title: Onivara_Flagleaf_Panicle

city: Bangalore

first: Shivaprasad

last: Padubidri V.

address: GKVK Campus, Bellary road

institute: National Center for Biological Sciences

data_processing:
Adapter was removed and low quality bases were trimmed from sequenced reads.
small RNAs matching rRNA and tRNA are filtered out
20-21nt small RNA reads were size selected
Supplementary_files_format_and_content: Text files including read sequence and its count for each sample.

organism: Oryza nivara

source_name: Flagleaf and Panicle

extract_protocol:
Total RNA from three different tissues, 4-week old seedling and, flagleaf and panicle (equal concentration of flagleaf RNA and panicle RNA were mixed) of two rice species were extracted using Trizol (Invitrogen) reagent.
Degradome cDNA libraries were construction according to J. Zhai et al., 2014, Methods, 67 (84–90) protocol with slight modifications.

value: Flagleaf and Panicle


title: BS_F1(rdr126 cmt23 X drm2 suvh456)_rep1

status: Public on Sep 30 2020

type: SRA

city: Bunkyo-ku

first: Taiko

middle: Kim

last: To

state: Tokyo

address: 7-3-1 Hongo

department: Biological Science

country: Japan

institute: University of Tokyo

library_source: genomic

data_processing:
WGBS: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). Mapping to the reference genome (TAIR10), deduplication, and methylation extraction were performed using Bismark version 0.10.1 (Krueger and Andrews, 2011). The parameters used for mapping is -n 1 –l 20 –e 90. Uniquely aligned reads were used and reads with more than one alignment with same read quality were removed.
RNA-seq: The adaptor sequences and low quality regions were trimmed using Trimmomatic (Bolger et al. 2014). The quality filtered reads were mapped to genes (TAIR10) were counted through STAR algorithm (Dobin et al., 2013).
ChIP-seq: The reads were quality-filtered using Trimmomatic (Bolger et al. 2014) and mapped to TAIR10 genome using Bowtie (Langmead et al., 2009) with option -M 1 --best.
Genome_build: TAIR10
Supplementary_files_format_and_content: WGBS: CX_report file
Supplementary_files_format_and_content: RNA-seq: STAR ReadsPerGene output file
Supplementary_files_format_and_content: ChIP-seq: bowtie output file

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: WGBS: Plants were grown on soil.

extract_protocol:
WGBS: Genomic DNA was isolated from rosette leaves using the Nucleon Phytopure genomic DNA extraction kit (GE Healthcare).
WGBS: Genomic DNA was fragmented using Covaris S220, and the size between 300-450bp were gel-purified. The libraries were prepared using TruSeq DNA LT Sample Prep Kit (Illumina) and subjected to bisulfite conversion using MethylCode Bisulfite Conversion Kit (Life Technologies). Bisulfite-treated DNA were amplified with KAPA HiFi HotStart Uracil ReadyMix (Kapa Biosystems), and then purified with Agencourt AMPure XP (Beckman Coulter).

tag: genotype

tag: tissue

value: Leaves


title: X1 - EP155 + P74-3

city: Ottawa

first: Myron

last: Smith

state: Ontario

address: 1125 Colonel By drive

department: Biology

country: Canada

institute: Carleton University

description: NS.1339.004.NEBNext_dual_i7_163---NEBNext_dual_i5_163.X1

library_source: transcriptomic

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality sequence to about 100bp length. Then mapped to C.parasitica whole genome v.2 using STAR v2.7
Novel transcripts from regions of the genome that showed significant expression, but were not previously annotated as genes were identified using StringTie v.2.1.3
Raw Count table was created using SummarizedExperiment R package.
Genome_build: C.parasitica v.2, FASTA for novel transcripts is available on the series record.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Cryphonectria parasitica

source_name: mycelium

extract_protocol:
Cultures for RNA extraction were grown in 8.5 cm Petri plates on potato dextrose agar (PDA, BD Difco Brand, NJ, USA) overlaid with sterile semi-permeable cellophane membranes. Total RNA was extracted using the Qiagen RNeasy Plant RNA extraction kit following manufacturer manual (Qiagen, Valencia, CA, USA) with DNAse treatment step.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mix of EP155 + P74-3

value: mycelium


title: BS_cmt23 h2az

value: cmt2 cmt3 hta8 hta9 hta11


title: granulocyte rep1

status: Public on Sep 29 2020

city: Beijing

first: Jiahuan

last: HE

state: Beijing

address: Dong dan san tiao wu hao xie he ji chu suo

department: Department of Biochemistry and Molecular Biology

country: China

institute: Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College

data_processing:
DNA-seq reads were mapped with bwa, RNA-seq reads were mapped with bwa for RNA editing sites identification. RNA-Seq reads were mapped with tophat for RPKM calculation
ChIP-seq data were mapped with tophat and peaks were called through macs2
Differential gene expressions were calculated with Featurecounts and DESeq2 for RNA-seq.
Genome_build: GRCm38
Genome_build: annotation build: ensembl GRCm38.85
Supplementary_files_format_and_content: bigwig for ChIP-seq; expression matix for Ddx1 knock down/control data, bed format for 12 populations of hematopoietic cells

organism: Mus musculus

source_name: granulocyte

extract_protocol:
hematopoietic cells were sorted and RNA was harvested using an RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: granulocyte

tag: treatment


title: granulocyte rep2


title: BS_cmt23 H2AZ

value: cmt2 cmt3


title: E2 - EP155

description: NS.1326.001.NEBNext_dual_i7_154---NEBNext_dual_i5_154.E2


title: RNAseq_cmt23_H2AZ_rep1

source_name: seedling

growth_protocol: RNA-seq and ChIP-seq: Seedlings were grown on MS medium with 1% sucrose and 0.8% agar with 16h light / 8h dark.

extract_protocol:
RNA-seq: Total RNAs were purified from 12-day-old plants grown on MS Agar plates using RNeasy Plant Mini Kit (QIAGEN), and then treated with DNase I (TaKaRa)
RNA-seq: RNA Fragmentation was performed at 94°C for 7 min. Libraries were constructed using the KAPA Stranded RNA-seq Library Preparation Kit according to the manufacturer’s instruction.

value: seedling


title: P4 - P74-3

description: NS.1339.004.NEBNext_dual_i7_159---NEBNext_dual_i5_159.P4


title: MK rep2

source_name: MK

value: MK


title: Onivara_Seedling

department: Plant epigenetics

country: India

source_name: Four weeks old seedlings

value: Four weeks old seedlings


title: GMP rep1

source_name: GMP

value: GMP


title: GMP rep2


title: BS_F1_in_ibm1(ibm1+/- cmt23 X ibm1+/- suvh456)


title: MEP rep1

source_name: MEP

value: MEP


title: monocyte rep1

source_name: monocyte

value: monocyte


title: monocyte rep2


title: Ery-B rep2

source_name: Ery-B

value: Ery-B


title: BS_F1(rdr126 cmt23 X drm2 suvh456)_rep2


title: macrophage rep2

source_name: macrophage

value: macrophage


title: MPP rep2

source_name: MPP

value: MPP


title: MPP rep1


title: LT-HSC rep2

source_name: LT-HSC

value: LT-HSC


title: LT-HSC rep1


title: ST-HSC rep1

source_name: ST-HSC

value: ST-HSC


title: Ery-B rep1


title: Ery-A rep2

source_name: Ery-A

value: Ery-A


title: Ery-A rep1


title: V6.5_ES_epiLC_24hr_shBcat_rep2

city: Kansas City

first: Shiyuan

middle: (Cynthia)

last: Chen

state: MO

department: Computational Biology

country: USA

institute: Stowers Institute for Medical Research

description:
Trizol extraction
RSEM_TPM_table_2984.csv

data_processing:
Basecalling and bcl to fastq generation was done using bcl2fastq2 v2.18 from illumina.
RNA-seq was aligned to genome mm10 from UCSC using STAR aligner
TPM expression was generated using RSEM
ChIP-seq was aligned to genome mm10 using bowtie2
Bigwig files are normalized and extended to fragment length for IP samples
Genome_build: mm10
Supplementary_files_format_and_content: RNA-seq TPM in excel file, ChIP-seq in bigwig files

growth_protocol: 2i media

extract_protocol:
RNA was isolated by first homogenizing cells in 1ml TRIzol reagent (Invitrogen 15596026) through triturating the cell lysate through a 27-gauge needle a minimum of 7 times. Homogenized samples were mixed with 200µ l chloroform and vigorously shaken by hand for 30sec. Samples were then incubated at RT for 10min before centrifuging at 12,000g for 10min at RT. The aqueous phase containing RNA was transferred to a new tube, mixed with 100µ l chloroform, and subjected to a second round of shaking, incubation and centrifuging.  The aqueous phase was transferred to a new tube containing 1.5µ l 20mg/ml glycogen, and mixed with 450µ l isopropanol to pre- cipitate RNA. Samples were gently mixed and incubated at RT for 10min before centrifuging at 4 °C for 15min. The supernatant was discarded and the pellet was washed by 1ml 75% ethanol. After the wash the RNA pellet was dried at RT for 20min and resuspended in RNase-free water. Yield and purity of RNA was determined by spectrophotometry with Nano drop (Thermo Scien- tific). The RNA was treated with DNase (Promega M6101)
RNA-seq and ChIP-seq libraries were prepared using the TruSeq RNA kit for sequencing,

treatment_protocol: Beta-catenin knowndown in ES cell and epiLC

value: epiblast-like cell

tag: culture condition

value: epiLC media


title: MK rep1


title: V6.5_ES_epiLC_48hr_shBcat_rep2


title: V6.5_ES_epiLC_48hr_shBcat_rep1


title: V6.5_ES_epiLC_48hr_rep1

description:
Trizol extraction
RSEM_TPM_table_2804.csv


title: V6.5_ES_epiLC_24hr_rep2


title: macrophage rep1


title: MEP rep2


title: V6.5_ES_2i_rep1

value: embryonic stem cell


title: QKO_ES_shGFP_2i_48hr_rep2

description:
Trizol extraction
RSEM_TPM_table_2742.csv


title: QKO_ES_shGFP_2i_48hr_rep1


title: CMP rep1

source_name: CMP

value: CMP


title: CMP rep2


title: QKO_ES_shGFP_2i_48hr_rep3


title: QKO_ES_shBcat_2i_48hr_rep1


title: V6.5_ES_2i_rep2


title: V6.5_ES_epiLC_96hr_shBcat_rep1


title: ST-HSC rep2


title: V6.5_ES_epiLC_96hr_shBcat_rep2


title: V6.5_ES_epiLC_96hr_rep1


title: V6.5_ES_epiLC_96hr_rep2


title: V6.5_ES_epiLC_48hr_rep2


title: NSC11_m6A_Input_rep1

city: Cleveland

first: Briana

last: Prager

state: OH

address: 9500 Euclid Ave.

institute: Cleveland Clinic

data_processing:
FASTQ files were processed using Trim Galore v0.4.5 and cutadapt v2.1 to trim adaptors.
FASTQ files were aligned using STAR v2.7 to hg19 and sorted and indexed using SAMtools v1.3.
Indexed bams were processed to generate individual and differential peaksets using m6a Viewer v1.6. Peaks were detected using default settings comparing meRIP-seq to input at a minimum 2-fold enrichment and false discovery rate (FDR) < 0.05 using Benjamini-Hotchberg correction. To generate consensus peaksets for each cell model, overlapping peaks were used.
Differential peaks between NSCs and GSCs were called using the R package MeTDiff with an FDR cutoff of 0.05 and differential fold enrichment of 1.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in CSV format

organism: Homo sapiens

growth_protocol: Cells were cultured as spheres in Neurobasal medium supplemented with B27, L-glutamine, sodium pyruvate, 1% penicillin/streptomycin, 10 ng/ml basic fibroblast growth factor (bFGF), and 10 ng/ml epidermal growth factor (EGF).

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen). RNA was treated with RNAse free DNAse I (Roche) to deplete DNA contamination. PolyA RNA was purified using GenEluteª mRNA Miniprep Kit (Sigma Aldrich) per manufacturer's instruction. PolyA RNA was fragmented using RNA fragmentation kit (Ambion). Two microgram fragmented RNA was saved as input. Two hundred microgram fragmented RNA was incubated with 3 microgram anti-m6A antibody (Synaptic Systems) in RIP buffer (150mM NaCl, 10mM Tris, 0.1% NP40) for 2 hrs at 4 oC, followed by the addition of washed protein A/G magnetic beads (Millipore) and incubation at 4 oC for additional 2 hrs. Beads were washed 6 times in RIP buffer and incubated with 50 microliter IP buffer containing 0.5mg/mL to elute RNA. IP'ed RNA was extracted with phenol/chloroform.
The Scriptseq v.2 RNA-seq Library Preparation method was performed on 40 ng of RNA for each sample. We followed the protocol given in the Scriptseq v.2 RNA-seq Library Preparation manual (Epicentre, an Illumina company), except DNA Clean & Concentratorª-5 - PCR/DNA clean columns (Zymo Research) were used to isolate the cDNA prior to PCR step. 15 cycles of PCR were performed on the cDNA and the resulting DNA products were purified on 2% E-Gel¨ EX Agarose Gels (Invitrogen). The products were visualized using a blue light transluminator and selected regions of the gel were excised corresponding to 200-400 bp products. The gel slices were dissolved in agarose dissolving buffer and the DNA was isolated on DNA Clean & Concentratorª-5 - PCR/DNA clean columns. The isolated DNA products were then analyzed and quantitated on an Agilent Bioanalyzer 2100.  Samples were pooled and loaded into one lane of a HiSeq2000 v3 flowcell (Illumina) and sequenced for 100 bases with separate 7 base indexing read.

tag: cell line

value: neural stem cells (NSCs)

tag: ip antibody

value: none (input)


title: V6.5_ES_epiLC_24hr_shBcat_rep1


title: HNP1_m6A_IP_rep2

value: anti-m6A antibody (Synaptic Systems)


title: HNP1_m6A_IP_rep1


title: V6.5_ES_epiLC_24hr_rep1


title: QKO_ES_shBcat_2i_48hr_rep3


title: NSC11_m6A_IP_rep2


title: QKO_ES_shBcat_2i_48hr_rep2


title: HNP1_m6A_Input_rep1


title: NSC11_m6A_IP_rep1


title: 4121_m6A_IP_rep2

value: Patient derived glioblastoma stem cells (GSCs)


title: 4121_m6A_Input_rep2


title: 4121_m6A_Input_rep1


title: 387_m6A_IP_rep2


title: HNP1_m6A_Input_rep2


title: 4121_m6A_IP_rep1


title: v6.5_input

description: ChIP with Flag antibody

extract_protocol:
A total of 2×10^7 ES cells were used per ChIP assay. Cells were washed with 1 x PBS and crosslinked with 1% paraformaldehyde for 10 min at RT and quenched with 1ml 2.5M glycine. Cells were washed with cold PBS three times and resuspended in 300μl lysis buffer. The cell suspension was sonicated in Bioruptor Pico sonication device with the setting of 30 sec on, 30 sec off for 16 cycles followed with centrifuga- tion at maximum speed for 10 min. The supernatant was saved and mixed with antibody coated protein G dynabeads(Invitrogen 10003D) at a ratio of 5μl per 1μg antibody for immunoprecip- itation overnight at 4°C . The next day the protein G dynabeads were washed with 800μl RIPA buffer three times. After the elution, 4μ l RNase A(10μ g/ml) was then added with the beads being incubated at 37°C for 2 hours, after which 2μl Protease K(Invitrogen 20mg/ml) was added and the beads were incubated at 55 °C for 2 hours. After the RNase A and Protease K treatment, the beads were incubated at 55 °C overnight for decrosslinking. The next day the DNA on beads was extracted by 300 μl phenol chloroform isoamyl alcohol(25:24:1) with centrifugation at 12,000 rpm for 5 min at RT. The supernatant was transferred to a new 1.5ml tube with 12μl of 5M NaCl and 2μl glycogen (20mg/ml). The DNA was precipitated by 750μl cold 100% ethanol with at least 30 min incubation at - 80 °C . The sample was centrifuged for 30 min in 4 °C at maximum speed and the ethanol was decanted. The pellet was washed with 800 μ l cold 70% ethanol, centrifuged and air dried. The DNA was resuspended in 55μl nuclease-free water.
RNA-seq and ChIP-seq libraries were prepared using the TruSeq RNA kit for sequencing,

tag: antibody

value: Flag


title: 387g1

data_processing:
FASTQ sequencing reads were trimmed using Trim Galore.
Transcript quantification was performed using Salmon in the quasi-mapping mode.
Salmon “quant” files were converted using Tximport.
Differential expression analysis was performed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Salmon quant files

source_name: GSCs_YTHDF2 sgRNA

extract_protocol:
Cells were collected in TriZol reagent and RNA was extracted using Rneasy Mini kit (Qiagen #74104)
RNA libraries were prepared for sequencing using standard rRNA depletion protocol

treatment_protocol: Transduced cells were selected with 2mg/ml Puromycin for 3 days.

tag: genotype/variation

value: YTHDF2 sgRNA


title: v6.5_Hmga2_CST

description: ChIP with Hmga2 antibody


title: 387_m6A_IP_rep1


title: 4121nt

source_name: GSCs_control sgRNA

value: Control sgRNA


title: 387_m6A_Input_rep2


title: 387_m6A_Input_rep1


title: NSC11_m6A_Input_rep2


title: ES_2i_control_H3K4me3_2

description: ChIP


title: 4121g1


title: ES_2i_control_H3K27me3_2

description: ChIP


title: v6.5_Flag_Hmga2_input

description: Sonicated whole cell extract


title: 4121g2


title: 965-M1

status: Public on Sep 28 2020

city: Baltimore

first: Konstantinos

last: Konstantopoulos

state: MD

address: 3400 N Charles St

department: Chemical and Biomolecular Engineering

institute: Johns Hopkins University

description: Each sample was split and run on four lanes, creating four read files

data_processing:
Quality control using FASTQC
RNA-seq reads were mapped to hg38 reference genome using HISAT2 aligner
StringTie for transcript assembly using most recent gencode gtf file (gencode.v32)
Htseq-count command from the HTSeq framework was used to quantify read counts per gene from aligned reads using human ENSEMBL 86 (GRCh38.p7) gene models
The Bioconductor/R package DESeq2 was used for normalization and differential gene expression analysis.
Genome_build: human ENSEMBL 86 (GRCh38.p7) gene models
Supplementary_files_format_and_content: Gene symbols and normalized reads contains a list of features recognized by the sequencing data and the normalized reads associated with each gene.

source_name: Primary glioblastoma cells

growth_protocol: The primary GBM cells were grown as adherent cultures on tissue culture flasks pre-coated with laminin (Trevigen) at a density of 1 µg/cm2 surface area diluted with PBS without magnesium and calcium for 3 h at 37°C. The culture media consisted of 1:1 Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F12, Invitrogen), Gem21 NeuroplexTM without vitamin A serum-free supplement (Gemini), 1´ antibiotic/antimycotic solution (Sigma-Aldrich), 10 ng/ml of recombinant human fibroblast growth factor (Peprotech) and 20 ng/ml of recombinant human epidermal growth factor (Peprotech). Accutase solution (Sigma-Aldrich) was used to dissociate cells from the laminin-coated tissue culture flasks instead of trypsin.

extract_protocol:
RNA was isolated from samples of ~1000 migratory or unsorted cells using the RNeasy Micro Kit (Qiagen). RNA was evaluated by Bioanalyzer using the Agilent RNA 60000 Pico kit. Samples with RNA Integrity Number (RIN) 8.4-9.3 were used.
335pg of RNA of each sample were used to prepare complementary DNA (cDNA) libraries using the Smart-seq v4 kit (Takara). cDNAs were purified by AMPure XP beads, fragmented by sonication to ~400bp, and subjected to barcoding and single-end sequenced on Nextseq 500 with 75 cycles. Raw sequencing depth ranged 38.7 – 76.1 million reads with >97.2% of reads mappable to the human genome.

treatment_protocol: Prior to RNA isolation, cells were passed from tissue culture flasks and seeded in microfluidic devices as described in Wong, BS et al Nature Biomedical Engineering 2020. Highly motile (migratory) cells were isolated and compared to the unsorted (ctl) population.

value: Primary glioblastoma cells

tag: patient id

tag: group

value: migratory


title: 965-M3


title: 897-M1


title: ES_2i_control_H3K4me3_1

description: ChIP


title: 965-B1

value: unsorted bulk


title: 387g2


title: ES_2i_control_H3K27me3_1

description: ChIP


title: 965-M2


title: BioR_Flag_ctnnb1

description: Biorupter sonicated whole cell extract


title: 897-M2


title: 965-B2


title: 965-B3


title: 387nt


title: IRI M PTs rep 2 [4_tub_IR_M]

status: Public on Sep 09 2020

first: Theodore

last: Perkins

state: ON

address: 501 Smyth Rd.

department: Cellular and Molecular Medicine

institute: Ottawa Hospital Research Institute

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
4-2

data_processing:
Reads quantified against transcripts from the GENCODE vM19 assembly using salmon v0.13.1 (flags --gcBias --validateMappings)
Fold change analsyis performed using DESeq2
Transcript quantification data read using the tximport library. Count matrix filtered to retain only genes with 5+ reads in at least two samples.
Separate DESeqDataSet objects constructed for endothelial and proximal tubule cells. Technical replicates for sample 9_tub_SHAM_M combined using collapseReplicates(). Calculation of size factors and differential expression using the model '~condition' where condition is the combination of AKI or No Injury plus sex
Fold changes calculated between IRI and uninjured for Male and Female animals, and between male and female animals in uninjured and IRI conditions using the lfcShrink() function with the 'apeglm' method.
pvalue and padj recalculated without outlier detection (call to results() with cooksCutoff=F), and substituted for pvalue and padj calculated with lfcShrink. Values of pvalue and padj from lfcShrink added to results as pvalue.cooks and padj.cooks respectively
Genome_build: GRCm38
Supplementary_files_format_and_content: Salmon transcript quantification: tab-delimited text
Supplementary_files_format_and_content: DESeq2 differential expression results: tab-delimited text

extract_protocol:
RNA was isolated from PTs or renal endothelial cells from 3 male and 3 female mice in each experimental group, using the RNeasy Plus Micro Kit (Qiagen Inc., Toronto, Ontario, Canada). RNA quality was assessed using the Fragment Analyzer (Advanced Analytical Technologies, Inc., Ames, LA, USA). Only RNA with RQN scores of >7 was selected for further analysis
Library construction was performed with the NEB Next Ultra II RNA Library Prep Kit for Illumina using the polyA mRNA workflow (New England Biolabs Ltd., Ipswich, MA, USA). For each sample, 20 ng of total RNA was used as input for the library preparation. Following library construction, the samples were pooled to minimize potential sequencing bias and run on NextSeq 500 (Illumina, San Diego, CA, USA). A total of six 75 cycle high output flow cells were run to achieve approximately 40 million reads per sample.

treatment_protocol: Endothelial an proximal tubular cells were isolated from kidneys after enzymatic digestion, CD31+ microbeads were used to obtain endothelial cells and proximal tubular cell were collected by microdissection.

value: FVB

tag: Sex

value: Male

value: Acute Kidney injury

value: kidney

value: Proximal tubular cells


title: IRI M PTs rep 3 [7_tub_IR_M]

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
7-2


title: 897-B1


title: Sham M PTs rep 3B [9_tub_SHAM_M]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
9-2_libB

value: No injury


title: 897-B2


title: Sham M PTs rep 2 [6_tub_SHAM_M]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
6-2


title: Sham M PTs rep 1 [5_tub_SHAM_M]

description:
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
5-2


title: IRI M endo rep 1 [3_endo_IR_M]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
3-1

value: endothelial cells


title: v6.5_Flag_Hmga2

description: ChIP with Flag antibody

value: embryonic stem cell


title: Sham M endo rep 2 [6_endo_SHAM_M]

description:
processed data file:
endo.SHAM.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
6-1


title: bulk Primed H3K9me3 replicate

status: Public on Aug 22 2020

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
The aligment files of bulk  ChIP-seq and micro ChIP-seq were merge together, and Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

source_name: Embryonic stem cell

growth_protocol: Naive cells were cultured in serum+LIF condition on feeders, primed cells were cultured in bFGF+Activin A condition on feeders.

extract_protocol:
The ULI-NChIP procedure was performed as previously described(Brind'Amour et al., 2015; Wang et al., 2018).
Sequencing libraries were generated using AT seq library following manufacturer's recommendations and index codes were added. The library quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina HiSeq x platform and 150 bp paired-end reads were generated
Ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP)

treatment_protocol: For ULI-NChIP-seq, about 50000 naïve or primed cells were used per reaction. For bulk ChIP-seq, about 5000000 naïve or primed cells were used per reaction.

value: C57 x CBA

value: Embryonic stem cell

tag: condition

value: primed

tag: passage

tag: chip anitbody

value: H3K9me3 abcam ab176916


title: Sham M endo rep 1 [5_endo_SHAM_M]

description:
processed data file:
endo.SHAM.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
5-1


title: micro Naive Dnmt3b

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal

value: mESCs

value: Naïve

tag: passages

tag: chip antibody

value: Dnmt3b abcam ab2851


title: IRI M PTs rep 1 [3_tub_IR_M]

description:
processed data file:
tub.IR.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
3-2

tag: tissue


title: IRI M endo rep 2 [4_endo_IR_M]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
4-1

tag: strain


title: micro Primed Dnmt3b

tag: cell type

value: Primed


title: bulk Primed H3K9me3


title: IRI M endo rep 3 [7_endo_IR_M]

description:
processed data file:
endo.IR.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
7-1

tag: treatment


title: bulk Primed H3K9me2

value: H3K9me2 abcam ab32521


title: bulk Primed H3K9me2 replicate


title: bulk Naive H3K9me3


title: bulk Naive H3K9me3 replicate


title: bulk Naive H3K9me2 replicate


title: bulk Naive H3K9me2


title: P23H_11

status: Public on Aug 21 2020

city: Irvine

first: Henri

last: Leinonen

state: California

address: 829 Health Sciences Rd

department: Ophthalmology

institute: University of California, Irvine

data_processing:
Original image data file from high-throughput sequencing (Illumina) was transformed into sequenced reads by CASAVA base recognition (Base Calling).
Data quality control was performed by inspecting error rates and QC content distribution
Data was filteterd as follows: (1) Reads with adaptor contamination were removed, (2) Reads when uncertain nucleotides constituted more than 10 percent of either read (N > 10%) were removed, (3) Removal of reads when low quality nucleotides (Base Quality less than 20) constituted more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
The gene expression data were aligned with a reference genome (mus musculus mm10) using Tophat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
The gene expression level was measured by transcript abundance and reported as Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM) sequenced.
Genome_build: mm10
Supplementary_files_format_and_content: FPKMs, mRNA abundances, GO/KEGG/reactome pathway enrichments, in xlsx. format

source_name: RhoP23H/WT_whole retina

extract_protocol:
Animals were euthanized by cervical dislocation, retinas were removed and snap-frozen using liquid nitrogen. RNA was harvested using Qiagen RNAeasy Mini-Kit. Genomic DNA was removed by on-column digestion.
RNA libraries were prepared for sequencing using standard Illumina protocols (RNA-seq provided by commercial supplier; Novogene)

treatment_protocol: None. Animals never anesthetized.

tag: strain background

value: RhoP23H/WT (mutant)

tag: age

value: Postnatal day 90

value: Whole retina


title: P23H_13

value: Male


title: WT_9

source_name: RhoWT_whole retina

value: RhoWT (wild-type)

value: Female


title: Sham M PTs rep 3 [9_tub_SHAM_M]

description:
Two libraries sequenced from this sample and quantified separately. Technical replicates combined in DESeq2 analysis
processed data file:
tub.SHAM.M_vs_F.txt
tub.IR_vs_SHAM.M.txt
9-2

value: FVB

value: No injury

value: kidney

value: Proximal tubular cells


title: P23H_6


title: P23H_8


title: Empty_plasmid_pUC57_rep1

status: Public on Aug 20 2020

city: Dunedin

first: Christopher

middle: Michael

last: Brown

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

data_processing:
Adapter sequences were trimmed using Skewer v0.2.2 (-N -n -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA)
Reads were aligned to human and HBV genomes using STAR 2.5.2b in 2-pass mode (--runMode alignReads --twopassMode Basic --twopass1readsN -1 --readFilesCommand zcat --outFilterType BySJout --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --sjdbOverhang 100 --sjdbScore 1 --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 2815365604)
Read counting was carried out using mmquant (-a gencode.v19.annotation.gtf -r Aligned.sortedByCoord.out.bam -s RF -e Y)
Differential gene expression was performed using DESeq2 (using batch as a linear term in the DESeqDataSetFromMatrix function)
Genome_build: hg19 and HBV genotypes A2, B2, C2, and D3
Supplementary_files_format_and_content: DESeq2 normalized counts

source_name: Liver tumor

growth_protocol: DMEM supplemented with 10% Fetal Bovine Serum, and 1% antibiotic-antimycotic cocktail (streptomycin, amphotericin B and Penicillin)

extract_protocol:
Total RNA samples were purified using RNeasy kit (Qiagen, Hilden, Germany).
Ribosomal RNA depletion using Ribo-Zero kit; random selection by shearing; paired-end

treatment_protocol: Huh7 cells were seeded in 6-well plates at partial confluence. After overnight incubation, the cells were transiently transfected with pUC57 constructs harboring 1.3-mer HBV genomes (genotypes A2, B2, C2, and D3) using FuGene 6 transfection reagent according to the manufacturer’s instructions (Promega, WI, USA).

tag: disease

value: hepatocellular carcinoma

tag: hbv transfection

value: No


title: bulk Naive Dnmt3b

value: C57 x CBA

value: mESCs


title: HBV_D3_rep2

value: Yes

tag: hbv genotype


title: HBV_C2_rep1


title: bulk Primed Dnmt3b

value: Primed

value: Dnmt3b abcam ab2851


title: HBV_D3_rep1


title: Sham M endo rep 3 [9_endo_SHAM_M]

description:
processed data file:
endo.SHAM.M_vs_F.txt
endo.IR_vs_SHAM.M.txt
9-1

value: endothelial cells


title: HBV_B2_rep2


title: HBV_B2_rep1


title: HBV_C2_rep2


title: HBV_A2_rep1


title: HBV_A2_rep2


title: WT_12

tag: genotype/variation

value: Postnatal day 90


title: Empty_plasmid_pUC57_rep2


title: Patient_6-1

status: Public on Aug 05 2020

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

description:
Sample 8
supplement.h5ad

data_processing:
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Doublets were identified and removed with scrublet v0.2.1. Ambient RNA was corrected with FastCAR (https://github.com/LungCellAtlas/FastCAR).
Samples were processed with scanpy v1.5.1, low-quality cells were removed and samples were integrated with BBKNN v1.3.12
Sample 16 contained cells from patients A and B. To assign cells to correct patients, we used souporcell v2.0 with the list of common variants for GRCh38 genome, provided on the souporcell page (https://github.com/wheaton5/souporcell) on samples 14, 15 and 16 with the number of clusters k=2. We used Pearson correlation between genotypic clusters in samples 14 & 16 and 15 & 16 to determine which genotypic clusters come from the same patients. Genotypic doublets and unassigned cells were discarded.
Genome_build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
Supplementary_files_format_and_content: gene expression count matrices; anndata objects; cell metadata

source_name: Sorted macrophages and T cells

extract_protocol: Libraries were prepared with 10x Genomics 5' gene expression (GEX) reagents according to the manufacturer protocol (CG000086_RevM).

tag: individual

tag: disease state

value: COVID-19 Negative

tag: time

value: 1 day after intubation

tag: sample type

value: BAL

value: Sorted macrophages and T cells


title: Patient_3-2

description:
Sample 4
main.h5ad
supplement.h5ad

value: COVID-19 Positive


title: Patient_3-1

description:
Sample 3
main.h5ad
supplement.h5ad


title: Patient_1-1

description:
Sample 5
main.h5ad
supplement.h5ad

value: 2 days after intubation


title: Patient_1-2

description:
Sample 6
main.h5ad
supplement.h5ad


title: WT_7

value: RhoWT (wild-type)

tag: Sex

value: Female

value: Whole retina


title: CB_donor2_γδT_transcriptome

status: Public on Jul 31 2020

city: Hamburg

first: Immo

last: Prinz

address: Falkenried 94

department: Institute of Systems Immunology

country: Germany

institute: University medical center Hamburg Eppendorf

data_processing:
Data processing of single-cell RNA sequencing libraries:
To generate the cell (barcode)-gene matrices, raw sequencing data were demultiplexed to individual fastq files, then aligned and quantified by Cell Ranger v3.1 (10xGenomics) under default setting. Human genome GRCh38 (UCUS) was adopted as reference. Ambient RNA in raw cell-gene matrices were cleaned based on the nUMI-barcode saturation curves.
Cell clustering and differentially expressed gene profile:
The R package Seurat v3.1 was used under R v3.6 for scRNA-seq data trimming, analyzing, and visualization (Butler et al., 2018; Stuart et al., 2019). Briefly, cell-gene matrices were exported to R as Seurat projects. Cells contain less than 1,500 unique molecular identifiers (UMIs) or more than 6,000 UMIs, or greater than 11% mitochondrial RNA content were trimmed from analysis. Cell cycling score and cell phases were assigned by the function ‘CellCycleScoring’ according to a gene list of cell cycle markers (Kowalczyk et al., 2015). Raw data matrices were then normalized and scaled by regularized negative binomial regression by ‘SCTransform’ function (Hafemeister and Satija, 2019); contents of mitochondrial genes and ribosomal genes, donor batch effects, and cycling scores were regressed out as unwanted heterogeneity during normalization. Datasets from different donor groups (adult versus newborns) were integrated by Seurat data integration pipeline (Stuart et al., 2019), 3,000 genes represent the correspondences between cells in two groups were used as ‘anchors’ to harmonize and integrate the datasets. Integrated data were subject to a principal component analysis (PCA), 100 components were calculated. The significance of each component was evaluated by Jackstraw score. The significant components were then selected for K-nearest neighbor (KNN) based unsupervised clustering with resolution = 0.8, and Uniform Manifold Approximation and Projection (UMAP) visualization. After clustering, clusters with no CD3 expression (CD3D, CD3E) were trimmed as contamination.
Differentially expressed genes (DEGs) were identified by bimod method as average log2-fold change (logFC) ≥ 0.25, expressed in minimal percentage cells in at least 1 test group (min.pct) ≥ 15%, and adjust p-value ≤ 0.01.
Clusters defined by unsupervised-clustering were further adjusted according to the DEGs:  We calculated the DEGs between neighboring clusters and set the cutoff of DEG as logFC ≥ 0.5. Two neighboring clusters which have less than 30 non-mitochondrial/ribosomal DEGs were merged as one cluster. Therefore, we reduced the cluster number from 16 to 12.
The integrated neonatal and adult single-cell transcriptome dataset was export as Human_gdt_seurat_proj.rds
Single-cell TCR sequencing analysis: Cell Ranger VDJ pipeline (10xGenomics) under default parameters was performed to generate scTCR annotations on the assembled contigs and on the clonotype consensus sequences. Human genome GRCh38 was used as reference for alignment. The two scTCR annotation tables from two rounds of sequencing of a same sample were merged together after removing duplicates. The merged annotation tables were exported as processed data. Further, by matching the cellular barcodes, scTCR data was joined into the metadata of scRNA Seurat project (Human_gdt_seurat_proj.rds) we created above.
Genome_build: GRCh38
Supplementary_files_format_and_content:  scRNA-seq: matrix.mtx, features.tsv, barcodes.tsv. TCR-seq: TCR.csv

source_name: γδ T cells, neonate

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) and cord blood mononuclear cells (CBMCs) were isolated from fresh blood samples stored in EDTA using a density gradient media (Pancoll, PAN-Biotech). After isolation, mononuclear cells were washed twice in PBS 10% FBS (Sigma-Aldrich) and cryopreserved at -80°C in freezing medium (50% FBS (Sigma-Aldrich), 40% RPMI 1640 (Gibco), 10% DMSO (Roth)). Cells were cultured overnight in X-Vivo 15 medium (Lonza) before antibody staining and cell sorting and treated with 5% FcR block in buffer (PBS with 3% FCS, 4 mM EDTA) right before staining. Cells were stained with hCD3 FITC (1:100; clone BW264/56; Miltenyi), hTCR γδ PE (1:50; clone 11F2; Miltenyi), and DAPI (0.1 μg/ml) to determine living cells. For sequencing experiments, DAPI−, CD3+, γδ+ T cells were sorted on a FACS Aria Fusion cytometer (BD) and subsequently used for the preparation of single-cell libraries using the single-cell immune profiling platform of 10x Genomics.
scRNA-seq and single-cell TCR libraries were prepared using the Chromium Single Cell V(D)J Reagent Kit (10x Genomics). For each sample, 3*10e4 γδ T cells mixed with a master mix for cDNA generation were used in a droplet-based approach for the generation of Gel Bead-in-emulsion (GEMs). 5’ Gel beads contain adapters and oligonucleotides for amplification and barcoding of sequences (Illumina R1 sequence (read 1 sequencing primer), 10x barcode, unique molecular identifier (UMI) and template switch oligo (TSO)). Subsequently, pooled GEMs of each sample were used for the construction of two libraries, the scRNA library containing the 5’ gene expression profile and the single-cell TCR library comprising single-cell TRG and TRD sequences. Downstream processing and library construction, including clean-up steps, were performed according to the protocol provided by 10x Genomics. Agilent Bioanalyzer High Sensitivity chips were applied for quality control. To amplify γδ TCR chains, the primers were used for the enrichment of γδ TCR chains instead of primers for αβ TCR profiling (10x Genomics User Guide CG000086, Step 4, Target Enrichment from cDNA).    The scRNA-seq libraries were sequenced on the NextSeq 550 platform using read lengths of 26 base pairs (bp) read1 and 100 bp read2. The single-cell TCR libraries were sequenced by Illumina MiSeq.

value: gamma delta T cells

value: cord blood

value: neonate


title: flox/flox

status: Public on Jul 24 2020

city: Saint Louis

first: Jonathan

last: Kipnis

address: 4515 McKinley Ave

department: Pathology and Immunology

institute: Washington University in Saint Louis

description: Hoechst positive, NeuN positive sorted nuclei after elevated plus maze task (4 mice pooled)

data_processing:
Fastq files were generated with the Illumina bcl2fastq2 software and mapped to an mm10 pre-mrna reference genome using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag and files for each well index were specified using --samples flag. The cellranger count pipeline, resulted in one UMI count matrix for each of our samples (SynCre:Il17rafl/fl, SynCre, and Il17ra fl/fl), which are uploaded here. Further quality control and analysis were performed in R.
Genome_build: mm10
Supplementary_files_format_and_content: Folders containing the raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Prefrontal Cortex

growth_protocol: standard 12h light/dark cycle conditions in rooms equipped with control for temperature and humidity

extract_protocol:
10x Genomics Chromium single nuclei preparation
NGS Illumina Next Seq

tag: celltype

value: Neurons

value: 8-10 weeks

value: male


title: Syn-Cre


title: CB_donor1_γδT_transcriptome


title: Syn-Cre:Il17ra-flox/flox


title: DG WT nonengram

description: mKate2-, Hoechst+ from fear trained mice

data_processing:
Fastq files were generated with the cellranger mkfastq command and mapped to an mm10 pre-mrna reference genome using the Cellranger count pipeline. Fastq files from each run were specified using the --fastqs flag and files for each well index were specified using --samples flag. The cellranger count pipeline, resulted in one UMI count matrix for each of our sample conditions ( WT engram and WT nonengram), which are uploaded here. Further quality control and analysis were performed in R.
Genome_build: mm10
Supplementary_files_format_and_content: Folders containing the raw UMI count matrices for each sample as well as matrices with cell barcodes and gene symbols.

source_name: Dentate Gyrus

growth_protocol: Standard 12h light/dark cycle conditions in rooms equipped with control for temperature and humidity. Mice were purchased from Jackson Laboratory.

treatment_protocol: 4 WT mice were fed with doxycycline food for 1 week. The mice were then injected with AAV-RAM-d2TTA::TRE-NLS-mKate2-WPRE pA in the dentate gyrus and were kept on doxycycline food. Two weeks after injection, the mice were taken off of doxycycline food for 24 hours and were trained with contextual fear conditioning. The mice were euthanized 24 hours after training. The dentate gyrus was dissected out and kept at aCSF prior to nuclei extraction.

value: Neuronal nuclei

value: 6-8 weeks


title: PB_donor2_γδT_transcriptome

source_name: γδ T cells, adult

value: peripheral blood

value: adult


title: Sample 2_1_Spleen Pup

description: CD45+, TCRb-, TCRgd+ sorted cells from spleen of mouse pups

data_processing:
Illumina bcl2fastq software used for basecalling
UMI count matrices generated using the Cellranger count pipeline. The cellranger count pipeline, resulted in raw count matrices for each of our 4 sample conditions ( Meninges Pup, Meninges Adult, Spleen Pup, Spleen Adult).
Data was read into R using the DropletUtils package and barcodes were identified as cells or empty droplets using the EmptyDrops method.
Filtered matrices were saved as gene by count matrices with gene symbols as rownames and cell barcodes as column names.
Genome_build: mm10
Supplementary_files_format_and_content: Compressed csv files containing the raw UMI count matrices for each sample, with gene symbols and sample names and barcodes .  Additionally, a compressed csv file containing a matrix with raw UMI counts from each sample, merged by gene symbols.

source_name: Spleen Pup

growth_protocol: Standard 12 h light/dark cycle conditions in rooms equipped with control for temperature and humidity. Mice were purchased from the Jackson Laboratory and bred in-house.

extract_protocol:
10x Genomics Chromium single cell preparation
NGS Illumina Next Seq

treatment_protocol: Naïve adult animals (8-weeks old) and pups (at P7) were euthanized and transcardially perfused. Their meninges were dissected, digested and stained for the single cell sequencing experiment.

value: Jax strain 000664 (C57BL6)

value: gd T cells

value: unknown

value: spleen


title: Patient_4

description:
Sample 1
main.h5ad
supplement.h5ad

value: COVID-19 Positive

value: 1 day after intubation

value: BAL

value: Sorted macrophages and T cells


title: DG WT engram

description: mKate2+, Hoechst+ from fear trained mice


title: Sample 4_1_Meninges Pup

description: CD45+, TCRb-, TCRgd+ sorted cells from meninges of mouse pups

source_name: Meninges Pup

value: meninges


title: Sample 3_1_Meninges Adult

description: CD45+, TCRb-, TCRgd+ sorted cells from meninges of adult mice

source_name: Meninges Adult

value: 8 weeks

value: Male


title: Sample 1_1_Spleen Adult

description: CD45+, TCRb-, TCRgd+ sorted cells from spleen of adult mice

source_name: Spleen Adult


title: Patient_6-2

description:
Sample 9
supplement.h5ad

value: COVID-19 Negative


title: IgG_TSA

status: Public on Jul 17 2020

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

data_processing:
Read adapters and poly-A tails were removed using cutadapt software. Trimming of low-quality tails was performed using sickle in paired-end mode, reads with the length less than 20 bp after trimming were discarded.
The remaining reads were aligned to build version danRer11 of the Danio rerio genome using Bowtie version 2 in paired-end mode (with enabling options --no-discordant --no-mixed). Only reads that aligned exactly one time concordantly were passed to further analysis.  After alignment read duplicates were removed using Picard MarkDuplicates function.
The coverage track (bedGraph) was obtained by calculation enrichment of each test signal against appropriate IgG control signal with deeptools2 bamCompare tool (with options --operation=ratio --extendReads) for merged replicates bam file.
The tracks signal was averaged using 500bp windows.
Genome_build: danRer11
Supplementary_files_format_and_content: Processed data was obtained by deeptools2 bamCompare and includes: values of ratio between sample and corresponding IgG averaged using 500 bp windows (bedGraph).

organism: Danio rerio

source_name: fibroblasts

growth_protocol: Zebrafish fibroblasts AB.9 were received from American Type Culture Collection (ATCC, CRL2298). The cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 15% fetal bovine serum (FBS) at 28°C under 5% CO2.

extract_protocol:
Cells were harvested and nuclei were prepared by incubation in buffer, containing 10 mM Tris–HCl (pH, 8.0), 100 mM NaCl, 50 mM KCl, 0.32 M sucrose, 0.5 mM CuSO4 and 1 % Triton X-100. All solutions contained protease inhibitor cocktail (Bimake), and for histone panacetylation analysis 5 mM sodium butyrate was included to inhibit histone deacetylase activity. After 15 min of incubation on ice, the nuclei were pelleted and then resuspended in the same buffer without CuSO4. Next, the nuclei were washed twice with digestion buffer (50 mM Tris–HCl [pH 8.0], 3 mM MgCl2, 1 mM CaCl2, 0.3 M sucrose, and 100 mM NaCl) and treated with 60 U/μl micrococcal nuclease (Thermo Fisher Scientific) for 10 min at 28 °C. The reactions were stopped by the addition of EDTA to a final concentration of 10 mM. The solubilized chromatin was extracted with hypotonic buffer (1 mM Tris–HCl [pH 8.0], 1 mM EDTA). After purification and concentration with Amicon Ultra 30K centrifugal filter devices (Millipore), the chromatin was used for further analysis. Immunoprecipitation reactions were performed overnight at 4 °C in 1 ml of solution containing 50 mM NaCl, 20 mM Tris–HCl (pH 8.0), 5 mM EDTA, 20 mM sodium butyrate, protease inhibitor cocktail and 5 μg of rabbit polyclonal antibodies against modified histones. Histone  H3ac (pan-acetyl) antibody (Active Motif, # 39139), histone H4ac (pan-acetyl) antibody (Active Motif, # 39243) and histone H3K27me3 antibody (Active Motif, # 39155) were used. Rabbit IgG (Jackson ImmunoResearch, #011-000-002) was used as a negative ChIP control. Immune complexes were collected using magnetic beads coated with immobilized protein G (Thermo Fisher Scientific). Immobilized complexes were washed two times for 10 min at 4◦C in low salt buffer (20 mM Tris–HCl, pH 8.0, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100) and high salt buffer (20 mM Tris–HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, 1% Triton X-100). Samples were incubated with RNase A (Thermo Fisher Scientific) for 30 min at 37°C. The DNA was eluted from the beads by proteinase K digestion overnight at 55◦C and purified using phenol/chloroform extraction.
ChIP samples containing 10 ng of precipitated DNA were prepared for next-generation sequencing using a standard protocol including DNA end repair, A-tailing, and Illumina Y-adapter ligation. Biotinylated probes for targeted enrichment of ChIP-seq libraries (C-TALE) were generated from BACs bearing the locus of interest. We produced hybridization baits using BACs CH211-225L23 and CH211-197P7 (CHORI BACPAC) covering the genomic region chr3: 54945766-55214549.

treatment_protocol: For HDAC inhibition experiments Danio rerio fibroblasts were treated with increasing concentrations (0,1, 1, 5, 10, 20 µM) of trichostatin A (TSA) for 24 h.

tag: cell line

value: fibroblast

value: TSA

tag: antibody

value: IgG


title: IgG_fib


title: Patient_2

description:
Sample 7
main.h5ad
supplement.h5ad

value: 0 days after intubation


title: Patient_5

description:
Sample 2
main.h5ad
supplement.h5ad


title: H4panac_TSA


title: H4panac_fib


title: H3panac_fib


title: H3panac_TSA


title: PB_donor1_γδT_transcriptome

value: gamma delta T cells

tag: tissue

value: peripheral blood

value: adult


title: H3K27me3_fib

tag: cell type


title: 11-10T-Old

status: Public on Jul 07 2020

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-seq reads (including ERCC spike-in controls) were aligned to the human reference genome (assembly GRCh37.75/hg19 concatenated with the sequence of the ERCC transcripts) using STAR with default parameters. Only alignments with mapping score MAPQ of 10 and above were retained.
Read counts for the ERCC spike-in transcripts were counted using samtools idxstat function. FeatureCounts was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Genome_build: hg19
Supplementary_files_format_and_content: read count per gene

source_name: Frozen postmortem brain tissue

extract_protocol:
RNA isolated from tissue was spiked with the ERCC Spike-In Mix (equal quantities) and subject to ribosomal RNA removal and sequencing library preparation.
Libraries were sequenced (75 bp, single-end) on a NextSeq 550 platform (Illumina) in accordance with the manufacturer’s protocol.

value: Lateral temporal lobe

value: old


title: 25-5T-AD

value: Alzheimer's disease


title: 31-7T-AD


title: 24-3T-AD


title: 8-15A-Young

value: young


title: 29-6T-AD


title: 6-14A-Young


title: 9-16A-Young


title: 4-13A-Young


title: 2-12A-Young


title: 17-9A-Old


title: 22-2T-AD


title: 18-10A-Old


title: 19-11A-Old


title: 14-7A-Old


title: 12-6A-Old


title: 10-8A-Old


title: 5-18T-Young


title: 7-19T-Young


title: 30-9T-AD


title: 23-2A-AD


title: 27-5A-AD


title: 21-1A-AD


title: 3-17T-Young


title: 20-1T-AD


title: 16-14T-Old


title: 26-3A-AD


title: 13-11T-Old


title: 28hpf poly(A)+

status: Public on Jun 28 2020

city: Pittsburgh

first: Miler

middle: T

last: Lee

address: 4249 Fifth Ave

department: Biological Sciences

institute: University of Pittsburgh

description:
zf_tpm.tsv
28hpf_polyA

data_processing:
Reads were mapped to the X. laevis v9.2 or GRCz11 (zebrafish) genomes using HISAT2 v2.0.5 (--no-mixed --no-discordant)
Mapped reads were assigned to genes (Xenbase v9.2 models for X. laevis and Ensembl r99 for zebrafish) using featureCounts v1.5.1 in reversely-stranded paired-end mode with default parameters.
Transcripts per million per gene were calculated in R using gene lengths output by featureCounts
Genome_build: X. laevis v9.2
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab-delimited transcripts per million (TPM) per gene

molecule: polyA RNA

source_name: Whole embryos

extract_protocol:
For X. laevis, 2 embryos were pooled for RNA extraction; for D. rerio, 20 embryos or 10 fin clips were pooled. Samples were snap frozen in a 1.5ul tube and homogenized with a pestle in 500ul of TRIzol Reagent (Invitrogen #15596026) followed by 100ul of chloroform. Tubes were spun at 18,000 x g at 4C for 15 minutes, the aqueous phase was transferred to a fresh tube with 340 ul of isopropanol and 1 ul of GlycoBlue (Invitrogen #AM9515), then precipitated at -80C for 1 hour. Precipitated RNA was washed with cold 75% ethanol and resuspended in 50ul of nuclease-free water. Concentration was determined by NanoDrop. RNA was stored at -80C until use.
For rRNA depletion, 1ul of antisense nuclear rRNA oligos (final concentration 0.4 uM per oligo) and 1ul of antisense mitochondrial rRNA (plus any other targeted gene) oligos (final concentration 0.1 uM per oligo) were combined with 1ug of total RNA in a 10ul buffered reaction volume (100mM Tris-HCl  pH 7.4, 200mM NaCl, 10mM DTT), heated at 95C for 2 minutes and cooled to 22C at a rate of 0.1C/s in a thermocycler. Next, 10U of thermostable RNaseH (NEB #M0523S) and 2uL of provided 10X RNaseH buffer were added and volume brought to 20uL with nuclease-free water. The reaction was incubated at 65C for 5 minutes (standard) or 45C for 30 minutes, then 5U of TURBO DNase (Invitrogen #AM2238) and 5uL of provided 10x buffer was added, volume brought to 50uL with nuclease-free water and incubated at 37C for 30 minutes. The reaction was purified and size selected to >200 nts using Zymo Clean and Concentrator-5 (Zymo #D4013) according to manufacturer’s protocol, eluting in 10uL of nuclease-free water. For poly(A) selection, the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490L) was used according to the manufacturer’s protocol: 1 ug of total RNA was denatured at 65C for 5 minutes then hybridized to buffered dT magnetic beads at room temperature for 2 minutes. Selected RNA was eluted in 50uL of Tris buffer at 80C for 2 minutes and rehybridized to the same beads for a second round of selection at room temperature for 2 minutes. Re-selected RNA was eluted in a final volume of 17 uL of Tris buffer. Strand-specific RNA-seq libraries were constructed using NEB Ultra II RNA-seq library kit (NEB #E7765) according to manufacturer’s protocol with fragmentation in first-strand buffer at 94C for 15 minutes. Following first and second strand synthesis, DNA was purified with 1.8X AmpureXP beads (Beckman #A63880), end repaired, then ligated to sequencing adaptors diluted 1:5. Ligated DNA was purified with 0.9X AmpureXP beads and PCR amplified for 8 cycles, then purified again with 0.9X AmpureXP beads. Libraries were verified by Qubit dsDNA high sensitivity (Invitrogen #Q32851) and Fragment Analyzer prior to multiplexed sequencing (paired end 38/37bp) on an Illumina NextSeq 500 at the Health Sciences Sequencing Core at Children's Hospital of Pittsburgh.

tag: strain

value: TUAB

tag: developmental stage


title: 28-8T-AD


title: 15-13T-Old


title: 28hpf somatic rRNA deplete

description:
zf_tpm.tsv
28hpf_rrna_som

tag: processing

value: somatic rRNA depleted


title: 28hpf untreated

description:
zf_tpm.tsv
28hpf_untreat


title: 28hpf mix rRNA deplete

description:
zf_tpm.tsv
28hpf_rrna_mix

value: all rRNA depleted


title: Stage 5 rRNA deplete

description:
xl_tpm.tsv
st5_rrna

organism: Xenopus laevis

value: rRNA depleted


title: 28hpf maternal rRNA deplete

description:
zf_tpm.tsv
28hpf_rrna_mat

value: maternal rRNA depleted


title: Stage 8 untreated

description:
xl_tpm.tsv
st8_untreat


title: P23h14_3

status: Public on Jun 16 2020

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h14_3

data_processing:
Original image data file from high-throughput sequencing (Illumina) was transformed into sequenced reads by CASAVA base recognition (Base Calling).
Data quality control was performed by inspecting error rates and QC content distribution
Data was filteterd as follows: (1) Reads with adaptor contamination were removed, (2) Reads when uncertain nucleotides constituted more than 10 percent of either read (N > 10%) were removed, (3) Removal of reads when low quality nucleotides (Base Quality less than 20) constituted more than 50 percent of the read. The Qscore (Quality value) of over 50% bases of these read is <= 5.
The gene expression data were aligned with a reference genome (mus musculus mm10) using Tophat2 (http://ccb.jhu.edu/software/tophat/index.shtml).
The gene expression level was measured by transcript abundance and reported as Fragments Per Kilobase of transcript sequence per Millions base pairs (FPKM) sequenced.
Genome_build: mm10
Supplementary_files_format_and_content: xls. or xlts., FPKMs or GO/KEGG/reactome pathway enrichments
Supplementary_files_format_and_content: Differential mRNA abundance
Supplementary_files_format_and_content: Significant GO pathway changes
Supplementary_files_format_and_content: Significant KEGG pathway changes
Supplementary_files_format_and_content: Significant predicted protein reactome changes

source_name: Whole retina

tag: background strain

tag: genotype

value: RhoP23H/WT (mutant)

value: Female

tag: age

value: Postnatal day 30


title: Stage 5 poly(A)+

description:
xl_tpm.tsv
st5_polyA


title: P23h12_7

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_7

value: RhoWT (wild-type)


title: P23h13_1

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h13_1

value: Male


title: P23h12_5

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_5


title: P23h12_6

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_6


title: P23h11_4

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h11_4


title: P23h11_3

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h11_3


title: P23h12_3

description:
Table S2 Differentially expressed genes WT males vs females
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_3


title: P23h11_2

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h11_2


title: P23h12_4

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_4


title: P23h12_1

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_1


title: P23h11_1

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h11_1


title: LUM0321: 7287656

status: Public on Jun 13 2020

city: Leiden

first: Pietro

last: Spitali

state: Zuid Holland

address: Postzone S4-P, Albinusdreef 2

department: Human Genetics

country: Netherlands

institute: Leiden University Medical Center

description: internal code: LUM0321

data_processing:
Data were aligned with STAR
Expression was quantified with cufflinks
Genome_build: mm10
Supplementary_files_format_and_content: count table

source_name: tibialis anterior muscle

growth_protocol: Mice were fasted for 4-6 hours with access to water before collecing the blood sample. Blood was collected at 6, 12, 18, 24 and 30 weeks of age. About 100μl of blood were collected frmo the tail into RNA protecting tubes. Mice were anaesthetised during blood collection with 2% isoflurane in oxygen and a solution of lidocaine was applied on the tail after the procedure. Mice were sacrificed at 30 weeks of age when the tibialis anterior muscle was also collected.

extract_protocol:
Total RNA was purified from blood using the Rneasy Protect Animal blood kit and the globin mRNA content was reduced using the globin clear kit. Muscle RNA was purified with Tripure reagent.
Trueseq v2 paired end sequencing

tag: genotype/variation

value: mdx/utrn+/-

value: tibialis anterior muscle

tag: mouse id

tag: group

tag: origin

value: total RNA

tag: week

tag: weight before fasting (g)

tag: weight after fasting (g)

tag: time food removed

tag: time collection


title: LUM0327: 7289306

description: internal code: LUM0327

value: mdx/utrn-/-

tag: tissue

tag: sample type


title: LUM0324: 9086178

description: internal code: LUM0324


title: P23h12_8

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_8

tag: Sex


title: Stage 8 poly(A)+

description:
xl_tpm.tsv
st8_polyA

tag: strain

tag: developmental stage


title: P23h12_2

description:
Table S1 Differentially expressed genes P23H females vs males
Table S3 Downregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S4 Upregulated genes arranged by log-fold change P23H vs WT retinas sexes pooled
Table S5 Significantly downregulated GO enrichment in P23H vs WT littermates
Table S6 Significantly upregulated GO enrichment in P23H vs WT littermates
Table S7 Significantly downregulated KEGG enrichment in P23H vs WT littermates
Table S8 Significantly upregulated KEGG enrichment in P23H vs WT littermates
Table S9 Predicted downregulated protein-protein interaction reactome P23H vs WT littermates
Table S10 Predicted upregulated protein-protein interaction reactome P23H vs WT littermates
P23h12_2

tag: background strain


title: LUM0316: 9086176

description: internal code: LUM0316

value: mdx/utrn+/+


title: LUM0318: 7283823

description: internal code: LUM0318


title: LUM0314: 9089165

description: internal code: LUM0314

value: mdx


title: LUM0325: 7286381

description: internal code: LUM0325


title: LUM0313: 9089164

description: internal code: LUM0313


title: LUM0317: 7281384

description: internal code: LUM0317


title: LUM0315: 9086174

description: internal code: LUM0315


title: LUM0311: 9089370

description: internal code: LUM0311


title: LUM0312: 9089371

description: internal code: LUM0312


title: LUM0323: 7289304

description: internal code: LUM0323


title: LUM0310: 9087926

description: internal code: LUM0310


title: LUM0326: 7289305

description: internal code: LUM0326


title: LUM0308: 9090753

description: internal code: LUM0308

value: WT


title: LUM0307: 7280769

description: internal code: LUM0307


title: LUM0328: 7291053

description: internal code: LUM0328


title: LUM0306: 7280768

description: internal code: LUM0306


title: LUM0302: 9084398

description: internal code: LUM0302


title: LUM0303: 9084142

description: internal code: LUM0303


title: LUM0304: 7271717

description: internal code: LUM0304


title: LUM0319: 7286382

description: internal code: LUM0319


title: LUM0320: 9086175

description: internal code: LUM0320


title: LUM0300: 9084143

description: internal code: LUM0300


title: LUM0299: 9084141

description: internal code: LUM0299


title: LUM0329: 7291056

description: internal code: LUM0329


title: LUM0296: 9082254

description: internal code: LUM0296


title: LUM0298: 7265906

description: internal code: LUM0298


title: LUM0297: 7269921

description: internal code: LUM0297


title: LUM0294: 7263678

description: internal code: LUM0294


title: LUM0291: 7269917

description: internal code: LUM0291


title: LUM0292: 9084396

description: internal code: LUM0292


title: LUM0293: 7263675

description: internal code: LUM0293


title: LUM0290: 7265911

description: internal code: LUM0290


title: LUM0288: 9083387

description: internal code: LUM0288


title: LUM0284: 9081310

description: internal code: LUM0284


title: LUM0280: 7269956

description: internal code: LUM0280


title: LUM0282: 9084390

description: internal code: LUM0282


title: LUM0286: 9083377

description: internal code: LUM0286


title: LUM0285: 9081311

description: internal code: LUM0285


title: LUM0281: 9083831

description: internal code: LUM0281


title: LUM0279: 7269955

description: internal code: LUM0279


title: LUM0276: 7289304

description: internal code: LUM0276

source_name: blood globin reduced

value: blood

value: blood globin reduced

tag: total ng rna

value: globin reduced


title: LUM0277: 7291053

description: internal code: LUM0277


title: LUM0274: 7286382

description: internal code: LUM0274


title: LUM0275: 7287656

description: internal code: LUM0275


title: LUM0273: 7283823

description: internal code: LUM0273


title: LUM0295: 7265907

description: internal code: LUM0295


title: LUM0271: 9089164

description: internal code: LUM0271


title: LUM0270: 9089371

description: internal code: LUM0270


title: LUM0272: 7281384

description: internal code: LUM0272


title: LUM0287: 9083378

description: internal code: LUM0287


title: LUM0289: 7263677

description: internal code: LUM0289


title: LUM0269: 9089370

description: internal code: LUM0269


title: LUM0267: 7289502

description: internal code: LUM0267


title: LUM0268: 9087926

description: internal code: LUM0268


title: LUM0266: 9090753

description: internal code: LUM0266


title: LUM0265: 7280769

description: internal code: LUM0265


title: LUM0264: 7280768

description: internal code: LUM0264


title: LUM0263: 9086807

description: internal code: LUM0263


title: LUM0261: 7291053

description: internal code: LUM0261


title: LUM0258: 7286382

description: internal code: LUM0258


title: LUM0259: 7287656

description: internal code: LUM0259


title: LUM0256: 7281384

description: internal code: LUM0256


title: LUM0278: 7291056

description: internal code: LUM0278


title: LUM0257: 7283823

description: internal code: LUM0257


title: LUM0260: 7289304

description: internal code: LUM0260


title: LUM0250: 9090753

description: internal code: LUM0250


title: LUM0251: 7289502

description: internal code: LUM0251


title: LUM0253: 9089370

description: internal code: LUM0253


title: LUM0254: 9089371

description: internal code: LUM0254


title: LUM0248: 7280768

description: internal code: LUM0248


title: LUM0246: 7291056

description: internal code: LUM0246


title: LUM0247: 9086807

description: internal code: LUM0247


title: LUM0249: 7280769

description: internal code: LUM0249


title: LUM0243: 7287656

description: internal code: LUM0243


title: LUM0245: 7291053

description: internal code: LUM0245


title: LUM0244: 7289304

description: internal code: LUM0244


title: LUM0242: 9086175

description: internal code: LUM0242


title: LUM0238: 9086176

description: internal code: LUM0238


title: LUM0241: 7286382

description: internal code: LUM0241


title: LUM0240: 7283823

description: internal code: LUM0240


title: LUM0237: 9086174

description: internal code: LUM0237


title: LUM0230: 7280769

description: internal code: LUM0230


title: LUM0262: 7291056

description: internal code: LUM0262


title: LUM0234: 9089370

description: internal code: LUM0234


title: LUM0236: 9089164

description: internal code: LUM0236


title: LUM0235: 9089371

description: internal code: LUM0235


title: LUM0232: 7289502

description: internal code: LUM0232


title: LUM0233: 9087926

description: internal code: LUM0233


title: LUM0229: 7280768

description: internal code: LUM0229


title: LUM0228: 9086807

description: internal code: LUM0228


title: LUM0225: 7289304

description: internal code: LUM0225


title: LUM0224: 7287656

description: internal code: LUM0224


title: LUM0222: 7286382

description: internal code: LUM0222


title: LUM0223: 9086175

description: internal code: LUM0223


title: LUM0226: 7291053

description: internal code: LUM0226


title: LUM0218: 9086174

description: internal code: LUM0218


title: LUM0239: 7281384

description: internal code: LUM0239


title: LUM0221: 7283823

description: internal code: LUM0221


title: LUM0214: 9089370

description: internal code: LUM0214


title: LUM0216: 9089164

description: internal code: LUM0216


title: LUM0217: 9089165

description: internal code: LUM0217


title: LUM0213: 9087926

description: internal code: LUM0213


title: LUM0211: 9090753

description: internal code: LUM0211


title: LUM0220: 7281384

description: internal code: LUM0220


title: LUM0219: 9086176

description: internal code: LUM0219


title: LUM0212: 7289502

description: internal code: LUM0212


title: LUM0231: 9090753

description: internal code: LUM0231


title: LUM0210: 7280769

description: internal code: LUM0210


title: LUM0207: 7291056

description: internal code: LUM0207


title: LUM0209: 7280768

description: internal code: LUM0209


title: LUM0208: 9086807

description: internal code: LUM0208


title: LUM0227: 7291056

description: internal code: LUM0227


title: LUM0203: 7286381

description: internal code: LUM0203


title: LUM0204: 7289305

description: internal code: LUM0204


title: LUM0202: 9086178

description: internal code: LUM0202


title: LUM0198: 9086175

description: internal code: LUM0198


title: LUM0206: 7291053

description: internal code: LUM0206


title: LUM0201: 7289304

description: internal code: LUM0201


title: LUM0197: 7286382

description: internal code: LUM0197


title: LUM0200: 9090499

description: internal code: LUM0200


title: LUM0192: 9089165

description: internal code: LUM0192


title: LUM0191: 9089164

description: internal code: LUM0191


title: LUM0190: 9089371

description: internal code: LUM0190


title: LUM0196: 7283823

description: internal code: LUM0196


title: LUM0194: 9086176

description: internal code: LUM0194


title: LUM0186: 9090753

description: internal code: LUM0186


title: LUM0195: 7281384

description: internal code: LUM0195


title: LUM0205: 7289306

description: internal code: LUM0205


title: LUM0188: 9087926

description: internal code: LUM0188


title: LUM0187: 7289502

description: internal code: LUM0187


title: LUM0184: 7280768

description: internal code: LUM0184


title: LUM0193: 9086174

description: internal code: LUM0193


title: 24hpf_EM-seq_rep2

status: Public on May 26 2020

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

country: Australia

institute: Garvan Institute of Medical Research

data_processing:
library strategy: EM-seq (enzymatic methylation sequencing)
APOBEC-converted (EM-seq) sequence reads were trimmed with Trimmomatic (ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:20) (Bolger et al. 2014), and mapped using WALT (-m 5 -t 20 -N 10000000) (Chen et al. 2016) onto the bisulfite-converted GRCz11 reference (UCSC) containing λ and puc19 sequences  added as separate chromosomes. The resulting alignments in BAM format were processed with CGmapTools (Guo et al. 2018) (convert bam2cgmap) to obtain methylation calls. ATCGmap files were parsed to discard the CH positions that showed evidence of a CG position in the reads discordant with the reference genome CH annotation.
Genome_build: GRCz11
Supplementary_files_format_and_content: CGmap file: (1) chromosome, (2) nucleotide on Watson (+) strand, (3) position, (4) context (CG/CHG/CHH), (5) dinucleotide-context (CA/CC/CG/CT), (6) methylation-level = #_of_C / (#_of_C + #_of_T), (7) #_of_C (methylated C, the count of reads showing C here), (8) = #_of_C + #_of_T (all Cytosines, the count of reads showing C or T here)

source_name: 24hpf embryos

growth_protocol: Adult wild type (AB/Tubingen) Danio rerio (zebrafish) were bred in a 1 male:1 female ratio. Embryos were collected 0 hours post-fertilization (hpf) and incubated in 1X E3 medium (0.03% NaCl, 0.005% CaCl2, 0.0013% KCl, 99.9557% H2O, 0.008% H14MgO11S) for 24 hours at 28.5°C.

extract_protocol:
24hpf embryos were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted from 24hpf embryos using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.
EM-seq library construction was performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs, Ipswich, MA, USA) according to manufacturer instructions with modifications. 0.02ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) and 0.0001ng of pUC19 plasmid methylated at 100% of CpG sites (New England BioLabs, Ipswich, MA, USA) were used as spike-in controls to determine the efficiency of APOBEC deamination and TET2 oxidation, respectively. Briefly, 200ng of zebrafish gDNA was sonicated to an average insert size of 300bp. Input DNA concentration was selected according to the optimal input amount as recommended by the manufacturer. Sonicated DNA was end repaired followed by ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was treated with TET2 for one hour. Following TET2 oxidation DNA was denatured with 0.1M NaOH then treated with APOBEC for three hours. DNA was PCR amplified (8 cycles). Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. 300pmol of the combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode)
EM-seq (enzymatic methylation sequencing)

tag: age

value: whole embryos

value: Mixed AB and Tubingen


title: LUM0189: 9089370

description: internal code: LUM0189

tag: genotype/variation


title: Castor bean infected by S. sclerotiorum rep3

status: Public on Apr 15 2020

city: Castanet tolosan

first: Sylvain

last: Raffaele

address: 28 chemin de borde rouge

country: France

institute: INRAE

data_processing:
HiSeq control software 2.2.58, RTA 1.18.64.0, Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genomes using the RNA-seq analysis function of the CLC genomics software with default settings.
Read count per gene were calculated using the RNA-seq analysis function of the CLC genomics software with default settings.
Genome_build: Helianthus annuus HanXRQr1.0; Beta vulgaris BETVU1.2.2; Ricinus communis RICCO1.1; Phaseolus vulgaris PVULG_BAT93
Supplementary_files_format_and_content: tab-delimited text files include total count of uniquely mapped reads per gene for each Sample

organism: Ricinus communis

source_name: Periphery of ~20mm wide disease lesion on leaves

growth_protocol: Plants were  grown in Jiffy pots under controlled conditions at 23°C, with a 9 hour light period at intensity of 120 μmol/m²/s.

extract_protocol:
The edge and center of developed mycelial colonies (~20 mm diameter) was harvested and stored in liquid nitrogen. Samples were ground with metal beads (2.5 mm) in a Retschmill apparatus (24hertz for 2x1min) before solubilizing in 1mL Trizol reagent (ThermoFisher) and left for 5 min at RT. Chloroform (200 µL) was added and mixed thoroughly before incubating for 3 min at RT. After centrifugation at ~12,000g (4°C) for 15min, the upper aqueous phase was recovered and nucleic acids were precipitated by adding 2µL GlycoBlue (Ambion) and 500µL isopropanol (10 min at -20°C). After centrifugation at ~15,000g (4°C) for 15min, pellets were washed twice with 70% ethanol before drying and resuspended in RNAse-free water. To eliminate chloroform traces, water resuspended nucleic acids were further cleaned using an RNA extraction kit (Quiagen) following manufacturer’s instructions. Genomic DNA was removed by DNase treatment (TURBO DNase; Ambion) following manufacturer’s instructions. The quality and concentrations of RNAs preparations were assessed with an Agilent apparatus and chips (nano).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: S. sclerotiorum strain 1980 was subcultured on Potato Dextrose Agar plates at 22°C. For inoculations, a 5-mm wide agar plug containing actively growing S. sclerotiorum mycelium was placed at the center of a Petri dish or on the adaxial surface of leaves on 5-week old plants. The border (ring of ~5mm wide) and center of colonies were collected with a scalpel and frozen in liquid nitrogen.

tag: cultivar

value: Hale

value: Leaves of 5-week old plants

tag: infection

value: infected (Ss)


title: Castor bean infected by S. sclerotiorum rep2


title: 24hpf_EM-seq_rep1

description:
EM-seq library construction was performed using the NEBNext Enzymatic Methyl-seq Kit (New England BioLabs, Ipswich, MA, USA) according to manufacturer instructions with modifications. 0.02ng of unmethylated lambda phage DNA (Promega, Madison, WI, USA) and 0.0001ng of pUC19 plasmid methylated at 100% of CpG sites (New England BioLabs, Ipswich, MA, USA) were used as spike-in controls to determine the efficiency of APOBEC deamination and TET2 oxidation, respectively. Briefly, 200ng of zebrafish gDNA was sonicated to an average insert size of 300bp. Input DNA concentration was selected according to the optimal input amount as recommended by the manufacturer. Sonicated DNA was end repaired followed by ligation of adapters to DNA overnight using NEXTFLEX Bisulfite-Seq Barcodes (PerkinElmer, Waltham, MA, USA). DNA was treated with TET2 for one hour. Following TET2 oxidation DNA was denatured with 0.1M NaOH then treated with APOBEC for three hours. DNA was PCR amplified (8 cycles). Library concentration was quantified through qPCR using KAPA Library Quantification Kit (Sigma-Aldrich, St. Louis, MO, USA) according to manufacturer instructions. 300pmol of the combined libraries with 15% PhiX spike-in was sequenced on the Illumina HiSeq 10X platform using 150bp paired-end sequencing (high output mode)
EM-seq (enzymatic methylation sequencing)

extract_protocol: 24hpf embryos were snap frozen in liquid nitrogen and stored at -80°C prior to DNA extraction. Genomic DNA (gDNA) was extracted from 24hpf embryos using the QIAGEN DNeasy Blood & Tissue Kit (QIAGEN, Chadstone, VIC, Australia) according to manufacturer instructions in two biological replicates.


title: Castor bean infected by S. sclerotiorum rep1


title: LUM0183: 9086807

description: internal code: LUM0183

tag: mouse id

tag: group

tag: origin


title: Beetroot infected by S. sclerotiorum rep3

organism: Beta vulgaris subsp. vulgaris


title: Sunflower infected by S. sclerotiorum rep2

organism: Helianthus annuus

tag: genotype

value: XRQ


title: Beetroot infected by S. sclerotiorum rep2


title: Sunflower infected by S. sclerotiorum rep3


title: Common bean infected by S. sclerotiorum rep3

organism: Phaseolus vulgaris

tag: accession


title: Beetroot infected by S. sclerotiorum rep1


title: Sunflower infected by S. sclerotiorum rep1


title: Common bean infected by S. sclerotiorum rep2


title: Common bean infected by S. sclerotiorum rep1


title: Day24 pLN_002 eff non-TFH

status: Public on Mar 17 2020

city: Durham

first: Chen-Hao

last: Yeh

state: NC

address: 207 Research Drive

department: Immunology

institute: Duke University

data_processing:
Reads were initially trimmed using TrimGalore
Reads were mapped to the GRCm38v73 version of the mouse genome and transcriptome using the STAR aligner
The number of reads mapping to each gene was compiled using HTSeq
Genome_build: GRCm38v73
Supplementary_files_format_and_content: HTSeq raw counts for each sample

source_name: NP-OVA/Alum immunized pLN

extract_protocol:
RNA was extracted from sorted cell populations using the Direct-zol RNA Kits (Zymo Research).
Prior to cDNA synthesis, the quantification and quality assessment of RNA was performed using a Qbit 4.0 fluorimeter with the RNA IQ Assay (Thermo Fisher Scientific) and Bioanalyzer with Agilent RNA 6000 Pico Kit (Agilent). The cDNA was produced using the SMART-Seq® v4 Ultra Low Input RNA Kit following manufacturer’s recommendations (Takara Bio USA Inc.). Adapters were used as template for cDNA synthesis and downstream PCR for the cDNA amplification. The resulting cDNA was purified using the KAPA Pure Beads (Roche Sequencing and Life Science), and quantification and quality assessment was performed using a Qbit 4.0 fluorimeter with the dsDNA HS Assay Kit (Thermo Fisher Scientific). The DNA library was constructed using the KAPA HyperPlus Kit following manufacturer’s recommendations (Roche Sequencing and Life Science).

treatment_protocol: FoxP3-eGFP mice were footpad immunized with 20µg of NP-OVA in alum and harvested at days 8, 12, 16 and 24. CD90lowGCTFH, Cd90hiGCTFH, TFR and EffNonTFH cells were sorted from the same pLN and subjected to ultra-low RNA sequencing.

value: FoxP3-eGFP (Jax 006772)

value: Popliteal LN

tag: time point

value: Day 24


title: LUM0185: 7280769

description: internal code: LUM0185

tag: tissue

value: total RNA

tag: week

tag: weight before fasting (g)

tag: weight after fasting (g)

tag: time food removed

tag: time collection


title: Day24 pLN_001 eff non-TFH

tag: strain


title: Day24 pLN_002 TFR

value: TFR (CD4+FoxP3+CXCR5hiPD-1hi)


title: Day24 pLN_003 eff non-TFH


title: Day24 pLN_003 CD90hi GCTFH-like


title: Day24 pLN_002 CD90hi GCTFH-like


title: Day16 pLN_003 eff non-TFH

value: Day 16


title: Day16 pLN_003 TFR


title: Day24 pLN_003 CD90neglo GCTFH


title: Day24 pLN_001 TFR


title: LUM0305: 9086807

description: internal code: LUM0305

value: tibialis anterior muscle

tag: sample type


title: Day24 pLN_001 CD90hi GCTFH-like

tag: genotype/variation


title: Day24 pLN_003 TFR


title: Day16 pLN_003 CD90hi GCTFH-like


title: Day16 pLN_002 CD90hi GCTFH-like


title: Day16 pLN_003 CD90neglo GCTFH


title: Day16 pLN_002 TFR


title: Day16 pLN_002 eff non-TFH


title: Day24 pLN_002 CD90neglo GCTFH


title: Day16 pLN_002 CD90neglo GCTFH


title: Day16 pLN_001 TFR


title: Day16 pLN_001 eff non-TFH


title: Day16 pLN_001 CD90hi GCTFH-like


title: Day16 pLN_001 CD90neglo GCTFH


title: Day12 pLN_003 TFR

value: Day 12


title: Day24 pLN_001 CD90neglo GCTFH


title: Day12 pLN_003 CD90hi GCTFH-like


title: Day12 pLN_002 CD90neglo GCTFH


title: Day12 pLN_003 CD90neglo GCTFH


title: Day12 pLN_002 eff non-TFH


title: Day12 pLN_001 eff non-TFH


title: Day12 pLN_002 CD90hi GCTFH-like


title: Day12 pLN_002 TFR


title: Day12 pLN_001 TFR


title: Day8 pLN_003 CD90hi GCTFH-like

value: Day 8


title: Day8 pLN_003 eff non-TFH


title: Day12 pLN_001 CD90neglo GCTFH


title: Day12 pLN_001 CD90hi GCTFH-like


title: Day8 pLN_003 TFR


title: Day12 pLN_003 eff non-TFH


title: Day8 pLN_003 CD90neglo GCTFH


title: Day8 pLN_001 eff non-TFH


title: Day8 pLN_001 TFR


title: Day8 pLN_002 CD90neglo GCTFH


title: Day8 pLN_002 TFR


title: Day8 pLN_001 CD90hi GCTFH-like


title: 10007608-1

status: Public on Mar 13 2020

city: Rochester

first: Xiaojia

last: Tang

state: MN

address: 200 1st ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using fastQC
Alignment and gene counts were obtained through MAPR-Seq pipeline v2.0.
Genome_build: hg19
Supplementary_files_format_and_content: GeneCount_raw.txt

source_name: Tissue Biopsy

extract_protocol:
Biopsy samples were thawed on ice, homogenized, and centrifuged at 13,000 RPM, and the supernatant was transferred to a new tube.
RNA was prepared using the RNeasy Mini Kit (QIAGEN, Hilden, Germany).

tag: age

tag: bmi

tag: gender

value: F

tag: cohort

value: Constipation


title: 10007606-1


title: 10007602-1


title: 10007613-1

value: Healthy


title: 10007541-1


title: Day8 pLN_002 eff non-TFH


title: 10007557-1


title: 10007616-1


title: 10007615-1


title: 10007564-1


title: 10007563-1


title: Day8 pLN_001 CD90neglo GCTFH


title: 10007595-1


title: 10007607-1


title: 10007562-1


title: 10007610-1


title: Day8 pLN_002 CD90hi GCTFH-like


title: 10007583-1


title: 10007590-1

value: Diarrhea


title: 10007581-1


title: 10007565-1


title: 10007559-1

value: Diarrheaiarrhea


title: 10007589-1


title: 10007603-1


title: 10007558-1


title: 10007547-1


title: 10007542-1


title: BCALI

status: Public on Feb 20 2020

city: New Haven

first: Allison

middle: M

last: Greaney

state: CT

address: 10 Amistad St

department: Biomedical Engineering

institute: Yale University

description: 10x Genomics

data_processing:
FASTQ read 2 sequences were trimmed of the reverse complement sequence of the template switch oligo, as well as for poly(A) contaminants. Paired reads with a trimmed read 2 less than 30 bp long were discarded.
Downstream processing was conducted with zUMIs v 0.4 (44) with the default parameters; the top 10,000 cell barcodes ranked by reads were output for each sample.
Genome_build: Ensembl Rnor6.0 release 92 was used to align the data to the rat transcriptome.
Supplementary_files_format_and_content: sparse matrix of raw counts
Supplementary_files_format_and_content: barcodes (column names for .mtx file)
Supplementary_files_format_and_content: genelist (rownames for .mtx file)

organism: Rattus norvegicus

source_name: peBC at ALI

growth_protocol: Native rat tracheal epithelial scapings (TE1ep) were plated and peBC expanded on collagen-coated TCP using a pharmacologic expansion media (Propagenix)(BCP1, BCP3, BCP6).

extract_protocol:
Samples were rendered to a single cell suspension for sequencing enzymatically using platform-specific protocols (Greaney 2020).
Single-cell libraries were prepared using the standard 10x Genomics v2 processing workflow. Cell loadings were designed to yield 5000-10000 cells per library.
10x genomics standard library preparation. Sequencing on Illumina HiSeq 4000 sequencers, indexed to a depth of 160-220 million reads per library. Read 1 sequencing was 26 bp long, read 2 sequencing was 98 bp long.

treatment_protocol: peBC were differentiated on four in vitro culture platforms, including organoids in matrigel (BCO1), at air-liquid interface (BCALI), in engineered trachea (BCT1), and in engineered lung (BCL5). All differentiation was performed in Propagenix Airway Differentiation Medium (PADM).

tag: group

value: differentiated cells

tag: protocol

value: air-liquid interface


title: BCT1

description: 10x Genomics

source_name: peBC in engineered trachea

value: engineered trachea


title: EGR1_MACRO_D3_CUTRUN

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

country: United Kingdom

institute: Imperial College London

description: EGR1 CUT&RUN was performed on differenting macrophages (day 3)

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control: FastQC
Adapter Trimming: TRIM-GALORE
alignment (RNA-seq): STAR
alignment (ChIPseq, CUT&RUN, ATAC-seq): BWA
tag density files: deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: DIFFERENTIATING MACROPHAGES

growth_protocol: CD34 were cultured andf differentiated in IMDM, with heatinactivated FBS and  M-CSF. Primary Monocytes were cultured differentiated in IMDM with heat inactivated FBS and 25 ng/ul GM-CSF

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: M-CSF  14 days (monocyte diff); GM-CSF 5 days (macrophages)

tag: cell type

value: DIFFERENTIATING MACROPHAGES

tag: chip antibody

value: EGR1 BETHYL RABBIT POLICLONAL A303


title: 10007548-1


title: EGR1_MACRO_D2_CUTRUN

description: EGR1 CUT&RUN was performed on differenting macrophages (day 2)


title: EGR1_M5_CUTRUN

description: EGR1 CUT&RUN was performed on differenting CD34 into monocytes (day 5)

source_name: DIFFERENTIATING MONOCYTES

value: DIFFERENTIATING MONOCYTES


title: TE1ep

description: 10x Genomics

source_name: Native trachea scraping

value: native cells


title: EGR1_MACRO_D4_CUTRUN

description: EGR1 CUT&RUN was performed on differenting macrophages (day 4)


title: EGR1_CD34_CUTRUN

description: EGR1 CUT&RUN was performed on CD34+ cells

source_name: CD34+ cells

value: CD34+ cells


title: BCP6

description: 10x Genomics

source_name: peBC at P6

value: cultured cells

value: collagen-coated TCP using a pharmacologic expansion media (Propagenix)


title: EGR1_MACRO_D1_CUTRUN

description: EGR1 CUT&RUN was performed on differenting macrophages (day 1)


title: EGR1_MACRO_D6_CUTRUN

description: EGR1 CUT&RUN was performed on differenting macrophages (day 6)


title: 10007584-1


title: 10007554-1


title: EGR1_M13_CUTRUN

description: EGR1 CUT&RUN was performed on differenting CD34 into monocytes (day 13)


title: SC75.LB19004

status: Public on Feb 12 2020

city: Houston

first: Yuanxin

last: Xi

state: TX

address: 1400 Pressler St

department: Bioinformatics and Computational Biology

institute: The University of Texas MD Anderson Cancer Center

data_processing:
Seqeuncing reads were processed using Cell Ranger v2.0 pipeline (10x Genomics)
Genome_build: hg38
Supplementary_files_format_and_content: UMI reads count were calculated by Cell Ranger v2.0

growth_protocol: Tumors were grown in mice to between 500-800 mm3

extract_protocol:
Tumors were collected and RNA extracted using Trizol reagent and purified with a Qiagen RNeasy kit
Sequencing library were constructed following 10x Genomics Chromiun v2 library preparation protocol.

treatment_protocol: Mice were untreated

tag: tissue

value: CDX flank

tag: patient diagnosis

value: small cell lung cancer (SCLC)

tag: treatment

value: untreated


title: SC55.LB19001


title: BCP3

description: 10x Genomics

source_name: peBC at P3


title: 10007556-1

value: F

value: Constipation


title: SC68.LB19002

value: vehicle-treated


title: SC68_cr.LB19003

value: cisplatin, relapsed


title: SC4_Talazoparib.LB17011

value: talazoparib, relapsed


title: SC4_Talazoparib.LB17015


title: EGR1_MONO_CUTRUN

description: EGR1 CUT&RUN was performed on monocytes

source_name: PERIPHERAL MONOCYTES

value: PERIPHERAL MONOCYTES


title: SC4_LY2606368.LB17016

value: prexasertib, relapsed