title: ESC, TET-TKO, TET3, Dox 12h, C, 5hmC

city: Dunedin

first: Oscar

middle: Javier

last: Ortega-Recalde

state: Otago

address: 60 Hanover Street

department: Anatomy

country: New Zealand

institute: University of Otago

data_processing:
Library strategy: ACE-seq
Trimming using TrimGalore ! (v0.6.4), quality threshold 20, hard trimming 10bp
Reads were aligned against Mus musculus genome version 38 (GRCm38) using Bismark (v0.22.3)
BAM files were deduplicated and CpG calls were extracted using bismark_methylation_extractor
Assembly: GRCm38
Supplementary files format and content: Processed files contain individual CpG calls processed by Bismark

growth_protocol: Once a stable mTET3-CD complemented TET-TKO line was produced, media supplemented with 50 μg/ml ascorbate was added to cells plated at low-density in 12-well plates overnight.

extract_protocol:
Total nucleic acids were purified using the Bio-On-Magnetic-Beads (BOMB) approach. Briefly, a guanidine isothiocyanate lysis buffer was used to homogenize cells, and then was combined with TE-diluted Sera-Mag Magnetic SpeedBeads (GE Healthcare, GEHE45152105050250) and isopropanol in volumetric ratio of 2:3:4 (beads:lysate:isopropanol). Beads were captured with a neodymium magnet and washed once with isopropanol, twice with 70% ethanol and resuspended in milliQ water.
For ACE-seq, 10 ng of purified DNA was enzymatically fragmented to ~300 bp with dsDNA Fragmentase (#M0348 NEB), according to the manufacturer instructions, with the reaction scaled down 50%, and incubation time of 37 °C for 32 min. Fragmented DNA was concentrated using PEG-diluted SPRI beads. In a total volume of 5 μl, 5hmC was glucosylated with 5 U T4- βGT in NEB buffer 4 supplemented with 2 mM UDP-Glucose at 37 °C for 1 h. Glucosylated DNA was denatured in the presence of 20% DMSO at 95 °C for 5 min then swiftly transferred to a pre-cooled PCR tube rack on dry ice for snap-cooling. The single stranded glucosylated DNA was then deaminated in 50 mM Bis-Tris (pH 6.0), 0.1% Triton X-100 (APOBEC Reaction Buffer, EM-seq component E7134AA, NEB), 20 µg BSA (NEB) using 0.2 µg of APOBEC3A (EM-seq component E7133AA, NEB), in a total volume of 10 μl. DNA was deaminated by APOPBEC3A at 4 °C for 10 minutes, then ramping from 4 to 50 °C over 2 h followed by 50 °C for 10 min as previously reported (46). First strand synthesis, second strand synthesis for adapter tagging, and PCR, was completed as described above for PBAT. Library integrity was determined by agarose gel electrophoresis, libraries were pooled and size selected by gel extraction (MinElute® Gel Extraction Kit, Qiagen) and sequenced over 3 Illumina iSeq100 runs using 150bp chemistry.
APOBEC-coupled epigenetic sequencing (ACE-seq)

treatment_protocol: Mouse TET 1-3 triple-KO ESC line with doxycycline inducible mouse TET3 catalytic domain were treatet with 1 μM doxycycline.

value: Embryonic stem cells

tag: dox inducible tet3-cd

value: Dox 12h


title: Bacteria injection - ultrasound Stimulation R225

status: Public on Jun 13 2022

type: SRA

city: Niskayuna

first: John

last: Graf

state: New York

address: One Research Circle

country: USA

institute: GE Global Research

library_source: transcriptomic

data_processing:
Fastq files of the paired end reads were merged into two files for each sample, one for R1 and one for R2 using Unix commands.
Base quality control was checked using Fast QC v0.10.1 from Babraham Bioinformatics.
Sequencing reads were mapped to the annotated rat genome version, Rattus norvegicus Rnor 6.0.91, using STAR_2.5.3a aligner.
Transcript abundance estimates were generated from the sorted BAM files using RSEM.
Transcript abundance normalization was performed on all samples using the DESeq2 tool.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: rsem_genes.csv : comma-delimited text file that includes the table of RSEM output for every gene and every sample
Supplementary_files_format_and_content: rsem_isoforms.csv : comma-delimited text file that includes the table of RSEM output for every transcript and every sample
Supplementary_files_format_and_content: transcript_read_counts.csv : comma-delimited text file that includes the table of raw read counts for every transcript and every sample
Supplementary_files_format_and_content: transcript_normalized_abundance.csv : comma-delimited text file that includes the table of Median Ratio normalization (MRN) abundances for every transcript and every sample

molecule: total RNA

organism: Rattus norvegicus

source_name: blood 18 hours post injection and 2 hours post ultrasound

growth_protocol: Adult male Sprague-Dawley rats (age 9-11 weeks) weighing 300-400 gm were used in this study under the approval of Institutional Animal Care and Use Committee (IACUC) at the Feinstein Institutes for Medical Research. Streptococcus Pneumoniae Serotype 19F (49619, American Type Culture Collection (ATCC)) was cultured in Brain Heart Infusion broth until it reached the log phase with an optic density of 0.5 at 600nm. It was then aliquoted in 1.8 ml cryogenic vials with 30% glycerol and stored in a -80C freezer.

extract_protocol:
Blood was collected at the terminal time point 2 hours post ultrasound treatment from cardiac puncture. RNA extraction from tissues and RNA sequencing were performed at the Feinstein Institutes for Medical Research (FIMR), Genomics Shared Resource, Manhassett, New York.
Sequencing RNA libraries were prepared using the Rat TruSeq Stranded Total RNA with Ribo-Zero Globin Sample Preparation Kit (Illumina, San Diego, CA) according to the manufacturer’s instructions.

treatment_protocol: Lung instillation was performed on rats anesthetized with isoflurane (5% for induction and 2-3% for maintenance). A catheter was placed in the trachea below the larynx (IV Catheter 20G x 1-3/4in L, Jelco). A polyethylene tube (PE-10) was then inserted inside the catheter. Either saline or a bacterial dose of 3E5 suspended in 200 ul saline was instilled. Splenic ultrasound stimulation was delivered at 16 hours after bacteria or saline inoculation. The rats were anesthetized using isoflurane. The location of the spleen was identified using diagnostic imaging ultrasound. Animals either received 5 minutes of ultrasonic stimulus (1.1 MHz, 200mV per pulse, 150 burst cycles, 200 ms burst period) or Sham stimulus where no energy was applied. The ultrasound system consists of RF power amplifier (E&I 350L), a function generator (Agilent 33120A), a matching network (Sonic Concept), and High-Frequency Focused Ultrasound Probe/transducer (Sonic Concept H106).

tag: tissue

value: blood

tag: injection

value: Bacteria

tag: ultrasound

value: Stimulation

tag: series


title: Bacteria injection - ultrasound Sham R219

value: Sham


title: large-vs-small-kit: small-kit 4np (LKC1)

city: Oxford

first: Robert

middle: A

last: Beagrie

address: Headley Way

department: Molecular Haematology Unit

country: United Kingdom

institute: MRC Weatherall Institute of Molecular Medicine

library_source: genomic

data_processing:
Library strategy: Genome Architecture Mapping
Reads were aligned to the mm9 build of the mouse genome using bowtie v2.1.
GAMtools (https://gam.tools) was used to discard poorly or non-uniquely mapped reads, remove PCR duplicates and call positive 40kb windows based on the level of read coverage. Samples with less than 15% of reads mapping to the Mouse genome were not taken forward for further analysis but can be found in a separate GEO submission under the same super-series.
Genome_build: mm9
Supplementary_files_format_and_content: GAM segregation table: Each row represents one 40kb window from the mouse genome, each column indicates one sequencing sample (containing three nuclear profiles). Values indicate whether the given window was present (1) or absent (0) from the given sample.

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse ES Cells

growth_protocol: Cells were grown at 37°C in a 5% CO2 incubator in Glasgow Modified Eagles Medium, supplemented with 10% fetal bovine serum, 2 ng/ml LIF and 1 mM 2-mercaptoethanol, on 0.1% gelatin-coated dishes. Cells were passaged every other day. After the last passage 24h before harvesting, ES cells were re-plated in serum-free ESGRO Complete Clonal Grade medium (Millipore Inc.)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines

tag: cell type

tag: strain


title: Bacteria injection - ultrasound Stimulation R223


title: eosin-test: eosin-etoh 4np (EOH3)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with sterile-filtered eosin (0.5 % w/v in 40% ethanol) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: ESC, TET-TKO, TET3, Dox 12h, A, 5hmC

source_name: Mouse TET 1-3 triple-KO ESC line with doxycycline inducible mouse TET3 catalytic domain

tag: cell line

tag: treatment


title: eosin-test: eosin-etoh 4np (EOG3)


title: Bacteria injection - ultrasound Sham R209


title: ESC, TET-TKO, TET3, Dox 12h, B, 5hmC

value: Mouse TET 1-3 triple-KO ESC line with doxycycline inducible mouse TET3 catalytic domain


title: Bacteria injection - ultrasound Stimulation R226


title: eosin-test: unstained 4np (EOA4)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: sybrgold-test: stained-sybrgold 4np (SGD1)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Samples were then frozen and stored overnight at -20 ∞C. The next day, whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: large-vs-small-kit: small-kit 4np (LKA1)


title: eosin-test: eosin-etoh 4np (EOF3)


title: Bacteria injection - ultrasound Sham R208


title: ESC, TET-TKO, TET3, Dox 6h, B, 5hmC

value: Dox 6h


title: eosin-test: eosin-etoh 4np (EOE3)


title: ESC, TET-TKO, TET3, Dox 6h, A, 5hmC


title: Bacteria injection - ultrasound Sham R207


title: Bacteria injection - ultrasound Sham R206


title: ESC, TET-TKO, TET3, Ctr 0h, C, 5hmC

value: Ctr 0h


title: eosin-test: eosin-etoh 4np (EOC3)


title: eosin-test: eosin-h2o 4np (EOH2)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with sterile-filtered eosin (0.5 % w/v in water) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: Saline injection - ultrasound Sham R201

value: Saline


title: Saline injection - ultrasound Sham R202


title: eosin-test: eosin-etoh 4np (EOB3)


title: eosin-test: eosin-h2o 4np (EOG2)


title: eosin-test: eosin-h2o 4np (EOF2)


title: ESC, TET-TKO, TET3, Ctr 0h, B, 5hmC


title: ESC, TET-TKO, TET3, Ctr 0h, A, 5hmC


title: Saline injection - ultrasound Sham R200


title: eosin-test: eosin-h2o 4np (EOD2)


title: eosin-test: eosin-etoh 4np (EOD3)


title: eosin-test: eosin-h2o 4np (EOC2)


title: eosin-test: eosin-h2o 4np (EOB2)


title: Saline injection - ultrasound Sham R198


title: cresyl-violet-test: crystal-violet 4np (CVG4)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with sterile-filtered crystal violet (1 % w/v in water) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: eosin-test: eosin-h2o 4np (EOA2)


title: Saline injection - ultrasound Sham R197


title: cresyl-violet-test: crystal-violet 4np (CVH4)


title: eosin-test: eosin-etoh 4np (EOA3)


title: cresyl-violet-test: crystal-violet 4np (CVE4)


title: Bacteria injection - ultrasound Sham R193


title: cresyl-violet-test: crystal-violet 4np (CVD4)


title: Bacteria injection - ultrasound Sham R192


title: cresyl-violet-test: crystal-violet 4np (CVB4)


title: HEK293_K57N_rep1

type: RNA

city: Minato-ku

first: Mutsuhiro

last: Takekawa

state: Tokyo

address: 4-6-1, Shirokanedai

country: Japan

institute: Institute of Medical Science, The University of Tokyo

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes and hybridized to Agilent SurePrint G3 Human GE 8x60k Ver2.0 for 17 hours at 65°C using Agilent Gene Expression Hybridization kit in a rotating hybridization oven.

scan_protocol: Slides were scanned after washing on the Agilent DNA Microarray Scanner (G2539A) according to the AgilentG3_GX_1Color protocol (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software10.10.1.1 (Agilent) using default parameters (protocol GE1_1010_Sep10 and Grid: 039494_D_F_20120628). Raw expression values were further normalized by quantile method (percentile Shift=75) using GeneSpring GX.

organism: Homo sapiens

source_name: HEK293 cells stably expressing K57N

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the Low Input Quick Amp labeling kit (one-color, Agilent), followed by RNAeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 and Agilent 2100 Bioanalyzer.

extract_protocol: RNA was prepared using QIAGEN miRNeasy Mini Kit following the manufacturer's recommendations. RNA was quantified using Nanodrop ND 1000 and quality was monitored with the Agilent 2100 Bioanalyzer and RNA6000 Nanokit.

tag: expression


title: cresyl-violet-test: crystal-violet 4np (CVA4)


title: eosin-test: eosin-h2o 4np (EOE2)


title: Bacteria injection - ultrasound Stimulation R116


title: Saline injection - ultrasound Sham R199


title: cresyl-violet-test: crystal-violet 4np (CVH3)


title: HEK293_K57N_rep3


title: HEK293_K57N_rep2


title: HEK293_F53S_rep2

source_name: HEK293 cells stably expressing F53S


title: cresyl-violet-test: crystal-violet 4np (CVF4)


title: Bacteria injection - ultrasound Stimulation R105


title: HEK293_F53S_rep1


title: Bacteria injection - ultrasound Stimulation R114


title: cresyl-violet-test: crystal-violet 4np (CVF3)


title: cresyl-violet-test: crystal-violet 4np (CVE3)


title: Bacteria injection - ultrasound Stimulation R102


title: cresyl-violet-test: crystal-violet 4np (CVB3)


title: HEK293_F53S_rep3


title: HEK293_WT_rep3

source_name: HEK295 cells stably expressing WT

value: WT


title: cresyl-violet-test: crystal-violet 4np (CVG3)


title: Bacteria injection - ultrasound Stimulation R101


title: cresyl-violet-test: crystal-violet 4np (CVC3)


title: cresyl-violet-test: crystal-violet 4np (CVC4)


title: cresyl-violet-test: unstained 4np (CVG2)


title: cresyl-violet-test: water-control (CVH2)

extract_protocol:
An adhesive 8-strip LCM collection cap was left empty during laser microdissection to act as a negative control. Whole genome amplification was performed on the empty cap using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: HEK293_WT_rep2

source_name: HEK294 cells stably expressing WT


title: HEK293_WT_rep1

source_name: HEK293 cells stably expressing WT


title: cresyl-violet-test: crystal-violet 4np (CVD3)


title: Saline injection - ultrasound Stimulation R97


title: Bacteria injection - ultrasound Stimulation R99


title: cresyl-violet-test: unstained 4np (CVC1)


title: cresyl-violet-test: unstained 4np (CVB1)


title: cresyl-violet-test: unstained 4np (CVD2)


title: Saline injection - ultrasound Stimulation R96


title: cresyl-violet-test: unstained 4np (CVA2)


title: WT_CRE2

city: Baltimore

first: Peisong

last: Gao

state: MARYLAND

address: 5501 Hopkins Bayview Circle

institute: Johns Hopkins Asthma & Allergy Center

data_processing:
RNAseq reads were aligned to the  mouse reference genome GRCm38 using STAR aligner version 2.7.2b.
BAM file outputs from  STAR were annotated using Partek Genomic Suite (v6.6) and the RefSeq database.
The gene  expression levels were defined as counts by Salmon
Assembly: GRCm38(mm10)
Supplementary files format and content: tab-delimited text files include FPKM and count values for each Sample

source_name: AT2 cells from AhRfl/fl mice

extract_protocol:
Mouse AT2 cells were isolated from AhRfl/fl mice and Sftpc-Cre;AhRflox/flox mice. Briefly, mice were euthanized with ketamine and xylazine intraperitoneally. Lung  tissues from these mice were digested with Dispase (50 units/ml, Gibco) at room temperature for  45 min, and then incubated with AT2 isolation medium consisting of a 1:1 mixture of  Dulbecco’s modified Eagle’s medium (DMEM) and Ham’s F-12 (DMEM/F-12; Sigma)  supplemented with 0.01% DNase I (Sigma), 100 U/ml sodium penicillin G, and 100 μg/ml  streptomycin. The mixed cells were filtered through cell strainers, stained with biotinylated anti_x0002_CD16/32, anti-CD45, anti-Ter119, and anti-Sca-1 (Biolegend), and incubated at 37 °C shaking  incubator for 30 min. These cells were further negatively selected with streptavidin-conjugated  magnetic beads for 30 min at RT. Cells were centrifuged for 10 min at 300g at 4 °C, and  incubated on dishes pre-coated with mouse IgG. After incubation for 2 h, non-adherent cells  were collected, centrifuged and re-suspended with AT2 isolation medium.
RNA-Seq libraries were prepared for sequencing using Illumina TruSeq stranded mRNA sample  preparation kit following the manufacturer’s recommended procedure. Briefly, total RNA was  extracted using RNeasy Mini Kit (QIAGEN). mRNA was enriched using oligo dT beads and  then fragmented chemically by incubating at 94℃ for 8 min. cDNA was synthesized with  SuperScript II. After purification using AMPure XP beads, the double-stranded cDNA was  ligated to TruSeq RNA adapters followed by 15 cycles of amplification and library purification.

treatment_protocol: Isolated AT2 cells were cultured on 12-well plate coated with Collagen I, then the cells were treated with or without 50 ug/ml CRE for 24h. RNA were extracted after treatment.

value: AT2 cells from AhRfl/fl mice

tag: genotype

value: CRE


title: WT_PBS1

value: PBS


title: WT_PBS2


title: WT_PBS3


title: wga-pcr-cycles-test: 23-pcr-cycles 4np (F43A2)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 23 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: wga-pcr-cycles-test: 20-pcr-cycles 4np (F43A3)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 20 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: wga-pcr-cycles-test: 25-pcr-cycles 4np (F43B1)


title: cresyl-violet-test: crystal-violet 4np (CVA3)


title: wga-pcr-cycles-test: 20-pcr-cycles 4np (F43D3)


title: WT_CRE3


title: wga-pcr-cycles-test: 25-pcr-cycles 4np (F43A1)


title: Saline injection - ultrasound Stimulation R89


title: WT_CRE1


title: early-freezing-test: frozen-late 4np (F42A2)


title: Saline injection - ultrasound Stimulation R87


title: Saline injection - ultrasound Stimulation R95


title: AhR_PBS2

source_name: AT2 cells isolated from Sftpc-Cre;AhRfl/fl mice

value: KO


title: Saline injection - ultrasound Stimulation R86


title: full-collection-4np: gdna-control (G1H12)

extract_protocol:
An adhesive 8-strip LCM collection cap was left empty during laser microdissection. After laser microdissection, 5 ng of Human genomic DNA was added to the cap to act as a positive control. Whole genome amplification was performed on the cap containing the gDNA using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: AhR_PBS1

value: AT2 cells isolated from Sftpc-Cre;AhRfl/fl mice


title: AhR_CRE3


title: AhR_PBS3


title: early-freezing-test: frozen-late 4np (F42G1)


title: Gut_500ppb_flx

city: Sainte-Anne-de-Bellevue

first: Krittika

last: Mittal

state: Quebec

address: 21,1111 Lakeshore Blvd, Apt #2

country: Canada

institute: McGill University

description: RTgutCC

data_processing:
Raw reads were preprocessed and filtered by fastp with a minimum reads quality score of 25 and minimum read length of 15
Salmon, an ultra-fast pseudo-alignment tool for transcript quantification of RNA-seq data was used to map and quantify the filtered reads
Assembly: Rainbow trout reference genome: USDA O.mykiss version 1.1
Supplementary files format and content: Raw fastq files were filtered as mentioned above and provided count matrices. These were analyzed for gene expression and benchmark dose response, resulting in tables of differentially expressed genes and list of genes with transcriptomic benchmark dose response values.

organism: Oncorhynchus mykiss

source_name: Intestinal Epithelium

growth_protocol: Cells were grown at 19C in 100 mm petri dishes with L-15 culture medium (without phenol red) containing 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
RNA was isolated from cells using the Qiagen Rneasy kit with the aid of the QIAcube
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 101-bp paired-end reads.

treatment_protocol: For the methylmercury experiment two replicates were treated with a range of 5 concentrations plus control for 24 h. For fluoxetine single replicates were treated with a range of 9 concentrations plus two controls for 24 h.

tag: passage #


title: early-freezing-test: frozen-early 4np (F42A4)


title: Gut_1000ppb_flx

description: RTgutCC


title: full-collection-4np: 4np (G1F12)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with cresyl violet (1 % w/v in water) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Caps were frozen and stored for up to two weeks. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: full-collection-4np: water-control (G1G12)

extract_protocol:
An adhesive 8-strip LCM collection cap was left empty during laser microdissection to act as a negative control. Whole genome amplification was performed on the empty cap using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.95 µl library preparation mastermix (3.3 µl library preparation buffer, 1.65 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 4.5 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 85 µl amplification master mix (11 µl amplification buffer, 66.5 µl H2O, 7.5 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: AhR_CRE2


title: Gut_100ppb_flx

description: RTgutCC


city: South San Francisco

first: Matthew

middle: R

last: Grimmer

state: CA

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

description: in vivo mouse xenograft HCC2302 A947 rep5 + A947

data_processing:
Raw sequencing reads for in vitro samples were mapped to the UCSC human genome (GRCh38) using GSNAP software.
In order to remove potential mouse stromal contamination for in vivo xenograft samples, raw sequencing reads were stripped of reads showing complete alignment to the UCSC mouse genome (mm10) using Xenome software.
Remaining reads not showing complete alignment to mm10 were then mapped to GRCh38/hg38 using GSNAP software. Gene expression counts were obtained by quantifying the number of reads uniquely mapping to each gene locus.
Lowly expressed genes were removed from all samples using a high-pass filter for genes with at least 15 counts in at least 10% of samples.
Quantile normalized Log2 counts per million (LogCPM) of sufficiently covered genes were generated using the voom function of the limma analysis pipeline.
Assembly: GRCh38
Supplementary files format and content: SAM*.analyzed.bam: BAM and reads aligned to human GRCh38, as described above
Supplementary files format and content: counts_voomed.txt: text file and Log2CPM, normalized using limma::voom

source_name: lung

growth_protocol: Cells were maintained in RPMI1640 supplemented with 10% Fetal Bovine Serum (FBS) and 2mM L-Glutamine, under 5% CO2 at 37ºC

extract_protocol:
For in vitro gene expression studies, cells were treated with DMSO or A947(100nM) for both 24h and 96h prior to isolation of total RNA using the MagMax mirVana total RNA isolation kit (ThermoFisher Scientific, A27828). In addition, HCC2302-shNTC and HCC2302-shSMARCA2 cells were treated for 168h prior to isolation of RNA. For in vivo gene expression studies, total RNA was isolated from xenograft tissues as above. RNA concentrations were measured by NanoDrop8000 (ThermoFisher).
Integrity of RNA was assessed by Bioanalyzer 2100 prior to library generation using 500ng RNA. Libraries were prepared using the TruSeq Stranaded Total RNA Library Prep Kit (Illumina), multiplexed and sequenced on Illumina HiSeq2500 (Illumina) to generate ~30M single end, 50 base pair reads.

treatment_protocol: Inducible SMARCA2 knockdown cell lines were generated using shRNAs directed against SMARCA2 tandemly delivered in a modified pBH1.2 piggy-bac system (Smarca2_iKD_dual62_pBH1.2). The following shRNAs were utlilized: shRNA6:GATCCGTCTCGTCGAGCAATCATTTGGTTGTAGTGAAATAtATATTAAACAACCAAATGATTG CTCGACGTTACGGTAC and shRNA2:GATCCGTCTGACTGTTCACGTTCATCCTGGTAGTGAAATAtATATTAAACCAGGATGAACGTG AACAGTCTTACGGTAC. pBO (Piggybac transposase) were co- transfected with Smarca2_iKD_dual62_pBH1.2 into HCC2302 cells by using lipofectamine 2000 (ThermoFisher Scientific). Cells were selected with 2 μg/mL puromycin (Gibco) 3 days after transfection and subsequently subcloned.

value: lung

value: lung adenocarcinoma

value: SMARCA2 mutant


title: full-collection-4np: 4np (G1C12)


description: in vivo mouse xenograft HCC2302 A947 rep1 + A947


description: in vivo mouse xenograft HCC2302 A947 rep4 + A947


title: full-collection-4np: 4np (G1D12)


title: Gut_200ppb_flx

description: RTgutCC


title: Perk KO astrocytes, TM-treated, Biol. Rep. 3

city: Amsterdam

first: Wiep

last: Scheper

address: De Boelelaan 1085

department: Department of Functional Genomics, Center for Neurogenomics and Cognitive Research  (CNCR)

country: Netherlands

institute: Amsterdam University Medical Centers (UMC) Location Vrije Universiteit

description:
A_KO_CvsA_KO_TM_DEG.xls
A_WT_TMvsA_KO_TM_DEG.xls

data_processing:
Raw data were processed through fastp and clean data were mapped to the reference mouse genome (ensembl_mus_musculus_grcm38_p6_gca_000001635_8) using HISAT2 software.
Featurecounts software was used to count the read numbers mapped of each gene (readcounts) and Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) of each gene were calculated.
Differential expression analysis between two conditions (three biological replicates per condition) was performed using the obtained readcounts and DESeq2 R package, calculating the log2FoldChange, p-values, and adjusted p-values (padj) using the Benjamini and Hochberg's approach for controlling the false discovery rate.
Assembly: ensembl_mus_musculus_grcm38_p6_gca_000001635_8
Supplementary files format and content: fpkm_genename.xls includes FPFM values for each Sample
Supplementary files format and content: fpkm_readcount.xls includes readcount values for each Sample
Supplementary files format and content: _DEG.xls includes differenctial expression analysis

source_name: Astrocytes

growth_protocol: Neuron and astrocyte cultures were maintained in neurobasal medium (NB) supplemented with 2% B-27, 1.8% HEPES, 0.25%   GlutaMAX and 0.1% pen-strep at 37°C/5% CO2

extract_protocol:
Cells were washed with ice-cold PBS and cell lysates were prepared by incubation and scraping in TRI Reagent   solution (Invitrogen). Cell lysates were loaded on Phase Lock Gel-Heavy tubes (Quantabio) and mixed 1:5 with chloroform (VWR Chemicals). The organic   and aqueous phase were separated by centrifugation at 12000 g for 15 min at 4°C. The aqueous phase was mixed 1:1 with Isopropanol (VWR Chemicals) and 150 mg/mL glycoblue (Invitrogen) and centrifuged at 12000 g for 10 min at 4°C to precipitate RNA. Precipitated RNA was washed with 75% ethanol (Sigma-Aldrich) and centrifuged 7500 g for 5 min. After removal of ethanol, the pellet was air-dried and dissolved in RNase-free H2O.
Transcriptome analysis was performed by Novogene (UK) Company Limited, Cambridge, United Kingdom. Quantity and quality of isolated RNA was assessed by agarose gel electrophoresis, spectrophotometry using the NanoPhotometer (IMPLEN) and the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent). Only qualified samples were used for RNA sequencing. First, sequencing libraries were generated, using 1 µg RNA per sample and   the NEBNext Ultra TM RNA Library Prep Kit for Illumina (New England BioLabs), according to the manufacturer’s protocol and index codes were added to attribute sequences. PCR products were purified using the AMPure XP system and library quality was assessed using the Bioanalyzer 2100 system (Agilent). Clustering of the index-coded samples was performed using a cBot Cluster Generation System and PE Cluster Kit cBot-HS (Illumina), according to the manufacturer’s protocol. Finally, the library preparations were sequenced on a NovaSeq 6000 platform (Illumina) and paired-end reads were generated.

treatment_protocol: To induce ER-stress cells were treated with 5 µg/mL tunicamycin (TM; Sigma-Aldrich) for 24 hours at days in vitro (DIV) 14. Equal volumes of DMSO were added to the controls.

value: Astrocytes

value: Perk KO

value: TM


description: in vivo mouse xenograft HCC2302 A947 rep3 + A947


description: in vivo mouse xenograft HCC2302 A947 rep2 + A947


title: full-collection-4np: 4np (G1A12)


title: full-collection-4np: 4np (G1B12)


title: Gut_20ppb_flx

description: RTgutCC


title: Gut_8ppb_flx

description: RTgutCC


title: Perk KO astrocytes, TM-treated, Biol. Rep. 1


title: Perk KO astrocytes, Control, Biol. Rep. 3

description:
A_KO_CvsA_KO_TM_DEG.xls
A_WT_CvsA_KO_C_DEG.xls

value: DMSO


description: in vivo mouse xenograft HCC2302 Veh rep5 + Vehicle

value: Vehicle


description: in vivo mouse xenograft HCC2302 Veh rep4 + Vehicle


title: Gut_4ppb_flx

description: RTgutCC


title: Perk KO astrocytes, Control, Biol. Rep. 2


description: in vivo mouse xenograft HCC2302 Veh rep3 + Vehicle


title: full-collection-4np: 4np (G1C11)


title: full-collection-4np: 4np (G1F11)


description: in vivo mouse xenograft HCC2302 Veh rep2 + Vehicle


title: AhR_CRE1


title: Gut_ctrl_flx

description: RTgutCC


title: Gut_1.6ppb_flx

description: RTgutCC


description: in vivo mouse xenograft HCC2302 Veh rep1 + Vehicle


title: full-collection-4np: water-control (G1H10)


title: Perk KO astrocytes, TM-treated, Biol. Rep. 2


title: full-collection-4np: 4np (G1H11)


title: Liv_1000ppb_flx

source_name: Liver


title: Gut_40ppb_flx

description: RTgutCC


title: full-collection-4np: 4np (G1F10)


title: WT astrocytes, TM-treated, Biol. Rep. 3

description:
A_WT_CvsA_WT_TM_DEG.xls
A_WT_TMvsA_KO_TM_DEG.xls


title: Perk KO astrocytes, Control, Biol. Rep. 1


title: WT astrocytes, TM-treated, Biol. Rep. 1


title: WT astrocytes, TM-treated, Biol. Rep. 2


title: full-collection-4np: 4np (G1C10)


title: full-collection-4np: 4np (G1D10)


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Dox rep2 + Dox

value: Dox


title: WT astrocytes, Control, Biol. Rep. 3

description:
A_WT_CvsA_WT_TM_DEG.xls
A_WT_CvsA_KO_C_DEG.xls


title: Gut_H2O_flx

description: RTgutCC


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Dox rep3 + Dox


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Dox rep1 + Dox


title: Liv_500ppb_flx


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Veh rep2 + Vehicle


title: WT astrocytes, Control, Biol. Rep. 2


title: Liv_200ppb_flx


title: Liv_40ppb_flx


title: full-collection-4np: 4np (G1B10)


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Veh rep1 + Vehicle


title: full-collection-4np: 4np (G1D9)


title: WT astrocytes, Control, Biol. Rep. 1


title: full-collection-4np: water-control (G1H8)


title: Perk KO neurons, TM-treated, Biol. Rep. 2

description:
N_KO_CvsN_KO_TM_DEG.xls
N_WT_TMvsN_KO_TM_DEG.xls

source_name: Neurons

value: Neurons


title: full-collection-4np: 4np (G1A10)


title: Liv_20ppb_flx


title: full-collection-4np: 4np (G1G8)


title: Perk KO neurons, TM-treated, Biol. Rep. 3


title: in vitro HCC2302-shNTC Dox rep3

description: in vitro HCC2302-shNTC Dox rep3 + Dox


description: in vitro HCC2302-shSMARCA2-dual62 cl2 Veh rep3 + Vehicle


title: full-collection-4np: 4np (G1D8)


title: Liv_4ppb_flx


title: Liv_8ppb_flx


title: Liv_100ppb_flx


title: in vitro HCC2302-shNTC Dox rep1

description: in vitro HCC2302-shNTC Dox rep1 + Dox


title: in vitro HCC2302-shNTC Veh rep3

description: in vitro HCC2302-shNTC Veh rep3 + Vehicle


title: full-collection-4np: 4np (G1F8)


title: Perk KO neurons, Control, Biol Rep. 2

description:
N_KO_CvsN_KO_TM_DEG.xls
N_WT_CvsN_KO_C_DEG.xls


title: Perk KO neurons, Control, Biol Rep. 3


title: Liv_H2O_flx


title: full-collection-4np: 4np (G1C8)


title: Liv_1.6ppb_flx


title: Perk KO neurons, Control, Biol Rep. 1


title: Liv_ctrl_flx


title: Gill_1000ppb_flx

source_name: Gill


title: KM-155 24h-3

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

description: Human myoblast differentiated for 24h replicate-3

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Genome_build: hg19
Supplementary_files_format_and_content: text files containing counts

source_name: Human myoblast differentiate

growth_protocol: Human myoblasts were cultured in growth medium (equal volume mixture of Hamm's F10 media with 20% FBS and Promocell Skeletal Muscle Cell Growth Medium).  Human myoblasts were induced to differentiate by growth to high density and replacement of the growth medium with differentiation medium (DMEM with 2% horse serum)

extract_protocol:
Total RNA from cultured cells was isolated using the Direct-zol™ RNA MiniPrep kit (Zymo Research), which includes a digestion step using DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human myoblast

tag: cell status

value: Differentiated for 24h


title: WT neurons, TM-treated, Biol. Rep. 2

description:
N_WT_CvsN_WT_TM_DEG.xls
N_WT_TMvsN_KO_TM_DEG.xls

value: WT


title: full-collection-4np: 4np (G1F7)


title: WT neurons, TM-treated, Biol. Rep. 3


title: Gill_500ppb_flx


title: full-collection-4np: 4np (G1A8)


title: in vitro HCC2302-shNTC Dox rep2

description: in vitro HCC2302-shNTC Dox rep2 + Dox


title: Perk KO neurons, TM-treated, Biol. Rep. 1


title: in vitro HCC2302-shNTC Veh rep1

description: in vitro HCC2302-shNTC Veh rep1 + Vehicle


title: WT neurons, TM-treated, Biol. Rep. 1


title: KM-155 24h-2

description: Human myoblast differentiated for 24h replicate-2


title: in vitro HCC2302-shNTC Veh rep2

description: in vitro HCC2302-shNTC Veh rep2 + Vehicle


title: Gill_100ppb_flx


title: full-collection-4np: 4np (G1B7)


title: Gill_40ppb_flx


title: full-collection-4np: 4np (G1B8)


title: Gill_200ppb_flx


title: KM-155 0h-2

description: Proliferating human myoblast replicate-2

source_name: Proliferating human myoblast replicate

value: Proliferating


title: WT neurons, Control, Biol. Rep. 3

description:
N_WT_CvsN_WT_TM_DEG.xls
N_WT_CvsN_KO_C_DEG.xls


title: KM-155 24h-1

description: Human myoblast differentiated for 24h replicate-1


title: WT neurons, Control, Biol. Rep. 1


title: full-collection-4np: 4np (G1A7)

source_name: Mouse ES Cells


title: full-collection-4np: gdna-control (G1H6)


title: KM-155 0h-1

description: Proliferating human myoblast replicate-1


title: Gill_20ppb_flx


title: Gill_4ppb_flx


title: full-collection-4np: 4np (G1A6)


title: full-collection-4np: 4np (G1A5)


title: WT neurons, Control, Biol. Rep. 2


title: KM-155 0h-3

description: Proliferating human myoblast replicate-3


title: Gill_H2O_flx


title: m16Carrier6

city: Cambridge

first: Kamal

last: Kishore

address: Robinson Way

department: Bioinformatics Core

institute: CRUK CI

data_processing:
Reads were aligned to the mouse genome version GRCm38 using STAR v2.5.3a
Read counts were obtained using feature Counts function in Subread v1.5.267
Read counts were normalized and tested for differential gene expression using the DESeq2 workflow
Multiple testing correction was applied using the Benjamini–Hochberg method
Assembly: GRCm38
Supplementary files format and content: text files include raw counts of sequencing reads for each Sample

source_name: Spleen/peripheral lymph nodes

growth_protocol: Spleens were harvested and placed into ice-cold sterile DPBS (Gibco, cat no. 14190094, hereafter referred to as PBS). Spleens were dissociated through a 70 μm filter (Greiner, cat no. 542070) using the top of the plunger from a 2 ml syringe. Filters were washed with ice-cold, sterile MACS Buffer, made with PBS + 2% fetal calf serum (FCS, Biosera, cat no. 1001, 500ml) + 2 mM EDTA and then centrifuged at 1200 rpm for 10 min at 4°C. Naïve murine CD4+ T cells were isolated using a negative-selection MACS approach (Naïve CD4+ T Cell Isolation Kit, cat no. 130-104-453, Miltenyi Biotec). MACS separation was performed by loading the labelled cell suspension through a 50µm sterile CellTrics Partec filter (Wolflabs, cat no. 04-004-2327) onto the LS column (Miltenyi Biotec, cat no. 130-042-401). The purity of the sorted populations was above 95%. CD4+ T cells were plated onto a 96-well plate pre-coated overnight at 4°C with 2.5 µg/ml anti-CD3e and 2 µg/ml anti-CD28 antibody. For Th polarization experiments CD4+ T cells were plated at a final concentration of 1x106 cells/ml in complete IMDM supplemented with 10ng/ml IL-1b, 20ng/ml IL-6, 10ng/ml IL-23, 1ng/ml TGF-b (all Peprotech), 5ug/ml anti-IL-4 monoclonal antibody (Biolegend Cat No. 504115) and 10ug/ml anti-IFNg monoclonal antibody (Biolegend Cat No. 517904).

extract_protocol:
RNA was extracted using the RNAqeous™-Micro Total RNA Isolation Kit according to the manufacturer’s instructions. RNA quality was assessed using a capillary electrophoresis system (4200 Tapestation, Agilent) using RNA ScreenTape (Agilent, cat no. 5067-5576) as per the manufacturer’s instructions. RNA concentrations were quantified using the Qubit™ RNA BR Assay kit (Thermo, cat no. 10210) as instructed by the manufacturer
Libraries were generated using the TruSeq stranded mRNA kit (Illumina) following the manufacturer’s instructions

treatment_protocol: Th17 cells were polarised as described for 3 days in culture in the presence of cyclopamine (5uM or 7.5uM as indicated) or carrier control (ethanol).

value: Spleen/peripheral lymph nodes

value: Primary CD4+ T cells

value: Carrier


title: full-collection-4np: water-control (G1H4)


title: m18CYA75uM6

value: 7.5uM Cyclopamine


title: m17CYA5uM6

value: 5uM Cyclopamine


title: full-collection-4np: water-control (G1G6)


title: full-collection-4np: 4np (G1G4)


title: Gill_ctrl_flx


title: m14CYA5uM5


title: Gut_1_2_Hg

description: RTgutCC


title: full-collection-4np: 4np (G1C4)


title: full-collection-4np: 4np (G1A4)


title: Gill_8ppb_flx


title: full-collection-4np: 4np (G1C6)


title: Control

city: New York

first: Takayuki

last: Fujii

state: NY

address: 515 E 71st St

institute: Hospital for Special Surgery

data_processing:
Using CellRanger v3.0, sequenced reads were mapped on mm10, and cell-calling was performed.
Cell filtering, read count normalization, scaling, variable feature detection were performed using scran and Seurat. scDblFinder was used for doublet detection.
Data aggregation with CCA, dementionality reduction with PCA and UMAP, clustering and differentially expression analysis was performed with Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table of gene raw counts is in matrix.mtx, cell barcodes are barcodes.tsv, and gene names are features.tsv for every sample.

source_name: Mouse naïve bone cells

extract_protocol:
25,000 cells were used for library prep using Chromium Single Cell 3' Reagent Kits (v3 Chemistry)
Single-cell RNA-seq

value: Non-erythroid cells

tag: time

value: Control


title: full-collection-4np: 4np (G1E3)


title: Gut_1_1_Hg

description: RTgutCC


title: Gill_1.6ppb_flx


title: m12CYA75uM4


title: Day14-W1-D14-Neuts

data_processing:
Sequenced reads were mapped with STAR. Raw counts were normalized and differential analysis was performed using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: Raw read counts are provided by Raw_counts.csv

source_name: Mouse interface tissue after ACLR

extract_protocol:
Cells were sorted according to the gatings with flow cytometry and total RNA was extracted with RNeasy plus micro kit (Qiagen)
SMART-Seq Stranded Kit (Takara)

value: myeloid cell populations

tag: cell sorting

value: Live, Lin-, CD45+, Ly6G+, Ly6C+


title: Gut_0.5_2_Hg

description: RTgutCC


title: m13Carrier5


title: m15CYA75uM5


title: Gut_0.5_1_Hg

description: RTgutCC


title: m10Carrier4


title: Gut_0.1_2_Hg

description: RTgutCC


title: full-collection-4np: water-control (G1H2)


title: full-collection-4np: 4np (G1B2)


title: full-collection-4np: 4np (G1A2)


title: Day14-W1-D14-F4-80-


title: m8CYA5uM3


title: Day14-W2-D14-F4-80-


title: Day14-W1-D14-CX3R1


title: Gut_0.01_2_Hg

description: RTgutCC


title: Gut_0.01_1_Hg

description: RTgutCC


title: Gut_0.1_1_Hg

description: RTgutCC


title: m6CYA75uM2


title: full-collection-4np: 4np (G1B1)


title: Day14-W2-D14-CD9


title: m5CYA5uM2


title: m11CYA5uM4


title: m9CYA75uM3


title: freezing-after-incubation: frozen-post-incubation 4np (F41A3)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: m7Carrier3


title: Day14-W2-D14-CX3R1


title: m3CYA75uM1


title: freezing-after-incubation: unfrozen 4np (F41E2)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: freezing-after-incubation: frozen-post-incubation 4np (F41A4)


title: Gut_0.001_2_Hg

description: RTgutCC


title: full-collection-4np: 4np (G1A1)


title: Day01-WT2-F4-80-


title: freezing-after-incubation: unfrozen 4np (F41H1)


title: Day14-W2-D14-Neuts


title: m4Carrier2


title: Day01-WT2-Neuts


title: m2CYA5uM1


title: freezing-after-incubation: frozen-post-incubation 4np (F41D3)


title: Day14-W1-D14-CD9


title: Gut_0.001_1_Hg

description: RTgutCC


title: m1Carrier1


title: Day01-WT1-CX3R1


title: Gut_ctrl_2_Hg

description: RTgutCC


title: Day01-WT1-Neuts


title: Day01-WT1-CD9


title: Liv_0.5_1_Hg


title: Liv_0.1_1_Hg


title: VP_Cocaine_24h_2

city: Bordeaux cedex

first: Michel

last: Engeln

address: Zone nord Bat 2 2ème étage

country: France

institute: Institut de Neurosciences Cognitives et Intégratives d'Aquitaine (INCIA)

data_processing:
Base calls were performed using the built-in Illumina basecaller
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mouse GRCm38 reference using the TopHat splice-aware aligner
Reads counts were calculated for each sample.
Differential expression of genes were computed between saline and cocaine samples using Deseq
Assembly: M. musculus (GRCm38)
Supplementary files format and content: read counts, LFC, p value, FDR

source_name: Ventral pallidum neurons

growth_protocol: Room temperature 18-23°C, 12 hour light/dark cycle

extract_protocol:
RNA was extracted using Trizol (Invitrogen) and the RNeasy Micro kit (Qiagen: 74004) with a DNase step (#79254, Qiagen).
Libraries were prepared from 90 ng of RNA from each sample using the NEBNext Ultra kit (New England BioLabs). Samples were sequenced on an Illumina HiSeq 4000 with a 75 bp paired-end read.

value: Cocaine self-administration

value: Bulk VP neurons

value: wild-type


title: Day01-WT1-F4-80-


title: Gut_ctrl_1_Hg

description: RTgutCC


title: VP_Saline_24h_4

value: Saline self-administration


title: Liv_0.01_2_Hg


title: VP_Cocaine_24h_4


title: Liv_1_2_Hg


title: Liv_1_1_Hg


title: Liv_0.5_2_Hg


title: pk-volume-titration: 8ul-mdc-pk 4np (F40F6)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (12.3 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.8 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: Day01-WT2-CX3R1


title: pk-volume-titration: 8ul-mdc-pk 4np (F40G6)


title: VP_Cocaine_24h_3


title: pk-volume-titration: 8ul-mdc-pk 4np (F40A6)


title: Day01-WT2-CD9


title: VP_Cocaine_24h_1


title: Liv_0.01_1_Hg


title: pk-volume-titration: 8ul-mdc-pk 4np (F40D6)


title: pk-volume-titration: 8ul-mdc-pk 4np (F40E6)


title: VP_Saline_24h_2


title: Liv_0.1_2_Hg


title: pk-volume-titration: 8ul-mdc-pk 4np (F40C6)


title: pk-volume-titration: 8ul-mdc-pk 4np (F40B6)


title: VP_Saline_24h_3


title: pk-volume-titration: 4ul-mdc-pk 4np (F40G5)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (12.7 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.4 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: Rloop_BRD2_BRD3_untreated_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

country: China

institute: Peking University

data_processing:
All libraries were sequenced using an Illumina Hiseq sequencer and 150 bp paired-end format.
The 150 bp paired-end reads were pre-processed by Cutadapt and then aligned to the mm10 mouse genome assembly using Bowtie2.
Unmapped reads, low quality mapped reads and PCR duplicates were discarded. Only uniquely mapped were retained for downstream analysis.
Peaks were called against input control using the MACS2 function callpeak on each replicate in default parameters and q-value threshold of 0.05 to ensure high confidence. Repeatable peaks between the replicates were detected by IDR software using IDR threshold of 0.05.
The ChIP reads at each genomic position were normalized and converted to bigwig format using bamCoverage from deeptools toolkit. Rloop datasets were normalized by the spike-in reads that mapped to the E.coli T7 genome.
Genome_build: mm10
Supplementary_files_format_and_content: The bigwig files of ChIP-seq data were generated using deepTools.

source_name: mouse embryonic stem cells

growth_protocol: For BRD2-degron cells and BRD2-degron_BRD3-knockout cells ChIP-seq, BRD2-mAID tagged mES (V6.5) cell lines and BRD2-mAID BRD3-knockout mES (V6.5) cell lines were cultured with 2i medium containing 15% FBS, leukaemia inhibiting factor (mLIF), L-glutamine, β-mercaptoethanol, non-essential amino acids, 3 μM CHIR99021, and 1 μM PD0325901 in ES-qualified Dulbecco’s modified Eagle’s medium (DMEM), incubated at 37 °C with 5% CO2. mES cells were cultured with mESC EB medium without mLIF to form embryonic bodies (EBs).

extract_protocol:
The crosslinked cells were isolated into chromatin and digested using MNase (15 min at 37 °C), and then, sonicated in Bioruptor Sonication Device (high energy for 30s on and 60s off, work on 16 cycles).  Lysates were centrifuged twice, 40 μl supernatant were sampled as input, and the rest supernatant were transferred into 2 new DNase free tubes, 2 μg of BRD2 abs (CST, D89B4), 2 μg of BRD3 abs (Proteintech, 11859-1-AP), 2 μg of BRD4 abs (Abcam, ab128874), 1 μg of CTCF abs (ABclonal, A1133), 1 μg of Smc1a abs (Bethyl, A300-055A), 1 μg of Rpb1NTD abs (CST, D8L4Y) , 1 μg of Rpb1 PSer2 abs (CST, E1Z3G), 2.5 μg of TAF1 abs (CST, D6J8B), 2.5 μg of TAF3 abs (Proteintech, 18901-1-AP), 2.5 μg of TBP abs (Proteintech, 22006-1-AP), 4 μg of XRN2 abs (Proteintech, 11267-1-AP), and 1 μl GFP abs (Abcam, ab290) were added for each ChIP reaction, respectively, and equal isotype IgG control (Millipore, 12-370, 12-371) and incubated overnight at 4 °C with low speed rotation, the antibody enriched DNA was extracted by Tris saturated equilibrium phenol (25:24:1) (pH8.0).
BRD2-degron mES, BRD2, BRD3, BRD4, GFP, CTCF, SMC1, Pol II-NTD, Pol II-S2P, TAF1, TAF3, TBP, and XRN2 ChIPed DNA were subjected for library construction using the NEBNext Ultra II DNA library prep kit, according to the manufacturer-supplied protocol, and then the 200~400 bps length amplified DNA were recovered and analyzed with Qubit assays and Fragment Analyzer, and finally subject to HiSeq Xten PE150 sequencing (Novogene, Beijing).

treatment_protocol: BRD2-degron mES cells for 4 days were treated with 1 μg/ml Doxycycline (Dox) for 18 hrs and 500 μM auxin (indole-3-acetic acid) for 3 hrs to induce the BRD2 degradation. Then, cells were harvested and crosslinked using 1% formaldehyde for 10 min at room temperature, finally, cells were subjected for ChIP.

value: embryonic stem cells

tag: genotype/variation

value: untreated BRD2-degron mES

tag: antibody


title: Rloop_BRD2_BRD3_untreated_rep1


title: Rloop_BRD2_BRD3_RNaseA_rep2

value: untreated mES


title: VP_Saline_24h_1


title: Rloop_BRD2_BRD3_RNaseA_rep1


title: Liv_0.001_2_Hg


title: pk-volume-titration: 4ul-mdc-pk 4np (F40F5)


title: Liv_0.001_1_Hg


title: WT-CD8 [WGBS]

first: Yiouli

last: Ktena

state: MD

address: 1800 Orleans Street

department: SOM Onc Pediatric Oncology

institute: JHU; School of Medicine

data_processing:
base calls and demultiplexing: bcl2fastq v1.8.4
Trim Galore! v0.3.6
Bismark v0.12.3
InformME
Genome_build: mm10
Supplementary_files_format_and_content: bigWig format.  Tracks include mean methylation level (MML), normalized methylation entropy (NME), and differential quantities of the above between samples (dMML, dNME) and Jensen Shannon Distance (JSD) to measure epigenetic discordance between samples, as well as tracks of differentially methylated regions (DMR) based on JSD.

source_name: sorted splenic donor T-cells

extract_protocol:
Epicentre DNA extraction kit
Illumina TruSeq, NEBNext

value: primary

tag: age (weeks)

value: Donors 6-12 weeks, Recipients 8-12 weeks

tag: cytogenetics

value: DNMT3a WT littermates

tag: time point

value: Day +10 post-transplant

value: sorted splenic donor T-cells


title: Rloop_BRD2_BRD3_BRD3_KO_rep2

value: BRD3 KO mES


title: pk-volume-titration: 4ul-mdc-pk 4np (F40E5)


title: Liv_ctrl_2_Hg


title: WT-CD4 [WGBS]

tag: tissue


title: pk-volume-titration: 4ul-mdc-pk 4np (F40D5)


title: pk-volume-titration: 4ul-mdc-pk 4np (F40C5)


title: pk-volume-titration: 4ul-mdc-pk 4np (F40B5)


title: Liv_ctrl_1_Hg


title: KO-DP [WGBS]

value: DNMT3a KO (CD4-Cre 2loxP)


title: Rloop_BRD2_BRD3_BRD2_degron_rep2

value: BRD2 degron 3h mES


title: Gill_1_2_Hg


title: Rloop_BRD2_BRD3_BRD2_degron_rep1


title: Gill_1_1_Hg


title: Rloop_BRD2_BRD3_BRD3_KO_rep1


title: pk-volume-titration: 4ul-mdc-pk 4np (F40A5)


title: KO-CD8 [WGBS]


title: pk-volume-titration: 3ul-mdc-pk 4np (F40G4)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (12.8 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.3 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: KO-CD4 [WGBS]


title: Gill_0.5_2_Hg

extract_protocol:
RNA was isolated from cells using the Qiagen Rneasy kit with the aid of the QIAcube
Library was prepared according to Illumina instructions for NovaSeq 6000 S4 PE100 101-bp paired-end reads.


title: Rloop_BRD2_BRD3_BRD2_degron_BRD3_KO_rep2

value: BRD2 degron 3h & BRD3 KO mES


title: WT2-CD8

data_processing:
polyA RNA extraction with Qiagen rneasy kit per manufacturer protocol
Stranded mRNA libraries were sequenced on an Illumina HiSeq 4000 instrument using 47bp paired-end dual indexed reads
Reads were aligned to GRCm38 using STAR version 2.7.2b
We generated summarized experiment objects using the gtf file Homo_sapiens.GRCm38.gtf and the following command from the Bioconductor package ‘GenomicAlignments’: summarizeOverlaps
Differential expression analysis and statistical testing was performed using DESeq2 software
Counts generated using built in DEseq2 functions normalized counts()
Genome_build: mm10
Supplementary_files_format_and_content: abundance measurements

molecule: polyA RNA

extract_protocol: RNA-Seqstudies,strand specific mRNA libraries were generated using the NEBNext Ultra II Directional RNA library prep Kit for Illumina (New England BioLabs #E7760), mRNA was isolated using Poly(A) mRNA magnetic isolation module (New England BioLabs#E7490). Preparation of libraries followed the manufacturer’s protocol (Version 2.2 05/19). Input was 1microgram.


title: WT6-CD8


title: Gill_0.01_2_Hg


title: Rloop_BRD2_BRD3_BRD2_degron_BRD3_KO_rep1


title: WT5-CD4


title: pk-volume-titration: 3ul-mdc-pk 4np (F40F4)


title: ChIP-Seq_TBP_BRD2_untreated_rep2

value: Tbp


title: Gill_0.5_1_Hg


title: Gill_0.001_2_Hg


title: WT5-CD8


title: ChIP-Seq_XRN2_BRD2_untreated_rep1


title: ChIP-Seq_XRN2_BRD2_untreated_rep2


title: WT3-CD4


title: ChIP-Seq_TBP_BRD2_untreated_rep1


title: ChIP-Seq_TBP_BRD2_degron_3h_rep2


title: Gill_0.1_2_Hg


title: WT3-CD8


title: WT2-CD4


title: pk-volume-titration: 3ul-mdc-pk 4np (F40E4)


title: pk-volume-titration: 2ul-mdc-pk 4np (F40C3)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (12.9 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.2 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: pk-volume-titration: 3ul-mdc-pk 4np (F40A4)


title: Gill_0.1_1_Hg


title: pk-volume-titration: 3ul-mdc-pk 4np (F40D4)


title: ChIP-Seq_XRN2_BRD2_degron_3h_rep2


title: WT6-CD4


title: ChIP-Seq_XRN2_BRD2_degron_3h_rep1


title: pk-volume-titration: 3ul-mdc-pk 4np (F40C4)


title: ChIP-Seq_TBP_BRD2_degron_3h_rep1


title: Gill_0.01_1_Hg


title: KO3-DP


title: ChIP-Seq_TAF3_BRD2_untreated_rep2


title: ChIP-Seq_TAF3_BRD2_untreated_rep1


title: Root_HMg_AM_rep3

city: Guangzhou

first: Jinzhuan

last: Qin

address: Wushan Road

institute: South China Agricultural University

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Remove reads with adaptors;Remove reads in which unknown bases(N) are more than 10%;Remove low quality reads (we define the low quality read as the percentage of base which quality is lesser than 15 is greater than 50% in a read).
We use Bowtie2 to map clean reads to reference gene and use HISAT to reference genome.
RSEM is a quantification tool and FPKM methodis usedincalculatedexpressionlevel.
we used DEseq2 algorithms to detect the DEGs.DEseq2:Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05
Genome_build: Glycine max Wm82.a2.v1
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample .

organism: Glycine max

extract_protocol:
Ethanol precipitation protocol and CTAB-PBIOZOL reagent for the purification of total RNA from the plant tissue
BGI RNA-Seq kit

tag: mg concentration

value: High Mg

tag: inoculation treatment

value: Rhizophagus irregularis

value: root


title: Gill_0.001_1_Hg


title: KO4-DP

tag: strain

tag: cell type


title: pk-volume-titration: 3ul-mdc-pk 4np (F40B4)


title: Gill_ctrl_2_Hg


title: pk-volume-titration: 1ul-csc-pk 4np (F40G1)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. 5.35 µl library preparation mastermix (3.57 µl library preparation buffer, 1.78 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 5.35 µl library preparation enzyme (diluted 3x with H2O) was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 108.9 µl amplification master mix (13.4 µl amplification buffer, 86.6 µl H2O, 8.9 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: Gill_ctrl_1_Hg


title: pk-volume-titration: 1ul-mdc-pk 4np (F40E2)


title: KO1-DP


title: Root_HMg_AM_rep2


title: ChIP-Seq_TAF3_BRD2_degron_3h_rep2


title: KO4-CD8


title: ChIP-Seq_TAF3_BRD2_degron_3h_rep1


title: pk-volume-titration: 1ul-csc-pk 4np (F40D1)


title: Root_HMg_AM_rep1


title: pk-volume-titration: 1ul-csc-pk 4np (F40F1)


title: pk-volume-titration: 1ul-csc-pk 4np (F40C1)


title: ChIP-Seq_SMC1_BRD2_untreated_rep1


title: KO3-CD8


title: pk-volume-titration: 1ul-csc-pk 4np (F40E1)


title: Root_HMg_NM_rep3


title: ChIP-Seq_SMC1_BRD2_untreated_rep2


title: pk-volume-titration: 1ul-mdc-pk 4np (F40B2)


title: KO2-DP


title: Root_HMg_NM_rep2


title: KO1-CD8


title: KO4-CD4


title: pk-volume-titration: 1ul-csc-pk 4np (F40B1)


title: ChIP-Seq_SMC1_BRD2_degron_3h_rep2


title: Root_LMg_AM_rep3

value: Low Mg


title: KO3-CD4


title: Root_LMg_AM_rep2


title: Root_LMg_AM_rep1


title: pi-staining-and-freezing: unstained 4np (F38A1)


title: KO2-CD8


title: ChIP-Seq_Pol2_S2P_BRD2_untreated_rep1

value: embryonic stem cells

value: Pol2 s2p


title: ChIP-Seq_Pol2_S2P_BRD2_untreated_rep2

value: untreated BRD2-degron mES


title: KO2-CD4

value: primary


title: Root_HMg_NM_rep1


title: Root_LMg_NM_rep3


title: KO1-CD4

value: Donors 6-12 weeks, Recipients 8-12 weeks


title: ChIP-Seq_Pol2_S2P_BRD2_degron_3h_rep2


title: Root_LMg_NM_rep2


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38G8)

extract_protocol:
220 nm cryosections were collected in sucrose droplets and transferred to steel frame PEN membrane slides. Slides were washed in 1x PBS (3 times, 5 min each), then with water (3 times, 5 min each). Staining was performed with propidium iodide (10 µg/ml in PBS) for 10 min, followed by 2 washes with water (30 s each) and air dryed for 15 minutes. Nuclear profiles were laser microdissected into adhesive 8-strip LCM collection caps, with four profiles dissected into each cap. Whole genome amplification was performed using the Sigma WGA4 kit. 14.5 µl of lysis and fragmentation mastermix (13 µl H2O, 1.4 µl lysis and fragmentation buffer, 0.1 µl proteinase K) was added to each well of a 96 well plate, caps with microdissected material were used to close the wells, then the plate was inverted and centrifuged upside-down at 3000 xg for 2 min such that the fragmentation mastermix was collected in the cap. Plates were incubated upside-down for 4 h at 50 ∞C then inverted and centrifuged right-way-up at 3000 xg for 2 min to collect the extracted DNA in the bottom of the well. Samples were then heat inactivated at 99 ∞C for 4 min then cooled on ice for 2 min. Samples were then frozen and stored overnight at -20 ∞C. The next day, 4.32 µl library preparation mastermix (2.88 µl library preparation buffer, 1.44 µl library stabilisation solution) was added to each sample, incubated at 95 ∞C for 2 min, cooled on ice for 2 min then centrifuged at 3000 xg for 2 min. 1.4 µl library preparation enzyme was added to each tube, then samples were incubated at 16 ∞C for 20 min, then 24 ∞C for 20 min, 37 ∞C for 20 min and 75 ∞C for 5 min. Finally, 87.84 µl amplification master mix (10.8 µl amplification buffer, 69.84 µl H2O, 7.2 µl WGA polymerase) was added to each tube and samples were amplified by PCR (initial denaturation 95 ∞C for 3 min, then 25 cycles of denaturation 95 ∞C for 30 s and annealing/extension 65 ∞C for 5 min).
WGA amplified DNA fragments larger than 500bp were purified using Ampure XP beads and prepared for sequencing using the Illumina Nextera kit, following the manufacturer's guidelines


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38H8)


title: postoperative day 14

value: Non-erythroid cells

value: postoperative day 14


title: Root_LMg_NM_rep1


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38H7)


title: ChIP-Seq_SMC1_BRD2_degron_3h_rep1


title: ChIP-Seq_Pol2_NTD_BRD2_untreated_rep2

value: Pol2 ntd


title: ChIP-Seq_Pol2_S2P_BRD2_degron_3h_rep1


title: postoperative day 7

value: postoperative day 7


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38G7)


title: sample_8

city: Milano

first: Michela

last: Riba

address: via Olgettina 60

department: COSR, Center for Omics Sciences

country: Italy

institute: IRCCS, Ospdale San Raffaele

description: kidney ephitelial cell line A498, treated with IL1β, 4 hours

data_processing:
alignment with STAR_2.5.3a (--outFilterMismatchNmax 10)
counting reads with featureCounts
Differential Gene Expression with LIMMA
Assembly: Hg38; genome annotation: basic annotation Hg38 Gencode v31
Supplementary files format and content: xls with count data

source_name: kidney epithelial cell line A498, treated with IL1β, 4 hours

growth_protocol: Cells were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of IL1β 30 ng/ml for 4h hours.  The supernatant was removed, cells were washed with PBS, trypsinized and harvested. Pellets were washed with PBS and resuspendend in RLT buffer (QIAGEN)

extract_protocol:
Total RNA was extracted using RNeasy plus mini kit  (Qiagen). RNA quantification was carried out using Qubit Fluorimetric Quantification (Life Technologies) and 100ng of RNA were used to prepare the library.
Illumina_TruSeq_stranded

treatment_protocol: A498 cells were grown in RPMI medium containing 10% FBS, and supplemented with penicillin (10000 units/ml), streptomycin (10 mg/ml), in a standard incubator (37°C, 5% CO2).

tag: cell line

tag: treatment

value: IL1Beta, 4 hours


title: postoperative day 1

extract_protocol:
25,000 cells were used for library prep using Chromium Single Cell 3' Reagent Kits (v3 Chemistry)
Single-cell RNA-seq

value: postoperative day 1


title: ChIP-Seq_Pol2_NTD_BRD2_untreated_rep1


title: sample_7


title: postoperative day 3

value: postoperative day 3


title: ChIP-Seq_Pol2_NTD_BRD2_degron_3h_rep2

value: BRD2 degron 3h mES


title: pk-volume-titration: 1ul-csc-pk 4np (F40A1)


title: pi-staining-and-freezing: pi_stained_frozen 4np (F38F8)