title: InputB_sgKDM6A_236L_1

first: Michael

last: Tolstorukov

address: 360 Longwood Avenue

department: Informatics

institute: Dana Farber Cancer Institute

data_processing:
ChIP-seq reads were aligned to the mm10 genome using Bowtie2 version 2.4.2.
Peaks were called using MACS3 version 3.0.0a7 with parameters -f BAM -g mm -B -q 0.01 –broad. Alignment files InputAB* were used as control conditions for H3K27me3 and H3K4me2 ChIP-Seq peaks. Alignment files InputD* were used as control conditions for KDM6A ChIP-Seq peaks. Alignment files InputB* were used as control conditions for H3K4me1 ChIP-Seq peaks.
Assembly: mm10
Supplementary files format and content: bam
Supplementary files format and content: bigwig
Supplementary files format and content: broadPeak

source_name: sgKdm6a RPP 236L

growth_protocol: Early passage 236L and 236R cell lines derived from sgKdm6a RPP tumors (Kdm6a-Mutant) and early passage 1014 and 159-1 cell lines derived from sgControl RPP tumors (Kdm6a-WT) grown in complete media containing [10% FBS, P/S, and HITES (10 nM hydrocortisone (Sigma Aldrich # H0135), Insulin-Transferrin-Selenium (Gemini #400-145), and 10 nM beta-estradiol (Sigma Aldrich# E2257), 100 U/mL of penicillin (P), and 100 µg/mL of streptomycin (S)], were plated in ultra-low attachments plates at 0.4 X 10^6 cells/mL in 12mLs (4.8 X 10^6 cells total) or 20mLs (8 X 10^6 cells total) of complete media for H3K27me3/H3K4me2 or KDM6A ChIP, respectively. sgControl RPP cell lines (1014 and 159-1) were also plated at the same density to perform control IgG ChIP for each experiment. 24 hours later, cells were collected, and centrifuged. for ChIP experiments.

extract_protocol:
KDM6A ChIP sequencing experiments were performed by first cross-linking cells with 2 mM disuccinimidyl glutarate (DSG) with rocking for 30 minutes at room temperature prior to fixation with 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. H3K4me2 and H3K27me3 ChIP was performed by fixation with 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. Excess formaldehyde was quenched by dropwise addition of freshly made Glycine at a final concentration 1.25 M. The cells were then resuspended in 1 mL of lysis buffer (50mM Hepes-NaOH pH 8, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. Intact nuclei were then collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the pellet was resuspended in 1 mL of wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, supplemented with a protease inhibitor cocktail and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the tube was rinsed with 500 µL of shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 supplemented with protease inhibitors and phosphatase inhibitors). The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C, the supernatant was carefully removed, and the pellet was gently resuspended in 1mL shearing buffer and transferred to a 1mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator at 100 peak incident power, 10% duty cycles, 200 cycles per burst, water level 15 (left indicator)/10 (right indicator) for 900 seconds. The samples were then transferred to 1.5 mL Eppendorf tubes and centrifuged in an Eppendorf microcentrifuge at 15,900 x g for 5 minutes at 4°C. 900 µL of the supernatants were transferred to a new Eppendorf tube, to which 1% Triton X-100 and 150 mM NaCl were added. 20µl of Dynabeads Protein G (ThermoFisher #10004D), prewashed with Shearing Buffer, was then added and samples were rotated for 1 hour at 4°C to pre-clear the sonicated chromatin. The Dynabeads were then removed using a magnetic stand and the supernatants were transferred to new tubes. 2.5% of the total lysate was removed to make genomic DNA to be used for the ChIP-sequencing input DNA. For the H3K27me3 and H3K4me2 ChIP, the remaining lysate (95% of total) were equally distributed into two Eppendorf tubes to perform the H3K27me3 and H3K4me2 ChIPs. 3 µg of the rabbit anti-H3k27me3 (C36B11) (Cell signaling, #9733) or 3 µg of the rabbit anti-H3K4me2 (Abcam #Ab32356) primary antibodies were added. For the KDM6A ChIP, the remaining 95% were incubated with 10 µg of the rabbit anti-KDM6A [Bethyl lab, A302-374A (UTX antibody)]. Same amount of rabbit IgG isotype control (Cell Signaling #3900) with the same amount of lysate was used as a control for each ChIP. All samples were incubated overnight while rotating at 4°C. The following morning, 50µL of Dynabeads, prewashed with Shearing buffer, were added and the samples were incubated for another 2 hours while rotating at 4°C. A magnetic stand was used to isolate the Dynabeads.  The supernatant was removed and the Dynabeads were washed once in 1mL of low salt immune complex wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 0.1% SDS, 1% TX-100, 2mM EDTA) and incubated for 5 minutes while rotating at 4°C.  The beads were again isolated using a magnetic stand.  Following removal of the supernatant the Dynabeads were washed once in 1mL of high salt immune complex wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 0.1% SDS, 1% TX-100, 2mM EDTA) and incubated for 5 minutes while rotating at 4°C.  The beads were again pelleted with a magnetic stand.  Following removal of the supernatant, the Dynabeads were washed once in 1mL of Lithium Chloride immune complex wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% SDS, 1% NP-40, 1mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were then washed twice in TE pH8 at room temperature and the beads were then resuspended in 100µL TE pH8.
RNase A (Qiagen) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, proteinase K was then added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and then an additional 6 hours at 65°C. 300 µL QG buffer and 100 µL of isopropanol was then added to each sample and a magnetic stand was used to pellet the Dynabeads. The supernatant was then collected and DNA was isolated using QIAquick gel extraction kit (Qiagen) according to the manufacturer’s instructions. DNA concentration was determined using the Nanodrop 8000 (Thermofisher Scientific) and sample were stored at -80°C.

treatment_protocol: No treatment

tag: cell line

value: sgKdm6a RPP 236L

value: mouse small cell lung cancer cell line (SCLC) derived from a mouse tumor


title: MG_Cort_ATGLi_p47

status: Public on Jun 08 2023

type: SRA

city: Baton Rouge

first: Jaroslaw

last: Staszkiewicz

state: LA

address: 6400 Perkins Rd

department: Genomics Core Facility

country: USA

institute: Pennington Biomedical Research Center

library_source: transcriptomic

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.6.1, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.24.0 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

molecule: total RNA

organism: Mus musculus

source_name: mixed gastrocnemius

extract_protocol:
Mice were euthanized using CO2 and cervical dislocation. Tissues were collected, flash-frozen in liquid nitrogen, and stored at -80C until processed. Tissues were powdered and 20-25mg was used for RNA isolation using an Rneasy kit using the manufacturers protocol for skeletal muscle tissue.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

treatment_protocol: Male C57BL6J mice were provided with vehicle (1% EtOH) or corticosterone (cort; 100ug/ml) within their drinking water for two weeks.  A subset of animals treated with either vehicle or cort were provided with the ATGL inhibitor, atglistatin (571mg/kg) milled into their food (Teklad 8640), in order to reduce lipolysis.

tag: tissue

value: mixed gastrocnemius

tag: strain

tag: treatment

value: Cort ATGLi

tag: disease state

value: Nondiabetic (ND)

tag: glucose (fed)

tag: insulin


title: InputB_sgCTRL_1014_1

city: Boston

state: MA

library_source: genomic

molecule: genomic DNA

source_name: sgControl RPP 1014

value: sgControl RPP 1014

tag: cell type


title: MG_EtOH_ATGLi_p14

value: EtOH ATGLi


title: InputB_sgKDM6A_236R_1

source_name: sgKdm6a RPP 236R

value: sgKdm6a RPP 236R


title: InputB_sgCTRL_159_1

source_name: sgControl RPP 159-1

value: sgControl RPP 159-1


title: H3K4me1_sgCTRL_159_1


title: MG_Cort_CON_p45

value: Cort CON

value: Diabetic (Db)


title: H3K4me1_sgKDM6A_236L_1


title: H3K4me1_sgCTRL_1014_1


title: MG_EtOH_ATGLi_p13


title: H3K4me1_sgKDM6A_236R_1


title: MG_Cort_ATGLi_p41


title: 6AF 10µM_72h

type: RNA

city: Sendai-shi

first: Susumu

last: Suzuki

country: Japan

institute: Tohoku Medical and Pharmaceutical University

hyb_protocol: standard Affymetrix Protocol

scan_protocol: standard Affymetrix Protocol

data_processing: The data were analyzed using Transcriptome Analysis Console (TAC) Software (Thermo Fisher Scientific).

label: biotin

organism: Homo sapiens

source_name: NB4 cell

label_protocol: standard Affymetrix Protocol

growth_protocol: RPMI containing 10% heat-inactivated fetal bovine serum (FBS) under 5% CO2 at 37°C in a humidified atmosphere.

extract_protocol: RNA extraction was performed using Sepasol®-RNA I Super G (nacali tesque) according to the manufacturer's instructions.

treatment_protocol: Cells were seeded at a density of 2-3×10^5 cells/ml and treated with DMSO, 100 nM ATRA, 10 µM 6AF and 100 nM ATRA+10 µM 6AF for 72h.

value: acute promyelocytic leukemia


title: MG_Cort_ATGLi_p40


title: MG_Cort_ATGLi_p39


title: 1314-1_sgKdm6aRPP

first: Yixiang

last: Li

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell ranger version 6.0.2 pipeline (10×Genomics) was used to align sequencing data to the custom mouse reference genome and generate the gene-level counts matrix.
Assembly: Custom reference genome was established by adding EGFP and Cas9 sequence to the mouse genome (mm10-2020-A).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung tumor

extract_protocol:
3 independent sgKdm6a RPP were euthanized and lung tumors dissected and finely minced mechanically using a razor blade and then enzymatically digested with Mouse Tumor Dissociation Kit (Miltenyi Biotec, #130-096-730) following the manufacturer’s instruction.
For each sample, about 16,000 cells were loaded onto a10×GenomicsChromiumTMinstrument (10×Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2 kit (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq were normalized to 4 nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform

value: Lung tumor

value: IMSR_JAX:026175:Rosa26-LSL-Cas9 knockin on B6J

tag: age

value: tumor cell

tag: genotype

value: sgKdm6a RPP


title: 1274_sgKdm6aRPP

description: 10x Genomics


title: Ctrl(DMSO)_72h


title: MG_Cort_CON_p37


title: MG_Cort_CON_p35


title: MG_Cort_ATGLi_p38


title: MG_Cort_ATGLi_p42


title: Tcf1_CUT&RUN_KO

city: Tampa

first: Dorina

last: Avram

state: Fl

address: 12902 Magnolia Drive, MRC4

department: Department of Immunology

institute: Moffitt Cancer Center

data_processing:
Fastq files were prepared using Illumina FASTQ Generation application. Fastq files were trimmed using Trimmomatic.
Reads were mapped to the mm10 genome using Bowtie2 (v. 2.2.5) with the following parameters: --dovetail --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
The resulting SAM files were pruned (Q > 30), converted to BAM format, and sorted using SAMtools. Duplicate reads were removed using Picard tools.
MACS2 was used for peak calling, with the following parameters: macs2 callpeak --call-summits -g mm -p 0.00001 -f BAMPE --SPMR -B. Bedgraph files produced by MACS2 were lambda control subtracted. Resulting files were converted to bigWig format.
Due to technical challenges, only one biological replicate of suitable quality was used for downstream analysis of CUT&RUN samples for each genotype.
Differential analysis was conducted using MAnorm with the following parameters: --pe -w 1000. Only peaks with P < 0.05 were used for downstream analyses and these were in some instances additionally filtered for |log2FC|>1. P value was adjusted for the FDR by the Benjamini-Hochberg adjustment.
Assembly: mm10
Supplementary files format and content: narrowPeak files contain CUT&RUN peaks produced by MACS2
Supplementary files format and content: bigWig files were generated from lambda control subtracted bedgraph files produced by MACS2
Supplementary files format and content: bed file contains output from MAnorm representing differential peaks between Bcl11b-deficient and WT cells
Library strategy: CUT&RUN

source_name: Trm-like CD8+ T cells

extract_protocol:
Following sorting, CUT&RUN was performed on 350,000 cells/sample using the ChIC/CUT&RUN Kit (EpiCypher #14-1048) and anti-Tcf1 antibody (clone C46C7, Cell Signaling Technology Cat. No. 2206). The procedure followed the manufacturer's protocol with the following modifications. No spike-in controls were used, 1.5 μl anti-Tcf1 antibody/sample was used. pAG-MNase binding was performed for 30 min at 4C while rotating. MNase digestion was performed for 40 min at 4C while rotating. eBioscience Perm Buffer (Invitrogen/Thermo Fisher Scientific Cat. No. 00-8333) was used at 1x concentration (0.1% saponin) supplemented with Spermidine and cOmplete™EDTA-free Protease Inhibitor (Roche Cat. No. 11836170001) during the incubation step with pAG-MNase. 0.5x eBioscience Perm Buffer was used during the wash step post-pAG-MNase and at later steps of the protocol.
Sequencing libraries were prepared with the NEBNext Ultra II Library Prep Kit (New England Biolabs Cat. No. E7645) and the Magnetic SPRI beads (Beckman Coulter Cat. No. B23317) for purification. PCR amplification conditions were: 14 cycles of DNA melting at 98˚C for 15 seconds, annealing plus extension at 60˚C for 10 seconds, followed by final extension at 72˚C for 1 minute. Libraries were quality-checked and quantified by Bioanalyzer (Agilent) and Qubit (ThermoFisher) and sequenced as PE150 on Illumina NovaSeq 6000.

treatment_protocol: CD8+ T cells were isolated from naïve Bcl11bf/fGzmbCre+Rosa26eYFP+ OT-I and wild type OT-I mice. Purified cells were activated with anti-CD3/anti-CD28 beads (Invitrogen, Cat. No. 114525D) at 250,000 cells/mL in 10% FBS MEM alpha supplemented with 100U/mL IL-2 (Shenandoah Biotechnology, Cat. No. 100-12) for 48 hours at 37°C, 5% CO2, when cells were split 1:3 in fresh media supplemented with 10ng/mL TGFb1 (Shenandoah Biotechnologies, Cat. No. 100-39) and 100ng/mL IL-33 (Shenandoah Biotechnologies, Cat. No. 200-36), for an additional 48 hours.

value: Spleen, LN

value: Bcl11bF/F GzmbCre+ Rosa26+/

tag: cut&run antibody

value: anti-Tcf1 (clone C46C7, Cell Signaling Technology Cat. No. 2206)


title: Tcf1_CUT&RUN_WT

value: wild type


title: ATRA 100nM_72h

value: ATRA 100nM_72h


title: H3K4me3_CUT&RUN_KO

data_processing:
Fastq files were prepared using Illumina FASTQ Generation application. Fastq files were trimmed using Trimmomatic.
Reads were mapped to the mm10 genome using Bowtie2 (v. 2.2.5) with the following parameters: --dovetail --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700.
The resulting SAM files were pruned (Q > 30), converted to BAM format, and sorted using SAMtools. Duplicate reads were removed using Picard tools.
MACS2 was used for peak calling, with the following parameters: macs2 callpeak --call-summits -g mm -p 0.00001 -f BAMPE --SPMR -B. Bedgraph files produced by MACS2 were lambda control subtracted. Resulting files were converted to bigWig format.
Due to technical challenges, only one biological replicate of suitable quality was used for downstream analysis of CUT&RUN samples for each genotype.
Differential analysis was conducted using MAnorm with the following parameters: --pe -w 2000. Only peaks with P < 0.05 were used for downstream analyses and these were in some instances additionally filtered for |log2FC|>1. P value was adjusted for the FDR by the Benjamini-Hochberg adjustment.
Assembly: mm10
Supplementary files format and content: narrowPeak files contain CUT&RUN peaks produced by MACS2
Supplementary files format and content: bigWig files were generated from lambda control subtracted bedgraph files produced by MACS2
Supplementary files format and content: bed file contains output from MAnorm representing differential peaks between Bcl11b-deficient and WT cells
Library strategy: CUT&RUN

extract_protocol:
CUT&RUN was performed on 300,000 cells/sample using the ChIC/CUT&RUN Kit (EpiCypher #14-1048) and anti-H3K4me3 (EpiCypher Cat. No. 13-0041). The procedure followed the manufacturer's protocol with the following modifications. 1 μl anti-H3K4me3 antibody/sample was used. Following spike-in controls were used: K-MetStat Panel (2 μl of stock diluted 1:3) and 0.37 μl E. coli. pAG-MNase binding was performed for 20 min at RT while rotating. MNase digestion was performed for 120 min at 4C while rotating.
Sequencing libraries were prepared with the NEBNext Ultra II Library Prep Kit (New England Biolabs Cat. No. E7645) and the Magnetic SPRI beads (Beckman Coulter Cat. No. B23317) for purification. PCR amplification conditions were: 14 cycles of DNA melting at 98˚C for 15 seconds, annealing plus extension at 60˚C for 10 seconds, followed by final extension at 72˚C for 1 minute. Libraries were quality-checked and quantified by Bioanalyzer (Agilent) and Qubit (ThermoFisher) and sequenced as PE150 on Illumina NovaSeq 6000.


title: Ileal IgG_Trichuris_5AGImmunized_E

type: protein

city: St. Louis

first: Bruce

middle: A

last: Rosa

state: MO

address: 4444 Forest Park Ave

department: Medicine

institute: Washington University in St Louis

description: Arrays were incubated overnight at 4°C with agitation, washed three times with Tris-buffered saline (TBS)–0.05% Tween 20, and incubated with Goat anti-Swine IgG (Bethyl Laboratories, Montgomery, TX) diluted 1:500 in blocking buffer at room temperature. Arrays were washed three times with TBS–0.05% Tween 20 and incubated with Cy5 Donkey Anti-Goat IgG (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer at room temperature, protected from light. Arrays were washed three times with TBS–0.05% Tween 20, three times with TBS, and once with water and then air dried by being centrifuged at 1,000 × g for 4 min and left overnight in a desiccator before scanning. Probed microarrays (slides) were scanned using a GenePix 4300A high-resolution microarray scanner (Molecular Devices, Sunnyvale, CA).

hyb_protocol: Briefly, the clone library was created through an in vivo recombination cloning process with PCR-amplified coding sequences from cDNA, and a complementary linearized expressed vector transformed into chemically competent E. coli cells was amplified by PCR and cloned into the pXI vector using a high-throughput PCR recombination cloning method. The cloning methodology is described in detail elsewhere (Davies et al., 2005). All the clones were sequenced (Retrogen, Inc., San Diego, CA), and the results matched the correct target for the selected genes.  From each clone, the corresponding protein was expressed using an in vitro transcription and translation (IVTT) system, the E. coli cell-free rapid translation system (RTS) kit (Biotechrabbit, Berlin, Germany), as previously described (Davies et al., 2005). Each expressed protein includes a 5′ polyhistidine epitope tag and a 3′ hemagglutinin (HA) epitope tag. After expressing the proteins according to the manufacturer's instructions, translated proteins were printed onto nitrocellulose-coated glass AVID slides (Grace Bio-Labs, Inc., Bend, OR) using an ArrayJet Marathon Argus robotic microarray non-contact printer (ArrayJet, Roslin, UK). Each slide contained 16 nitrocellulose pads on which the expressed proteins along with controls were printed (this allowed sixteen samples to be probed per slide using sealed chambers that isolate the arrays). Microarray chip printing and protein expression were quality checked by probing random slides with anti-His and anti-HA monoclonal antibodies with fluorescent labeling.

scan_protocol: Probed microarrays (slides) were scanned using a GenePix 4300A high-resolution microarray scanner (Molecular Devices, Sunnyvale, CA), and an image file (.tiff) was saved for each array using GenePix pro 7 software. The signals in the scanned images were quantified using the Mapix software (Innopsys) autogridding feature. For this process, two input files are required: (i) a .gal file that defines the array and subarray layout, and (ii) the .tiff image file for an array. Once the autogridding is complete, the overlays of the mapped array, subarray, and individual spot locations are shown in the graphical user interface (GUI). If the automatic gridding fails to map to the correct positions, the mapping can be manually adjusted using the GUI. The final raw intensity is the foreground intensity minus the local background intensity. The raw signals were automatically extracted and saved as .csv files in data matrix format, with array spots as rows and samples as columns, using R (http://www.R-project.org).

data_processing:
Initial processing of the raw array data was performed as previously described (Li et al., 2017). First, raw values were transformed using the base 2 logarithm. Next, the data set was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT control spots for each sample. Since the IVTT control spots carry not only the chip, sample, and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding versus the nonspecific antibody binding to the IVTT controls. With the normalized data, a value of 0.0 means that the intensity is no different than that of the IVTT controls, and a value of 1.0 indicates a doubling with respect to IVTT control spots. Log2 relative fluorescence values (relative to the median of the negative control probes) were calculated for each protein and each sample (one sample per array). Principal components analysis (PCA) was performed using the “prcomp” package in R, using only the proteins with relative Log2 fluorescence >0 relative to negative controls.
The Protein IDs come from the PRJNA80881 Ascaris suum genome annotation, retrieved from https://parasite.wormbase.org/Ascaris_suum_prjna80881/Info/Index

label: Cy5 Donkey Anti-Goat IgG

molecule: protein

organism: Sus scrofa

source_name: Pig_Ileal IgG_Trichuris_5AGImmunized

label_protocol: Cy3 Goat Anti-Rabbit IgG, Cy5 Donkey Anti-Goat IgG

extract_protocol: Cloning and expression was performed using standard techniques. All sequences were PCR amplified from cDNA using sequence specific forward and reverse primers that encompassed the mature protein and contained Sac I (forward) and Xho I (reverse) restriction sites for downstream subcloning. Translation stop sites were incorporated into all reverse primers. Amplified sequences were first cloned into pCR2.1-TOPO by TA cloning then transformed into DH5α cells for sequence verification. Validated sequences were restriction enzyme digested and subcloned into the pSUMO bacterial expression vector (Life Sensors) and transformed into BL21 cells for protein production. Expression was performed using overnight cultures to spike 500ml of LB medium containing ampicillin (100 µg/ml) which was induced at OD = 0.7 for 5 hrs. with isopropyl β-D-1-thiogalactopyranoside (0.3 mM final). Pelleted cells were lysed with 1 mg/ml lysozyme, frozen overnight then sonicated. Because all clones formed inclusion bodies during production, the sonicated pellets were first washed 3X with 2% Triton X-100, solubilized in 8M Urea (made fresh) and batch purified by affinity chromatography using 2 ml of Ni-NTA. All mixtures were added to columns, washed with 6M urea (3X), then wash buffer containing 50 mM sodium phosphate, pH 8.0, 300 mM sodium chloride and 20 mM imidazole. Recombinant proteins were eluted with 5 ml of wash buffer containing 500 mM imidazole and 12 mM sodium lauryl sarkosine.

treatment_protocol: Experimental pig barrows were obtained from a pig farrowing facility at the Beltsville Agricultural Research Center, Beltsville, MD. Pigs were derived from boars from a four-way crossbred composite BX line (Duroc X maternal Landrace X terminal Landrace X Yorkshire) designed by scientists at the USDA/ARS/US Meat Animal Research Center, Clay Center, NE to be genetically similar to genetics in the commercial swine industry at the time they were born; the genetics of the gilts are predominantly of the BX composite line. Pigs were from a herd screened yearly for porcine reproductive and respiratory syndrome virus (PRRSV), influenza (H1N1 and H3N2), pseudorabies, brucellosis and intestinal worm parasites by the Veterinary Services Group at the Beltsville Agricultural Research Center and have been negative for these infections. They were individually housed in stalls with a non-absorptive concrete floor surface covered with rubber mats with ad libitum access to water and a nutritionally adequate corn/soybean-based diet. All animal experiments and procedures were conducted in accordance with guidelines established and approved by the Beltsville Area Animal Care and Use Committee under protocol 17-019. Pigs in the infection only cohort included 1) three pigs inoculated five times every 10 days with 10,000 T. suis eggs and bled 10 days after the last inoculation, 2) six pigs inoculated eight times every other day with 10,000 A. suum eggs and bled 25 days after the last inoculation, and 3) three pigs inoculated with 10,000 T. suis eggs and bled 53 days later (these pigs were worm free and considered as a resistant phenotype). The second group of six pigs in the vaccination cohort were immunized with 400µg of recombinant protein (80µg each of the five-parasite antigen cocktail in Seppic Montanide ISA 61 VG which was injected subcutaneously). The pigs were immunized a second time four weeks later and again after two weeks later and followed by a challenge infection with either 10,000 infective A. suum or T. suis eggs. The A. suum-infected pigs were bled and euthanized 27 days after inoculation and the T. suis infected pigs 37 after inoculation to collect blood and ileal wash fluid (contents from the ileum were removed and spun at 10,000 rpm and the supernatant fluid decanted and frozen at -80C until used) from the small intestine (3 - immunized/A. suum infected).

tag: tissue type

value: Ileal IgG

tag: infection status

value: Trichuris suis

tag: immunization status

value: Immunized with 5_antigen cocktail


title: 1314-2_sgKdm6aRPP

description: 10x Genomics


title: MG_Cort_CON_p33

value: mixed gastrocnemius

value: Nondiabetic (ND)


title: MG_Cort_CON_p34

value: Cort CON


title: MG_Cort_CON_p32


title: H3K4me3_CUT&RUN_WT

value: anti-H3K4me3 (EpiCypher Cat. No. 13-0041)


title: MKN1 overexpressing RHOA Y42C

city: Kashiwa

first: Shogo

last: Kumagai

state: Chiba

address: 6-5-1 Kashiwanoha

institute: National Cancer Center

description: MKN1 overexpressing RHOA Y42C

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix GeneChip Command Console Software and Affymetrix Expression Console Software.

label: puromycin

source_name: human gastric cancer cell line

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

growth_protocol: The cell lines were cultured in 37℃ in RPMI with 10% FBS.

extract_protocol: RNA was extracted using the RNeasy Mini Kit (QIAGEN).

treatment_protocol: MKN1 was transfected with pBABE RHOA wild-type or pBABE RHOA Y42C and selected by puromycin.

value: human gastric cancer cell line

tag: overexpressed gene

value: RHOA Y42C


title: Ileal IgG_Trichuris_5AGImmunized_B


title: Ileal IgG_Ascaris_5AGImmunized_E

source_name: Pig_Ileal IgG_Ascaris_5AGImmunized

value: Ascaris suum


title: 1270_sgKdm6aRPP

description: 10x Genomics

value: Lung tumor

value: IMSR_JAX:026175:Rosa26-LSL-Cas9 knockin on B6J

value: tumor cell


title: MG_Cort_CON_p36


title: H3K27ac_ChIPseq_KO1

data_processing:
Fastq files were prepared using Illumina FASTQ Generation application. Fastq files were trimmed using Trimmomatic.
Reads were mapped to the mm10 genome using Bowtie2 (v. 2.2.5) with the default parameters.
The resulting SAM files were pruned (Q > 30), converted to BAM format, and sorted using SAMtools. Duplicate reads were removed using Picard tools.
MACS2 was used for peak calling, with the following parameters: macs2 callpeak --call-summits --nomodel -g mm -p 0.01 -f BAM --SPMR -B. Bedgraph files produced by MACS2 were lambda control subtracted. A single representative file for each experiment was created as a mean of two biological replicates. Resulting files were converted to bigWig format.
Irreproducible discovery rate (IDR) tool was used to generate a single peak dataset from two biological replicates and peaks with an IDR value <= 0.05 were kept.
Differential analysis was conducted using MAnorm with default parameters. Only peaks with P < 0.05 were used for downstream analyses and these were in some instances additionally filtered for |log2FC|>1. P value was adjusted for the FDR by the Benjamini-Hochberg adjustment.
Assembly: mm10
Supplementary files format and content: narrowPeak files contain ChIP-seq peaks produced by MACS2
Supplementary files format and content: bigWig files were generated from lambda control subtracted bedgraph files produced by MACS2 and they represent mean of two biological replicates
Supplementary files format and content: bed files contain H3K27ac ChIP-seq peaks as non-filtered output of IDR combining two biological replicates; and separately output from MAnorm representing differential peaks between Bcl11b-deficient and WT cells

extract_protocol:
Following sorting, ChIP was performed using the ChIP-IT High Sensitivity Kit (Active Motif, Cat. No. 53040). The procedure followed the manufacturer recommended protocol with specific modifications: (i) the nuclear pellet of 10M cells was lysed in 500 μl ChIP buffer and the chromatin was sheared to an average of 200 to 600 base pairs using the Sonicator Q125 (QSonica, Newtown, CT, USA); (ii) the immunoprecipitation was performed with 4 μL of anti-acetyl-H3 (Lys27) (D5E4) (Cell Signaling Technology, Cat. No. 8173).
Sequencing libraries were prepared using the Next Gen DNA Library kit (Active Motif, Cat. No. 53216) and Next Gen Indexing Kit (Active Motif, Cat. No. 53264) for Illumina. Libraries were purified with the Magnetic SPRI beads (Beckman Coulter #B23317) and amplified with 9 PCR cycles (Mastercycler Nexus, Eppendorf). Quality of amplified libraries was validated using ChIP-IT qPCR Analysis Kit (Active Motif, Cat. No. 53029) and libraries were sequenced as PE150 on Illumina NovaSeq 6000.

value: Spleen, LN

value: Bcl11bF/F GzmbCre+ Rosa26+/

tag: chip antibody

value: anti-H3K27ac (D5E4; Cell Signaling Technology; #8173)


title: MG_Cort_CON_p30

value: Diabetic (Db)


title: MG_Cort_CON_p29


title: H3K27ac_ChIPseq_WT2

value: wild type


title: MKN1 overexpressing RHOA wild-type

description: MKN1 overexpressing RHOA wild-type

value: RHOA wild-type


title: Ileal IgG_Trichuris_5AGImmunized_D

value: Ileal IgG

value: Trichuris suis

value: Immunized with 5_antigen cocktail


title: H3K27ac_ChIPseq_WT1


title: Ileal IgG_Ascaris_5AGImmunized_D


title: MG_Cort_CON_p28

value: mixed gastrocnemius

value: Cort CON


title: Ileal IgG_Trichuris_5AGImmunized_C


title: MG_Cort_CON_p27


title: Ahr_ChIPseq_KO2

data_processing:
Fastq files were prepared using Illumina FASTQ Generation application. Fastq files were trimmed using Trimmomatic.
Reads were mapped to the mm10 genome using Bowtie2 (v. 2.2.5) with the default parameters.
The resulting SAM files were pruned (Q > 30), converted to BAM format, and sorted using SAMtools. Duplicate reads were removed using Picard tools.
MACS2 was used for peak calling, with the following parameters: macs2 callpeak --call-summits --nomodel -g mm -q 0.05 -f BAM --SPMR -B. Bedgraph files produced by MACS2 were lambda control subtracted. A single representative file for each experiment was created as a mean of two biological replicates. Resulting files were converted to bigWig format.
Irreproducible discovery rate (IDR) tool was used to generate a single peak dataset from two biological replicates. Due to technical challenges of Ahr ChIP-seq, no IDR filtering was performed for this dataset.
Differential analysis was conducted using MAnorm with the following parameters: --pe -w 1000. Only peaks with P < 0.05 were used for downstream analyses and these were in some instances additionally filtered for |log2FC|>1. P value was adjusted for the FDR by the Benjamini-Hochberg adjustment.
Assembly: mm10
Supplementary files format and content: narrowPeak files contain ChIP-seq peaks produced by MACS2
Supplementary files format and content: bigWig files were generated from lambda control subtracted bedgraph files produced by MACS2 and they represent mean of two biological replicates
Supplementary files format and content: bed files contain Ahr ChIP-seq peaks as non-filtered output of IDR combining two biological replicates; and separately output from MAnorm representing differential peaks between Bcl11b-deficient and WT cells

extract_protocol:
Following sorting, ChIP was performed using the ChIP-IT High Sensitivity Kit (Active Motif, Cat. No. 53040). The procedure followed the manufacturer's recommended protocol with specific modifications: (i) the nuclear pellet of 10M cells was lysed in 500 μl ChIP buffer and the chromatin was sheared to an average of 200 to 600 base pairs using the Sonicator Q125 (QSonica, Newtown, CT, USA); (ii) the immunoprecipitation was performed with 4 μL of anti-Ahr (Enzo Life Sciences, Cat. No. BML-SA210–0100).
Sequencing libraries were prepared using the Next Gen DNA Library kit (Active Motif, Cat. No. 53216) and Next Gen Indexing Kit (Active Motif, Cat. No. 53264) for Illumina. Libraries were purified with the Magnetic SPRI beads (Beckman Coulter #B23317) and amplified with 9 PCR cycles (Mastercycler Nexus, Eppendorf). Quality of amplified libraries was validated using ChIP-IT qPCR Analysis Kit (Active Motif, Cat. No. 53029) and libraries were sequenced as PE150 on Illumina NovaSeq 6000.

treatment_protocol: CD8+ T cells were isolated from naïve Bcl11bf/fGzmbCre+Rosa26eYFP+ OT-I and wild type OT-I mice. Purified cells were activated with anti-CD3/anti-CD28 beads (Invitrogen, Cat. No. 114525D) at 250,000 cells/mL in 10% FBS MEM alpha supplemented with 100U/mL IL-2 (Shenandoah Biotechnology, Cat. No. 100-12) for 48 hours at 37°C, 5% CO2, when cells were split 1:3 in fresh media supplemented with 10ng/mL TGFb1 (Shenandoah Biotechnologies, Cat. No. 100-39) and 100ng/mL IL-33 (Shenandoah Biotechnologies, Cat. No. 200-36), for an additional 48 hours. Cells were treated with the Ahr ligand 6-formylindolo[3,2-b]carbazole (FICZ, final concentration 200 nM; Enzo Life Sciences Cat. No. BML-GR206) for 4 hours before harvesting.


title: Ileal IgG_Ascaris_5AGImmunized_C


title: H3K27ac_ChIPseq_KO2


title: Ileal IgG_Ascaris_5AGImmunized_B


title: Ahr_ChIPseq_KO1

value: anti-Ahr (Enzo Life Sciences, Cat. No. BML-SA210–0100)


title: MG_Cort_ATGLi_p25

value: Cort ATGLi

value: Nondiabetic (ND)


title: Ileal IgG_Trichuris_5AGImmunized_A


title: Ileal IgG_Ascaris_5AGImmunized_A

value: Ascaris suum


title: Ileal IgG_Trichuris_NoImmunization_H

source_name: Pig_Ileal IgG_Trichuris_NoImmunization

value: No Immunization


title: Ahr_ChIPseq_WT2


title: MG_Cort_ATGLi_p24


title: Ahr_ChIPseq_WT1


title: Ileal IgG_Trichuris_NoImmunization_G


title: MG_EtOH_ATGLi_p12

value: EtOH ATGLi


title: Ileal IgG_Trichuris_NoImmunization_F


title: Abdominal aorta, Prdm16 knockout, rep3

city: Ann Arbor

first: Zhenguo

last: Wang

state: MI

address: 2800 Plymouth Road, NCRC BLDG26, Rm214N

department: MM Int Med-Cardiology

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files. The reads were trimmed using Cutadapt v2.3.
The reads were evaluated with FastQC (Andrews, 2010) (v0.11.8) to determine quality of the data.
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq.
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7.
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: Tpm_geo.csv: Comma-separated matrix table with transcripts per kilobase million (tpm) for every gene and every sample.

molecule: polyA RNA

source_name: Abdominal aorta

extract_protocol:
Total RNA from abdominal aorta were isolated with the RNeasy® micro kit (Cat# 74004, Qiagen).
The RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) with poly A selection. This pool was subjected to 151 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). An average of 40 million paired-reads per samples were generated.

value: Abdominal aorta

value: Prdm16 knockout

tag: Sex

value: male


title: MG_EtOH_ATGLi_p11


title: Abdominal aorta, Prdm16 knockout, rep2


title: Abdominal aorta, Prdm16 knockout, rep1


title: Ileal IgG_Trichuris_NoImmunization_E


title: MG_EtOH_ATGLi_p10


title: MG_EtOH_ATGLi_p09


title: Ileal IgG_Trichuris_NoImmunization_D


title: Abdominal aorta, control, rep3

value: control


title: Ileal IgG_Trichuris_NoImmunization_C


title: Abdominal aorta, control, rep2


title: MG_Cort_ATGLi_p17


title: Ileal IgG_Trichuris_NoImmunization_B


title: MG_Cort_ATGLi_p23


title: Skeletal Muscle, AHRmKO, snRNA-seq

city: Gainesville

first: Terence

middle: E.

last: Ryan

state: Florida

address: 1864 Stadium Rd

department: Applied Physiology and Kinesiology

institute: University of Florida

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger software v7.0.1
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Tibialis Anterior

extract_protocol:
Nuclei were isolated using the 10x Genomica Chromium nuclei isolation kit.
Library was performed according to the manufacter's instructions (Chromium Next GEM Single Cell 3’ HT Reagent kits v3.1, 10x Genomics).

value: Skeletal Muscle

value: Tibialis Anterior

value: AHRtm3.1Bra/J, Jackson Laboratories, Stock No. 006203 crossed with Tg(ACTA1-cre/Esr1*)2Kesr/J, Jackson Laboratories, Stock No. 025750

value: 16-20 weeks


title: MG_EtOh_CON_p16

value: EtOH CON


title: Skeletal Muscle, AHRfl/fl, snRNA-seq

description: 10x Genomics


title: Ileal IgG_Trichuris_NoImmunization_A

value: Ileal IgG

value: Trichuris suis


title: MG_EtOh_CON_p15

value: mixed gastrocnemius


title: Ileal IgG_Ascaris_NoImmunization_L

source_name: Pig_Ileal IgG_Ascaris_NoImmunization


title: 656_KDM6A [scATAC-seq]

first: Yingtian

last: Xie

address: 450 BROOKLINE AVE

institute: DANA FARBER CANCER INSTITUTE INC

data_processing:
Illumina Bcl2fastq v2.18
Reads were aligned to mm10 using BWA
Assembly: mm10

source_name: sclc

extract_protocol:
dissociated cells were resuspended in DPBS with 0.04% UltraPure BSA and cell counts were measured with a Vi-CELL XR Cell Viability Analyzer (Beckman Coulter). Cells were then diluted in 0.04% BSA/DPBS at a cell concentration of 1000 cells/μL. About 16,000 cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s instructions
nuclei were transposed according to 10XGenomics specifications. Approximately 10,000 cells were targeted for each tissueanalyzed and pooled and processed according to the 10x Genomics scATAC-seq sample preparation protocol (Chromium Single Cell ATAC Library & Gel Bead Kit, 10x Genomics) to obtain a single sequencing library

value: sclc

value: tissue

value: kdm6a KO


title: MG_Cort_ATGLi_p14

value: Cort ATGLi

value: Nondiabetic (ND)


title: Ileal IgG_Ascaris_NoImmunization_I

value: Ascaris suum

value: No Immunization


title: Ileal IgG_Ascaris_NoImmunization_K


title: MG_Cort_ATGLi_p13


title: MG_EtOh_CON_p12


title: Tumor_1122

data_processing:
Burrows-Wheeler Aligner (BWA) to map sequencing reads to the reference genome
MACS2 for peakcalling
Assembly: mm9
Supplementary files format and content: pileup.bw

source_name: tissue

extract_protocol:
Cells was fixed using 1% formaldehyde and chromatin sheared to 300-500 bp in size using the Covaris E220 ultrasonicator. Resulting chromatin was incubated overnight with indicated antibodies. Purified immunoprecipitates were isolated and quantified by Qubit fluorometer.
DNA sequencing libraries were prepared using the ThruPLEX-FD Prep kit (Rubicon Genomics). Libraries were sequenced using 75-bp reads on the Illumina platform at the Dana-Farber Cancer Institute.

value: kdm6a ko


title: Ileal IgG_Ascaris_NoImmunization_H


title: MG_Cort_ATGLi_p18


title: Abdominal aorta, control, rep1

value: Abdominal aorta

value: control

value: male


title: Ileal IgG_Ascaris_NoImmunization_G


title: Tumor_1117


title: Tumor_1121


title: MG_EtOh_CON_p10


title: Ileal IgG_Ascaris_NoImmunization_F


title: Tumor_165

value: wt


title: Ileal IgG_Ascaris_NoImmunization_J


title: MG_EtOH_ATGLi_p08

value: EtOH ATGLi


title: MG_EtOH_ATGLi_p07


title: Tumor_645

data_processing:
ChIP reads were aligned to the mm9 genome assembly using BWA
ChIP-seq peaks were called using MACS 2.0
DEseq2 was used to assign differential intensities and statistics
Differential binding sites was determined by filtering out insignificant peaks (adjusted p-value<0.05) and then determining log2FC values between samples for each region using a log2 FC >0 or <0
Assembly: mm9
Supplementary files format and content: Analysis was done using the CoBRA workflow


title: MG_EtOH_ATGLi_p06


title: 236R_KDM6A [scATAC-seq]


title: Tumor_535


title: Ileal IgG_Ascaris_NoImmunization_C


title: MG_EtOH_ATGLi_p05


title: Ileal IgG_Uninfected_NoImmunization_S

source_name: Pig_Ileal IgG_Uninfected_NoImmunization

value: Uninfected


title: Ileal IgG_Ascaris_NoImmunization_A

value: Ileal IgG


title: Ileal IgG_Ascaris_NoImmunization_B


title: MG_EtOh_CON_p04

source_name: mixed gastrocnemius

value: EtOH CON


title: Tumor_236L


title: MG_EtOh_CON_p09

value: mixed gastrocnemius


title: Ileal IgG_Ascaris_NoImmunization_D


title: Ileal IgG_Ascaris_NoImmunization_E


title: MG_EtOh_CON_p02


title: Tumor_18_227

value: sclc


title: Ileal IgG_Uninfected_NoImmunization_R


title: Ileal IgG_Uninfected_NoImmunization_Q


title: Tumor_656

value: tissue


title: Ileal IgG_Uninfected_NoImmunization_P


title: 1121_sgKdm6aRPP

description: 10x Genomics

data_processing:
Cell ranger version 6.0.2 pipeline (10× Genomics) was used to align sequencing data to the custom mouse reference genome and generate the gene-level counts matrix.
Assembly: Custom reference genome was established by adding EGFP and Cas9 sequence to the mouse genome (mm10-2020-A).
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
3 independent sgKdm6a RPP (numbers) and 3 independent sgControl RPP mice (numbers) were euthanized and lung tumors dissected and finely minced mechanically using a razor blade and then enzymatically digested with Mouse Tumor Dissociation Kit (Miltenyi Biotec, #130-096-730) following the manufacturer’s instruction.
For each sample, about 16,000 cells were loaded onto a 10× Genomics ChromiumTM instrument (10× Genomics) according to the manufacturer’s instructions. The scRNA-seq libraries were processed using Chromium Next GEM Single Cell 5' Kit v2 kit (10× Genomics). Quality controls for amplified cDNA libraries and final sequencing libraries were performed using Bioanalyzer High Sensitivity DNA Kit (Agilent). The sequencing libraries for scRNAseq were normalized to 4 nM concentration and pooled. The pooled sequencing libraries were sequenced on Illumina NovaSeq S4 300 cycle platform

value: Lung tumor

value: IMSR_JAX:026175:Rosa26-LSL-Cas9 knockin on B6J

value: tumor cell

value: sgKdm6a RPP


title: MG_EtOh_CON_p01

value: Nondiabetic (ND)


title: 1119_sgKdm6aRPP

description: 10x Genomics


title: Ileal IgG_Uninfected_NoImmunization_O

value: No Immunization


title: Liver_Cort_CON_p50

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.6, Rstudio V1.3.1056 and biomaRt V2.24.1
DESeq2  V1.24.0 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

source_name: liver

extract_protocol:
Mice were euthanized using CO2 and cervical dislocation. Tissues were collected, flash-frozen in liquid nitrogen, and stored at -80C until processed. Tissues were powdered and 15-20mg was used for RNA isolation using an Rneasy kit using the manufacturers protocol for liver.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

value: liver

value: Cort CON

value: Diabetic (Db)


title: Tumor_236R

value: kdm6a KO


title: Liver_Cort_CON_p49


title: 1198_RPPControl

description: 10x Genomics

value: sgCtrl RPP


title: Ileal IgG_Uninfected_NoImmunization_N

value: Uninfected


title: Ileal IgG_Uninfected_NoImmunization_M

value: Ileal IgG


title: MG_EtOh_CON_p03

value: EtOH CON


title: Liver_Cort_ATGLi_p48

value: Cort ATGLi


title: Liver_Cort_ATGLi_p47


title: 168_RPPControl

description: 10x Genomics


title: Ileal IgG_Uninfected_NoImmunization_L


title: Ileal IgG_Uninfected_NoImmunization_K


title: 165_RPPControl

description: 10x Genomics


title: Ileal IgG_Uninfected_NoImmunization_J


title: Liver_Cort_CON_p46


title: Liver_Cort_CON_p45


title: Input_KDM6A_sgCTRL_1014

data_processing:
ChIP-seq reads were aligned to the mm10 genome using Bowtie2 version 2.4.2.
Assembly: mm10
Peaks were called using MACS3 version 3.0.0a7 with parameters -f BAM -g mm -B -q 0.01 broad. Alignment files InputAB* were used as control conditions for H3K27me3 and H3K4me2 ChIP-Seq peaks. Alignment files InputD* were used as control conditions for KDM6A ChIP-Seq peaks. Alignment files InputB* were used as control conditions for H3K4me1 ChIP-Seq peaks.

source_name: sgControl RPP 1014

tag: antibody

value: input

tag: cell line

value: sgControl RPP 1014

value: mouse small cell lung cancer cell line (SCLC) derived from a mouse tumor


title: Liver_EtOH_ATGLi_p14

tag: tissue

tag: strain

value: EtOH ATGLi


title: Input_KDM6A_sgCTRL_159-1

source_name: sgControl RPP 159-1

value: sgControl RPP 159-1


title: Liver_EtOH_ATGLi_p13

tag: treatment

tag: disease state


title: Ileal IgG_Uninfected_NoImmunization_H


title: 1117_sgKdm6aRPP

description: 10x Genomics

value: Lung tumor

value: IMSR_JAX:026175:Rosa26-LSL-Cas9 knockin on B6J

value: tumor cell

value: sgKdm6a RPP


title: Liver_Cort_ATGLi_p42

value: liver

value: Nondiabetic (ND)

tag: glucose (fed)

tag: insulin


title: Ileal IgG_Uninfected_NoImmunization_I

value: No Immunization


title: KDM6A_sgCTRL_159-1

tag: cell type


title: Liver_Cort_ATGLi_p41


title: Ileal IgG_Uninfected_NoImmunization_E


title: Ileal IgG_Uninfected_NoImmunization_F


title: InputH3K4me2_H3K27me3_sgCTRL_236R

source_name: sgKdm6a RPP 236R

value: sgKdm6a RPP 236R


title: Liver_Cort_ATGLi_p38


title: InputH3K4me2_H3K27me3_sgCTRL_1014


title: Ileal IgG_Uninfected_NoImmunization_C

value: Uninfected


title: Liver_Cort_CON_p37

value: Cort CON

value: Diabetic (Db)


title: InputH3K4me2_H3K27me3_sgCTRL_236L

source_name: sgKdm6a RPP 236L

value: sgKdm6a RPP 236L


title: Ileal IgG_Uninfected_NoImmunization_B

value: Ileal IgG


title: InputH3K4me2_H3K27me3_sgCTRL_159-1

value: input


title: Liver_Cort_ATGLi_p40

value: Cort ATGLi


title: Liver_Cort_CON_p35


title: Ileal IgG_Uninfected_NoImmunization_G


title: Ileal IgG_Uninfected_NoImmunization_D


title: Liver_Cort_CON_p36


title: KDM6A_sgCTRL_1014

value: sgControl RPP 1014

value: mouse small cell lung cancer cell line (SCLC) derived from a mouse tumor


title: Ileal IgG_Uninfected_NoImmunization_A


title: H3K4me2_sgKDM6A_236R


title: Serum_Trichuris_5AGImmunized_E

description: Arrays were incubated overnight at 4°C with agitation, washed three times with Tris-buffered saline (TBS)–0.05% Tween 20, and incubated with Rabbit Anti-Pig IgG (MilliporeSigma, Burlington, MA) diluted 1:500 in blocking buffer at room temperature. Arrays were washed three times with TBS–0.05% Tween 20 and incubated with Cy3 Goat Anti-Rabbit IgG (Jackson ImmunoResearch, West Grove, PA) diluted 1:200 in blocking buffer at room temperature, protected from light. Arrays were washed three times with TBS–0.05% Tween 20, three times with TBS, and once with water and then air dried by being centrifuged at 1,000 × g for 4 min and left overnight in a desiccator before scanning. Probed microarrays (slides) were scanned using a GenePix 4300A high-resolution microarray scanner (Molecular Devices, Sunnyvale, CA).

label: Cy3 Goat Anti-Rabbit IgG

value: Serum

value: Trichuris suis

value: Immunized with 5_antigen cocktail


title: 535_Ctrl  [scATAC-seq]

value: sclc

tag: genotype

value: tissue

value: control


title: H3K4me2_sgKDM6A_236L


title: Liver_Cort_CON_p32

value: liver

value: Nondiabetic (ND)


title: Liver_Cort_CON_p33


title: H3K27me3_sgKDM6A_236L


title: H3K4me2_sgCTRL_1014


title: Serum_Trichuris_5AGImmunized_A


title: Liver_Cort_CON_p34


title: H3K4me2_sgCTRL_159-1

value: sgControl RPP 159-1


title: Serum_Trichuris_5AGImmunized_D


title: Liver_Cort_CON_p28

value: Cort CON


title: Serum_Trichuris_5AGImmunized_C


title: CD1-brain-M-5M-DNA-5

city: Loma Linda

first: Isaac

middle: Jacob

last: Kremsky

state: CA

address: 11175 Campus St., Chan Shun Pavilion, Room A1022

department: Basic Sciences

institute: Loma Linda University

data_processing:
Adaptors were trimmed from raw sequencing reads using trimmomatic version 0.38.
Germline transposable elements were determined using TEMP2.
SNPs and indels were called upsing GATK HaployTypeCaller, and then filtered with GATK VariantFiltration, and then separated into Uniform and non-Uniform variants using GATK SelectVariants
Assembly: mm10
Supplementary files format and content: Gzipped vcf files quantifying CD-1 variants, in mm10 coordinates. These including Uniform SNPs between CD-1 and mm10 (Cd1_UnifromSNPs.mm10.vcf.gz), Uniform Indels between CD-1 and mm10 (Cd1_UniformIndels.mm10.vcf.gz), non-Uniform SNPs within CD-1 (Cd1_NonuniformSNPs.mm10.vcf.gz), non-Uniform Indels within CD-1 (Cd1_NonuniformIndels.mm10.vcf.gz), and all SNPs/Indels called prior to processing (Cd1_SNPsandIndels_filtered_unprocessed.mm10.vcf.gz). The file Cd1_NonuniformSNPs.mm10.vcf.gz contains all regions that were N-maskedn For reserachers simply wishing to blacklist non-uniform variants, use Cd1_NonuniformSNPs.mm10.vcf.gz and/or Cd1_NonuniformIndels.mm10.vcf.gz.
Supplementary files format and content: Bed files with the mm10 coordiantes of germ-line Transposable elements gained and lost in CD-1, relative to mm10.
Supplementary files format and content: Cd1_final.fa.gz is the reference genome for Cd1 (gzip compressed fasta file), converted from mm10 using the called variants. Repeat elements are soft-masked.
Supplementary files format and content: Cd1_genes.gtf.gz is the gene annotation file which may be used for gene quantification (gzip compressed gtf file).  This file was derived using liftoff to convert the NCBI refSeq gene annotation for mm10 to Cd1 coordinates.
Supplementary files format and content: Cd1_repeatMasker.out.gz is the (gzip compressed) file output by RepeatMasker characterizing the repeat elements that were masked in the Cd1 reference fasta.
Supplementary files format and content: Cd1tomm10.chain.gz and mm10toCd1.chain.gz are gzip compresed .chain files which may be used by liftOver or similar software to convert data between mm10 and Cd1 coordinates.

source_name: Whole Brain

extract_protocol:
Dounce homogenizers were used for each cortex sample in a general lysis buffer containing 0.1 M Tris-pH8, 0.2M NaCl, 5 mM EDTA, 10% SDS, 150 mM DTT and proteinase K. The genomic DNA was extracted from the lysate using phenol:chloroform:isoamyl alcohol extraction followed by EtOH precipitation.
2 µg of genomic DNA was sheared with Diagenode Bioruptor to yield DNA fragments that are approximately 300 bp. DNA fragments were end repaired, A-tailed, and ligated to Illumina adaptors followed by PCR amplification for 7 cycles. The final libraries were size selected using AMPure XP beads, so the fragments were between the size of 200-400 bp long.
Each library was subject to paired-end sequencing for 150 bp reads using Illumina NovaSeq platform.

value: Whole Brain

tag: tissue region

value: cortex

value: CD-1 IGS

tag: age

value: 2-5 months old

tag: developmental stage

value: adult


title: Liver_Cort_CON_p30

value: Diabetic (Db)


title: CD1-brain-M-4M-DNA-3


title: H3K27me3_sgKDM6A_236R

extract_protocol:
KDM6A ChIP sequencing experiments were performed by first cross-linking cells with 2 mM disuccinimidyl glutarate (DSG) with rocking for 30 minutes at room temperature prior to fixation with 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. H3K4me2 and H3K27me3 ChIP was performed by fixation with 1% paraformaldehyde diluted in PBS for 10 minutes at room temperature. Excess formaldehyde was quenched by dropwise addition of freshly made Glycine at a final concentration 1.25 M. The cells were then resuspended in 1 mL of lysis buffer (50mM Hepes-NaOH pH 8, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% TX-100 supplemented with a protease inhibitors and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. Intact nuclei were then collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the pellet was resuspended in 1 mL of wash buffer (10mM Tris-HCl pH 8.0, 200mM NaCl, 1mM EDTA, supplemented with a protease inhibitor cocktail and phosphatase inhibitors) and incubated by rotating for 10 minutes at 4°C. The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C. The supernatant was then gently aspirated and the tube was rinsed with 500 µL of shearing buffer (0.1% SDS, 1 mM EDTA, 10 mM Tris-HCl pH 8.0 supplemented with protease inhibitors and phosphatase inhibitors). The nuclei were again collected by centrifugation at 1900 x g for 5 minutes at 4°C, the supernatant was carefully removed, and the pellet was gently resuspended in 1mL shearing buffer and transferred to a 1mL AFA fiber tube (Covaris #520130). The chromatin was then sonicated using a Covaris E220 sonicator at 100 peak incident power, 10% duty cycles, 200 cycles per burst, water level 15 (left indicator)/10 (right indicator) for 900 seconds. The samples were then transferred to 1.5 mL Eppendorf tubes and centrifuged in an Eppendorf microcentrifuge at 15,900 x g for 5 minutes at 4°C. 900 µL of the supernatants were transferred to a new Eppendorf tube, to which 1% Triton X-100 and 150 mM NaCl were added. 20µl of Dynabeads Protein G (ThermoFisher #10004D), prewashed with Shearing Buffer, was then added and samples were rotated for 1 hour at 4°C to pre-clear the sonicated chromatin. The Dynabeads were then removed using a magnetic stand and the supernatants were transferred to new tubes. 2.5% of the total lysate was removed to make genomic DNA to be used for the ChIP-sequencing input DNA. For the H3K27me3 and H3K4me2 ChIP, the remaining lysate (95% of total) were equally distributed into two Eppendorf tubes to perform the H3K27me3 and H3K4me2 ChIPs. 3 µg of the rabbit anti-H3k27me3 (C36B11) (Cell signaling, #9733) or 3 µg of the rabbit anti-H3K4me2 (Abcam #Ab32356) primary antibodies were added. For the KDM6A ChIP, the remaining 95% were incubated with 10 µg of the rabbit anti-KDM6A [Bethyl lab, A302-374A (UTX antibody)]. Same amount of rabbit IgG isotype control (Cell Signaling #3900) with the same amount of lysate was used as a control for each ChIP. All samples were incubated overnight while rotating at 4°C. The following morning, 50µL of Dynabeads, prewashed with Shearing buffer, were added and the samples were incubated for another 2 hours while rotating at 4°C. A magnetic stand was used to isolate the Dynabeads.  The supernatant was removed and the Dynabeads were washed once in 1mL of low salt immune complex wash buffer (20mM Tris-HCl pH 8.0, 150mM NaCl, 0.1% SDS, 1% TX-100, 2mM EDTA) and incubated for 5 minutes while rotating at 4°C.  The beads were again isolated using a magnetic stand.  Following removal of the supernatant the Dynabeads were washed once in 1mL of high salt immune complex wash buffer (20mM Tris-HCl pH 8.0, 500mM NaCl, 0.1% SDS, 1% TX-100, 2mM EDTA) and incubated for 5 minutes while rotating at 4°C.  The beads were again pelleted with a magnetic stand.  Following removal of the supernatant, the Dynabeads were washed once in 1mL of Lithium Chloride immune complex wash buffer (10mM Tris-HCl pH 8.0, 250mM LiCl, 1% SDS, 1% NP-40, 1mM EDTA) and incubated for 5 minutes while rotating at 4°C. The beads were then washed twice in TE pH8 at room temperature and the beads were then resuspended in 100µL TE pH8.
RNase A (Qiagen) was then added to a final concentration of 0.2 mg/mL and the samples were incubated for 30 minutes at 37°C. To reverse the formaldehyde crosslinking and remove protein, proteinase K was then added to a final concentration of 0.8 mg/mL and the samples were incubated for 30 minutes at 42°C and then an additional 6 hours at 65°C. 300 µL QG buffer and 100 µL of isopropanol was then added to each sample and a magnetic stand was used to pellet the Dynabeads. The supernatant was then collected and DNA was isolated using QIAquick gel extraction kit (Qiagen) according to the manufacturer’s instructions. DNA concentration was determined using the Nanodrop 8000 (Thermofisher Scientific) and sample were stored at -80°C.

value: sgKdm6a RPP 236R

value: mouse small cell lung cancer cell line (SCLC) derived from a mouse tumor


title: Serum_Ascaris_5AGImmunized_E

tag: tissue type

value: Serum

tag: infection status

value: Ascaris suum

tag: immunization status


title: Serum_Trichuris_5AGImmunized_B

value: Trichuris suis

value: Immunized with 5_antigen cocktail


title: Serum_Ascaris_5AGImmunized_D


title: Liver_Cort_ATGLi_p26

value: Cort ATGLi


title: H3K27me3_sgCTRL_159-1


title: Liver_Cort_ATGLi_p25

value: liver


title: Serum_Ascaris_5AGImmunized_F


title: CD1-brain-M-3M-DNA-1


title: Serum_Ascaris_5AGImmunized_B


title: Liver_Cort_CON_p27


title: Serum_Ascaris_5AGImmunized_A


title: Serum_Uninfected_5AGImmunized_K

value: Uninfected


title: CD1-brain-M-4M-DNA-2


title: Serum_Ascaris_5AGImmunized_C


title: Liver_Cort_ATGLi_p24

value: Nondiabetic (ND)


title: Liver_EtOH_ATGLi_p12

value: EtOH ATGLi


title: CD1-brain-M-2M-DNA-4

value: Whole Brain


title: H3K27me3_sgCTRL_1014

value: sgControl RPP 1014


title: Liver_Cort_ATGLi_p23


title: Liver_Cort_CON_p29

value: Cort CON


title: Serum_Uninfected_5AGImmunized_I


title: cre2

city: Vienna

first: Thomas

last: Weichhart

address: Waehringerstraße 10

department: Center for Pathobiochemistry and Genetics

country: Austria

institute: Medical University of Vienna

data_processing:
Demultiplxing, alignment, feature counting and filtering was performed with the 10x Genomics Cell Ranger pipeline version 5.0.1 against reference transcriptome mm10-2020-A.
Genome_build: GRCm38 UCSC mm10
Supplementary_files_format_and_content: GNU Tar archive of barcode.tsv.gz, feature.tsv.gz and matrix.mtx.gz files, sample specific and aggreagted (AGGR).

source_name: duodenum cell suspension

extract_protocol: 10x Genomics Single Cell 3' v3

tag: Sex

value: female

value: Tsc2fl/fl Lyz2cre/+

value: CD68+ macrophages


title: Liver_Cort_ATGLi_p18


title: BPAF3, Adipose, ATACseq, Rep2

data_processing:
Raw fastq files were trimmed using trim_galore.
Trimmed fastq files were then mapped using bowtie2 version 2.3.5.1, with the flag “-X 2000” to allow for DNA fragments up to 2 kb. Reads that did not map uniquely to one location were removed, and then reads were sorted, and PCR duplicates were removed with samtools markdup.
Peaks were called with macs2 callpeak version 2.2.7.1.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: Adipose

extract_protocol:
Visceral adipose tissue (1g) was placed in the cold 1× homogenization buffer (320 mM sucrose, 0.1 mM EDTA, 0.1% NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.8, 1× protease inhibitors (Roche, cOmplete), and 167 μM β-mercaptoethanol, in water), homogenized with Dounce homogenizer, and residual debris were precleared by using 80 um nylon mesh filter. The nuclei were then collected by layering with iodixanol mixture.
50,000 counted nuclei were transferred to a tube containing the transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl water) and mixed by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns. Library amplification was done with 2x KAPA HiFi mix (Kapa Biosystems) and 1.25 µM indexed primers using the following PCR conditions: 72°C for 5 min; 98°C for 30 s; and 10-11 cycles at 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.
ATAC-seq was carried out using the Omni-ATAC protocol.

value: Adipose

value: 8-weeks old

value: BPA


title: BPAF3, Adipose, ATACseq, Rep1


title: Liver_EtOH_ATGLi_p11


title: f2

value: Tsc2fl/fl Lyz2+/+


title: Serum_Uninfected_5AGImmunized_J

value: Serum


title: Liver_EtOH_ATGLi_p10


title: Liver_EtOH_ATGLi_p09


title: KO_TE_3

data_processing:
Fastq files were trimmed using Seqtk
Trimmed fastq files were aligned to the mm10 genome via Hisat2
Raw counts were extracted from bam files using htseq
Differential analysis was performed on raw counts with DESeq2
Normalized counts were calculated with DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Normalized_counts.txt contains normalized count values for each sample generated by DESeq2.

source_name: Bcl11b deficient

extract_protocol:
Cells were lysed and RNA was isolated using Qiagen Rneasy Plus Micro Kit (Qiagen #74034). RNA quality was determined on a bioanalyzer (Agilent RNA 6000 Nano #5067-1511)
Libraries were prepared using New England Biolabs NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (cat# E7770S) according to the manufacturer's instructions. Library quality and concentration was checked on a bioanalyzer (Agilent High Sensitivity DNA Kit #5067-4626) and by Qubit (Qubit™ dsDNA HS Assay Kit #Q32854). Libraries were sequenced on a NextSeq500 or NovaSeq6000.

treatment_protocol: Adoptively co-transferred Bcl11b KO and WT splenic MP and TE, and small intestine intrapithelial Trmp were sorted from mice 9 days post Listeria monocytogenes infection.

value: Bcl11b KO

value: Bcl11bF/F GzmbCre-Cre+ Rosa26+/-

value: Terminal effector cells


title: Serum_Uninfected_5AGImmunized_H

value: Uninfected

value: Immunized with 5_antigen cocktail


title: Liver_Cort_ATGLi_p13

value: liver

value: Cort ATGLi

value: Nondiabetic (ND)


title: cre1


title: Serum_Uninfected_5AGImmunized_G


title: Serum_Uninfected_5AGImmunized_A


title: Liver_Cort_ATGLi_p17


title: Serum_Uninfected_5AGImmunized_F


title: WT_TE_3

source_name: Bcl11b WT

value: Bcl11b WT

value: Bcl11bF/F GzmbCre-Cre- Rosa26+/-


title: Liver_EtOh_CON_p11

value: EtOH CON


title: Serum_Trichuris_NoImmunization_L

value: Trichuris suis

value: No Immunization


title: Serum_Uninfected_5AGImmunized_E


title: Liver_EtOh_CON_p16


title: Serum_Uninfected_5AGImmunized_D


title: WT_TE_2


title: WT_TE_1


title: Liver_EtOh_CON_p15


title: Serum_Uninfected_5AGImmunized_C


title: Serum_Uninfected_5AGImmunized_B


title: Liver_Cort_ATGLi_p14


title: f1

value: female

value: CD68+ macrophages


title: Liver_EtOH_ATGLi_p07

value: EtOH ATGLi


title: Liver_EtOH_ATGLi_p08


title: KO_MP_2

value: Memory precursor cells


title: KO_MP_3

value: Bcl11b KO


title: KO_TE_2

value: Bcl11bF/F GzmbCre-Cre+ Rosa26+/-


title: KO_MP_1


title: Liver_EtOh_CON_p12


title: WT_MP_3


title: KO_TE_1

value: Terminal effector cells


title: Liver_EtOh_CON_p10


title: Liver_EtOH_ATGLi_p05


title: WT_MP_2


title: Serum_Trichuris_NoImmunization_K

value: Serum


title: WT_MP_1


title: Liver_EtOh_CON_p09


title: Serum_Trichuris_NoImmunization_J


title: Liver_EtOH_ATGLi_p06


title: Serum_Trichuris_NoImmunization_I


title: Serum_Trichuris_NoImmunization_F


title: Serum_Trichuris_NoImmunization_D


title: Serum_Trichuris_NoImmunization_E


title: iTrm_1 [CHIP-seq]

description: WT iTrm

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2 on bam files
Reproducible peaks were determined using the two replicate peak files using IDR
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files were generated from Macs2 output

source_name: CD8+ T cells

extract_protocol:
Isolated cells were fixed with 1% formaldehyde in PBS for 10 minutes, then quenched with glycine.  After washing, DNA was extracted using the Illumina SimpleChIP Enzymatic ChIP kit (#9003S). Briefly, nuclei were isolated by incubating in 1ml buffer A for 10 min on Ice, followed by centrifugation and resuspension in 1 ml Buffer B.  Chromatin was sheared to roughly 200-1000bp. Samples were centrifuged to clear lysates, and the supernatant containing the DNA was transferred to a fresh tube for overnight antibody complexing.  Next day, protein G dynabeads were added to each tube, incubated, washed, and isolated with magnet.  DNA complexes were then released from the beads, decrosslinked, and phenol:choloroform:isolamyl alcohol extracted for library prep.
DNA libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina.  Briefly, DNA ends were repaired, followed by ligation of adapter sequences.  DNA was cleaned with AMPure XP beads, and then DNA was PCR amplified with 7-8 cycles.  After final cleaup with AMPure XP Beads, libraries were quantified using Agilent Bioanalyzer high sensitivity DNA kit and were subsequently sequenced.

treatment_protocol: Purified cells were activated with anti-CD3/anti-CD28 beads (Invitrogen, Cat. No. 114525D) at 2.5 x 105 cells/mL in  1mL 10% RPMI supplemented with 100U/mL IL-2 (Shenandoah Biotechnology, Cat. No. 100-12) for 48 hours at 37°C, 5% CO2. 2mL of fresh warmed 10% RPMI supplemented with a final concentration of 10ng/mL TGFb1 (Shenandoah Biotechnologies, Cat. No. 100-39) and 100ng/mL IL-33 (Shenandoah Biotechnologies, Cat. No. 200-36), split into 2 more additional wells and incubated at 37°C, 5% CO2 for an additional 48 hours.

value: Secondary lymphoid organs

value: WT

tag: chip antibody

value: 4ug each of Anti-Bcl11b Antibodies:Abcam ab18465,  Bethyl A300-385, and 20ul of CST D6F1

tag: group

value: Control


title: Serum_Trichuris_NoImmunization_G

data_processing:
Initial processing of the raw array data was performed as previously described (Li et al., 2017). First, raw values were transformed using the base 2 logarithm. Next, the data set was normalized to remove systematic effects by subtracting the median signal intensity of the IVTT control spots for each sample. Since the IVTT control spots carry not only the chip, sample, and batch-level systematic effects, but also antibody background reactivity to the IVTT system, this procedure normalizes the data and provides a relative measure of the specific antibody binding versus the nonspecific antibody binding to the IVTT controls. With the normalized data, a value of 0.0 means that the intensity is no different than that of the IVTT controls, and a value of 1.0 indicates a doubling with respect to IVTT control spots. Log2 relative fluorescence values (relative to the median of the negative control probes) were calculated for each protein and each sample (one sample per array). Principal components analysis (PCA) was performed using the “prcomp” package in R, using only the proteins with relative Log2 fluorescence >0 relative to negative controls.
The Protein IDs come from the PRJNA80881 Ascaris suum genome annotation, retrieved from https://parasite.wormbase.org/Ascaris_suum_prjna80881/Info/Index


title: iTrm_2 [CHIP-seq]

description: WT iTrm

tag: tissue


title: Liver_EtOh_CON_p03

value: liver

tag: strain

value: Nondiabetic (ND)


title: Liver_EtOh_CON_p04

tag: treatment

value: EtOH CON


title: Serum_Trichuris_NoImmunization_H

value: Trichuris suis


title: WT_Trmp_2 [ATAC-seq]

data_processing:
Fastq files prepared using Illumina FASTQ Generation application
Fastq files were trimmed using Trimmomatic
Reads were aligned to the mm10 genome using Bowtie2
Duplicate reads were removed using PicardTools
Peaks were called using Macs2 on bam files
Reproducible peaks were determined using the two replicate peak files using IDR
Genome_build: mm10
Supplementary_files_format_and_content: Bedgraph files

extract_protocol:
DNA from 20,000-50,000 CD8+ T-cells was prepared as previously described by others (Buenrostro, J.D., Wu, B., Chang, H.Y., and Greenleaf, W.J. (2015). ATAC-seq: A Method for Assaying Chromatin Accessibility Genome-Wide. Curr Protoc Mol Biol 109, 21.29.21-29.) Briefly, cells were lysed and the nuclei underwent the transposition reaction at 37oC for 30 minutes.
DNA was purified after transposition reaction using Qiagen MinElute PCR Purification Kit and libraries were generated by amplifying DNA with 12-15 cycles. Necessary cycles determined by qPCR. DNA was purified using AMPure XP beads, quality and quantity was determined by Agilent bioanalyzer (high sensitivity DNA kit), and the libraries were subsequently sequenced.

value: Small intestine intraepithelial lymphocytes

value: Bcl11bF/F GzmbCre-Cre- Rosa26+/-

value: Resident memory precursor cells


title: Liver_EtOh_CON_p02

tag: disease state


title: WT_Trmp_1 [ATAC-seq]


title: Serum_Trichuris_NoImmunization_B

extract_protocol: Cloning and expression was performed using standard techniques. All sequences were PCR amplified from cDNA using sequence specific forward and reverse primers that encompassed the mature protein and contained Sac I (forward) and Xho I (reverse) restriction sites for downstream subcloning. Translation stop sites were incorporated into all reverse primers. Amplified sequences were first cloned into pCR2.1-TOPO by TA cloning then transformed into DH5α cells for sequence verification. Validated sequences were restriction enzyme digested and subcloned into the pSUMO bacterial expression vector (Life Sensors) and transformed into BL21 cells for protein production. Expression was performed using overnight cultures to spike 500ml of LB medium containing ampicillin (100 µg/ml) which was induced at OD = 0.7 for 5 hrs. with isopropyl β-D-1-thiogalactopyranoside (0.3 mM final). Pelleted cells were lysed with 1 mg/ml lysozyme, frozen overnight then sonicated. Because all clones formed inclusion bodies during production, the sonicated pellets were first washed 3X with 2% Triton X-100, solubilized in 8M Urea (made fresh) and batch purified by affinity chromatography using 2 ml of Ni-NTA. All mixtures were added to columns, washed with 6M urea (3X), then wash buffer containing 50 mM sodium phosphate, pH 8.0, 300 mM sodium chloride and 20 mM imidazole. Recombinant proteins were eluted with 5 ml of wash buffer containing 500 mM imidazole and 12 mM sodium lauryl sarkosine.

value: No Immunization


title: KO_Trmp_2 [ATAC-seq]


title: WT_Trmp_3

value: Bcl11b WT


title: Serum_Trichuris_NoImmunization_C


title: KO_Trmp_1 [ATAC-seq]


title: Liver_EtOh_CON_p01

tag: glucose (fed)


title: Serum_Trichuris_NoImmunization_A


title: WT_Trmp_1


title: Serum_Ascaris_NoImmunization_H

value: Ascaris suum


title: WT_Trmp_2


title: KO_Trmp_3

value: Bcl11b KO

value: Bcl11bF/F GzmbCre-Cre+ Rosa26+/-


title: Serum_Ascaris_NoImmunization_G

value: Serum


title: aRBC_Hic_Rep2

city: Mexico City

first: Mayra

last: Furlan-Magaril

state: Mexico City

address: Circuito exterior s/n

department: Molecular Genetics

country: Mexico

institute: IFC-UNAM

data_processing:
Hi-C experiments were processed following the HiC-Pro (v2.11.1) pipeline using the merge data from both replicates to generate .validPairs files with interacting regions.
.validPairs files were normalized to contain the same number of interacting pairs.
Assembly: GRCg6a
Supplementary files format and content: .validPairs files containing the interacting pairs for each sample. validPairs files can be used to generate Hi-C matrices with HiC-Pro.

organism: Gallus gallus

source_name: Primary red blood cells from adult hens (28-38 weeks old)

growth_protocol: Primary fibroblasts and HD3 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; GIBCO) supplemented with 10% fetal bovine serum (Biowest), 2% chicken serum and penicillin/streptomycin (Invitrogen).

extract_protocol:
10 x 106 cells were fixed with formaldehyde 2% for 10 minutes at room temperature. Chromatin was digested with MboI overnight and 5′ overhangs were filled with Biotin-14-dATP and religated in nuclei. DNA fragments were purified and shared to an average size of 500 bp using a Covaris machine.
Hi-C libraries were generated using the TruSeq Illumina system.


title: Erythroblasts_Hic_Rep2

tag: cell line

value: Chicken erythroblasts


title: Serum_Ascaris_NoImmunization_E


title: eRBC_Hic_Rep2

source_name: Primary embryonic red blood cells (Embryonic day 10)

tag: cell type

value: WT


title: KO_Trmp_2

tag: genotype


title: Fibroblasts_Hic_Rep1

source_name: Primary fibroblasts

value: Primary fibroblasts


title: Fibroblasts_Hic_Rep2


title: KO_Trmp_1


title: Serum_Ascaris_NoImmunization_F


title: aRBC_ATACseq_Rep2

data_processing:
ATAC-seq reads were mapped to the GRCg6a genome using Bowtie2 (v2.3.5). Duplicates and reads longer than 150 bp were removed with Samtools (v1.9).
Peaks were called with MACS2 (v2.1.2) with a significance level of 0.01 and the peaks conserved between two biological replicates were used for analysis
Assembly: GRCg6a
Supplementary files format and content: NarrowPeak file with the consensus accessible peaks shared between 2 biological replicates per cell type.

extract_protocol:
Nuclei extraction of 150,000 cells was treated with the Tn5 enzyme (Illumina) for 30 min. Following tagmentation, DNA was extracted using MinElute columns (Qiagen).
ATAC-seq libraries were amplified for 10 PCR cycles using the Nextera barcode system (Illumina).

value: Primary red blood cells from adult hens (28-38 weeks old)


title: Fibroblasts_ATACseq_Rep2


title: Serum_Ascaris_NoImmunization_D


title: Fibroblasts_ATACseq_Rep1


title: Serum_Ascaris_NoImmunization_C


title: Serum_Ascaris_NoImmunization_B


title: MIA Paca-2,GEM-SEN, INPUT

city: Guangzhou

first: Rui

address: 651 Dongfeng East Road

country: China

institute: Sun Yat-sen University Cancer Center

data_processing:
The input reads were trimmed to the same length as the m6A-IP reads using fastx_trimmer from FASTX-Toolkit.
Clean reads were mapped to the hg38 genome using STAR. MACS2 and MeTPeak were used to call peaks, and the cut-off P value for a significant peak for MACS2 was 1e-6.
Only m6A peaks identified by both peak-calling methods were retained and merged using BEDTools. The human annotation file (GENCODE v27) from the GENCODE database was used to perform the m6A annotation. Homer was used to search the motif enriched in m6A peaks.
The read coverage in m6A-IP and input of each peak were calculated using Multicov from BEDTools with RPKM for normalization (reads per kilobase million). The ratio of m6A-IP RPKM to input RPKM was used to calculate the enrichment of each m6A peak.
Differentially modified m6As with a P value of < 0.05 and the absolute value of fold change of > 1.5 were treated as differentially methylated m6As.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: MIA Paca-2

growth_protocol: total RNA extracted from cell lines was treated with DNase I to eliminate DNA and purified to mRNA using poly-T oligo-attached magnetic beads.

extract_protocol:
One tenth of the fragmented RNA served as an input control in RNA sequencing.
RNA fragments from the m6A-IP and input samples were used for cDNA library preparation and sequenced on an Illumina HiSeqX Ten PE150 platform.

treatment_protocol:
Purified mRNA was fragmented and incubated with anti-m6A antibody (Synaptic Systems, 202003)-conjugated beads in RIP reaction buffer overnight at 4 °C
After incubation, the bound RNAs were purified via proteinase K treatment, acidic phenol/chloroform extraction and ethanol precipitation

value: MIA Paca-2

value: PDAC cells

tag: phenotype

value: GEM-SEN

tag: rip antibody


title: Serum_Uninfected_NoImmunization_T

value: Uninfected


title: Serum_Ascaris_NoImmunization_A


title: Serum_Uninfected_NoImmunization_S


title: Serum_Uninfected_NoImmunization_R


title: HPC-Y5,GEM-SEN, INPUT


title: BI-3802 30min_IFNγ 24hr_EC3

city: Los Angeles

first: Nicole

last: Valenzuela

state: California

address: 1000 Veteran Avenue, Room 1-520

institute: UCLA

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
The reads were mapped by STAR 2.7.9a [1] and read counts per gene were quantified using the human genome GRCh38.
In Partek Flow [2], read counts were normalized by CPM +1.0E-4. All results of differential gene expression analysis utilized the statistical analysis tool, DESeq2 [3].
P-value (p<0.01), FDR (<0.01), and fold change (FC>2-fold) filters were applied for differentially expressed gene lists prior to downstream analysis.
Assembly: GRCh38
Supplementary files format and content: txt matrix file with normalized CPM

source_name: aorta

growth_protocol: cells were cultured to confluence in a 6 well tissue culture treated plate

extract_protocol:
RNA was prepared using the Rneasy Kit
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: Cells were treated in M199 + 10% HI FBS, in normal medium or with 30min pre-treatment with ruxolitinib (2uM), FX1, BI-3812 or BI-3802 (each at 100uM) prior to 24hr treatment with IFNg

value: aorta

value: primary

value: endothelial cell

value: BI-3802 30min_IFNγ 24hr


title: BI-3802 30min_IFNγ 24hr_EC2


title: BXPC-3,GEM-SEN, INPUT


title: Serum_Uninfected_NoImmunization_Q

value: No Immunization


title: CAPAN-2,GEM-INS, INPUT

value: GEM-INS


title: BI-3802 30min_IFNγ 24hr_EC1


title: BI-3812 30min_IFNγ 24hr_EC3

value: BI-3812 30min_IFNγ 24hr


title: PANC-1,GEM-INS, INPUT


title: HPAF-II, GEM-INS, INPUT

source_name: HPAF-II

value: HPAF-II


title: aRBC_ATACseq_Rep1

description: Lane 2 of aRBC_ATACseq_Rep1 was sequenced on a Novaseq instrument


title: BI-3812 30min_IFNγ 24hr_EC2


title: BI-3812 30min_IFNγ 24hr_EC1


title: Serum_Uninfected_NoImmunization_P

value: Serum


title: MG_EtOh_CON_p11

data_processing:
Lexogen Quantseq pipeline V1.8.8 on the Bluebee platform, quality control, mapping, and read count tables
Annotation and preparation for analysis, R V3.6.1, Rstudio V1.1.423 and biomaRt V2.24.1
DESeq2  V1.24.0 differential gene expression
JMP Genomics V9 quality control, principal components, ANOVA, hierarchical clustering
Assembly: mouse- GRCm38.84
Supplementary files format and content: tab-delimited text containing DESeq2 normalized counts

source_name: mixed gastrocnemius

extract_protocol:
Mice were euthanized using CO2 and cervical dislocation. Tissues were collected, flash-frozen in liquid nitrogen, and stored at -80C until processed. Tissues were powdered and 20-25mg was used for RNA isolation using an Rneasy kit using the manufacturers protocol for skeletal muscle tissue.
Lexogen Quant-Seq; indexed and pooled samples, 50bp forward read

value: mixed gastrocnemius

value: EtOH CON

value: Nondiabetic (ND)

tag: insulin


title: Serum_Uninfected_NoImmunization_O

tag: tissue type


title: Serum_Uninfected_NoImmunization_N

tag: infection status


title: MIA Paca-2,GEM-SEN, IP


title: Serum_Uninfected_NoImmunization_M

tag: immunization status


title: FX1 30min_IFNγ 24hr_EC3

value: FX1 30min_IFNγ 24hr


title: HPC-Y5,GEM-SEN, IP


title: FX1 30min_IFNγ 24hr_EC2


title: Serum_Uninfected_NoImmunization_L


title: BXPC-3,GEM-SEN, IP


title: Serum_Uninfected_NoImmunization_J


title: CAPAN-2,GEM-INS, IP


title: PANC-1,GEM-INS, IP


title: Serum_Uninfected_NoImmunization_K


title: FX1 30min_IFNγ 24hr_EC1


title: ruxo 30min_IFNγ 24hr_EC3

value: ruxo 30min_IFNγ 24hr


title: Serum_Uninfected_NoImmunization_I


title: ruxo 30min_IFNγ 24hr_EC1


title: HPAF-II, GEM-INS, IP

value: PDAC cells


title: PANC-1 si-LINC00261-3 (X261S3)

city: Chongqing

first: Songsong

last: Liu

state: Chongqing

address: No. 30 Gaotanyan Street, Shapingba District

institute: Army Medical University

data_processing:
Sequenced raw reads were preprocessed by removing rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads with Seqtk (https:// github.com/lh3/seqtk).
Obtained clean reads were mapped to the mouse mm10 reference genome with two mismatches by Hisat2 (version 2.0.4). After genome mapping, Cufflinks v2.1.1 was run with a reference annotation to generate FPKM (fragments per kilobase of exon model per million mapped reads)values for known gene models.
The p-value significance threshold was set by the false discovery rate (FDR) strictly controlled using the Benjamini and Hochberg algorithm. The fold-changes were estimated according to the FPKM in each sample. Differentially expressed genes were identified using Cuffdiff with the following filter criteria: FDR≤0.05 and fold-change≥2.
Genome_build: mm10

growth_protocol: Pancreatic cancer cell line PANC-1 cells were used for our research.

extract_protocol:
Total RNA was extracted from the samples using the TRIzol method. The total RNA extracted from the samples was tested by a NanoDrop 2000 and denaturing gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: PANC-1 cells were transfected with LINC00261 siRNA and control siRNA.

value: Pancreatic cancer cell line


title: IFNγ 24hr_EC3

value: IFNγ 24hr


title: Serum_Uninfected_NoImmunization_H

value: Uninfected


title: PANC-1 si-LINC00261-2 (X261S2)


title: IFNγ 24hr_EC2

value: aorta

value: primary


title: Serum_Uninfected_NoImmunization_G


title: PANC-1 si-LINC00261-1 (X261S1)


title: Serum_Uninfected_NoImmunization_F


title: PANC-1 si-NC3 (X261N3)


title: Serum_Uninfected_NoImmunization_D


title: untreated 24hr_EC3

value: endothelial cell

value: untreated 24hr


title: Serum_Uninfected_NoImmunization_E

value: No Immunization


title: ruxo 30min_IFNγ 24hr_EC2


title: Serum_Uninfected_NoImmunization_C


title: untreated 24hr_EC2


title: PANC-1 si-NC1 (X261N1）


title: Serum_Uninfected_NoImmunization_A


title: PDAC, EtOH, 6 hrs, ERalpha ab

status: Public on Jun 07 2023

city: La Jolla

first: Ruth

middle: T

last: Yu

address: 10010 N Torrey Pines Rd

department: Gene Expression Lab

institute: Salk Institute

data_processing:
For human samples, reads were aligned using Bowtie2 to GRCh37 and SE peaks were called using HOMER v4.11.1 default settings (-style super, Fold change >4, p-value <0.0001).
For mouse samples, reads were aligned using Bowtie2 to MGSCv37 (mm9) and differential peaks were called using HOMER’s79 default settings (Fold change >4, p-value <0.0001) using '-style factor'.
Data tracks were visualized using IGV v2.3.90.
Assembly: GRCh37 (human) and MGSCv37 (mm9) for mouse
Supplementary files format and content: bedGraph, bed

source_name: PDAC

extract_protocol:
Briefly, cells were fixed, nuclei were isolated, lysed, and sheared with a Diagenode Bioruptor to yield DNA fragment sizes of 200 –1,000 bp, and active chromatin was immunoprecipitated.
Libraries were prepped and sequenced on the Illumina HiSeq4000 using barcoded multiplexing and a single-end 100bp length.

value: PDAC

tag: treatment duration

value: 6 hrs

value: ERα

value: p48-Cre; LSL-KrasG12D; Rosa26LSL-MycERT2 (KMp48) mice

value: EtOH


title: PDAC, 4-OHT, 6 hrs, Myc ab

tag: chip antibody

value: Myc


title: PDAC, EtOH, 6 hrs, Myc ab


title: PDAC, 4-OHT, 6 hrs, ERalpha ab


title: PDAC, EtOH, 24 hrs, ERalpha ab

value: 24 hrs


title: pancreas , Dox_25wks

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

data_processing:
The sequencing outputs for all Visium datasets were preprocessed using SpaceRanger-v1.2.1 and mapped to either the latest human or mouse reference genome and the filtered matrices were converted to Seurat objects in R and used for downstream analyses.
Assembly: mm10
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz : Compressed tar archives include Filtered feature-barcode matrices from Space Ranger
Supplementary files format and content: spatial.tar.gz : Compressed tar archives include processed output from Space Ranger with spatial information
Supplementary files format and content: filtered_feature_bc_matrix.h5 : Filtered feature-barcode matrices in HDF5 format
Supplementary files format and content: GNASmouse_onlydox_merge.rds : RDS file both samples merged
Library strategy: Spatial Transcriptomics Visium 10x genomics

source_name: p48-Cre;LSL-KrasG12D;Rosa26R-LSL-rtTA-TetO-GnasR201C, on 0.0060% doxycycline diet

extract_protocol:
Samples were flash frozen in liquid nitrogen, cryo-sectioned and H&E stained. After sectioning onto the Visium slides, sample processing was performed as described in the Visium 10x Genomics protocol for fresh-frozen tissue samples (15 minutes were used for permealization time)
Library preparation was performed as described in the Visium 10x genomics protocol for fresh-frozen tissue samples.  After library preparation, samples were pooled and sequenced using a NextSeq 550 (Ilumina, CA, USA).

value: pancreas

value: 0.0060% doxycycline diet

tag: age

value: 33 weeks


title: PDAC, EtOH, 24 hrs, Myc ab

tag: tissue


title: IFNγ 24hr_EC1

value: IFNγ 24hr


title: PDAC, 4-OHT, 24 hrs, Myc ab


title: 81_vm1.5yr_7_C57BL/6NCrl

first: Jing

address: 1425 San Pablo St.

department: Department of Regenerative Medicine  & Stem Cell Biology

institute: University of Southern California

data_processing:
For sample 1- 145, RNA-seq reads from fastq with length lower than 20, average quality lower than 20 were filtered through Fastp version 0.20.1. Filtered reads were then aligned to the Ensembl release 103 primary assembly by STAR version 2.7.9a. Gene counts were derived from featureCount version 2.0.1.
For sample 146 - 188, RNA-seq reads were aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32.
Assembly: Mus_musculus.GRCm39.dna.primary_assembly.fa; For sample 1 - 145: Mus_musculus.GRCm39.103.gtf; For sample 146 - 188: Mus_musculus.GRCm39.101.gtf
Supplementary files format and content: 1_WashU_50SE_counts.txt; 2_BGI_PE150_counts.txt; 3_WashU_PE150_counts.txt
Supplementary files format and content: 146_155_all.gene_counts.txt, 156_188_all.gene_counts.txt

source_name: kidney

extract_protocol:
Whole kidney total RNA were extracted using Qiagen’s RNeasy Mini Kit.
Sample 1- 67 and sample 98 - 188 were submitted to the Genome Access Technology Center at the McDonnell Genome Institute at University of Washington in St. Louis. Samples 1- 67, sample 98 - 145 were prepared according to Clontech SMARTer library kit manufacturer’s protocol, sample 146 - 188 were prepared according to polyA selection library kit manufacturer’s protocol. Sample 1- 67 were indexed, pooled, and sequenced on Illumina HiSeq2500 platform for 50-bp single-end. Sample 98 - 188 were indexed, pooled, and sequenced on llumina NovaSeq S4 2X150 (4 lanes). Sample 68 to Sample 97 were indexed, pooled and sequenced at BGI genomics with DNBseq platform according to the manufacturer's protocol. For sample 146 - 188, Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation.  Library preparation was performed with 5 to 10ug of total RNA with a Bioanalyzer RIN score greater than 8.0. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented in reverse transcriptase buffer and heating to 94 degrees for 8 minutes. mRNA was reverse transcribed to yield cDNA using SuperScript III RT enzyme (Life Technologies, per manufacturer's instructions) and random hexamers. A second strand reaction was performed to yield ds-cDNA. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

value: kidney

tag: Sex

value: M

value: Virgin

tag: time

tag: fragment length

tag: library kit

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: 79_vf1.5yr_5_C57BL/6NCrl

value: F

tag: treatment


title: PANC-1 si-NC2 (X261N2)

value: Pancreatic cancer cell line

tag: cell line


title: 76_vf1.5yr_2_C57BL/6NCrl

tag: genotype


title: Serum_Uninfected_NoImmunization_B

value: Serum

value: Uninfected

value: No Immunization


title: 75_vf1.5yr_1_C57BL/6NCrl


title: 82_vm1.5yr_8_C57BL/6NCrl


title: 78_vf1.5yr_4_C57BL/6NCrl


title: 83_vm1.5yr_9_C57BL/6NCrl


title: 77_vf1.5yr_3_C57BL/6NCrl


title: 46_castrated_C57BL/6NCrl

value: corn oil

value: 24 hours


title: untreated 24hr_EC1

value: aorta

value: primary

tag: cell type

value: endothelial cell

value: untreated 24hr


title: 80_vm1.5yr_6_C57BL/6NCrl


title: 44_TES1_castrated_C57BL/6NCrl

value: 15mg/kg Testosterone (Sigma:T1500)


title: 45_TES2_castrated_C57BL/6NCrl


title: pancreas, Dox_15wks

value: pancreas

value: 0.0060% doxycycline diet

value: 23 weeks


title: 41_TES1_ovariectomized_C57BL/6NCrl

value: kidney


title: 42_TES2_ovariectomized_C57BL/6NCrl

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: PDAC, 4-OHT, 24 hrs, ERalpha ab

value: PDAC

value: 24 hrs

value: ERα

value: p48-Cre; LSL-KrasG12D; Rosa26LSL-MycERT2 (KMp48) mice


title: 43_ovariectomized_C57BL/6NCrl

value: F


title: 38_castrated_C57BL/6NCrl

value: M


title: 40_ovariectomized_C57BL/6NCrl


title: 37_castrated_C57BL/6NCrl


title: 67_M1.5y_5_C57BL/6NCrl

value: Retired breeder


title: 66_M1.5y_4_C57BL/6NCrl


title: 39_ovariectomized_C57BL/6NCrl


title: 64_M1.5y_2_C57BL/6NCrl


title: 71_F1.5y_4_C57BL/6NCrl


title: 70_F1.5y_3_C57BL/6NCrl


title: 69_F1.5y_2_C57BL/6NCrl


title: 68_F1.5y_1_C57BL/6NCrl


title: 4_M4_8wk_C57BL/6J


title: 1_M1_8wk_C57BL/6J


title: 3_M3_8wk_C57BL/6J


title: 6_F1_8wk_C57BL/6J


title: 7_F2_8wk_C57BL/6J


title: 10_F5_8wk_C57BL/6J


title: 9_F4_8wk_C57BL/6J


title: 15_M5_4wk_C57BL/6J


title: 8_F3_8wk_C57BL/6J


title: 5_M5_8wk_C57BL/6J


title: 12_M2_4wk_C57BL/6J


title: 65_M1.5y_3_C57BL/6NCrl


title: 63_M1.5y_1_C57BL/6NCrl


title: 13_M3_4wk_C57BL/6J


title: 11_M1_4wk_C57BL/6J


title: 18_F3_4wk_C57BL/6J


title: 20_F5_4wk_C57BL/6J


title: 29_M4_2wk_C57BL/6J


title: 16_F1_4wk_C57BL/6J


title: 30_M5_2wk_C57BL/6J


title: 2_M2_8wk_C57BL/6J


title: 72_F1.5y_5_C57BL/6NCrl


title: 28_M3_2wk_C57BL/6J


title: 25_M1_2wk_C57BL/6J


title: 26_F5_2wk_C57BL/6J


title: 24_F4_2wk_C57BL/6J


title: 27_M2_2wk_C57BL/6J


title: 14_M4_4wk_C57BL/6J


title: 34_M2_P0_C57BL/6J


title: 23_F3_2wk_C57BL/6J


title: 35_M3_P0_C57BL/6J


title: 21_F1_2wk_C57BL/6J


title: 36_M4_P0_C57BL/6J


title: 31_F1_P0_C57BL/6J


title: 32_F2_P0_C57BL/6J


title: 33_M1_P0_C57BL/6J


title: 19_F4_4wk_C57BL/6J


title: 17_F2_4wk_C57BL/6J


title: Rax-GFP ESCs, input control Rep 1

city: Chicago

first: NOZOMU

last: TAKATA

state: Illinois

address: 303 East Superior Street, 10-220

department: Center for Vascular and Developmental Biology

institute: Northwestern University Feinberg School of Medicine

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using Bowtie2 version 2.4.5
Peak calling and bigWig generation was performed using HOMER v4.10.4
Assembly: mm10
Supplementary files format and content: bigWig files

source_name: ESC-derived eye organoids (Rax-GFP ESCs)

growth_protocol: DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

value: eye organoid

value: retina progenitors

value: Rax-GFP knockin Het

tag: antibody

value: no antibody control


title: Rax-GFP ESCs, input control Rep 2


title: 22_F2_2wk_C57BL/6J


title: Rax-GFP ESCs, H3K27ac rescue Rep 1

value: Acetyl-Histone H3 (Lys27) (Cell Signaling technology, #8173S)


title: Rax-GFP ESCs, H3K27ac rescue Rep 2


title: Rax-GFP ESCs, H3K27ac antagonist Rep 1


title: Rax-GFP ESCs, H3K27ac control Rep 1


title: Rax-GFP ESCs, H3K27ac control Rep 2


title: Rax-GFP ESCs, day 6, three biological replicate pool, scRNAseq

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Single cell data was further processed with Seurat, version 2.3.4
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

growth_protocol: The method was descrived previously Nature Protocols volume 7, pages69–79 (2012).

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).  Chromium Single Cell v2 Reagent Kit and Controller (10X Genomics, Pleasanton, CA, USA)

value: culture day 6


title: Rax-GFP ESCs, rescued-4 (GNE-140+lactate)

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: mm10
Supplementary files format and content: raw counts

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: pretreated with lactate for 12 hours and GNE-140 was added for 3 days.

value: Rax-GFP knockin hets

value: rescued (GNE-140+lactate)

tag: time point

value: Day 7


title: Rax-GFP ESCs, rescued-3 (GNE-140+lactate)


title: Rax-GFP ESCs, treated-3 (GNE-140)

value: treated (GNE-140)


title: Rax-GFP ESCs, treated-4 (GNE-140)


title: 74_fp0_3_C57BL/6J

value: kidney

value: mRNA-Seq.cDNA Amplification - Clontech SMARTer


title: Rax-GFP ESCs, control-4

value: control


title: 73_fp0_3_C57BL/6J


title: Rax-GFP ESCs, rescued-1 (GNE-140+lactate)


title: Rax-GFP ESCs, rescued-2 (GNE-140+lactate)


title: Rax-GFP ESCs, control-3


title: Rax-GFP ESCs, treated-2 (GNE-140)


title: Rax-GFP ESCs, control-1


title: Rax-GFP ESCs, control-2


title: Rax-GFP ESCs, treated-1 (GNE-140)