title: IGF1_rep3, RNA-seq

city: Goiania

first: Bruno

middle: Oliveira Silva

last: Duran

state: GO

address: Esperança Avenue, Campus Samambaia, Biological Sciences Institute

department: Department of Histology, Embryology and Cell Biology

country: Brazil

institute: Federal University of Goias

data_processing:
Transcriptome was obtained through the NovaSeq 6000 platform (Illumina, USA) with 150 base pairs, paired-end, and 6 GB data per sample.
Adapters and low-quality reads were removed using an in-house perl scripts and then mapped against the latest gilthead sea bream genome available (https://www.ensembl.org/index.html; accessed in January 2023) using HISAT2 software.
Transcripts were assembled followed by mRNA expression profiling analysis using StringTie, and expressing the results as FPKM (fragments per kilobase of exon per million fragments mapped).
Differences in transcription levels between treatments obtained from RNAseq data were biological relevant when log2-fold change (log2FC) was ≤ −1 and ≥ 1, and corrected p-values (False Discovery Rate, FDR) was ≤ 0.05.
Assembly: Gilthead sea bream genome (fSpaAur1.1) available in https://www.ensembl.org/index.html
Supplementary files format and content: Matrix table (.xlsx) with FPKM values for the identified mRNAs in each sample. Spreadsheets show comparisons between treatments (AA vs C; IGF1 vs C; IGF1 vs AA). Differences between treatments for each mRNA and differential expression are indicated as corrected p-value (qval) and log2Fold-change.
Supplementary files format and content: Matrix table (.xlsx) with FPKM values for the identified lncRNAs in each sample. Differences between treatments for each lncRNA are indicated as corrected p-value (qval).

organism: Sparus aurata

source_name: Fast-twitch skeletal muscle

growth_protocol: Cells were isolated from gilthead sea bream fast-twitch muscle and grown in complete medium until the 8th day of culture.

extract_protocol:
Total RNA was extracted using Trizol, as recommended by manufacturer. The material was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation.
Poly(A) RNA sequencing library using Illumina's protocol.

treatment_protocol: C (control) group cells were cultured in nutrient restriction medium for 36 hours. AA (amino acids) group cells were cultured in nutrient restriction medium for 12 hours followed by 24 hours of AA supplementation. IGF1 (insulin-like growth factor 1) group cells were cultured in nutrient restriction medium for 12 hours followed by 24 hours of IGF1 supplementation.

value: Fast-twitch skeletal muscle

value: Muscle cells

value: IGF1 treatment for 24 hours


title: IGF1_rep2, RNA-seq

status: Public on Apr 17 2024

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: cell type

tag: treatment


title: WT_S2_11

city: Grugliasco

first: IVAN

last: VISENTIN

state: Seleziona uno Stato

address: Largo Braccini 2

department: DISAFA

country: Italy

institute: University of Turin

data_processing:
Clean reads were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome (SL3.0) using the HISAT2 software.
HTSeq was used to count the read numbers mapped of each gene, including known and novel genes; then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: ITAG SL3.0
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Solanum lycopersicum

source_name: Leaf

growth_protocol: Seeds were sterilized in 4% (v/v) sodium hypochlorite containing 0.02% (v/v) Tween 20, rinsed thoroughly with sterile water, and then placed for 48 h on moistened filter paper at 25°C in darkness. Germinated seedlings were grown for two weeks in a walk-in climate chamber (16/8h light/dark 25°C, 65% humidity, and 200 µmol s–1 m–2 of photosynthetic photon flux density) in a seedbed with standard soil (Terra Nature, NPK 12:14:24) and then moved into 1-liter pots filled with vermiculite and kept under the same conditions.

extract_protocol:
Total RNA was extracted from leaves using the Spectrum Plant Total RNA Kit (Sigma Aldrich). After digestion of contaminant DNA by DNAse I (ThermoScientific) at 37°C for 30 min, RNA quantity and quality were determined with a Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Wilmington, DE, United States).
cDNA libraries were prepared from 1 µg total RNA using NEBnext Ultra TM RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s recommendations. A total of 21 libraries (three each for wt and SL- leaves, plus wt treated with GR245DS) were constructed and quantified using a Qubit 2.9 fluorometer (Life Technologies) and sequenced on an Illumina platform to generate paired-end reads.

treatment_protocol: Time-course experiments were performed by gently uprooting plants of both wt and SL- genotypes, transferring them in vermiculite hydrated with only 20 ml of water (stressed group), or transferred in wet vermiculite (well-watered controls). After having completely recovered, the stressed plants were subjected to a second identical cycle of dehydration and rewatering. Unstressed, well-watered controls were sampled before transfer to new wet substrates. GR245DS treatment was carried out by leaf spraying of a 5 uM solution until drip-off 24 h before sampling, which corresponded with the beginning of the drought time-course (hence, untreated irrigated wt plants are an appropriate control group for this condition as well).

tag: cultivar

value: Leaf

tag: genotype

value: WT

value: Water recovery 2

tag: time


title: CTCF_d80_170_adult_HA_2

city: Moscow

first: Natalia

last: Klimenko

address: 34/5 Vavilova Street

country: Russia

institute: Institute of Gene Biology (IGB) of the Russian Academy of Sciences

library_source: genomic

data_processing:
Adapters, poly-N and poly-A read ends were removed using cutadapt software (Martin 2011). Cutadapt was also used for trimming low-quality ends (quality threshold was set to 20, reads with the length less than 20 bp after trimming were discarded).
The remaining reads were aligned to build version dm6 of the Drosophila melanogaster genome using Bowtie version 2 (Langmead and Salzberg 2012). Only reads that aligned concordantly exactly one time were passed to further analysis.
After alignment, read duplicates were removed using Picard MarkDuplicates function (http://broadinstitute.github.io/picard/). Also, peaks overlapping with blacklist regions were discarded (blacklist regions were previously converted from dm3 to dm6 genome built version) (https://sites.google.com/site/anshulkundaje/projects/blacklists)
Chip-seq coverage tracks (BedGraph) were obtained using deepTools (Ramírez et al. 2014) bamCoverage function with bin width 50 bp and RPKM normalization.
Assembly: dm6
Supplementary files format and content: Processed data was obtained by deeptools bamCoverage (bedGraph)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole organism

growth_protocol: Drosophila strains were maintained on standard medium at 25°C and 50-60% humidity.

extract_protocol:
After 3 rounds of washing with lysis buffer supplemented with 500 mM NaCl, and TE buffer (10 mM Tris-HCl, pH 8; 1 mM EDTA), the DNA was eluted with elution buffer (50 mM Tris-HCl, pH 8.0; 1 mM EDTA, 1% SDS), the cross-links were reversed, and the precipitated DNA was extracted by the ChIP DNA Clean &Concentrator kit (Zymoresearch).
Libraries were prepared according to manufacturers recommendations with small modifications. In short, 1-10ng of purified, RNase treated, and reverse cross-linked genomic DNA was end-repaired and terminal adenosine residues were added using the NEBNext reagents. Custom-made indexed adapters were ligated, after which the material was size selected at ~200-600 bp with Ampure XP beads (Beckman Coulter). PCR amplification was performed using PE1.0 and PE2.0 primers (custom-made) for 12 cycles for Input samples and 14 to 15 cycles for IP-ed samples using the Q5 Hot Start HiFi PCR Master Mix (NEB). The PCR-amplified library was purified using Ampure XP beads and its quality was assessed on a Bioanalyzer 2100 system (Agilent). The libraries were sequenced on aNovaSeq 6000 (Illumina) in pair-end mode.

treatment_protocol: Chromatin was prepared from two- to three-day-old adult flies. A 1 g of adult flies was ground in a mortar in liquid nitrogen and resuspended in 20 mL of buffer A (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 13 mM EDTA, 0.1 mM EGTA, 0.15 mM spermine, 0.5 mM spermidine, 0.5% NP-40, 0.5 mM DTT) supplemented with 0.5 mM PMSF and Calbiochem Cocktail V. The suspension was then homogenized subsequently in a Potter and Dounce homogenizer with tight pestle, filtered through 100 µm Nylon Cell Strainer (Miltenyi Biotec, United States), and cross-linked with 1% formaldehyde for 15 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 125 mM. The nuclei were washed with three 10-mL portions of wash buffer (15 mM HEPES-KOH, pH 7.6, 60 mM KCl, 15 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 0.1% NP-40, protease inhibitors), one 5-mL portion of nuclear lysis basic buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, protease inhibitors) and resuspended in 1 mL of nuclear lysis buffer (15 mM HEPES, pH 7.6, 140 mM NaCl, 1 mM EDTA, 0.1 mM EGTA, 1% Triton X-100, 0.5 mM DTT, 0.1% sodium deoxycholate, 0.5% SLS, 0.1% SDS, protease inhibitors). The suspension was sonicated in a Covaris ME220 focused-ultrasonicator (40 alternating 15-s ON and 45-s OFF intervals, peak power 75, duty % factor 25), and 50-µL aliquots were used to test extent of sonication and to measure DNA concentration. Debris was removed by centrifugation at 14 000 g, 4°C, for 10 min, and chromatin was pre-cleared with Protein A Dynabeads (Invitrogen). Corresponding antibodies were incubated for 1 hour at room temperature with 20 µL aliquots of Protein A (anti-CTCF C, 1:200) or G (anti-CP190, 1:200) Dynabeads (Invitrogen) mixed with 200 µL of PBST. Then antibodies-Dynabeads complexes and anti-HA Magnetic beads (Pierce) were washed and equilibrated in nuclear lysis buffer. Chromatin samples containing 10–20 µg of DNA equivalent in 200 µL of nuclear lysis buffer (2 µL aliquots of such pre-cleared chromatin being stored as input material) were incubated overnight, at 4°C, with antibodies-Dynabeads complexes.

tag: development stage

value: adult

tag: protein

value: dCTCF

tag: antibody source

value: HA

tag: strain

value: Oregon-R


title: WT_S2_8


title: CTCF_d80_170_adult_HA_1


title: AA_rep3, RNA-seq

value: AA treatment for 24 hours


title: WT_S1_4

value: Water recovery 1


title: CTCF_hN_adult_C-CTCF_2

value: rabbit

value: dCTCFhN


title: RSEM_siCYP3A5_1

city: Memphis

first: William

middle: C.

last: Wright

state: Tennessee

address: 262 Danny Thomas Pl

department: Computational Biology

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Raw sequence files were merged across lanes according to sample and subjected to a first round of quality control using the FastQC tool (www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Illumina universal adapters were trimmed from all samples using Trim Galore ([www.bioinformatics.babraham.ac.uk/projects/trim_galore/) and samples were then subjected to a second round of quality control
Reads were mapped to the human Hg38 reference genome using Bowtie2
The edgeR package with Limma/Voom was used for linear modeling, empirical Bayes smoothing, TMM normalization, generation of Log2(CPM), and statistical analysis
Genome_build: Hg38
Supplementary_files_format_and_content: Log2(Normalized Counts per Million + 1)

organism: Homo sapiens

growth_protocol: All cells were maintained according to respective ATCC recommended culture conditions

extract_protocol:
Total RNA was extracted from each cell line using the Maxwell 16 LEV automation system and simplyRNA purification kit (Promega, Cat. No. 1280) according to the manufacturer’s protocol. The extracted RNA was quantified by spectrophotometry using a NanoDrop 8000 (ThermoFisher Scientific, Waltham, MA) to ensure a reading of OD260/OD280 between 1.8 and 2.0.
RNA libraries were prepared for sequencing using TruSeq Stranded mRNA Library Preparation Kit (Illumina)

treatment_protocol: Cells were not drug treated

tag: cell line

value: pancreatic cancer cell line

tag: disease

value: cancer

value: Pancreas

tag: genotype/variation

value: CYP3A5 knockdown


title: RSEM_siCYP3A5_3


title: WT_S1_13


title: RSEM_CT_3

value: control


title: WT_S1_1


title: RSEM_siCYP3A5_2


title: CTCF_hN_adult_C-CTCF_1


title: CC_S2_8

value: Strigolactone-depleted line 6936


title: AA_rep1, RNA-seq

value: Fast-twitch skeletal muscle

value: Muscle cells


title: RSEM_CT_1


title: CTCF_wt_adult_C-CTCF_2

value: dCTCFwt


title: RSEM_3A5OE_3

value: CYP3A5 over-expression


title: C_rep2, RNA-seq

value: Nutrient restriction for 36 hours (control)


title: CTCF_wt_adult_C-CTCF_1

value: adult

value: dCTCF


title: CC_S2_13

value: Leaf

value: Water recovery 2


title: C_rep1, RNA-seq


title: IGF1_rep1, RNA-seq

value: IGF1 treatment for 24 hours


title: CTCF_wt_adult_CP190_2

value: rat

value: Oregon-R


title: RSEM_3A5OE_2

value: pancreatic cancer cell line

value: cancer


title: AA_rep2, RNA-seq

value: AA treatment for 24 hours


title: CC_S1_17

value: Water recovery 1


title: 1' Myoblast Hypoxia 4% pO2  PT2385

city: Athens

first: Hang

last: Yin

state: GA

address: 325 Riverbend Rd

department: Center for Molecular Medicine

institute: The University of Georgia

description:
Hypoxia_4%_PT2385
Chronic_Hypoxia_HIF-2A.gct

data_processing:
Raw RNA-seq reads (.fastq) were mapped to mouse genome by HISAT2 (2.1.0) using  --dta-cufflinks -f -q  arguments. Mapping results were sorted by samtools (1.3.1). Gene expression levels were called by Cufflinks/Cuffdiff (2.2.1) with mouse transcripts annotation (Mus_musculus.GRCm38.95.gtf). FPKM values at the gene level were converted into GenePattern (.gct) format (Chronic_Hypoxia_HIF-2A.gct).
Assembly: mm10 (Mus_musculus.GRCm38.100.gtf)
Supplementary files format and content: FPKM values at the gene level are included in Chronic_Hypoxia_HIF-2A.gct

organism: Mus musculus

source_name: Primary Myoblast, Hypoxia 4% pO2 Growth Medium, PT2385 1uM treatment (48h)

extract_protocol:
Zymo Research  RNA extract and clean kits
We sent the whole RNAs to BGI directly, and they made libraries to run on their platform.

value: Primary Myoblast

value: Hypoxia 4% pO2, PT2385


title: 1' Myoblast Hypoxia 4% pO2  Vehicle

description:
Hypoxia_4%_DMSO
Chronic_Hypoxia_HIF-2A.gct

source_name: Primary Myoblast, Hypoxia 4% pO2 Growth Medium, DMSO 0.1% treatment (48h)

value: Hypoxia 4% pO2, DMSO


title: Hi-C: wild-type replicate 1

city: Bern

first: Peter

last: Meister

state: Schweiz

address: Baltzerstrasse 4

department: Institute of Cell Biology

country: Switzerland

institute: University of Bern

data_processing:
HiC-Pro pipeline (Servant et al. 2015), version 3.0.0.
Hicpro matrices were converted to cool format using the hicpro2higlass.sh utility from hicpro.
Assembly: ce11
Supplementary files format and content: Cool files with a bin size of 2000bp.

organism: Caenorhabditis elegans

source_name: L3 animals

extract_protocol:
Hi-C was done as in Jimenez et al. 2021, with minor modifications. In short, the frozen worm pellet was resuspended in 2% formaldehyde prepared in M9 buffer and incubated for 30 mins in the rotator. Formaldehyde was quenched with glycine at 125 mM (final) and incubated for 5 mins. The worms were pelleted, washed with M9 and about 100 ul of the packed animals were transferred to 1.5 ml microcentrifuge tubes. Each tube with the worms were washed with 1 ml 1x PBS and protease inhibitors, washed again with 1 ml 1x PBS, snap frozen in liquid nitrogen and stored at -80°C. Cross-linked frozen worms were ground using a SPEX 6775 freezer/mill at 5 cycles per second for 1 minute with a total of 2 cycles. The ground worm powder was dissolved in 5 ml 1x PBS and immediately cross-linked with 500 μl TC buffer (100 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 50 mM Hepes pH 8.0, 22% formaldehyde), to a final concentration of 2% formaldehyde for 20 minutes at room temperature. Cross-linking was stopped by addition of 289 ul of Stop Solution 1 (provided in the Arima Hi-C kit) and 5 minutes incubation at RT. Samples were pelleted at 2000g for 15 mins at RT and resuspended in 5 ml 1x PBS before 10 aliquots were distributed into 1.5 ml microcentrifuge tubes. The amount of DNA acquired from a single aliquot was estimated and accordingly the subsequent Hi-C experiment was done as per the manufacturer’s instructions.
Modified protocol from Arima Genomics for the KAPA Hyper Prep Kit was used.

treatment_protocol: Synchronised L1 animals are seeded on NGM plates, incubated for 3 hours at 22℃, heat-shocked for 30 mins at 34℃. Then they are incubated again for 19 hours at 22℃. The degron strain was seeded on 1mM auxin plates and heat-shocked as described earlier. All animals were collected by washing thrice with M9 buffer, pelleted and stored at -80°C.

value: whole body

value: untreated

value: L3 larvae

value: wildtype


title: CTCF_d132_170_adult_HA_2

value: adult

value: dCTCF

value: HA


title: RSEM_CT_2

value: Pancreas

value: control


title: CC_S1_16

value: Leaf

value: Strigolactone-depleted line 6936


title: RSEM_3A5OE_1

value: pancreatic cancer cell line

value: cancer

value: CYP3A5 over-expression


title: C_rep3, RNA-seq

value: Fast-twitch skeletal muscle

value: Muscle cells

value: Nutrient restriction for 36 hours (control)


title: CTCF_d132_170_adult_HA_1

value: Oregon-R


title: IR64_flag_leaf_H3K27me3_2

city: Wuhan

first: feng

last: zhao

state: Hubei

address: No. 1, Shizishan Street, Hongshan District

country: China

institute: Huazhong Agricultural University

data_processing:
*library strategy: CUT&Tag
Raw reads of all sequencing data were trimmed using fastp (v0.20.1)
Assembly: MSU7.0
Supplementary files format and content: bw

organism: Oryza sativa Indica Group

extract_protocol:
Take 100mg of fresh flag leaf, use scissors or a blade to chop the flag leaf until homogenized. Resuspend tissue samples with 20 ml 1×PBS (+1% 50x protease inhibitor).Filter homogenized solution through Miracloth (Millipore, cat. no. 3536029) into a new 50 ml centrifuge tube.Centrifuge at 600 g for 5 min at 4 °C and remove the supernatant.Resuspend product with 1 ml NEB2 buffer and transfer to a new 1.5 ml centrifuge tube. Centrifuge at 600 g for 5 min at 4 °C and remove the supernatant.
The library was constructed using the CUT&Tag kit (Hyperactive® Universal CUT&Tag Assay Kit for Illumina, Vazyme Biotech Co.,Ltd).

value: wild type


title: CC_WW_7

value: Well-watered


title: CTCF_wt_adult_CP190_1

value: rat

value: dCTCFwt


title: CC_S2_11

value: Water recovery 2


title: 1' Myoblast Hypoxia 1% pO2  PT2385

description:
Hypoxia_1%_PT2385
Chronic_Hypoxia_HIF-2A.gct

source_name: Primary Myoblast, Hypoxia 1% pO2 Growth Medium PT2385 1uM treatment (48h)

value: Primary Myoblast

value: Hypoxia 1% pO2, PT2385


title: 1' Myoblast Hypoxia 1% pO2  Vehicle

description:
Hypoxia_1%_DMSO
Chronic_Hypoxia_HIF-2A.gct

source_name: Primary Myoblast, Hypoxia 1% pO2 Growth Medium DMSO 0.1% treatment (48h)

value: Hypoxia 1% pO2, DMSO


title: CTCF_d80_170_adult_C-CTCF_1

value: adult

value: dCTCF

value: rabbit


title: CTCF_wt_adult_HA_2

value: HA


title: 1' Myoblast Normoxia 20% pO2 PT2385

description:
Normoxia_PT2385
Chronic_Hypoxia_HIF-2A.gct

source_name: Primary Myoblast, Normoxia 20% pO2 Growth Medium PT2385 1uM treatment (48h)

value: Normoxia 20% pO2, PT2385


title: CC_WW_6

value: Leaf

value: Strigolactone-depleted line 6936


title: CTCF_wt_adult_HA_1


title: IR64_flag_leaf_H3K4me3_2

value: H3K4me3(Abcam, #ab8580)


title: CC_S1_12

value: Water recovery 1


title: 1' Myoblast Normoxia 20% pO2 Vehicle

description:
Normoxia_DMSO
Chronic_Hypoxia_HIF-2A.gct

source_name: Primary Myoblast, Normoxia 20% pO2 Growth Medium DMSO 0.1% treatment (48h)

value: Normoxia 20% pO2, DMSO


title: CC_WW_3

value: Well-watered


title: IR64_flag_leaf_H3K4me3_1

value: wild type


title: WTl_DMSO_Biol_Rep2

status: Public on Apr 16 2024

city: Berkeley

first: Gloria

last: Brar

state: CA

address: 616 Barker Hall

department: Molecular and Cell Biology

institute: UC Berkeley

description: The Illumina NovaSeq X was used as the sequencing instrument.

data_processing:
Read alignment was performed with STAR.
Raw counts were calculated using featureCounts from the Rsubread package.
Assembly: SK1 genome (http://cbio.mskcc.org/public/SK1_MvO/).
Supplementary files format and content: *.counts.txt: Tab-delimited text files include raw counts.

molecule: polyA RNA

organism: Saccharomyces cerevisiae SK1

source_name: yeast cells

growth_protocol: Strains were grown, shaking, in YEPD at 30C.

extract_protocol:
Cells were spun down and pellets were flash frozen. RNA extraction was performed as described in Higdon et al. 2023.
PolyA selection was performed using NEXTFLEX Poly(A) Beads 2.0 kit with 5ug total RNA (NOVA-512992). RNA-seq libraries were prepared from the resulting poly-A selected RNA using the NEXTFLEX Rapid Directional RNA-Seq Kit 2.0 (NOVA-5198-02).

treatment_protocol: Cells were treated with either aTC or DMSO upon dilution from overnight cultures, cells were collected at 3h post-dilution.

value: yeast cells

tag: condition

value: 3h in YEPD

value: MATa/alpha his3::pTetO7.1-altPus1-3V5::HIS3; ura3::pRNR2-TetR-Tup1, pTetO7.1-TetR::URA3

value: DMSO


title: WTl_aTC_Biol_Rep1

value: aTC


title: WTl_DMSO_Biol_Rep1


title: WT_aTC_Biol_Rep2


title: Pus1del_DMSO_Biol_Rep2

value: MATa/alpha his3::pTetO7.1-altPus1-3V5::HIS3; ura3::pRNR2-TetR-Tup1, pTetO7.1-TetR::URA3; pus1::KanMX


title: Pus1del_DMSO_Biol_Rep1


title: Pus1del_aTC_Biol_Rep2


title: Pus1del_aTC_Biol_Rep1


title: KK-16: Cgsnf2 mutant, Macrophage internalized for 10 h; Replicate-2

city: Hyderabad

first: Rupinder

last: Kaur

state: Telangana

address: Inner ring road, Uppal

country: India

institute: Centre for DNA Fingerprinting and Diagnostics

data_processing:
RNA-seq reads were aligned to the Candida glabrata CBS138 genome and quantified using the reference gene model in HISAT 2.1.0 aligner.
Differential expression of the genes was estimated from aligned reads using DESeq2 program.
Differentially-expressed genes were filtered with the following setting: Fold change in expression (≥ 2) and adjusted p value (≤ 0.05).
Assembly: Candida glabrata CBS138 genome
Supplementary files format and content: text files; File contain target_id and normalized_read_count

organism: Nakaseomyces glabratus

source_name: Cgsnf2∆ mutant cells

growth_protocol: Cell samples were collected in two biological replicates.Collection of RPMI-grown C. glabrata cells: C. glabrata wild-type and Cgsnf2Δ strains were inoculated in YPD medium and incubated for 16 h at 30⁰C under shaking conditions (200 rpm). These cultures were inoculated in the RPMI medium containing 10% FBS at an initial density of 1 million cells per ml, and incubated in tissue culture condition (37°C with 5% CO2).  At 2 h and 10 h, wild-type and Cgsnf2Δ cells were collected. Collection of macrophage-internalized C. glabrata cells: Human THP-1 monocytic cells were treated with phorbol 12-myristate 13-acetate (16 nM) (PMA) for 12 h for differentiation into macrophages at 37°C with 5% CO2, followed by 12 h cell recovery in RPMI medium containing 10% FBS. THP-1 macrophages were infected with overnight, YPD medium-grown cells of wild-type and Cgsnf2Δ strains at a multiplicity of infection (MoI) of 1.0. Non-phagocytosed C. glabrata cells were removed after 2 h, and the infection was continued for another 8 h. At 2 h and 10 h post-infection, extracellular C. glabrata cells were removed with PBS, THP-1 cells were lysed in water to collect macrophage-internalized C. glabrata cells.

extract_protocol:
RNA extraction from collected cells of wild-type and Cgsnf2Δ strains was done using Qiagen RNeasy kit following manufacturers’ protocol.
The NEBNext Poly(A) mRNA Magnetic Isolation Module is used for the enrichment of mRNA. Poly (A) purified RNA sample is used for library preparation using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® as per manufacturer protocol. In short, following purification, the RNA is fragmented using divalent cations under elevated temperature. Next, the cDNA is synthesized using Reverse transcriptase and random hexamers in a first-strand synthesis reaction. Subsequently, the cDNA is converted to double-stranded cDNA where Uracil is added instead of Thymine. The strand specificity is preserved by a USER enzyme-based digestion of the second strand, thereby leaving one functional strand which maps to the DNA strand from which it was transcribed from. The USER digested single strand molecules were enriched and indexed in a limited cycle PCR, followed by AMPure bead purification to create the final cDNA library for sequencing.

tag: growth phase

value: 10 h grown

value: Macrophage internalized

value: Cgsnf2 mutant


title: IR64_flag_leaf_H3K27me3_1


title: KK-15: Cgsnf2 mutant, RPMI-grown for 10 h; Replicate-2

description: RPMI-grown for 10 h; Replicate-2

value: RPMI grown


title: KK-12: Cgsnf2 mutant, Macrophage internalized for 10 h; Replicate-1


title: KK-10: wild-type, Macrophage internalized for 10 h; Replicate-1

source_name: wild-type cells

value: wild-type


title: KK-13: wild-type, RPMI-grown for 10 h; Replicate-2

description: RPMI-grown for 10 h; Replicate-2


title: KK-11: Cgsnf2 mutant, RPMI-grown for 10 h; Replicate-1

description: RPMI-grown for 10 h; Replicate-1


title: KK-14: wild-type, Macrophage internalized for 10 h; Replicate-2


title: KK-8: Cgsnf2 mutant, Macrophage internalized for 2 h; Replicate-2

value: 2 h grown


title: KK-7: Cgsnf2 mutant, RPMI-grown for 2 h; Replicate-2

description: RPMI-grown for 2 h; Replicate-2


title: KK-5: wild-type, RPMI-grown for 2 h; Replicate-2

description: RPMI-grown for 2 h; Replicate-2


title: KK-6: wild-type, Macrophage internalized for 2 h; Replicate-2


title: KK-3: Cgsnf2 mutant, RPMI-grown for 2 h; Replicate-1

description: RPMI-grown for 2 h; Replicate-1


title: KK-4: Cgsnf2 mutant, Macrophage internalized for 2 h; Replicate-1


title: KK-2: wild-type, Macrophage internalized for 2 h; Replicate-1


title: KK-1: wild-type, RPMI-grown for 2 h; Replicate-1

description: RPMI-grown for 2 h; Replicate-1


title: KK-4: RPMI-grown for 2 h; Replicate-2

description: RPMI-grown for 2 h; Replicate-2

data_processing:
Processed sequence reads were aligned to the C. glabrata genome version s04-m01-r06 (www.candidagenome.org) using bowtie2, version 2.5.0.
Nucleosome position and dynamics were analysed using the DANPOS3 software.
Dynamic nucleosomes were identified using the following criteria:  Position shift: ≥ 50 bp shift; Occupancy change: ≥ 2-fold change (FDR ≤ 0.05); or Fuzziness change: ≥ 1.5-fold change (FDR ≤ 0.05).
Assembly: Candida glabrata CBS138 genome version s04-m01-r06
Supplementary files format and content: text files; File contain: chr, start, end, smt_pos, smt_value, fuzziness_score, txStart, txEnd, CAGL ID, strand and distance

growth_protocol: Cell samples were collected in two biological replicates.THP-1 monocytes were treated with phorbol 12-myristate 13-acetate (PMA; 16 nM) for 12 h for their differentiation into macrophages, followed by 12 h recovery in the fresh RPMI medium containing 10% FBS. PMA-activated THP-1 (2.2 x 107) cells were infected with YPD medium-grown C. glabrata wild-type at a MoI (multiplicity of infection) of 1.0. After 2 h and 10 h of infection, macrophage-internalized C. glabrata cells were collected, by lysing infected macrophages in ice-cold water. To separate C. glabrata cells from macrophage debris, macrophage lysates were gently vortexed, and centrifuged at 6000 rpm for 5 min at 4°C. The C. glabrata cell pellet was collected and suspended in ice-cold water. As a control, overnight YPD medium-grown C. glabrata cells were grown in 10% FBS-containing RPMI medium for 2 h and 10 h, and cell pellets were collected.

extract_protocol:
Cell pellets were dissolved in MNase-digestion buffer [10 mM Tris-Cl (pH 8.0) and 1 mM CaCl2], and lysed using glass beads. Cell lysates (1 mg) were incubated with MNase (10 units/1 mg lysate) at 37°C for 60 min. The digestion was stopped by adding the Stop Buffer (8.6% SDS and 0.007 M EDTA), followed by proteinase K (20 mg/ml) digestion in two steps, first incubation at room temperature for 30 min, and later at 65°C for overnight. DNA was isolated with PCI (Phenol:Chloroform:Isoamyl alcohol) extraction, precipitated with sodium acetate and ethanol, and was suspended in nuclease-free water, followed by RNase A digestion for 30 min at 37°C. DNA was run on 2% agarose gel, and bands of ~ 150 bp, corresponding to mononucleosomal DNA fragments, were excised, and purified using the QIAquick extraction kit.
The prepared libraries were sequenced (2x100 bp paired-end sequencing) on the HiSeq 2500 (Illumina) platform.


title: KK-4: RPMI-grown for 2 h; Replicate-1

description: RPMI-grown for 2 h; Replicate-1


title: KK-3: Macrophage internalized for 2 h; Replicate-1


title: KK-2: RPMI-grown for 10 h; Replicate-2

description: RPMI-grown for 10 h; Replicate-2


title: KK-1: Macrophage internalized for 10 h; Replicate-2


title: KK-2: RPMI-grown for 10 h; Replicate-1

description: RPMI-grown for 10 h; Replicate-1


title: larval, experimental group, Day30

city: Dalian

first: Zihao

last: Yan

state: Liaoning

address: Ganjingzi District

department: School of Life Science

institute: Liaoning Normal University

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platformand 150 bppaired-endreadswere generated. About 40-50 M raw reads for each sample were generated.
Raw reads of fastq formatwere firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then about 41-47 M clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: ASM1570882v1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Lethenteron reissneri

source_name: larval

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) accordingtothemanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop2000spectrophotometer (Thermo Scientific, USA).RNA integrity was assessed usingtheAgilent2100Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructedusingVAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: larval

value: CDA1 knockout


title: KK-1: Macrophage internalized for 10 h; Replicate-1


title: larval, control, Day30

value: WT


title: KK-9: wild-type, RPMI-grown for 10 h; Replicate-1

description: RPMI-grown for 10 h; Replicate-1


title: Liver, CG-1

city: Lanzhou

first: guiyan

address: Yingmen Village 1

institute: Gansu Agricultural University

data_processing:
Sequencing was performed on an Illumina HiSeq™ X10 platform at Gene Denovo Biotechnology
The raw Ribo-seq data underwent quality control to remove low-quality sequences and rRNA. Clean reads were then aligned to the chromosome-level genome of the rainbow trout (www.ncbi.nlm.nih.gov/genome/?term=oncorhynchus+mykiss) using Bowtie2 software
DEGs were identified using the edgeR package, defined as having an absolute fold change values ≥ 2 and FDR < 0.05,
The three-nucleotide periodic distribution was successfully constructed using the riboWaltz R package
Assembly: Oncorhynchus mykiss Omyk_1.1
Supplementary files format and content: ribo-CG-vs-HS.txt  (includes count values and FPKM values for each Sample)
Library strategy: Ribo-seq

molecule: nuclear RNA

organism: Oncorhynchus mykiss

source_name: the control group involve placing rainbow trout liver  in  18°C

extract_protocol:
According to the manufacturer's protocol, RFs from the liver of rainbow trout was extracted using RNA Clean and Concentrator-25 kit (Zymo Research, Beijing, China). .
Ribo-seq libraries were assembled utilizing the NEBNext® Multi-Small RNA Library Prep Set for Illumina®
Ribosome profiling sequencing

treatment_protocol:
the control group involve placing rainbow trout liver  in  20°C
the experimental group is subjected to heat stress by treating the rainbow trout liver  in  24°C for a duration of 8 h

value: Liver

value: control


title: Liver, HS-1

source_name: the experimental group is subjected to heat stress by treating the rainbow trout liver  in  24°C for a duration of 8 h

value: heat stress


title: Liver, CG-3


title: Liver, HS-3


title: Liver, CG-2


title: NHEK_CTLi_1

city: Beer Sheva

first: Idan

last: Cohen

address: David Ben Gurion Blvd 1

department: Microbiology, Immunology and Genetics

country: Israel

institute: Ben-Gurion University

data_processing:
The sequences were quality trimmed and filtered using Trim Galore (v0.4.5) and cutadapt (v1.15).
Alignment of the reads to the human genome (GRCh38) was done using STAR (v2.5.2a).
The number of reads per gene per sample was counted using RSEM (v1.2.28).
Quality assessment (QA) of the process was carried out using FASTQC (v0.11.8) and MultiQC (v1.0.dev0).
We analyzed read counts for differential gene expression using the DESeq2 R package
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Skin

extract_protocol:
Primary neonatal human epidermal keratinocytes were cultured in KGM-Gold media (Lonza). Cells were infected with either CASZ1 shRNA or control shRNA lentiviral particles, and selected in the presence of 0.4ug/ml puromycine. To induce epidermal differentiation, growth media was supplemented with 1.4mM CaCl2 and cells were grown for six days. Cells were then dissociated by warm 0.25% Trypsin for 10 min at 37°C. Cells were then centrifuged at 200 g for 4 min at 4°C, washed twice with 1x PBS and incubated in 350 µl Trizol for 10 min at room temp. Total RNA was purified using TriRNA Pure Kit (Geneaid) according to manufacturer’s instructions.
of total RNA per sample was used. Enrichment for poly(A) mRNA was done using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). The RNA-seq libraries were then constructed following standard protocol for the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).  The concentration and quality of the libraries were determined using Qubit (Invitrogen) and Bioanalyzer (Agilent). Constructed RNA-seq libraries were sequenced on the Illumina NextSeq 2000 platform, obtaining 100-nucleotide single reads.

value: Skin

value: Neonatal keratinocytes

value: Normal Human Epidermal Keratinocytes (NHEK)

value: Control shRNA


title: NHEK_CASZ1i_1

value: CASZ1 shRNA


title: NHEK_CASZ1i_2


title: NHEK_CTLi_3


title: lib87645

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

data_processing:
Base calls were processed to FASTQs on BaseSpace (Illumina), and a base call quality-trimming step was applied to remove low-confidence base calls from the ends of reads. The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a and gene counts were generated using htseq-count (v0.4.1). Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
Assembly: GRCh38 release 91
Supplementary files format and content: counts.csv: Gene count matrix in text file

source_name: Islet TMR+ CD8 T cells

growth_protocol: Cryopreserved PBMC were thawed and rested at 37C for 3h in RPMI with 10% commercial human serum. After resting PBMC were cultures with overlapping peptide libraries (20 aa in length, 12 aa overlap) from the islet proteins GAD65, IGRP, ZnT8, and preproinsulin in the presence of anti-CD40 antibody for 14h.

extract_protocol:
Sorted cells were lysed, followed by reverse transcription (SMART-Seq v1 Ultra Low Input RNA Kit; Takara, Mountain View, CA).
Sequencing libraries were prepared using Nextera XT DNA kits (Illumina, San Diego, CA).

treatment_protocol: After 14h cutlture CD154+ activated T cells were enriched by magnetic bead enrichment and single cell sorted to isolate CD4+CD154+CD69+ T cells. Cells were sorted directly into wells of a 96 w plate containing SMART-seq v1 Ultra Low Input RNA buffer and then processed for library preparation.

value: Islet TMR+ CD8 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides

tag: donorid

tag: project number

tag: study group

value: >1 Aab+ any age


title: lib87646

tag: cell type


title: NHEK_CTLi_2

tag: tissue

tag: treatment


title: lib87643


title: lib87642


title: lib87647


title: lib87641


title: lib87648


title: lib87644


title: lib87639


title: KK-3: Macrophage internalized for 2 h; Replicate-2

value: Macrophage internalized

tag: genotype


title: Liver, HS-2


title: lib87638


title: lib87637


title: lib87640


title: lib87635


title: lib87636


title: lib87634


title: NHEK_CASZ1i_3


title: lib87633


title: lib87649


title: lib87631


title: lib87632


title: lib87629


title: lib87628


title: lib87630


title: lib87626


title: lib87627


title: lib87622


title: lib87624


title: lib87621


title: lib87620


title: lib87618


title: lib87625


title: lib87623


title: lib87617


title: lib87615


title: lib87613


title: lib87612


title: lib87616


title: lib87614


title: lib87610


title: lib87611


title: lib87609


title: lib87608


title: lib87607


title: lib87606


title: lib87605


title: lib87604


title: lib87603


title: lib87600


title: lib87598


title: lib87601


title: lib87599


title: lib87619


title: lib87597


title: lib87594


title: lib87593


title: lib87591


title: lib87595


title: lib87590


title: lib87596


title: lib87589


title: lib87592


title: lib87588


title: lib87586


title: lib87584


title: lib87587


title: lib87582


title: lib87583


title: lib87585


title: lib87580


title: lib87578


title: lib87577


title: lib87575


title: lib87576


title: lib87602


title: lib87574


title: lib87573


title: lib87572


title: lib87570


title: lib87569


title: lib87571


title: lib87568


title: lib87567


title: lib87565


title: lib87564


title: lib87563


title: lib87559


title: lib87581


title: lib87558


title: lib87579


title: lib87556


title: lib87557


title: lib87562


title: lib87554


title: lib87552

value: Aab negative


title: lib87553


title: lib87551


title: lib87555


title: lib87548


title: lib87547


title: lib87549


title: lib87546


title: lib87566


title: lib87544


title: lib87542


title: lib87543


title: lib87561


title: lib87541


title: lib87540


title: lib87560


title: lib87536


title: lib87538


title: lib87537


title: lib87534


title: lib87533


title: lib87535


title: lib87530


title: lib87529


title: lib87550


title: lib87539


title: lib87526


title: lib87525


title: lib87527


title: lib87528


title: lib87523


title: lib87521


title: lib87545


title: lib87522


title: lib87532


title: lib87520


title: lib87517


title: lib87518


title: lib87519


title: lib87512


title: lib87514


title: lib87515


title: lib87513


title: lib87510


title: lib87531


title: lib87509


title: lib87508

source_name: CD154+CD69+ CD4 T cells

value: CD154+CD69+ CD4 T cells


title: lib87511


title: lib87505


title: lib87504


title: lib87506


title: lib87507


title: lib87503


title: lib87524


title: lib87500


title: lib87501


title: lib87499


title: lib87498


title: lib87497


title: lib87496


title: lib87495


title: lib87516


title: lib87493


title: lib87494


title: lib87492


title: lib87491


title: lib87487


title: lib87485


title: lib87488


title: lib87486


title: lib87490


title: lib87484


title: lib87489


title: lib87483


title: lib87482


title: lib87478


title: lib87479


title: lib87477


title: lib87481


title: lib87475


title: lib87476


title: lib87502


title: lib87472


title: lib87473


title: lib87470


title: lib87474


title: lib87469


title: lib87468


title: lib87466


title: lib87465


title: lib87467


title: lib87464


title: lib87463


title: lib87462


title: lib87460


title: lib87457


title: lib87458


title: lib87459


title: lib87454


title: lib87480


title: lib87455


title: lib87449


title: lib87447


title: lib87471


title: lib87446


title: lib87445


title: lib87450


title: lib87448


title: lib87452


title: lib87441


title: lib87442


title: lib87451


title: lib87391


title: lib87443


title: lib87389


title: lib87390


title: lib87392


title: lib87388


title: lib87444


title: lib87387


title: lib87386


title: lib87461


title: lib87456


title: lib87453


title: lib87384


title: lib87385


title: lib87383


title: lib87381


title: lib87380


title: lib87379


title: lib87382


title: lib87377


title: lib87378


title: lib87372


title: lib87375


title: lib87376


title: lib87373


title: lib87374


title: lib87371


title: lib87369


title: lib87370


title: lib87368


title: lib87367


title: lib87364


title: lib87362


title: lib87363


title: lib87365


title: lib87358


title: lib87359


title: lib87360


title: lib87357


title: lib87356


title: lib87352


title: lib87353


title: lib87351


title: lib87350


title: lib85452


title: lib85451


title: lib85450


title: lib87366


title: lib85447


title: lib85448


title: lib87361


title: lib85449


title: lib85445


title: lib85442


title: lib85443


title: lib85440


title: lib87355


title: lib85439


title: lib85437


title: lib85435


title: lib85434


title: lib87354


title: lib85433


title: lib85438


title: lib85436


title: lib85431


title: lib85427


title: lib85430


title: lib85428


title: lib85429


title: lib85426


title: lib85432


title: lib85446


title: lib85424


title: lib85444


title: lib85421


title: lib85422


title: lib85419


title: lib85425


title: lib85423


title: lib85420


title: lib85441


title: lib85417


title: lib85416


title: lib85418


title: lib85413


title: lib85415


title: lib85414


title: lib85411


title: lib85410


title: lib85408


title: lib85409


title: lib85407


title: lib85406


title: lib85405


title: lib85404


title: lib85403


title: lib85402


title: lib85401


title: lib85400


title: lib85399


title: lib85398


title: lib85397


title: lib85394


title: lib85393


title: lib85395


title: lib85396


title: lib85389


title: lib85390


title: lib85412


title: lib85391


title: lib85384


title: lib85385


title: lib85383


title: lib85381


title: lib85387


title: lib85379


title: lib85378


title: lib85382


title: lib85376


title: lib85377


title: lib85374


title: lib85373


title: lib85372


title: lib85375


title: lib85371


title: lib85392


title: lib85370


title: lib85368


title: lib85369


title: lib85367


title: lib85388


title: lib85365


title: lib85364


title: lib85362


title: lib85361


title: lib85363


title: lib85366


title: lib85386


title: lib85380


title: lib85358


title: lib85357


title: lib85360


title: lib85354


title: lib85355


title: lib85353


title: lib85359


title: lib85352


title: lib85351


title: lib85350


title: lib85348


title: lib85347


title: lib85349


title: lib85343


title: lib85340


title: lib85346


title: lib85344


title: lib85342


title: lib85345


title: lib85334


title: lib85339


title: lib85337


title: lib85332


title: lib85341


title: lib85330


title: lib85338


title: lib85329


title: lib85328


title: lib85327


title: lib85331


title: lib85356


title: lib85333


title: lib85326


title: lib85324


title: lib85322


title: lib85323


title: lib85335


title: lib85321


title: lib85336


title: lib85320


title: lib85319


title: lib85318


title: lib85315


title: lib85316


title: lib85312


title: lib85310


title: lib85309


title: lib85314


title: lib85311


title: lib85308


title: lib85325


title: lib85304


title: lib85302


title: lib85301


title: lib85305


title: lib85317


title: lib85298


title: lib85303


title: lib85300


title: lib85299


title: lib85295


title: lib85297


title: lib85296


title: lib85307


title: lib85294


title: lib85293


title: lib85291


title: lib85289


title: lib85292


title: lib85313


title: lib85306


title: lib84979


title: lib84972


title: lib84977


title: lib84975


title: lib84971


title: lib84976


title: lib84973


title: lib84974


title: lib84964


title: lib84965


title: lib84970


title: lib84960


title: lib84961


title: lib84966


title: lib84959


title: lib84967


title: lib85290


title: lib84968


title: lib84962


title: lib84969


title: lib84956


title: lib84954


title: lib85288


title: lib84958


title: lib84953


title: lib84978


title: lib84952


title: lib84951


title: lib84963


title: lib84945


title: lib84947


title: lib84948


title: lib84946


title: lib84940


title: lib84944


title: lib84941


title: lib84942


title: lib84950


title: lib84949


title: lib84936


title: lib84957


title: lib84937


title: lib84935


title: lib84933


title: lib84934


title: lib84943


title: lib84955


title: lib84931


title: lib84932


title: lib84930


title: lib84929


title: lib84928


title: lib84927


title: lib84925


title: lib84926


title: lib84924


title: lib84939


title: lib84923


title: lib84938


title: lib84920


title: lib84919


title: lib84921


title: lib84916


title: lib84913


title: lib84914


title: lib84922


title: lib84912


title: lib84918


title: lib84562


title: lib84563


title: lib84915


title: lib84559


title: lib84917


title: lib84910


title: lib84911


title: lib84560


title: lib84557


title: lib84555


title: lib84556


title: lib84554


title: lib84553


title: lib84551


title: lib84552


title: lib84549


title: lib84548


title: lib84545


title: lib84561


title: lib84544


title: lib84546


title: lib84547


title: lib84541


title: lib84542


title: lib84543


title: lib84539


title: lib84532


title: lib84558


title: lib84540


title: lib84533


title: lib84536


title: lib84529


title: lib84535


title: lib84526


title: lib84525


title: lib84534


title: lib84530


title: lib84531


title: lib84528


title: lib84527


title: lib84521


title: lib84524


title: lib84523


title: lib84550


title: lib84515


title: lib84516


title: lib84510


title: lib84509


title: lib84538


title: lib84522


title: lib84537


title: lib84520


title: lib84519


title: lib84506


title: lib84505


title: lib84518


title: lib84517


title: lib84513


title: lib84514


title: lib84501


title: lib84499


title: lib84497


title: lib84508


title: lib84504


title: lib84507


title: lib84511


title: lib84496


title: lib84503


title: lib84502


title: lib84500


title: lib84512


title: lib84492


title: lib84498


title: lib84494


title: lib84491


title: lib84495


title: lib84490


title: lib84493


title: lib84489


title: lib84485


title: lib84487


title: lib84488


title: lib84486


title: lib84484


title: lib84481


title: lib84479


title: lib84478


title: lib84474


title: lib84470


title: lib84476


title: lib84475


title: lib84471


title: lib84469


title: lib84459


title: lib84467


title: lib84473


title: lib84460


title: lib84472


title: lib84461


title: lib84466


title: lib84464


title: lib84456


title: lib84458


title: lib84477


title: lib84482


title: lib84457


title: lib84462


title: lib84468


title: lib84454


title: lib84463


title: lib84453


title: lib84480


title: lib84483


title: lib84465


title: lib84450


title: lib84452


title: lib84451


title: lib84449


title: lib84448


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title: lib84442


title: lib84455


title: lib84439


title: lib84443


title: lib84441


title: lib84444


title: lib84438


title: lib84432


title: lib84433


title: lib84436


title: lib84431


title: lib84430


title: lib84434


title: lib84437


title: lib84429


title: lib84435


title: lib84428


title: lib84425


title: lib84424


title: lib84426


title: lib84447


title: lib84440


title: lib84419


title: lib84420


title: lib84421


title: lib84422


title: lib84418


title: lib84427


title: lib84413


title: lib84417


title: lib84412


title: lib84411


title: lib84416


title: lib84410


title: lib84415


title: lib84409


title: lib84406


title: lib84408


title: lib84405


title: lib84407


title: lib84403


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title: lib84401


title: lib84399


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title: lib84400


title: lib84397


title: lib84423


title: lib84396


title: lib84414


title: lib84394


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title: lib84393


title: lib84392


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title: lib84388


title: lib84385


title: lib84387


title: lib84386


title: lib84383


title: lib84384


title: lib84380


title: lib84379


title: lib84381


title: lib84382


title: lib84375


title: lib84378


title: lib84377


title: lib82682


title: lib84376


title: lib82680


title: lib82676


title: lib82681


title: lib82678


title: lib82679


title: lib84391


title: lib82677


title: lib82675


title: lib82672


title: lib84389


title: lib82674


title: lib82673


title: lib82670


title: lib82667


title: lib82668


title: lib82664


title: lib82665


title: lib82663


title: lib82661


title: lib82662


title: lib82659


title: lib82660


title: lib84402


title: lib82657


title: lib82656


title: lib82655


title: lib82654


title: lib82658


title: lib82652


title: lib82653


title: lib82649


title: lib82650


title: lib82648


title: lib82666


title: lib82651


title: lib82647


title: lib82645


title: lib82671


title: lib82640


title: lib82643


title: lib82644


title: lib82642


title: lib82638


title: lib82634


title: lib82669


title: lib82636


title: lib82639


title: lib82641


title: lib82631


title: lib82630


title: lib82627


title: lib82635


title: lib82633


title: lib82626


title: lib82629


title: lib82632


title: lib82646


title: lib82620


title: lib82628


title: lib82618


title: lib82617


title: lib82625


title: lib82624


title: lib82623


title: lib82621


title: lib82622


title: lib82619


title: lib82606


title: lib82605


title: lib82604


title: lib82603


title: lib82637


title: lib82601


title: lib82598


title: lib82599


title: lib82615


title: lib82616


title: lib82597


title: lib82609


title: lib82612


title: lib82595


title: lib82607


title: lib82610


title: lib82593


title: lib82613


title: lib82611


title: lib82591


title: lib82600


title: lib82590


title: lib82596


title: lib82602


title: lib82588


title: lib82614


title: lib82592


title: lib82608


title: lib82589


title: lib82594


title: lib82584


title: lib82586


title: lib82583


title: lib82582


title: lib82580


title: lib82578


title: lib82579


title: lib82581


title: lib82577


title: lib82574


title: lib82572


title: lib82570


title: lib82569


title: lib82571


title: lib82576


title: lib82568


title: lib82567


title: lib82566


title: lib82585


title: lib82564


title: lib82587


title: lib82563


title: lib82565


title: lib82562


title: lib82561


title: lib82559


title: lib82557


title: lib82558


title: lib82554


title: lib82575


title: lib82555


title: lib82560


title: lib82553


title: lib82549


title: lib82550


title: lib82551


title: lib82552


title: lib82573


title: lib82547


title: lib82546


title: lib82548


title: lib82545


title: lib82543


title: lib82544


title: lib82541


title: lib82540


title: lib82539


title: lib82538


title: lib82536


title: lib82537


title: lib82533


title: lib82535


title: lib82556


title: lib82532


title: lib82529


title: lib82534


title: lib82528


title: lib82525


title: lib82526


title: lib82527


title: lib82531


title: lib82524


title: lib82530


title: lib82523


title: lib82522


title: lib82542


title: lib82519


title: lib82520


title: lib82518


title: lib82517


title: lib82514


title: lib82516


title: lib82512


title: lib82511


title: lib82509


title: lib82510


title: lib82508


title: lib82506


title: lib82507


title: lib82505


title: lib82503


title: lib82504


title: lib82501


title: lib82502


title: lib82500


title: lib82499


title: lib82521


title: lib82496


title: lib82498


title: lib82497


title: lib82515


title: lib82493


title: lib82491


title: lib82492


title: lib82488


title: lib82513


title: lib82487


title: lib82490


title: lib82495


title: lib82489


title: lib82494


title: lib82482


title: lib82481


title: lib82485


title: lib82486


title: lib82484


title: lib82483


title: lib82480


title: lib82479


title: lib82478


title: lib82476


title: lib82436


title: lib82435


title: lib82434


title: lib82433


title: lib82432


title: lib82430


title: lib82428


title: lib82427


title: lib82425


title: lib82422


title: lib82423


title: lib82424


title: lib82421


title: lib82420


title: lib82419


title: lib82416


title: lib82417


title: lib82418


title: lib82415


title: lib82414


title: lib82413


title: lib82407


title: lib82406


title: lib82431


title: lib82405


title: lib82477


title: lib82403


title: lib82402


title: lib82412


title: lib82401


title: lib82410


title: lib82397


title: lib82396


title: lib82395


title: lib82409


title: lib82408


title: lib82404


title: lib82393


title: lib82429


title: lib82426


title: lib82411


title: lib82400


title: lib82389


title: lib82388


title: lib82399


title: lib82385


title: lib82386


title: lib82387


title: lib82383


title: lib82394


title: lib82392


title: lib82381


title: lib82384


title: lib82382


title: lib82398


title: lib82379


title: lib82390


title: lib82380


title: lib82378


title: lib82377


title: lib82374


title: lib82391


title: lib82371


title: lib82376


title: lib82372


title: lib82370


title: lib82375


title: lib82367


title: lib82369


title: lib82365


title: lib82364


title: lib82361


title: lib82368


title: lib82359


title: lib82363


title: lib82360


title: lib82373


title: lib82357


title: lib82362


title: lib82355


title: lib82353


title: lib82356


title: lib82354


title: lib82348


title: lib82358


title: lib82351


title: lib82350


title: lib82349


title: lib82347


title: lib82345


title: lib82346


title: lib82339


title: lib82337


title: lib82336


title: lib82335


title: lib82352


title: lib82333


title: lib82330


title: lib82366


title: lib82342


title: lib82344


title: lib82340


title: lib82338


title: lib82332


title: lib82343


title: lib82321


title: lib82331


title: lib82326


title: lib82322


title: lib82320


title: lib82328


title: lib82327


title: lib82317


title: lib82329


title: lib82313


title: lib82318


title: lib82315


title: lib82316


title: lib82309


title: lib82312


title: lib82323


title: lib82325


title: lib82341


title: lib82307


title: lib82319


title: lib82334


title: IRAK4-KD-3

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

description:
poly(A) RNA from hippocampus
D3

data_processing:
2x150bp  reads, Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

source_name: Hippocampus

extract_protocol:
QIAGEN miRNEasy Micro Kit
KAPA HyperPrep mRNA

value: Hippocampus

tag: age

value: 10 months


title: C57-3

description:
poly(A) RNA from hippocampus
C3


title: C57-2

description:
poly(A) RNA from hippocampus
C2


title: lib82301


title: lib82314


title: lib82302


title: lib82311


title: MRL-IRAK4-KD-3

description:
poly(A) RNA from hippocampus
B3


title: lib82310


title: lib82306


title: lib82324


title: MRL-IRAK4-KD-2

description:
poly(A) RNA from hippocampus
B2


title: IRAK4-KD-1

description:
poly(A) RNA from hippocampus
D1


title: lib82298


title: lib82299


title: lib82305


title: MRL-IRAK4-KD-1

description:
poly(A) RNA from hippocampus
B1


title: lib82308


title: lib82304


title: lib82303


title: MRL-4

description:
poly(A) RNA from hippocampus
A4

value: MRL


title: MRL-2

description:
poly(A) RNA from hippocampus
A2


title: MRL-3

description:
poly(A) RNA from hippocampus
A3


title: lib82295


title: C57-1

description:
poly(A) RNA from hippocampus
C1


title: MRL-IRAK4-KD-4

description:
poly(A) RNA from hippocampus
B4


title: lib82300


title: lib82294


title: IRAK4-KD-2

description:
poly(A) RNA from hippocampus
D2


title: lib82297


title: lib82296


title: lib82293


title: lib82291


title: lib82292


title: P8_WT_lung

city: Houston

first: Dalia

last: Hassan

state: TX

department: Pulmonary Medicine

institute: MD Anderson Cancer Center

description: wild type mouse lung

library_source: genomic single cell

data_processing:
Chromium single-cell ATAC-seq output was processed with Cell Ranger using “cellranger count” and “cellranger aggr”.
Bams were filtered using Picard and Samtools with the commands MarkDuplicates and –f 3 –F 4 –F 256 –F 1024 –F 2048 –q 30
Barcodes were extracted from processed cell clusters in Seurat and Signac and used with Sinto to partition the cellranger output bam file into smaller cell type bams
Further analysis can be achieved using the Cell Ranger ATAC’s functions “cellranger-atac count”. Downstream analysis was performed using Seurat R package (4.3) Signac (1.9)
Peaks were then called using Macs on the -braod setting whereupon peaks were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Rds files can be opened with Signac (R package) and analyzed
Supplementary files format and content: bw files can be opened with igv genomic browser

source_name: lung

extract_protocol:
Perfused lungs were collected from anesthetized mice as described above. Previously published protocols for cell dissociation and sorting cells were used with minor modifications11. Extra-pulmonary airways and connective tissues were removed from lungs, which were then minced with forceps and digested in Liebovitz media (Gibco, 21083-027) for scRNA-seq, ATAC-seq, or scATAC-seq with 2 mg/mL collagenase type I (Worthington, CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington, D, LS002007), and 2 mg/mL elastase (Worthingon, ESL, LS002294) for 30 min at 37 °C. To stop the digestion, fetal bovine serum (FBS, Invitrogen, 10082-139) was added to a final concentration of 20%. Tissues were triturated until homogenous and filtered through a 70 µm cell strainer (Falcon, 352350) on ice in a 4 °C cold room and transferred to a 2 mL tube. The sample was then centrifuged at 1,537 rcf for 1 min; then 1 mL red blood cell lysis buffer (15 mM NH4Cl, 12 mM NaHCO3, 0.1 mM EDTA, pH 8.0) was added and incubated for 3 min before centrifugation again at 1,537 rcf. The red blood cell lysis buffer incubation was repeated to remove residual red blood cells. Liebovitz+10% FBS was used to wash and resuspend samples, which were then filtrated through a 35 mm cell strainer into a 5 mL glass tube and had SYTOX Blue (1:1000, Invitrogen, S34857) added. After refiltering, samples were for ATAC-seq were sorted for GFP positive cells from a RosaSun1GFP reporter activated by Wnt3aCre, Rtkn2CreER, or SftpcCreER on a BD FACSAria IIIu cell sorter with a 70 mm nozzle. Samples for scRNA-seq or scATAC-seq were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min followed by a wash and being resuspended with Liebovitz meda+10% FBS and addition of SYTOX Blue. Samples were then filtered through a 35 mm cell strainer into a 5 mL glass tube again and sorted by a BD FACSAria Fusion sorter or a with a 70 mm nozzle.
FACS-purified FACS-purified lung epithelial, immune, endothelial, and mesenchymal c, were processed using the 3′ Library and Gel Bead Kit following the manufacturer’s users guide (v2 rev D) on the Chromium Single-Cell Gene Expression Solution Platform (10X Genomics).
Libraries were then sequenced using Illumina Novaseq6000 with a 50-paired-end format with index1 for 8 cycles and index2 for 16 cycles.

value: lung

value: epithelial, mesenchymal, endothelial and immune

value: WT

value: postnatal day8

value: no treatment

tag: Sex

value: pooled male and female


title: E18.5_WT_lung

description: wild type mouse lung

value: Embryonic day 18.5


title: lib82288


title: KO_VD_3

city: Guangzhou

first: Xuejiao

last: Fan

state: Guangdong

address: Tianhe District, Jinsui Road

department: Institute of Pediatrics

institute: Guangzhou Women and Children’s Medical Centre

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Alignment, filtering, barcode counting, and unique molecular identifier (UMI) counting were performed with Cell Ranger count module to generate feature-barcode matrix and determine clusters.
Assembly: mm10
Supplementary files format and content: barcodes files, features files, matrix files

source_name: aorta

extract_protocol:
The aorta was washed three times in PBS, incubated at 37 °C for 40 minutes with an enzymatic dissociation cocktail (0.55 mg/mL collagenase I, 0.15 mg/mL collagenase IV and 0.07 mg/mL hyaluronidase in RPMI-1640 medium) and minced. The cell suspensions were filtered through 70 µm strainers and then pelleted by centrifugation at 400g for 5 minutes. The enzyme solution was then discarded and cells were resuspended in fresh PBS containing 0.04% BSA.
Cell suspension was loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads-in-emulsion (GEMs). Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual GEMs. Reverse transcription was performed on a Thermal Cycler. Libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1 according to the manufacturer’s protocol.

value: aorta

value: male

value: 8 weeks old


title: lib82286

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides

value: >1 Aab+ any age


title: MRL-1

description:
poly(A) RNA from hippocampus
A1


title: lib82285


title: WT_VD_2

description: 10x Genomics


title: lib82290


title: KO_VD_2

description: 10x Genomics


title: lib82284


title: WT_3

description: 10x Genomics

value: vehicle


title: 9-wks_WT

description: wild type mouse lung


title: lib82283

value: CD154+CD69+ CD4 T cells


title: KO_VD_1

description: 10x Genomics


title: WT_VD_3

description: 10x Genomics


title: lib82277


title: Spleen, NN

city: Nantong

first: Qianqian

last: Luo

state: Jiangsu

address: No.9, Seyuan Road, Chongchuan district, Nantong, Jiangsu Province, China

institute: Nantong University

description: control

data_processing:
The BD Rhapsody WTA Analysis Pipeline(version 1.8) was used to create sequencing libraries from single cell transcriptomes without specifying a targeted panel.
After sequencing, the analysis pipeline takes the FASTQ files, a reference genome file (human: GRCh38,mouse:mm10) and a transcriptome annotation file (human:GENCODE v32/Ensembl 98,mouse:GENCODE vM23/Ensembl 98) for sequence alignment.
Assembly: reference genome file (human: GRCh38,mouse:mm10) and transcriptome annotation file (human:GENCODE v32/Ensembl 98,mouse:GENCODE vM23/Ensembl 98)
Supplementary files format and content: The pipeline generates a unique molecular identifier (UMI) count matrix which will be processed using python package Scanpy (version 1.8) for further analysis.

source_name: Spleen

growth_protocol: C57BL/6J mice were exposed to a hypobaric hypoxia (HH) chamber for 7 days to establish an animal model simulating high altitude exposure at 6000 meters, while the control group animals were kept in a similar chamber under normobaric normoxia (NN) conditions for 7 days.

extract_protocol:
BD Rhapsody system was used to capture the transcriptomic information of the (XX sample-derived) single cells. Single-cell capture was achieved by random distribution of a single-cell suspension across >200,000 microwells through a limited dilution approach. Beads with oligonucleotide barcodes were added to saturation so that a bead was paired with a cell in a microwell. The cells were lysed in the microwell to hybridize mRNA molecules to barcoded capture oligos on the beads.
Beads were collected into a single tube for reverse transcription and ExoI digestion. Upon cDNA synthesis, each cDNA molecule was tagged on the 5′ end (that is, the 3′ end of a mRNA transcript) with a unique molecular identifier (UMI) and cell barcode indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Rhapsody single-cell whole-transcriptome amplification (WTA) workflow including random priming and extension (RPE), RPE amplification PCR and WTA index PCR. The libraries were quantified using a High Sensitivity D1000 ScreenTape (Agilent) and High Sensitivity D1000 Reagents (Agilent) on a 4150 TapeStation System (Agilent) and the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific).
Sequencing was performed by illumina sequencer (Illumina, San Diego, CA) on a 150 bp paired-end run.

treatment_protocol: The spleen tissues were surgically removed and stored in MACS Tissue Storage Solution (Miltenyi Biotec, Bergisch Gladbach, Germany) until processing. Single-cell dissociation was performed by the experimentalists at the GENECHEM laboratory (Shanghai, China).

value: Spleen

value: Normobaric normoxia exposure for 7 days


title: lib82280


title: lib82287


title: lib82275


title: KIKO_1

city: Roma

first: Andrea

last: Ninni

state: RM

address: Via della Ricerca Scientifica

department: Biology

institute: Tor Vergata University

data_processing:
Alignment w/ Hisat2
Annotation w/ featureCounts
Analysis w/ R 4,3,1
Analysis w/ DESeq2
Assembly: mm10
Supplementary files format and content: txt file

source_name: Cerebellum

extract_protocol:
the total RNA were extracted using the QUIAGEN RNAse Lipid Tissue
the Library were prepared with Illumina stranded RNA kit

value: Cerebellum

value: KIKO


title: lib82274


title: WT_VD_1

description: 10x Genomics


title: lib82273


title: WT_1


title: WT_2

description: 10x Genomics


title: lib82271


title: lib82282


title: WT_1

description: 10x Genomics


title: lib82279


title: lib82281


title: ipsilateral sham injured cortical astrocytes  [a9_11_IPSI_C]

city: Blacksburg

first: Michelle

middle: Lynne

last: Olsen

state: VA

address: 970 Washington Street SW

department: School of Neuroscience

institute: Virginia Tech

data_processing:
Bases with quality scores less than 30 and adapters were trimmed from raw sequencing reads by Trim Galore (v 0.6.4)
After trimming, only reads with length greater than 30bp were mapped to mm10 by RSEM (v1.2.28) with bowtie2 (v 2.4.1)
The raw counts were used to identify differentially expressed genes by DESeq2 (v 1.36.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

extract_protocol:
Ambion’s PureLink RNA Mini Isolation
TakaraSMARTSeq V4 ultra-low input RNA kit

value: astrocytes

value: WT CD31 Sham

value: Ipsi SHAM

tag: time

value: 4 months post injury


title: lib82270


title: KIKO_2


title: ipsilateral sham injured cortical astrocytes  [a9_10_IPSI_C]


title: lib82268


title: Spleen, HH

description: treatment

value: WT

value: Hypobaric hypoxia exposure for 7 days


title: lib82289


title: ipsilateral sham injured cortical astrocytes  [a8_16_IPSI_C]


title: Cerebellum_KIKO

data_processing:
Alignment w/ CellRanger 7,0,1
Analysis w/ R 4,3,1
Analysis w/ Seurat 4,3,0
Assembly: mm10
Supplementary files format and content: Barcodes – tsv file
Supplementary files format and content: Features – tsv file
Supplementary files format and content: Matrix – sparse matrix file

extract_protocol:
The cells were isolated with 10x Chromium Next GEM Single Cell 3’ v3.1(Dual Index) Protocol
The library were prepared with 10x 3’ Library Prep


title: lib82267


title: Cerebellum_WT


title: ipsilateral injured cortical astrocytes PTE- [a9_20_IPSI_C]

value: WT CD31 Injured

value: Ipsi PTE-


title: lib82278


title: E16.5_WT_lung

description: wild type mouse lung

value: lung

value: epithelial, mesenchymal, endothelial and immune

value: Embryonic day 16.5

value: no treatment

value: pooled male and female


title: lib82265

value: CD154+CD69+ CD4 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides

value: >1 Aab+ any age


title: KIKO_3

value: Cerebellum

value: KIKO


title: ipsilateral injured cortical astrocytes PTE- [a9_15_IPSI_C]

value: astrocytes


title: ipsilateral injured cortical astrocytes PTE- [a9_14_IPSI_C]


title: lib82262


title: lib82276


title: ipsilateral injured cortical astrocytes PTE- [a9_13_IPSI_C]


title: WT_3


title: WT_2


title: lib82272


title: lib82269


title: ipsilateral sham injured cortical astrocytes  [a9_9_IPSI_C]

value: WT CD31 Sham

value: Ipsi SHAM


title: ipsilateral injured cortical astrocytes PTE- [a8_14_IPSI_C]

value: 4 months post injury


title: lib82260


title: lib82258


title: ipsilateral injured cortical astrocytes PTE- [a8_11_IPSI_C]


title: lib82257


title: lib82256


title: lib82266


title: ipsilateral injured cortical astrocytes PTE+ [a9_18_IPSI_C]

value: Ipsi PTE+


title: lib82263


title: ipsilateral injured cortical astrocytes PTE- [a9_16_IPSI_C]

value: WT CD31 Injured


title: lib82264


title: lib81511

value: Aab negative


title: lib82261


title: contralateral sham injured cortical astrocytes  [a9_11_contra_C]

value: Contra SHAM


title: lib81508


title: ipsilateral injured cortical astrocytes PTE- [a9_12_IPSI_C]

value: Ipsi PTE-


title: lib82259


title: contralateral sham injured cortical astrocytes  [a9_9_contra_C]


title: ipsilateral injured cortical astrocytes PTE- [a8_13_IPSI_C]


title: lib81507


title: ipsilateral injured cortical astrocytes PTE- [a8_9_IPSI_C]


title: ipsilateral injured cortical astrocytes PTE+ [a9_19_IPSI_C]


title: lib81505


title: lib82255


title: lib81503


title: contralateral injured cortical astrocytes PTE- [a9_15_contra_C]

value: Contra PTE-


title: ipsilateral sham injured cortical astrocytes  [a8_15_IPSI_C]


title: lib81512


title: contralateral injured cortical astrocytes PTE- [a9_12_contra_C]


title: lib81509


title: ipsilateral injured cortical astrocytes PTE+ [a9_17_IPSI_C]


title: ipsilateral injured cortical astrocytes PTE+ [a8_10_IPSI_C]


title: lib81499


title: contralateral injured cortical astrocytes PTE- [a8_11_contra_C]


title: contralateral injured cortical astrocytes PTE- [a8_13_contra_C]


title: contralateral injured cortical astrocytes PTE- [a8_9_contra_C]


title: lib81496


title: lib81510


title: lib81498


title: contralateral sham injured cortical astrocytes  [a8_15_contra_C]


title: contralateral sham injured cortical astrocytes  [a8_16_contra_C]


title: contralateral injured cortical astrocytes PTE+ [a9_18_contra_C]

value: Contra PTE+


title: lib81504


title: contralateral injured cortical astrocytes PTE+ [a8_17_contra_C]


title: lib81493


title: contralateral injured cortical astrocytes PTE+ [a8_10_contra_C]


title: contralateral injured cortical astrocytes PTE- [a9_16_contra_C]


title: contralateral injured cortical astrocytes PTE- [a9_13_contra_C]


title: lib81502


title: contralateral sham injured cortical astrocytes  [a9_10_contra_C]


title: lib81501


title: lib81500


title: lib81490


title: lib81489


title: SAVI Tnfr 1/2 KO 1

city: Bonn

first: Rayk

last: Behrendt

state: North Rhine-Westphalia

address: Venusberg-Campus 1

department: Nucleic Acid Immunity & Genome Defense

country: Germany

institute: Institute for Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn

data_processing:
bcl2fastq2 2.20.0
Fragments were aligned to the mouse reference (GRCm39) with support of the Ensembl 104 gene annoation using the aligner gsnap (v2020-12-16) (-d GRCm39 --gunzip -A sam -t 12 --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000  -B 5 -n 1 -m 0.6 -s EnsemblGene-104.ss.GRCm39.iit -N 0)
Fragments per gene and samples were obtained based on the overlap of the uniquely mapped fragments with the same Ensembl gene annotation using featureCounts (v2.0.1) (-a EnsemblGene-104.GRCm39.TR.gtf -s 2 -p -o genecount/bfx1909.GRCm39.e104.txt -Q 1 -T 8)
Assembly: GRCm39
Comma separated text file from FeatureCounts. Each columns is either the listing of gene characteristics or Samples and each row show the specific gene details / fragments per gene per sample

extract_protocol:
FACS sorting
mRNA was isolated from on average 50 ng total RNA by poly-dT enrichment using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s instructions. Samples were then directly subjected to the workflow for strand-specific RNA-Seq library preparation (Ultra II Directional RNA Library Prep, NEB). For ligation NEB Next Adapter for Illumina of the NEB Next Multiplex Oligos for Illumina Kit were used. After ligation, adapters were depleted by an XP bead purification (Beckman Coulter) adding the beads solution in a ratio of 0.9:1 to the samples. Unique dual indexing was done during the following PCR enrichment (14 cycles) using amplification primers carrying the same sequence for i7 and i5 index (Primer 1: AAT GAT ACG GCG ACC ACC GAG ATC TAC AC NNNNNNNN ACA TCT TTC CCT ACA CGA CGC TCT TCC GAT CT, Primer 2: CAA GCA GAA GAC GGC ATA CGA GAT NNNNNNNN GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC T). After two more XP bead purifications (0.9:1), libraries were quantified using the Fragment Analyzer (Agilent). Libraries were sequenced on an Illumina NovaSeq 6000 in 100 bp paired-end mode with an average of 30 million fragments per library.

value: lung

value: ex vivo

value: Tmem173 N154S KI/WT Tnfr1/2 KO/KO


title: lib81488

value: CD154+CD69+ CD4 T cells

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Tnfr1/2 KO 4

value: Tnfr1/2 KO/KO


title: contralateral injured cortical astrocytes PTE- [a8_14_contra_C]

value: astrocytes


title: Tnfr1/2 KO 3


title: lib81486


title: contralateral injured cortical astrocytes PTE+ [a9_17_contra_C]


title: lib81506


title: contralateral injured cortical astrocytes PTE- [a9_20_contra_C]


title: Tnfr1/2 KO 1


title: lib81497


title: SAVI 4

value: Tmem173 N154S KI/WT


title: lib81494


title: lib81483


title: lib81481


title: lib81492


title: SAVI Tnfr 1/2 KO 4


title: WT CTRL 3

value: Tmem173 N154S WT/WT


title: SAVI Tnfr 1/2 KO 3


title: WT CTRL 1


title: lib81479


title: SAVI Tnfr 1/2 KO 2


title: lib81495


title: lib81474


title: PVN,ZT8 treatment, replicate 2,scRNA-seq

first: Yulin

last: Dai

address: 7000 fannin, suite 600

department: School of Biomedical Informatics

institute: University of Texas health science center at Houston

description: 10x Genomics

data_processing:
The Cell Ranger™ Single Cell Software Suite v.7.0.0 was used and The reads were aligned to the human transcriptome reference (cellranger mm10-2020-A) with STAR 2.6
Assembly: cellranger-mm10-2020-A
Supplementary files format and content: standard output of cellranger with gzipped barcode, features (gene), and Unique Molecular Identifier (UMI)

source_name: PVN

extract_protocol:
PVN ncueli was obtained from compiling 5 micorpunched PVNs together and then carrying out nuceli isolation using a sucrose gradient. The nuceli morpholohy and quantity were checked under the microscope by staining
Single cell Gene Expression Library was prepared according toChromium Next GEM Single Cell 3' Reagent Kits v3(10x Genomics). In Brief, single nuclei suspension, reverse transcription (RT) reagents, Gel Beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller (10x Genomics) to generate single cell GEMS (Gel Beads-In-Emulsions) where full length cDNA was synthesized and barcoded for each single cell. Subsequently the GEMS are broken and cDNA from each single cell are pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA is amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. Final library was generated by amplification.

value: PVN

value: PVN cells

value: Male


title: PVN,ZT20 treatment, replicate 1,scRNA-seq

description: 10x Genomics


title: Tnfr1/2 KO 2


title: lib81472

value: Aab negative


title: lib81484


title: lib81477


title: lib81491


title: lib81470


title: lib81469


title: XL413_UT_0h

city: Milan

first: Francesco

last: Gualdrini

address: Via Adamello, 16

department: Department of Experimental Oncology

institute: European Institute of Oncology

description: ChIPseq

data_processing:
Reads were quality filtered according to the illumina pipeline
Single end reads were mapped to the mouse mm10 genome (Illumina's iGenomes reference annotation downloaded from UCSC http://support.illumina.com/sequencing/sequencing_software/igenome.html) by exploiting the mapping steps of ShortStack (Johnson et al. 2016).Briefly, ShortStack exploits bowtie to identify all best-matched alignments for each read. It will compute a probability for each alignment to different loci in the genome. To do so the frequency of uniquely aligned reads mapping within the vicinity of multi-mapping reads is used to redistribute multi-mapping reads accordingly.
Mapped reads were filtered in order to remove randomly placed multi-mappers and unmapped reads using SAMtools standard procedure (version 1.9)(Li et al. 2009).
In order to identify high confidence genome wide site of enrichment per antibody we implemented three strategies accordingly to the type of signal distribution evaluated after visual inspection of bigwig tracks on IGV (Robinson et al. 2011):   For H2K27ac we used peaks identified in ATACseq samples (see below) expanding the ATAC peaks by 1.5 kb on both sides.
Read counts per samples at the identified loci were retrieved using the R/Bioconductor package GenomicRanges and GenomicAlignment (Lawrence et al. 2013). Sample normalization was achieved by selecting invariant peaks across samples (Gualdrini et al. 2016). Briefly, we modelled the frequency distribution of the differences in reads counts across samples with a log-normal distribution. Peaks laying within 1σ of the best fitted mean difference were considered as invariant and used to normalize the samples.
Assembly: mm10
Supplementary files format and content: .bw are BigWig normalised files

source_name: mouse bone marrow derived macrophages

extract_protocol:
genomic DNA
ChIPseq was carried out as previously described (XXXXXXX). Briefly, 2 x 106 BMDM cells were fixed with 1% of formaldehyde (Merck cod. 252549) for 10 min at RT and lysed to prepare nuclear extracts. After chromatin shearing by sonication with a Bioruptor® Pico, lysates were incubated overnight at 4°C with protein G Dynabeads (Invitrogen, cod.10009D) previously coupled with 2 μg of H3K27ac antibody (ab4729). After immunoprecipitation, beads were recovered using a magnetic stand and washed six times with FA/SDS buffer (50mM Hepes pH 8, 1% Triton-X, 0.1% Na-deoxycholate, 0.1% SDS, 1mM EDTA, 650mM Nacl), four times with Wash buffer (10mM Tris pH 8, 0.25M LiC, 1mM EDTA, 0.5% NP40, 0.5% Na-deoxycholate), followed by two washes with TEbuffer plus 50mM NaCl. Immunoprecipitated chromatin was eluted and cross-link reverted overnight at 65°C. DNA was purified with QIAquick PCR Purification Kit (QIAGEN) and then quantified with QuantiFluor (Cod.E2670, Promega. DNA libraries were prepared for NextSeq500 sequencing as described (Gualdrini et al 2022). The purified DNA libraries were quantified with the Quantifluor reagent (Cod.E2670, Promega) and the quality of the size was controlled with the Tapestation instrument (Agilent) using the High Sensitivity Assay HD5000 (Agilent cod.5067-5592). Library DNA were diluted to a working concentration of 4 nM and Single Reads (76bp) sequenced on an Illumina NextSeq500 platform.

treatment_protocol: Individual samples have been pre-treated with each compound separately for 1h before stimulating the cells with either LPS (10ng/mL) or IL4 (10 ng/mL) for 30minutes, 1h, 2h or 4h.

value: BMDM

value: 1h pre-treatment with XL413 followed by 4h UT

value: wild type

tag: antibody


title: SAVI 3


title: lib81482


title: SAVI 2


title: XL413_LPS_1h

description: ChIPseq

value: 1h pre-treatment with XL413 followed by 1h LPS 10ng/mL


title: SAVI 1

value: lung


title: lib81471


title: lib81487


title: lib81480


title: WT CTRL 4

value: ex vivo


title: lib81478


title: WT CTRL 2


title: lib81485


title: lib81476


title: X396_UT_0h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 4h UT


title: PVN,ZT20 treatment, replicate 2,scRNA-seq

description: 10x Genomics


title: lib81475

value: CD154+CD69+ CD4 T cells


title: lib81473

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib81460


title: X396_LPS_1h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 1h LPS 10ng/mL


title: KO GFP+

city: Columbus

first: Tyler

middle: Joseph

last: Dause

state: Ohio

address: 1835 Neil Avenue

department: Psychology

institute: The Ohio State University

description:
Cluster0 eNB
Cluster1 NSPCs
Cluster2 IPC1
Cluster3 IPC2
Cluster4 NB
Cluster5 qNSC2
Cluster6 aNSCs
Cluster7 qNSC1
Cluster8 IN2
Cluster9 Astrocytes
Cluster10 IN1
Cluster11 Undefined

data_processing:
10X single-cell reads were demultiplexed using cellranger (v7.0.1) mkfastq using default parameters
Demultiplexed fastq files were then grouped by cellbarcode, UMI collapsed, aligned, and analyzed using cellranger (v7.0.1) count using default parameters
Basecalls performed using Casava 1.8.2
Reads were trimmed using AdapterRemoval v2.2.0 to remove sequencing adapters
Reads were aligned against the human decontaminome using HISAT2 v2.0.6 using default parameters
Unaligned deconaminome reads were aligned against the human genome using HISAT2 v2.0.6 using default parameters
Reads were quantified using Subread FeatureCounts using GENCODE release M14
Assembly: Genome_build: GRCh38
Supplementary files format and content: TSV Counts (WT and KO) tables generated using Subread FeatureCounts, Unfiltered; Seurat v4.1.1 was used to post-process 10X generated counts table using default workflow: Transcripts present in less than 5 cells were filtered out; Cells with less than 2000 or greater than 5000 transcripts were filtered out; Cells with more than 2% mitochondrial counts were filtered out; The resulting counts table was log-normalized; Cells in resulting counts table were ordered by cluster according to Seurat's default clustering algorithm with parameters reduction = 'pca', dims=1:10, and resolution = 0.5

source_name: Adult Mouse Dentate Gyrus

extract_protocol:
DGs from 5 WT and 5 KO adult mice were harvested and mechanically dissosciated then resuspended and washed in HBSS before cell sorting for EYFP+ cells for input into 10x genomics chip as per manufacturer instructions.
10X Genomic's RNA-seq library was sequenced using paired-end 150bp approach on an IlluminaNovaSeq 6000sequencer. CellRanger v7.0.1 was used to demultiplex, align, and deduplicate sequencing reads in BCL files. Single-cell data in feature-barcode matrices were then processed using Seurat v4.1.1s default pipeline to identify unsupervised cell clusters and generate a t-Distributed Stochastic Neighbor Embedding (t-SNE) plot. Seurat's feature expression analysis was used to visualize genes markers known to be expressed in cell populations displayed in the t-SNE plot.

value: Adult Mouse Dentate Gyrus

value: Tamoxifen


title: WT GFP+


title: XL413_LPS_30

description: ChIPseq

value: 1h pre-treatment with XL413 followed by 30 LPS 10ng/mL


title: X396_IL4_30

description: ChIPseq

value: 1h pre-treatment with X396 followed by 30 IL4 10ng/mL


title: lib81468


title: PVN,ZT8 treatment, replicate 1,scRNA-seq

description: 10x Genomics

value: PVN

value: PVN cells


title: lib81467

value: Aab negative


title: lib81456


title: XL413_IL4_4h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with XL413 followed by 4h IL4 10ng/mL


title: lib81466


title: VX702_LPS_4h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 4h LPS 10ng/mL

value: wild type


title: lib81453


title: lib81465


title: XL413_IL4_30

description: ChIPseq

value: 1h pre-treatment with XL413 followed by 30 IL4 10ng/mL


title: X396_IL4_1h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 1h IL4 10ng/mL


title: XL413_IL4_1h

description: ChIPseq

value: 1h pre-treatment with XL413 followed by 1h IL4 10ng/mL


title: lib81464

value: CD154+CD69+ CD4 T cells


title: lib81463

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: X396_LPS_4h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 4h LPS 10ng/mL


title: lib81462


title: lib81461


title: X396_LPS_30

description: ChIPseq

value: 1h pre-treatment with X396 followed by 30 LPS 10ng/mL


title: lib81451


title: VX702_LPS_1h_b

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 1h LPS 10ng/mL


title: lib81449


title: lib81448


title: lib81459


title: VX702_IL4_30

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 30 IL4 10ng/mL


title: X396_LPS_2h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 2h LPS 10ng/mL


title: X396_IL4_4h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 4h IL4 10ng/mL


title: lib81458


title: lib81457


title: X396_IL4_2h

description: ChIPseq

value: 1h pre-treatment with X396 followed by 2h IL4 10ng/mL


title: lib81446

value: Aab negative


title: lib81447


title: lib81455


title: VX702_IL4_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with VX702 followed by 1h IL4 10ng/mL


title: lib81444


title: Volasertib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 4h UT


title: Volasertib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 4h LPS 10ng/mL

value: wild type


title: Volasertib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 30 LPS 10ng/mL


title: lib81450


title: lib81442


title: VX702_UT_0h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 4h UT


title: lib81454

value: CD154+CD69+ CD4 T cells


title: VX702_LPS_30

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 30 LPS 10ng/mL


title: lib81452

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: VX702_LPS_2h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 2h LPS 10ng/mL


title: lib79996

value: Islet TMR+ CD8 T cells


title: VX702_IL4_4h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 4h IL4 10ng/mL


title: VX702_LPS_1h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 1h LPS 10ng/mL


title: VX702_IL4_2h

description: ChIPseq

value: 1h pre-treatment with VX702 followed by 2h IL4 10ng/mL


title: lib81445


title: Volasertib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 1h IL4 10ng/mL


title: lib81443

value: Aab negative


title: Vatalanib_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Vatalanib followed by 4h UT


title: lib79991


title: lib79989


title: lib81441


title: Volasertib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 2h LPS 10ng/mL


title: lib79995


title: lib79988


title: Vatalanib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 4h IL4 10ng/mL


title: lib79987


title: lib79994


title: lib79992


title: Volasertib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 2h IL4 10ng/mL

value: wild type


title: Volasertib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 30 IL4 10ng/mL


title: Vatalanib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 30 LPS 10ng/mL


title: lib79985


title: Volasertib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 1h LPS 10ng/mL


title: lib79993

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79990


title: lib79983


title: Vatalanib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 2h LPS 10ng/mL


title: Vatalanib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 1h LPS 10ng/mL


title: Vatalanib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 2h IL4 10ng/mL


title: Vandetanib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 4h UT


title: Volasertib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Volasertib followed by 4h IL4 10ng/mL


title: lib79984

value: Islet TMR+ CD8 T cells


title: Vatalanib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 30 IL4 10ng/mL


title: Vandetanib_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Vandetanib followed by 1h LPS 10ng/mL


title: lib79979


title: lib79978


title: Vatalanib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 4h LPS 10ng/mL


title: Vandetanib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 4h IL4 10ng/mL


title: lib79986


title: lib79982


title: Vandetanib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 30 IL4 10ng/mL


title: lib79981


title: Vandetanib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 30 LPS 10ng/mL

value: wild type


title: Vandetanib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 2h LPS 10ng/mL


title: lib79976


title: Vandetanib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 1h IL4 10ng/mL


title: Vatalanib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Vatalanib followed by 1h IL4 10ng/mL


title: lib79977

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: Vandetanib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 2h IL4 10ng/mL


title: lib79972


title: lib79973


title: lib79975


title: lib79971


title: Ulixertinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 4h UT


title: Ulixertinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 30 LPS 10ng/mL


title: lib79974


title: Ulixertinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 2h LPS 10ng/mL


title: lib79980

value: Islet TMR+ CD8 T cells


title: Vandetanib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Vandetanib followed by 4h LPS 10ng/mL


title: lib79970


title: Ulixertinib_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Ulixertinib followed by 1h LPS 10ng/mL


title: Ulixertinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 4h IL4 10ng/mL


title: lib79969


title: lib79968


title: Ulixertinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 2h IL4 10ng/mL


title: Ulixertinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 30 IL4 10ng/mL


title: lib79966


title: lib79964


title: Tofacitinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 4h UT


title: lib79967


title: lib79963


title: Tofacitinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 30 LPS 10ng/mL

value: wild type


title: lib79965


title: Ulixertinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 1h IL4 10ng/mL


title: Tofacitinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 2h LPS 10ng/mL


title: Tofacitinib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 1h LPS 10ng/mL


title: lib79961

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79959


title: Ulixertinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Ulixertinib followed by 4h LPS 10ng/mL


title: Tofacitinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 2h IL4 10ng/mL


title: Tofacitinib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 4h IL4 10ng/mL


title: Tofacitinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 30 IL4 10ng/mL


title: Tofacitinib_IL4_1h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 1h IL4 10ng/mL


title: lib79955

value: Islet TMR+ CD8 T cells


title: lib79956


title: TG100572_UT_0h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with TG100572 followed by 4h UT


title: lib79957


title: TG100572_LPS_4h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 4h LPS 10ng/mL


title: Tofacitinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Tofacitinib followed by 4h LPS 10ng/mL


title: lib79954


title: lib79953


title: lib79952


title: lib79950


title: TG100572_IL4_4h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 4h IL4 10ng/mL


title: TG100572_LPS_30

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 30 LPS 10ng/mL


title: lib79949


title: TG100572_LPS_1h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 1h LPS 10ng/mL

value: wild type


title: TG100572_LPS_2h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 2h LPS 10ng/mL


title: lib79951


title: TG100572_IL4_30

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 30 IL4 10ng/mL


title: lib79960

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: lib79958


title: TG100572_IL4_2h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 2h IL4 10ng/mL


title: lib79947


title: TG100572_IL4_1h

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 1h IL4 10ng/mL


title: lib79944


title: TG100115_LPS_4h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 4h LPS 10ng/mL


title: lib79946


title: lib79943


title: TG100115_LPS_30_b

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 30 LPS 10ng/mL


title: TG100572_IL4_2h_b

description: ChIPseq


title: lib79945


title: TG100115_LPS_30

description: ChIPseq


title: TG100115_UT_0h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 4h UT


title: lib79941

value: Islet TMR+ CD8 T cells


title: lib79942


title: TG100115_LPS_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with TG100115 followed by 1h LPS 10ng/mL


title: lib79948


title: lib79939


title: TG100572_UT_0h_b

description: ChIPseq

value: 1h pre-treatment with TG100572 followed by 4h UT


title: lib79937


title: lib79938


title: lib79936


title: TG100115_IL4_1h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 1h IL4 10ng/mL


title: TG100115_IL4_30

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 30 IL4 10ng/mL


title: lib79935


title: Telatinib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 4h UT


title: lib79934


title: TG100115_IL4_4h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 4h IL4 10ng/mL


title: Telatinib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 4h LPS 10ng/mL

value: wild type


title: lib79933


title: lib79932


title: Telatinib_LPS_2h

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 2h LPS 10ng/mL


title: Telatinib_LPS_30

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 30 LPS 10ng/mL


title: Telatinib_IL4_30

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 30 IL4 10ng/mL


title: lib79931

value: 20mer GAD/ IGRP/ ZnT8+PPI library peptides


title: TG100115_LPS_2h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 2h LPS 10ng/mL


title: lib79928


title: lib79930


title: Telatinib_IL4_2h

description: ChIPseq

value: 1h pre-treatment with Telatinib followed by 2h IL4 10ng/mL


title: TG100115_IL4_2h

description: ChIPseq

value: 1h pre-treatment with TG100115 followed by 2h IL4 10ng/mL


title: Tanzisertib_UT_0h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 4h UT


title: lib79929

value: Islet TMR+ CD8 T cells


title: Telatinib_IL4_1h

description: ChIPseq

value: BMDM

value: 1h pre-treatment with Telatinib followed by 1h IL4 10ng/mL


title: lib79927


title: Tanzisertib_LPS_4h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 4h LPS 10ng/mL


title: lib79925


title: lib79926


title: lib79923


title: lib79922


title: Tanzisertib_IL4_4h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 4h IL4 10ng/mL


title: Tanzisertib_LPS_1h

description: ChIPseq

value: 1h pre-treatment with Tanzisertib followed by 1h LPS 10ng/mL


title: lib79924


title: lib79920