title: 6-week-old Sec15 KO mouse liver re2

type: RNA

city: Shanghai

first: Mingdian

last: Tan

state: Shanghai

address: No. 320, Yueyang Rd, Xuhui District

institute: Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences

description: Sec15 KO mouse withou any treatment

hyb_protocol: Step 5 Hybridization  Kit and Instruments:  Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242):  10X Blocking Agent  25X Fragmentation Buffer  2x GEx Hybridization Buffer HI-RPM  Hybridization Chamber, stainless (Agilent p/n G2534A)  Hybridization Chamber gasket slides (Agilent p/n G2534-60003)  Hybridization oven (Agilent p/n G2545A)  Hybridization oven rotator for Agilent Microarray Hybridization Chambers (Agilent p/n G2530-60029)    Procedure:  1. Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube:  For 1*244K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.5ug  10X Blocking Agent 50ul  Nuclease-free water ×ul  25X Fragmentation Buffer 10ul  Total volume 250ul    For 2*105K array Amount  cyanine 3-labeled, linearly amplified cRNA 1. 5ug  10X Blocking Agent 25ul  Nuclease-free water ×ul  25X Fragmentation Buffer 5ul  Total volume 125ul    For 4*44K array Amount  cyanine 3-labeled, linearly amplified cRNA 1.65ug  10X Blocking Agent 11ul  Nuclease-free water ×ul  25X Fragmentation Buffer 2.2ul  Total volume 55ul    For 8*15K array Amount  cyanine 3-labeled, linearly amplified cRNA 0.6ug  10X Blocking Agent 5ul  Nuclease-free water ×ul  25X Fragmentation Buffer 1ul  Total volume 25ul    4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  cRNA from Fragmentation Mix 250ul 125ul 55ul 25ul  2* GEx Hybridization Buffer HI-RPM 250ul 125ul 55ul 25ul    7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  Volumes per hybridization  Components 1*244K 2*105K 4*44K 8*15K  Volume Prepared 500ul 250ul 110ul 50ul  Hybridization Sample Volume 490ul 245ul 100ul 40ul    12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.     Step 6 Microarray Wash  Kit and Instruments:  Gene Expression Wash Buffer 1 (Agilent p/n 5188-5325)  Gene Expression Wash Buffer 2 (Agilent p/n 5188-5326)  Magnetic stir bar (Corning p/n 401435)  Magnetic stir plate (Corning p/n 6795-410)  Slide-staining dish, with slide rack (Thermo Shandon p/n 121)    Procedure:  1. Prewarm enough volume of Gene Expression Wash Buffer 2 to 37°C.  2. Add the slide rack and stir bar to the staining dish.  3. Transfer the staining dish with the slide rack and stir bar to a magnetic stir plate.  4. Fill the staining dish with 100% acetonitrile.  5. Turn on the magnetic stir plate and adjust the speed to a setting of 4 (medium speed).  6. Wash for 5 minutes.  7. Discard the acetonitrile as is appropriate for your site.  8. Repeat step 2 to step 7.  9. Air dry the staining dish in the vented fume hood.  10. Wash all dishes, racks, and stir bars with Milli-Q water.   11. Completely fill slide-staining dish #1 with Gene Expression Wash Buffer 1 at room temperature.  12. Place a slide rack into slide-staining dish #2. Add a magnetic stir bar. Fill slide-staining dish #2 with enough Gene Expression Wash Buffer 1 at room temperature to cover the slide rack. Place this dish on a magnetic stir plate.  13. Place the empty dish #3 on the stir plate and add a magnetic stir bar. Do not add the prewarmed (37°C) Gene Expression Wash Buffer 2 until the first wash step has begun.  14. Remove one hybridization chamber from incubator and record time. Record whether bubbles formed during hybridization and if all bubbles are rotating freely.   15. Prepare the hybridization chamber disassembly.  a) Place the hybridization chamber assembly on a flat surface and loosen the thumbscrew, turning counterclockwise.  b) Slide off the clamp assembly and remove the chamber cover.  c) With gloved fingers, remove the array-gasket sandwich from the chamber base by grabbing the slides from their ends. Keep the microarray slide numeric barcode facing up as you quickly transfer the sandwich to slide-staining dish #1.  d) Without letting go of the slides, submerge the array-gasket sandwich into slide-staining dish #1 containing Gene Expression Wash Buffer 1.  16. With the sandwich completely submerged in Gene Expression Wash Buffer 1, pry the sandwich open from the barcode end only:  a) Slip one of the blunt ends of the forceps between the slides.  b) Gently turn the forceps upwards or downwards to separate the slides.  c) Let the gasket slide drop to the bottom of the staining dish.  d) Remove the microarray slide and place into slide rack in the slide-staining dish #2 containing Gene Expression Wash Buffer 1 at room temperature.   17. When all slides in the group are placed into the slide rack in slide-staining dish #2, stir using setting 4 for 1 minute.  18. During this wash step, remove Gene Expression Wash Buffer 2 from the 37°C water bath and pour into the slide-staining dish #3.  19. Transfer slide rack to slide-staining dish #3 containing Gene Expression Wash Buffer 2 at elevated temperature. Stir using setting 4 for 1 minute.   20. Slowly remove the slide rack minimizing droplets on the slides. It should take 5 to 10 seconds to remove the slide rack.  21. Scan slides immediately to minimize the impact of environmental oxidants on signal intensities.

scan_protocol: Step 7 Scanning  Instrument:  Agilent Microarray Scanner (Agilent p/n G2565BA)    Procedure:  1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.   Parameters  Scan region Scan Area (61 x 21.6 mm)  Scan resolution (μm) 5  5μm scanning mode Single Pass  eXtended Dynamic range (selected)  Dye channel Green  Green PMT   XDR Hi 100%   XDR Lo 10%  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Step 8 Extract data using Agilent Feature Extraction Software  Software:  Agilent Feature Extraction    Procedure:  1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

source_name: 6-week-old Sec15 KO mouse liver replicate 2

label_protocol: Kit:  Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)    Procedure:  1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.   Volume(ul) per reaction  5×First Strand Buffer 4  0.1M DTT 2  10mM dNTP mix 1  MMLV-RT 1  RNaseOut 0.5  Total volume 8.5  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.   Volume(ul) per reaction  Nuclease-free water 15.3  4X Transcription Buffer 20  0.1 M DTT 6  NTP mix 8  50% PEG 6.4  RNaseOUT 0.5  Inorganic pyrophosphatase 0.6  T7 RNA Polymerase 0.8  Cyanine-3-CTP 2.4  Total volume 60  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.     Step 4 Purify the labeled/amplified RNA and labeled cRNA QC  Kit and instrument:  RNeasy Mini Kit (Qiagen p/n 74104)  NanoDrop ND-1000    Procedure:  1. Add 20 μL of nuclease-free water to your cRNA sample, for a total volume of 100 μL.  2. Add 350 μL of Buffer RLT and mix well by pipetting.  3. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  4. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  5. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  6. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  7. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  8. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  9.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000( Passed-please see report ”Labeling Efficiency-QC”).   From the main menu, choose MicroArray Measurement. Go to the Sample Type pull-down menu and select DNA-50.   Blank the instrument with 1.5 μL of 1x labeling solution.   Use 1.5 μL of purified labeled genomic DNA for quantitation. Measure the absorbance at A260nm (DNA), A550nm (cyanine 3).   The specific activity (pmol dyes per μg genomic DNA) of the labeled genomic DNA can be obtained by the following calculation:  (Concentration of Cy3)  Specific Activity =——————————————— = pmol Cy3 per μg cRNA  (Concentration of cRNA) * 1000  * If the yield is <1.65 μg and the specific activity is <9.0 pmol Cy3 per μg cRNA do not proceed to the hybridization step. Repeat cRNA preparation.

extract_protocol: Kits and Reagents:  TRIzol® Reagent (Invitrogen life technologies)  Biopulverizer(biospec)  Mini-Bead-Beater-16(biospec)    Procedure:  1. Homogenization  a. Tissues  a) Cryopulverization of tissue using the Biopulverizer   Place the BioPulverizer™ in a shallow container and cool thoroughly with either liquid nitrogen.   Place prefrozen tissue in the well of the mortar.   Remove the mortar from the shallow container, place it on the lab bench and pulverize the tissue with one or two blows to the pestle with a hammer (models 59012MS).   Empty the powdered contents for subsequent homogenization or extraction procedures.               b) Homogenization using the Mini-Bead-Beater-16   Fill the 2 ml screw-cap microtube one-half full with 1.0mm beads. Then add TRIzol and tissue, being sure to fill the microtube almost to the top. Exclude as much air from the microtube as possible. Use screw-cap microtubes with integral o-ring seals in order to eliminate aerosol formation during the homogenization. Be sure there are no beads on the threads of the microtubes when screwing down the cap.    Insert 1 to 16 microtubes into the holder. Distribute them symmetrically as you would do with a centrifuge. Screw in the black plastic chamber cap until it is in contact with the tops of the microtube caps. Tighten the lid by hand so the vials are firmly held in place. Do not overtighten.   Set the timer depending on the type of sample. Start the machine.   b. Cells Grown in Monolayer  Lyse cells directly in a culture dish by adding 1 ml of TRIzol Reagent to a 3.5 cm diameter dish, and passing the cell lysate several times through a pipette. The amount of TRIzol Reagent added is based on the area of the culture dish (1 ml per 10 cm2) and not on the number of cells present.   c. Cells Grown in Suspension  Pellet cells by centrifugation. Lyse cells in TRIzol Reagent by repetitive pipetting. Use 1 ml of the reagent per 5-10 × 106 of animal, plant or yeast cells, or per 1 × 107 bacterial cells. Washing cells before addition of TRIzol Reagent should be avoided as this increases the possibility of mRNA degradation. Disruption of some yeast and bacterial cells may require the use of a homogenizer.  2. Phase Separation  Incubate the homogenized samples for 5 minutes at 15 to 30°C to permit the complete dissociation of nucleoprotein complexes. Add 0.2 ml of chloroform per 1 ml of TRIzol Reagent. Cap sample tubes securely. Shake tubes vigorously by hand for 15 seconds and incubate them at 15 to 30°C for 2 to 3 minutes. Centrifuge the samples at 12,000 × g for 15 minutes at 4°C. Following centrifugation, the mixture separates into a lower red, phenol-chloroform phase, an interphase, and a colorless upper aqueous phase. RNA remains exclusively in the aqueous phase. The volume of the aqueous phase is about 60% of the volume of TRIzol Reagent used for homogenization.  3. RNA Precipitation  Transfer the aqueous phase to a fresh tube. Precipitate the RNA from the aqueous phase by mixing with isopropyl alcohol. Use 0.5 ml of isopropyl alcohol per 1 ml of TRIzol Reagent used for the initial homogenization. Incubate samples at 15 to 30°C for 10 minutes and centrifuge at 12,000 × g for 10 minutes at 4°C.   4. RNA Wash  Remove the supernatant. Wash the RNA pellet once with 75% ethanol, adding at least 1 ml of 75% ethanol per 1 ml of TRIzol Reagent used for the initial homogenization. Mix the sample by vortexing and centrifuge at 7,500 × g for 5 minutes at 4°C.  5. Redissolving the RNA  At the end of the procedure, air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 85ul or less RNase-free water by passing the solution a few times through a pipette tip, and incubating for 10 minutes at 55 to 60°C.     Step 2 Total RNA Clean-up and RNA QC  Kits and Reagents:  RNasey Mini Kit(Qiagen p/n 74104):      Buffer RPE  Buffer RLT  RNeasy Mini spin column  NanoDrop ND-1000  Baseline-ZERO DNase(EPICENTRE, Cat. Nos. DB0711K)    Things to do before starting:  1. Buffer RPE is supplied as a concentrate. Before using for the first time, add 4 volumes of ethanol (96–100%) as indicated on the bottle to obtain a working solution.    Procedure:  1. Mix the following in a microcentrifuge tube:  Redissolved RNA ≤85ul  10×Reaction buffer 10ul  Baseline-ZERO DNase 5ul  RNase-free water X ul  Total volume 100ul  2. Incubate at 37°C for 30 minutes.  3. Add 350 μl Buffer RLT, and mix well.  4. Add 250 μl ethanol (96–100%) to the diluted RNA, and mix well by pipetting. Do not centrifuge. Proceed immediately to step 5.  5. Transfer the sample (700 μl) to an RNeasy Mini spin column placed in a 2 ml collection tube. Close the lid gently, and centrifuge for 15 s at ≥8000 x g (≥10,000 rpm). Discard the flow-through.  6. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 15 s at≥8000 x g (≥10,000 rpm) to wash the spin column membrane. Discard the flow-through.  7. Add 500 μl Buffer RPE to the RNeasy spin column. Close the lid gently, and centrifuge for 2 min at ≥8000 x g (≥10,000 rpm) to wash the spin column membrane.  8. Place the RNeasy spin column in a new 2 ml collection tube, and discard the old collection tube with the flow-through. Close the lid gently, and centrifuge at full speed for 1 min.  9. Place the RNeasy spin column in a new 1.5 ml collection tube. Add appropriate RNase-free water (please see report ”RNA-QC”) directly to the spin column membrane. Close the lid gently, and centrifuge for 1 min at ≥8000 x g (≥10,000 rpm) to elute the RNA.  10. RNA quantification and quality control(Passed-please see report ”RNA-QC”).

treatment_protocol: No treatment

value: Liver tissue

tag: gender

tag: age

value: Sec15 KO


title: 6-week-old Sec15 KO mouse liver re3

status: Public on Nov 14 2024

country: China

description: Sec15 KO mouse withou any treatment

molecule: total RNA

organism: Mus musculus

source_name: 6-week-old Sec15 KO mouse liver replicate 3

tag: tissue

value: male

tag: genotype


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 3

type: genomic

city: Ariel

first: Mali

last: Salmon-Divon

address: Ariel university, Ariel Israel, Ramat HaGolan St 65, Ari'el

country: Israel

institute: Department of Molecular Biology, Ariel University

description:
LCH3
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

hyb_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

data_processing:
ChAMP package in R environment (v 2.21.1)
BMIQ normalized beta

label: Cy3 and Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: bone

extract_protocol: ChemagicSTAR FFPE DNA Extraction Protocol

value: bone

tag: disease state

value: histiocytoses

tag: Sex

value: female


title: F1.KP.CO.c

type: SRA

city: Amsterdam

first: Arezo

last: Torang

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description:
F1.KP.CO.c
AK45

library_source: transcriptomic

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

source_name: Colon

growth_protocol: Intestinal organoids were maintained in Advanced DMEM/F12 (ADF) media supplemented with penicillin (100ug/ml), 5ml 200 mM Glutamax, 5ml 10mM Hepes, B27 supplement (Invitrogen) and N2 supplement (Invitrogen). In addition to ADF we also use 50ng/ml recombinant Mouse EGF (Tebu-BIO), mouse Noggin-FC supernatant (~100ng/ml) and R-Spondin-FC supernatant(~ 500ng/ml). Cultures were maintained at 37 degrees celsius and checked monthly for mycoplasma contamination.

extract_protocol:
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.

value: Colon

tag: cell type

value: In Vitro organoids

value: KP

tag: batch


title: 6-week-old Sec15 KO mouse liver re1

description: Sec15 KO mouse withou any treatment

source_name: 6-week-old Sec15 KO mouse liver replicate 1


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 2

description:
LCH2
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

scan_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

source_name: soft tissue

value: soft tissue


title: Bone Marrow, TNFKO + 5mg-kg LPS, m11, d0.5

city: Chicago

first: Denis

last: Cipurko

state: IL

address: 900 E 57th St

department: Biological Sciences Division

country: USA

institute: University of Chicago

description:
BM_d0.5_11
Bone Marrow_cpm_counts.txt

data_processing:
Sequencing read files were processed to generate UMI (unique molecular identifier) count matrices using the python toolkit from the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/). In brief, reads were aligned to the mouse mm10 transcriptome with RapMap (https://github.com/COMBINE-lab/RapMap). Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/), Qualimap, MultiQC (https://github.com/ewels/MultiQC). Samples were demultiplexed using barcodes stored in Read 1 (first 6 bases) and raw UMI count matrices were computed using UMIs stored in Read 1 (bases 7 to 16) (https://github.com/vals/umis). Differential expression (DE) analysis was done using custom scripts in R (http://www.R-project.org). Raw count matrices were filtered to keep genes with at least 20 counts per million (cpm) or 5 UMIs in 2 samples and normalized across samples using the calcNormFactor function in edgeR (https://github.com/StoreyLab/edge).
Assembly: mm10
Supplementary files format and content: All count matrices are in tsv format. The first seven columns contain sample metadata (Organ, Treatment, Mouse ID, Mouse genotype, etc.). The remaining columns consist of normalized cpm counts. Matrices include all replicates for the organ.

molecule: polyA RNA

source_name: Bone Marrow

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies). For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293).
Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Bone Marrow

tag: mouse id

tag: time point

value: 12 hours

tag: treatment

value: 5mg-kg LPS


title: Bone Marrow, 5mg-kg LPS, m7, d0.5

description:
BM_d0.5_7
Bone Marrow_cpm_counts.txt


title: DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis 1

description:
LCH1
DNA from histyocitic infiltrated tissues of Langerhans cell histiocytosis

source_name: skin

label_protocol: Standard Illumina Procedure for MethylationEPIC platform with FFPE restoration step

value: skin


title: F1.KP.SIP.c

description:
F1.KP.SIP.c
AK44

source_name: Small Intestine

value: Small Intestine


title: Plasma exosome Healthy_2

city: Guangzhou

first: MinQiang

last: Lu

state: Guangdong

address: No.1, Panfu Road, Yuexiu District

department: HBP II Surgery

institute: Guangzhou First People's Hospital

data_processing:
Illumina NextSeq 500 was used for base-calling
Trimmed data after raw sequencing data went through quality control, and trimmed data after removing adapter sequences from Reads and short clips.
MiRNA expression was quantified by software miRDeep2, which compared the results to known genomes and counted them.
The miRNA expression threshold was set to those mirnas whose average CPM (Counts per million reads) in each group exceeded 1, which were considered to be expressed in the grouping and counted.
Assembly: miRDeep2
Supplementary files format and content: All differentially expressed miRNAs were obtained by comparing CPM between sample groups.

source_name: Plasma exosome

extract_protocol:
Exosome samples from plasma were centrifuged at 150,000 × g for 2 hours for twice.RNA was extracted by TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. RNA was quantified using a Nano-Drop spectrophotometer (Thermo Fisher Scientific)
miRNA sequencing libraries were prepared using the total RNA of each sample, denatured into single-stranded DNA molecules, captured on Illumina Flow cell, amplified into clusters in situ, and sequenced for 51 cycles on the Illuminia Nextseq 500 according to the supplier's instructions.

value: Plasma exosome

tag: disease

value: non-Hepatocellular carcinoma


title: Plasma exosome Healthy_3


title: 6-week-old mouse liver re2

description: WT mouse withou any treatment

source_name: 6-week-old mouse liver replicate 2

value: Liver tissue

value: WT


title: Bone Marrow, TNFKO + 5mg-kg LPS, m10, d0.5

description:
BM_d0.5_10
Bone Marrow_cpm_counts.txt


title: Bone Marrow, 5mg-kg LPS, m5, d0.5

description:
BM_d0.5_5
Bone Marrow_cpm_counts.txt


title: F1.BPN.CO.c

description:
F1.BPN.CO.c
AK43

value: BPN


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 6

description:
ECD6
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease

source_name: colon

value: colon


title: Plasma exosome Healthy_1


title: Bone Marrow, CTRL, m4, d0.5

description:
BM_d0.5_4
Bone Marrow_cpm_counts.txt

value: PBS


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 5

description:
ECD5
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease

source_name: brain

value: brain

value: histiocytoses

value: male


title: F1.BPN.SIP.c

description:
F1.BPN.SIP.c
AK42

value: In Vitro organoids


title: Plasma exosome HCC_3

value: Hepatocellular carcinoma


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 4

description:
ECD4
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease

source_name: pleura

value: pleura


title: Plasma exosome HCC_2


title: Bone Marrow, CTRL, m2, d0.5

description:
BM_d0.5_2
Bone Marrow_cpm_counts.txt

value: Bone Marrow

value: 12 hours


title: F1.BPN.SIP.b

description:
F1.BPN.SIP.b
AK40


title: Bone Marrow, 5mg-kg LPS, m6, d0.5

description:
BM_d0.5_6
Bone Marrow_cpm_counts.txt

value: 5mg-kg LPS


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 3

description:
ECD3
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease

value: skin

value: female


title: 6-week-old mouse liver re3

description: WT mouse withou any treatment

source_name: 6-week-old mouse liver replicate 3


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 2

description:
ECD2
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease


title: Plasma exosome HCC_1

value: Plasma exosome


title: Bone Marrow, CTRL, m1, d0.5

description:
BM_d0.5_1
Bone Marrow_cpm_counts.txt


title: F1.AK.SIP.c

description:
F1.AK.SIP.c
AK3

value: Small Intestine

value: AK


title: DNA from histyocitic infiltrated tissues of Erdheim-Chester disease 1

description:
ECD1
DNA from histyocitic infiltrated tissues of Erdheim-Chester disease


title: F1.BPN.CO.a

description:
F1.BPN.CO.a
AK39

value: Colon

value: BPN


title: 6-week-old mouse liver re1

description: WT mouse withou any treatment

source_name: 6-week-old mouse liver replicate 1

value: Liver tissue

value: WT


title: Seeds, abi3-12 dog1-4 cyp707a2, 26d+ after pollination, Batch B, rep2

city: Wageningen

first: Mariana

middle: Aline

last: Silva Artur

address: Droevendaalsesteeg 1

department: Plant Sciences

institute: Wageningen University & Research

data_processing:
Mapping was done with hisat2 v2.1.0 (command: hisat2 -p 12 --rna-strandness R -t --dta-cufflinks -x TAIR11 -U $f -S $name.sam)
Sorting of alignments (command: samtools sort -@ 12 -o $name.bam $name.sam)
Transcript quantification was done with stringtie v1.3.2 (command: stringtie -e -B -p 12 -G Araport11_GFF3_genes_transposons.201606.gtf -o ballgown/$name/$name.gtf $name.bam)
Raw counts were extracted using the script prepDE.py, available at StringTie GitHub repository (https://github.com/gpertea/stringtie/blob/master/prepDE.py).
Assembly: TAIR10 genome,Araport11gene annotation
Supplementary files format and content: comma-delimited text file with raw counts for every sample

organism: Arabidopsis thaliana

source_name: Seed

growth_protocol: Plants were grown on 4 x 4 cm Rockwool blocks in a growth chamber at 20°C/18°C (day/night) under a 16-h photoperiod of artificial light (150 μmol m-2 s-1) and 70% relative humidity. Plants were watered three times per week with standard nutrient solution Hyponex (He et al. 2014).

extract_protocol:
Total RNA was extracted using a hot borate method modified from Wan and Wilkins (1994). The homogenized seeds were mixed with an extraction buffer (0.2 M Na borate decahydrate (Borax), 30 mM EGTA, 1% SDS, 1% Na deoxy-cholate (Na-DOC)) containing 1.6 mg DTT and 48 mg PVP40 which had been heated to 80ºC. One mg proteinase K was added to this suspension and incubated for 15 min at 42ºC. After adding 64 μL of 2 M KCl the samples were incubated on ice for 30 min and subsequently centrifuged for 20 min at 12,000 g. 270 μL of ice-cold 8 M LiCl was added to the supernatant in a final concentration of 2 M and the tubes were incubated overnight on ice. After centrifugation for 20 min at 12,000 g at 4ºC, the pellets were washed with 750 μL ice-cold 2 M LiCl. The samples were centrifuged for 10 min at 10,000 g at 4ºC and the pellets were re-suspended in 100 μL DEPC treated water. The samples were cleaned with phenol chloroform and treated with DNAse (RQ1 DNase, Promega).
RNA was processed for RNA-seq using mRNA enrichment polyA capture (Illumina). The RNA-seq library was prepared for sequencing with strand-specific cDNA synthesis using random hexamer priming.

treatment_protocol: Several flowers were tagged in every plant of all genotypes just before anthesis to allow follow up on days after pollination (DAP). For each round of experiments plants were grown together and seeds were harvested from 12 DAP to 26 DAP in 2 days intervals. For each sample four biological replicates were used, and each biological replicate consisted of 4 to 6 siliques. Fresh siliques were immediately dissected, and the seeds were carefully removed. The samples for RNA extraction were frozen in liquid nitrogen and stored at -80°C. For extraction, three replicates of a pool of seeds from 4 siliques for each treatment were homogenized. The experiment was repeated 3 times, we refer to the different experiments as rounds 1 to 3. Round 1 consisted of pre-tests, and only RNA-Seq data of experimental rounds 2 and 3 is shared, as batch A and batch B, respectively.

value: Seed

tag: accession

tag: genetic modification

value: triple knock-out

tag: maturation stage

value: dry-stage

value: B

tag: experimental round

tag: replicate


title: Brown Adipose Tissue, TNFKO + 5mg-kg LPS, m11, d0.5

description:
BF_d0.5_11
Brown Adipose Tissue_cpm_counts.txt

source_name: Brown Adipose Tissue

value: Brown Adipose Tissue


title: DNA from non-neoplastic histiocytic infiltrates of suture granulomas 4

description:
Sut_Gran4
DNA from non-neoplastic histiocytic infiltrates of suture granulomas

value: control, suture granulomas

value: male


title: F1.BPN.SIP.a

description:
F1.BPN.SIP.a
AK38

value: In Vitro organoids


title: Brown Adipose Tissue, TNFKO + 5mg-kg LPS, m12, d0.5

description:
BF_d0.5_12
Brown Adipose Tissue_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: F1.BPN.CO.b

description:
F1.BPN.CO.b
AK41


title: F1.BP.SIP.c.OE

description:
F1.BP.SIP.c.OE
AK37

value: BP


title: Bone Marrow, CTRL, m3, d0.5

description:
BM_d0.5_3
Bone Marrow_cpm_counts.txt

value: Bone Marrow

value: PBS


title: Brown Adipose Tissue, TNFKO + 5mg-kg LPS, m10, d0.5

description:
BF_d0.5_10
Brown Adipose Tissue_cpm_counts.txt


title: Seeds, abi3-12 dog1-4 cyp707a2, 24d after pollination, Batch B, rep3


title: Seeds, abi3-12 dog1-4 cyp707a2, 26d+ after pollination, Batch B, rep1


title: F1.BP.SIP.c

description:
F1.BP.SIP.c
AK36

value: Small Intestine


title: Brown Adipose Tissue, TNFKO + 5mg-kg LPS, m9, d0.5

description:
BF_d0.5_9
Brown Adipose Tissue_cpm_counts.txt


title: DNA from non-neoplastic histiocytic infiltrates of suture granulomas 1

description:
Sut_Gran1
DNA from non-neoplastic histiocytic infiltrates of suture granulomas

value: skin

value: female


title: Seeds, abi3-12 dog1-4 cyp707a2, 24d after pollination, Batch B, rep2


title: Seeds, abi3-12 dog1-4 cyp707a2, 26d+ after pollination, Batch B, rep3


title: Brown Adipose Tissue, 5mg-kg LPS, m8, d0.5

description:
BF_d0.5_8
Brown Adipose Tissue_cpm_counts.txt


title: Brown Adipose Tissue, 5mg-kg LPS, m7, d0.5

description:
BF_d0.5_7
Brown Adipose Tissue_cpm_counts.txt


title: Seeds, abi3-12 dog1-4 cyp707a2, 24d after pollination, Batch B, rep1


title: F1.BP.SIP.b

description:
F1.BP.SIP.b
AK34


title: Seeds, abi3-12 dog1-4 cyp707a2, 22d after pollination, Batch B, rep3


title: E-cadherin knock out 1

city: Paris

first: Rene-Marc

last: Mege

address: 15 Rue Helene Brion

country: France

institute: Institut Jacques Monod

data_processing:
After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplex and control the quality of the raw data (based of FastQC modules / version 0.11.5). Obtained fastq files were then aligned using STAR algorithm (version 2.5.2b) and quality control of the alignment obtained with Picard tools (version 2.8.1). Reads were then counted using Featurecount (version Rsubread 1.24.1) and the statistical analyses on the read counts were performed with the DESeq2 package version 1.14.1 to determine the proportion of differentially expressed genes between the two conditions. From the initial DESeq2 file containing 11191 genes without duplicates, we then performed the Gene Set Enrichment Analysis with the ClusterProfiler package on R~\cite{yu_clusterprofiler_2012}. We used the canis familiaris (Cf) annotation and performed the GSEA from ENSEMBL to SYMBOL annotations without permutation and with p-value and p-value adjusted cutoffs set at 0.05.
We then looked at the Molecular Signatures Database (MSigDB) to find if these up or downregulated genes were present in the gene sets related to specific cellular processes as cell-cell adhesion or cell death, apoptosis and oxidative stress or cell substrate adhesion regulation
Assembly: canis familiaris (Cf) annotation and performed the GSEA from ENSEMBL to SYMBOL annotations
Supplementary files format and content: WT_KO_Analysis.xlsx

organism: Canis lupus familiaris

source_name: Kidney

growth_protocol: MDCK WT and MDCK E-cad KO cells were grown in DMEM + 10% FBS and 1% PS until 70-80% confluency.

extract_protocol:
RNA was extracted using the RNeasy kit (Qiagen, Cat.No./ID:74104). Briefly cells were lysed with RLT buffer and disrupt using cell shredder. Following RNA collection following the kit protocol, RNA concentrations were obtained using nanodrop or a fluorometric Qubit RNA assay (Life Technologies, Grand Island, New York, USA).
250 ng of high quality total RNA sample ($RIN > 8$) was processed using Stranded mRNA Prep kit (Illumina) according to manufacturer instructions. Briefly, after purification of poly-A containing mRNA molecules, mRNA molecules are fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis will permit to achieve the strand specificity. Addition of a single A base to the cDNA is followed by ligation of Illumina adapters. Libraries were quantified by Q bit and profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-lengths read V2 chemistry in a paired-end mode.

value: Kidney

tag: cell line

value: MDCK Type II Ecadherin KO

value: Madin-Darby canine kidney(MDCK)cells

value: MDCK Type II

value: e-cadherin loss of function


title: Brown Adipose Tissue, 5mg-kg LPS, m6, d0.5

description:
BF_d0.5_6
Brown Adipose Tissue_cpm_counts.txt

value: Brown Adipose Tissue


title: F1.KP.SIP.bv1

description:
F1.KP.SIP.bv1
VW2.KP 7.5.D

value: KP


title: DNA from non-neoplastic histiocytic infiltrates of suture granulomas 3

description:
Sut_Gran3
DNA from non-neoplastic histiocytic infiltrates of suture granulomas

value: control, suture granulomas


title: Seeds, abi3-12 dog1-4 cyp707a2, 22d after pollination, Batch B, rep1

value: Seed

value: triple knock-out

value: B


title: F1.BP.CO.a.OE

description:
F1.BP.CO.a.OE
AK32

value: Colon

value: In Vitro organoids

value: BP


title: Brown Adipose Tissue, 5mg-kg LPS, m5, d0.5

description:
BF_d0.5_5
Brown Adipose Tissue_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: DNA from non-neoplastic histiocytic infiltrates of suture granulomas 2

description:
Sut_Gran2
DNA from non-neoplastic histiocytic infiltrates of suture granulomas

value: skin

value: female


title: Brown Adipose Tissue, CTRL, m4, d0.5

description:
BF_d0.5_4
Brown Adipose Tissue_cpm_counts.txt

value: PBS


title: F1.A.CO.c

description:
F1.A.CO.c
AK2

value: A


title: HSMM_siAEBP1-1

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description: HSMM transfected with AEBP1 siRNA1

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

source_name: HSMM

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: Human skeletal muscle myoblasts (HSMMs) were purchased from Lonza (Basel, Switzerland), and were cultured in SKBM-2 Skeletal Muscle Cell Growth Basal Medium-2 (Lonza) with SKGM-2 Skeletal Muscle Cell Growth Medium-2 SingleQuots Supplements and Growth Factors (Lonza).

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: For knockdown of AEBP1, 5^10E4 cells were transfected with Silencer Select Pre-designed siRNA (100 pmol each; AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) or Silencer Select Negative Control No. 1 siRNA (Thermo Fisher Scientific) using TransIT-X2 Dynamic Delivery System (Mirus Bio, Madison, WI, USA). Cells were harvested 72 h after transfection. For co-culture experiments, HSMMs (5^10E4 cells/well in 6-well plates) were indirectly co-cultured with OSCC cells (1^10E5 cells in culture inserts) for 72 h.

tag: sirna

value: AEBP1 siRNA1


title: HSMM_siAEBP1-2

description: HSMM transfected with AEBP1 siRNA2

value: AEBP1 siRNA2


title: F1.AKPS.CO.c

description:
F1.AKPS.CO.c
AK26

source_name: Colon

tag: tissue

value: AKPS


title: F1.BP.SIP.b.OE

description:
F1.BP.SIP.b.OE
AK35

value: Small Intestine

tag: genotype


title: Seeds, abi3-12 dog1-4 cyp707a2, 20d after pollination, Batch B, rep3


title: Brown Adipose Tissue, CTRL, m3, d0.5

description:
BF_d0.5_3
Brown Adipose Tissue_cpm_counts.txt

value: Brown Adipose Tissue


title: HSMM_d8_SAS

description: HSMM co-cultured with SAS


title: HSMM_siCONT

description: HSMM transfected with control siRNA

value: control siRNA


title: Seeds, abi3-12 dog1-4 cyp707a2, 20d after pollination, Batch B, rep2

value: Seed

value: triple knock-out


title: HSMM_d8

description: HSMM at day 8


title: F1.BP.SIP.a.OE

description:
F1.BP.SIP.a.OE
AK33


title: F1.AKPS.CO.b

description:
F1.AKPS.CO.b
AK24

value: Colon


title: Brown Adipose Tissue, CTRL, m1, d0.5

description:
BF_d0.5_1
Brown Adipose Tissue_cpm_counts.txt


title: Seeds, abi3-12 dog1-4 cyp707a2, 20d after pollination, Batch B, rep1

value: B


title: F1.AKPS.SIP.c

description:
F1.AKPS.SIP.c
AK25

value: In Vitro organoids


title: Seeds, abi3-12 dog1-4 cyp707a2, 22d after pollination, Batch B, rep2


title: F1.AKPS.SIP.b

description:
F1.AKPS.SIP.b
AK23


title: wlim2a flg22 3

city: Thuwal

first: Prabhu

last: Manickam

state: Jeddah

address: 4700 KAUST

department: BESE

country: Saudi Arabia

institute: KAUST

data_processing:
Reads were quality controlled using FASTQC v0.11.5
Trimmometric was used for quality trimming. Parameters for read quality filter were set as follows: Minimum length of 36 bp; Mean Phred quality score greater than 30; Leading and trailing bases removal with the base quality below 3; sliding window of 4:15.
TopHat v2.1.1 was used to alignment of short reads to the Arabidopsis thaliana TAIR 10
cufflinks for transcripts assembly, and differentially expression levels (fragment per kilobase of transcript per million mapped reads, FPKM).
The differentially expressed genes (DEGs) were identified using Cufflinks and the limma package in R. Cuffdiff v2.2.1 (Trapnell et al., 2012) with quartile normalization to find the significant gene expression.
Assembly: TAIR10
Supplementary files format and content: geneid_lim2moc_lim2flg22_wtflg22_wtmock.xlsx

organism: Arabidopsis

source_name: Seedlings

growth_protocol: 14-day-old WT and mutant Arabidopsis seedlings were grown in three independent biological replicates on½ MS agar at 22C in a growth Percival

extract_protocol:
total RNA was isolated with the RNeasy midi kit (Qiagen).
RNA libraries were prepared for transcriptome sequencing by GATC Biotech AG, an Eurofins Genomics Company, using standard Illumina protocols in frame of the INVIEW Transcriptome Explore protocol. For library preparation, mRNA was fragmented, and random hexamer-primed cDNA synthesis was performed. Illumina pair-end read (SR) sequencing with guaranteed 30 million reads per sample was performed by the Genome Sequencer Illumina HiSeq, in the sequence mode HiSeq 4000.

treatment_protocol: 14-day-old WT and mutant Arabidopsis seedlings were grown in three independent biological replicates on½ MS agar, moved to ½MS liquid media overnight, and then treated for one hour with 1 µM flg22,a peptide synthesized by GeneScript, and water (mock)

value: Seedlings

value: Mutant


title: White Adipose Tissue, TNFKO + 5mg-kg LPS, m12, d0.5

description:
WF_d0.5_12
White Adipose Tissue_cpm_counts.txt

source_name: White Adipose Tissue

value: White Adipose Tissue

value: 12 hours

value: 5mg-kg LPS


title: White Adipose Tissue, TNFKO + 5mg-kg LPS, m10, d0.5

description:
WF_d0.5_10
White Adipose Tissue_cpm_counts.txt


title: HSMM_d3

description: HSMM at day 3


title: F1.AKPS.SIP.a

description:
F1.AKPS.SIP.a
AK21


title: wlim2a flg22 1


title: White Adipose Tissue, TNFKO + 5mg-kg LPS, m11, d0.5

description:
WF_d0.5_11
White Adipose Tissue_cpm_counts.txt


title: F1.AKPS.CO.a

description:
F1.AKPS.CO.a
AK22


title: Brown Adipose Tissue, CTRL, m2, d0.5

description:
BF_d0.5_2
Brown Adipose Tissue_cpm_counts.txt

value: PBS


title: Seeds, abi3-12 dog1-4 cyp707a2, 18d after pollination, Batch B, rep2


title: Seeds, abi3-12 dog1-4 cyp707a2, 18d after pollination, Batch B, rep1


title: wlim2a flg22 2


title: Seeds, abi3-12 dog1-4 aba2-1, 26d+ after pollination, Batch B, rep3

value: dry-stage


title: Seeds, abi3-12 dog1-4 cyp707a2, 18d after pollination, Batch B, rep3


title: F1.AKP2.CO.c

description:
F1.AKP2.CO.c
AK20


title: wlim2a mock 3

value: Mock


title: White Adipose Tissue, 5mg-kg LPS, m8, d0.5

description:
WF_d0.5_8
White Adipose Tissue_cpm_counts.txt


title: wlim2a mock 1


title: Seeds, abi3-12 dog1-4 aba2-1, 26d+ after pollination, Batch B, rep2


title: White Adipose Tissue, TNFKO + 5mg-kg LPS, m9, d0.5

description:
WF_d0.5_9
White Adipose Tissue_cpm_counts.txt


title: F1.A.SIP.c

description:
F1.A.SIP.c
AK1

value: A


title: White Adipose Tissue, 5mg-kg LPS, m7, d0.5

description:
WF_d0.5_7
White Adipose Tissue_cpm_counts.txt


title: Seeds, abi3-12 dog1-4 aba2-1, 26d+ after pollination, Batch B, rep1


title: Seeds, abi3-12 aba2-1, 26d+ after pollination, Batch B, rep3

value: double knock-out


title: wlim2a mock 2


title: WT-flg22 3

value: Witd Type


title: F1.AKP2.SIP.c

description:
F1.AKP2.SIP.c
AK19

value: Small Intestine


title: Seeds, abi3-12 aba2-1, 26d+ after pollination, Batch B, rep2

value: Seed


title: F1.AKP2.CO.b

description:
F1.AKP2.CO.b
AK18


title: WT-flg22 2


title: Seeds, abi3-12 aba2-1, 26d+ after pollination, Batch B, rep1


title: WT-flg22 1


title: F1.AKP2.CO.a

description:
F1.AKP2.CO.a
AK16


title: White Adipose Tissue, 5mg-kg LPS, m6, d0.5

description:
WF_d0.5_6
White Adipose Tissue_cpm_counts.txt


title: White Adipose Tissue, CTRL, m4, d0.5

description:
WF_d0.5_4
White Adipose Tissue_cpm_counts.txt


title: F1.AKP.CO.c

description:
F1.AKP.CO.c
AK14

value: AKP


title: White Adipose Tissue, CTRL, m3, d0.5

description:
WF_d0.5_3
White Adipose Tissue_cpm_counts.txt


title: WT-Mock 3


title: Seeds, dog1-4 aba2-1, 26d+ after pollination, Batch B, rep1

value: dog1-4 aba2-1


title: WT-Mock 1


title: F1.AKP2.SIP.b

description:
F1.AKP2.SIP.b
AK17


title: Seeds, dog1-4 aba2-1, 26d+ after pollination, Batch B, rep2

value: B


title: WT-Mock 2


title: F1.AP2.CO.c

description:
F1.AP2.CO.c
AK11

value: Colon

value: In Vitro organoids


title: F1.AK.SIP.a4

description:
F1.AK.SIP.a4
ROE124ASIP

value: AK


title: Muscle, TNFKO + 5mg-kg LPS, m12, d0.5

description:
MU_d0.5_12
Muscle_cpm_counts.txt

source_name: Muscle

value: Muscle


title: MDA-MB-231 Control (biol rep 2)

city: New York

first: Hee Won

last: Yang

state: NY

institute: Columbia University

description:
est_counts_genes_kallisto.txt
HE008

data_processing:
BCL files were converted to FASTQ format using bases2fastq version 1.7.0.1196148384, including adapter trimming.
FASTQ files were pseudoaligned to a Kallisto index based on Ensembl v111 transcriptomes (Human: GRCh38.p14) using Kallisto version 0.50.1.
Assembly: Human: GRCh38.p14
Supplementary files format and content: Txt files with raw counts.

extract_protocol:
MDA-MB-231 cells expressing with mCerulean-tagged Geminin (a.a 1−110) were treated with the indicated drugs for 42 hr. Cells were then dissociated, and mCerulean-positive cells were isolated by FACS. Collected cells were immediately lysed in TRIzol LS Reagent (Invitrogen, 25 #10296010) with an additional 0.2 ml of chloroform per 1ml of TRIzol to facilitate phase separation. Following centrifugation at 12,000 rpm for 15 min at 4°C, the aqueous phase was transferred and RNA was precipitated by adding 0.5 ml of isopropyl alcohol (per 1 ml of TRIzol) along with Glycoblue (50 µg/ml) (Applied Biosystems, AM9515), then incubated overnight at - 35 20°C. Precipitated RNA was centrifuged at 12,000 rpm for 10 min at 4°C, the supernatant was discarded, and the RNA pellet was washed with 75% ethanol. After a final centrifugation at 7,500 rpm for 5 min at 4°C, the RNA pellet was air-dried and resuspended in RNase-free water.
cDNA synthesis was carried out using the Clontech Ultra Low v4 kit, followed by library construction with NexteraXT.

value: Epithelial

value: Control


title: MDA-MB-231 CDK7i (biol rep 2)

description:
est_counts_genes_kallisto.txt
HE007


title: F1.AKP.SIP.c

description:
F1.AKP.SIP.c
AK13


title: Muscle, TNFKO + 5mg-kg LPS, m11, d0.5

description:
MU_d0.5_11
Muscle_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: White Adipose Tissue, CTRL, m2, d0.5

description:
WF_d0.5_2
White Adipose Tissue_cpm_counts.txt

value: White Adipose Tissue

value: PBS


title: Seeds, abi3-12 dog1-4, 26d+ after pollination, Batch B, rep1

value: double knock-out

value: dry-stage


title: F1.AK.SIP.b4

description:
F1.AK.SIP.b4
ROE123ESIP

value: Small Intestine


title: Muscle, TNFKO + 5mg-kg LPS, m10, d0.5

description:
MU_d0.5_10
Muscle_cpm_counts.txt


title: White Adipose Tissue, CTRL, m1, d0.5

description:
WF_d0.5_1
White Adipose Tissue_cpm_counts.txt


title: Seeds, abi3-12 dog1-4, 26d+ after pollination, Batch B, rep3

value: Seed


title: Seeds, abi3-12 dog1-4, 26d+ after pollination, Batch B, rep2


title: F1.AKPN.SIP.b4

description:
F1.AKPN.SIP.b4
RKW52BSIP

value: AKPN


title: F1.AK.CO.a4

description:
F1.AK.CO.a4
ROE124ACO


title: MDA-MB-231 CDK4/6i (biol rep 2)

description:
est_counts_genes_kallisto.txt
HE006


title: Muscle, 5mg-kg LPS, m8, d0.5

description:
MU_d0.5_8
Muscle_cpm_counts.txt


title: MDA-MB-231 CDK7i (biol rep 1)

description:
est_counts_genes_kallisto.txt
HE003


title: F1.APN.SIP.a4.OE

description:
F1.APN.SIP.a4.OE
RKW51ASIPOE

value: APN


title: Seeds, abi3-12 dog1-4, 24d after pollination, Batch B, rep3

value: B


title: MDA-MB-231 CDK4/6i+CDK7i (biol rep 1)

description:
est_counts_genes_kallisto.txt
HE005


title: White Adipose Tissue, 5mg-kg LPS, m5, d0.5

description:
WF_d0.5_5
White Adipose Tissue_cpm_counts.txt


title: Seeds, dog1-4 aba2-1, 26d+ after pollination, Batch B, rep3

value: dog1-4 aba2-1


title: MDA-MB-231 CDK4/6i+CDK7i (biol rep 2)

description:
est_counts_genes_kallisto.txt
HE004


title: Seeds, abi3-12 dog1-4, 24d after pollination, Batch B, rep2


title: Muscle, 5mg-kg LPS, m7, d0.5

description:
MU_d0.5_7
Muscle_cpm_counts.txt


title: Seeds, abi3-12 dog1-4, 24d after pollination, Batch B, rep1


title: Muscle, 5mg-kg LPS, m5, d0.5

description:
MU_d0.5_5
Muscle_cpm_counts.txt


title: MDA-MB-231 CDK4/6i (biol rep 1)

description:
est_counts_genes_kallisto.txt
HE002


title: Seeds, abi3-12 dog1-4, 22d after pollination, Batch B, rep1


title: F1.AKPN.CO.b4

description:
F1.AKPN.CO.b4
RKW52BCO

value: Colon

value: In Vitro organoids


title: F1.AKPN.CO.a4

description:
F1.AKPN.CO.a4
RKW101BCO


title: F1.KP.SIP.b4

description:
F1.KP.SIP.b4
RKAC75DSIP

value: KP


title: Seeds, abi3-12 dog1-4, 22d after pollination, Batch B, rep3


title: Muscle, 5mg-kg LPS, m6, d0.5

description:
MU_d0.5_6
Muscle_cpm_counts.txt

value: Muscle


title: MDA-MB-231 Control (biol rep 1)

description:
est_counts_genes_kallisto.txt
HE001

value: Epithelial

value: Control


title: Seeds, abi3-12 dog1-4, 20d after pollination, Batch B, rep2


title: F1.KP.SIP.a4

description:
F1.KP.SIP.a4
RKAC85ASIP


title: Muscle, TNFKO + 5mg-kg LPS, m9, d0.5

description:
MU_d0.5_9
Muscle_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: Seeds, abi3-12 dog1-4, 20d after pollination, Batch B, rep1


title: Seeds, abi3-12 dog1-4, 22d after pollination, Batch B, rep2


title: flu infection reporter guide RNA #3

city: San Diego

first: Alistair

middle: Brian

last: Russell

state: CA

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

description: RNA reporter econding guide RNA

library_source: other

data_processing:
Data were processed with a custom pipeline described in the associated manuscript.
Assembly: Gecko V2
Supplementary files format and content: Individual counts of guide sequences and associated gene targets

molecule: other

growth_protocol: Samples were from infections of A549-Cas9 cells bearing a CRITR-seq library with a type III interferon reporter with guides cloned from the GECKO library. Cells were allowed to undergo editing for 10 days, after which they were infected by A/WSN/1933 bearing segment 8 from A/PR/8 with stop codons interrupting the NS1 reading frame at an MOI of 2 in influenza growth media. RNA and DNA harvested at 8 hours post infection.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010), DNA by the Monarch spin gDNA extraction kit (NEB #T3010).
Custom amplicon sequencing

treatment_protocol: Infection at MOI 2 by A/WSN/1933 with segment 8 from A/PR/8 bearing stop codons in the NS1 reading frame for 8 hours.

value: CRITR-Seq with infection by flu lacking NS1


title: flu infection reporter guide RNA #2

description: RNA reporter econding guide RNA


title: flu infection genomic guide DNA #3

description: DNA encoding guide RNA


title: Muscle, CTRL, m3, d0.5

description:
MU_d0.5_3
Muscle_cpm_counts.txt

value: PBS


title: Seeds, abi3-12 dog1-4, 20d after pollination, Batch B, rep3

value: double knock-out


title: Seeds, abi3-12 dog1-4, 18d after pollination, Batch B, rep3


title: flu infection reporter guide RNA #1

description: RNA reporter econding guide RNA


title: Heart, TNFKO + 5mg-kg LPS, m12, d0.5

description:
HE_d0.5_12
Heart_cpm_counts.txt

source_name: Heart

value: Heart


title: Muscle, CTRL, m4, d0.5

description:
MU_d0.5_4
Muscle_cpm_counts.txt


title: F1.KP.SIP.b4.OE

description:
F1.KP.SIP.b4.OE
RKAC75DSIPOE

source_name: Small Intestine

value: Small Intestine


title: Muscle, CTRL, m2, d0.5

description:
MU_d0.5_2
Muscle_cpm_counts.txt


title: F1.KPN.SIP.a4.OE

description:
F1.KPN.SIP.a4.OE
RKA281GSIPOE

value: KPN


title: Muscle, CTRL, m1, d0.5

description:
MU_d0.5_1
Muscle_cpm_counts.txt


title: Heart, TNFKO + 5mg-kg LPS, m11, d0.5

description:
HE_d0.5_11
Heart_cpm_counts.txt


title: Seeds, abi3-12 dog1-4, 18d after pollination, Batch B, rep2

value: Seed


title: flu infection genomic guide DNA #2

description: DNA encoding guide RNA


title: F1.KP.CO.a4

description:
F1.KP.CO.a4
RKAC85ACO


title: Heart, TNFKO + 5mg-kg LPS, m10, d0.5

description:
HE_d0.5_10
Heart_cpm_counts.txt


title: F1.AKP.SIP.b4

description:
F1.AKP.SIP.b4
RCB221ESIP

value: AKP


title: Seeds, abi3-12 dog1-4, 18d after pollination, Batch B, rep1

value: B


title: F1.AKP.SIP.a4

description:
F1.AKP.SIP.a4
RCB164ASIP


title: F1.AKP.CO.a4

description:
F1.AKP.CO.a4
RCB164ACO

value: Colon


title: Seeds, L2-1 Col-0 + DOG1-Cvi, 26d+ after pollination, Batch B, rep3

value: L2-1 Col-0 + DOG1-Cvi

value: transgenic line

value: dry-stage


title: F1.AP2.SIP.b4

description:
F1.AP2.SIP.b4
RCB162DSIP

value: In Vitro organoids


title: Heart, 5mg-kg LPS, m8, d0.5

description:
HE_d0.5_8
Heart_cpm_counts.txt


title: Heart, TNFKO + 5mg-kg LPS, m9, d0.5

description:
HE_d0.5_9
Heart_cpm_counts.txt


title: F1.KPN.CO.b4

description:
F1.KPN.CO.b4
RKA205ACO


title: flu infection genomic guide DNA #1

description: DNA encoding guide RNA


title: Seeds, L2-1 Col-0 + DOG1-Cvi, 26d+ after pollination, Batch B, rep2


title: Seeds, L2-1 Col-0 + DOG1-Cvi, 26d+ after pollination, Batch B, rep1


title: Seeds, aba2-1, 26d+ after pollination, Batch B, rep3

value: knock-out


title: F1.AP2.SIP.a4

description:
F1.AP2.SIP.a4
RCB161BSIP


title: F1.AP2.CO.b4

description:
F1.AP2.CO.b4
RCB162DCO


title: D1_Treg_RNA/ABO

city: Oxford

first: Oliver

last: McCallion

address: John Radcliffe Hospital, Headley Way, Headington

country: United Kingdom

institute: University of Oxford

data_processing:
Raw fastq files were processed initially using the BD Rhapsody Analysis pipeline. Briefly, low quality read pairs were filtered by length, quality score, and base complexity. R1 reads were annotated to identify cell IDs and UMIs and R2 reads were mapped to reference panel sequences using Bowtie2.38 Valid R1 and R2 pairs were then filtered using recursive substitution error correction (RSEC) to mitigate UMI errors whereby molecules differing by one base within the UMI sequence are amalgamated.
Assembly: panel.rna.csv
Supplementary files format and content: RDS files containing Seurat Objects of either RNA or ABO matrices per sample

source_name: Regulatory T cells

extract_protocol:
Cryopreserved aliquots of TR001 (Treg cell therapy) and paired PBMC samples isolated at 24-weeks and 60-weeks post-transplant from 4 patients were thawed. Treg were enriched by FACS sorting and stained with AbSeq antibodies before loading onto a BD Rhapsody cartridge
Libraries were constructed as per the manufacturers protocol. Briefly, cDNA was initially amplified for 11 cycles (PCR1) and then for a further 10 cycles (PCR2). PCR2 products were adjusted to 2.5 ng/μl (mRNA), 1.1 ng/μl (Sample Tag) and 0.7 ng/μl (AbSeq) and underwent a final round of amplification (6 cycles for mRNA and Sample Tag and 7 cycles for AbSeq) using indexes for Illumina sequencing to prepare the final libraries

value: Regulatory T cells


title: D3_Treg_RNA/ABO


title: D4_Treg_RNA/ABO


title: D2_Treg_RNA/ABO


title: H3K27ac, replicate 2

city: Philadelphia

first: Ryan

middle: Patrick

last: Calhoun

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

library_source: genomic

data_processing:
Reads were aligned using bowtie2 to hg38 genome
Macs2 was utilized for peak calling on the bam files
Homer was utilized for annotation and motif enrichment
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: adipose

extract_protocol:
H3K27ac CUT & RUN experiment was similarly performed in hAPC following manufacturer’s protocol (86652, Cell Signaling). DNA bound by H3K27Ac (Active Motif) or IgG (Millipore) was collected.
Libraries were prepared and sent for next-generation sequencing according to manufacturer’s specifications (Novogene)

value: adipose

value: adipocyte precursor cells


title: Heart, 5mg-kg LPS, m6, d0.5

description:
HE_d0.5_6
Heart_cpm_counts.txt

value: 12 hours

value: 5mg-kg LPS


title: Heart, 5mg-kg LPS, m7, d0.5

description:
HE_d0.5_7
Heart_cpm_counts.txt

value: Heart


title: F1.AP2.CO.a4

description:
F1.AP2.CO.a4
RCB161BCO


title: Heart, 5mg-kg LPS, m5, d0.5

description:
HE_d0.5_5
Heart_cpm_counts.txt


title: Seeds, aba2-1, 26d+ after pollination, Batch B, rep1


title: Heart, CTRL, m4, d0.5

description:
HE_d0.5_4
Heart_cpm_counts.txt

value: PBS


title: IRF2BP2 Overexpression, Replicate 1

data_processing:
The raw paired-end Fastq files were trimmed using the tool TrimGalore (version 0.6.5) with default parameters and paired option enabled.
The trimmed files were then aligned to the GRCh38 (version 104) genome using kallisto (version 0.46.1) with the default parameters of the kallisto quant command for paired-end data.
Kallisto output files were read into R (version 4.3.0) and differentially expressed genes were generated by EdgeR (version 4.0.2)
Assembly: hg38
Supplementary files format and content: Raw counts in a comma-separated file for GFP and IRF1 samples
Supplementary files format and content: Raw counts in a comma-separated file for ctrl and IRF2BP2KD samples

extract_protocol:
Tissue RNA was harvested using Trizol (Invitrogen) according to the manufacturer’s protocol.
Extracted cellular total RNA samples were sequenced by NovaSeq 6000 PE150 (Novogene)

value: primary adipocyte

value: IRF2BP2 Overexpression


title: F1.K.SIP.b3

description:
F1.K.SIP.b3
RZP71ISIP

value: Small Intestine

value: K


title: Seeds, aba2-1, 26d+ after pollination, Batch B, rep2

value: Seed

value: B


title: H3K27ac, replicate 1


title: GFP Overexpression, Replicate 2

value: GFP Overexpression


title: Heart, CTRL, m3, d0.5

description:
HE_d0.5_3
Heart_cpm_counts.txt


title: Seeds, dog1-4, 26d+ after pollination, Batch B, rep3

value: dry-stage


title: F1.K.CO.b3

description:
F1.K.CO.b3
RZP71ICO

value: Colon

value: In Vitro organoids


title: Heart, CTRL, m2, d0.5

description:
HE_d0.5_2
Heart_cpm_counts.txt


title: Seeds, dog1-4, 26d+ after pollination, Batch B, rep2

value: knock-out


title: Seeds, dog1-4, 26d+ after pollination, Batch B, rep1


title: F1.K.SIP.a3

description:
F1.K.SIP.a3
RZP71CSIP


title: Seeds, dog1-4, 24d after pollination, Batch B, rep2


title: F1.A.SIP.a3

description:
F1.A.SIP.a3
ROE124BSIP

value: A


title: IRF2BP2 Knockout, Replicate 1

value: adipose

value: IRF2BP2 Knockout


title: Lung, TNFKO + 5mg-kg LPS, m11, d0.5

description:
LU_d0.5_11
Lung_cpm_counts.txt

source_name: Lung

value: Lung

value: 12 hours

value: 5mg-kg LPS


title: IRF2BP2 Overexpression, Replicate 2

value: primary adipocyte


title: GFP Overexpression, Replicate 1


title: F1.K.CO.a3

description:
F1.K.CO.a3
RZP71CCO


title: Lung, TNFKO + 5mg-kg LPS, m10, d0.5

description:
LU_d0.5_10
Lung_cpm_counts.txt


title: Seeds, dog1-4, 24d after pollination, Batch B, rep1


title: F1.AK.SIP.a3

description:
F1.AK.SIP.a3
ROE124ASIP

value: AK


title: Seeds, dog1-4, 24d after pollination, Batch B, rep3


title: F1.A.CO.a3

description:
F1.A.CO.a3
ROE124BCO


title: Heart, CTRL, m1, d0.5

description:
HE_d0.5_1
Heart_cpm_counts.txt

value: Heart

value: PBS


title: IRF2BP2 Knockout, Replicate 2


title: Control, Replicate 2

value: WT


title: Seeds, dog1-4, 22d after pollination, Batch B, rep3

value: Seed

value: B


title: Control, Replicate 1


title: Lung, 5mg-kg LPS, m8, d0.5

description:
LU_d0.5_8
Lung_cpm_counts.txt


title: StitchR 3.0 GFP Nt-GFP + Ct-GFP Biological Replicate 2

city: Rochester

first: Tyler

last: Stahl

address: 601 Elmwood Ave

institute: University of Rochester Medical Center School of Medicine and Dentistry

data_processing:
Data Formatting bcltofastq-2.19.1
Data Cleaning fastp 0.23.1, parameters: --length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y –r
Genome Alignment bowtie2 2.4.4, parameters: -k 2
Deeptools BamCoverage, parameters:  -bs 1  --normalizeUsing CPM
Assembly: Custom GFP Reference
Supplementary files format and content: bigwigs

extract_protocol:
The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
TruSeq Stranded Total Sample Preparation Kit (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, ribosomal-depletion was performed on 200ng total RNA with biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads, followed by RNA fragmentation. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis using dUTP incorporation for strand marking. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA and amplified with PCR primers specific to the adaptor sequences to generate cDNA amplicons of approximately 200-500bp in size. The amplified libraries were sequenced using the NovaSeq 6000 (Illumina, San Diego, CA).


title: StitchR 3.0 GFP Nt-GFP + Ct-GFP Biological Replicate 1


title: Seeds, dog1-4, 22d after pollination, Batch B, rep1


title: Lung, TNFKO + 5mg-kg LPS, m9, d0.5

description:
LU_d0.5_9
Lung_cpm_counts.txt


title: Seeds, dog1-4, 22d after pollination, Batch B, rep2


title: Lung, TNFKO + 5mg-kg LPS, m12, d0.5

description:
LU_d0.5_12
Lung_cpm_counts.txt


title: F1.AK.SIP.b3

description:
F1.AK.SIP.b3
ROE123ESIP

value: Small Intestine


title: Seeds, dog1-4, 20d after pollination, Batch B, rep3


title: F1.AK.CO.b3

description:
F1.AK.CO.b3
ROE123ECO

value: Colon


title: Healthy donor 3 DCs, after CCL21-transduction

city: Los Angeles

first: Linh

middle: My

last: Tran

state: California

department: Medicine - Pulmonary & Critical Care

institute: University of Los Angeles

description: 10X Genomics Chromium™ Single Cell 3’ v3.1 Dual Index

library_source: transcriptomic single cell

data_processing:
The demultplexing, barcoded processing, and gene count were made using the CellRanger 6.0
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: PBMCs

growth_protocol: PBMCs were plated in GMP DC Media (CellGenix) at a concentration of 12.5-15 x 106 cells/mL (250-300 x 106 cells per T175 flask) and allowed to adhere by incubating for 1.5 hours in a 37C incubator supplemented with 5% CO2. The flasks were then gently washed twice with sterile normal saline to remove non-adherent cells. DC medium supplemented with 800 IU/mL granulocyte-macrophage colony-stimulating factor (GM-CSF; Sanofi) and 400 IU/mL interleukin-4 (IL-4; Miltenyi) was added to each flask.  Cells were incubated at 37C for 6-7 days with DC media freshly supplemented with GM-CSF and IL-4 added to the culture flasks on day 4. DCs were then harvested by firmly pipetting off loosely adherent cells. The resulting cell suspension was collected and resuspended in serum-free RPMI media.

extract_protocol:
Single cell suspensions obtained after treatment were utilized for single cell RNA library construction.
Library was performed according to the manufacter’s instructions (Chromium Next Gem Single Cell 3’ v3 protocol, 10x Genomics) to capture a target of 10,000 cells per sample

treatment_protocol: AdCCL21 vector was added at multiplicity of infection (MOI) of 100:1 (virus:total cells) and cells aliquoted in 1.5 mL microcentrifuge tubes for centrifugation at 2000 x g at room temperature for 2 hours. The supernatant was discarded, and cells were washed two times in sterile saline.

value: PBMCs

value: monocyte-derived DCs

value: AdCCL21 vector

value: male


title: Healthy donor 2 DCs, after CCL21-transduction

value: female


title: F1.A.CO.b3

description:
F1.A.CO.b3
ROE113ACO

value: In Vitro organoids

value: A


title: Lung, 5mg-kg LPS, m5, d0.5

description:
LU_d0.5_5
Lung_cpm_counts.txt

value: Lung

value: 12 hours

value: 5mg-kg LPS


title: Seeds, dog1-4, 20d after pollination, Batch B, rep1

value: knock-out


title: Healthy donor 1 DCs, after CCL21-transduction


title: F1.AP.SIP.b3

description:
F1.AP.SIP.b3
RCB241ASIP

value: AP


title: F1.AK.CO.a3

description:
F1.AK.CO.a3
ROE124ACO

value: AK


title: F1.AP.CO.b3

description:
F1.AP.CO.b3
RCB241ACO


title: Lung, CTRL, m4, d0.5

description:
LU_d0.5_4
Lung_cpm_counts.txt

value: PBS


title: Patient 3 DCs, after CCL21-transduction

description: 10X Genomics Chromium™ Single Cell 3’ v3 Single Index


title: Seeds, abi3-12, 26d+ after pollination, Batch B, rep3

value: Seed

value: dry-stage

value: B


title: Lung, CTRL, m3, d0.5

description:
LU_d0.5_3
Lung_cpm_counts.txt


title: Patient 3 DCs, before CCL21-transduction

value: PBMCs

value: Untreated


title: Seeds, abi3-12, 26d+ after pollination, Batch B, rep2


title: Lung, 5mg-kg LPS, m7, d0.5

description:
LU_d0.5_7
Lung_cpm_counts.txt


title: F1.AP.SIP.a3

description:
F1.AP.SIP.a3
RCB231BSIP

value: Small Intestine


title: Lung, CTRL, m1, d0.5

description:
LU_d0.5_1
Lung_cpm_counts.txt


title: F1.A.SIP.b3

description:
F1.A.SIP.b3
ROE113ASIP


title: F1.AKP.SIP.b3

description:
F1.AKP.SIP.b3
RCB221ESIP

value: AKP


title: Patient 2 DCs, after CCL21-transduction

value: monocyte-derived DCs

value: AdCCL21 vector

value: female


title: Lung, CTRL, m2, d0.5

description:
LU_d0.5_2
Lung_cpm_counts.txt

value: Lung


title: Lung, 5mg-kg LPS, m6, d0.5

description:
LU_d0.5_6
Lung_cpm_counts.txt

value: 12 hours


title: F1.AKP.SIP.a3

description:
F1.AKP.SIP.a3
RCB164ASIP

value: In Vitro organoids


title: Seeds, abi3-12, 26d+ after pollination, Batch B, rep1

value: knock-out


title: Kidney, TNFKO + 5mg-kg LPS, m12, d0.5

description:
KI_d0.5_12
Kidney_cpm_counts.txt

value: Kidney

value: 5mg-kg LPS


title: Seeds, abi3-12, 24d after pollination, Batch B, rep3


title: Seeds, abi3-12, 24d after pollination, Batch B, rep2


title: Seeds, dog1-4, 20d after pollination, Batch B, rep2


title: Kidney, TNFKO + 5mg-kg LPS, m11, d0.5

description:
KI_d0.5_11
Kidney_cpm_counts.txt


title: Kidney, TNFKO + 5mg-kg LPS, m10, d0.5

description:
KI_d0.5_10
Kidney_cpm_counts.txt


title: Patient 2 DCs, before CCL21-transduction


title: Patient 1 DCs, after CCL21-transduction

value: male


title: Seeds, abi3-12, 24d after pollination, Batch B, rep1

value: Seed


title: Seeds, abi3-12, 22d after pollination, Batch B, rep3


title: F1.AKP.CO.a3

description:
F1.AKP.CO.a3
RCB164ACO

value: Colon


title: Patient 1 DCs, before CCL21-transduction


title: IP_CUR_3

city: Fuzhou

first: Jiaxin

last: Wen

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: mm10
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

source_name: placenta

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: placenta

value: trophoblast

value: Wild type

value: treat with curdione

tag: rip antibody


title: F1.AP.CO.a3

description:
F1.AP.CO.a3
RCB231BCO

value: AP


title: Kidney, 5mg-kg LPS, m8, d0.5

description:
KI_d0.5_8
Kidney_cpm_counts.txt


title: F1.AP2.CO.b3

description:
F1.AP2.CO.b3
RCB162DCO


title: IP_CUR_2


title: Seeds, abi3-12, 22d after pollination, Batch B, rep2

value: B


title: IP_CUR_1


title: F1.AP2.SIP.b3

description:
F1.AP2.SIP.b3
RCB162DSIP

value: Small Intestine


title: Seeds, abi3-12, 22d after pollination, Batch B, rep1


title: F1.AP2.SIP.a3

description:
F1.AP2.SIP.a3
RCB161BSIP


title: Kidney, 5mg-kg LPS, m7, d0.5

description:
KI_d0.5_7
Kidney_cpm_counts.txt


title: Kidney, TNFKO + 5mg-kg LPS, m9, d0.5

description:
KI_d0.5_9
Kidney_cpm_counts.txt


title: Seeds, abi3-12, 20d after pollination, Batch B, rep3


title: Kidney, 5mg-kg LPS, m6, d0.5

description:
KI_d0.5_6
Kidney_cpm_counts.txt


title: IP_Con_2

value: Control


title: Seeds, abi3-12, 20d after pollination, Batch B, rep2


title: F1.K.SIP.b2

description:
F1.K.SIP.b2
RZP71ISIP

value: K


title: Kidney, 5mg-kg LPS, m5, d0.5

description:
KI_d0.5_5
Kidney_cpm_counts.txt

value: 12 hours


title: F1.AP2.CO.a3

description:
F1.AP2.CO.a3
RCB161BCO

value: In Vitro organoids


title: F1.K.CO.b2

description:
F1.K.CO.b2
RZP71ICO


title: IP_Con_1


title: Seeds, abi3-12, 20d after pollination, Batch B, rep1

value: knock-out


title: Seeds, abi3-12, 18d after pollination, Batch B, rep2


title: Input_CUR_3

value: none (input)


title: F1.K.SIP.a2

description:
F1.K.SIP.a2
RZP71CSIP


title: Seeds, abi3-12, 18d after pollination, Batch B, rep1


title: Input_CUR_2


title: Kidney, CTRL, m4, d0.5

description:
KI_d0.5_4
Kidney_cpm_counts.txt

value: Kidney

value: PBS


title: Kidney, CTRL, m3, d0.5

description:
KI_d0.5_3
Kidney_cpm_counts.txt


title: Seeds, abi3-6, 26d+ after pollination, Batch B, rep3

value: Seed

value: dry-stage


title: Input_Con_3

value: placenta


title: F1.K.CO.a2

description:
F1.K.CO.a2
RZP71CCO

value: Colon


title: Kidney, CTRL, m2, d0.5

description:
KI_d0.5_2
Kidney_cpm_counts.txt


title: F1.A.CO.a2

description:
F1.A.CO.a2
ROE124BCO

value: A


title: F1.A.SIP.a2

description:
F1.A.SIP.a2
ROE124BSIP


title: Thymus, TNFKO + 5mg-kg LPS, m12, d0.5

description:
TH_d0.5_12
Thymus_cpm_counts.txt

source_name: Thymus

value: Thymus

value: 5mg-kg LPS


title: Input_CUR_1

value: trophoblast

value: Wild type

value: treat with curdione


title: Kidney, CTRL, m1, d0.5

description:
KI_d0.5_1
Kidney_cpm_counts.txt


title: Seeds, abi3-6, 26d+ after pollination, Batch B, rep2

value: B


title: Input_Con_2

value: Control


title: Seeds, abi3-6, 26d+ after pollination, Batch B, rep1


title: IP_Con_3


title: Thymus, TNFKO + 5mg-kg LPS, m11, d0.5

description:
TH_d0.5_11
Thymus_cpm_counts.txt

value: 12 hours


title: F1.A.CO.b2

description:
F1.A.CO.b2
ROE113ACO

value: In Vitro organoids


title: F1.A.SIP.b2

description:
F1.A.SIP.b2
ROE113ASIP

value: Small Intestine


title: Seeds, abi3-6, 24d after pollination, Batch B, rep3

value: knock-out


title: Seeds, abi3-6, 24d after pollination, Batch B, rep2


title: Group 3 Medulloblastoma - UPN1433

city: Denver

first: Pluto

last: Bio

state: CO

address: 3575 Ringsby Ct Suite 414

institute: Pluto Bio

description: Primary patient tumor

data_processing:
Arima-HiC libraries were sequenced via an IlluminaÒ sequencer in “paired-end” mode with a 2x150bp read length.
The resulting Arima-HiC data was analyzed using Juicer v1.6
No sample-to-sample normalization was performed.
The Juicer pipeline (version 1.6) was run on all samples using default parameters. The reads were aligned to the GRCh37 reference genome. The pipeline was run in a Linux environment using 24 CPU cores and 96Gb of RAM.
Chromatin loop calls were identified using HiCCUPS (Hi-C Computational Unbiased Peak Search) algorithm with KR (Knight-Ruiz) normalization using 12 GPU cores and 48Gb of RAM.
TADs (Topologically Associating Domains) were identified using Arrowhead algorithm at multiple resolutions using 12 GPU cores and 48Gb of RAM.
Assembly: GRCh37
Supplementary files format and content: Hi-C contact matrix file for each sample, zipped

source_name: Medulloblastoma

extract_protocol:
Primary patient tumor tissue was formalin fixed and paraffin embedded according to clinical histopathology standard. Hi-C data was generated using the Arima-HiC kit, according to the manufacturer protocols. Briefly, whole genome DNA was extracted from FFPE sample and crosslinked in 2% formaldehyde. Crosslinked chromatin was digested using restriction enzyme mix for 30 min at 37C followed by 20 min at 62C.  5'-overhangs were then filled with biotinylated nucleotide (buffer/enzyme B 45 min at 25C) before the DNA fragments were  proximally ligated using buffer/enzyme C mix at 15 min at 25C. Purified ligated DNA was fragmented using Biorupter Plus (Diagenode) for goal size 400-600 bp. Biotin enrichment is then performed prior to adapter ligation.
Libraries were prepared using the Illumina TruSeq adapter kit according to manufacturer specifications.

value: Medulloblastoma


title: F1.APN.CO.b2.OE

description:
F1.APN.CO.b2.OE
RKW51CCOOE

value: APN


title: Thymus, TNFKO + 5mg-kg LPS, m9, d0.5

description:
TH_d0.5_9
Thymus_cpm_counts.txt


title: Thymus, TNFKO + 5mg-kg LPS, m10, d0.5

description:
TH_d0.5_10
Thymus_cpm_counts.txt


title: Group 3 Medulloblastoma - UPN1355

description: Primary patient tumor


title: F1.APN.CO.b2

description:
F1.APN.CO.b2
RKW51CO


title: Thymus, 5mg-kg LPS, m8, d0.5

description:
TH_d0.5_8
Thymus_cpm_counts.txt


title: D458 cells, IgG, replicate 2, ChIP

description: genome build/assembly: GRCh37

data_processing:
FASTQ files were processed using the nf-core CUT&RUN pipeline (v3.0.0).
Adapter sequences were removed with Cutadapt.
Reads were aligned with Bowtie2 to either GRCh38 or GRCh37 and duplicates were removed for only control samples using picard.
Peaks were called with seacr (normalization mode: CPM), and were defined as regions where at least one of the target samples significantly exceeds its matched IgG control for a given genomic region.
Consensus peaks were merged across all samples using BEDTools and annotated to the nearest gene transcriptional start site using HOMER.
Peak counts were generated using featureCounts.
Supplementary files format and content: comma-delimited text files includes raw consensus peak counts for each Sample
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Myc-amplified medulloblastoma

growth_protocol: D458 cell lines were cultured in DMEM supplemented with 10% FBS (Sigma-Aldrich), 1 mM sodium pyruvate (GIBCO), 1 × penicillin/streptomycin solution (Cellgro), and with 1 × L-glutamine (Cellgro).

extract_protocol:
Beads were prepared using 10 ul/sample of CUTANA Concavalin A Conjugated Paramagnetic Beads (EpiCypher, SKU:21-1401). Beads were transferred to a 1.5 ml tube and placed in a magnetic separation rack. Supernatant was removed and beads were washed 2 times with 100 ul/sample of cold Bead Activation Buffer (20 mM HEPES pH7.9, 10 mM Kcl, 1 mM CaCl2, 1 mM MnCl2). Beads were then resuspended in 10 ul/sample of cold Bead Activation Buffer and aliquot 10 ul/sample of activated bead slurry into 8-strip tube and kept on ice.  Cells were collected using 0.05% trypsin and washed with 100 ul/sample of Wash Buffer (20 mM HEPES pH7.5, 150 mM NaCl, 0.5 mM Spermidine, 1x Roche cOmplete EDTA-free Protease Inhibitor (1187358001)) at room temperature and centrifuged at RT, 600 g for 3min, for a total of two washes. Cells were resuspended in 100 ul/sample RT Wash Buffer and then aliquot of 100ul washed cells to each 8-strip tube containing 10 ul of activated beads and mixed by pipetting. Cells were incubated with bead slurry for 10 min at RT. Tube strip was placed on a magnetic separation rack until slurry clears and the supernatant was removed. 50 ul of cold Antibody Buffer was added to each sample and mixed by pipetting; 1 ul of antibody, IgG (Rabbit IgG Negative Control, EpiCypher, 13-0042K), PolI (Rpb1 CTD (4H8), Cell Signaling, #2629S), pPolI (pRpb1 CTD (S2), Cell Signaling, #13499S), Brd4 (Brd4, EpiCypher, 13-2003), ENL (MLLT1/ENL (D9M4B);Cell Signaling, #14893) was added to each sample, mixed and incubated on a nutator overnight at 4oC. Tube was placed on a magnet until slurry clears and the supernatant was removed. While beads were on magnet, 250 ul of cold Digitonin Buffer was added directly onto beads of each sample and then pipet to remove supernatant, for a total of 2-washes. 50 ul of cold Digitonin Buffer was added to each sample and mixed. 2.5 ul of CUTANA pAG-MNase (20Xstock) was added to each sample, mixed and incubated for 10min at RT. Tube was placed on a magnet and supernatant was removed. Beads were washed 2 times with cold Digitonin Buffer. Supernatant and 50 ul of cold Digitonin Buffer was added to each sample and mixed. Tubes were placed on ice and 1 ul of 100 mM CaCl2 was added to each sample, mixed, and then incubated on nutator 2 hrs at 4oC. 33 ul/sample of Stop buffer, to stop the MNase activity by chelating Ca++ ions, containing 0.5 ng/sample of E.coli Spike-in DNA, was added to the samples, mixed by pipetting  and incubated for 10 min at 37oC in a thermocycler. Tubes were placed on a magnet stand until slurry cleared and the supernatant was transferred to a 1.5ml tube. Finally, the DNA was purified using CUTANA DNA Purification Kit (EpiCypher, 14-0050) according to the manufactory instructions and 1ul of DNA was used to be quantified using Qubit and library preparation.
The NEBNext Ultra DNA Library Prep Kit for Illumina (NEB #E7645S) with Dual Index Primers (NEB #E7600) were used to library preparation for ChiPseq and Cut and Run samples sequencing.   For the NEBNext end prep, 1x TE was added to the DNA to get final volume of 50 ul and mixed with 3ul of NEBNext Ultra II End Prep Enzyme Mix and 7ul of NEBNext Ultra II End Prep Reaction Buffer, placed in thermocycler with heated lid set to 75oC and run the program 30 minutes at 20oC, 60 minutes at 50oC and hold at 4oC. The adaptor ligation reaction was performed with 60u l of Prep Reaction Mixture, 2.5ul of NEBNext Adaptor for Illumina diluted following the manufacture recommendations, 30 ul of NEBNext Ultra Ligation Master Mix and 1ul of NEBNext Ligation Enhancer, incubated at 20oC for 15 min with heated lid off. 3 ul of USER Enzyme was added to the reaction and incubated at 37oC for 15 min with heated led set to 47oC. For the cleanup of the adaptor-ligated DNA without size selection, 1.1x of AMPure XP Beads were added to the Adaptor Ligation reaction and samples were incubated for 5min at room temperature. Tubes were placed on a magnetic stand to separate beads from supernatant, after 5 min, supernatant was removed, and beads were washed 2 times with 200ul of 80% freshy prepared ethanol. Beads were air dried for up 5 min while tubes were on magnet with lid open. DNA was eluted from the beads by adding 17 ul of 0.1XTE buffer.  For the PCR enrichment of adaptor-ligated DNA step, to 15 ul of the Adaptor Ligated DNA fragments was added 25ul of NEBNext Ultra Q5 Master Mix, 5 ul of Index primer i7 and 5ul Universal PCR Primer i5, and PCR amplification was performed following the cycling conditions: 98oC for 45s, 98oC 15s and 60oC 10s for 16 cycles, 72oC for 1 min and hold at 4oC. Followed by a Clean Up of the PCR reaction using AMPure XP Beads.  The DNA was quantified using Qubit and the quality and size of libraries were checked with the Bioanalyzer and sent for sequencing at the Genomics Shared Resource (sequencing core) of CU Anschutz Medical Campus.

treatment_protocol: Cells were either treated with 200 nM TG02 or DMSO control and collected at 24 hours, or were collected without additional treatment.

value: Myc-amplified medulloblastoma

tag: cut&run antibody

value: IgG Negative Control; EpiCypher Cat. #13-0042

tag: dosage

tag: timepoint


title: Seeds, abi3-6, 22d after pollination, Batch A, rep2

source_name: Seed

value: Seed

tag: batch


title: Thymus, 5mg-kg LPS, m6, d0.5

description:
TH_d0.5_6
Thymus_cpm_counts.txt

tag: mouse id

tag: time point


title: D458 cells, H3K4me1, replicate 2, ChIP

description: genome build/assembly: GRCh37

tag: cell type

value: H3K4me1; EpiCypher Cat. #13-0057

tag: treatment


title: D458 cells, IgG, replicate 1, ChIP

description: genome build/assembly: GRCh37


title: F1.AKPN.SIP.a2

description:
F1.AKPN.SIP.a2
RKW101BSIP

data_processing:
The quality of raw data was assessed using FastQC (v.0.11.9) and MultiQC (v.1.9) prior to processing the data.
The first 12 bases as well as low-quality bases (Phred score < 20) were trimmed from each sequence using Cutadapt (v1.18).
STAR (v.2.7.4.a) was applied to align sequences to the mouse genome (GRCm38) and to determine counts per gene.
After log2 transformation and quantile normalization, data were visualized using PCA plots to assess the quality of data after alignment and possible batch effects.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes normalized values for each Sample

extract_protocol:
RNA was isolated using Bioke Nucleospin RNA isolation kit (Bioke) according to the manufacturer’s protocol. DNA degradation was performed using Bioke RNase-Free DNase. We assessed the quality of our RNA samples using Agelent 2100 Bioanalyzer (Agilent Technologies) and only high quality RNA samples were selected based on RIN value.
The organoid RNAseq libraries were prepared using KAPA mRNA HyperPrep (Roche) following the manufacturer’s protocol. They were barcoded, quantified using the Qubit DNA HS kit from Thermofisher and Tapestation 4200 from Agilent, pooled and multiplex sequencing was performed on the Illumina Novaseq6000 platform.

value: AKPN


title: Seeds, abi3-6, 22d after pollination, Batch A, rep1

tag: accession

tag: genetic modification

value: A


title: F1.KPN.SIP.a2

description:
F1.KPN.SIP.a2
RKA281GSIP

value: KPN


title: Seeds, abi3-6, 20d after pollination, Batch A, rep2

tag: maturation stage

tag: experimental round


title: Thymus, 5mg-kg LPS, m5, d0.5

description:
TH_d0.5_5
Thymus_cpm_counts.txt

data_processing:
Sequencing read files were processed to generate UMI (unique molecular identifier) count matrices using the python toolkit from the bcbio-nextgen project version 1.1.5 (https://bcbio-nextgen.readthedocs.io/en/latest/). In brief, reads were aligned to the mouse mm10 transcriptome with RapMap (https://github.com/COMBINE-lab/RapMap). Quality control metrics were compiled with a combination of FastQC (http:bioinformatics.babraham.ac.uk/projects/fastqc/), Qualimap, MultiQC (https://github.com/ewels/MultiQC). Samples were demultiplexed using barcodes stored in Read 1 (first 6 bases) and raw UMI count matrices were computed using UMIs stored in Read 1 (bases 7 to 16) (https://github.com/vals/umis). Differential expression (DE) analysis was done using custom scripts in R (http://www.R-project.org). Raw count matrices were filtered to keep genes with at least 20 counts per million (cpm) or 5 UMIs in 2 samples and normalized across samples using the calcNormFactor function in edgeR (https://github.com/StoreyLab/edge).
Assembly: mm10
Supplementary files format and content: All count matrices are in tsv format. The first seven columns contain sample metadata (Organ, Treatment, Mouse ID, Mouse genotype, etc.). The remaining columns consist of normalized cpm counts. Matrices include all replicates for the organ.

extract_protocol:
Whole-tissue RNA extraction was performed as described previously (Surya et al., 2020). Briefly, tissues stored in RNA-preserving solution were thawed and transferred to 2 mL tubes containing 700-1500 µL (depending on tissue) of PureZOL (Bio-Rad, 7326890) or homemade Trizol-like solution (38% phenol, 0.8 M guanidine thiocyanate, 0.4 M ammonium thiocyanate, 0.1 M sodium acetate, 5% glycerol). Tissues were lysed by adding 2.8-mm ceramic beads (OMNI International, 19-646) and running 1-3 cycles of 5-45 s at 3500 rpm on the PowerLyzer 24 (QIAGEN). For liver, brain, and small intestine samples, tissues were lysed with 3-5 mL using M tubes (Miltenyi biotec, 130-096-335) and running 1-4 cycles of the RNA_02.01 program on the gentleMACS Octo Dissociator (Miltenyi biotec). Next, lysates were processed in deep 96-well plates (USA Scientific 1896-2000) by adding chloroform for phase separation by centrifugation, followed by precipitation of total RNA in the aqueous phase using magnetic beads coated with silane (Dynabeads MyOne Silane; TermoFisher Scientific 37002D), buffer RLT (QIAGEN 79216), and ethanol. Genomic DNA contamination was removed by on-bead DNase I (ThermoFisher Scientific AM2239) treatment at 37 °C for 20 min. After washing steps with 80% ethanol, RNA was eluted from beads. This RNA extraction protocol was performed on the Bravo Automated Liquid Handling Platform (Agilent). Sample concentrations were measured using a Nanodrop One (Termo Scientific). RNA quality was confirmed using a Tapestation 4200 (Agilent Technologies). For each tissue sample, full-length cDNA was synthesized in 20 µl final reaction volume containing the following: (1) 10 µl of 10 ng/µl RNA; (2) 1 µl containing 2 pmoles of a custom RT primer biotinylated in 5’ and containing sequences from 5’ to 3’ for the Illumina read 1 primer, a 6-bp sample barcode (up to 384), a 10-bp unique molecular identifier (UMI), and an anchored oligo(dT)30 for priming; and (3) 9 µl of RT mix containing 4 µl of 5X RT buffer, 1 µl of 10 mM dNTPs, 2 pmoles of template switching oligo (TSO), and 0.25 µl of Maxima H Minus Reverse Trascriptase (Thermo Scientific, EP0753). First, barcoded RT primers were added to RNA, which were then denatured at 72°C for 1 min and snap cooled on ice. Second, the RT mix was added, and plates were incubated at 42°C for 120 min. For each library, double stranded cDNA from up to 384 samples were pooled using DNA Clean & Concentrator-5 columns (Zymo Research, D4013), and residual RT primers were removed using exonuclease I (New England Biolabs, M0293).
Full-length cDNAs were amplified with 5 to 8 cycles of single-primer PCR using the Advantage 2 PCR Kit (clontech 639206) and cleaned up using SPRIselect magnetic beads (Beckman Coulter B23318). cDNA was quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific 32851) and 50 ng of cDNA per pool of samples was tagmented using the Tagment DNA Enzyme I (Illumina 20034197) and amplified using the NEBNext Ultra II Q5 Master Mix (NEW ENGLAND BioLabs M0544L). Libraries were gel purified using 2% E-Gel EX Agarose Gels (ThermoFisher Scientific G402002), quantified with a Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Scientific Q32851) and a Tapestation 4200 (Agilent Technologies), and sequenced on the NextSeq 550 platform (Illumina).

value: Thymus

value: 5mg-kg LPS


title: F1.KPN.SIP.b2

description:
F1.KPN.SIP.b2
RKA205ASIP


title: D458 cells, H3K4me1, replicate 1, ChIP

description: genome build/assembly: GRCh37

tag: cell line


title: Input_Con_1

value: placenta

value: trophoblast

value: Wild type

value: none (input)


title: Thymus, CTRL, m4, d0.5

description:
TH_d0.5_4
Thymus_cpm_counts.txt

value: 12 hours

value: PBS


title: Seeds, abi3-6, 20d after pollination, Batch A, rep1

value: knock-out

tag: replicate


title: Seeds, abi3-6, 24d after pollination, Batch B, rep1

tag: tissue

value: B


title: D458 cells, Myc, TG02, replicate 2, ChIP

description: genome build/assembly: GRCh38

value: Myc-amplified medulloblastoma

value: Myc; Cell Signaling #13987S

value: 24 hours


title: Thymus, CTRL, m3, d0.5

description:
TH_d0.5_3
Thymus_cpm_counts.txt

tag: genotype


title: Seeds, abi3-6, 18d after pollination, Batch A, rep1

value: Seed


title: F1.AP.SIP.b2

description:
F1.AP.SIP.b2
RCB241ASIP

value: Small Intestine

value: In Vitro organoids

value: AP


title: F1.AP.CO.b2

description:
F1.AP.CO.b2
RCB241ACO

value: Colon


title: Thymus, CTRL, m2, d0.5

description:
TH_d0.5_2
Thymus_cpm_counts.txt

value: Thymus


title: Seeds, abi3-6, 16d after pollination, Batch A, rep2

value: A


title: D458 cells, Myc, TG02, replicate 1, ChIP

description: genome build/assembly: GRCh38


title: D458 cells, IgG, TG02, replicate 2, ChIP

description: genome build/assembly: GRCh38

value: IgG Negative Control; EpiCypher Cat. #13-0042


title: F1.AP.SIP.a2

description:
F1.AP.SIP.a2
RCB231BSIP


title: Thymus, CTRL, m1, d0.5

description:
TH_d0.5_1
Thymus_cpm_counts.txt


title: F1.APN.SIP.a2

description:
F1.APN.SIP.a2
RKW51ASIP

value: APN


title: Thymus, 5mg-kg LPS, m7, d0.5

description:
TH_d0.5_7
Thymus_cpm_counts.txt

value: 5mg-kg LPS


title: D458 cells, IgG, TG02, replicate 1, ChIP

description: genome build/assembly: GRCh38


title: F1.K.SIP.b1

description:
F1.K.SIP.b1
RZP71ISIP

value: K


title: Seeds, Col-0, 26d+ after pollination, Batch B, rep3

value: wild-type

value: dry-stage


title: D458 cells, Myc, DMSO, replicate 2, ChIP

description: genome build/assembly: GRCh38

value: DMSO


title: Seeds, Col-0, 26d+ after pollination, Batch B, rep2

value: B


title: D458 cells, Myc, DMSO, replicate 1, ChIP

description: genome build/assembly: GRCh38

value: Myc-amplified medulloblastoma

value: Myc; Cell Signaling #13987S


title: F1.K.CO.b1

description:
F1.K.CO.b1
RZP71ICO


title: Seeds, abi3-6, 18d after pollination, Batch A, rep2

value: Seed

value: knock-out


title: Colon, TNFKO + 5mg-kg LPS, m10, d0.5

description:
CO_d0.5_10
Colon_cpm_counts.txt

value: 12 hours


title: Seeds, Col-0, 26d+ after pollination, Batch B, rep1


title: F1.K.SIP.a1

description:
F1.K.SIP.a1
RZP71CSIP

value: Small Intestine

value: In Vitro organoids


title: D458 cells, IgG, DMSO, replicate 2, ChIP

description: genome build/assembly: GRCh38

value: 24 hours


title: Colon, TNFKO + 5mg-kg LPS, m9, d0.5

description:
CO_d0.5_9
Colon_cpm_counts.txt

value: Colon


title: D458 cells, IgG, DMSO, replicate 1, ChIP

description: genome build/assembly: GRCh38

value: IgG Negative Control; EpiCypher Cat. #13-0042


title: Seeds, abi3-6, 16d after pollination, Batch A, rep1

value: A


title: Seeds, Col-0, 24d after pollination, Batch B, rep2


title: Colon, 5mg-kg LPS, m7, d0.5

description:
CO_d0.5_7
Colon_cpm_counts.txt

value: 5mg-kg LPS


title: F1.A.SIP.a1

description:
F1.A.SIP.a1
ROE124BSIP


title: Colon, 5mg-kg LPS, m6, d0.5

description:
CO_d0.5_6
Colon_cpm_counts.txt


title: Seeds, Col-0, 22d after pollination, Batch B, rep3


title: F1.A.CO.a1

description:
F1.A.CO.a1
ROE124BCO


title: F1.AK.SIP.a1

description:
F1.AK.SIP.a1
ROE124ASIP

value: AK


title: Seeds, Col-0, 24d after pollination, Batch B, rep1

value: wild-type


title: F1.AP.CO.a2

description:
F1.AP.CO.a2
RCB231BCO

value: AP


title: Colon, TNFKO + 5mg-kg LPS, m12, d0.5

description:
CO_d0.5_12
Colon_cpm_counts.txt


title: Colon, 5mg-kg LPS, m5, d0.5

description:
CO_d0.5_5
Colon_cpm_counts.txt


title: Seeds, Col-0, 22d after pollination, Batch B, rep2


title: Colon, TNFKO + 5mg-kg LPS, m11, d0.5

description:
CO_d0.5_11
Colon_cpm_counts.txt


title: Colon, CTRL, m4, d0.5

description:
CO_d0.5_4
Colon_cpm_counts.txt

value: PBS


title: F1.AK.CO.a1

description:
F1.AK.CO.a1
ROE124ACO


title: Seeds, Col-0, 22d after pollination, Batch B, rep1

value: B


title: F1.AK.SIP.b1

description:
F1.AK.SIP.b1
ROE123ESIP


title: Colon, CTRL, m3, d0.5

description:
CO_d0.5_3
Colon_cpm_counts.txt


title: Seeds, Col-0, 20d after pollination, Batch B, rep3


title: F1.AK.CO.b1

description:
F1.AK.CO.b1
ROE123ECO


title: Seeds, Col-0, 24d after pollination, Batch B, rep3


title: Seeds, Col-0, 20d after pollination, Batch B, rep2


title: Colon, CTRL, m2, d0.5

description:
CO_d0.5_2
Colon_cpm_counts.txt


title: Colon, CTRL, m1, d0.5

description:
CO_d0.5_1
Colon_cpm_counts.txt


title: Colon, 5mg-kg LPS, m8, d0.5

description:
CO_d0.5_8
Colon_cpm_counts.txt


title: F1.A.SIP.b1

description:
F1.A.SIP.b1
ROE113ASIP


title: Seeds, Col-0, 20d after pollination, Batch B, rep1


title: F1.K.CO.a1

description:
F1.K.CO.a1
RZP71CCO

value: K


title: Spleen, TNFKO + 5mg-kg LPS, m12, d0.5

description:
SP_d0.5_12
Spleen_cpm_counts.txt

source_name: Spleen

value: Spleen


title: F1.A.CO.b1

description:
F1.A.CO.b1
ROE113ACO


title: Seeds, Col-0, 18d after pollination, Batch B, rep3

value: Seed


title: F1.APN.CO.b1.OE

description:
F1.APN.CO.b1.OE
RKW51CCOOE

value: APN


title: Spleen, TNFKO + 5mg-kg LPS, m11, d0.5

description:
SP_d0.5_11
Spleen_cpm_counts.txt

value: 12 hours


title: Spleen, TNFKO + 5mg-kg LPS, m10, d0.5

description:
SP_d0.5_10
Spleen_cpm_counts.txt


title: F1.APN.CO.b1

description:
F1.APN.CO.b1
RKW51CO


title: Spleen, TNFKO + 5mg-kg LPS, m9, d0.5

description:
SP_d0.5_9
Spleen_cpm_counts.txt


title: Seeds, Col-0, 18d after pollination, Batch B, rep1


title: F1.APN.SIP.a1

description:
F1.APN.SIP.a1
RKW51ASIP

value: Small Intestine


title: Seeds, Col-0, 18d after pollination, Batch B, rep2


title: Seeds, Col-0, 26d+ after pollination, Batch A, rep3

value: dry-stage


title: F1.AKPN.SIP.a1

description:
F1.AKPN.SIP.a1
RKW101BSIP

value: In Vitro organoids

value: AKPN


title: Seeds, Col-0, 26d+ after pollination, Batch A, rep2


title: F1.KPN.SIP.a1

description:
F1.KPN.SIP.a1
RKA281GSIP

value: KPN