bedgraph files that can be uploaded to the UCSC genome browser as custom tracks.
Supplementary_files_format_and_content: Tab-separated file with normalized Ensembl gene expression values in Fragments per Kilobase per Million mapped reads (FPKM) for all samples, as calculated by the cufflinks program.

molecule: total RNA

organism: Rattus norvegicus

source_name: PFC, SERT KO70

extract_protocol:
RNA extraction was carried out using RNeasy lipid tissue kit (QIAGEN, Venlo, The Netherlands)
2.5 μg RNA was used for rRNA depletion using the Ribo‐Zero rRNA Removal Kit (Human/Mouse/Rat, Epicentre, Madison, Wisconsin, USA) according to the manufacturer's recommendations. RNA fragmentation reactions were performed using fragmentation buffer (5x; 200 mM Tris‐Ac, 500 mM potassium‐Ac, 150 mM magnesium‐Ac, pH 8.2) in a final concentration of 1x per reaction. Fragmentation reactions were incubated at 95°C for 4 min on a thermal cycler and placed on ice for 10 min. Fragmented rRNA-depleted RNA was purified using ethanol precipitation, First and second strand synthesis was performed as described by Kouwenhoven and colleagues (2015). samples were prepared for sequencing by end repair of 5 ng total DNA as measured by Qubit dsDNA HS (Invitrogen). NEXTflex adaptors (Bioo scientific, Austin, Texas, USA) were ligated to the DNA fragments, followed by post-ligation cleanup using Agencourt AMPure XP beads (Beckman Coulter, Woerden, The Netherlands), library amplification by PCR (10 cycles) and size selection (∼300 bp) using Agencourt AMPure XP beads (Beckman Coulter). Quality control of DNA libraries prepared for sequencing was performed by qPCR and by running the products on a Bioanalyzer (Bio-Rad, Veenendaal, The Netherlands). Cluster generation and sequencing (50 bp, single end reads) was performed with the Illumina HiSeq 2000 sequencer according to standard Illumina protocols. Samples were sequenced to a depth of approximately 29 million reads per sample. Reads were aligned to the rn4 rat genome assembly using the gsnap program

tag: strain

value: Wistar

tag: genotype/variation

value: SERT knock-out

tag: developmental stage

value: Post-natal day 70

tag: tissue

value: prefrontal cortex


title: PFC-SERT-KO70-5-2


title: PFC-SERT-KO70-1-2


title: PFC-WT21-14-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107385

source_name: PFC, WT21

value: WT

value: Post-natal day 21


title: PFC-SERT-KO35-9-3

source_name: PFC, SERT KO35

value: Post-natal day 35


title: PFC-WT14-21-3

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107384

source_name: PFC, WT14

value: Post-natal day 14


title: PFC-SERT-KO35-7-3


title: PFC-SERT-KO35-7-2


title: PFC-WT14-19-1

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107380


title: PFC-SERT-KO21-17-2

source_name: PFC, SERT KO21


title: PFC-SERT-KO21-13-4


title: PFC-SERT-KO21-18-1


title: PFC-SERT-KO14-23-3

source_name: PFC, SERT KO14


title: PFC-SERT-KO21-17-1


title: PFC-SERT-KO14-24-2


title: PFC-WT8-25-2

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107375

source_name: PFC, WT8

value: Post-natal day 8


title: PFC-SERT-KO14-24-1


title: PFC-SERT-KO21-13-1


title: PFC-SERT-KO14-22-1


title: PFC-SERT-KO8-30-5

source_name: PFC, SERT KO8


title: PFC-SERT-KO8-30-1


title: PFC-SERT-KO35-9-5


title: PFC-SERT-KO8-29-4


title: PFC-SERT-KO8-28-1


title: PFC-SERT-KO35-12-3


title: RNAseq_Tcells_Candida_albicans_IMQ_rep2

status: Public on Sep 22 2020

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

country: USA

institute: NIH

description: mRNA

data_processing:
RNA-seq samples were trimmed and subsequently mapped to the mm10 mouse genome with STAR and quality control was performed with FastQC. Gene expression was assessed using HOMER’s analyzeRepeats with parameters rna, mm10, -count exons -condenseGenes. Raw data is shown as TPM (transcripts per million). Principle component analysis (PCA) was done with R. Differential expression was calculated using DESeq2. Genes were considered differentially expressed with false discovery rate (FDR) < 0.01 and fold change > 2. Gene ontology analysis was done with metascape or Ingenuity Pathway Analysis (IPA) (Qiagen).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include TPM values for each sample.

organism: Mus musculus

source_name: CD4+CD90.2+TCRb+Foxp3- from ear pinnae

growth_protocol: Whole tissue were taken from whole ear pinnae of mice. CD45+CD4+CD90.2+TCCRb+Foxp3-DAPI- Tcells were sorted on a BD FACs Aria from ear pinnae of mice.

extract_protocol:
RNA was extracted using a Arcturus PicoPure RNA Isolation Kit (Applied Biosystems).
For T cell RNA-seq the Clontech SMARTer Ultra low mRNA library preparation kit was used and samples were sequenced paired-end on an Illumina HiSeq 4000. For whole tissue RNA-seq, the RNeasy Fibrous Tissue Mini Kit (Qiagen) was used and samples were sequenced single-end on an Illumina NextSeq 500.

treatment_protocol: Candida albicans was associated topically for 8 days every other day. Imiquimod was applied every day for 5 days.

value: Skin, T cells

tag: treatment

value: Candida albicans and IMQ association


title: PFC-SERT-KO8-29-5


title: RNAseq_Tcells_Candida_albicans_IMQ_rep3

description: mRNA


title: RNAseq_Tcells_IMQ_rep1

description: mRNA

value: IMQ association


title: RNAseq_Tcells_Candida_albicans_rep2

description: mRNA

value: Candida albicans association


title: RNAseq_Tcells_Candida_albicans_IMQ_rep1

description: mRNA


title: RNAseq_Tcells_Candida_albicans_rep1

description: mRNA


title: RNAseq_Tcells_IMQ_rep3

description: mRNA


title: RNAseq_Tcells_IMQ_rep2

description: mRNA


title: RNAseq_whole_tissue_Candida_albicans_IMQ_rep2

description: mRNA

source_name: Whole tissue from ear pinnae

value: Skin, whole tissue


title: RNAseq_whole_tissue_Candida_albicans_IMQ_rep3

description: mRNA


title: PFC-SERT-KO14-22-3


title: RNAseq_whole_tissue_Candida_albicans_rep3

description: mRNA


title: RNAseq_whole_tissue_Candida_albicans_IMQ_rep1

description: mRNA


title: RNAseq_whole_tissue_Candida_albicans_rep2

description: mRNA


title: RNAseq_whole_tissue_Candida_albicans_rep1

description: mRNA


title: RNAseq_whole_tissue_IMQ_rep1

description: mRNA


title: RNAseq_whole_tissue_IMQ_rep2

description: mRNA


title: RNAseq_whole_tissue_naive_rep3

description: mRNA

value: Naive


title: PFC-WT14-20-6

description:
rat_WT_PFC_FPKM_table.txt
Identical (raw data, processed data) to GSM2107383


title: RNAseq_whole_tissue_naive_rep2

description: mRNA


title: RNAseq_whole_tissue_naive_rep1

description: mRNA


title: RNAseq_Tcells_Candida_albicans_rep3

description: mRNA


title: RNAseq Mbd5 shRNA

status: Public on Sep 14 2020

data_processing:
Reads were aligned using the STAR version 2.5.2b
Count files (Read counts per gene) were then used in differential expression analysis performed with the DESeq2  package
Genome_build: RNOR 6.0.88 Rat Genome
Supplementary_files_format_and_content: counts

source_name: primary Cortical neurons

growth_protocol: primary neurons were isolated from embryonic day 18 brians and cultured for 21 days in vitro

extract_protocol:
21 days old neurons were isolated,  RNA was harvested using Trizol reagent.500 ng of total RNA for the construction of sequencing libraries.
The library quantification was performed with the KAPA Library Quantification Kit (Kapa Biosystems #KK4844) followed by pair-ended sequencing with NextSeq500 (Ilumina)

tag: days in vitro

value: 21 days in vitro


title: RNAseq Mll3 shRNA


title: RNAseq Smarcb1 shRNA


title: RNAseq control


title: RNAseq Ehmt1 shRNA


title: Input DNA

status: Public on Sep 10 2020

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

description: input genomic DNA

library_source: genomic

data_processing:
75-nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the mouse genome mm9 using the BWA algorithm.
Only the unique tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.

molecule: genomic DNA

source_name: control, input DNA

growth_protocol: Mice were virgin, aged to at least 7.5 months on normal rodent chow.

extract_protocol:
Chromatin samples were prepared by Active Motif Services - Factor Path assays
Libraries were prepared by Active Motif Services - Factor Path assays

treatment_protocol: Ovarian neoplasia tissue was flash frozen and sent to Active Motif for factor path chromatin immunoprecipitation and sequencing.

value: ovarian tumor

tag: genotype

value: PGRcre/+mPGRBLsL/+

tag: chip antibody


title: Ovarian tumor PGR-ChIPseq

description: PGR-bound genomic DNA

source_name: Ovarian tumor PGR-ChIPseq

value: Progesterone Receptor (Santa Cruz, sc-7208)


title: RNAseq_whole_tissue_IMQ_rep3

description: mRNA


title: tumor_RU486_rep3

type: RNA

description: RNA isolated from tumor treated with RU486 pellet

hyb_protocol: Hybridized on GeneTAC HybStation according to manufacturer's protocol.

scan_protocol: ScanArray 5000 was utilized to scan the products according to manufacturer's instructions.

data_processing: Data was processed using Partek Genomics Suite with Gene Expression Platform

label_protocol: Total RNA was labeled with Amino-Allyl of total RNA with Cy3

growth_protocol: Mice were housed and provided normal rodent chow.

extract_protocol: RNA was isolated using TRIzol reagent (Invitrogen) and aqueous phase isolation was performed twice with 1-Bromo-3-chloropropane and chloroform. RNA was precipitated with ethanol and applied to the Qiagen mRNEasy RNA mini prep kit for cleanup and elution following manufacturer's protocol (Qiagen). RNA quality control was assessed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: PGR-B expressing mice with an ovarian tumor size between 0.5-1 cm in diameter were treated with chronic release RU486 or placebo pellet for 24 hours before tissue harvest.

value: Pgrcre/+mPgrLsL/+


title: tumor_placebo_rep1

description: RNA isolated from tumor treated with placebo pellet

value: placebo


title: G1

status: Public on Aug 18 2020

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Data were analyzed using Cell Ranger™ v3.0.1 pipelines which is available in 10x Genomics website.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: h5: Contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis.
Supplementary_files_format_and_content: *tsv, *mtx: Gene barcode matrices and feature barcode matrix.

source_name: day 5

extract_protocol:
Cardiac cells were collected at different time points after myocardial infarction (no infarct/Day 0: n=5; Day 1: n=5; Day 3: n=5, Day 5: n=5; Day 7: n=3) as described above. Cell suspensions were incubated for 10 minutes at 4°C with 10μg/ml Fc Block (purified rat anti-mouse CD16/CD32, Biolegend TruStain FcX anti-mouse) to block non-specific binding of antibodies to Fc Receptors and then incubated at 4°C for 30 minutes with anti-CD45-PE (1:300, Thermofisher Scientific, Clone 30-F11), anti-Ly6G-V450 (1:300, BD Biosciences, Clone 1A8) and Fixable Viability Staining e780 (1:1000, Thermofisher Scientific). All staining and washing steps were performed in PBS containing 1% FCS, except the last wash and sorting that were made in PBS supplemented with 0.04% BSA (Sigma Aldrich, SRE0036). Right before sorting, cells were passed through a 40µm cell strainer. In this experiment, a neutrophil reduction step was performed to increase the proportion of monocyte/macrophages at early time points. Viable CD45.2 (intravenous)-negative/CD45+ cells were sorted using a FACS-Aria III (BD Biosciences) with a 100µm nozzle, counted and loaded into the 10X Genomics Chromium.
Cells were loaded in the 10X Genomics Chromium at concentrations recommended by the manufacturer. Libraries were prepared with Chromium Single Cell 3’ Reagents Kit v2 Chemistry.

treatment_protocol: Mice were anesthetized with isoflurane (4.0%), received an intravenous injection of 5µg of anti-CD45.2-APC (clone 104, ThermoFisher Scientific) in 100µl of PBS, and left under isoflurane anesthesia for 5-10 minutes before being killed by cervical dislocation. Induction of myocardial infarction was macroscopically confirmed and mice received an intracardiac perfusion of PBS and the hearts were collected. The right ventricle was removed as well as the viable myocardium right above the ligature site, so that the infarcted area, its border zone and the adjacent viable myocardium were processed. A similar part of the left ventricle was processed for non-infarcted hearts. The excised hearts were rinsed in 4°C RPMI and gently massaged to expel excess blood, minced with surgery scissors and digested in RPMI containing 450U/ml collagenase I (Sigma-Aldrich C0130), 125U/ml collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich H3506) for 1 hour at 37°C in a Thermomixer (Eppendorf) with shaking set at 1000rpm. The resulting cell suspension was filtered through a 70µm cell strainer, and incompletely digested pieces of myocardium were gently dissociated using a syringe plunger. Cells were then washed in 50ml 4°C PBS containing 1% Fetal Bovine Serum (centrifugation 8 minutes at 300rcf).

tag: Sex

value: Male

tag: condition

value: Myocardial infarction

tag: cell type

value: CD45+ total leukocytes from heart

tag: time point

value: Day 5


title: F12

source_name: day 3

value: Day 3


title: tumor_placebo_rep2


title: Pgrcre/+ ovary, bioreplicate 6

description: Gene expression of ovary at 23wk diestrus stage

hyb_protocol: The labeled RNA was added with 3X SSC, 2X Denhardt's, 0.3X SDS, heated for 2min at 100°C, incubated for 10min at RT.

scan_protocol: The probe array cartriage was scanned using the GeneChip Scanner 3000,

data_processing: The summary of probe cell indensity data (CEL file) was generated using GeneChip Command Console Software.

label: biotin

source_name: Ovaries from Pgrcre/+ mice at 23 weeks old diestrus stage

label_protocol: 10µg RNA was mixed with 35µg Cy3, 35µg Cy5, 8µg polyA RNA, 20µg tRNA yeast, and bring to 26µl by TE buffer.

growth_protocol: The female mice were fed with normal chow, and housed with its female littermates until 23 weeks old.

extract_protocol: RNA was extracted using Trizol and aqueophase separation method, and futher purified by Qiagen Rneasy mini kit.

treatment_protocol: The estrous stage of the female mice were evaluated by vagina smear. At diestrus, the mice were euthanized, and the ovary was collected for RNA isolation.

value: ovary

value: Pgrcre/+

tag: tumor progression stage

value: No tumor


title: Pgrcre/+PgrBLsL/+ stage I ovary, bioreplicate 1

source_name: Ovaries from Pgrcre/+PgrBLsL/+ mice at 23 weeks old diestrus stage

value: Pgrcre/+PgrBLsL/+

value: Stage I


title: Pgrcre/+PgrBLsL/+ stage II ovary, bioreplicate 1

value: Stage II


title: Pgrcre/+PgrBLsL/+ stage II ovary, bioreplicate 2


title: Pgrcre/+PgrBLsL/+ stage II ovary, bioreplicate 3


title: Pgrcre/+ ovary, bioreplicate 2


title: Ovarian Neoplasia_cycling_rep1

description:
RNA isolated from total ovarian neoplasm
39423_LsL/+

source_name: ovarian neoplasia, cycling, rep1

treatment_protocol: Cycling mice were euthanized and ovaries obtained and flash frozen

value: ovarian neoplasia

tag: disease state

value: tumorigenic


title: Pgrcre/+ ovary, bioreplicate 3


title: RNA-seq: T_Cell_KO_Thymus_rep4

status: Public on Jul 29 2020

city: Amsterdam

first: Fred

last: van Leeuwen

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
Mapped reads were counted using htseq-count version 0.9.1 and Ensembl GRCm38.90 gtf files with the following arguments: ‘-m union -s no -f bam’
Genome_build: mm10
Supplementary_files_format_and_content: comma seperated values with one column per sample and one row per gene containing raw counts

source_name: KO Thymus

extract_protocol:
CD8 T cell subsets were flow cytometrically sorted and resuspended in Trizol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of Flow cytometrically purified cells were resuspended in Trizol (Ambion Life Technologies) and total RNA was extracted according to the manufacturer’s protocol. Quality and quantity of the total RNA was assessed by the 2100 Bioanalyzer using a Nano chip (Agilent). Only RNA samples having an RNA Integrity Number (RIN) > 8 were subjected to library generation.
Strand-specific cDNA libraries were generated using the TruSeq Stranded mRNA sample preparation kit (Illumina) according to the manufacturer’s protocol. The libraries were analyzed for size and quantity of cDNAs on a 2100 Bioanalyzer using a DNA 7500 chip (Agilent), diluted and pooled in multiplex sequencing pools. The libraries were sequenced as 65 base single reads on a HiSeq2500 (Illumina).

value: Thymus CD8 SP


title: Ovary_cycling_rep3

description:
RNA isolated from total cycling ovary
40549_WT

source_name: ovary, cycling, rep1

value: healthy

value: Wildtype


title: Pgrcre/+PgrBLsL/+ stage I ovary, bioreplicate 3


title: RNA-seq: T_Cell_KO_Thymus_rep3


title: Pgrcre/+ ovary, bioreplicate 5


title: Pgrcre/+ ovary, bioreplicate 4


title: tumor_RU486_rep2

value: Pgrcre/+mPgrLsL/+


title: Ovary_cycling_rep1

description:
RNA isolated from total cycling ovary
39503_WT


title: Ovarian Neoplasia_cycling_rep4

description:
RNA isolated from total ovarian neoplasm
39426_LsL/+


title: Ovary_cycling_rep2

description:
RNA isolated from total cycling ovary
39504_WT


title: tumor_placebo_rep3

value: placebo


title: Ovarian Neoplasia_cycling_rep5

description:
RNA isolated from total ovarian neoplasm
39427_LsL/+


title: Ovarian Neoplasia_cycling_rep2

description:
RNA isolated from total ovarian neoplasm
39424_LsL/+


title: Ovarian Neoplasia_cycling_rep3

description:
RNA isolated from total ovarian neoplasm
39425_LsL/+


title: tumor_RU486_rep1


title: Pgrcre/+ ovary, bioreplicate 1


title: Pgrcre/+PgrBLsL/+ stage I ovary, bioreplicate 2


title: RNA-seq: T_Cell_KO_Thymus_rep2


title: RNA-seq: T_Cell_KO_Thymus_rep1


title: RNA-seq: T_Cell_WT_Thymus_rep3

source_name: WT Thymus


title: RNA-seq: T_Cell_WT_Thymus_rep2


title: RNA-seq: T_Cell_WT_Thymus_rep1


title: Stage 8 rRNA deplete

status: Public on Jun 28 2020

city: Pittsburgh

first: Miler

middle: T

last: Lee

state: PA

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description:
xl_tpm.tsv
st8_rrna

data_processing:
Reads were mapped to the X. laevis v9.2 or GRCz11 (zebrafish) genomes using HISAT2 v2.0.5 (--no-mixed --no-discordant)
Mapped reads were assigned to genes (Xenbase v9.2 models for X. laevis and Ensembl r99 for zebrafish) using featureCounts v1.5.1 in reversely-stranded paired-end mode with default parameters.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: X. laevis v9.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited transcripts per million (TPM) per gene

organism: Xenopus laevis

source_name: Whole embryos

extract_protocol:
For X. laevis, 2 embryos were pooled for RNA extraction; for D. rerio, 20 embryos or 10 fin clips were pooled. Samples were snap frozen in a 1.5ul tube and homogenized with a pestle in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -80C for 1 hour. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop. RNA was stored at -80C until use.
For rRNA depletion, 1ul of antisense nuclear rRNA oligos (final concentration 0.4 uM per oligo) and 1ul of antisense mitochondrial rRNA (plus any other targeted gene) oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 minutes (standard) or 45C for 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo Clean and Concentrator-5 (Zymo #D4013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. For poly(A) selection, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L) was used according to the manufacturer’s protocol: 1 ug of total RNA was denatured at 65C for 5 minutes then hybridized to buffered dT magnetic beads at room temperature for 2 minutes. Selected RNA was eluted in 50uL of Tris buffer at 80C for 2 minutes and rehybridized to the same beads for a second round of selection at room temperature for 2 minutes. Re-selected RNA was eluted in a final volume of 17 uL of Tris buffer. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing (paired end 38/37bp) on an Illumina NextSeq 500 at the Health Sciences Sequencing Core at Children's Hospital of Pittsburgh.

tag: processing

value: rRNA depleted


title: C57 IMQ Dermis

status: Public on May 13 2020

city: Shanghai

first: Fangzhou

last: Lou

address: 280 South Chongqing Road

department: Shanghai Institute of Immunology

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were processed using Cell Ranger software provided by 10x Genomics.
Genome_build: mm10
Supplementary_files_format_and_content: tsv files with barcodes and genes
Supplementary_files_format_and_content: mtx files with gene counts for every gene and every cell with a unique barcode

source_name: skin

extract_protocol:
Single cell suspensions were generated through enzyme digestion and dead cells were removed using FACS.
Libraries were generated using Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.

treatment_protocol: C57BL/6 mice were treated with imiquimod for 5 consecutive days on the ear.

value: wild type

value: dermis

tag: age

value: 10 week

value: imiquimod


title: RNAseq_MHCII_neg_keratinocytes_control_epidermis_rep4

status: Public on Apr 14 2020

description: RNA-seq from MHCII negative keratinocytes from epidermis under control condition - replicate 4

data_processing:
Sequencing quality of the raw read data was assessed using FASTQC v0.11.5, following which FASTQ files were used as input for RSEM v1.3.01 (which was internally configured to use the bowtie2 aligner, version 2.2.6). Expected read counts from RSEM were imported into the DESeq2 Bioconductor package2, normalized using the geometric-mean based approach built into this package and then tested for differential expression between groups using a Wald test with multiple testing correction using the Benjamini-Hochberg False Discovery Rate method.
Genome_build: mm10

extract_protocol:
Keratinocytes were FACsorted from the epidermis of ear pinnae of C57BL/6 mice from naïve mice or day 14 post topical association with S. epidermidis NIHLM087. CD49f+Sca-1+ Keratinocytes were sorted as CD45-CD31-CD34- cells and further separated based on their expression of MHCII. RNA was extracted from 60 000 keratinocytes per replicate using the RNAeasy micro Kit for RNA Isolation (Qiagen), as per manufacturer’s instructions.
mRNA libraries were constructed using SMARTer Ultra Low Input RNA kit (Clonetech) + Nextera XT DNA library prep kit (Illumina).
mRNA samples were pooled and sequenced paired-end for 75bp on 1 lane of a Illumina NextSeq500.

treatment_protocol: Staphylococcus epidermidis strain  NIHLM087 was cultured for 18 hours in tryptic soy broth at 37°C. For topical association of bacteria, each mouse was associated with a bacterial suspension (approximately 109 CFU/ml) across the surface of the ear pinnae (approximately 36 cm2) using a sterile cotton swab. Application of bacterial suspension was repeated four times every other day before analysis.

value: epidermis

value: MHCII negative keratinocytes

value: Ctrl


title: RNAseq_MHCII_pos_keratinocytes_D14_Sepi_epidermis_rep1

description: RNA-seq from MHCII positive keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 1

value: Staph. Epi. D14


title: RNAseq_MHCII_neg_keratinocytes_D14_Sepi_epidermis_rep3

description: RNA-seq from MHCII negative keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 3


title: RNAseq_MHCII_neg_keratinocytes_D14_Sepi_epidermis_rep2

description: RNA-seq from MHCII negative keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 2


title: RNAseq_MHCII_neg_keratinocytes_D14_Sepi_epidermis_rep4

description: RNA-seq from MHCII negative keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 4


title: RNAseq_MHCII_pos_keratinocytes_D14_Sepi_epidermis_rep2

description: RNA-seq from MHCII positive keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 2


title: C2C12, MH2A1.1 ChIP-seq sample

status: Public on Apr 03 2020

city: Badalona

first: Roberto

last: Malinverni

state: Barcelona

address: Josep Carreras Building, Ctra de Can Ruti,

country: Spain

institute: Josep Carreras Leukaemia Research Institute

data_processing:
Illumina Casava1.7 software used for basecalling.
After data cleaning and trimming, reads were aligned to the mouse genome (mm9) using Bowtie 2 version 2.0.6, with sensitive pre-setting option (-D 15 -R 2-L 22 -i S,1,1.15). Enriched genomic regions for multiple overlapping ((peaks) EPIC2) were used to identify enriched regions using default parameters.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig files for DM1-11 sample and IPDM input
Supplementary_files_format_and_content: bed file with peaks calling results

source_name: myoblast

growth_protocol: Proliferative C2C12 grow in growth medium (GM) composed of DMEM (Gibco) with 20% FBS (Invitrogen) supplemented with 1% Pyruvate, 1% Glutamate and 1% Penicillin-Streptomycin (Gibco). Differentiation of C2C12 cells was achieved by replacing GM to differentiation media (DM) were FBS was exchanged by 2% of horse serum (Gibco). Fresh medium was added every two days. Proliferative C2C12 and mature myotubes were collected by scraping after PBS washing.

extract_protocol:
Chromatin immunoprecipitation were performed as in Buschbeck et al., 2009. 10 ng of enriched DNA was used for library generation and parallel sequencing on Illumina genome Analyzer at the CRG Genomics Unit (CRG Core Facilities). DNA quality was controled by High Sensitivity Qubit. From 10 ng of DNA, the sequencing was performed on single read (SR), with an average length of reads of 50 bp, 30 000 reads per sample, on an Illumina HiSeq2500 sequencer.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: cell line

value: Wild Type

value: anti-macroH2A1.1 (generated by laboratory of Prof. Kerstin Bistriky)


title: KD mH2A1.2 rep2

data_processing:
Illumina Casava1.7 software used for basecalling.
For “quasi”aligmen and raw reads counts : salmon software 0.13.1 (Patro et al., Nature Methods. 2017) -salmon quant -l A
Satatistical analysis preformed using DESq2
Genome_build: mm10
Supplementary_files_format_and_content: Comma separated table with raw counts  for all samples (one sample for each column)
Supplementary_files_format_and_content: Comma separated table with normalized counts  for all samples (one sample for each column)

growth_protocol: Proliferative C2C12 grow in growth medium (GM) composed of DMEM (Gibco) with 20% FBS (Invitrogen) supplemented with 1% Pyruvate, 1% Glutamate and 1% Penicillin-Streptomycin (Gibco). Differentiation of C2C12 cells was achieved by replacing GM to differentiation media (DM) were FBS was exchanged by 2% of horse serum (Gibco). Fresh medium was added every two days. Mature C2C12 were collected by scraping after PBS washing at day 4 of differentiation.

extract_protocol:
The transcriptomic of myotubes at day 4 was analysed. RNA was extracted (as described in the section "RNA isolation and cDNA synthesis") using the PureLinkTM RNA Mini Kit (Ambion, Life Technologies), including on-Column PureLink DNase treatment. RNA concentration was checked using Nanodrop (ThermoScientific). RNA was sent for library preparation to the CRG Genomics Unit (CRG Core Facilities). RNA quality control showed RNA integrity number (RIN) was between 9.9 and 10. RNA was amplified using mRNAseq which selects polyA. From 1ug of total RNA, the sequencing was performed on single read (SR), with an average length of reads of 50 bp, on an Illumina HiSeq2500 sequencer.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For the knock-down of macroH2A1 isoforms we used siRNAs (Primer table, ordered from Invitrogen) previously described (Dardenne et al., 2012). For all siRNAs, 10nM was found to be the optimal concentration to use. Briefly, in a 6-well plate, 20 000 C2C12 cells were seeded. C2C12 cells were then transfected with the transfection reaction composed of 500ul of OptiMEM (Gibco) 3,12 ul of lipofectamine RNAiMAX Transfection Reagent (Invitrogen) and 10nM of siRNA. For knockdown in myotubes, siRNA was repeatedly delivered at day +1 after seed (-1 of differentiation), the day of medium change for differentiation (D0) and 2 days after (D2). In the case of p15 plate, 300 000 C2C12 were seeded and transfected with 7,5ml Optimem, 45ul lipofectamine and siRNA at a final concentration of 10nM.

value: si KD mH2A1.2


title: RNAseq_MHCII_neg_keratinocytes_control_epidermis_rep1

description: RNA-seq from MHCII negative keratinocytes from epidermis under control condition - replicate 1

tag: strain


title: U87siCT

status: Public on Jun 08 2020

city: Charlottesville

first: Zhongqiu

last: Xie

state: VA

address: 345 Crispell Dr,  Charlottesville

department: Pathology

institute: University of Virginia

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

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

organism: Homo sapiens

source_name: GBM

label_protocol: siRNA transfeced and overexpress stable cell select

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

tag: time

tag: sirna

value: U87siCT(Knock down control)

value: glioblastoma


title: RNAseq_MHCII_pos_keratinocytes_D14_Sepi_epidermis_rep4

description: RNA-seq from MHCII positive keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 4

tag: tissue


title: KD mH2A1.2 rep1


title: C2C12, input sample

description: IPDM


title: KD mH2A1.1 rep3

value: si KD mH2A1.1


title: RNAseq_MHCII_neg_keratinocytes_control_epidermis_rep3

description: RNA-seq from MHCII negative keratinocytes from epidermis under control condition - replicate 3

tag: treatment


title: KD mH2A1.1 rep2


title: RNAseq_MHCII_neg_keratinocytes_control_epidermis_rep2

description: RNA-seq from MHCII negative keratinocytes from epidermis under control condition - replicate 2


title: KD mH2A1.1 rep1


title: RNAseq_MHCII_pos_keratinocytes_D14_Sepi_epidermis_rep3

description: RNA-seq from MHCII positive keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 3


title: WT rep2


title: U87/CT

value: U87/CT(over-express control)


title: RNAseq_MHCII_neg_keratinocytes_D14_Sepi_epidermis_rep1

description: RNA-seq from MHCII negative keratinocytes from epidermis 14 days after association with Staph. Epi - replicate 1


title: KD mH2A1.2 rep3


title: Tn5_EA39

status: Public on Apr 01 2020

city: Stanford

first: Seung

last: Kim

state: CA

address: 279 Campus Dr B303

department: Developmental Biology

institute: Stanford University

data_processing:
Reads were mapped to mm10 using PEPATAC pipeline (Smith et al 2021, PMID: 34859208)
Peaks were called using the PEPATAC pipeline (Smith et al 2021, PMID: 34859208)
genome build/assembly: mm10
processed data files format and content: bigWig

source_name: pancreas

extract_protocol:
Qiagen Minelute column DNA purification
ATAC-Seq libraries were prepared as described in Buenrostro et al 2013 (PMID:24097267)
Nextera Tagmentation (Buenrostro et al 2013, PMID:24097267)

value: Pancreas

tag: developmental stage

value: embryonic day 15.14


title: Tn5_EA38

value: Duct

value: embryonic day 15.13

tag: genotype


title: U87/AVIL

value: U87/AVIL (over-express AVIL)


title: Tn5_EA36

value: Endocrine

value: embryonic day 15.11


title: Tn5_EA60

value: embryonic day 15.19


title: Tn5_EA57

value: embryonic day 15.17


title: Tn5_EA34

value: embryonic day 15.9


title: Tn5_EA37

value: Neurog3 null

value: embryonic day 15.12


title: Tn5_EA40

value: embryonic day 15.15


title: Tn5_EA20

value: embryonic day 15.5


title: WT rep3

value: Wild Type


title: Tn5_EA41

value: embryonic day 15.16


title: Donor_2_LPS_2hr

status: Public on Feb 19 2020

city: Worcester

first: Katherine

middle: A

last: Fitzgerald

state: Massachusetts

address: 364 Plantation Street

department: Medicine

institute: Umass Chan Medical

data_processing:
Sequencing reads were aligned with Bowtie
Gene expression level were calculated with RSEM
Genome_build: hg38
Supplementary_files_format_and_content: results.txt file

growth_protocol: human monocytes were isoldated from PBMCs with Miltenyi CD14 positive selection beads, and then were differentiated with human GMCSF and IL4 for 10 days into dendritic cells.

extract_protocol:
total RNA was extracted with Qiagen RNeasy Mini Kit
Library was prepared with illumina TruSeq Stranded Total RNA Library Prep Kit

treatment_protocol: dendritic cells were treated with 100ng/ml of LPS for 0, 1, 2, 6hrs

tag: individual

value: monocytes derived dendritic cells

value: LPS


title: Tn5_EA33

value: Pancreas

value: embryonic day 15.8


title: Donor_1_LPS_2hr


title: Tn5_EA35

value: Duct

value: embryonic day 15.10


title: U87siAVIL

value: U87siAVIL(Knock down AVIL)

value: glioblastoma


title: Donor_2_LPS_6hr


title: Donor_3_LPS_6hr


title: Tn5_EA32

value: embryonic day 15.7


title: Donor_3_LPS_0hr


title: WT rep1


title: Tn5_EA23

value: embryonic day 15.6


title: Donor_1_LPS_1hr


title: Donor_2_LPS_1hr


title: Donor_3_LPS_1hr


title: D21_HSV_2hr

treatment_protocol: dendritic cells were infected with IAV PR8 (MOI=0.5) or HSV 7134 (MOI=10) for 0, 2, 6 hr


title: Donor_2_LPS_0hr

value: PBS


title: D22_HSV_6hr


title: Tn5_EA59

value: Endocrine

value: embryonic day 15.18


title: Donor_3_LPS_2hr


title: Donor_1_LPS_0hr


title: D21_HSV_6hr


title: D22_HSV_2hr


title: D22_IAV_6hr

value: IAV PR8


title: D21_IAV_6hr


title: D22_IAV_2hr


title: D22_untreated


title: D21_untreated


title: D21_IAV_2hr


title: Stromal Cell _Downstage_76

status: Public on Jan 18 2020

city: São Paulo

first: Maria Lucia

middle: Hirata

last: Katayama

state: São Paulo

address: Av Dr Arnaldo

department: Radiology and Oncology

country: Brazil

institute: Faculty of Medicine University São Paulo

hyb_protocol: Competitive hybridization of each sample of interest-Cy5 and Universal Reference-Cy3 Fluorescent cRNAs (300 ng each) was performed in the SurePrint G3 8×60K slides  at 60oC, during 20 hours.  The accuracy and efficiency of hybridization was evaluated considering spike controls.

scan_protocol: After having washed the slides, the microarrays were scanned at 5-μm resolution with the Agilent Bundle Model B Microarray Scanner System . Scanned image files were visually inspected for artifacts, and the fluorescence intensities were extracted and pre- processed with Agilent Feature Extraction software (v10.7.1).

data_processing:
Normalization was done using GeneSpring GX12.1 software (Agilent Technologies).
Comparisons of expression levels were performed using MeV (MultiExperiment Viewer, version 4.5.1.) software applying SAM (Significance analysis of microarrays). Analysis was done using all sequences (without filtering). Unsupervised hierarchical clustering based on Euclidean distance and average linkage was used to verify association patterns. The reliability of the clustering was assessed by the Bootstrap technique using MEV.

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_76

label_protocol: Competitive microarray assays was performed using two-round RiboAmp HS Plus 2-round and Low Input Quick Amp kit protocols, which were adapted to optimize the amplification for the small number of cells isolated by  Laser Capture Microdissection (LCM). Spikes A and B (Agilent RNA Spike-In Kit) were added to Eniversal Reference RNA and samples, respectively, and used in microarray experiments as amplification and hybridization quality control. During the last in vitro transcription, samples and the Universal Reference, were labelled with cyanine 5 (CY5) or cyanine 3 (CY3), respectively. After fragmentation at 60 o C during 10 minutes, samples were analyzed to calculate the yield and specific activity. Samples selected for the hybridization step were those presenting yields ≥0.825pg and specific activity ≥6.

extract_protocol:
Fresh frozen breast tumor fragments were cut in 10 µm slices, dehydrated, using Histogene® Refill Kit, and eosin stained. Stromal cells were visualized and aptured by the transfer film bounded to the lower surface of a cap (CapSure HS LCM), through infrared pulses, shot by Pix Cell II Laser Capture Microdissection  (LCM)
Lysis solution (12 μl) was added to the cap forExtraction of a cell lysate, which was then placed in a preconditioned RNA purification column, which was washedwith buffer,and spun, twice, and eluted in 30 μl elution buffer (Arcturus PicoPure RNAisolation.

tag: gender

value: female

value: Ductal

value: Triple negative

source_name: Strategene Universal Human Reference RNA (Catalog #740000)

tag: reference


title: Stromal Cell _Non-Downstage_81

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_81

value: Luminal B

value: Strategene Universal Human Reference RNA


title: Stromal Cell _Non-Downstage_67

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_67

value: D/L

value: Luminal A


title: Stromal Cell _Non-Downstage_62

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_62


title: Stromal Cell _Downstage_66

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_66


title: Donor_1_LPS_6hr

tag: cell type

value: monocytes derived dendritic cells

value: LPS


title: Stromal Cell _Downstage_63

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_63


title: Stromal Cell _Non-Downstage_69

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_69


title: Stromal Cell _Non-Downstage_72

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_72


title: Stromal Cell_Non-Downstage_51

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_51


title: Stromal Cell _Non-Downstage_73

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_73


title: Stromal Cell _Non-Downstage_70

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_70

value: D/oth


title: Stromal Cell _Non-Downstage_55

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_55


title: Stromal Cell _Downstage_79

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_79


title: Stromal Cell _Non-Downstage_75

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_75


title: Stromal Cell _Non-Downstage_64

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_64


title: Stromal Cell _Non-Downstage_59

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_59


title: Stromal Cell _Non-Downstage_58

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_58


title: Stromal Cell _Non-Downstage_68

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_68

source_name: Strategene Universal Human Reference RNA (Catalog #740000)


title: Stromal Cell_Downstage_61

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_61


title: Stromal Cell_Non-Downstage_54

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_54


title: Stromal Cell _Non-Downstage_71

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_71

value: D/IS


title: Stromal Cell _Non-Downstage_99

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_99


title: Stromal Cell _Non-Downstage_80

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_80


title: Stromal Cell _Non-Downstage_45

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_45

value: Lobular

value: triple negative


title: Stromal Cell _Downstage_49

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_49


title: Stromal Cell _Non-Downstage_52

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_52


title: Stromal Cell _Downstage_60

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_60


title: Stromal Cell _Non-Downstage_56

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_56


title: Stromal Cell _Non-Downstage_37

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_37


title: Stromal Cell _Non-Downstage_30

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_30

value: Luminal


title: Stromal Cell _Non-Downstage_36

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_36


title: Stromal Cell _Downstage_38

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_38


title: Stromal Cell _Non-Downstage_11

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_11


title: Peripheral serum, disease group, patient 25

status: Public on Dec 31 2019

city: Beijing

first: Yanqiong

last: Zhang

address: No 16, Nanxiaojie, Dongzhimennei

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

description: Gene expression data of SONFH patients

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were normalized by RMA algorithm, Affy packages in R.

source_name: Human peripheral serum

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip  3'IVT PLUS Reagent Kit (Cat#902416, Affymetrix, Santa Clara, CA, US)followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: A total of 30 patients with SONFH (disease group n=30, 13 men, 17 women; ARCO Ⅰ-Ⅱ 10, stage Ⅲ 10, stage Ⅳ 10; mean age: 23.07±3.01 years)and 10 patients who did not develop SONFH (control group n=10, 7 men, 3 women; mean age 25.02±2.87 years) following steroid administration were included in the study.

extract_protocol: Total RNA was extracted and purified using PAXgene Blood RNA Kit (Cat#762174, QIAGEN, GmBH, Germany) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).The concentration of total RNA was measured using a NanoDrop spectrophotometer (Nanodrop technologies, Montchanin, DE, USA). Total RNA was eluted in 15 μl of RNase-free water and stored at − 80°C.mRNA expression proile obtained from disease and control groups were respectively detected using Affymetrix EG1.0 array carried out by Shanghai GMINIX Biotechnology Corporation, Shanghai, China.

treatment_protocol: Peripheral serum samples (2.5 mL) were collected before treatment.

tag: tissues

value: The peripheral serum

value: Female

tag: disease

value: SONFH


title: Stromal Cell _Non-Downstage_18

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_18

value: female

source_name: Strategene Universal Human Reference RNA (Catalog #740000)


title: Stromal Cell _Downstage_84

source_name: Stromal cell from Tissue, Breast Cancer_Downstage_84


title: Peripheral serum, disease group, patient 28

description: Gene expression data of SONFH patients


title: Stromal Cell

source_name: Stromal cell from Tissue Breast Cancer_Non-Downstage_6

value: Ductal


title: Stromal Cell _Non-Downstage_9

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_9


title: Peripheral serum, disease group, patient 19

description: Gene expression data of SONFH patients


title: Stromal Cell _Non-Downstage_7

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_7


title: Stromal Cell _Non-Downstage_20

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_20


title: Stromal Cell _Non-Downstage_44

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_44


title: Peripheral serum, disease group, patient 27

description: Gene expression data of SONFH patients


title: Stromal Cell _Non-Downstage_17

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_17


title: Peripheral serum, disease group, patient 30

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 24

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 22

description: Gene expression data of SONFH patients


title: Stromal Cell _Non-Downstage_13

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_13

value: Triple negative


title: Stromal Cell _Non-Downstage_33

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_33

value: Luminal B


title: Stromal Cell _Non-Downstage_19

source_name: Stromal cell from Tissue, Breast Cancer_Non-Downstage_19

value: Strategene Universal Human Reference RNA


title: Peripheral serum, disease group, patient 17

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 21

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 23

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 26

description: Gene expression data of SONFH patients

value: Male


title: Peripheral serum, disease group, patient 29

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 20

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 16

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 18

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 15

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 13

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 9

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 8

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 12

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 5

description: Gene expression data of SONFH patients


title: Myometrial tissue, subject TP2 (ChIP-Seq)

status: Public on Nov 27 2019

description: The PGR occupancy profile in human myometrial tissue, subject TP2

data_processing:
50nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the human genome hg19 using the BWA algorithm.
Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: Myometrium

growth_protocol: Not applicable

treatment_protocol: Not applicable

tag: Stage

value: 38-42 weeks estimated gestational age

value: myometrial tissue

tag: chip antibody

value: Anti-PGR antibody (sc-7208, Santa Cruz Biotechnology, Dallas, TX)


title: Peripheral serum, disease group, patient 7

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 10

description: Gene expression data of SONFH patients


title: Myometrial tissue, subject TP-C (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject TP-C

data_processing:
Raw reads of 101 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the human genome (UCSC hg19) using Tophat version 2.0.4 and assembled using Cufflinks version 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

extract_protocol:
RNA was extracted using TRIzol according to manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Myometrial tissue, subject NP2 (ChIP-Seq)

description: The PGR occupancy profile in human myometrial tissue, subject NP2

value: Nonpregnant at the proliferative phase


title: Myometrial tissue, subject TP-B (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject TP-B


title: Myometrial tissue, subject NP1 (ChIP-Seq)

description: The PGR occupancy profile in human myometrial tissue, subject NP1


title: Myometrial tissue, subject TP1 (ChIP-Seq)

description: The PGR occupancy profile in human myometrial tissue, subject TP1


title: Myometrial tissue, subject TP5 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject TP5

data_processing:
50nt sequence reads were processed with trim_galore to trim the adaptor and keep the reads at least 20nt long  with quality higher than 20 .
Reads were mapped to the mouse genome hg19 using bowtie allowing 2 mismatches.
Only the first 9nt of tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.


title: Myometrial tissue, subject TP-A (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject TP-A


title: Myometrial tissue, subject TP4 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject TP4


title: Peripheral serum, disease group, patient 4

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 11

description: Gene expression data of SONFH patients


title: Peripheral serum, disease group, patient 2

description: Gene expression data of SONFH patients


title: Myometrial tissue, subject NP6 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject NP6


title: Myometrial tissue, subject NP-B (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject NP-B


title: Myometrial tissue, subject NP-C (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject NP-C


title: Myometrial tissue, subject NP7 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject NP7


title: Myometrial tissue, subject TP3 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject TP3


title: Peripheral serum, control group, patient 10

description: Gene expression data of non-SONFH patients

value: non-SONFH


title: Peripheral serum, control group, patient 7


title: Peripheral serum, control group, patient 6


title: Myometrial tissue, subject NP5 (ATAC-Seq)

description: The accessible genome profile in the human myometrial tissue, subject NP5


title: Peripheral serum, control group, patient 1


title: Peripheral serum, disease group, patient 6

description: Gene expression data of SONFH patients


title: Peripheral serum, control group, patient 9


title: Peripheral serum, disease group, patient 14

description: Gene expression data of SONFH patients


title: Peripheral serum, control group, patient 5


title: Peripheral serum, control group, patient 4


title: Peripheral serum, disease group, patient 1

description: Gene expression data of SONFH patients


title: Peripheral serum, control group, patient 8


title: Midsecretory rep2 input

description:
genomic DNA
N274-input

data_processing:
The raw ChIP-Seq reads were initially processed by filtering with average quality scores greater than 20.
Then the reads were aligned to the human reference genome (UCSC hg19) using Bowtie version 1.1.2 with unique mapping and up to 2 mismatches for each read (-m 1 -v 2)
The duplicated reads with the same sequence were discarded
Genome_build: hg19
Supplementary_files_format_and_content: biWig files were generated from normalized bedgraph files using bedGraphToBigWig; Scores represent normalized mapped read coverage

source_name: control, input DNA

extract_protocol:
Lysates were clarified from sonicated nuclei and PGR-bound DNA were isolated with PGR antibody.
True Seq RNA kit

tag: menstrual cycle phase

value: mid-secretory

value: endometrium/whole endometrium


title: Proliferative rep2 PGR-ChIPseq

description:
PGR bound chromatin
N293

source_name: Proliferative rep2 PGR-ChIPseq

value: proliferative

value: Progesterone Receptor (Santa Cruz, sc-7208)


title: Pooled input

description:
genomic DNA
Pooled-input


title: Myometrial tissue, subject NP-A (RNA-seq)

description: The transcriptome profile in the human myometrial tissue, subject NP-A


title: Human endometrium/Epithelium only Midsecretory-rep5_RNAseq

data_processing:
Raw reads of 100 nucleotides, paired-end filtered for quality score > 20.
Reads were mapped to the human genome (UCSC hg19) using Tophat version 2.0.4 and assembled using Cufflinks version 2.0.2.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM was calculated for each gene in each sample by using Cufflinks version 2.0.2.

source_name: Human endometrium/Epithelium only at mid-secretory stage

value: endometrium/Epithelium only


title: Human endometrium/Epithelium only Midsecretory-rep4_RNAseq


title: Proliferative rep1 PGR-ChIPseq

description:
PGR bound chromatin
N252

source_name: Proliferative rep1 PGR-ChIPseq


title: Human endometrium/Epithelium only Midsecretory-rep1_RNAseq


title: Proliferative rep2 input

description:
genomic DNA
N293-input


title: Human endometrium/Epithelium only Midsecretory-rep3_RNAseq


title: Human endometrium/Epithelium only Proliferative-rep2_RNAseq

source_name: Human endometrium/Epithelium only at proliferative stage


title: Peripheral serum, control group, patient 2

source_name: Human peripheral serum

value: The peripheral serum


title: Human endometrium/Epithelium only Proliferative-rep3_RNAseq


title: Human endometrium/Epithelium only Proliferative-rep4_RNAseq


title: Human endometrium/Epithelium only Proliferative-rep1_RNAseq


title: Midsecretory rep1 PGR-ChIPseq

description:
PGR bound chromatin
N275

source_name: Midsecretory rep1 PGR-ChIPseq


title: Human endometrium Midsecretory-rep4_RNAseq

source_name: Human endometrium at mid-secretory stage


title: Human endometrium/Epithelium only Midsecretory-rep2_RNAseq


title: Human endometrium Midsecretory-rep2_RNAseq


title: Human endometrium Midsecretory-rep3_RNAseq


title: Human endometrium Proliferative-rep5_RNAseq

source_name: Human endometrium at proliferative stage


title: Peripheral serum, control group, patient 3


title: Human endometrium Proliferative-rep2_RNAseq


title: Human endometrium Proliferative-rep6_RNAseq


title: Human endometrium Proliferative-rep1_RNAseq


title: HTO-counts_MAIT cells from different tissues

status: Public on Oct 28 2019

description: oligonucleotides to barcode samples

data_processing:
I1 read: contains the sample index.
R1 read: contains the cell barcode (first 16 nt) and UMI (next 10 nt).
R2 read: contains the RNA sequence.
Data was demultiplexed using Cell Ranger 3.0.1 resulting in data for 6,463 cells. HTO libraries were processed using CITE-seq-Count. Subsequently, data was analyzed using Seurat 3.0. Cells with less than 900 or more than 3,000 gene counts, more than 5% mitochondrial contamination, or more than 10,000 RNA counts were filtered out, leaving 5,678 cells for downstream analysis. Data was normalized, scaled, PCA was performed, and neighbors were found using 5 dimensions. UMAP reduction was performed on this dataset with 10 dimensions. HTO were read in and assigned to the single cells and only singlets were used for further analysis leaving 585 cells. To define origins of cells, number of HTOs per cluster were considered and classified as “Skin”, “Spleen/Lung/Liver”, or not assigned (“NA”). To analyze gene expression between tissues, all cells, including cells without HTO from the respective clusters were used.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv, features.tsv, matrix.mtx

source_name: Hash-tagged oligonucleotide counts for scRNA-seq

growth_protocol: MAIT cells were sorted DAPI-, CD45+, Thy1.2+, TCRgd-, TCRb+, MR1 tetramer+, and additionally labelled with a oligo-nucleotide antibody unique per tissue

extract_protocol:
single cell RNA-seq was performed using the 10X Genomics platform
Libraries were performed according to manufactor's instruction. HTO libraries were constructed following the CITE-seq protocol (Stoeckius et al., Nature Methods, 2017)

value: Ctrl

value: skin, spleen, lung, liver

value: mucosal-associated invariant T (MAIT) cells


title: Peripheral serum, disease group, patient 3

description: Gene expression data of SONFH patients

value: Female

value: SONFH


title: Human endometrium Midsecretory-rep5_RNAseq


title: scRNASeq_MAIT cells from different tissues

description: single cell RNA

source_name: MAIT cells from different tissues


title: RNASeq_MAIT_Sepi_rep1

data_processing:
RNA-seq reads were mapped with STAR to the mm10 reference genome with default parameters. Read counts were assessed with HOMER’s analyzeRepeats with the option rna and parameters -noadj and -condenseGenes for two replicates per condition. Differential gene expression was assessed with DESeq2 using HOMER’s getDiffExpression.pl using a false discovery rate (FDR) of 5% and a fold change of 2. Metascape was used for analyzing enriched GO terms.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: MAIT T cells from skin

growth_protocol: MAIT cells were sorted DAPI-, CD45+, Thy1.2+, TCRgd-, TCRb+, MR1 tetramer+, while CD4+ T cells were sorted DAPI-, CD45+, Thy1.2+, TCRgd-, TCRb+, MR1 tetramer-, CD4+, CD8b-, CD25-.

extract_protocol:
RNA was extracted using a Arcturus PicoPure RNA Isolation Kit (Applied Biosystems)
DNase-treated total RNA (100 ng) was reverse transcribed into cDNA with Omniscript RT kit (QIAGEN) following manufacturer’s instructions.

treatment_protocol: S. epidermidis LM061 was topically applied to the skin of 7-week-old WT C57BL/6 female mice on days 0, 2, 4, and 6. 14 days after the initial application, animals were euthanized and compared to unassociated age- and gender-matched control animals.

value: Staph. Epi association

tag: Sex

value: female

value: skin

value: MAIT T cells


title: Human endometrium Midsecretory-rep1_RNAseq


title: RNASeq_MAIT_naive_rep1

tag: strain


title: RNASeq_CD4_Sepi_rep2

source_name: CD4+CD25- T cells from skin

value: CD4+CD25- T


title: RNASeq_MAIT_Sepi_rep2


title: RNASeq_CD4_Sepi_rep1


title: Human endometrium Proliferative-rep4_RNAseq


title: RNASeq_MAIT_naive_rep2


title: RNASeq_CD4_naive_rep1


title: Limbal-TERT-cloneW-50-12597

status: Public on Oct 22 2019

data_processing:
Sequencing reads were aligned to human genome assembly hg19 (NCBI version 37) using STAR 2.5.0 with default options
Read counts representing gene expression levels were calculated by using STAR 2.5.0 with default options.
Genes with the mean of DESeq2-normalized counts (“baseMean”) > 10 are considered to be expressed, and genes with non-adjusted P value < 0.001 are consider to be  Differential expressed genes  (DEG).
Genome_build: hg19
Supplementary_files_format_and_content: Counts and DEGs

source_name: Limbal-TERT-cloneW

extract_protocol:
Lysates were purified using Nuleospin RNA (Macherey-Nagel, cat# 740955.250)
Libraries were prepared according to NuGEN’s instructions accompanying the NuGEN Ovation RNA-seq kit (NuGENcat #7102-32). RNA-seq libraries were amplified using 10 cycles.

value: limbal epithelial cells

value: PAX6 mutation


title: RNASeq_CD4_naive_rep2


title: Limbal-TERT-wt-35-12595

source_name: Limbal-TERT-wt

value: WT


title: Limbal-TERT-cloneW-49-12596


title: 973_FBN

status: Public on Sep 10 2019

city: Minneapolis

first: Shijia

last: Zhu

state: Minnesota

address: 1200 Washington Avenue S Suite #175

department: Department of Laboratory Medicine and Pathology

institute: University of Minnesota Medical School

description: affected NRXN1 deletion hiPSC-neurons single cell

data_processing:
Whole-tanscriptome RNA-seq: Reads were aligned with STAR (version 2.4.0c)
Whole-tanscriptome RNA-seq:genes annotated in Gencode v18 were quantified with featureCounts (v1.4.3-p1)
Whole-tanscriptome RNA-seq: Normalization and differential expression was done with the Bioconductor package DESeq2
10X Genomics single-cell seq: Reads from each cell per sample was determined using the standard CellRanger Pipeline
10X Genomics single-cell seq: Filtering, clustering and differential expression was done using Seruat
Genome_build: 10X Genomics single-cell seq: hg38
Genome_build: Whole-tanscriptome RNA-seq: hg19
Supplementary_files_format_and_content: Whole-tanscriptome RNA-seq: raw read counts (.txt)
Supplementary_files_format_and_content: 10X Genomics single-cell seq: Each sample has three files including barcodes.tsv, genes.tsv and matrix.mtx file which can be used to contruct a count matrix

source_name: hiPSC-neurons

growth_protocol:
hiPSC-NPCs: were derived from hiPSCs through an EB intermediate and cultured at high-density on matrigel splitting every week
hiPSC-neurons were differentiatiated from hiPSC-NPCs through the addition of growth factors for 6 weeks before harvest
NGN2-induced hiPSC-neurons were differentiated from hiPSC-NPCs for 3 weeks and treated with Ara-C before harvest
ASCL1/DLX2-induced hiPSC-neurons were differentiated from hiPSC-NPCs for 5 weeks and treated with Ara-C before harvest

extract_protocol:
Whole-transcriptome RNA-seq samples: Trizol was added to cells while in the plate, then phenol-chloroform extraction was performed.
10X Genomics single-cell seq: hiPSC-neurons were lifted from plate using TryplE and gently dissociated to form a single cell suspension
Whole-tanscriptome RNA-seq samples: Kapa Total 350bp kit using standard Illumina protocols.
10X Genomics single-cell seq: Chromium platform (10x Genomics) with the 3’ gene expression (3’ GEX) V2 kit, using an input of ~10,000 cells

tag: diagnosis

value: Case

tag: nrxn1 status

value: 5' NRXN1 intragenic deletion

tag: hipsc-clone

value: Clone 1

tag: relationship

value: Proband 2


title: 972_FBN

value: Mother 2


title: 641_FBN

value: 3' NRXN1 intragenic deletion

value: Proband 1


title: Limbal-TERT-wt-34-12594


title: 553_FBN

description: control hiPSC-neurons single cell

value: Control


title: 972_GABA

description:
affected NRXN1 deletion ASCL1/DLX2-induced hiPSC-neurons
NRXN1_hiPSCderived_CellType_ReadCounts.tsv

source_name: ASCL1/DLX2-induced hiPSC-neurons


title: 973_GABA


title: 641_GABA


title: 3084_NGN

description:
control NGN2-induced hiPSC-neurons
NRXN1_hiPSCderived_CellType_ReadCounts.tsv

source_name: NGN2-induced hiPSC-neurons


title: 641_NGN

description:
affected NRXN1 deletion NGN2-induced hiPSC-neurons
NRXN1_hiPSCderived_CellType_ReadCounts.tsv


title: fetal-dlPFC

description:
control human fetal dlPFC
Postmortem_dlPFC_Read Counts.txt

source_name: fetal post-mortem PFC


title: 553_NGN


title: 553_GABA

description:
control ASCL1/DLX2-induced hiPSC-neurons
NRXN1_hiPSCderived_CellType_ReadCounts.tsv


title: 972_NGN


title: 2607_GABA


title: 973_NGN


title: 2607_NGN


title: 14-34-dlPFC

description:
control human adult dlPFC
Postmortem_dlPFC_Read Counts.txt

source_name: adult post-mortem dlPFC


title: 2607_FBN

description: control hiPSC-neurons single cell


title: Oral keratinocytes, P2

hyb_protocol: 17 hours at 45 degrees in Affymetrix hybridization oven at 60 rpm,washing and staining in  Fluidics station 450 using stain cocktails: SAPE and antibody solution, (protocol FS450_0001)

scan_protocol: GeneChip scanner 3000 7G

data_processing:
Partek (Partek Genomic Suite software, version 6.4; Partek Inc.) where only core exons were extracted and normalized using the RMA algorithm with GC background correction.
Core transcript summaries were calculated using the mean intensities of the corresponding probe sets

source_name: Oral keratinocytes

label_protocol: Genome U133 Plus 2.0 Array® (Affymetrix)

growth_protocol: Palatal keratinocytes (passage 3) were thawed and cultured in T75 flasks in 10 ml keratinocyte serum free medium (K-SFM) (Gibco, Invitrogen, 10744019) with supplements and incubated at 37°C. Once the cells reached 80-90% confluence, they were cultured for an additional 24 hours in fresh medium.

extract_protocol: Subsequently, the cells were washed with cold phosphate-buffered saline (PBS), lysed in RLT buffer (RNeasy Mini Kit®) containing β-mercaptoethanol, and stored at -80°C.

tag: tissue

value: Cultured from tissue biopsies

tag: condition

value: patient pool


title: 12-27-dlPFC


title: Oral keratinocytes, C5

value: control pool


title: 106751-dlPFC


title: 3084-2-2-NPC

description:
control hiPSC-NPCs
NRXN1Cohort_NPC_FBN_ReadCounts.txt

source_name: hiPSC-NPCs

value: Clone 2


title: Oral keratinocytes, C2


title: 3084-1-1-NPC


title: Oral keratinocytes, C3


title: Oral keratinocytes, P5


title: Oral keratinocytes, P3


title: 3084-1-1-FB

description:
control hiPSC-neurons
NRXN1Cohort_NPC_FBN_ReadCounts.txt


title: 973-5-2-NPC

description:
affected NRXN1 deletion hiPSC-NPCs
NRXN1Cohort_NPC_FBN_ReadCounts.txt


title: Oral keratinocytes, C1


title: Oral keratinocytes, P1


title: Oral keratinocytes, C4


title: 973-5-2-FB

description:
affected NRXN1 deletion hiPSC-neurons
NRXN1Cohort_NPC_FBN_ReadCounts.txt


title: Oral keratinocytes, P4


title: 973-2-3-NPC


title: 973-1-3-NPC

value: Clone 3


title: 973-1-3-FB


title: 972-2-2-NPC


title: 972-5-2-FB


title: 972-5-2-NPC


title: 3084-2-2-FB


title: 972-1-1-NPC


title: 642-1-1-NPC

description:
affected hiPSC-NPCs
NRXN1Cohort_NPC_FBN_ReadCounts.txt

value: Mother 1


title: 972-1-1-FB


title: 642-2-1-NPC


title: 641-8-2-NPC


title: 641-8-2-FBN


title: 973-2-3-FB


title: 641-6-2-NPC


title: 641-7-2-FBN


title: 581-3-1-NPC

value: Proband 1A


title: 581-3-1-FBN


title: 641-6-2-FBN


title: 581-2-1-NPC


title: 553-1-1-NPC


title: 553-x-C-FBN


title: 553-1-1-FBN


title: 581-2-1-FBN


title: 553-3-1-NPC


title: 553-x-C-NPC


title: 2607-3-1-NPC


title: 2607-4-1-FBN


title: 642-2-1-FBN

description:
affected hiPSC-neurons
NRXN1Cohort_NPC_FBN_ReadCounts.txt


title: 2607-2-1-NPC


title: 642-1-1-FBN


title: 553_NGN2

description:
NRXN1 cDNA was synthesized from total TNA then NRXN1 transcripts were PCR amplified
TargetRNAseqReadCount.txt

data_processing:
Illumina Amplicon short-read seqeuncing: Raw cDNA reads are aligned to the hg19 reference with the spliced gap aligner STAR, with count-based quantitation carried out via the Subread package featureCounts at the geneic levels for annotation builds.
Genome_build: Illumina Amplicon short-read seqeuncing: hg19
Supplementary_files_format_and_content: Illumina Amplicon short-read seqeuncing: raw read counts (.txt)

extract_protocol:
Trizol was added to cells while in the plate, then phenol-chloroform extraction was performed. NRXN1 cDNA was synthesized from total RNA then NRXN1 transcripts were PCR amplified
PacBio long-read sequencing: PCR products were purified with Agencourt AMPure XP magnetic beads (Beckman Coulter) at a volume ratio of 0.5:1.
Illumina Amplicon short-read seqeuncing: PCR product was then run on a 1% agarose gel and gel extracted using the Genejet gel extraction and DNA cleanup micro kit.
PacBio long-read sequencing: SMRT bell sequencing libraries were prepared using Pacific Biosciences DNA Template Prep Kit according to the 5-kb template preparation and sequencing protocol provided by Pacific Biosciences prior to purification and size binning to proper molecular range using Sage BluePippin
Illumina Amplicon short-read seqeuncing:  Library preped using Nextera XT DNA library preparation kit (Genewiz)


title: 641_NGN2


title: Fetal_2


title: Midsecretory rep2 PGR-ChIPseq

description:
PGR bound chromatin
N274

source_name: Midsecretory rep2 PGR-ChIPseq

value: mid-secretory

value: endometrium/whole endometrium

value: Progesterone Receptor (Santa Cruz, sc-7208)


title: 553_GABA


title: 2607-4-1-NPC


title: 641-7-2-NPC

value: Case


title: Fetal_3


title: Fetal_1


title: 553-3-1-FBN


title: Adult_3


title: 2607-3-1-FBN


title: 642

value: Clone 1


title: 641


title: 553


title: 581


title: Adult_2


title: PGRA_ChIPseq

status: Public on Aug 29 2019

description: Antibody: Santa Cruz #sc-7208

data_processing:
36-nt sequence reads were identified by the Sequencing Service (using Illumina’s Genome Analyzer 2).
Reads were mapped to the mouse genome mm9 using the BWA algorithm.
Only tags that map uniquely, have no more than 2 mismatches, and that pass quality control filtering are used in the subsequent analysis.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bedGraphToBigWig from UCSC.

source_name: whole uterus

growth_protocol: Mice were fed on normal chow and ovariectomized at 8-10 weeks of age.

extract_protocol:
The PGR ChIP reactions were performed using 30ug of ovarian chromatin with 20µL of PGR antibody (Santa Cruz #sc-7208).
The number of unique alignments without duplicate reads was totaled and MACS analysis was performed at a pvalue 1e-7. At this threshold, >30,000 peaks were identified at an emipirical FDR value of <0.17%.

treatment_protocol: Mice were ovariectomized at 8-10 weeks of age, rested for 2 weeks, and treated with progesterone for 1 hour before harvesting and flash freezing whole uterine tissue.

tag: antibody

value: PGR antibody (Santa Cruz #sc-7208)

tag: age

value: 8-10 weeks

value: C57BL6/6J, 129 mixed strain

value: ovariectomized


title: WT-3

status: Public on Aug 30 2019

city: Bordeaux

first: Nicolas

middle: J.

last: Tourasse

address: 146 rue Leo Saignat

department: INSERM U1212, CNRS UMR5320

country: France

institute: University of Bordeaux

description: strain transformed with a wild-type aapA3/IsoA3 locus PCR product; biological replicate 3

data_processing:
Raw FASTQ files were generated by the sequencing platform.
Reads were first trimmed of low-quality 3’ ends using cutadapt 1.1 (option “-q 28”). Then, reads having an average base quality lower than 28 were discarded using prinseq-lite 0.20.4 (“-min_qual_mean 28”). Read pairs for which both mates passed the quality filtering steps were recovered by means of cmpfastq, and mates were assembled into a single sequence using PANDAseq run with options “-N -o 30 -O 0 -t 0.6 -A simple_bayesian -C empty”. About 5 million read pairs (combining the three biological replicates) could be assembled for the WT and pIsoA3* (inactivated IsoA3 antitoxin promoter) samples.
The assembled reads were aligned onto the 426-nt reference sequence by the BWA-SW algorithm of BWA 0.7.12 run with options “-a 1 -b 3 -q 5 -r 2 -z 1” to produce alignments in BAM format. Mapped sequences of length 426 showing a single substitution compared to the reference were then extracted using utilities from the samtools 1.2 and bamtools 2.3.0 packages based on the various flags and tags in the BAM files (in particular the CIGAR string and NM tag). This gave a dataset of 1,653,406 WT and 2,559,164 mutated single-substitution sequences. Mapped sequences of length 425 and 427 harboring a single deletion or insertion, respectively, were also extracted (40,998 WT and 100,754 pIsoA3* single-deletion sequences; 4,799 WT and 7,048 pIsoA3* single-insertion sequences).
Statistical analyses of the differential distribution of substitutions in the WT and pIsoA3* single-substitution sequences were carried out. To determine whether substitutions were enriched at particular positions in the pIsoA3* compared to WT sequences, a “positional” analysis was conducted by summing together the counts of all sequences that showed a substitution at a given position, regardless of the identity of the substituted nucleotide. A “nucleotide-specific” analysis comparing the amount of each individual sequence was also done to determine whether particular nucleotides were enriched at specific positions. Differential analyses were conducted following the protocol of Haas et al. (Nature Protocols 2013, 8: 1494-1512) using tools from the Trinity 2.2.0 and DESeq2 1.10.1 packages, taking into account variability among the three biological replicates. The sequence abundance estimation step was not performed; actual sequence counts were used. Substitutions were considered as significantly over- or under-represented in the pIsoA3* vs WT samples if the p-value adjusted for multiple testing (False Discovery Rate [FDR] calculated using the Benjamini-Hochberg [BH] method in DESeq2) was equal or lower than 5% (padj <= 0.05). Similar “positional” analyses were also carried out for single-insertion and single-deletion sequences to determine whether insertions or deletions were statistically enriched at particular positions in the pIsoA3* dataset.
Genome_build: AE000511.1:1502963-1503388
Supplementary_files_format_and_content: One Microsoft Excel spreadsheet with raw sequence counts, and four Microsoft Excel spreadsheets with log2 fold-changes and p-values computed using DESeq2

organism: Helicobacter pylori

source_name: cells

extract_protocol:
H. pylori genomic DNA was extracted using the Bacteria Genomic DNA extraction Kit (Neo Biotech).
After genomic DNA extraction, the aapA3/IsoA3 toxin-antitoxin locus was amplified with a specific primer pair generating an amplicon of 426 nt. The primers carried an overhang 5’-tail containing the adaptors for Illumina sequencing. Sequencing of the amplicon libraries was done on a MiSeq instrument in paired-end mode 2 x 250 nt (overlapping reads) at the Platforme GeT-PlaGe, Genotoul Centre INRA, Toulouse, France.

treatment_protocol: We performed series of chromosome manipulations in which PCR-generated constructs were used. This strategy involved the previous generation of a recipient H. pylori 26695 strain in which the aapA3/IsoA3 toxin-antitoxin locus was replaced by the rpsl-erm double-gene cassette on a rpsl K43R mutant (StrR) genetic background, strain named ΔaapA3/IsoA3::rpsl-erm/K43R (StrS, ErmR). The aapA3/IsoA3 locus was split into two fragments amplified with the high-fidelity enzyme Phusion Hot Start DNA polymerase (Thermo Fischer) and the primer pairs FA406/FA386 and FA409/FA387. Each of them was cloned into a separate pGEM®-T (Promega) plasmid and transformed into One Shot TOP10 chemically competent E. coli cells (Thermo Fischer). Note that the FA386 and FA387 primers have 25 nucleotides (nt) overlapping which will allow subsequent fragment assembly by PCR. The fragments contain 415 and 418 nt of upstream and downstream regions, respectively, to the aapA3/IsoA3 locus that will serve as homology regions to allow homologous recombination during transformation. Those plasmids were then used as template for site-directed-mutagenesis PCR using the PfuUltra high-fidelity DNA polymerase (Agilent). We used custom-designed overlapping oligonucleotides containing the desired mutations to inactivate IsoA3 -10 box (FA283/FA284) and AapA3 start codon (FA281/FA282). To inactivate the IsoA3 promoter (pIsoA3*) two point mutations on its -10 box were created (adenine residues at positions +87 and +90 from the aapA3 +1 transcription start site were mutated to cytosine and guanine, respectively). Next, the wild-type (WT) or pIsoA3* fragments were amplified from the previously generated and extracted plasmids, using 35 amplification cycles, the Phusion High-Fidelity Hot Start DNA Polymerase and the same primer pairs as those used for insert amplification prior to cloning. PCR assembly with 35 amplification cycles, the DreamTaq DNA polymerase (Thermo Fischer) and the external primers FA406/FA409 was next performed to generate the complete aapA3/IsoA3 desired locus variant (1294-nt amplicon). 1 μg of PCR assembly product was used to transform a 1 OD600 bacterial patch after 4 h growth in a CAB plate. Upon transformation, plates were incubated for another 16 hours. The assay was performed in independent biological triplicates using the WT or pIsoA3* PCR products. Transformation patches were recovered and resuspended in 1 mL BHI. Strains were isolated on streptomycin-containing plates by using optimized ten-fold dilutions adapted to each transformation case (9 plates/replicate of 10-1 dilution for pIsoA3* and 3 plates/replicate of 10-3 dilution for WT). Three days after transformation, isolated colonies were pooled (approximately 60,000 colonies per transformation) and genomic DNA was extracted. Next, the aapA3/IsoA3 locus was amplified with the primer pair FA395/FA396 (426-nt amplicon), which allows the introduction of the DNA adapters for Illumina paired-end sequencing. Importantly, to avoid amplification from phenotypic revertant strains (mutated rpsl gene), the FA395 and FA396 primers are nested to the ones used for locus deletion (FA407 and FA408), thus, binding to deleted regions that are re-introduced only upon recombination. For this PCR, the Phusion High-Fidelity Hot Start DNA polymerase and 35 amplification cycles were used. Finally, the samples were sent for sequencing at the Platforme GeT-PlaGe, Genotoul Centre INRA, Toulouse, France. Sequencing was done on an Illumina MiSeq instrument in paired-end mode 2 x 250 nt (overlapping reads).

tag: genotype

value: aapA3/IsoA3/rpsl K43R

tag: phenotype

value: wild-type


title: WT-2

description: strain transformed with a wild-type aapA3/IsoA3 locus PCR product; biological replicate 2


title: WT-1

description: strain transformed with a wild-type aapA3/IsoA3 locus PCR product; biological replicate 1


title: mut-2

description: strain transformed with a mutated IsoA3 promoter aapA3/pIsoA3* locus PCR product; biological replicate 2

value: aapA3/pIsoA3*/rpsl K43R

value: Toxicity suppressor strains


title: RNAseq_Spleen_DR_rep1

status: Public on Aug 22 2019

data_processing:
RNA-seq reads were mapped with STAR to the mm10 reference genome with default parameters. Read counts were assessed with HOMER’s analyzeRepeats with the option rna and parameters -noadj -condenseGenes and -count exons for three replicates per condition. Differential gene expression was assessed with DESeq2 using HOMER’s getDiffExpression.pl using a false discovery rate (FDR) of 5% and a fold change of 1.5. Metascape was used for analyzing enriched GO terms, and GSEA was used for gene set enrichment analysis. PCA was performed in R with prcomp, center = TRUE, scale. = TRUE.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: CD8+ T-cells (TCM) from spleen

extract_protocol:
RNA was extracted using a Arcturus PicoPure RNA Isolation Kit (Applied Biosystems), (bone marrow and spleen) as per manufacturer’s instructions or the Rneasy mini kit for the whole bone marrow
DNase-treated total RNA (100 ng) was reverse transcribed into cDNA with Omniscript RT kit (QIAGEN) following manufacturer’s instructions.

treatment_protocol: The daily intake of chowby a cage of mice was determined by giving a certain amount and weighing what was left 1 week later. Half of what was usually consumed was given to mice daily for up to 6 weeks.

tag: organ

value: spleen

value: CD8+ T-cells (TCM) from spleen

tag: treatment

value: dietary restriction


title: mut-3

description: strain transformed with a mutated IsoA3 promoter aapA3/pIsoA3* locus PCR product; biological replicate 3


title: RNAseq_Spleen_DR_rep3


title: 2607

value: Control


title: Adult_1


title: RNAseq_Spleen_DR_rep2


title: Human endometrium Proliferative-rep3_RNAseq

source_name: Human endometrium at proliferative stage

value: proliferative


title: RNAseq_Spleen_Ctrl_rep2

value: Ctrl


title: RNAseq_Spleen_Ctrl_rep3


title: RNAseq_Spleen_Ctrl_rep1


title: Input


title: mut-1

description: strain transformed with a mutated IsoA3 promoter aapA3/pIsoA3* locus PCR product; biological replicate 1


title: RNAseq_BM_DR_rep2

source_name: CD8+ T-cells (TCM) from bone marrow

value: bone marrow

value: CD8+ T-cells (TCM) from bone marrow


title: RNAseq_BM_Ctrl_rep3


title: RNAseq_BM_DR_rep1


title: RNAseq_BM_Ctrl_rep2


title: RNAseq_BM_Ctrl_rep1


title: RNAseq_whole_tissue_BM_DR_rep4

source_name: whole bone marrow

value: whole bone marrow


title: RNAseq_BM_DR_rep3


title: RNAseq_whole_tissue_BM_DR_rep3


title: 44130 Wnt7acre+mPRALsL/+ day 4.5

description: Gene expression of whole uterine tissue at day 4.5 natural pregnancy

hyb_protocol: Approximately 480ng of fragmented cRNA samples were loaded onto each of the Mouse G3 8x60K Expression arrays. The arrays were hybridized in an Agilent Hybridization Chamber for 17 hours at 65C with rotation at 10rpm.

scan_protocol: Once dry, the slides were scanned with the Agilent Scanner (G2565BA) using Scanner Version C and Scan Control software version A.8.5.1. Data extraction and quality assessment of the microarray data was completed using Agilent Feature Extraction Software Version 11.0.1.1.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: uterus, day 4.5 natural pregnancy

label_protocol: Twenty-five nanograms of total RNA, combined with RNA spike mix, were reverse transcribed using a T7 Primer Mix to produce cDNA. The cDNA product was transcribed using T7 RNA Polymerase, producing cyanine-3-labeled cRNA. The labeled cRNA was purified using a Qiagen RNeasy Mini Kit. Purified products were quantified using the NanoDrop spectrophotometer for yield and dye incorporation, and tested for integrity on the Agilent Bioanalyzer. Six hundred nanograms of the labeled cRNA were fragmented.

growth_protocol: Female mice were fed normal chow and were mated to vasectomized males at 8-10 weeks of age.

extract_protocol: RNA was isolated from frozen tissue using Trizol and aqueous phase separation techniques with the Qiagen RNEasy prep kit.

treatment_protocol: Female mice at breeding age were mated to vasectomized males and sacrificed 4 days after the presence of the post-coital plug. Uteri were harvested and frozen.

value: whole uterine

tag: gender

value: female

tag: genotype/variation

value: PGRA overexpression


title: 44125 Wnt7acre+ day 4.5

value: wild type


title: RNAseq_whole_tissue_BM_DR_rep2


title: RNAseq_whole_tissue_BM_DR_rep1


title: RNAseq_whole_tissue_BM_Ctrl_rep2


title: RNAseq_whole_tissue_BM_Ctrl_rep4


title: 44127 Wnt7acre+ day 4.5


title: 44126 Wnt7acre+ day 4.5


title: 44128 Wnt7acre+mPRALsL/+ day 4.5


title: 44129 Wnt7acre+mPRALsL/+ day 4.5


title: d30 RNA-seq rep2

status: Public on Aug 19 2019

data_processing:
RNA-seq reads were aligned to the hg19 genome assembly using hisat2 (version 2.1.0) with the default parameters.
Read counts representing gene expression levels were calculated by HTSeq (version 0.9.1) with the default parameters using Genecode database annotations (version 19).
Remove all non protein coding genes.
bigwig (bw) files were generated using deepTools bamCoverage (version 3.0.2) tools was used to generate bigwig files with the default parameters
Genome_build: hg19
Supplementary_files_format_and_content: bigwig (bw) files and read counts file

source_name: Pluripotent stem cells

growth_protocol: Undifferentiated and differentiated PSCs c were cultured under feeder-free conditions. Day 0 PSCs were cultured on Essential 8TM Flex basal medium (GIBCO, cat # A2858501). Day 4, 7 and 15 cells were cultured on KSFM (supplemented with 30 µg/mL BPE and 0.2 ng/mL EGF) + 0.3 mg/mL RA + 10 ng/mL BMP-4 and day 30 cells were cultured on Basal KSFM (GIBCO, cat#17005-042) (supplemented with 30 µg/mL BPE and 0.2 ng/mL EGF).  We cultured Primary keratinocytes (KRT) on Keratinocyte Basal Medium (KGM, Lonza, cat# 4131) supplemented with 100 units/mL P/S (GIBCO), 0.1 mM ethanolamine (Sigma-Aldrich), 0.1 mM O-phosphoethanolamine (Sigma Aldrich) 0.4% bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor (all Lonza cat # 4131).

tag: passages

tag: cell type

value: Pluripotent stem cells


title: RNAseq_whole_tissue_BM_Ctrl_rep3

tag: strain


title: d30 RNA-seq rep1


title: d7 RNA-seq rep1


title: d7 RNA-seq rep2


title: d15 RNA-seq rep1


title: d15 RNA-seq rep2


title: KRT RNA-seq rep1

source_name: Keratinocytes

value: KRT

value: Keratinocytes


title: d4 RNA-seq rep1


title: d4 RNA-seq rep2


title: d0 RNA-seq rep2


title: mutant2_day0_CTCF ChIP-Seq

status: Public on Jun 21 2019

data_processing:
Sequenced reads were aligned against the UCSC human reference genome (GRCh37/hg19) with Burrows-Wheeler Aligner (BWA) program with default parameters
The potential PCR and optical duplicates were removed using Picard MarkDuplicates option. The filtered BAM files were inputted to MACS2 for peak calling.
Genome_build: hg19
Supplementary_files_format_and_content: bw files contain continuous data that will be displayed in the Genome Browser as a graph

source_name: keratinocytes

growth_protocol: primary keratinocytes were cultured in Keratinocyte Basal Medium (KBM, Lonza #CC-4131) supplemented with 100 U/mL Penicillin/Streptomycin (Gibco Life Technology #15140122), 0.1 mM ethanolamine (Sigma Aldrich #141-43-5), 0.1 mM O-phosphoethanolamine (Sigma Aldrich #1071-23-4), 0.4% (vol/vol) bovine pituitary extract, 0.5 μg/mL hydrocortisone, 5 μg/mL insulin and 10 ng/mL epidermal growth factor (Lonza #CC-4131). Medium was refreshed every other day. When cells were more than 90% confluent, samples are collected for the proliferation stage. No mycoplasma contamination is found during cell culture.

extract_protocol:
Chromatin was incubated overnight at 4 °C in 1× incubation buffer (0.15% SDS, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES) supplemented with protease inhibitors and 0.1% BSA. A 50:50 mix of Protein A and G Dynabeads (Invitrogen) were added. Antibodies against H3K4me3 (Diagenode, C15410003, 1 μg), H3K27me3 (Diagenode, C15410069, 1.5 μg) and RUNX1 (ab23980, abcam, 4 μg) were used in each ChIP assay. The beads were washed twice with wash buffer 1 (0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), once with wash buffer 2 (wash buffer 1 with 500 mM NaCl), once with wash buffer 3 (250 mM LiCl, 0.5% sodium deoxycholate, 0.5% NP-50, 1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES), and twice with wash buffer 4 (1 mM EDTA, 0.5 mM EGTA, and 20 mM HEPES). After the washing steps, beads were rotated for 20 min at room temperature in elution buffer (1% SDS and 0.1 M NaHCO3). The supernatant was de-cross-linked with 200 mM NaCl and 100 μg/mL proteinase K for 4 h at 65 °C. De-cross-linked DNA was purified with MinElute PCR Purification columns (Qiagen). DNA amounts were determined with Qubit fluorometric quantification (ThermoFisher Scientific).
The pulled down DNA fragments were proceeded on with library construction using KAPA Hyper Prep Kit (Kapa Biosystems #KK8504) according to the standard protocol. The prepared libraries were then sequenced using the NextSeq 500 (Illumina) according to standard Illumina protocols.

treatment_protocol: no treatment

tag: cell line

tag: Stage

value: day0 (proliferation)

value: CTCF antibody (Millipore #07-729)


title: mutant2_day0-2_ATAC-Seq

data_processing:
Sequenced reads were aligned against the UCSC human reference genome (GRCh37/hg19) with Burrows-Wheeler Aligner (BWA) program with default parameters
The potential PCR and optical duplicates were removed using Picard MarkDuplicates option. The filtered BAM files were inputted to MACS2 for peak calling. For ATAC-seq, the open chromatin regions were predicted using default parameters except for using -f BAMPE option. Peaks overlapping with the consensus excludable ENCODE blacklist were dropped to avoid confounding by repetitive regions.
Genome_build: hg19
Supplementary_files_format_and_content: bw files contain continuous data that will be displayed in the Genome Browser as a graph

extract_protocol:
In brief, keratinocytes were treated with Accutase® solution on plates and well re-suspended into single cells.
Pellet cells for 5 min at 500 g. After twice wash with ice-old PBS, pellet the cells again. Re-suspend cells and take out 100,000 cells for lysis with ice-old freshly made lysis buffer (containing 10 mM Tris-HCl pH 7.5, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 detergent). Then perform tagmentation using 2 μl of Tn5 transposase and 12.5 ul 2 × TD buffer (Illumina # FC-121-1031) at 37°C for 1h with 650 rpm shaking. The resulted DNA fragments underwent two sequential seven-cycle PCR amplification, and in between the libraries were selected for <500 bp fragments using SPRI beads. The final PCR products were purified with QIAquick PCR Purification Kit (QIAGEN # 28106) and quantified with the KAPA Library Quantification Kit (Kapa Biosystems #KK4844), and then sequenced in a paired-ended manner using the NextSeq 500 (Illumina) according to standard Illumina protocols.


title: mutant2_day0-1_ATAC-Seq


title: KRT RNA-seq rep2


title: RNAseq_whole_tissue_BM_Ctrl_rep1


title: mutant1_day0_CTCF ChIP-Seq


title: mutant1_day0-2_ATAC-Seq


title: mutant1_day0-1_ATAC-Seq


title: d0 RNA-seq rep1


title: HKC_day0-2_ATAC-Seq


title: E16 Sox2-EGFP+ cochlear duct cells rep 2

city: Seattle

first: Olivia

last: Bermingham-McDonogh

state: WA

address: 1959  NE Pacific St box 357420

department: Biological Structure

institute: University of Washington

data_processing:
Basecalls performed by Genomics & Bioinformatics Shared Resource at the Fred Hutchinson Cancer Research Center (Illumina Hi-seq 2500) and Seattle Genomics (Illumina Next Seq 500)
Adapters were trimmed from reads and low-quality sequences (Phred <33) were removed using Trim Galore!
Reads were aligned to mm9 using Bowtie2 (option: --very-sensitive)
Duplicate reads were marked using Picard ‘MarkDuplicates’
Duplicate and mitochondrial reads were removed using SAMtools
Bigwigs were generated using a custom script (https://rpubs.com/achitsaz/98857)
Peaks were called using MACS2 (options: --nomodel --shift -100 --extsize 200)
Irreproducible peaks were filtered using BEDOPS107 (command: ‘bedops -e 1 replicate1.bed replicate2.bed’). Overlapping and nearby ATAC-seq peaks were merged using BEDtools108 (command: bedtools merge -i replicatedpeaks.bed -d 100). Peaks in regions previously found by ENCODE to produce artefactual signal109 (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/) were removed using BEDOPS command: -n 1.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig,  bed

source_name: E16 Sox2-EGFP+ cochlear duct cells

extract_protocol:
Cochlear ducts were microdissected from E12-E16 temporal treated with collagenase and dispase. Cochlear ducts were dissociated using the Worthington papain dissociation kit. Sox2-EGFP+ and Sox2-EGFP- cells were sorted by FACS.
Libraries were prepared from up to 50,000 cells using the Illumina Nextera kit as described by Buenrostro et al. Curr Protoc Mol Biol. 2015.

value: B6;129S-Sox2tm2Hoch/J (Jackson Stock No. 017592)

tag: stage (embryonic day)

value: cochlear duct


title: E16 Sox2-EGFP- cochlear duct cells rep 1

source_name: E16 Sox2-EGFP- cochlear duct cells


title: E14.5 Sox2-EGFP+ cochlear duct cells rep 2

source_name: E14.5 Sox2-EGFP+ cochlear duct cells


title: HKC_day0-1_ATAC-Seq


title: E14.5 Sox2-EGFP- cochlear duct cells rep 2

source_name: E14.5 Sox2-EGFP- cochlear duct cells


title: E16 Sox2-EGFP- cochlear duct cells rep 2


title: E16 Sox2-EGFP+ cochlear duct cells rep 1


title: E12 Sox2-EGFP+ cochlear duct cells rep 2

source_name: E12 Sox2-EGFP+ cochlear duct cells


title: HKC_day0_CTCF ChIP-Seq


title: E12 Sox2-EGFP+ cochlear duct cells rep 1


title: E14.5 Sox2-EGFP+ cochlear duct cells rep 1


title: genomic DNA from monocytes 45

status: Public on Jun 20 2019

type: genomic

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner protocol

data_processing: GenomeStudio v2011.1 and Methylation module (within GenomeStudio) v1.9 was used.

label: Cy3, Cy5

source_name: RRMS patient with Low BMI

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from CD14+ sorted blood monocytes using Qiagen DNeasy Kit according to standard instructions

value: F

tag: bmi

tag: therapy

value: Naive

tag: disease state

value: CIS

value: blood monocytes


title: genomic DNA from monocytes 37

value: RRMS


title: genomic DNA from monocytes 47

source_name: RRMS patient with High BMI


title: genomic DNA from monocytes 42


title: genomic DNA from monocytes 33


title: genomic DNA from monocytes 39


title: genomic DNA from monocytes 26

value: M


title: genomic DNA from monocytes 38


title: genomic DNA from monocytes 29


title: genomic DNA from monocytes 34


title: genomic DNA from monocytes 44


title: genomic DNA from monocytes 43


title: genomic DNA from monocytes 41


title: genomic DNA from monocytes 36


title: genomic DNA from monocytes 40


title: genomic DNA from monocytes 46


title: genomic DNA from monocytes 32


title: genomic DNA from monocytes 30


title: genomic DNA from monocytes 21


title: genomic DNA from monocytes 48


title: genomic DNA from monocytes 24


title: genomic DNA from monocytes 27


title: genomic DNA from monocytes 20


title: genomic DNA from monocytes 22


title: genomic DNA from monocytes 49


title: genomic DNA from monocytes 35


title: genomic DNA from monocytes 31


title: genomic DNA from monocytes 23


title: genomic DNA from monocytes 25


title: genomic DNA from monocytes 28