title: D0_Mll2-KO_H3K4me2_repA

status: Public on Oct 01 2025

city: Santander

first: Lucio

last: Di Filippo

address: PCTCAN - Cl. Albert Einstein, 22

country: Spain

institute: IBBTEC

description: Library name: Sample 39

data_processing:
Basic read quality check was performed using FastQC (Babraham Bioinformatics) and MultiQC. The removal of read adapters and low-quality filtering was done with trimgalore(v0.6.7).
Reads were mapped to the mm10 reference genome with STAR v2.6.1d (--outSAMtype BAM Unsorted --runMode alignReads --outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 3 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 350 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 30000 --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000 --readFilesCommand zcat).
Duplicate reads were marked with picard tool (3.1.1)
Bigwig files were generated with deepTools v3.5.1 using bamCoverage (--normalizeUsing 'RPGC').
Assembly: mm10

source_name: Mll2-KO mESC

growth_protocol: mESC were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM (Thermo Fisher Scientific, 10829018) supplemented with 15% fetal bovine serum (FBS; Thermo Fisher Scientific, A5256801), 1x antibiotic and antimycotic solution (Sigma-Aldrich, A5955), 1x glutaMAX (Thermo Fisher Scientific, 35050038), 1x non-essential amino acids (NEAA; Thermo Fisher Scientific, 11140035), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific, 21985023) and leukemia inhibitory factor (LIF; made in-house). Cells were maintained at 37 °C with 5% CO2. For the multilineage differentiation, cells were grown on 0.1% gelatin-coated plates, using KnockOutTM DMEM supplemented with 10% FBS, 2 mM L-glutamine (Thermo Fisher Scientific, 25030024), 0.1 nM β-mercaptoethanol, 1x NEAA, 1x antibiotic and antimycotic solution and 1 µM retinoic acid (RA; Sigma-Aldrich, R2625) for 4 days.

extract_protocol:
Approximately 10 million and 40 million cells were used for histone PTMs and COMPASS subunits ChIPs, respectively.  For histone modification ChIP assays, cells were crosslinked with 1% formaldehyde for 10 minutes at room temperature (RT) before being quenched with 0.125 M glycine for another 10 minutes, while for COMPASS subunits ChIP assays cells were double crosslinked with ChIP cross-link Gold (Diagenode, C01019027) and 1% formaldehyde according to the manufactor’s instructions. Chromatin was isolated through sequential incubation with three distinct lysis buffers: LB1 (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), and LB3 (10 mM Tris-HCl pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine). Chromatin sonication was carried out in LB3 using an EpiShearTM sonicator (Active Motif; 4-5 minutes, 20 seconds ON and 30 seconds OFF at 25% amplitude). The sheared chromatin was then incubated O/N at 4 °C with either 5 or 10 μg of antibody for histone PTMs or COMPASS subunits respectively.
DNA libraries were prepared using the TruSeq ChIP-seq sample preparation kit. 10 ng of ChIP DNA was used as starting material.

treatment_protocol: Starting from a previously described Cre-inducible Mll2-KO mESC line, Mll1-KO mESC were generated via CRISPR editing. Two sg-RNAs were designed flanking the region to-be deleted for each line, using Benchling’s CRISPR tool (https://www.benchling.com/crispr). For each sgRNA, two oligonucleotides were synthesized , annealed and cloned into a CRISPR-Cas9 expression vector (pX330-hCas9-long-chimeric-grna-g2p, provided by Leo Kurian’s lab). mESC were transfected with CRISPR-Cas9 constructs using LipofectamineTM 3000 (Thermo Fisher Scientific, L3000001).  For the generation of Mll2-KO and double-KO mESC lines, cells were treated with (Z)-4-Hydroxytamoxifen (4-OHT; Sigma-Aldrich, H7904) at a final concentration of 800 nM for 48 hours.

tag: cell line

value: Mll2-KO mESC

value: mESC

value: H3K4me2 antibody (Active Motif, 39141)


title: m3 Old Rep1 ATAC

status: Public on Apr 17 2024

type: SRA

city: La Jolla

first: Peter

middle: D.

last: Adams

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

description: m3 Old technical rep1, biological rep1

library_source: genomic

data_processing:
Raw reads quality were checked using FastQC v0.10.0
Raw reads were trimmed with threshold quality score > 20 using Trimgalore v0.3.0
Trimmed reads were aligned to mm9 using bowtie2
Duplicated reads were marked using Picard Tools v1.98.
Peaks were called using macs2 with parameter --nomodel
Assembly: mm9
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

molecule: genomic DNA

organism: Mus musculus

source_name: liver

extract_protocol:
Nuclei were extracted from whole liver and lysed using diluted 10x (LB): 100mM Tris.Hcl pH 7.5, 100mM NaCl, 30mM MgCl2, 1% Igepal CA-630 with 2% BSA and protease inhibitor diluted in PBS.
Tagmentation reaction was for 30 minutes at 37C then DNA was isolated and 6-PCR cycles (72C 3m, 95C 30s, (95C for 10s, 63C for 30s, 72C for 1 min) X15, 72C for 3 min, 4C) with i5xx and i7xx primers followed by a gel size selection of 220-1000bp.

treatment_protocol: Mice were aged for 6 and 23 months under IACUC supervision and provided normal CHOW (Teklad global 18% protein)

tag: tissue

value: liver

tag: strain

tag: Sex

value: male

tag: age (months)

tag: treatment

value: Aging


title: tbsP_a_noglu

status: Public on Dec 01 2023

city: Durham

first: Amy

middle: K

last: Schmid

state: NC

address: 124 Science Dr

institute: Duke University

library_source: transcriptomic

data_processing:
Merged FASTQ files for samples that were loaded onto multiple lanes of a given flowcell, respecting read pair assignment. Ex) cat *_L001_R1_001.fastq.gz *_L002_R1_001.fastq.gz
Adapter sequences were removed with Trim_galore! 0.4.3, cutadapt 2.3, and and sample quality assessed with FastQC 0.11.7 using default parameters.
Reads were aligned to the Haloferax volcanii DS2 reference genome (GCA_000025685.1, accessed 2023-09-11) with Bowtie2 2.3.5.1. Alignment by Bowtie2 required stand-specific read orientation for libraries constructed in the 2021 experiment. Only pairs aligning concordantly in the --rf orientation were considered.
Aligned sequence files were converted to binary format, sorted, and indexed using samtools 1.10.
Reads (for samples from 2019) or read paris (2021 samples) aligning to ORFs were counted using featureCounts 2.0.1 with arguments -p -B -s 2 and the DS2 reference genome  annotation (GCA_000025685.1, accessed 2023-09-11). For 2021 samples, fragments were required to align concordantly in the correct strand orientation (reverse) to be tallied.
In R, counts from 2019 and 2021 experiments were normalized relative to library size and batch corrected with DeSeq2 1.34.0. Pairwise correlations were computed using normalized counts for samples within each genotype+condition group, and samples with average R < 0.7  were considered outliers and were not used in downstream analyses.
Assembly: GCA_000025685.1
Supplementary files format and content: Text file of fragments mapping to genes. Each column is a sample, and rows are counts mapping to a given gene.

molecule: total RNA

organism: Haloferax volcanii DS2

source_name: H26 ∆pyrE2∆tbsP (HVO_2861)

growth_protocol: Four single colonies of DF60 and ASK133 or AKS319 from 10-day old plates were inoculated in 5 mL YPC23 medium supplemented with 0.1% glucose and grown aerobically (250 rpm shaking) at 37C to stationary phase (optical density at 600nm ~ 4). Cells were washed twice with Hh-CA medium without glucose and transferred into fresh 50 mL Hh-CA with or without 0.1\% glucose at an initial optical density of ~ 0.4. After 24 hours cultures were collected and flash frozen with liquid nitrogen.

extract_protocol:
After 24 hours storage in -80C, RNA was extracted from cell pellets using Absolutely RNA Miniprep kit (Agilent Technologies, Santa Clara, CA).  For all samples, the absence of DNA contamination was determined on 200 ng samples of RNA in 25 cycles of PCR and total RNA was quantified using Agilent Bioanalyzer RNA Nano 6000 chip (Agilent Technologies, Santa Clara, CA). For 2019 samples,  ribosomal RNA was removed with Ribo-Zero rRNA Removal Kit (now discontinued, Illumina, San Diego, CA). For 2021 samples, extraction was followed by additional DNAse treatment with Turbo DNAse (Invitrogen), and ribosomal RNA was removed from total RNA with the PanArchaea riboPOOL kit according to the manufacturer protocol (siTOOLs Biotech, Germany) and checked for depletion using Agilent Bioanalyzer RNA Nano 6000 chip as described as described in Pastor et al. 2022.
For 2019 samples, rRNA-depleted RNA was used to construct the sequencing libraries with KAPA Stranded RNA-seq Library preparation (Kapa Biosystems) following manufacturer protocol. Fragment size of final libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on Illumina HiSeq4000 at the Duke Sequencing and Genomic Technologies Core Facility at Duke University (Durham, NC). For 2021 samples, sequencing libraries were constructed with NEBNext UltraII Directional RNA Library Preparation Kit (New England BioLabs, #E7760). The fragment size of all libraries was measured using Agilent Bioanalyzer DNA 1000 chip and then pooled and sequenced on NovaSeq6000 at the Center for Genomic and Computational Biology at Duke University (Durham, NC).

tag: genotype

value: H26 {delta}pyrE2{delta}tbsP (HVO_2861)

tag: cell type

value: archaeal cell culture

value: HvCA + uracil

tag: time

tag: year-flowcell


title: deltadelta_b_noglu

source_name: H26 ∆pyrE2∆trmB∆tbsP

value: H26 {delta}pyrE2{delta}trmB{delta}tbsP


title: tbsP_a_glu

value: HvCA + uracil + 0.1% glucose (w/v)


title: deltadelta_a_noglu


title: tbsP_d_glu


title: trmB_c_glu

source_name: H26 ∆pyrE2∆trmB

value: H26 {delta}pyrE2{delta}trmB


title: tbsP_b_noglu


title: trmB_b_noglu


title: tbsP_b_glu


title: deltadelta_a_glu


title: trmB_c_noglu


title: tbsP_c_noglu


title: deltadelta_d_noglu


title: deltadelta_c_glu


title: parental strain no iron repl 2

status: Public on Nov 16 2023

address: 125 Science Dr.

department: Biology

description: ∆pyrE

data_processing:
50bp paired reads were quality checked using FastQC, adapter sequences trimmed using Trim Galore and Cutadapt.
Result sequences were aligned to the Haloferax volcanii DS2 genome (RefSeq GCF_000025685.1) using Bowtie2.
BAM files were generated using samtools, they were inputs to generate count files using HTSeq (count files associated with each sample are included in this GEO dataset)
Count files were input into DeSeq2 to generate normalised counts, exclude outlier samples, and generate lists of differentially expressed genes in pairwise comparisons.
Assembly: GCF_000025685.1
Supplementary files format and content: tab-delimited text file with raw counts for each gene

organism: Haloferax volcanii

source_name: archaeal cells

growth_protocol: Triplicate cultures of strains ∆pyrE (control strain) and  ∆troR (TF knockout strain) were grown in rich media overnight and then washed and resuspended in minimal media  supplemented with iron until stationary phase; finally,  cells were subcultured in minimal media with or without iron  until  mid-log phase (OD600 ~0.4). Cells were then pelleted, freezed with N2 and processed.

extract_protocol:
RNA was extracted using the Agilent Kit as per the manufacturer's protocol, quantified by bioanalyzer and checked for quality by PCR to ensure that it was not contaminated by gDNA. rRNA removal using RiboZero
Libraries were constructed using the KAPA Hyper Prep kit and Illumina TruSeq adapters according to manufactuer's instructions. DNA library quality was assessed by Bioanalyzer using a High Sensitivity DNA chip (Agilent). Samples were pooled and run in a single lane on an Illumina HiSeq 4000 (Duke Sequencing and Genomics Technologies core).

treatment_protocol: Cells were grown in Minimal Media (PR) with 100 microM Fe2SO4 or PR treated with iron chelator BPS and without iron addition.

value: archaeal cell

value: {delta}pyrE

tag: growth phase

value: mid-log

tag: condition

value: iron chelated


title: parental strain no iron repl 1

description: ∆pyrE


title: tbsP_e_noglu


title: troR knockout repl 2

description: ∆pyrE ∆troR

value: {delta}pyrE {delta}troR

value: 100 mM Fe2SO4


title: deltadelta_b_glu


title: parental strain repl 3

description: ∆pyrE


title: deltadelta_d_glu


title: parental strain repl 1

description: ∆pyrE


title: RNAseq_H.volcanii_delta2753_p2_R2

status: Public on Nov 13 2023

city: Freiburg

first: Rick

last: Gelhausen

state: Baden Württemberg

address: Georges-Köhler-Allee 106

department: Department of Computer Science

country: Germany

institute: Albert-Ludwigs-University Freiburg

description: Total RNA extracted from delta HV0_2753 mutant strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.1 (cutadapt parameters: -q 20 --trim-n -m 10 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC) (HRIBO 1.6.0)
Mapping with segemehl 0.3.4 (HRIBO 1.6.0)
rRNA filtering was done using samtools 1.9 (HRIBO 1.6.0)
Coverage files were created using HRIBO 1.6.0
bigwig files were generated with full read coverage and normalized to the size of the minimal sample size among all samples.
Assembly: GCF_000025685.1
Supplementary files format and content: bigwig format files containing normalized read coverage for each sample

source_name: Haloferax volcanii DS2 H26

growth_protocol: H. volcanii cells were grown to exponential phase

extract_protocol:
Total RNA was extracted using  phenol-chloroform-isoamyl alcohol (25:24:1, Roth).
Total RNA was first rRNA-depleted, fragmented then subjected to cDNA library preparation. First, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified  using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and was analyzed by capillary electrophoresis.
Adapter ligation protocol for RNA-seq performed at Vertis Biotechnology

treatment_protocol: No treatment applied during growth.

value: delta HV0_2753 mutant strain


title: parental strain no iron repl 3

description: ∆pyrE


title: RNAseq_H.volcanii_delta2753_p2_R1


title: D0_Mll1-KO_H3K27ac_repB

description: Library name: Sample 31

source_name: Mll1-KO mESC

value: Mll1-KO mESC

value: mESC

value: H3K27ac antibody (Active Motif, 39133)


title: troR knockout repl 3

description: ∆pyrE ∆troR


title: RNAseq_H.volcanii_H26WT_p2_R2

description: Total RNA extracted from WT strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation (WT for delta  HV0_2753 mutant strain)

value: WT


title: RNAseq_H.volcanii_H26WT_p1_R1

description: Total RNA extracted from WT strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation (WT for delta  HV0_0758 mutant strain)


title: troR knockout repl 1

description: ∆pyrE ∆troR


title: WT IL, replicate 2, scRNAseq

status: Public on Nov 06 2023

city: Pittsburgh

first: Shanshan

last: Song

state: PA

address: 3501 Fifth Ave

institute: University of Pittsburgh

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics) analysis pipeline was used to perform alignment, filtering and counting of barcodes, and unique molecular identifiers. The sequencing data was aligned to the mouse genome mm10. Count matrices generated by Cell Ranger were imported into Partek Flow 8.0 for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain white matter (ipsilateral to stroke)

extract_protocol:
Single-cell RNA sequencing and bioinformatic analysis were performed in white matter tissues dissected from the WT or Nhe1 cKO brains at 3 days post-tMCAO. Briefly, mice were euthanized with an overdose of CO2 and transcardially perfused with ice-cold saline, as described before (10). The brains were dissected and cut into 4 coronal slices of 2 mm thickness in a brain slicer matrix. Cortices were removed and white matter tissues (corpus callosum and external capsules) were separated from the contralateral and ipsilateral hemispheres and dissociated into single-cell suspensions using a Neural Tissue Dissociation Kit with the gentleMAC Octo Dissociator (Miltenyi Biotech Inc., Germany). Myelin was removed using the 30/70 Percoll gradient method as described (10). Single-cell suspension was prepared as we described before 13 and used for droplet-based scRNAseq (10x Genomics).
The quality of the single-cell suspension was confirmed prior to the start of library preparation with an acridine-orange-propidium iodide stain (Nexcelcom Biosciences) and a Cellometer Auto 2000 Viability Counter (Nexcelcom Biosciences). Library Preparation (Chromium Next GEM Single Cell 3’ Reagent kit v3.1) was conducted as per the manufacturer’s protocol. The quality of the cDNA libraries was verified using a High Sensitivity D5000 ScreenTape and 4200 Tapestation system (Agilent Technologies).

treatment_protocol: Both genotypes of mice (male or female) at postnatal day 30-40 (P30-40) received tamoxifen (Tam, Sigma) (75 mg/kg body weight/day at a concentration of 20 mg/ml in corn oil, intraperitoneally) for 5 consecutive days. As Cx3cr1 is expressed by both brain resident microglia and peripheral infiltrating bone marrow-derived myeloid cells (BMDM), a 30-day post-injection waiting period was given for clearance of Tam 3-5 and for replenishing of Cx3cr1+ monocytes 6 prior to induction of ischemic stroke.

value: tamoxifen


title: WT CL, replicate 1, scRNAseq

description: 10x Genomics

source_name: brain white matter (contralateral to stroke)


title: CSF1 stimulated Input sgRNAs

status: Public on Oct 01 2023

city: Brookings

first: Natalie

last: Thiex

state: SD

address: 1066 Campanile Ave, Box 2022A ookings

department: Biology and Microbiology

institute: South Dakota State University

description:
This sample represents the sgRNAs used to transduce cells with for the CSF1 stimulated dextran uptake screen
CSF1stim.count.txt

library_source: other

data_processing:
20 base sgRNA reads were trimmed using Cutadapt 2.3, where 20bp sequence flanked by cgaaacaccg...gttttagagc was identifed from all fastq files. Cutadapt arguments= -g cgaaacaccg...gttttagagc, -o, --minimum-length 15, --discard-untrimmed, -e 0.2, --cores=8
Counts of sgRNA reads generated and mapped to Brie library sgRNAs using MAGeCK 0.5.9. arguments= count, -l BrieGuideLibwithNonTarg.csv, --sample-label, --fastq, -n, --unmapped-to-file, --pdf-report
We used the MAGeCK test command to identify enriched sgRNAs within the high and low populations. Arguments= test, -k, -c low, -t high, -n, --control-sgrna nontargets.txt --keep-tmp --pdf-reports
Assembly: Brie Library
Supplementary files format and content: .txt and .csv files contain the data files used to process the data.  The BrieGuideLibwithNonTarg.csv file contains the Brie library file used by MAGeCK to map the trimmed reads back to the library.  The readmapping step generated the "CSF1stim.count.txt" and "unstim.count.txt" files used for the MAGeCK test functions.  The MAGeCK test step used one of the count tables and the "nontargets.txt" file to identify sgRNAs enriched in the low and high fluroescence populations.  The MAGeCK test output includes the "CSF1_dexuptake_highlow.gene_summary.txt" and "unstim_dexuptake.gene_summary.txt" files.  The MAGeCK out files were used to identify genes regulating  dextran uptake.
Library strategy: CRISPR screen

molecule: other

organism: synthetic construct

source_name: Plasmid DNA used to make lentivirus

growth_protocol: BMDM were cultured in bone-marrow medium (BMM) containing Dulbecco’s Modified Eagle Medium (4 mM L-glutamine, 4500 mg/L glucose, 1 mM sodium pyruvate, and 1500 mg/L sodium bicarbonate), 20% heat-inactivated fetal bovine serum and 30% L-cell supernatant (a source of colony-stimulating factor-1), 10,000 IU penicillin and 10 mg/mL streptomycin, and 5.7 mM 2-mercaptoethanol.

extract_protocol:
Genomic DNA was extracted from cells using the GeneJET genomic DNA extraction kit (#K0721 Thermofisher) and the sgRNA library was amplified by a single-step PCR protocol (Broad Institute) for NGS using barcoded primers with staggered sequences. PCR product from multiple PCR reactions was pooled and gel purified and quantified by Qubit Fluorometer and subjected to sequencing on Illumina Nextseq 500 with 75 reads.
Mouse Brie CRISPR knockout pooled library developed by David Root and John Doench was obtained from Addgene (Addgene #73633) was amplified in Stable 3 competent E. coli (Thermofisher) and subjected to next-generation-sequencing (NGS) to determine the distribution of sgRNAs in the library. To produce Lentivirus, 1.8 x 106 NIH 293T cells were seeded in six 10-cm plates and transfected the following day with 6 μg sgRNA pooled library in lentiGuide-Puro (Addgene# 73633), 6 μg psPAX2 plasmid, 1 μg pVSVG plasmid, and 0.024 mg polyethyleneimine (PEI). After 48 h, the lentivirus was harvested, centrifuged, and aliquoted into multiple 15 mL tubes and stored at -80o C or - 150o C. The functional titer of the lentivirus was determined by live-cell counting after puromycin selection.
The parameters for how the library sequenced - chip: 75 high fidelity read

treatment_protocol: Primary Macrophages expressing Cas9-GFP were transduced with the Brie Library at low multiplicity of infection (MOI) (0.3) to achieve 50 fold representation of each sgRNA in the Brie Mouse library.  After 48 h, transduced cells were selected with 5 ug/ml puromycin for 2 days and cultured another 8 before sorting.  To identify genes regulating dextran uptake, cells were starved of CSF1 overnight in DMEM plus 10% FBS.  Then, cells were exposed to 300 ug/ml 40 kDa fluorescent dextran for 15 minutes in the presence or absence of CSF1.  Cells were then sorted based on their ability to internalize dextran using a BD FACs jazz flow cytometer.  We sorted the top (high fluorescence) and bottom (low fluorescence) quintiles based on dextran fluorescence and sequenced both samples to idenfity sgRNAs enriched in each sample.


title: Detached cells sgRNAs

description:
This sample represents the sgRNAs enriched within the cells that detached from the plate following CSF1 stimulation.
Unstim.count.txt

source_name: Bone Marrow Derived Macrophages

value: Primary Macrophage


title: RNAseq_H.volcanii_H26WT_p1_R2


title: parental strain repl 2

description: ∆pyrE


title: WT CL, replicate 2, scRNAseq

description: 10x Genomics

value: brain white matter (contralateral to stroke)


title: Unstimulated low dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the unstimulated low dextran uptake sample.  These sgRNAs induced a loss of function that decreased dextran uptake.
Unstim.count.txt


title: Unstimulated Presort sgRNAs

description:
This sample represents the sgRNAs present in the cell populations on sorting day for the unstimulated dextran uptake screen
Unstim.count.txt


title: CSF1 stimulated high dextran uptake sgRNAs

description:
This samples represents the sgRNAs present in the high dextran uptake sample and induced a gain of function that increased dextran uptake in response to CSF1 stimulation.
CSF1stim.count.txt


title: CSF1 stimulated low dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the low dextran uptake samples.  These sgRNAs induced a loss of function that reduced dextran uptake in response to CSF1 stimulation.
CSF1stim.count.txt


title: RNAseq_H.volcanii_d0758_p1_R1

description: Total RNA extracted from delta HV0_0758 mutant strain, DNaseI digested, rRNA depleted, fragmented and subjected to cDNA library preparation

value: delta HV0_0758 mutant strain


title: RNAseq_H.volcanii_d0758_p1_R2


title: Unstimulated Input sgRNAs

description:
This sample represents the sgRNAs used to transduce cells with for the unstimulated dextran uptake screen
Unstim.count.txt


title: CSF1 stimulated Presort sgRNAs

description:
This sample represents the sgRNAs present in the cell populations on sorting day for the CSF1 stimulated dextran uptake screen
CSF1stim.count.txt


title: RNAseq_H.volcanii_H26WT_p2_R1


title: WT IL, replicate 1, scRNAseq

description: 10x Genomics

value: brain white matter (ipsilateral to stroke)


title: genomic DNA from eutopic endometrium Sample_897

status: Public on Sep 12 2023

type: genomic

city: Herston

first: Sally

last: Mortlock

state: Queensland

address: AWaGHR Centre, School of Public Health, The University of Queensland

department: School of Public Health

country: Australia

institute: University of Queensland

description:
genomic DNA from eutopic endometrium
Control eutopic endometrium sample

hyb_protocol: All DNA samples were adjusted to the same volume and concentration for sodium bisulfite conversion followed by DNAm analysis on the Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Standard Illumina scan protocol was performed at the University of Southern California Epigenome Center.

data_processing:
Background correction with dye-bias, signal intensity normalization and Beta value generation performed using the SeSAME R package. Samples with a low overall intensity signal (median unmethylated or methylated signal <9), a detection p-value >0.05 in more than 1% of DNAm sites were removed. Probes with a detection p-value >0.05 in more than 10% of samples and probes not overlapping between batches were removed. Probes were masked based on the SeSAME package. 759,345 DNAm sites for 984 samples remained.
Normalized Beta and Normalized M-value

label: Cy3 and Cy5

organism: Homo sapiens

source_name: endometrium sample 897

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from endometrial samples

tag: gender

value: Female

tag: sample type

value: endometrium

tag: disease state

value: Control

tag: cycle phase

value: ESE

tag: plate

tag: terminus

tag: batch

tag: euro

value: EUR

tag: recruiment

tag: age


title: genomic DNA from eutopic endometrium Sample_896

source_name: endometrium sample 896

value: PE


title: Unstimulated high dextran uptake sgRNAs

description:
This sample represents the sgRNAs enriched within the unstimulated high dextran uptake sample.  These sgRNAs induced a loss of function that increased dextran uptake.
Unstim.count.txt

tag: strain


title: genomic DNA from eutopic endometrium Sample_894

description:
genomic DNA from eutopic endometrium
Endometriosis eutopic endometrium sample

source_name: endometrium sample 894

value: Endometriosis


title: genomic DNA from eutopic endometrium Sample_891

source_name: endometrium sample 891


title: genomic DNA from eutopic endometrium Sample_898

source_name: endometrium sample 898

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_889

source_name: endometrium sample 889

value: MSE


title: genomic DNA from eutopic endometrium Sample_888

source_name: endometrium sample 888


title: genomic DNA from eutopic endometrium Sample_885

source_name: endometrium sample 885


title: genomic DNA from eutopic endometrium Sample_886

source_name: endometrium sample 886


title: genomic DNA from eutopic endometrium Sample_899

source_name: endometrium sample 899


title: genomic DNA from eutopic endometrium Sample_887

source_name: endometrium sample 887


title: genomic DNA from eutopic endometrium Sample_895

source_name: endometrium sample 895


title: genomic DNA from eutopic endometrium Sample_893

source_name: endometrium sample 893


title: D0_WT_RING1B_repA

description: Library name: Sample 21

source_name: WT mESC

tag: cell line

value: WT mESC

value: mESC

tag: genotype

tag: treatment

value: RING1B antibody (Cell Signalling, 5694)


title: genomic DNA from eutopic endometrium Sample_892

source_name: endometrium sample 892


title: genomic DNA from eutopic endometrium Sample_890

source_name: endometrium sample 890


title: genomic DNA from eutopic endometrium Sample_881

source_name: endometrium sample 881


title: genomic DNA from eutopic endometrium Sample_883

source_name: endometrium sample 883


title: genomic DNA from eutopic endometrium Sample_882

source_name: endometrium sample 882


title: D0_Mll1-KO_H3K27me3_repA

description: Library name: Sample 32

source_name: Mll1-KO mESC

value: Mll1-KO mESC

tag: cell type

value: H3K27me3 antibody (Active Motif, 39155)


title: genomic DNA from eutopic endometrium Sample_884

source_name: endometrium sample 884


title: genomic DNA from eutopic endometrium Sample_878

source_name: endometrium sample 878


title: genomic DNA from eutopic endometrium Sample_879

source_name: endometrium sample 879


title: genomic DNA from eutopic endometrium Sample_877

source_name: endometrium sample 877


title: genomic DNA from eutopic endometrium Sample_880

source_name: endometrium sample 880


title: genomic DNA from eutopic endometrium Sample_875

source_name: endometrium sample 875


title: genomic DNA from eutopic endometrium Sample_874

source_name: endometrium sample 874


title: genomic DNA from eutopic endometrium Sample_876

source_name: endometrium sample 876


title: genomic DNA from eutopic endometrium Sample_871

source_name: endometrium sample 871


title: genomic DNA from eutopic endometrium Sample_872

source_name: endometrium sample 872


title: genomic DNA from eutopic endometrium Sample_873

source_name: endometrium sample 873


title: genomic DNA from eutopic endometrium Sample_869

source_name: endometrium sample 869


title: genomic DNA from eutopic endometrium Sample_867

source_name: endometrium sample 867

value: LSE


title: genomic DNA from eutopic endometrium Sample_866

source_name: endometrium sample 866


title: genomic DNA from eutopic endometrium Sample_870

source_name: endometrium sample 870


title: genomic DNA from eutopic endometrium Sample_868

source_name: endometrium sample 868


title: genomic DNA from eutopic endometrium Sample_864

source_name: endometrium sample 864


title: genomic DNA from eutopic endometrium Sample_863

source_name: endometrium sample 863


title: genomic DNA from eutopic endometrium Sample_865

source_name: endometrium sample 865


title: genomic DNA from eutopic endometrium Sample_862

source_name: endometrium sample 862


title: genomic DNA from eutopic endometrium Sample_861

source_name: endometrium sample 861


title: genomic DNA from eutopic endometrium Sample_859

source_name: endometrium sample 859


title: genomic DNA from eutopic endometrium Sample_860

source_name: endometrium sample 860


title: genomic DNA from eutopic endometrium Sample_858

source_name: endometrium sample 858


title: genomic DNA from eutopic endometrium Sample_857

source_name: endometrium sample 857


title: genomic DNA from eutopic endometrium Sample_856

source_name: endometrium sample 856


title: genomic DNA from eutopic endometrium Sample_855

source_name: endometrium sample 855


title: genomic DNA from eutopic endometrium Sample_853

source_name: endometrium sample 853


title: genomic DNA from eutopic endometrium Sample_854

source_name: endometrium sample 854


title: genomic DNA from eutopic endometrium Sample_852

source_name: endometrium sample 852


title: genomic DNA from eutopic endometrium Sample_850

source_name: endometrium sample 850


title: genomic DNA from eutopic endometrium Sample_851

source_name: endometrium sample 851


title: genomic DNA from eutopic endometrium Sample_849

source_name: endometrium sample 849


title: genomic DNA from eutopic endometrium Sample_847

source_name: endometrium sample 847


title: genomic DNA from eutopic endometrium Sample_844

source_name: endometrium sample 844


title: genomic DNA from eutopic endometrium Sample_843

source_name: endometrium sample 843


title: genomic DNA from eutopic endometrium Sample_848

source_name: endometrium sample 848


title: genomic DNA from eutopic endometrium Sample_842

source_name: endometrium sample 842


title: EC-3h-ΔΔ, replicate 2, scRNA-seq

status: Public on Feb 20 2024

city: Wuhan

first: Xiaodan

last: Yan

state: Hubei Province

address: Donghu Road, No. 115, Wuchang District,

department: Medical Research Institute

country: China

institute: Wuhan University

description:
RiboD-mSPLiT
0427-4
ECOLI rRNA and mRNA reads.txt

data_processing:
The demultiplexing, barcodes processing, gene counting and aggregation of scRNA-seq data were made by scripts compiled in Python 2.7.15 as previously described with some modifications. [lattman, W. Jiang, P. Oikonomou, S. Tavazoie, Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing. Nature microbiology 5, 1192 (Oct, 2020).]. Downstream analysis of single cell data was performed using pipelines detailed in Seurat v4.3.0.
For corralation analysis of bulk RNA-Seq and scRNA-seq data, scRNA-seq data was combined with the UMI sums of all cells. Single-cell and bulk transcriptomes of E.coli were compared by computing the Pearson correlation of log2 transcripts reads of each gene between the two measurements.
For scRNA-seq data mRNA / total RNA ratio analysis, we removed the barcodes sequence contained in the front, and the interference of the last ten bases, and kept only 20 bases for mapping. Then we mapped the data from the different species to the corresponding reference genomes.
(Detailed codes were saved in "Detailed Computational Pipeline.docx" and "scripts" compressed package .)
Assembly: E.coli MG1655 K12
Supplementary files format and content: matrix files
Supplementary files format and content: xlsx file include raw counts for RNA-seq and UMI sums of scRNA-seq data
Supplementary files format and content: tab-delimited files includes raw counts for samples of the same species

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacterial cell

extract_protocol:
For RiboD-mSPLiT, all  cells were from pure culture in vitro. Cells were harvested by centrifuge;
For RiboD-mSPLiT, library was performed accarding to the Materials and Methods section;

value: bacterial cell

value: WT

value: exponential growth phase


title: genomic DNA from eutopic endometrium Sample_846

source_name: endometrium sample 846

value: Female

value: endometrium


title: genomic DNA from eutopic endometrium Sample_840

source_name: endometrium sample 840


title: genomic DNA from eutopic endometrium Sample_837

source_name: endometrium sample 837

value: ESE


title: genomic DNA from eutopic endometrium Sample_839

source_name: endometrium sample 839

value: EUR


title: genomic DNA from eutopic endometrium Sample_841

source_name: endometrium sample 841


title: genomic DNA from eutopic endometrium Sample_838

source_name: endometrium sample 838


title: genomic DNA from eutopic endometrium Sample_836

source_name: endometrium sample 836

value: PE


title: genomic DNA from eutopic endometrium Sample_835

source_name: endometrium sample 835

value: Endometriosis


title: genomic DNA from eutopic endometrium Sample_834

source_name: endometrium sample 834

value: Control


title: genomic DNA from eutopic endometrium Sample_845

source_name: endometrium sample 845


title: genomic DNA from eutopic endometrium Sample_832

source_name: endometrium sample 832


title: genomic DNA from eutopic endometrium Sample_831

source_name: endometrium sample 831

value: SE


title: genomic DNA from eutopic endometrium Sample_830

source_name: endometrium sample 830


title: genomic DNA from eutopic endometrium Sample_829

source_name: endometrium sample 829


title: genomic DNA from eutopic endometrium Sample_828

source_name: endometrium sample 828


title: genomic DNA from eutopic endometrium Sample_827

source_name: endometrium sample 827


title: genomic DNA from eutopic endometrium Sample_833

source_name: endometrium sample 833


title: genomic DNA from eutopic endometrium Sample_824

source_name: endometrium sample 824


title: genomic DNA from eutopic endometrium Sample_826

source_name: endometrium sample 826


title: genomic DNA from eutopic endometrium Sample_825

source_name: endometrium sample 825

value: MSE


title: genomic DNA from eutopic endometrium Sample_821

source_name: endometrium sample 821


title: genomic DNA from eutopic endometrium Sample_822

source_name: endometrium sample 822


title: genomic DNA from eutopic endometrium Sample_823

source_name: endometrium sample 823


title: genomic DNA from eutopic endometrium Sample_819

source_name: endometrium sample 819


title: genomic DNA from eutopic endometrium Sample_820

source_name: endometrium sample 820


title: genomic DNA from eutopic endometrium Sample_817

source_name: endometrium sample 817


title: genomic DNA from eutopic endometrium Sample_818

source_name: endometrium sample 818


title: genomic DNA from eutopic endometrium Sample_816

source_name: endometrium sample 816


title: genomic DNA from eutopic endometrium Sample_815

source_name: endometrium sample 815


title: genomic DNA from eutopic endometrium Sample_813

source_name: endometrium sample 813


title: genomic DNA from eutopic endometrium Sample_812

source_name: endometrium sample 812


title: genomic DNA from eutopic endometrium Sample_814

source_name: endometrium sample 814


title: genomic_DNAmethylation_FT73_v

status: Public on Mar 12 2025

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

hyb_protocol: Bisulfite-converted DNA was processed and hybridized to the bead chips according to the standard Illumina protocol

scan_protocol: HiScan according to the standard Illumina settings

data_processing: minfi preprocessRaw function, betas extracted

label_protocol: Standard Illumina protocol

extract_protocol: DNA salt extraction & bisulfite conversion

tag: tissue

value: Villi

tag: sentrix

tag: Sex

value: F

tag: ga


title: genomic_DNAmethylation_PL290_v


title: genomic DNA from eutopic endometrium Sample_811

source_name: endometrium sample 811

tag: gender

tag: sample type

tag: disease state


title: genomic DNA from eutopic endometrium Sample_810

source_name: endometrium sample 810

tag: cycle phase

tag: plate

tag: terminus


title: genomic DNA from eutopic endometrium Sample_808

source_name: endometrium sample 808

tag: batch

tag: euro

tag: recruiment


title: genomic DNA from eutopic endometrium Sample_809

source_name: endometrium sample 809

tag: age


title: genomic DNA from eutopic endometrium Sample_807

source_name: endometrium sample 807


title: genomic DNA from eutopic endometrium Sample_803

source_name: endometrium sample 803


title: genomic DNA from eutopic endometrium Sample_806

source_name: endometrium sample 806


title: genomic DNA from eutopic endometrium Sample_799

source_name: endometrium sample 799


title: genomic DNA from eutopic endometrium Sample_805

source_name: endometrium sample 805


title: genomic DNA from eutopic endometrium Sample_798

source_name: endometrium sample 798


title: genomic DNA from eutopic endometrium Sample_801

source_name: endometrium sample 801


title: genomic DNA from eutopic endometrium Sample_795

source_name: endometrium sample 795


title: genomic DNA from eutopic endometrium Sample_794

source_name: endometrium sample 794


title: genomic DNA from eutopic endometrium Sample_797

source_name: endometrium sample 797


title: genomic DNA from eutopic endometrium Sample_796

source_name: endometrium sample 796


title: genomic DNA from eutopic endometrium Sample_802

source_name: endometrium sample 802


title: genomic DNA from eutopic endometrium Sample_804

source_name: endometrium sample 804


title: genomic DNA from eutopic endometrium Sample_793

source_name: endometrium sample 793


title: genomic DNA from eutopic endometrium Sample_790

source_name: endometrium sample 790


title: genomic DNA from eutopic endometrium Sample_791

source_name: endometrium sample 791


title: genomic DNA from eutopic endometrium Sample_792

source_name: endometrium sample 792


title: genomic DNA from eutopic endometrium Sample_800

source_name: endometrium sample 800


title: genomic DNA from eutopic endometrium Sample_787

source_name: endometrium sample 787


title: genomic DNA from eutopic endometrium Sample_785

source_name: endometrium sample 785


title: genomic DNA from eutopic endometrium Sample_786

source_name: endometrium sample 786


title: genomic DNA from eutopic endometrium Sample_781

source_name: endometrium sample 781


title: genomic DNA from eutopic endometrium Sample_782

source_name: endometrium sample 782


title: genomic DNA from eutopic endometrium Sample_783

source_name: endometrium sample 783


title: genomic DNA from eutopic endometrium Sample_780

source_name: endometrium sample 780


title: genomic DNA from eutopic endometrium Sample_778

source_name: endometrium sample 778


title: genomic DNA from eutopic endometrium Sample_777

source_name: endometrium sample 777


title: genomic DNA from eutopic endometrium Sample_776

source_name: endometrium sample 776


title: genomic DNA from eutopic endometrium Sample_774

source_name: endometrium sample 774


title: genomic DNA from eutopic endometrium Sample_771

source_name: endometrium sample 771


title: genomic DNA from eutopic endometrium Sample_773

source_name: endometrium sample 773


title: genomic DNA from eutopic endometrium Sample_768

source_name: endometrium sample 768


title: genomic DNA from eutopic endometrium Sample_772

source_name: endometrium sample 772


title: genomic DNA from eutopic endometrium Sample_779

source_name: endometrium sample 779


title: genomic DNA from eutopic endometrium Sample_765

source_name: endometrium sample 765


title: genomic DNA from eutopic endometrium Sample_764

source_name: endometrium sample 764


title: genomic DNA from eutopic endometrium Sample_760

source_name: endometrium sample 760


title: genomic DNA from eutopic endometrium Sample_758

source_name: endometrium sample 758


title: genomic DNA from eutopic endometrium Sample_757

source_name: endometrium sample 757


title: genomic DNA from eutopic endometrium Sample_759

source_name: endometrium sample 759


title: genomic DNA from eutopic endometrium Sample_761

source_name: endometrium sample 761


title: genomic DNA from eutopic endometrium Sample_754

source_name: endometrium sample 754


title: genomic DNA from eutopic endometrium Sample_755

source_name: endometrium sample 755


title: genomic DNA from eutopic endometrium Sample_752

source_name: endometrium sample 752


title: genomic DNA from eutopic endometrium Sample_751

source_name: endometrium sample 751


title: genomic DNA from eutopic endometrium Sample_750

source_name: endometrium sample 750


title: genomic DNA from eutopic endometrium Sample_749

source_name: endometrium sample 749


title: genomic DNA from eutopic endometrium Sample_746

source_name: endometrium sample 746


title: genomic DNA from eutopic endometrium Sample_747

source_name: endometrium sample 747


title: genomic DNA from eutopic endometrium Sample_745

source_name: endometrium sample 745


title: genomic DNA from eutopic endometrium Sample_744

source_name: endometrium sample 744


title: genomic DNA from eutopic endometrium Sample_741

source_name: endometrium sample 741


title: genomic DNA from eutopic endometrium Sample_740

source_name: endometrium sample 740


title: genomic DNA from eutopic endometrium Sample_742

source_name: endometrium sample 742


title: genomic DNA from eutopic endometrium Sample_739

source_name: endometrium sample 739


title: genomic DNA from eutopic endometrium Sample_738

source_name: endometrium sample 738


title: genomic DNA from eutopic endometrium Sample_737

source_name: endometrium sample 737


title: genomic DNA from eutopic endometrium Sample_736

source_name: endometrium sample 736


title: genomic DNA from eutopic endometrium Sample_734

source_name: endometrium sample 734


title: genomic DNA from eutopic endometrium Sample_733

source_name: endometrium sample 733


title: genomic DNA from eutopic endometrium Sample_732

source_name: endometrium sample 732


title: genomic DNA from eutopic endometrium Sample_735

source_name: endometrium sample 735


title: genomic DNA from eutopic endometrium Sample_730

source_name: endometrium sample 730


title: genomic DNA from eutopic endometrium Sample_729

source_name: endometrium sample 729


title: genomic DNA from eutopic endometrium Sample_789

source_name: endometrium sample 789


title: genomic DNA from eutopic endometrium Sample_727

source_name: endometrium sample 727


title: genomic DNA from eutopic endometrium Sample_726

source_name: endometrium sample 726


title: genomic DNA from eutopic endometrium Sample_724

source_name: endometrium sample 724


title: genomic DNA from eutopic endometrium Sample_723

source_name: endometrium sample 723


title: genomic DNA from eutopic endometrium Sample_722

source_name: endometrium sample 722


title: genomic DNA from eutopic endometrium Sample_721

source_name: endometrium sample 721


title: genomic DNA from eutopic endometrium Sample_720

source_name: endometrium sample 720


title: genomic DNA from eutopic endometrium Sample_775

source_name: endometrium sample 775


title: genomic DNA from eutopic endometrium Sample_718

source_name: endometrium sample 718

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_719

source_name: endometrium sample 719


title: genomic DNA from eutopic endometrium Sample_717

source_name: endometrium sample 717


title: genomic DNA from eutopic endometrium Sample_766

source_name: endometrium sample 766


title: genomic DNA from eutopic endometrium Sample_767

source_name: endometrium sample 767


title: genomic DNA from eutopic endometrium Sample_716

source_name: endometrium sample 716


title: genomic DNA from eutopic endometrium Sample_715

source_name: endometrium sample 715


title: genomic DNA from eutopic endometrium Sample_770

source_name: endometrium sample 770


title: genomic DNA from eutopic endometrium Sample_713

source_name: endometrium sample 713


title: genomic DNA from eutopic endometrium Sample_710

source_name: endometrium sample 710


title: genomic DNA from eutopic endometrium Sample_711

source_name: endometrium sample 711


title: genomic DNA from eutopic endometrium Sample_707

source_name: endometrium sample 707


title: genomic DNA from eutopic endometrium Sample_706

source_name: endometrium sample 706


title: genomic DNA from eutopic endometrium Sample_708

source_name: endometrium sample 708


title: genomic DNA from eutopic endometrium Sample_704

source_name: endometrium sample 704


title: genomic DNA from eutopic endometrium Sample_705

source_name: endometrium sample 705


title: genomic DNA from eutopic endometrium Sample_702

source_name: endometrium sample 702


title: genomic DNA from eutopic endometrium Sample_701

source_name: endometrium sample 701


title: genomic DNA from eutopic endometrium Sample_743

source_name: endometrium sample 743


title: genomic DNA from eutopic endometrium Sample_703

source_name: endometrium sample 703


title: genomic DNA from eutopic endometrium Sample_700

source_name: endometrium sample 700


title: genomic DNA from eutopic endometrium Sample_698

source_name: endometrium sample 698


title: genomic DNA from eutopic endometrium Sample_696

source_name: endometrium sample 696


title: genomic DNA from eutopic endometrium Sample_695

source_name: endometrium sample 695


title: genomic DNA from eutopic endometrium Sample_694

source_name: endometrium sample 694


title: genomic DNA from eutopic endometrium Sample_692

source_name: endometrium sample 692


title: genomic DNA from eutopic endometrium Sample_691

source_name: endometrium sample 691


title: genomic DNA from eutopic endometrium Sample_690

source_name: endometrium sample 690


title: genomic DNA from eutopic endometrium Sample_689

source_name: endometrium sample 689


title: genomic DNA from eutopic endometrium Sample_688

source_name: endometrium sample 688


title: genomic DNA from eutopic endometrium Sample_687

source_name: endometrium sample 687


title: genomic DNA from eutopic endometrium Sample_685

source_name: endometrium sample 685


title: genomic DNA from eutopic endometrium Sample_686

source_name: endometrium sample 686


title: genomic DNA from eutopic endometrium Sample_684

source_name: endometrium sample 684


title: genomic DNA from eutopic endometrium Sample_682

source_name: endometrium sample 682


title: genomic DNA from eutopic endometrium Sample_681

source_name: endometrium sample 681


title: Healthy donor, Buccal biopsy, HV077

status: Public on Jan 28 2025

city: Bethesda

first: Behdad (Ben)

last: Afzali

state: MD

address: 10 Center Drive, Building 10

department: NIDDK

institute: National Institutes of Health

description: Health buccal biopsy was obtained from an individual that met criteria for oral health.

data_processing:
Sequence reads were assessed for quality on fastqc and mapped to NCBI/GRCh38  using bowtie2 (--sensitive-local --no-unal)
Read count was calculated using Rsubread (with default parameter) tools while using the GTF file (gencode.v39.annotation.gtf.gz) obtained from https://www.gencodegenes.org/human/
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file contain RPKM values for each Sample

source_name: Buccal biopsy

extract_protocol:
Total RNA was extracted from whole tissue using TruSeq Stranded Total RNA Kit following manufacturer’s recommendations (Illumina, San Diego, CA).
Sequencing libraries were prepared by the Illumina Nextera XT method following manufacturer’s recommendations (Illumina, San Diego, CA).
Paired-end RNA-seq on NextSeq500 sequencer (Illumina)

treatment_protocol: Standardized 4mm long x 2mm wide gingival collar biopsies and/or 4mm buccal punch biopsies were obtained  from APECED patients (N = 3) and healthy donors (N = 3) under local anesthesia. Healthy donors had no signs of mucosal candidiasis, inflammation, or infection at the time of tissue harvesting. Oral tissue was homogenized using Miltenyi Gentlemacs M tube (cat# 130-093-236).

value: Buccal biopsy

tag: genotype

value: wild-type

value: Healthy donor

value: Baseline


title: genomic DNA from eutopic endometrium Sample_680

source_name: endometrium sample 680


title: genomic DNA from eutopic endometrium Sample_679

source_name: endometrium sample 679


title: genomic DNA from eutopic endometrium Sample_678

source_name: endometrium sample 678

value: LSE


title: genomic DNA from eutopic endometrium Sample_677

source_name: endometrium sample 677

value: Female


title: genomic DNA from eutopic endometrium Sample_673

source_name: endometrium sample 673

value: endometrium


title: genomic DNA from eutopic endometrium Sample_672

source_name: endometrium sample 672


title: genomic DNA from eutopic endometrium Sample_674

source_name: endometrium sample 674


title: genomic DNA from eutopic endometrium Sample_669

source_name: endometrium sample 669


title: Spleen, CD8 (GEX)

status: Public on Jan 19 2025

first: Jian

last: Cui

address: Assembly building, 5051 Centre Ave

department: Department of Immunology

data_processing:
Library strategy: CITE-seq
For demultiplexing of samples, cellranger (v6.0.0; 10X Genomics) was used with the defualt settings.
CellRanger was used to align gene expression data to the mm10 reference and generate feature barcode expression matrices using the default settings.
cite-seq-count was(v1.4.3) used to align oligonucleotide tags to TotalSeqC (Biolegend) sequences to create citeseq feature barcode expression matrices using the following custom settings: -cbf 1 -cbl 16 -umif 17 -umil 26 -trim 10.
Genome_build: mm10
Supplementary_files_format_and_content: Gene expression feature barcode matrices.  CITEseq feature barcode matrices.  The cite seq hash tags to distinguish different experimental settings.

source_name: spleen

extract_protocol: Splenocytes were harvested from Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP mice that remained naïve or were infected with Cl. 13. for 16d. T cells were enriched by negative selection. Briefly, single cell splenic suspensions were incubated with a cocktail of the following biotinylated antibodies at 4oC for 15 min: CD11b (M1/70), CD11c (N418), CD19 (6D5), CD45R/B220 (RA3-6B2), TCRgd (GL3), PanNK (DX5), CD105 (MJ7/18), CD16/32 (93) and Ter119 (TER-119). Non-T cells were removed by incubating the suspension with streptavidin-coated magnetic beads at 4oC for 15 min, followed by magnetic separation. The unbound pure T cells were incubated with pooled MHC class I tetramer (APC) (GP33, GP276, NP396) and then stained for viability using Live/Dead Fixable eFluor 780. T cells from individual mice were identified via labeling with a uniquely barcoded TotalSeq-C antibodies towards pan-CD45 and MHC at 1:100 according to manufacturer’s protocol during surface staining (Biolegend). Tregs and Tetramer+ CD8+ T cells purified via fluorescently activated cell sorting using a BD Aria. Live cells were spun down, resuspended in 0.04% PBS-BSA (Fisher #MT20031CV and Sigma #A9418-100G), and counted to determine a cell stock concentration.A cell suspension volume was calculated to capture approximately 7,000 cells per sub-population. Cells were added to a Master Mix containing Reagent mix, RT Primers, Additive A, and RT Enzyme Mix to create a reaction for Tregs and one for Tetramer+ CD8+ T cells. These reactions were then loaded into separate lanes on Chromium Chip A and run through the 10X Genomics Chromium Controller. All libraries were sequenced on a NovaSeq™ 6000 S2 kit for 150 cycles at the UPMC Genome Core. Each Gene Expression library was sequenced at a depth of at least 20,000 reads/cell. Each Feature Barcode and TCR library was sequenced at a minimum depth of 5,000 reads/cell.

value: Foxp3Cre-YFP or Ifngr1L/LFoxp3Cre-YFP

tag: infection

value: LCMV infected only

value: spleen


title: genomic DNA from eutopic endometrium Sample_666

source_name: endometrium sample 666

value: Endometriosis

value: EUR


title: genomic DNA from eutopic endometrium Sample_665

source_name: endometrium sample 665


title: C2 cells, BMP4 added, 6h, biol rep 4

status: Public on Dec 30 2024

city: Rehovot

first: Inbal

last: Eizenberg

address: 234 Herzl Street

department: Molecular Genetics

country: Israel

institute: Weizmann Institute of Science

data_processing:
Samples were analyzed using the UTAP pipeline (PMID: 30909881)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using cutadapt
Trimmed sequence reads were mapped to mm10 genome using STAR v2.4.2a (parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –alignSoftClipAtReferenceEnds No).
Read count extraction (UMI counts) was performed after marking duplicates using HTSeq-count in union mode.
Assembly: mm10
Supplementary files format and content: C2_countsUmiCorrectedMatrix.txt;
Supplementary files format and content: read count matrix

source_name: Mammary gland

growth_protocol: NMuMG-C2 dual reporter cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS), 1mM sodium pyruvate, 100 unit/ml penicillin, 100 μg/ml streptomycin, 2 mM L-glutamine and 1X MEM non-essential amino acids in a humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was produced using the RNeasy mini kit (Qiagen). 50ng of total RNA was used for the construction of sequencing libraries.
Library preparation protocol was bulk-adapted from MARS-seq

treatment_protocol: Cell were plated at 50% confluency in 24-wells plate with DMEM+ 10% FBS and cultured for 24h. Following 24h cells were added with the indicated treatment: BMP4 (31.25ng/ml, R&D), Control- no added ligand, TGFb1 (1.92ng/ml, R&D), or BMP4+ TGFb1 and cultured for additional 6h.

value: Mammary gland

tag: cell line

tag: cell type

value: Epithel

value: Double reporter cells with BMP RE mCherry and TGFb RE mCitrine

tag: treatment


title: Haloferax volcanii cells, pyrE parent control strain, rep4

status: Public on Nov 20 2024

description:
molecule is archaeal mRNA, depleted of rRNA using biotinylated probes (not polyA)
hvo_pyrE_4

data_processing:
RNA-seq data were processed using the fastp toolkit (Chen et al., 2018) to trim low-quality bases and sequencing adapters from the 3’ end of reads.
STAR (Dobin et al., 2013) RNA-seq alignment tool was used to map trimmed reads to the genome of Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively). Reads aligning to a single genomic location were summarized across genes.
For genes having an overlap of at least 10 reads, gene counts were normalized and differential expression was carried out using the DESeq2 (Love et al., 2014) Bioconductor (Huber et al., 2015) package implemented for the R programming environment. Consistent with the recommendation of the DESeq authors, independent filtering (Ignatiadis et al., 2016) was utilized prior to calculating adjusted p-values (Benjamini Y, 1995) and moderated log2 fold-changes were derived using the ashr package (Stephens, 2017). Genes were considered significantly differentially expressed if the log2 fold change ratio (∆rosR : parent) was >= |1| and adjusted p-value < 0.05.
Assembly: Haloferax mediterranii or Haloferax volcanii (using NCBI assemblies ASM540632v1 or ASM2568v1, respectively).
Supplementary files format and content: Hfx. mediterranei assembly ASM540632v1 refseq ID = GCF_005406325.1; Hfx. volcanii assembly ASM2568v1 refseq ID = GCF_000025685.1

molecule: polyA RNA

source_name: archaeal cells

growth_protocol: Hm∆rosR, Hv∆rosR, and corresponding parent strain cultures were grown in biological triplicate in rich medium to mid-exponential phase.

extract_protocol:
RNA was extracted using an Absolutely RNA Miniprep kit according to manufacturer instructions (Agilent, Santa Clara, CA). RNA quality was measured using RNA 6000 Nano kit on a 2100 Bioanalyzer (Aglient, Santa Clara, CA). PCR to verify lack of DNA contamination was  conducted on 300 ng of RNA sample using species-specific primers listed in Supplementary Table S2. Ribosomal RNA depletion was performed from 300 ng of each sample using NEBNextR RNA Depletion Core Reagent (#E7870 New England Biolabs) according to the manufacturer instructions. The resultant mRNA was purified using NEBNext RNA sample purification beads and eluted in 7 l of nuclease-free water. 1l of each sample was used for quantification and quality verification (free of rRNA) in a second round of Agilent Bioanalyzer analysis using 2100 Prokaryote Total RNA Nano kit (Aglient, Santa Clara, CA).
Libraries were constructed using 5 ml of mRNA using the Ultra II Directional RNA Library Preparation Kit (Agilent, Santa Clara. CA). Indexes were designed according to the kit specifications and obtained from Integrated DNA Technologies. Resultant libraries were tested for quality and quantity by Bioanalyzer using the 2100 expert High Sensitivity DNA Assay chip (Agilent Technologies)

tag: tissue

value: archaeal cells

value: deltapyrE

value: standard growth medium, control strain


title: Exp4_Control1_rep4

status: Public on Dec 17 2024

city: Saint Louis

first: Andrew

middle: Lee

last: Young

state: MO

address: 660 South Euclid Ave

department: Medicine

institute: Washington University in St. Louis

description: Library name: Exp4_Control1_rep4

data_processing:
For WGBS, reads were sequenced using NovaSeq platform. Reads were aligned to mm10,  deduplicated and CpG methylation extracted using Bismark.
Assembly: mm10
Supplementary files format and content: reads are aligned to mm10
Supplementary files format and content: bw

source_name: KSL

growth_protocol: 200 CD45.2 HSCs of the indicated genotypes were competitively transplanted with competetive 250,000 CD45.1 whole bone marrow cells in lethally irradiated primary recipient mice.  Serial transplant was performed by repeating this process.

extract_protocol:
For WGBS, genomic DNA (gDNA) was prepared from the cells using PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific #K1820-02).
For WGBS, using 200 ng of gDNA and 0.2% lambda DNA was bisulfite treated using EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research #D5042) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries.

treatment_protocol: No treatment

tag: Stage

value: Primary

value: KSL

value: Control

value: Vav-Cre


title: genomic DNA from eutopic endometrium Sample_664

source_name: endometrium sample 664

tag: gender

value: Female

value: SE


title: genomic DNA from eutopic endometrium Sample_663

source_name: endometrium sample 663

tag: sample type

value: endometrium

value: ESE


title: genomic DNA from eutopic endometrium Sample_661

source_name: endometrium sample 661

tag: disease state

value: LSE


title: genomic DNA from eutopic endometrium Sample_660

source_name: endometrium sample 660

tag: cycle phase

value: MSE


title: genomic DNA from eutopic endometrium Sample_659

source_name: endometrium sample 659

value: Endometriosis

value: PE

tag: plate

value: EUR


title: genomic DNA from eutopic endometrium Sample_658

source_name: endometrium sample 658

tag: terminus


title: genomic DNA from eutopic endometrium Sample_657

source_name: endometrium sample 657

tag: batch


title: genomic DNA from eutopic endometrium Sample_656

source_name: endometrium sample 656

tag: euro


title: genomic DNA from eutopic endometrium Sample_654

source_name: endometrium sample 654

tag: recruiment


title: genomic DNA from eutopic endometrium Sample_653

source_name: endometrium sample 653

tag: age


title: genomic DNA from eutopic endometrium Sample_652

source_name: endometrium sample 652


title: genomic DNA from eutopic endometrium Sample_651

source_name: endometrium sample 651


title: genomic DNA from eutopic endometrium Sample_650

source_name: endometrium sample 650


title: genomic DNA from eutopic endometrium Sample_649

source_name: endometrium sample 649


title: genomic DNA from eutopic endometrium Sample_648

source_name: endometrium sample 648


title: genomic DNA from eutopic endometrium Sample_647

source_name: endometrium sample 647


title: genomic DNA from eutopic endometrium Sample_646

source_name: endometrium sample 646


title: genomic DNA from eutopic endometrium Sample_645

source_name: endometrium sample 645


title: genomic DNA from eutopic endometrium Sample_644

source_name: endometrium sample 644


title: genomic DNA from eutopic endometrium Sample_643

source_name: endometrium sample 643


title: genomic DNA from eutopic endometrium Sample_683

source_name: endometrium sample 683


title: genomic DNA from eutopic endometrium Sample_642

source_name: endometrium sample 642


title: genomic DNA from eutopic endometrium Sample_641

source_name: endometrium sample 641


title: genomic DNA from eutopic endometrium Sample_640

source_name: endometrium sample 640

value: Menstrual


title: genomic DNA from eutopic endometrium Sample_676

source_name: endometrium sample 676


title: genomic DNA from eutopic endometrium Sample_639

source_name: endometrium sample 639


title: genomic DNA from eutopic endometrium Sample_638

source_name: endometrium sample 638


title: genomic DNA from eutopic endometrium Sample_675

source_name: endometrium sample 675


title: genomic DNA from eutopic endometrium Sample_637

source_name: endometrium sample 637


title: genomic DNA from eutopic endometrium Sample_636

source_name: endometrium sample 636


title: genomic DNA from eutopic endometrium Sample_635

source_name: endometrium sample 635


title: genomic DNA from eutopic endometrium Sample_670

source_name: endometrium sample 670


title: genomic DNA from eutopic endometrium Sample_634

source_name: endometrium sample 634


title: genomic DNA from eutopic endometrium Sample_671

source_name: endometrium sample 671


title: genomic DNA from eutopic endometrium Sample_633

source_name: endometrium sample 633


title: genomic DNA from eutopic endometrium Sample_632

source_name: endometrium sample 632


title: genomic DNA from eutopic endometrium Sample_668

source_name: endometrium sample 668


title: genomic DNA from eutopic endometrium Sample_631

source_name: endometrium sample 631


title: genomic DNA from eutopic endometrium Sample_626

source_name: endometrium sample 626


title: genomic DNA from eutopic endometrium Sample_667

source_name: endometrium sample 667


title: genomic DNA from eutopic endometrium Sample_627

source_name: endometrium sample 627


title: genomic DNA from eutopic endometrium Sample_630

source_name: endometrium sample 630


title: genomic DNA from eutopic endometrium Sample_629

source_name: endometrium sample 629


title: genomic DNA from eutopic endometrium Sample_625

source_name: endometrium sample 625


title: genomic DNA from eutopic endometrium Sample_624

source_name: endometrium sample 624


title: genomic DNA from eutopic endometrium Sample_628

source_name: endometrium sample 628


title: genomic DNA from eutopic endometrium Sample_623

source_name: endometrium sample 623


title: genomic DNA from eutopic endometrium Sample_622

source_name: endometrium sample 622


title: genomic DNA from eutopic endometrium Sample_620

source_name: endometrium sample 620


title: genomic DNA from eutopic endometrium Sample_621

source_name: endometrium sample 621


title: genomic DNA from eutopic endometrium Sample_618

source_name: endometrium sample 618


title: genomic DNA from eutopic endometrium Sample_617

source_name: endometrium sample 617


title: genomic DNA from eutopic endometrium Sample_619

source_name: endometrium sample 619


title: genomic DNA from eutopic endometrium Sample_616

source_name: endometrium sample 616


title: genomic DNA from eutopic endometrium Sample_615

source_name: endometrium sample 615


title: genomic DNA from eutopic endometrium Sample_614

source_name: endometrium sample 614


title: genomic DNA from eutopic endometrium Sample_610

source_name: endometrium sample 610


title: genomic DNA from eutopic endometrium Sample_611

source_name: endometrium sample 611


title: genomic DNA from eutopic endometrium Sample_609

source_name: endometrium sample 609


title: genomic DNA from eutopic endometrium Sample_608

source_name: endometrium sample 608


title: genomic DNA from eutopic endometrium Sample_612

source_name: endometrium sample 612


title: genomic DNA from eutopic endometrium Sample_662

source_name: endometrium sample 662


title: genomic DNA from eutopic endometrium Sample_607

source_name: endometrium sample 607


title: genomic DNA from eutopic endometrium Sample_613

source_name: endometrium sample 613


title: genomic DNA from eutopic endometrium Sample_606

source_name: endometrium sample 606


title: genomic DNA from eutopic endometrium Sample_605

source_name: endometrium sample 605


title: genomic DNA from eutopic endometrium Sample_603

source_name: endometrium sample 603


title: genomic DNA from eutopic endometrium Sample_604

source_name: endometrium sample 604


title: genomic DNA from eutopic endometrium Sample_600

source_name: endometrium sample 600


title: genomic DNA from eutopic endometrium Sample_601

source_name: endometrium sample 601


title: genomic DNA from eutopic endometrium Sample_602

source_name: endometrium sample 602


title: genomic DNA from eutopic endometrium Sample_598

source_name: endometrium sample 598


title: genomic DNA from eutopic endometrium Sample_599

source_name: endometrium sample 599


title: genomic DNA from eutopic endometrium Sample_597

source_name: endometrium sample 597


title: genomic DNA from eutopic endometrium Sample_596

source_name: endometrium sample 596


title: genomic DNA from eutopic endometrium Sample_595

source_name: endometrium sample 595


title: genomic DNA from eutopic endometrium Sample_593

source_name: endometrium sample 593


title: genomic DNA from eutopic endometrium Sample_594

source_name: endometrium sample 594


title: genomic DNA from eutopic endometrium Sample_589

source_name: endometrium sample 589


title: genomic DNA from eutopic endometrium Sample_590

source_name: endometrium sample 590


title: genomic DNA from eutopic endometrium Sample_592

source_name: endometrium sample 592


title: genomic DNA from eutopic endometrium Sample_655

source_name: endometrium sample 655


title: genomic DNA from eutopic endometrium Sample_586

source_name: endometrium sample 586


title: genomic DNA from eutopic endometrium Sample_591

source_name: endometrium sample 591


title: genomic DNA from eutopic endometrium Sample_587

source_name: endometrium sample 587


title: genomic DNA from eutopic endometrium Sample_588

source_name: endometrium sample 588


title: genomic DNA from eutopic endometrium Sample_788

source_name: endometrium sample 788


title: genomic DNA from eutopic endometrium Sample_585

source_name: endometrium sample 585


title: genomic DNA from eutopic endometrium Sample_584

source_name: endometrium sample 584


title: genomic DNA from eutopic endometrium Sample_582

source_name: endometrium sample 582


title: genomic DNA from eutopic endometrium Sample_580

source_name: endometrium sample 580


title: genomic DNA from eutopic endometrium Sample_581

source_name: endometrium sample 581


title: genomic DNA from eutopic endometrium Sample_583

source_name: endometrium sample 583


title: genomic DNA from eutopic endometrium Sample_579

source_name: endometrium sample 579


title: genomic DNA from eutopic endometrium Sample_578

source_name: endometrium sample 578


title: genomic DNA from eutopic endometrium Sample_577

source_name: endometrium sample 577


title: genomic DNA from eutopic endometrium Sample_575

source_name: endometrium sample 575


title: genomic DNA from eutopic endometrium Sample_576

source_name: endometrium sample 576


title: genomic DNA from eutopic endometrium Sample_574

source_name: endometrium sample 574


title: genomic DNA from eutopic endometrium Sample_573

source_name: endometrium sample 573


title: genomic DNA from eutopic endometrium Sample_763

source_name: endometrium sample 763


title: genomic DNA from eutopic endometrium Sample_572

source_name: endometrium sample 572


title: genomic DNA from eutopic endometrium Sample_568

source_name: endometrium sample 568


title: genomic DNA from eutopic endometrium Sample_569

source_name: endometrium sample 569


title: genomic DNA from eutopic endometrium Sample_570

source_name: endometrium sample 570


title: genomic DNA from eutopic endometrium Sample_566

source_name: endometrium sample 566


title: genomic DNA from eutopic endometrium Sample_571

source_name: endometrium sample 571


title: genomic DNA from eutopic endometrium Sample_567

source_name: endometrium sample 567


title: genomic DNA from eutopic endometrium Sample_562

source_name: endometrium sample 562


title: genomic DNA from eutopic endometrium Sample_563

source_name: endometrium sample 563


title: genomic DNA from eutopic endometrium Sample_564

source_name: endometrium sample 564


title: genomic DNA from eutopic endometrium Sample_565

source_name: endometrium sample 565


title: genomic DNA from eutopic endometrium Sample_561

source_name: endometrium sample 561


title: genomic DNA from eutopic endometrium Sample_748

source_name: endometrium sample 748


title: genomic DNA from eutopic endometrium Sample_560

source_name: endometrium sample 560


title: genomic DNA from eutopic endometrium Sample_559

source_name: endometrium sample 559


title: genomic DNA from eutopic endometrium Sample_557

source_name: endometrium sample 557


title: genomic DNA from eutopic endometrium Sample_558

source_name: endometrium sample 558


title: genomic DNA from eutopic endometrium Sample_556

source_name: endometrium sample 556


title: genomic DNA from eutopic endometrium Sample_555

source_name: endometrium sample 555


title: genomic DNA from eutopic endometrium Sample_554

source_name: endometrium sample 554


title: genomic DNA from eutopic endometrium Sample_552

source_name: endometrium sample 552


title: genomic DNA from eutopic endometrium Sample_553

source_name: endometrium sample 553


title: genomic DNA from eutopic endometrium Sample_551

source_name: endometrium sample 551


title: genomic DNA from eutopic endometrium Sample_550

source_name: endometrium sample 550


title: genomic DNA from eutopic endometrium Sample_548

source_name: endometrium sample 548


title: genomic DNA from eutopic endometrium Sample_545

source_name: endometrium sample 545


title: genomic DNA from eutopic endometrium Sample_543

source_name: endometrium sample 543


title: genomic DNA from eutopic endometrium Sample_544

source_name: endometrium sample 544


title: genomic DNA from eutopic endometrium Sample_546

source_name: endometrium sample 546


title: genomic DNA from eutopic endometrium Sample_542

source_name: endometrium sample 542


title: genomic DNA from eutopic endometrium Sample_540

source_name: endometrium sample 540


title: genomic DNA from eutopic endometrium Sample_541

source_name: endometrium sample 541


title: genomic DNA from eutopic endometrium Sample_538

source_name: endometrium sample 538


title: genomic DNA from eutopic endometrium Sample_537

source_name: endometrium sample 537


title: genomic DNA from eutopic endometrium Sample_536

source_name: endometrium sample 536


title: genomic DNA from eutopic endometrium Sample_535

source_name: endometrium sample 535


title: genomic DNA from eutopic endometrium Sample_534

source_name: endometrium sample 534


title: genomic DNA from eutopic endometrium Sample_533

source_name: endometrium sample 533


title: genomic DNA from eutopic endometrium Sample_532

source_name: endometrium sample 532


title: genomic DNA from eutopic endometrium Sample_531

source_name: endometrium sample 531


title: genomic DNA from eutopic endometrium Sample_530

source_name: endometrium sample 530


title: genomic DNA from eutopic endometrium Sample_528

source_name: endometrium sample 528


title: genomic DNA from eutopic endometrium Sample_527

source_name: endometrium sample 527


title: genomic DNA from eutopic endometrium Sample_524

source_name: endometrium sample 524


title: genomic DNA from eutopic endometrium Sample_525

source_name: endometrium sample 525


title: genomic DNA from eutopic endometrium Sample_523

source_name: endometrium sample 523


title: genomic DNA from eutopic endometrium Sample_521

source_name: endometrium sample 521


title: genomic DNA from eutopic endometrium Sample_520

source_name: endometrium sample 520


title: genomic DNA from eutopic endometrium Sample_522

source_name: endometrium sample 522


title: genomic DNA from eutopic endometrium Sample_519

source_name: endometrium sample 519


title: genomic DNA from eutopic endometrium Sample_714

source_name: endometrium sample 714


title: genomic DNA from eutopic endometrium Sample_518

source_name: endometrium sample 518


title: genomic DNA from eutopic endometrium Sample_517

source_name: endometrium sample 517


title: genomic DNA from eutopic endometrium Sample_516

source_name: endometrium sample 516


title: genomic DNA from eutopic endometrium Sample_515

source_name: endometrium sample 515


title: genomic DNA from eutopic endometrium Sample_514

source_name: endometrium sample 514


title: genomic DNA from eutopic endometrium Sample_513

source_name: endometrium sample 513


title: genomic DNA from eutopic endometrium Sample_512

source_name: endometrium sample 512


title: genomic DNA from eutopic endometrium Sample_511

source_name: endometrium sample 511


title: genomic DNA from eutopic endometrium Sample_507

source_name: endometrium sample 507


title: genomic DNA from eutopic endometrium Sample_509

source_name: endometrium sample 509


title: genomic DNA from eutopic endometrium Sample_508

source_name: endometrium sample 508


title: genomic DNA from eutopic endometrium Sample_510

source_name: endometrium sample 510


title: genomic DNA from eutopic endometrium Sample_505

source_name: endometrium sample 505


title: genomic DNA from eutopic endometrium Sample_506

source_name: endometrium sample 506


title: genomic DNA from eutopic endometrium Sample_504

source_name: endometrium sample 504


title: genomic DNA from eutopic endometrium Sample_501

source_name: endometrium sample 501


title: genomic DNA from eutopic endometrium Sample_549

source_name: endometrium sample 549


title: genomic DNA from eutopic endometrium Sample_503

source_name: endometrium sample 503


title: genomic DNA from eutopic endometrium Sample_502

source_name: endometrium sample 502


title: genomic DNA from eutopic endometrium Sample_547

source_name: endometrium sample 547


title: genomic DNA from eutopic endometrium Sample_499

source_name: endometrium sample 499


title: genomic DNA from eutopic endometrium Sample_498

source_name: endometrium sample 498


title: genomic DNA from eutopic endometrium Sample_697

source_name: endometrium sample 697


title: genomic DNA from eutopic endometrium Sample_500

source_name: endometrium sample 500


title: genomic DNA from eutopic endometrium Sample_497

source_name: endometrium sample 497


title: genomic DNA from eutopic endometrium Sample_496

source_name: endometrium sample 496


title: genomic DNA from eutopic endometrium Sample_495

source_name: endometrium sample 495


title: genomic DNA from eutopic endometrium Sample_494

source_name: endometrium sample 494


title: genomic DNA from eutopic endometrium Sample_539

source_name: endometrium sample 539


title: genomic DNA from eutopic endometrium Sample_492

source_name: endometrium sample 492


title: genomic DNA from eutopic endometrium Sample_490

source_name: endometrium sample 490


title: genomic DNA from eutopic endometrium Sample_493

source_name: endometrium sample 493


title: genomic DNA from eutopic endometrium Sample_489

source_name: endometrium sample 489


title: genomic DNA from eutopic endometrium Sample_488

source_name: endometrium sample 488


title: genomic DNA from eutopic endometrium Sample_487

source_name: endometrium sample 487


title: genomic DNA from eutopic endometrium Sample_486

source_name: endometrium sample 486


title: genomic DNA from eutopic endometrium Sample_485

source_name: endometrium sample 485


title: genomic DNA from eutopic endometrium Sample_484

source_name: endometrium sample 484


title: genomic DNA from eutopic endometrium Sample_491

source_name: endometrium sample 491


title: genomic DNA from eutopic endometrium Sample_483

source_name: endometrium sample 483


title: genomic DNA from eutopic endometrium Sample_482

source_name: endometrium sample 482


title: genomic DNA from eutopic endometrium Sample_529

source_name: endometrium sample 529


title: genomic DNA from eutopic endometrium Sample_481

source_name: endometrium sample 481


title: genomic DNA from eutopic endometrium Sample_480

source_name: endometrium sample 480


title: genomic DNA from eutopic endometrium Sample_478

source_name: endometrium sample 478


title: genomic DNA from eutopic endometrium Sample_479

source_name: endometrium sample 479


title: genomic DNA from eutopic endometrium Sample_477

source_name: endometrium sample 477


title: genomic DNA from eutopic endometrium Sample_526

source_name: endometrium sample 526


title: genomic DNA from eutopic endometrium Sample_474

source_name: endometrium sample 474


title: genomic DNA from eutopic endometrium Sample_476

source_name: endometrium sample 476


title: genomic DNA from eutopic endometrium Sample_475

source_name: endometrium sample 475


title: genomic DNA from eutopic endometrium Sample_473

source_name: endometrium sample 473


title: genomic DNA from eutopic endometrium Sample_470

source_name: endometrium sample 470


title: genomic DNA from eutopic endometrium Sample_471

source_name: endometrium sample 471


title: genomic DNA from eutopic endometrium Sample_472

source_name: endometrium sample 472


title: genomic DNA from eutopic endometrium Sample_468

source_name: endometrium sample 468


title: genomic DNA from eutopic endometrium Sample_467

source_name: endometrium sample 467


title: genomic DNA from eutopic endometrium Sample_469

source_name: endometrium sample 469


title: genomic DNA from eutopic endometrium Sample_461

source_name: endometrium sample 461


title: genomic DNA from eutopic endometrium Sample_464

source_name: endometrium sample 464


title: genomic DNA from eutopic endometrium Sample_462

source_name: endometrium sample 462


title: genomic DNA from eutopic endometrium Sample_465

source_name: endometrium sample 465


title: genomic DNA from eutopic endometrium Sample_466

source_name: endometrium sample 466


title: genomic DNA from eutopic endometrium Sample_458

source_name: endometrium sample 458


title: genomic DNA from eutopic endometrium Sample_460

source_name: endometrium sample 460


title: genomic DNA from eutopic endometrium Sample_463

source_name: endometrium sample 463


title: genomic DNA from eutopic endometrium Sample_457

source_name: endometrium sample 457


title: genomic DNA from eutopic endometrium Sample_454

source_name: endometrium sample 454


title: genomic DNA from eutopic endometrium Sample_455

source_name: endometrium sample 455


title: genomic DNA from eutopic endometrium Sample_453

source_name: endometrium sample 453


title: genomic DNA from eutopic endometrium Sample_456

source_name: endometrium sample 456


title: genomic DNA from eutopic endometrium Sample_452

source_name: endometrium sample 452


title: genomic DNA from eutopic endometrium Sample_449

source_name: endometrium sample 449


title: genomic DNA from eutopic endometrium Sample_450

source_name: endometrium sample 450


title: genomic DNA from eutopic endometrium Sample_451

source_name: endometrium sample 451


title: genomic DNA from eutopic endometrium Sample_448

source_name: endometrium sample 448


title: genomic DNA from eutopic endometrium Sample_447

source_name: endometrium sample 447


title: genomic DNA from eutopic endometrium Sample_445

source_name: endometrium sample 445


title: genomic DNA from eutopic endometrium Sample_446

source_name: endometrium sample 446


title: genomic DNA from eutopic endometrium Sample_443

source_name: endometrium sample 443


title: genomic DNA from eutopic endometrium Sample_444

source_name: endometrium sample 444


title: genomic DNA from eutopic endometrium Sample_441

source_name: endometrium sample 441


title: genomic DNA from eutopic endometrium Sample_439

source_name: endometrium sample 439


title: genomic DNA from eutopic endometrium Sample_442

source_name: endometrium sample 442


title: genomic DNA from eutopic endometrium Sample_440

source_name: endometrium sample 440


title: genomic DNA from eutopic endometrium Sample_438

source_name: endometrium sample 438


title: genomic DNA from eutopic endometrium Sample_437

source_name: endometrium sample 437


title: genomic DNA from eutopic endometrium Sample_434

source_name: endometrium sample 434


title: genomic DNA from eutopic endometrium Sample_433

source_name: endometrium sample 433


title: genomic DNA from eutopic endometrium Sample_435

source_name: endometrium sample 435


title: genomic DNA from eutopic endometrium Sample_431

source_name: endometrium sample 431


title: genomic DNA from eutopic endometrium Sample_432

source_name: endometrium sample 432


title: genomic DNA from eutopic endometrium Sample_430

source_name: endometrium sample 430


title: genomic DNA from eutopic endometrium Sample_429

source_name: endometrium sample 429


title: genomic DNA from eutopic endometrium Sample_436

source_name: endometrium sample 436


title: genomic DNA from eutopic endometrium Sample_428

source_name: endometrium sample 428


title: genomic DNA from eutopic endometrium Sample_427

source_name: endometrium sample 427


title: genomic DNA from eutopic endometrium Sample_426

source_name: endometrium sample 426


title: genomic DNA from eutopic endometrium Sample_425

source_name: endometrium sample 425


title: genomic DNA from eutopic endometrium Sample_424

source_name: endometrium sample 424


title: genomic DNA from eutopic endometrium Sample_423

source_name: endometrium sample 423


title: genomic DNA from eutopic endometrium Sample_422

source_name: endometrium sample 422


title: genomic DNA from eutopic endometrium Sample_421

source_name: endometrium sample 421


title: genomic DNA from eutopic endometrium Sample_418

source_name: endometrium sample 418


title: genomic DNA from eutopic endometrium Sample_419

source_name: endometrium sample 419


title: genomic DNA from eutopic endometrium Sample_420

source_name: endometrium sample 420


title: genomic DNA from eutopic endometrium Sample_417

source_name: endometrium sample 417


title: genomic DNA from eutopic endometrium Sample_416

source_name: endometrium sample 416


title: genomic DNA from eutopic endometrium Sample_415

source_name: endometrium sample 415


title: genomic DNA from eutopic endometrium Sample_414

source_name: endometrium sample 414


title: genomic DNA from eutopic endometrium Sample_413

source_name: endometrium sample 413


title: genomic DNA from eutopic endometrium Sample_412

source_name: endometrium sample 412


title: genomic DNA from eutopic endometrium Sample_411

source_name: endometrium sample 411


title: genomic DNA from eutopic endometrium Sample_410

source_name: endometrium sample 410


title: genomic DNA from eutopic endometrium Sample_409

source_name: endometrium sample 409


title: genomic DNA from eutopic endometrium Sample_407

source_name: endometrium sample 407


title: genomic DNA from eutopic endometrium Sample_406

source_name: endometrium sample 406


title: genomic DNA from eutopic endometrium Sample_408

source_name: endometrium sample 408


title: genomic DNA from eutopic endometrium Sample_404

source_name: endometrium sample 404


title: genomic DNA from eutopic endometrium Sample_402

source_name: endometrium sample 402


title: genomic DNA from eutopic endometrium Sample_403

source_name: endometrium sample 403


title: genomic DNA from eutopic endometrium Sample_405

source_name: endometrium sample 405


title: genomic DNA from eutopic endometrium Sample_401

source_name: endometrium sample 401


title: genomic DNA from eutopic endometrium Sample_400

source_name: endometrium sample 400


title: genomic DNA from eutopic endometrium Sample_399

source_name: endometrium sample 399


title: genomic DNA from eutopic endometrium Sample_397

source_name: endometrium sample 397


title: genomic DNA from eutopic endometrium Sample_396

source_name: endometrium sample 396


title: genomic DNA from eutopic endometrium Sample_398

source_name: endometrium sample 398


title: genomic DNA from eutopic endometrium Sample_393

source_name: endometrium sample 393


title: genomic DNA from eutopic endometrium Sample_395

source_name: endometrium sample 395


title: genomic DNA from eutopic endometrium Sample_394

source_name: endometrium sample 394


title: genomic DNA from eutopic endometrium Sample_392

source_name: endometrium sample 392


title: genomic DNA from eutopic endometrium Sample_391

source_name: endometrium sample 391


title: genomic DNA from eutopic endometrium Sample_390

source_name: endometrium sample 390


title: genomic DNA from eutopic endometrium Sample_388

source_name: endometrium sample 388


title: genomic DNA from eutopic endometrium Sample_389

source_name: endometrium sample 389


title: genomic DNA from eutopic endometrium Sample_387

source_name: endometrium sample 387


title: genomic DNA from eutopic endometrium Sample_385

source_name: endometrium sample 385


title: genomic DNA from eutopic endometrium Sample_386

source_name: endometrium sample 386


title: genomic DNA from eutopic endometrium Sample_384

source_name: endometrium sample 384


title: genomic DNA from eutopic endometrium Sample_383

source_name: endometrium sample 383


title: genomic DNA from eutopic endometrium Sample_382

source_name: endometrium sample 382


title: genomic DNA from eutopic endometrium Sample_381

source_name: endometrium sample 381


title: genomic DNA from eutopic endometrium Sample_379

source_name: endometrium sample 379


title: genomic DNA from eutopic endometrium Sample_378

source_name: endometrium sample 378


title: genomic DNA from eutopic endometrium Sample_377

source_name: endometrium sample 377


title: genomic DNA from eutopic endometrium Sample_376

source_name: endometrium sample 376


title: genomic DNA from eutopic endometrium Sample_380

source_name: endometrium sample 380


title: genomic DNA from eutopic endometrium Sample_375

source_name: endometrium sample 375


title: genomic DNA from eutopic endometrium Sample_373

source_name: endometrium sample 373


title: genomic DNA from eutopic endometrium Sample_371

source_name: endometrium sample 371


title: genomic DNA from eutopic endometrium Sample_374

source_name: endometrium sample 374


title: genomic DNA from eutopic endometrium Sample_370

source_name: endometrium sample 370


title: genomic DNA from eutopic endometrium Sample_366

source_name: endometrium sample 366


title: genomic DNA from eutopic endometrium Sample_367

source_name: endometrium sample 367


title: genomic DNA from eutopic endometrium Sample_368

source_name: endometrium sample 368


title: genomic DNA from eutopic endometrium Sample_372

source_name: endometrium sample 372


title: genomic DNA from eutopic endometrium Sample_369

source_name: endometrium sample 369


title: genomic DNA from eutopic endometrium Sample_365

source_name: endometrium sample 365


title: genomic DNA from eutopic endometrium Sample_364

source_name: endometrium sample 364


title: genomic DNA from eutopic endometrium Sample_363

source_name: endometrium sample 363


title: genomic DNA from eutopic endometrium Sample_362

source_name: endometrium sample 362


title: genomic DNA from eutopic endometrium Sample_360

source_name: endometrium sample 360


title: genomic DNA from eutopic endometrium Sample_361

source_name: endometrium sample 361


title: genomic DNA from eutopic endometrium Sample_359

source_name: endometrium sample 359


title: genomic DNA from eutopic endometrium Sample_357

source_name: endometrium sample 357


title: genomic DNA from eutopic endometrium Sample_358

source_name: endometrium sample 358


title: genomic DNA from eutopic endometrium Sample_356

source_name: endometrium sample 356


title: genomic DNA from eutopic endometrium Sample_355

source_name: endometrium sample 355


title: genomic DNA from eutopic endometrium Sample_354

source_name: endometrium sample 354


title: genomic DNA from eutopic endometrium Sample_353

source_name: endometrium sample 353


title: genomic DNA from eutopic endometrium Sample_351

source_name: endometrium sample 351


title: genomic DNA from eutopic endometrium Sample_350

source_name: endometrium sample 350


title: genomic DNA from eutopic endometrium Sample_349

source_name: endometrium sample 349


title: genomic DNA from eutopic endometrium Sample_347

source_name: endometrium sample 347


title: genomic DNA from eutopic endometrium Sample_348

source_name: endometrium sample 348


title: genomic DNA from eutopic endometrium Sample_346

source_name: endometrium sample 346


title: genomic DNA from eutopic endometrium Sample_345

source_name: endometrium sample 345


title: genomic DNA from eutopic endometrium Sample_344

source_name: endometrium sample 344


title: genomic DNA from eutopic endometrium Sample_341

source_name: endometrium sample 341


title: genomic DNA from eutopic endometrium Sample_343

source_name: endometrium sample 343


title: genomic DNA from eutopic endometrium Sample_340

source_name: endometrium sample 340


title: genomic DNA from eutopic endometrium Sample_339

source_name: endometrium sample 339


title: genomic DNA from eutopic endometrium Sample_342

source_name: endometrium sample 342


title: genomic DNA from eutopic endometrium Sample_338

source_name: endometrium sample 338


title: genomic DNA from eutopic endometrium Sample_335

source_name: endometrium sample 335


title: genomic DNA from eutopic endometrium Sample_336

source_name: endometrium sample 336


title: genomic DNA from eutopic endometrium Sample_337

source_name: endometrium sample 337


title: genomic DNA from eutopic endometrium Sample_334

source_name: endometrium sample 334


title: genomic DNA from eutopic endometrium Sample_332

source_name: endometrium sample 332


title: genomic DNA from eutopic endometrium Sample_330

source_name: endometrium sample 330


title: genomic DNA from eutopic endometrium Sample_329

source_name: endometrium sample 329


title: genomic DNA from eutopic endometrium Sample_328

source_name: endometrium sample 328


title: genomic DNA from eutopic endometrium Sample_331

source_name: endometrium sample 331


title: genomic DNA from eutopic endometrium Sample_333

source_name: endometrium sample 333


title: genomic DNA from eutopic endometrium Sample_326

source_name: endometrium sample 326


title: genomic DNA from eutopic endometrium Sample_327

source_name: endometrium sample 327


title: genomic DNA from eutopic endometrium Sample_325

source_name: endometrium sample 325


title: genomic DNA from eutopic endometrium Sample_324

source_name: endometrium sample 324


title: genomic DNA from eutopic endometrium Sample_352

source_name: endometrium sample 352


title: genomic DNA from eutopic endometrium Sample_323

source_name: endometrium sample 323


title: genomic DNA from eutopic endometrium Sample_321

source_name: endometrium sample 321


title: genomic DNA from eutopic endometrium Sample_320

source_name: endometrium sample 320


title: genomic DNA from eutopic endometrium Sample_322

source_name: endometrium sample 322


title: genomic DNA from eutopic endometrium Sample_319

source_name: endometrium sample 319


title: genomic DNA from eutopic endometrium Sample_318

source_name: endometrium sample 318


title: genomic DNA from eutopic endometrium Sample_317

source_name: endometrium sample 317


title: genomic DNA from eutopic endometrium Sample_315

source_name: endometrium sample 315


title: genomic DNA from eutopic endometrium Sample_314

source_name: endometrium sample 314


title: genomic DNA from eutopic endometrium Sample_316

source_name: endometrium sample 316


title: genomic DNA from eutopic endometrium Sample_312

source_name: endometrium sample 312


title: genomic DNA from eutopic endometrium Sample_313

source_name: endometrium sample 313


title: genomic DNA from eutopic endometrium Sample_310

source_name: endometrium sample 310


title: genomic DNA from eutopic endometrium Sample_309

source_name: endometrium sample 309


title: genomic DNA from eutopic endometrium Sample_311

source_name: endometrium sample 311


title: genomic DNA from eutopic endometrium Sample_308

source_name: endometrium sample 308


title: genomic DNA from eutopic endometrium Sample_305

source_name: endometrium sample 305


title: genomic DNA from eutopic endometrium Sample_307

source_name: endometrium sample 307


title: genomic DNA from eutopic endometrium Sample_306

source_name: endometrium sample 306


title: genomic DNA from eutopic endometrium Sample_303

source_name: endometrium sample 303


title: genomic DNA from eutopic endometrium Sample_304

source_name: endometrium sample 304


title: genomic DNA from eutopic endometrium Sample_300

source_name: endometrium sample 300


title: genomic DNA from eutopic endometrium Sample_299

source_name: endometrium sample 299


title: genomic DNA from eutopic endometrium Sample_298

source_name: endometrium sample 298


title: genomic DNA from eutopic endometrium Sample_297

source_name: endometrium sample 297


title: genomic DNA from eutopic endometrium Sample_296

source_name: endometrium sample 296


title: genomic DNA from eutopic endometrium Sample_295

source_name: endometrium sample 295


title: genomic DNA from eutopic endometrium Sample_294

source_name: endometrium sample 294


title: genomic DNA from eutopic endometrium Sample_293

source_name: endometrium sample 293


title: genomic DNA from eutopic endometrium Sample_292

source_name: endometrium sample 292


title: genomic DNA from eutopic endometrium Sample_291

source_name: endometrium sample 291


title: genomic DNA from eutopic endometrium Sample_290

source_name: endometrium sample 290


title: genomic DNA from eutopic endometrium Sample_289

source_name: endometrium sample 289


title: genomic DNA from eutopic endometrium Sample_287

source_name: endometrium sample 287


title: genomic DNA from eutopic endometrium Sample_286

source_name: endometrium sample 286


title: genomic DNA from eutopic endometrium Sample_285

source_name: endometrium sample 285


title: genomic DNA from eutopic endometrium Sample_284

source_name: endometrium sample 284


title: genomic DNA from eutopic endometrium Sample_283

source_name: endometrium sample 283


title: genomic DNA from eutopic endometrium Sample_282

source_name: endometrium sample 282


title: genomic DNA from eutopic endometrium Sample_281

source_name: endometrium sample 281


title: genomic DNA from eutopic endometrium Sample_280

source_name: endometrium sample 280


title: genomic DNA from eutopic endometrium Sample_279

source_name: endometrium sample 279


title: genomic DNA from eutopic endometrium Sample_278

source_name: endometrium sample 278


title: genomic DNA from eutopic endometrium Sample_277

source_name: endometrium sample 277


title: genomic DNA from eutopic endometrium Sample_276

source_name: endometrium sample 276


title: genomic DNA from eutopic endometrium Sample_275

source_name: endometrium sample 275


title: genomic DNA from eutopic endometrium Sample_274

source_name: endometrium sample 274


title: genomic DNA from eutopic endometrium Sample_273

source_name: endometrium sample 273


title: genomic DNA from eutopic endometrium Sample_272

source_name: endometrium sample 272


title: genomic DNA from eutopic endometrium Sample_271

source_name: endometrium sample 271