title: MNase-ChIP_Pob3_yFR116wt_R1

description:
Biological replicate 1 of 2. Pob3 occupancy by MNase-ChIP-seq in WT cells. Pob3 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Pob3.
processed data file (two biological replicates combined):  MNaseChIP_Pob3_yFR116WT_CJ1-CJ2comb_20200319.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 cycles using KOD Hot Start DNA polymerase (Millipore, 71086-3) and cleaned up using 1X KAPA Pure Beads. Libraries were qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 13 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq


title: delta-rpoN_3

status: Public on Jul 26 2021

type: SRA

city: Bloomington

first: Julia

middle: C

last: van Kessel

state: IN

address: 1001 E 3rd Street

department: Biology

country: USA

institute: Indiana University

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for quality and adapters using Trimmomatic (v0.38 for all samples) with the following parameters: ILLUMINACLIP:adapters.fa:3:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:30
Reads were mapped to the genome using bowtie2 (v2.3.4.3).
Read counts for genes and 100 bp intergenic regions were determined with custom perl scripts
Genome_build: Vibrio campbellii strain DS40M4 genome, accessions: CP030788.1, CP030789.1 and CP030790.1
Supplementary_files_format_and_content: Text files containing read counts for annotated genes and 100 bp intergenic regions

molecule: total RNA

organism: Vibrio campbellii

source_name: Bacterial lysate

growth_protocol: Cells were grown at 30°C in LM media to an OD600 of 0.5

extract_protocol: Trizol Reagent followed by Dnase I treatment

tag: genotype

value: {delta}rpoN (BDP029)


title: delta-rpoN_2


title: DS40M4_1

value: WT (CAS107)


title: DS40M4_3


title: DS40M4_2


title: delta-rpoN_1


title: delta-fliAp_3

value: {delta}fliA (BDP046)


title: M1

status: Public on Jul 27 2021

city: Bodø

first: Ioannis

last: Konstantinidis

state: Nordland

address: Universitetsalléen 11

department: Faculty of Biosciences and Aquaculture

country: Norway

institute: Nord University

data_processing:
RNA-seq reads were decontaminated by BBDuk (v. 37.61) using the following parameters ktrim=r k=23 mink=11 hdist=1 tpe tbo qtrim=r trimq=30 minlen=23
Reads were aligned to the genome by HISAT2 (v. 2.1.0) using the core hisat2 function with default parameters
Reads were counted by feature Counts of the Subread package
Genome_build: GCA_001858045.3
Supplementary_files_format_and_content: A plain text file is provided with the feature counts per gene per sample

organism: Oreochromis niloticus

source_name: Fast muscle

extract_protocol:
Fast muscle was stored in -80 C. RNA was extracted after homogenizing the tissue within the DNA/RNA Shield using the Quick-RNA miniprep plus kit (Zymo Research) according to manufacturer's protocol and recommendations.
After extracting the total RNA as described above, rRNA depletion was performed using the Ribo-Zero Gold rRNA removal kit (Illumina) according to manufacturer's protocol
RNA libraries were prepared using the NEBNext Ultra II directional RNA library prep kit for Illumina a ccording to manufacturer's protocol

tag: gender

value: male

tag: replicates

value: replicate 1

tag: age

value: 5 months

tag: tissue

value: Fast (white) muscle


title: delta-flaM_3

value: {delta}flaM (BDP031)


title: delta-flaM_2


title: delta-flaK_3

value: {delta}flaK (BDP030)


title: delta-flaK_2


title: delta-fliAp_2


title: delta-flaM_1


title: MNase-input_Pob3_yFR116wt_R2

city: Montreal

first: Francois

last: Robert

state: QC

address: 110 av des Pins Ouest

country: Canada

institute: IRCM

description:
Biological replicate 2 of 2. Input signal of WT cells. This Input DNA was obtained from the same yeast extract used to perform Pob3 MNase-ChIP-seq.
processed data file (two biological replicates combined):  MNaseInput_Pob3_yFR116WT_CJ5-CJ6comb_20200319.bw

library_source: genomic

data_processing:
Paired-end reads from MNase-ChIP-seq data where aligned on the S. cerevisiae genome version sacCer3 using Bowtie2 version 2.3.4.3 (Langmead and Salzberg, 2012) with the parameter “-X 1000” to include longer fragments. Unmapped and low-quality fragments were removed using SAMtools version 1.9 using the following parameters “view -f 2 -F 2048”. Duplicates were removed using SAMtools with the following parameter “fixmate -m” and then “markdup -r”. The aligned files were converted to BED using BEDTools version 2.27.1 using a custom software called seqtools version 1.0 available at https://github.com/francoisrobertlab/seqtools with the command “seqtools bam2bed” resulting in BED files containing the DNA fragments. The BED files of replicates were merged using seqtools with command “seqtools merge”. Genome coverage files were generated using customs scripts “seqtools” with commands “mnasetools prepgenomecov” and “seqtools genomecov” that require BEDTools version 2.27.1 and KentUtils (downloaded on July 16th 2018). The genome coverage files were converted to the bigWig format using the utilities from UCSC Genome Browser (Casper et al., 2018).
Genome_build: S. cerevisiae (UCSC sacCer3)
Supplementary_files_format_and_content: bigWig files for both individual replicates (beginning with "CJ") and the combined biological replicates (beginning with "MNase").

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: Yeast cell extract

growth_protocol: Cells were grown at 30°C and 200 rpm in YPD (yeast extract-peptone-2% glucose, supplemented with 44 µM adenine) medium as follow. Strains were streaked from glycerol stocks onto 2% agar YPD plates and grown at 30°C for 2-3 days. An isolated colony was then grown overnight in 20 mL of YPD. This preculture was used to inoculate 500 mL of YPD at an OD600 of 0.1 which was grown to an OD600 of 0.7-0.9.

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 cycles using KOD Hot Start DNA polymerase (Millipore, 71086-3) and cleaned up using 1X KAPA Pure Beads. Libraries were qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 21 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq

treatment_protocol: Cultures were crosslinked with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 30 min. Crosslinking was quenched with 125 mM glycine.

tag: strain name

tag: chip antibody


title: MNaseseq_IP_H4_yFR1206_WT_R1

description:
Barcode ID: UDI0032 from Illumina TruSeq Kits
Biological replicate 1 of 2. H4 occupancy by MNase-ChIP-seq in WT cells. H4 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against H4.
processed data file (two biological replicates combined): MNaseseq_IP_H4_yFR1206_WT_CJ11-CJ12_20201127-cov-1.1.bw

extract_protocol: MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 cycles using KOD Hot Start DNA polymerase (Millipore, 71086-3) and cleaned up using 1X KAPA Pure Beads. Libraries were qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.

value: anti-H4 (a gift from A. Verreault, 2 uL)


title: delta-flaK_1


title: Vitamin A+ 2

city: Boston

first: Jens

last: Rister

state: MASSACHUSETTS

address: 100 Morrissey Boulevard

institute: University of Massachusetts Boston

data_processing:
Raw reads were processed for quality control using fastqc (v.0.11.5)
Raw reads were trimmed using Trim Galore (v0.4.2)
Raw reads were aligned to dmel genome (r6.24, flybase.org ) using STAR (v2.5.3a)
Gene level read counts was produced by featureCounts from Subread (v1.6.2) package
Genome_build: r6.24, flybase.org
Supplementary_files_format_and_content: gene level read raw count (abundance measurements)

organism: Drosophila melanogaster

source_name: Vitamin A+_whole head

growth_protocol: Flies were raised on minimal food with or without addition of beta-carotene, inside incubators set at 25°C temperature and 50% relative humidity.

extract_protocol:
Total RNA was extracted from heads of four day old female flies using Trizol followed by Qiagen Rneasy protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Flies were raised on food with or without beta-carotene.

tag: strain/genotype

value: Wild type Canton S

tag: treatment

value: vitamin A replete

value: four day old

value: female

value: Whole head


title: Vitamin A+ 1


title: MNase-ChIP_Pob3_yFR930chd1D_R1

description:
Biological replicate 1 of 2. Pob3 occupancy by MNase-ChIP-seq in chd1D cells. Pob3 MNase-ChIP-seq was performed using a rabbit polyclonal antibody against Pob3.
processed data file (two biological replicates combined):  MNaseChIP_Pob3_yFR930chd1D_CJ3-CJ4comb_20200319.bw

extract_protocol:
MNase-ChIP experiments were performed in two biological replicates, as previously described (Rando, 2010) with minor modifications. Briefly, yeast cultures were grown in 500 mL of YPD to an OD600 of 0.7-0.9 before crosslinking with 1% formaldehyde (Fisher Scientific, BP531-500) at room temperature for 15 min and quenched with 125 mM glycine at room temperature for 5 min. Crosslinked cells were collected by centrifugation and washed twice with ice-cold ddH2O. Yeast cell wall digestion was then performed by resuspending cell pellets in 39 mL Buffer Z (1 M sorbitol and 50 mM Tris-HCl pH 7.4) containing 10 mM β-mercaptoethanol and 10 mg Zymolyase 100T (US Biological, Z1004) and incubating at 30˚C with agitation (20-40 min). When digestion was completed, the resulting spheroplasts were pelleted by centrifugation at 3,000 g for 5 min at 4°C and gently resuspended in 2.5 mL of NP buffer (1 M sorbitol, 50 mM NaCl, 10 mM Tris-HCl pH 7.4, 5 mM MgCl2, 1 mM CaCl2, 500 µM spermidine (Sigma-Aldrich, 85558), 1 mM β-mercaptoethanol and 0.075% NP-40) before being exposed to MNase (Worthington, LS004798) digestion titration to generate the appropriate size of chromatin fragments as follow. 700 µl of spheroplasts were incubated with 4.5, 9, 18, and 36 units of MNase (resuspended in 10 mM Tris-HCl pH 7.4 and 30% glycerol) at 37˚C for 20 min and reaction was stopped by adding 10 mM EDTA. To ensure IP conditions, 200 µL of adjusting buffer (50 mM HEPES-KOH pH7.5, 140 mM NaCl, 1% Triton X-100, and 0.1% Na-deoxycholate) were added to the digested chromatin sample. To determine the appropriate condition of MNase digestion, 45 µL (5%) of each MNase digested sample were taken and incubated with 5 μL of 10X TE/SDS at 65˚C for 16 hr to reverse crosslinking. Samples were then treated with RNase A (345 μL TE, 3 μL 10 mg/mL RNAse A, 2 μL 20 mg/mL Glycogen) at 37°C for 2 hr and subsequently subjected to Proteinase K (15 μL 10% SDS, 7.5 μL 20 mg/mL Proteinase K) digestion at 37°C for 2 hr. Samples were twice phenol/chloroform/isoamyl alcohol (25:24:1) extracted followed by precipitation with 200 mM NaCl and 100 % ethanol. Precipitated DNA was resuspended in 30 μL of TE, treated with 1µL of 10 mg/mL RNAse A at 37°C for 1 hr before being analyzed by electrophoresis on a 1.8% TAE-agarose gel stained with ethidium bromide. The digested samples were also qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA Kit (Agilent Technologies, 5067-4626). The condition giving approximately 65% mono-, 25% di- and 10% tri-nucleosomes was subjected to IP as follow. 45µL (5%) were saved as Input sample and the remaining digested chromatin was incubated overnight with the appropriate antibody-coupled Dynabeads as per our standard ChIP protocol (see above). Beads were then washed and samples reverse crosslinked, treated with RNase A, and subsequently subjected to Proteinase K before being twice phenol/chloroform/isoamyl alcohol extracted followed by precipitation with NaCl and ethanol. Precipitated DNA was resuspended in 50 μL of TE before being used in sequencing libraries.  Before proceeding with MNase-ChIP-seq libraries, ChIP and Input samples were subjected to a 2X cleanup using KAPA Pure Beads (Roche, 07983280001) according to the manufacturers’ instructions. Samples were eluted with 50 μL of Elution buffer (10 mM Tris pH 8.0) and quantified/qualified on an Agilent 2100 Bioanalyzer instrument using the High Sensitivity DNA kit.  1 ng of Input DNA and 40 μL of ChIP DNA were used for library preparation as follow. The ends of DNA were repaired by incubating in 70 μL of 1X NEBuffer 2 containing 0.6 units of T4 DNA polymerase (NEB, M0203L), 2 units of T4 polynucleotide kinase (NEB, M0201S), 0.09 nM dNTPs and 0.045 μg/μL of BSA at 12˚C for 30 min. Repaired DNA was then subjected to a 2X cleanup using KAPA Pure Beads before dA-tailing as follow. Beads containing the repaired DNA were resuspended in 50 μL of 1X NEBuffer 2 containing 0.1 mM dATP and 25 units of Klenow Fragment (3'→5' exo-) (NEB, M0212M), and incubated at 37˚C for 30 min. After a 2X cleanup with KAPA Pure Beads, dA-tailed DNA was ligated to index adapters (Roche, SeqCap Adapter kit A (07141530001) and SeqCap Adapter kit B (07141548001)) as follow. The beads were resuspended in 45 μL of 1X Ligase buffer containing 8 nM of adapter and 2.5 units of T4 DNA ligase and incubated at room temperature for 60 min. The ligated DNA was then subjected to a 1X cleanup with KAPA Pure Beads. Libraries were PCR-amplified with 10-12 cycles using KOD Hot Start DNA polymerase (Millipore, 71086-3) and cleaned up using 1X KAPA Pure Beads. Libraries were qualified on Agilent 2100 Bioanalyzer using High Sensitivity DNA kit and quantified by qPCR using NEBNext Library Quant kit for Illumina (NEB, E7630). Equal molarity of each library was pooled (12 libraries per pool) and subjected to sequencing on Illumina HiSeq 4000 or NovaSeq 6000 platform at the McGill University and Génome Québec Innovation Centre to generate 50 bp paired-end reads.
Barcode ID:Adapter 15 from SeqCap Adapter kits A and B (Roche, 07141530001 and 07141548001)
MNase-ChIP-Seq

value: anti-Pob3 (a gift from T. Formosa, 1 μL)


title: Vitamin A- 1

source_name: Vitamin A-_whole head

value: vitamin A deprived


title: Vitamin A- 3


title: Vitamin A- 2


title: Untreated NLRP3 reconstituted THP-1 macrophages rep 5

city: Melbourne

first: Jamie

last: Gearing

address: 27-31 Wright St

country: Australia

institute: Hudson Institute of Medical Research

data_processing:
De-multiplexing was done with bcl2fastq software v1.8.4. Sequnce software RTA v1.18.66.3 was used.
Raw reads were trimmed and Illumina adaptor sequences removed using Trimmomatic v0.36 (Bolger et al., 2014).
Trimmed reads were aligned to the Ensembl human reference genome GRCh38, with the Ensembl GRCh38 v94 GTF file, and gene-level counts were generated using STAR v2.5.3a_modified (Dobin et al., 2012).
Counts were subseuqently processed using the edgeR package v3.24.0.
Genome_build: hg38
Supplementary_files_format_and_content: Comma-delimited table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: THP-1 macrophages

growth_protocol: THP-1 monocytes were maintained in RPMI 10% FCS 1% PenStrep

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries were prepared with 50 ng of total cellular RNA or 30 ng of total vesicular RNA using the QuantSeq 3’ mRNA Library Prep Kit FWD for Illumina according to the manufacturer’s instructions. Libraries were sequenced on the Illumina Hiseq2500.

treatment_protocol:
Cells were left untreated.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: NLRP3 reconstituted

value: UT

tag: cell type

value: THP-1 macrophages

tag: cell fraction

value: Whole cell

tag: replicate

tag: batch


title: Untreated NLRP3 reconstituted THP-1 macrophages rep 4


title: Untreated NLRP3 KO THP-1 macrophages rep 4

value: NLRP3 KO


title: Untreated NLRP3 KO THP-1 macrophages rep 5


title: Untreated NLRP3 KO THP-1 macrophages rep 3


title: delta-fliAp_1

value: {delta}fliA (BDP046)


title: Untreated NLRP3 KO THP-1 macrophages rep 2


title: Untreated NLRP3 reconstituted THP-1 macrophages rep 2


title: Untreated NLRP3 KO THP-1 macrophages rep 1


title: Vitamin A+ 3


title: SEC_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 5

treatment_protocol:
Cells were incubated with SEC EVs, which had been isolated from wild type THP-1 macrophages that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R837 (120 min; Invivogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9. EVs were transferred to recipient THP-1 macrophages at a 40:1 EV donor to EV recipient cell ratio. EVs were co-incubated with recipient cells for 15 h in RPMI with 10% FCS, 1% PenStrep, which had been previously centrifuged at 100,000 g for 18 h to remove bovine EVs. Prior to RNA isolation, supernatants containing EVs were removed and cells were washed three times with PBS to remove attached EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: SEC_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 4


title: SEC_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: SEC_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: Untreated NLRP3 reconstituted THP-1 macrophages rep 1


title: SEC_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: SEC_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 3


title: SEC_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 4

treatment_protocol:
Cells were incubated with SEC EVs, which had been isolated from wild type THP-1 macrophages that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 10 µM nigericin (90 min; Invitrogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9. EVs were transferred to recipient THP-1 macrophages at a 40:1 EV donor to EV recipient cell ratio. EVs were co-incubated with recipient cells for 15 h in RPMI with 10% FCS, 1% PenStrep, which had been previously centrifuged at 100,000 g for 18 h to remove bovine EVs. Prior to RNA isolation, supernatants containing EVs were removed and cells were washed three times with PBS to remove attached EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: SEC_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 2


title: SEC_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: SEC_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 5


title: SEC_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 4


title: SEC_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: SEC_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 1


title: SEC_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: SEC_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: SEC_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 2


title: Untreated NLRP3 reconstituted THP-1 macrophages rep 3


title: SEC_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 1


title: R837-treated NLRP3 KO THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 20 µg/ml R837 (120 min; Invivogen).
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: SEC_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 4


title: R837-treated NLRP3 KO THP-1 macrophages rep 2


title: R837-treated NLRP3 KO THP-1 macrophages rep 4


title: R837-treated NLRP3 KO THP-1 macrophages rep 3


title: SEC_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: R837-treated NLRP3 KO THP-1 macrophages rep 1


title: R837-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: R837-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: R837-treated NLRP3 reconstituted THP-1 macrophages rep 4


title: R837-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: R837-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: Nig-treated NLRP3 reconstituted THP-1 macrophages rep 4

treatment_protocol:
Cells were treated with 10 µM nigericin (90 min; Invitrogen).
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: Nig


title: Nig-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: Nig-treated NLRP3 KO THP-1 macrophages rep 4


title: SEC_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 3


title: Nig-treated NLRP3 KO THP-1 macrophages rep 2


title: Nig-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: Nig-treated NLRP3 KO THP-1 macrophages rep 3


title: Nig-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: Nig-treated NLRP3 KO THP-1 macrophages rep 1


title: Nig-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: LPS-treated NLRP3 reconstituted THP-1 macrophages rep 5

treatment_protocol:
Cells were treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen).
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: LPS


title: LPS-treated NLRP3 KO THP-1 macrophages rep 5


title: LPS-treated NLRP3 reconstituted THP-1 macrophages rep 4


title: LPS-treated NLRP3 KO THP-1 macrophages rep 4


title: LPS-treated NLRP3 KO THP-1 macrophages rep 3


title: LPS-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: LPS-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: LPS-treated NLRP3 KO THP-1 macrophages rep 2


title: LPS-treated NLRP3 KO THP-1 macrophages rep 1


title: 10K_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 5

treatment_protocol:
Cells were incubated with 10K EVs, which had been isolated from wild type THP-1 macrophages that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R837 (120 min; Invivogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. EVs were transferred to recipient THP-1 macrophages at a 40:1 EV donor to EV recipient cell ratio. EVs were co-incubated with recipient cells for 15 h in RPMI with 10% FCS, 1% PenStrep, which had been previously centrifuged at 100,000 g for 18 h to remove bovine EVs. Prior to RNA isolation, supernatants containing EVs were removed and cells were washed three times with PBS to remove attached EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: 10K_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 4


title: 10K_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: Nig-treated NLRP3 KO THP-1 macrophages rep 5


title: 10K_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 4


title: 10K_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 3


title: 10K_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: 10K_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 2


title: 10K_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: 10K_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 5

treatment_protocol:
Cells were incubated with 10K EVs, which had been isolated from wild type THP-1 macrophages that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 10 µM nigericin (90 min; Invitrogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. EVs were transferred to recipient THP-1 macrophages at a 40:1 EV donor to EV recipient cell ratio. EVs were co-incubated with recipient cells for 15 h in RPMI with 10% FCS, 1% PenStrep, which had been previously centrifuged at 100,000 g for 18 h to remove bovine EVs. Prior to RNA isolation, supernatants containing EVs were removed and cells were washed three times with PBS to remove attached EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: 10K_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: 10K_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 4


title: 10K_LPS+R837-treated NLRP3 KO THP-1 macrophages rep 1


title: LPS-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: 10K_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 4


title: 10K_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 3


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 4

source_name: Extracellular vesicles from THP-1 macrophages

treatment_protocol:
EVs were isolated from cells that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R837 (120 min; Invivogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: Wild type

value: SEC EVs


title: 10K_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 1


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 5


title: 10K_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 3


title: 10K_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 1


title: 10K_LPS+R837-treated NLRP3 reconstituted THP-1 macrophages rep 5


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 3


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 2


title: SEC EVs from LPS+R837-treated THP-1 macrophages rep 1


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 4

treatment_protocol:
EVs were isolated from cells that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 10 µM nigericin (90 min; Invitrogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs. Supernatant was filtered using a 0.2 µm filter (Millipore) and then concentrated to a total volume of 0.5 ml using a 10K NMWL filter (Amicon Ultra, Sigma-Aldrich). The sample was then transferred onto a size exclusion chromatography column (qEV original, Izon). Fractions of 0.5 ml were collected, the SEC EVs referred to within this study comprise fraction 7, 8 and 9.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: LPS+Nig


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 1


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 5


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 3


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 4

treatment_protocol:
EVs were isolated from cells that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 20 µg/ml R837 (120 min; Invivogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.

value: 10K EVs


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 3


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 2


title: 10K_LPS+Nig-treated NLRP3 reconstituted THP-1 macrophages rep 2


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 4

treatment_protocol:
EVs were isolated from cells that had been treated with 200 ng/ml LPS (120 min; ultrapure EB, Invitrogen), followed by 10 µM nigericin (90 min; Invitrogen). For EV isolation, tissue culture supernatant was centrifuged at 340 g for 10 min to remove floating cells, 2,000 g for 20 min to pellet 2K EVs and 10,000 g for 40 min to pellet 10K EVs.
[Overview] THP-1 monocytes were differentiated with 100 nM PMA (Sigma) for 12 to 16 h. THP-1 macrophages were washed once with PBS and rested for 24 h prior to any stimulation. THP-1 macrophages were were primed with LPS and subsequently treated with an inflammasome activator, primed only, treated with an activator only, incubated with extracellular veiscles or left untreated.


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 5


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 3


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 1


title: 10K EVs from LPS+R837-treated THP-1 macrophages rep 1


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 5


title: 10K_LPS+Nig-treated NLRP3 KO THP-1 macrophages rep 2


title: MC38 tumor cells - SA scRNA-seq

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Cellranger
Genome_build: mm10
Supplementary_files_format_and_content: Cellranger output files

organism: Mus musculus

source_name: tumor infiltrating immune cells

growth_protocol: MC38 tumor cells were inoculated into WT and SA mice. Immune cells were isolated on day 14 post-inoculation for single cell RNA-seq analysis.

extract_protocol: standard 10X scRNA-seq protocol

treatment_protocol: No treatment.

value: tumor infiltrating CD8 T cells


title: MC38 tumor cells - WT scRNA-seq

value: wild-type


title: SEC EVs from LPS+Nig-treated THP-1 macrophages rep 2


title: Day 27 cells derived from HNF1B+/+ hiPSCs_3 (bulk)

city: Autonomous CIty of Buenos Aires

first: Santiago

middle: Andres

last: Rodriguez Segui

address: Intendente Guiraldes s/n

country: Argentina

institute: IFIBYNE-UBA-CONICET

description: RNA-seq time-course.xlsx

data_processing:
[Bulk RNAseq Processing Pipeline]  RNA sequencing analyses were carried out following standard procedures (Conesa et al., 2016).
[Bulk RNAseq Processing Pipeline]  Reads were aligned to the reference human genome assembly GRCh38 with TopHat v2.0.13.
[Bulk RNAseq Processing Pipeline]  Reads with Mapping Quality Value <10 were filtered out with SAMtools.
[Bulk RNAseq Processing Pipeline]  FeatureCounts was used on paired-end reads to count fragments in annotated gene features, and genes with no counts were filtered out.
[Bulk RNAseq Processing Pipeline]  Read counts were normalised into fragments per kilobase of transcript per million mapped reads (FPKM).
[10X scRNA-seq Processing Pipeline]  cellranger V2.01
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene expression in fragments per kilobase of transcript per million mapped reads (FPKM) for bulk RNA-seq samples.
Supplementary_files_format_and_content: cellranger filtered gene-barcode matrices for 10X scRNA-seq samples.

growth_protocol:
[Bulk RNAseq Protocol]  For the bulk RNA-seq experiments, one HNF1B+/+, one HNF1B+/- and one HNF1B-/- (targeted wild-type) clone from the FSPS13.B hiPSC line were differentiated along the pancreatic lineage.
[10X scRNA-seq Protocol]  Single cell libraries were generated from HNF1B+/+ and HNF1B+/- clones from the FSPS13.B hiPSC line, which were differentiated along the pancreatic lineage.

extract_protocol:
[Bulk RNAseq Protocol]  RNA was extracted using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to manufacturer’s protocol.
[Bulk RNAseq Protocol]  RNA-seq library construction and sequencing was carried out by the DNA pipelines core facility at the Wellcome Sanger Institute.
[Bulk RNAseq Protocol]  Standard Illumina unstranded poly-A enriched libraries were prepared and sequenced using Illumina HiSeq 2500 v4 (Illumina, San Diego, CA, USA), with 75bp paired-end reads per sample and a library fragment size of 100-1000 bp.
[10X scRNA-seq Protocol]  For the preparation of cells for single-cell sequencing we used the Chromium Single Cell 3′ library and gel bead kit v2 protocol.
[10X scRNA-seq Protocol]  Single cell libraries were generated using the Chromium Single Cell 3′ library and gel bead kit v2 (PN #120237) from 10x Genomics. Briefly, to reach a target cell number of 2000 cells per sample, 3500 cells per sample were loaded onto a channel of the 10x chip to produce Gel Bead-in-Emulsions (GEMs). This underwent reverse transcription to barcode RNA before cleanup and cDNA amplification followed by enzymatic fragmentation and 5′adaptor and sample index attachment. Libraries were sequenced on the HiSeq4000 (Illumina).
[10X scRNA-seq Protocol]  RNA-seq. Illumina-C HiSeq V4 Paired end sequencing

treatment_protocol:
[Bulk RNAseq Protocol]  Human iPSCs were passaged and seeded onto 12-well plates using E8 supplemented with Y27632 (Rho-associated, coiled-coil containing protein kinase, ROCK Inhibitor; 10μM). Cells were plated as single cells and the plating density was optimised for each hiPSC line (approximately 80,000 to 100,000 cells per well of a 12-well plate). After 24 hours, the media was replaced with fresh E8 media without ROCK Inhibitor. To induce definitive-endoderm differentiation (days 1-3), cells were cultured in CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml), Ly294002 (10μM) and CHIR99021 (3μM) on day 1, CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml) and Ly294002 (10μM) on day 2 then RPMI/B27 media containing Activin (100ng/ml), FGF2 (80ng/ml) on day 3. For primitive gut tube differentiation (days 4-6), cells were cultured in Adv-BSA media supplemented with SB-431542 (10μM), FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml) and L-Ascorbic acid (250μM) for 3 days. For posterior foregut differentiation (days 7-8), cells were cultured in Adv-BSA with FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml), KAAD-cyclopamine (0.238μM), PdBU (50nM) and L-Ascorbic acid (250μM). Pancreatic progenitor specification (days 9- 13) was induced by culturing cells in RA (1μM), Noggin (150μg/ml), KAAD-cyclopamine (200ng/ml), EGF (100ng/ml), Nicotinamide (10mM), and L-Ascorbic acid (250μM) for 5 days. Cells were then grown in Adv-BSA containing glucose (final concentration 25mM), B27 (1%), RA (100nM), DAPT (1μM), Alk5i (10μM) and the small molecule BNZ (0.1mM) for 3 days to induce maturation of pancreatic progenitors to endocrine progenitor cells (fifth stage; days 14-16). For maturation of endocrine cells and further differentiation into C-peptide-producing beta cells, cells were cultured for 3 additional days in Adv-BSA containing B27 (1%), RA (100nM) and Alk5i (10μM) followed by 11 days in Adv-BSA containing B27 (1%), RA (100nM) (sixth stage; days 17-27).
[10X scRNA-seq Protocol]  Human iPSCs were passaged and seeded onto 12-well plates using E8 supplemented with Y27632 (Rho-associated, coiled-coil containing protein kinase, ROCK Inhibitor; 10μM). Cells were plated as single cells and the plating density was optimised for each hiPSC line (approximately 80,000 to 100,000 cells per well of a 12-well plate). After 24 hours, the media was replaced with fresh E8 media without ROCK Inhibitor. To induce definitive-endoderm differentiation (days 1-3), cells were cultured in CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml), Ly294002 (10μM) and CHIR99021 (3μM) on day 1, CDM-PVA supplemented with Activin (100ng/ml), FGF2 (80ng/ml), BMP4 (10ng/ml) and Ly294002 (10μM) on day 2 then RPMI/B27 media containing Activin (100ng/ml), FGF2 (80ng/ml) on day 3. For primitive gut tube differentiation (days 4-6), cells were cultured in Adv-BSA media supplemented with SB-431542 (10μM), FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml) and L-Ascorbic acid (250μM) for 3 days. For posterior foregut differentiation (days 7-8), cells were cultured in Adv-BSA with FGF10 (50ng/ml), RA (3μM), Noggin (150μg/ml), KAAD-cyclopamine (0.238μM), PdBU (50nM) and L-Ascorbic acid (250μM). Pancreatic progenitor specification (days 9- 13) was induced by culturing cells in RA (1μM), Noggin (150μg/ml), KAAD-cyclopamine (200ng/ml), EGF (100ng/ml), Nicotinamide (10mM), and L-Ascorbic acid (250μM) for 5 days. Cells were then grown in Adv-BSA containing glucose (final concentration 25mM), B27 (1%), RA (100nM), DAPT (1μM), Alk5i (10μM) and the small molecule BNZ (0.1mM) for 3 days to induce maturation of pancreatic progenitors to endocrine progenitor cells (fifth stage; days 14-16). For maturation of endocrine cells and further differentiation into C-peptide-producing beta cells, cells were cultured for 3 additional days in Adv-BSA containing B27 (1%), RA (100nM) and Alk5i (10μM) followed by 11 days in Adv-BSA containing B27 (1%), RA (100nM) (sixth stage; days 17-27).

tag: day

tag: hnf1b genotype

value: WT


title: Day 27 cells derived from HNF1B+/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx

value: Het


title: Day 27 cells derived from HNF1B-/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx

value: Hom


title: Day 27 cells derived from HNF1B-/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: 10K EVs from LPS+Nig-treated THP-1 macrophages rep 2


title: Day 27 cells derived from HNF1B-/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 27 cells derived from HNF1B+/+ hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 27 cells derived from HNF1B+/+ hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 27 cells derived from HNF1B+/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 27 cells derived from HNF1B+/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: 14 hour Input

city: Heidelberg

first: Nina

last: Papavasiliou

address: Im Neuenheimer Feld 280

department: Division of Immune Diversity (D150) Deutsches Krebsforschungszentrum

country: Germany

institute: German Cancer Research Center (DKFZ)

description: Chromatin Immunoprecipitated DNA

data_processing:
Single-end reads were aligned to mm10 genome using the subread function in the Bioconductor Rsubread (Liao et al., 2013)
bigWig files for visualization were generated from aligned reads using the Bioconductor rtracklayer (Lawrence et al., 2009) and GenomicAlignments packages (Lawrence et al., 2013).
Quality metrics for ChIP-Seq data were assessed using ChIPQC bioconductor package (Carroll et al., 2014)
Reads mapping to more than one genomic location were filtered prior to peak calling using Model-based Analysis of ChIP-Seq (MACS2) (Feng et al., 2011; Zhang et al., 2008) with duplicate filtering applied and input DNA sample as a control
Genome_build: mm10
Supplementary_files_format_and_content: bigWig file contains normalised ChIP-Seq signal across the genome. Useful for display of the normalized ChIP-Seq signal at their location in the genome in a track format for uploading into a genome browser such as the UCSC genome browser or Broad Institute's IGV.
narrowPeak - contains the Peak calls using MACS2 in narrow peak format
Summits - Peak call summits in BED format.

growth_protocol: C2C12s were plated at ~70% confluence 12 hours prior to inducing differentiation (seed ~2x10^6 cells in 10cm plates) maintained in DMEM (ATCC, 30-2002) with 10%FBS. This was followed by media change to DMEM with 2% horse serum (Life Biotechnologies, 26050-088) to induce differentiation. The cells (~5x10^6 /10cm plate) were harvested at 24-hour or 34-hour after inducing differentiation.

extract_protocol:
Cells were fixed on plate with 1% PFA in PBS for 10 minutes at RT. Glycine was added to a final concentration of 125mM. Cells were washed 2 times with 1x PBS with protease inhibitor cocktail (PIC, Roche, 11836170001). They were lysed on the plate with cold Farnham lysis buffer to ~10x10^6 cells /mL (5mM PIPES pH 8.0, 0.5% NP-40, 85mM KCl,1mM EDTA, PIC) and incubated rotating for 15min at 4°C . Lysates were scraped off the plates, pelleted and resuspended in LB2 (10 mM Tris pH 8.0, 200 mM NaCl, 1 mM 128EDTA, 0.5 mM EGTA, PIC) and incubated rotating for 15 minutes at 4°C and then centrifuged. Pellets were resuspended to 5x10^7 cells/mL in LB3 (10 mM Tris pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium-deoxycholate, 0.5% sodium lauroyl sarcosinate, PIC) until suspension was homogenized. Samples were then sonicated using Covaris ultrasonicator model S220 for 15 minutes with the following settings: 140W peak power, 5% duty, 200 cycles per burst. TritonX-100 to a final concentration of 1% was added to the samples. Samples were clarified by centrifugation at 20,000 g for 10 minutes at 4°C. The supernatant is the soluble chromatin extract. The soluble fragmented chromatin from ~2.5x10^7 was used for each IP. For each IP 100ul Dynabeads (Thermofisher anti-rabbit M280, 11203D) were mixed with 10ul polyclonal rabbit-APOBEC2 antibodies (gift from Alin Vonica MD, PhD) incubating overnight (~16 hours). A magnetic stand was used to separate beads from the lysate and beads were washed one time each with for 5min in: low salt wash (0.1%SDS, 1%Triton X-100, 2mM EDTA, 20mM Tris pH8, 150mM NaCl, PIC), high salt wash (0.1%SDS, 1% Triton X- 100, 2mM EDTA, 20mM Tris pH8, 500mM NaCl, PIC), lithium chloride wash (150mM LiCl, 1% NP-40, 1% NaDOC, 1mM EDTA, 10mM TrispH8, PIC), TE wash (10mM Tris-HCl pH8, 1mM EDTA, 50mM NaCl, PIC). Beads were resuspended in 52 ul of elution buffer (50mM Tris-HCl pH8, 10mM EDTA, 1%SDS) and incubated at 30min at 65°C while shaking to prevent beads from settling. The eluate was transferred to a new tube, inputs of the same volume were incubated for 8 hours at 65°C to reverse the crosslink. The samples were treated with RNAse (Roche, Cat. No. 11 119 915 001) for 1 hour at 37°C, and with Proteinase K for 2 hours at 55°C. Fragmented DNA was purified 129 with Ampure beads (Agencourt AMPure XP beads A63881) as per the manufacter’s instructions.
ChIP-Seq libraries were prepared using NEBNext Ultra DNA Library Prep Kit as per manufacturer’s instructions.

tag: cell line

tag: hours after inducing differentiation

tag: antibody used for ip

value: none (input)


title: 14 hour IP #2

description: Chromatin Immunoprecipitated DNA

value: Apobec2 (polyclonal, produced in rabbit)


title: 34 hour Input

description: Chromatin Immunoprecipitated DNA


title: 34 hour IP #3

description: Chromatin Immunoprecipitated DNA


title: 34 hour IP #2

description: Chromatin Immunoprecipitated DNA


title: 14 hour IP #1

description: Chromatin Immunoprecipitated DNA


title: 14 hour IP #3

description: Chromatin Immunoprecipitated DNA


title: 34 hour IP #1

description: Chromatin Immunoprecipitated DNA


title: BoneMarrow_3_R1c2_JH3

city: New Haven

first: Helen

middle: Alexander

last: Beilinson

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

data_processing:
Library strategy: HTGTS-Rep-seq
Fastq-multx tool based demultiplexing.
Cutadapt was used to trim adaptors.
The joined Paired-end sequence reads were then aligned and further processed using HTGTSrep pipeline (VDJ)/LAM-HTGTS pipeline (DJ) with default settings.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.xlsx: Excel files

source_name: RAG1core bone marrow B220+IgM- cells

extract_protocol:
B cells were isolated from mice aged 5-7 weeks. Splenic B cells were isolated using B220 magnetic beads (Miltenyi Biotec) or by FACS sorting. B220+ IgM- cells were purified via FACS sorting from bone marrow. Genomic DNA samples were obtained using phenol-chloroform extraction of whole cell lysates.
HTGTS-Rep-seq libraries were prepared as previously described (Hu et al., 2016; Lin et al., 2016). Briefly, genomic DNA was sonicated and subjected to LAM-PCR using biotinylated JH1 or JH3 bait primers (Lin et al., 2016). LAM-PCR products were purified using Dynabeads MyONE C1 streptavidin beads (Life Technologies, 65002) and ligated to bridge adaptors. Adaptor-ligated products were amplified by nested PCR with indexed JH1/JH3 primers (8-bp indexes were unique to each sample) and primer annealed to the adaptor. PCR products were further tagged with Illumina sequencing adaptor sequences and size-selected via gel extraction. Libraries were sequenced by paired-end 300-bp sequencing on an Illumina MiSeq by the Yale Center for Genome Analysis.

tag: genotype

value: Bone marrow

tag: htgts-rep-seq bait


title: BoneMarrow_3_R1c1_JH3


title: BoneMarrow_3_R1c1_JH1


title: BoneMarrow_2_PG1_JH3

source_name: RAG1.P326G bone marrow B220+IgM- cells


title: BoneMarrow_3_R1c2_JH1


title: BoneMarrow_2_PG2_JH3


title: BoneMarrow_2_KR2_JH3

source_name: RAG1.K233R bone marrow B220+IgM- cells


title: Day 16 cells derived from HNF1B+/+ hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_2_KR1_JH3


title: Day 16 cells derived from HNF1B+/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B-/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B-/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B+/+ hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B+/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B+/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 16 cells derived from HNF1B-/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_2_d2152_JH3

source_name: RAG1d215 bone marrow B220+IgM- cells


title: BoneMarrow_2_WT2_JH3

source_name: WT bone marrow B220+IgM- cells


title: Day 16 cells derived from HNF1B+/+ hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_2_PG2_JH1


title: BoneMarrow_2_WT1_JH3


title: BoneMarrow_2_d2152_JH1


title: BoneMarrow_2_PG1_JH1


title: BoneMarrow_2_WT2_JH1


title: BoneMarrow_2_KR2_JH1


title: BoneMarrow_2_KR1_JH1


title: BoneMarrow_2_d2151_JH1


title: Day 8 cells derived from HNF1B-/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 8 cells derived from HNF1B+/+ hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 8 cells derived from HNF1B+/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B+/+ hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B+/+ hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 8 cells derived from HNF1B-/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B+/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B+/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B-/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_KR_JH3


title: BoneMarrow_2_WT1_JH1


title: BoneMarrow_1_PG_JH3


title: BoneMarrow_1_R1c_JH3


title: Day 8 cells derived from HNF1B+/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_d215_JH3


title: Day 8 cells derived from HNF1B-/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_WT_JH3


title: Day 13 cells derived from HNF1B+/+ hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B-/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 13 cells derived from HNF1B+/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_PG_JH1


title: Day 13 cells derived from HNF1B-/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B-/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_KR_JH1


title: BoneMarrow_1_d215_JH1


title: Day 6 cells derived from HNF1B+/- hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: BoneMarrow_1_WT_JH1


title: Day 6 cells derived from HNF1B+/+ hiPSCs_3 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B-/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Spleen_2_PG_JH3

description: Beilinson_et_al_HTGTS_Rep_seq_Spleen2.xlsx

source_name: RAG1.P326G splenic B220+ cells

value: Spleen


title: Spleen_2_KR_JH3

source_name: RAG1.K233R splenic B220+ cells


title: Day 8 cells derived from HNF1B+/+ hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Spleen_3_PG2_JH1

description: Beilinson_et_al_HTGTS_Rep_seq_Spleen3.xlsx


title: Spleen_3_WT2_JH1

source_name: WT splenic B220+ cells


title: BoneMarrow_1_R1c_JH1


title: Spleen_3_WT1_JH1


title: Day 8 cells derived from HNF1B+/+ hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B+/- hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Spleen_2_d215_JH3

source_name: RAG1d215 splenic B220+ cells


title: OC10.11

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Raw data were analyzed using the Hisat aligner with stand-specific settings.
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Genome_build: Homo sapiens GRCh38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Oseochondroma

growth_protocol: Cartilage caps were microdissected from human osteochondromas obtained at surgery, miced into 3-5 mm cubic and cultured inside a diffusion chamber

extract_protocol:
Osteochondroma explants were washed with PBS, stored in RNAlator and kept at -80C. The explants were placed on clean Kimwipe to absorb excess RNAlater solution and then were snap-frozen in liquid nitrogen. Frozen tissue fragments were placed on pre-chilled carbon steel block and crashed into powder by the steel hammer. We then purified total RNA using Qiagen RNeasy fibrous tissue mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Osteochondroma explants were treated with NRX202467 or Palovarotene at 50-300nM.

tag: subject

value: Patient #10

tag: disease state

value: Oseochondroma

value: Osteochondroma explant

tag: treated drug

value: Palovarotene

tag: concentration


title: OC10.10

tag: tissue


title: Spleen_2_R1c_JH3

source_name: RAG1core splenic B220+ cells


title: OC10.12


title: Spleen_2_WT_JH3


title: Day 8 cells derived from HNF1B+/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B+/+ hiPSCs_2 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B-/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Day 6 cells derived from HNF1B+/+ hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: OC10.9


title: Spleen_2_PG_JH1


title: Day 6 cells derived from HNF1B+/- hiPSCs_1 (bulk)

description: RNA-seq time-course.xlsx


title: Spleen_3_PG1_JH1


title: OC10.8


title: Spleen_2_R1c_JH1


title: OC10.7


title: OC10.6

value: 50 nM


title: Spleen_1_KR_JH3

description: Beilinson_et_al_HTGTS_Rep_seq_Spleen1.xlsx


title: Spleen_1_R1c_JH3


title: Spleen_1_PG_JH3


title: SjSHC34-DN

city: Utrecht

first: Anneline

last: Hinrichs

address: Postbus 85500

department: Rheumatology & Clinical Immunology

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Samples were sequenced on an Illumina HiSeq4000 generating approximately 20 million 150bp paired-ended reads
The sample qualities were assessed by FastQC.
HTSeq-count was used to generate read counts.
Variance-stabilizing transformation (VST) on the raw read counts was performed using R/Bioconductor package DESeq2 to obtain normalized read counts (NRC), which are log2 normalized.
Genome_build: The sequencing reads were aligned to human genome (GRCh38 build 79) using STAR aligner.
Supplementary_files_format_and_content: Matrix table with log2 normalized read counts for every gene and every sample (except for 2 HC CCR9+ samples that were excluded after quality contol using FastQC).

source_name: HC_CCR9-CXCR5- Th cell

extract_protocol:
Venapuncture from patient or control. Fresh peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll density gradient centrifugation from Li-heparin blood. PBMCs were stained with fluorochrome-conjugated antibodies against CD3, CD4, CXCR5 and CCR9. CCR9+CXCR5- (CCR9+), CXCR5+CCR9- (CXCR5+) and CCR9-CXCR5- Th cells were sorted with Fluorescence-activated cell sorting (FACS) using BD FACSARIAIII and harvested into tubes with RPMI 1640 containing 10% FCS and 1% penicillin/streptomycin. Cells were lysed in RLTplus buffer (Qiagen) with 1% beta-mercaptoethanol. RNA was extracted using the AllPrep Universal Kit in QIACube (both Qiagen)
TruSeq RNA Library Prep Kit (Illumina) according to manufacturer's instructions

value: HC

value: Peripheral blood

value: CCR9-CXCR5- Th cell


title: Spleen_2_WT_JH1


title: Spleen_1_d215_JH3


title: Spleen_1_WT_JH3


title: SjSHC34-CCR9

source_name: HC_CCR9+ Th cell

value: CCR9+ Th cell


title: Spleen_1_PG_JH1


title: OC10.2

value: Vehicle ethanol


title: OC10.5


title: OC10.1


title: Spleen_1_KR_JH1


title: Spleen_2_KR_JH1


title: Spleen_1_R1c_JH1


title: Spleen_1_d215_JH1


title: SjSHC33-CXCR5plus

source_name: HC_CXCR5+ Th cell

value: CXCR5+ Th cell


title: SjSHC33-CCR9plus


title: Spleen_2_d215_JH1


title: SjSHC32-DN


title: SjSHC33-DN


title: SjSHC32-CCR9plus


title: SjSHC3-DN


title: late endorsperm stage endorsperm RNA-seq [LEN-2]

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

institute: Agriculture and Agri-Food Canada

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Salmon was used for fast and accurate alignment of cleaned reads to released JGI v3.1 annotation of B. distachyon Bd21 downloaded from the Phytozome database (http://phytozome.jgi.doe.gov/).
Salmon was used to obtain TPM and CPM of each sample.
Genome_build: B. distachyon Bd21 downloaded from the Phytozome database (http://phytozome.jgi.doe.gov/)
Supplementary_files_format_and_content: Matrix table files include log 2 CPM for each Sample

organism: Brachypodium distachyon

source_name: endorsperm

growth_protocol: Plants were grown under 16h of light, 22°C and 8h of dark, 20°C photoperiod 100-120 μE m−2 s−1 light intensity.

extract_protocol:
Embryo, endosperm and seed coat isolations were performed using a dissecting microscope, fine forceps and needles in a 4.8% Sucrose solution that contained 0.1% RNALater solution.For seed coat isolation, the embryos were manually removed, and the remaining seed coat was kept. Total RNA was extracted from each stage embryo sample following the protocol of RNAqueous-micro kit.
RNA-seq libraries were prepared using TruSeq RNA kit (version 1, rev A).

treatment_protocol: Brachypodium flowers were emasculated and pollinated at the flower stage, to ensure sufficient and developmentally coordinated seed production for embryo isolation.

value: endorsperm

tag: developmental stage

value: late endorsperm

tag: ecotype


title: Spleen_1_WT_JH1

value: WT

tag: cell type


title: SC stage seed coat RNA-seq [SEC-2]

source_name: seed coat

value: seed coat

value: SC


title: early endorsperm stage endorsperm RNA-seq [EEN-2]

value: early endorsperm


title: SjSHC34-CXCR5


title: mature stage embryo RNA-seq [MAT-2]

source_name: embryo

value: embryo

value: mature


title: SjSHC3-CXCR5


title: SjSHC3-CCR9


title: leaf late stage embryo RNA-seq [LEL-2]

value: leaf late


title: SjSHC18-DN


title: leaf middle stage embryo RNA-seq [LEM-2]

value: leaf middle


title: leaf early stage embryo RNA-seq [LEE-2]

value: leaf early


title: SjSHC18-CXCR5plus

value: HC


title: SjSHC18-CCR9plus

value: Peripheral blood


title: SjSHC32-CXCR5plus


title: preembryo stage embryo RNA-seq [PEM-2]

value: preembryo


title: SjSHC17-DN

value: CCR9-CXCR5- Th cell


title: SjSHC11-DN


title: 2cell and quadrant stage embryo RNA-seq [TCQ-2]

value: 2cell and quadrant


title: No polyIC WT_3__IFE

city: Bethesda

first: Keisuke

middle: Chris

last: Nagao

state: Maryland

address: 9000 Rockville Pike, Bldg 10, Rm12N240B

institute: National Institute of Arthritis and Musculoskeletal and Skin Diseases

data_processing:
The FASTQ files were aligned to the reference mouse genome (mm10) using STAR software in Partek Flow and gene-level count matrix was generated.
Genome_build: mm10

source_name: Hair follicles

extract_protocol:
Total RNA was extracted using Direct-zol RNA MicroPrep (Zymo Research).
RNA libraries were prepared using a NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), NEBNext Ultra RNA Library Prep Kit for Illumina (New England BioLabs) and NEBNext Multiplex Oligos for Illumina (Index Primers Set) (New England BioLabs) according to manufacturer protocol.

treatment_protocol: Epidermis from C57BL/6 mice were harvested one day after saline or poly(I:C) i.p. injection and interfollicular epidermis (IFE) and bulge cells were sorted into Trizol.

tag: strain

value: skin

tag: experimental group

value: saline

tag: genotyping

value: wild type


title: With polyIC WT_4__IFE


title: No polyIC WT_1__IFE


title: No polyIC WT_2__IFE


title: With polyIC WT_2__IFE


title: SjSHC17-CXCR5plus

value: CXCR5+ Th cell


title: SjSHC11-CXCR5plus


title: late endorsperm stage endorsperm RNA-seq [LEN-1]

value: endorsperm

value: late endorsperm


title: No polyIC WT_4__IFE


title: With polyIC WT_4__Bulge


title: With polyIC WT_3__Bulge


title: WIth polyIC WT_1__IFE


title: early endorsperm stage endorsperm RNA-seq [EEN-1]

value: early endorsperm


title: transition stage embryo RNA-seq [TRA-2]

value: embryo

value: transition


title: SjS53-DN

source_name: pSS_CCR9-CXCR5- Th cell

value: pSS


title: No polyIC WT_3__Bulge


title: SjS53-CXCR5plus

source_name: pSS_CXCR5+ Th cell


title: No polyIC WT_4__Bulge


title: mature stage embryo RNA-seq [MAT-1]

value: mature


title: leaf late stage embryo RNA-seq [LEL-1]

value: leaf late


title: SjS53-CCR9plus

source_name: pSS_CCR9+ Th cell

value: CCR9+ Th cell


title: BoneMarrow_2_d2151_JH3

source_name: RAG1d215 bone marrow B220+IgM- cells

value: Bone marrow


title: SC stage seed coat RNA-seq [SEC-1]

value: seed coat

value: SC


title: No polyIC WT_1__Bulge


title: SjS52-DN

value: Peripheral blood

value: CCR9-CXCR5- Th cell


title: With polyIC WT_1__Bulge

value: skin


title: No polyIC WT_2__Bulge

value: saline

value: wild type


title: leaf middle stage embryo RNA-seq [LEM-1]

value: leaf middle


title: ADAM10;ROSA26YFP_Mx1 bulge_3

data_processing:
The FASTQ files were aligned to the reference mouse genome (mm10) using STAR software (2.6.1c).
Gene-level count matrix was generated from mapped reads via GenomicFeatures and GenomicAlignments tools on R platform and then used as an input for downstream analysis using DESeq2 or kallisto (ver. 0.44.0), a pseudoalignment tool and sleuth pipeline.
Genes with lower than 10 read count were filtered out from further analysis.
The differentially expressed genes were based on a threshold of false discovery rate below 0.1.
Genome_build: mm10

treatment_protocol: Epidermis from WT(ROSA26YFP_Mx1 ) and Adam10-KO (ADAM10;ROSA26YFP_Mx1) mice were harvested 4 days after saline or poly(I:C) i.p. injection and upper hair follicle cells YFP-positive cells and bulge cells were sorted into Trizol.

value: Adam10-KO (ADAM10;ROSA26YFP_Mx1)


title: leaf early stage embryo RNA-seq [LEE-1]

value: leaf early


title: ADAM10;ROSA26YFP_Mx1 bulge_4


title: ROSA26YFP_Mx1 bulge_3

value: WT

value: wild type (ROSA26YFP_Mx1)


title: SjS52-CCR9plus

value: pSS


title: ADAM10;ROSA26YFP_Mx1 bulge_1


title: ROSA26YFP_Mx1 bulge_4


title: SjS52-CXCR5

value: CXCR5+ Th cell


title: ADAM10;ROSA26YFP_Mx1 bulge_2


title: transition stage embryo RNA-seq [TRA-1]

value: embryo

value: transition


title: SjS5-CXCR5plus


title: ROSA26YFP_Mx1 bulge_2


title: ADAM10;ROSA26YFP_Mx1 YFP-positive upper HF_4


title: ROSA26YFP_Mx1 bulge_1


title: SjS5-DN


title: 2cell and quadrant stage embryo RNA-seq [TCQ-1]

value: 2cell and quadrant


title: preembryo stage embryo RNA-seq [PEM-1]

value: preembryo


title: ADAM10;ROSA26YFP_Mx1 YFP-positive upper HF_3


title: SjS5-CCR9plus

value: CCR9+ Th cell


title: SjS22-DN

value: Peripheral blood


title: ADAM10;ROSA26YFP_Mx1 YFP-positive upper HF_1


title: ROSA26YFP_Mx1 YFP-positive upper HF_3


title: SjS22-CXCR5


title: ROSA26YFP_Mx1 YFP-positive upper HF_2


title: ROSA26YFP_Mx1 YFP-positive upper HF_1


title: Mature hepatocytes_rep3

city: Dresden

first: Lenka

last: Belicova

state: Saxony

address: Pfotenhauerstr. 108

institute: MPI-CBG Dresden

data_processing:
Basic quality control of raw sequencing data was performed with FastQC v0.11.2
Reads were mapped to the mouse genome reference assembly GRCm38 and genes of the Ensembl release v92
Reads were quantified using STAR v2.5.2b
The read duplication level was assessed using MarkDuplicates from Picard tools v2.10.2 and dupRadar v1.8.0
The count data of the samples were filtered for genes with more than 10 counts in any of the samples
The count data were analyzed by DESeq2 v1.22.2
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: raw counts

source_name: primary liver cells

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen, Cat. No. 74104 50) including the DNase I treatment step (Qiagen, cat. No. 79254).
1 µg mRNA was isolated from the total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer’s instructions. RNA-Seq library was prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®. 75bp single read sequencing on Illumina HiSeq 2500.

tag: isolation age

value: 8-12 weeks

value: Mature hepatocytes


title: Mature hepatocytes_rep2


title: trichome_rep4

city: East Lansing

first: koichi

last: Sugimoto

state: MI

address: 612 Wilson Rd

institute: Michigan State University

data_processing:
Sequence reads were trimmed using the Trimmomatic software (Bolger et al., 2014) to eliminate adaptor sequences and low quality reads.
The remaining reads were mapped to the Solanum lycopersicum L. reference genome sequence (ITAG 2.5 genome) using Tophat2 software (Kim et al., 2003).
The mapped reads were then aligned using SAMtools (Li et al., 2009) and counted by HTSeq (Anders et al., 2015).
Genome_build: ITAG2.4_gene_models.gff3
Supplementary_files_format_and_content: Tab-delimited text files include cpm values for each sample.

organism: Solanum lycopersicum

source_name: glandular cells of type VI trichome

growth_protocol: Plants grew on the potted soil in the growth chamber under 250 μE and 28 ºC for 5 weeks.

extract_protocol:
Total RNA was extracted with RNeasy kit (Qiagen) according to the manufacturer's instructions.
Sequencing libraries were prepared from total RNA with the TruSeq RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: Glandular cells of type VI trichome was collected as described in Schilmiller et al. (2010) Plant Physiology 153: 1212-1223. Trichome shaved leaves were obtained by hand-scraped leaf from the same plants of trichome prep.

tag: cultivar

value: leaf type VI trichomes

tag: sampling time

value: complemented line #4


title: Mature hepatocytes_rep1


title: trichome_rep3


title: SjS22-CCR9


title: SjS21-DN

value: CCR9-CXCR5- Th cell


title: trichome_rep2


title: Mature hepatocytes_rep4


title: In vitro diff. hepatocytes_rep3

value: in vitro differetniated hepatocytes


title: leaf_rep3

source_name: leaf cells

value: trichome shaved leaf

value: af mutant


title: trichome_rep1


title: leaf_rep1


title: SjS21-CXCR5plu


title: In vitro diff. hepatocytes_rep2


title: ROSA26YFP_Mx1 YFP-positive upper HF_4

value: WT

value: skin

value: wild type (ROSA26YFP_Mx1)


title: ADAM10;ROSA26YFP_Mx1 YFP-positive upper HF_2

value: Adam10-KO (ADAM10;ROSA26YFP_Mx1)


title: SjS21-CCR9plus

value: pSS


title: In vitro diff. hepatocytes_rep1


title: SjS15-CXCR5

value: CXCR5+ Th cell


title: SjS15-CCR9plus


title: leaf_rep4


title: leaf_rep2


title: In vitro diff. hepatocytes_rep4


title: Hepatoblasts_rep3

value: Hepatoblasts


title: SjS14-DN


title: Hepatoblasts_rep2


title: SjS14-CXCR5


title: SjS15-DN


title: Hepatoblasts_rep1


title: SjS14-CCR9plus

value: CCR9+ Th cell


title: Hepatoblasts_rep4


title: LW_42

first: Maxwell

last: Lee

address: Building 37, Room 5120

department: CCR

institute: National Cancer Institute, NIH

description:
RNA-seq data from  flash frozen tissue
LW_RNASeq39.anno_rpkm

data_processing:
RNA-seq reads were aligned to the mouse mm10 genome assembly using TopHat Software
differentially expressed genes were determined using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: 4T1 Mammary tumor

extract_protocol:
Tumors were resected, flash frozen on dry ice and RNA was harvested using the RNeasy Kit (QIAGEN).
RNA libraries were prepared for sequencing using Illumina TruSeq® Stranded Total RNA LT, RS-122-2201 protocol

treatment_protocol: Mice orthotopically implanted with 4T1 tumor cells were treated with vehicle, control antibodies or therapeutic antibodies (5mg/Kg ip 3x q wk) for 12 days starting on day+1 after tumor cell implantation.

tag: mouse strain

value: BALB/c

value: Mammary tumor

tag: in vivo timepoint

value: 12 day treatment

tag: treatment

value: XPA.42.089 human anti-TGFbeta1+TGFbeta2 MoAb


title: LW_41


title: LW_40


title: ncd8_EP_S29

city: Memphis

first: Yong

last: Cheng

state: Tennessee

address: 262 Danny Thomas Place

department: Department of Hematology

institute: St. Jude Children’s Research Hospital

description: amplicon sequencing

data_processing:
Library strategy: Amplicon sequencing
Data was processed by CrisprEsso2
CRISPResso -r1 $COL1 -a $COL3 -g $COL2 -o ${label}_5_29 --discard_indel_reads
Genome_build: hg19
Supplementary_files_format_and_content: excel table

growth_protocol: HEK293T cells were seeded in a 48-well plate at density of ~5 × 104  per well, transfected 24 h post-seeding with PE plasmid, pegRNA plasmid, and nicking gRNA plasmid (750:250:83) and 0.78 μl TransIT (Mirus) (per well).

extract_protocol:
Cells were collected 72h after transfection and lysed in 150 μl prepared DNA lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS; 25μg/ml proteinase K). DNA lysates were incubated at 37 °C for 1h, followed by an 80 °C enzyme inactivation step for 30 min.
For each sample, the target regions were amplified by first round of PCR (PCR1) using gene-specific primers flanking the target sequence. The PCR1 was performed in a 25 μl volume including 100ng genomic DNA, 1.25 μl of 10 μM each primer, 12.5 μl 2 × Phusion High-Fidelity PCR mix (Thermo) and 0.75 μl DMSO. PCR1 reactions were carried out as follows: 98 °C for 2 min, then 34 cycles of (98 °C for 10 s, 65°C for 30 s, 72 °C for 30 s), and a final 72 °C extension for 5 min. PCR1 products were purified by electrophoresis in a 1.5% agarose gel or using AMPure beads. In a secondary ‘barcoding’ PCR (PCR2), the amplicons were indexed with primer pairs containing appropriate Illumina forward and reverse adaptor sequences. The 25 μl PCR2 was performed with 10ng purified PCR1 products, 2.5 μl of 10 μM forward and reverse barcoding primers, 12.5 μl 2 × Phusion High-Fidelity PCR mix (Thermo) and 0.75 μl DMSO. The PCR2 reactions were carried out as follows: 98 °C for 2 min, then 10 cycles of (98 °C for 10 s, 65 °C for 20 s, and 72 °C for 30 s), followed by a final 72 °C extension for 2 min. PCR2 products were purified by electrophoresis with a 1.5% agarose gel and DNA concentration was measured by fluorometric quantification (Qubit, Thermo). Amplicon libraries were sequenced on the Illumina MiSeq instrument according to the manufacturer’s protocols. After demultiplexing, FASTQ files were analyzed using CRISPResso2 with --discard_indel_reads.

tag: cell line

tag: control

value: No

value: Easy-Prime


title: MDA-MB-231 Cells Wild Yam Root Extract - High1 Duplicate

type: RNA

city: Tallahassee

first: Elizabeth

middle: A

last: Mazzio

state: Florida

address: 1515 MLK Blvd

department: College of Pharmacy & Pharmaceutical Science

institute: Florida Agricultural & Mechanical University

description: Gene expression data from MDA-MB-231 cells grown under variable experimental treatment

hyb_protocol: Hybrization was conducted according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

scan_protocol: Arrays were scanned with GeneAtlas Imaging station scanner  (Affymetrix, ThermoFisher Scientific)

data_processing:
The data was processed using Affymetrix (applied biosystems transcriptome analysis console software) (Affymetrix, ThermoFisher Scientific)
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label: Biotin

source_name: MDA-MB-231 ATCC® HTB-26™ cells - 3-O-Acetyl-β-boswellic acid 46ug/ml

label_protocol: cDNA was labeled using according to manufacturer's instructions as per the GeneChipTM WT PLUS Reagent Manual for Whole Transcript (WT) Expression Arrays. (Affymetrix, ThermoFisher Scientific).

growth_protocol: MDA-MB-231 cells were cultured in Dulbecco’s Modified Eagle’s Medium - high glucose with 4500 mg/L glucose, L-glutamine, sodium pyruvate, and sodium bicarbonate, supplemented with 7% FBS and 100 U/ml penicillin G sodium /100 μg/ml streptomycin sulfate. Cells were grown at 37°C with 95% air and 5% CO2 and sub-cultured every three to five days.

extract_protocol: After treatment, cells were washed three times in HBSS, rapidly frozen and stored at -80 C. Total RNA was isolated/ purified using the TRIzol/chloroform method, quality was assessed and concentration was equalized to 82ng/ul in nuclease free water

treatment_protocol: Wild Yam powder was purchased from Mountain Rose Herbs (Eugene, OR). Crude WYE was prepared by dissolving the root power in absolute ethanol at 50mg/mL, followed by vortexing and storage  in the dark at -20C. Serial dilutions of WYE were prepared in sterile HBSS.  Two concentations were tested and pre-confirmed as sublethal Low (15ug/mL) and sublethal High (30ug/mL).  Controls and treatments were grown in 75cm2 flasks , treatments added and at 24 hours, the cells were QC checked as having retained morphological shape, flask attachment and had no obvious signs of cell death.  At this point, cells were rapidly washed in HBSS 3x, spun and frozen at -80C.

value: MDA-MB-231 ATCC® HTB-26™

value: mammary gland/breast; derived from metastatic site:pleural effusion

value: 3-O-Acetyl-β-boswellic acid 46ug/ml


title: ncd8_PD_S34

description: amplicon sequencing

value: PrimeDesign


title: MDA-MB-231 Cells Wild Yam Root Extract - Low Triplicate 1

source_name: MDA-MB-231 ATCC® HTB-26™ cells - Boswellia Serrata Extract 128 ug/ml

value: Boswellia Serrata Extract 128 ug/ml


title: MDA-MB-231 Cells Wild Yam Root Extract - Low Triplicate 3


title: S_b09_6mo_b3_4

first: Alison

last: Goate

state: NY

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Paired end reads were trimmed for Illumina TruSeq adapters
Reads were aligned to the hg38 genome, and samples were counted for reads, both using the STAR aligner (v2.5.2b).
Genes were filtered by expression abundance (Counts per million (CPM) >0.1 in 5 or more samples)
Library sizes were estimated by the trimmed mean of M-values normalization (TMM) using edgeR (v3.26.8)
Differential gene expression was predicted by linear mixed model analysis using the variancePartition package (v1.14.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files of raw read counts

source_name: iPSC-derived cerebral organoid

growth_protocol: Cerebral organoids were generated as per previously published protocol - see Yoon et al. Nature Methods, 2019.

extract_protocol:
Total RNA was extracted from individual organoids in a single batch using the KingFisher Flex (ThermoFisher Scientific) automated system and MagMAX mirVana Total RNA isolation kit (ThermoFisher Scientific).
Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina, and sequenced as paired-end 150bp reads on the Illumina HiSeq 4000.

treatment_protocol: No treatment

value: iPSC-derived cerebral organoid

tag: age

tag: batch

tag: technical replicate

tag: genotype


title: S_b09_6mo_b3_2

tag: tissue


title: S_b09_6mo_b3_3


title: MDA-MB-231 Cells Control Triplicate 3

source_name: MDA-MB-231 ATCC® HTB-26™ cells - No treatment

tag: cell type

value: No treatment


title: S_b09_6mo_b3_1


title: ncd8_WT_S18

description: amplicon sequencing

value: Yes


title: LW_39


title: MDA-MB-231 Cells Wild Yam Root Extract - High2 Duplicate


title: MDA-MB-231 Cells Control Triplicate 1


title: MDA-MB-231 Cells Control Triplicate 2


title: HFD_rep2

city: Beijing

first: Qian

last: Zhang

address: No. 1 Shuaifuyuan, Dongcheng District

country: China

institute: Peking Union Medical College Hospital

description: gene expression data from livers of male mice from high-fat diet mother

hyb_protocol: The sample preparation and hybridation of each cDNAs on Affymetrix  GeneChip Mouse Transcriptome 1.0 ST Assay based on manufacturer's instruction.

scan_protocol: Arrays were scanned using the GeneChip® Scanner 3000 Affymetrix)

data_processing: All arrays were uploaded into Affymetrix Expression Console Software v1.0  for data normalization, quality control and first-pass analysis. Differentially expressed genes were then identified through fold change as well as P value calculated with t-test. The threshold set for differentially regulated genes was a fold change>1.5 or 1.2 and a P value<0.05.

label: biotin

source_name: offspring from high-fat diet mother, 8 weeks

label_protocol: biotin

extract_protocol: Total tissue RNA was extracted using TRIzol reagent.

value: liver

value: 8 week

tag: Sex

value: male


title: MDA-MB-231 Cells Wild Yam Root Extract - Low Triplicate 2


title: HFD-inulin_rep3

description: gene expression data from livers of male mice from inulin treated mother

source_name: offspring from inulin treated mother, 8 weeks


title: LW_38

value: BALB/c


title: HFD_rep1


title: HFD-inulin_rep1


title: HFD-inulin_rep2


title: LW_36

value: Mammary tumor


title: S_b09_6mo_b1_4


title: S_b09_6mo_b1_2


title: LW_33

value: 12 day treatment

value: XPA.42.681 human pan isoform anti-TGFbeta MoAb


title: S_b09_6mo_b1_3


title: LW_35


title: HFD_rep3


title: LW_34


title: LW_32


title: S_b09_6mo_b1_1


title: LW_30


title: 42 oC stress IR64 7-day-old seedling, Biological replicate 1

city: New Delhi

first: Jitendra

middle: Paul

last: Khurana

address: Benito Juarez Road

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi South Campus

description: Gene expression data of 42 oC for 2 h heat stressed 7-day-old IR64 seedling

hyb_protocol: Following fragmentation, 12.5 ug of aRNA were hybridized for 16 h at 450C on GeneChip Rice Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3300.

data_processing: First-order analysis was performed using Affymetrix Gene Chip Operating (GCOS) software 1.2.1. Normalization of data and differential expression analysis was done using ArrayAssist ver 5.5  (Stratagene, CA, USA).

organism: Oryza sativa Indica Group

source_name: 7-day-old seedling

label_protocol: Biotinylated aRNA were prepared according to the revised 3' IVT Affymetrix protocol from 500ng total RNA.

growth_protocol: Seeds of each variety were surface sterilized with 70% ethanol followed by 0.1 % HgCl2 with repeated rinses with Mili-Q water, and were allowed to imbibe in water for 16 h. The seedlings were grown hydroponically for seven days on rice growth medium (RGM), pH 4.8.

extract_protocol: Trizol extraction of total RNA of whole seedlings was performed according to the manufacturer's instructions.

treatment_protocol: The seven-day-old seedings of each variety were subjected to heat stress by first pre-treating them at 37 oC for 1 h followed by 42 oC for 2 h at approximately 40 % relative humidity, respectively. Control tissues were maintained on RGM for 3 h at 28±1oC.

tag: stress

value: 42 oC heat stress

tag: time

value: seedling


title: 37 oC stress IR64 7-day-old seedling, Biological replicate 3

description: Gene expression data of 37 oC for 1 h heat stressed 7-day-old IR64 seedling

value: 37 oC heat stress


title: 42 oC stress IR64 7-day-old seedling, Biological replicate 3


title: S_b09_4mo_b3_2


title: S_b09_4mo_b3_3


title: 42 oC stress Annapurna 7-day-old seedling, Biological replicate 2

description: Gene expression data of 42 oC for 2 h heat stressed 7-day-old Annapurna seedling

value: Annapurna


title: 42 oC stress IR64 7-day-old seedling, Biological replicate 2


title: 42 oC stress Annapurna 7-day-old seedling, Biological replicate 3


title: 37 oC stress Annapurna 7-day-old seedling, Biological replicate 1

description: Gene expression data of 37 oC for 1 h heat stressed 7-day-old Annapurna seedling


title: S_b09_4mo_b3_1


title: 37 oC stress IR64 7-day-old seedling, Biological replicate 1


title: Control Annapurna 7-day-old seedling, Biological replicate 3

description: Gene expression data of control unstressed 7-day-old Annapurna seedling

value: control unstressed

value: control


title: 42 oC stress Annapurna 7-day-old seedling, Biological replicate 1


title: 37 oC stress Annapurna 7-day-old seedling, Biological replicate 2


title: Control IR64 7-day-old seedling, Biological replicate 3

description: Gene expression data of control unstressed 7-day-old IR64 seedling


title: Control IR64 7-day-old seedling, Biological replicate 1


title: 37 oC stress IR64 7-day-old seedling, Biological replicate 2


title: Control IR64 7-day-old seedling, Biological replicate 2


title: 37 oC stress Annapurna 7-day-old seedling, Biological replicate 3


title: S_b09_4mo_b1_2


title: LW_27

value: Anti-KLH control human MoAb


title: 1909_Controls uninflamed ascending/descending colon

city: South San Francisco

first: Jason

last: Hackney

state: CA

address: 1 DNA Way

department: Department of Bioinformatics and Computational Biology

institute: Genentech, Inc.

hyb_protocol: Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.

scan_protocol: Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 10.7.

data_processing: Raw intensity data were background subtracted using the normal + exponential method from the limma Bioconductor package. The test/reference ratio was log2 transformed and normalized using loess normalization for each array. Loess normalized log2 ratios were then subjected to quantiles normalization across all arrays in the dataset.

label_protocol: Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Quick Amp Labeling Kit (Agilent). For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal human reference (Stratagene, La Jolla, CA).

extract_protocol: RNA was extracted with Qiagen RNeasy Plus kit with removal of genomic DNA.

value: not determined

tag: diagnosis

value: Healthy control

tag: inflammation

value: Uninflamed

value: Colon

source_name: Universal human reference (UHR) from Stratagene

tag: sample type

value: pooled human reference RNA


title: LW_29

tag: mouse strain


title: S_b09_4mo_b1_4

value: iPSC-derived cerebral organoid


title: Control Annapurna 7-day-old seedling, Biological replicate 2

tag: cultivar


title: 1911_Controls uninflamed sigmoid colon

source_name: Controls uninflamed sigmoid colon


title: S_b09_4mo_b3_4


title: LW_26

value: BALB/c

tag: in vivo timepoint

tag: treatment


title: S_b09_4mo_b1_3

tag: cell line


title: S_b09_4mo_b1_1

tag: age


title: LW_31

value: Mammary tumor


title: 1909_Controls uninflamed sigmoid colon

tag: batch