title: Abisporus RNA-seq rep2

first: Christopher

last: Benner

address: 9500 Gilman Dr. MC 0640

institute: University of California, San Diego (UCSD)

description: abisporus-tsr.txt

data_processing:
For csRNA-seq, sequencing reads were trimmed for 3’ adapter sequences using HOMER (“homerTools trim -3 AGATCGGAAGAGCACACGTCT -mis 2 -minMatchLength 4 -min 20”) and aligned to the appropriate genome using STAR with default parameters[PMID: 23104886]. Only reads with a single, unique alignment (MAPQ >=10) were considered in the downstream analysis. Furthermore, reads with spliced or soft clipped alignments were discarded. Transcription Start Regions (TSRs), representing loci with significant transcription initiation activity (i.e. ‘peaks’ in csRNA-seq), were defined using HOMER’s findcsRNATSS.pl tool, which uses short input RNA-seq, traditional total RNA-seq, and annotated gene locations to eliminate loci with csRNA-seq signal arising from non-initiating, high abundance RNAs that nonetheless are captured and sequenced by the method (Duttke et al. for more details[PMID:31649059]). Replicate experiments were first pooled to form meta-experiments for each condition prior to identifying TSRs. Annotation information, including gene assignments, promoter distal, stable transcript, and bidirectional annotations are provided by findcsRNATSS.pl.
For RNA-seq, reads from accession GSE171286 were downloaded and aligned to the C. immitis genome (ASM14933v2)  using STAR with default parameters. Reference-guided transcranscript assembly was performed using StringTie2 (Kovaka et al. 2019) with the Ensembl gene annotation (GTF file) and additional parameters “-m 100 --rf”. Assembled transcripts were compared to the existing C. immitis annotation using cuffcompare.
Genome_build: C. immitis (ASM14933v2), S. cerevisiae (R64-1-1/sacCer3), S. pombe (ASM294v2), A. bisporus (gca_000300555/Agabi_varbur_1)
Supplementary_files_format_and_content: Tab-delimited Text file describing TSR positions and annotations, GTF formated transcript definition files

source_name: Agaricus bisporus fruiting body

extract_protocol:
Trizol extraction after tissue homogenisation
For RNA-Seq, strand-specific, paired-end libraries were prepared from total RNA by ribosomal depletion using the Yeast Ribo-Zero rRNA Removal Kit (Illumina) and then using the TruSeq Stranded total RNA-Seq kit (Illumina) according to manufacturer's instructions. Then 100 bases were sequenced from both ends using a HiSeq 4000 according to the manufacturer's instructions (Illumina).    csRNA-seq was performed as described in (Duttke et al. 2019). Small RNAs of ~20-60 nt were size selected from 0.4-2 µg of total RNA by denaturing gel electrophoresis. A 10% input sample was taken aside and the remainder enriched for 5’-capped RNAs. Monophosphorylated RNAs were selectively degraded by Terminator 5´-Phosphate-Dependent Exonuclease (Lucigen) and RNAs were 5’dephosporylation by quickCIP (NEB). Input (sRNA) and csRNA-seq libraries were prepared as described in (Hetzel et al. 2016) using RppH (NEB) and the NEBNext Small RNA Library Prep kit, amplified for 14 cycles and sequenced SE75 on the Illumina NextSeq 500.
csRNA-seq, sRNA-seq, total RNA-seq

value: brown

tag: tagtreatment

value: untreated

tag: method

value: ribo-0 total RNA-seq


title: D481_Blood_Flu CMV_CD8

status: Public on Jan 05 2022

type: SRA

city: New York

first: Donna

last: Farber

address: 650 West 168th Street

country: USA

institute: Columbia University Medical Center

description:
DM038_S10
201028_NS500289_0872_AH27F2BGXH_DM038_S10

library_source: transcriptomic

data_processing:
RTA (Illumina) for base calling on Illumina Illumina Novaseq 6000
extract UMIs and barcodes with "umi_tools extract"
align reads with STAR
assign alignments to genes with featureCounts
sort & index bam with samtools
make count matrix from bam with "umi_tools count", pandas, and scipy
Genome_build: GRCm38
Supplementary_files_format_and_content: plate_matrix.csv: raw gene counts for each barcode
Supplementary_files_format_and_content: plate_meta.csv: barcode, well, and cell type table

molecule: total RNA

organism: Homo sapiens

source_name: Blood CD8 T cells

extract_protocol:
lysis buffer 0.2% Triton X-100, 1 U/uL SUPERaseIN, 2mM dNTPs, 2uM well-specific RT primer
pooled 3' end scRNA-Seq

treatment_protocol: Mononuclear cells were thawed,  dead cells were removed, and cells were left to rest overnight (5% CO2, 37C). Cells were then stimulated by the addition of individual virus-specific peptide megapools (1ug/mL) for 24 hrs. Antigen-responsive cells were stained using the IFN-gamma Secretion Assay – Detection Kit, human (Miltenyi Biotec, cat# 130-054-202) then stained with fluorochrome-conjugated antibodies to label cell surface markers. IFN-gamma+ CD69+ CD8+ T cells were sorted using BD Influx Cell Sorter directly into 96-well plates containing 7.5 μl of lysis buffer [0.2% Triton X-100 (Sigma), SUPERaseIN (1 U/μl) (Thermo Fisher Scientific), 2 mM deoxyribonucleotides (dNTPs) (Thermo Fisher Scientific), and 2 μM reverse transcriptase (RT) primer (Integrated DNA Technologies)].

tag: cell type

value: Blood CD8 T cells

tag: stimulation condition

value: Flu or CMV stimulated CD8


title: M9 Min Glu #1, RNA polymerase ChIP, replicate 1

city: Ann Arbor

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

department: Biological Chemistry

institute: University of Michigan

description:
wt_minglu1_chip_vs_inp_lograt.bed
wt_minglu1_chip_vs_inp_lograt.gr

library_source: genomic

data_processing:
Adapter removal using the common Illumina Truseq adapter sequences with cutadapt 1.8.1
Read ends were trimmed using Trimmomatic 0.33 in paired end mode, with the trimming steps ‘TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:10’
Reads were aligned using bowtie2 version 2.1.0 with ‘very sensitive’ end-to-end presets, and dovetailed alignments allowed
We performed gene-level quantitation with htseq-count, using union mode for scoring and all mode for non-unique assignments
Differential expression calling was then performed using deseq2 with default settings
Genome_build: U00096.3
Supplementary_files_format_and_content: .gr files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. The first column gives a location and the second column gives the corresponding value
Supplementary_files_format_and_content: .csv files for RNA: Tabular output from DeSeq2, using as a sign convention log(cond2/cond1), where cond1 is the first condition listed and log2 the second condition listed in the file name
Supplementary_files_format_and_content: .bed files: Occupancies (expressed as log2(chip/input) for ChIP samples, and robust z-scores (as defined in https://doi.org/10.1101/2020.01.29.924811) for IPOD samples. Standard bed-formatted files

molecule: genomic DNA

organism: Escherichia coli

source_name: Culture lysate

growth_protocol: Overnight cultures (in M9 minimal media + 0.02% glucose) were back diluted to an OD600 0.003 in fresh, prewarmed M9 minimal medium including 0.2% glucose at 37°C. After growth to an OD of 0.2, the Glu #1 sample was harvested. Remaining cells were diluted to an OD of ~0.1 in M9 ninimal medium including 0.2% 5-keto D-gluconic acid, and grown to an OD of 0.2, at which point the KDG sample was harvested. Remaining cells were diluted in M9 minimal media plus 0.2% glucose to an OD of 0.003, and grown to an OD of 0.2, at which point the Glu #2 sample was harvested.

extract_protocol:
DNA samples: Frozen cell pellets were resuspended in 1x IPOD lysis buffer (10 mM Tris HCl, pH 8.0; 50 mM NaCl) containing 1x protease inhibitors (Roche Complete Mini, EDTA free) and 52.5 kU/mL of ready-lyse (Epicentre); 600 uL per pellet (stationary phase cells were diluted 10x prior to lysis due to the much higher biomass of those pellets). We incubated the resuspended pellet for 15 minutes at 30 C, and then placed it on ice. We then sonicated the cells using a Branson digital sonicator at 25% power, using three 10 second bursts with 10 second pauses between bursts. The cells were maintained in a wet ice bath throughout sonication. We then performed a calibrated DNA digestion to sub-200 bp fragments, by adding to the sonicated lysates 60 ug RNase A (Thermo Fisher), 6 uL DNase I (Fisher product #89835), 5.4 uL 100 mM MnCl2, and 4.5 uL 100 mM CaCl2, and then incubating on ice. While the appropriate digestion time must be calibrated for each particular sample type and batch of DNase, 30 minutes of digestion proved appropriate for all samples here. Reactions were quenched after completion by the addition of 50 uL 500 mM EDTA (pH 8.0), typically yielding 50-200 bp fragments. Samples were clarified by centrifugation for 10 minutes at 16,9000xg at 4 C. After clarification, the lysate was mixed with 1 volume of 100 mM Tris base and 2 volumes of 25:24:1 phenol:chloroform:isoamyl alcohol, vortexed, and then incubated for 10 minutes at room temperature. After incubation, the sample was spun at 21,130xg for two minutes at room temperature, allowing formation of a white disc at the aqueous-organic interface enriched for protein-DNA complexes. The complete aqueous phases were removed and discarded, and the remaining disc washed again with 350 microliters TE (10 mM Tris, pH 8.0; 1 mM EDTA), 350 microliters 100 mM Tris base, and 700 microliters 24:1 chloroform:isoamyl alcohol. The resulting mixture was vortexed vigorously, and again centrifuged for 2 minutes at 21,130xg. All liquid was again removed, and the wash was repeated using 700 microliters TE and 700 microliters 24:1 chloroform:isoamyl alcohol. After vortexing, centrifugation, and removal of the final wash (exactly as above), any residual liquid was removed by wicking with a laboratory wipe (if any substantial pools of liquid were present). Finally, the interface was resuspended in 500 microliters of elution buffer (described above), vortexed vigorously, and reverse crosslinked overnight at 65 C. After allowing the samples to cool to room temperature, we then added 100ug of RNase A (Thermo-Fisher), incubated 2 hours at 37 C, then added 200ug of proteinase K (Fermentas) and incubated an additional 2 hours at 50 C. DNA was then recovered via standard phenol-chloroform extraction and ethanol precipitation, following protocols from (Ausubel, 1998). We used Glycoblue (Ambion) as a co-precipitant, NaCl as a precipitating salt (due to the presence of SDS in our solution), and washed with ice-cold 95% ethanol to avoid loss of low molecular weight DNA. RNA: RNA was harvested using Qiagen RNAProtect. RNA was isolated, and rRNA depletion was performed according to the Illumina Ribo-Zero rRNA Removal Kit for Bacteria.
DNA samples: NEB Nebnext Ultra 2 DNA kit, but with a spin column replacing the first bead cleanup (see the accompanying paper for details).

treatment_protocol: Upon the harvest points noted under ‘growth protocol’, 1 mL of sample was preserved in Qiagen RNAprotect bacterial reagent following the manufacturer’s instructions

tag: strain

tag: genotype

value: wild type

tag: media

value: M9 minimal media + glucose

tag: time of harvest

value: logarithmic phase


title: Abisporus RNA-seq rep1

city: La Jolla

state: California

department: Medicine

description: abisporus-tsr.txt

organism: Agaricus bisporus

growth_protocol: C. immitis R.S. strain was grown as mycelia or spherules as previously described (Viriyakosol et al. 2013). To grow mycelia, 2×10^6 arthroconidia/ml were incubated in 250 ml flat-bottom Erlenmeyer flasks (Corning) in 50 ml GYE media. Flasks were cultured in a 30°C incubator without shaking for 5 days. To grow spherules, arthroconidia were washed 2 times in modified Converse media (Converse 1956). The spores were inoculated at 4×106 arthroconidia/ml into a 250 ml baffled Erlenmeyer flask containing 50 ml of modified Converse media. Flasks were set up and grown on a shaker at 160 rpm, in 14% CO2 at 42°C. Four flasks were harvested 2 days after inoculation and the remaining four flasks after 8 days. Fresh Converse media was not added.  The spherules did not rupture and release endospores within that time in this culture system. Saccharomyces cerevisiae (strain RYH2863) was grown as described previously (Neal et al. 2018). Schizosaccharomyces pombe (strain TH972) was generously provided by Tony Hunter (SALK Institute for Biological Sciences) and grown in Yeast Extract with Supplements (YES)(Leverson et al. 2002). White and brown ecotypes of Agaricus bisporus, better known as ‘Champignon’ or ‘crimini mushroom’ were kindly provided by Monterey Mushroom farms.

treatment_protocol: untreated

value: white


title: M9 Min Glu #1, Input, replicate 1

description:
wt_minglu1_chip_vs_inp_lograt.bed
wt_minglu1_chip_vs_inp_lograt.gr
wt_minglu1_v6rz_chipsub.bed
wt_minglu1_v6rz_chipsub.gr


title: Patient NR2

status: Public on Jan 04 2022

type: RNA

city: Zurich

first: Thomas

middle: F.

last: Müller

address: Rämistrasse

country: Switzerland

institute: University Hospital Zurich

hyb_protocol: Forty-eight target-mRNA-specific oligonucleotides A1,2,..48 and oligonucleotides B1,2,..48 were synthesized by Integrated DNA TechnologiesTM. Each 7 µL of the oligonucleotides A (present at 0.6 nM) and B (present at 3 nM) were mixed with 70 µL containing the unique fluorescent “barcode” reporter tag and the universal capture tag (provided by NanoStringTM), generating a so called Master MixTM. For hybridisation 8 µL of the Master MixTM were added to 7 µL of FFPE RNA sample with subsequent incubation at 67°C for minimum 16 hours.

scan_protocol: In a purification process all the mRNA/oligonucleotides not bound to a plate (through the universal capture tag) were washed away. After an alignment of all the hybridized unique fluorescent barcodes bound to the target mRNA in an electromagnetic field, analysis followed: the number of mRNA copies bound to their unique fluorescent barcode was counted.

data_processing: The number of mRNA copies bound to their unique fluorescent barcode was counted.

label: specific unique olgionucleotide produced byintegrated DANN TechnologiesTM

source_name: kidney transplant, caABMR, therapy non responder

label_protocol: Based on the target mRNA sequence two specially designed oligonucleotides A and B were synthesized for each one of he 48 target mRNAs.Oligonucleotide A specifically binds the target mRNA sequence and a unique fluorescent barcode reporter specific for the target mRNA sequence.  Oligonucleotide B specifically binds the target mRNA sequence and a universal capture tag able to fix the target mRNA on a plate.

growth_protocol: To obtain high quality transcriptome measurements in stored FFPE tissues we chose the NanoStringTM technology that allows robust mRNA analysis without further amplification

extract_protocol: After deparaffinization RNA was extracted and its quality checked.

treatment_protocol: For NanoStringTM analysis around 100 ng total RNA is needed, i.e. 3 to 4 cuts of 20 um each from the FFPE block

tag: postoperative day

tag: postoperative year

tag: age at transplantation

tag: age at biopsy


title: control_2

city: Hangzhou

first: Yuhan

last: Shu

address: Ling Yin Street, Road 38 West Lake District

country: China

institute: Zhejiang University

data_processing:
We performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
Cutadapt software was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100). And After removed the low quality bases and undetermined bases ,we used HISAT2 software  to map reads to the genome,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam). The mapped reads of each sample were assembled using StringTie with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam). The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR or DESeq2,and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.
Genome_build: Ensembl v96
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
Supplementary_files_format_and_content: differential expression genes between treated and control

source_name: colon cancer cells

growth_protocol: Cells were maintained in high glucose dulbecco's modified eagle medium (DMEM, HyClone) and supplemented with 10% FBS, 100 units/ml penicillin, 100 mg/ml streptomycin, 1 mM sodium pyruvate and 1 mM nonessential amino acids.

extract_protocol:
Total RNA was extracted using  Trizol buffer (Beyotime, Shanghai, China)  following the manufacturer's procedure
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: SW620 cells were seeded in 6-cm dishes overnight and treated with 12.5μM DHOK for 24 h in a 5% CO2 incubator.


title: Patient NR3


title: Patient NR5


title: Patient NR4


title: Patient NR6


title: Patient R4

source_name: kidney transplant, caABMR, therapy responder


title: Patient NR1


title: Patient R1


title: Patient R2


title: Patient R3


title: S15_scrambleOVA

city: Cold Spring Harbor

first: Ran

last: Yan

state: New York

address: 1 Bungtown Rd

institute: CSHL

data_processing:
NOT PROVIDED; REQUESTED
Genome_build: mm10
Supplementary_files_format_and_content: gene expression text file

molecule: polyA RNA

organism: Mus musculus

source_name: Subcutaneous PDA tumor

extract_protocol:
Qiagen RNAeasy
Illumina TruSeq; 10nM, 12 cycles for cDNA amplification

tag: genotype/variation

value: scrambleOVA

tag: tumor stage

value: 2 weeks after inoculation

tag: cancer cell type

value: 1242 KPC cell

tag: host strain


title: S5_scramble

value: scramble


title: S2_scrambleOVA


title: S18_scrambleOVA


title: S16_scrambleOVA


title: S4_scramble


title: Well-paired-seq_species-mixing_sample4

city: Xiamen

first: Li

last: Lin

state: Fujian

address: 422 Road, Siming District,  Xiamen, China

institute: Xiamen University

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample4_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample4_mouse_raw_dge.txt.gz

data_processing:
Well-paired-seq sequencing libraries produced paired-end reads: read 1 contains a cell barcode (12 bases) and a UMI (8 bases); read 2 contains the sequence of the transcript.
Data preprocessing and read alignment were implemented by using the Drop-seq core computational program (https://github.com/broadinstitute/Drop-seq/releases/tag/v2.3.0).
Briefly, the program extracted cell barcodes and UMIs from raw reads, filtered out low-quality reads, trimmed unusable read 2 sequences, performed the read alignment, added gene tags, repaired cell barcodes, and generated a digital gene expression matrix.
Reads filtration aimed to remove reads where the cell barcode or UMI had at least 1 base with quality lower than 10. At least five contiguous bases of the adapter and at least six contiguous bases of A with no mismatch were hard clipped off the read 2. After trimming, the reads were aligned to the hg19 or hg19_mm10 reference genome using STAR version 2.7.1a33 with default parameters. Thus, a gene tag “GE” was added to each read and multi-mapping reads were discarded.
Cell barcodes correlation, including detection and repairing of substitution errors and indel synthesis errors, were then carried out. UMIs for a gene with one edit distance were merged together. The total number of unique UMIs for each gene were counted as the number of transcripts of that gene for a given cell to generate digital gene expression.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: digital gene expression and sample annotation in text file

organism:
Homo sapiens
Mus musculus

source_name: Species Mixing 4 (K562 + 3T3)

extract_protocol:
Cells were lyzed and mRNA captured on barcoded beads were reverse transcripted and amplified using PCR.
RNA libraries were prepared for sequencing using standard TruePrep® DNA Library Prep Kit V2 for Illumina® (Vazyme, cat#TD502) according to the manufacturer’s protocols

treatment_protocol: Drug-treated group was treated by vorinostat at 0, 0.1, 1, or 10 µM for 36 hours

value: K562 and NIH/3T3

tag: treatment


title: Well-paired-seq_species-mixing_sample1

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample1_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample1_mouse_raw_dge.txt.gz

source_name: Species Mixing 1 (K562 + 3T3)


title: Well-paired-seq_species-mixing_sample3

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample3_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample3_mouse_raw_dge.txt.gz

source_name: Species Mixing 3 (K562 + 3T3)


title: Well-paired-seq_species-mixing_sample5

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample5_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample5_mouse_raw_dge.txt.gz

source_name: Species Mixing 5 (K562 + 3T3)


title: Well-paired-seq_species-mixing_sample6

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample6_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample6_mouse_raw_dge.txt.gz

source_name: Species Mixing 6 (K562 + 3T3)


title: Patient R8


title: Patient R5


title: Patient R6


title: Patient R7


title: Well-paired-seq_species-mixing_sample2

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample2_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample2_mouse_raw_dge.txt.gz

source_name: Species Mixing 2 (K562 + 3T3)


title: S1_scramble


title: Well-paired-seq_species-mixing_sample7

description:
the human/mouse gene expression matirx (txt file)
Well-paired-seq_species-mixing_sample7_human_raw_dge.txt.gz
Well-paired-seq_species-mixing_sample7_mouse_raw_dge.txt.gz

source_name: Species Mixing 7 (K562 + 3T3)


title: Patient R10


title: Patient R9


title: Whole glucan particles (WGP) treated pancreatic myeloid cells, replicate 3

city: Louisville

first: Eric

middle: Christian

last: Rouchka

state: Kentucky

address: 522 East Gray Street

department: Biochemistry and Molecular Genetics

institute: University of Louisville

data_processing:
Fastq sequences were aligned to the GRCm38.p6 mouse mm10 genome using STAR v2.6 and ENSEMBL93 transcripts.
Gene counts were calculated using HTSeq v0.10.0 with htseq-count and parameters --stranded=forward --mode=intersection-nonempty
Differential gene expression was performed using DESeq2 with a q-value cutoff of 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited htseq raw transcript counts

source_name: pancreatic myeloid cells

extract_protocol:
RNAs were extracted using a QIAGEN RNAeasy Kit (QIAGEN).
Libraries were prepared using the Universal Plus mRNA-Seq with NuQuant (NuGEN Cat# 0508).

treatment_protocol: 7 days following administration of PBS or WGP IP, pancreata were harvested, processed into a single cell suspension, stained for viability, CD45 and CD11b, and sorted using a FACS Aria III. Samples were prepared in triplicate for each experimental group. Once these myeloid cells were isolated, cells were washed 2x with ice cold PBS and then lysed with Trizol (Invitrogen).

value: pancreatic myeloid cells

value: WGP treated


title: WGP Treated, 3 Day

data_processing:
Samples were processed using the 10x Genomics CellRanger Suite Version 3.1.0.
Raw bcl files were demultiplexed into fastq files using cellranger mkfastq with a base mask of Y28, I8, Y125.
Gene counts were determined using cellranger count with the mouse mm10 transcriptome (v3.0.0) and 5000 expected cells.
Further analysis was performed using a custom R pipeline utilizing Seurat, DropletUtils, and other single cell sequencing packages.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes-- gzip cell barcode file from cellranger count
Supplementary_files_format_and_content: features -- gzip feature (gene) file from cellranger count
Supplementary_files_format_and_content: matrix -- gzip count matrix from cell ranger count

source_name: pancreas CD45+ cells

extract_protocol:
Cells were run through a cell sorter, where only live CD45+ cells were acquired.  Cells were washed with 400ug/mL BSA 2x and then counted.
Libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 3' GEM, Library and Gel Bead Kit v3.1, 4 rxns (PN-1000128); Next GEM Chip G Single Cell Kit, 16 rxns (PN-1000127); and i7 Multiplex Kit, 96 rxns (PN_120262).  Libraries were prepared using the manufacturers instructions following the Chromium Next GEM Single Cell 3' Reagents Kits v3.1 User Guide CG000204 Rev D. Samples were barcoded with Chromium Shared Sample Indexes.
scRNA-Seq

treatment_protocol: The pancreas of the mice were harvested, digested, and stained with viability dye and an anti-CD45 fluorescent antibody.

value: pancreas CD45+ cells

value: WGP

tag: time

value: 3 days prior to euthanization


title: WGP Treated, 7 Day

value: 7 days prior to euthanization


title: PBS control pancreatic myeloid cells, replicate 3

value: PBS control


title: PBS control pancreatic myeloid cells, replicate 1


title: Whole glucan particles (WGP) treated pancreatic myeloid cells, replicate 2


title: mFAMIN_KO_4

city: Cambridge

first: Gavin

last: Sewell

state: Cambridgeshire

address: Puddicombe Way

department: Jeffrey Cheah Biomedical Centre, University of Cambridge

country: United Kingdom

institute: Cambridge Institute of Therapeutic Immunology and Infectious Disease

data_processing:
FastQ files were quality-checked (FastQC) and any residual adaptor sequences were removed (TrimGalore).
Reads were then aligned to the reference genome (mm10, UCSC) using HISAT2.
Differential gene expression analysis was performed on read count files using the limma package in R with the Voom transformation.
Genome_build: mm10
Supplementary_files_format_and_content: cpm data

source_name: BMDCs (cDC1 subset)

growth_protocol: Bone marrow-derived dendritic cells from 6-10 week old Faminp.254I, Faminp.254V and Faminp.284R mice (as described in Cader et. al 2016) were cultured in the presence of 100ng/mL Flt3L for 9 days. cDC1 subsets were separated by negative selection using anti-PE microbeads (Miltenyi, 130-048-80) following labelling with SIRP?-PE antibody (Biolegend, 144011) and B220 (Biolegend, 103207).

extract_protocol:
Total RNA was extracted using the Rneasy Mini Kit (QIAGEN, 74104) in accordance with the manufacturer's instructions.
RNA libraries were prepared for sequencing using the TruSeq stranded mRNA library prep kit (Illumina, 20020594), using 400ng total RNA per sample in accordance with the manufacturer's instructions.

treatment_protocol: Isolated cDC1 cells were stimulated with 1mg/mL LPS (O111:B4, Sigma, LPS25) for 18 hours prior to extraction.

value: Bone marrow-derived dendritic cells

tag: age

value: 6-10 week old


title: mFAMIN_WT_4

tag: cell type


title: mFAMIN_KO_3


title: mFAMIN_KO_2


title: mFAMIN_KO_1


title: PBS control pancreatic myeloid cells, replicate 2


title: mFAMIN_WT_3


title: mFAMIN_WT_2


title: mFAMIN_WT_1


title: PBS Treated

value: PBS


title: Whole glucan particles (WGP) treated pancreatic myeloid cells, replicate 1


title: KO_1_SS_S5

data_processing:
Sequencing of libraries was performed using an Illumina NextSeq 500 platform with NextSeq 500-Mid Output kit generating 1x75bp reads
Quality control of the reads was performed using FastQC v0.11.4.
Reads were trimmed using TrimGalore v0.4.1.
Mapping of reads was performed using STAR v2.5.2a. using Ensembl Mus_musculus.GRCm38 (release 84) reference genome
Differential Gene Expression Analysis assessed using the counted reads and the R package edgeR version 3.16.5 (R version 3.4.1).
Genome_build: Mus_musculus.GRCm38 - mm10

source_name: T cells

growth_protocol: CD8+ T cells were isolated from spleens and lymph nodes of OT-I;Rag–/– mice, stimulated with anti-CD3 and CD28 in the presence of supernatant obtained from Famin-/- or Famin+/+ dendritic cells for 2 hours

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (QIAGEN, 74104) in accordance with the manufacturer's instructions
Libraries were prepared using TruSeq stranded mRNA library prep kit (Illumina, 20020594)

value: OT-I;Rag-/-

value: CD8+ T cells

value: Famin-/- supernatant-primed


title: KO_4_SS_S8


title: WT_3_SS_S3

value: Famin+/+ supernatant-primed


title: KO_2_SS_S6


title: KO_3_SS_S7


title: WT_2_SS_S2


title: WT_1_SS_S1


title: Liver_S2_11

city: Gainesville

first: Peter

middle: James

last: Hansen

state: FL

address: 2250 SW Shealy Drive

department: Animal Sciences

institute: University of Florida

data_processing:
Trimming sequences: Fastq files were trimmed of adapters and low quality sequence with Trimmomatric v0.33. Samples prepped with the Takara Bio kit were also trimmed of the first 3 bp  of the read.
Aligning sequences: Trimmed reads were mapped to the Bos taurus genome (ARS-UCD1.2) using HiSat2 (v2.1.0).
Quantifying gene features: Gene features were quantified with featureCounts from the subread package with RF strand specificity.
Differential Expression Analysis: Significant DEGs were determined using the edgeR package in R.
Genome_build: Bos taurus (ARS-UCD1.2)
Supplementary_files_format_and_content: Raw per-gene expression counts file contains all of the samples prepared with each protocol (TruSeq or SMARTer Takara Pico Mammalian) and are in tab-delimited text format

organism: Bos taurus

source_name: Liver

extract_protocol:
RNeasy Plus Universal kit
TruSeq Stranded mRNA sample prep or SMARTer Stranded Total RNA-Seq Pico Mammalian Kit

tag: tissue

value: Liver

tag: breed

value: Senepol

tag: mrna selection protocol

value: SMARTer Stranded Total RNA-Seq Pico Mammalian Kit v2 from Takara Bio


title: WT_4_SS_S4

tag: strain

tag: genotype


title: Liver_S1_5


title: p254I_5

description: Experiment 2

growth_protocol: Bone marrow-derived dendritic cells from 6-10 week old Faminp.254I, Faminp.254V and Faminp.284R mice (as described in Cader et. al 2016) were cultured in the presence of 100ng/mL Flt3L for 9 days. cDC1 subsets were separated by negative selection using anti-PE microbeads (Miltenyi, 130-048-80) following labelling with SIRPα-PE antibody (Biolegend, 144011) and B220 (Biolegend, 103207).


title: p284R_1

description: Experiment 1


title: p254V_2

description: Experiment 1

data_processing:
FastQ files were quality-checked (FastQC) and any residual adaptor sequences were removed (TrimGalore).
Reads were then aligned to the reference genome (mm10, UCSC) using HISAT2.
Differential gene expression analysis was performed on read count files using the limma package in R with the Voom transformation.
Batch normalisation was conducted using sva package in R
Genome_build: mm10
Supplementary_files_format_and_content: cpm data and batch-corrected cpm data


title: p254I_1

description: Experiment 1


title: p254V_6


title: p284R_3

description: Experiment 2


title: p284R_2

description: Experiment 1


title: p284R_5


title: p254I_2

description: Experiment 1


title: p254I_4

description: Experiment 2


title: p254I_3


title: p254V_1

description: Experiment 1


title: p254V_3

description: Experiment 1


title: p284R_4

description: Experiment 2


title: p254V_5


title: Liver_S1_4


title: Liver_S1_3


title: p254V_4

description: Experiment 2


title: Liver_S2_5


title: Liver_S2_7


title: Liver_S1_2


title: 2014-635_M2-4_Dyak_Caf_in_Dmel

city: Chicago

first: Manyuan

last: Long

state: IL

address: 5801 S. Ellis Ave.

institute: University of Chicago

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

organism: Drosophila melanogaster

source_name: Whole body

extract_protocol:
Chromatin from whole flies (150 flies per technical replicate) was isolated according to standard modENCODE protocols using formaldehyde as the crosslinking agent and sonication. Immunpreciptation was performed using anti-FLAG antibody (Sigma) and protein G beads (GE Healthcare)
Libraries for sequencing were prepared using the Ovation Ultra-Low Library System (NuGEN) and sequenced on the Illumina HiSeq platform by IGSB at The University of Chicago

value: Whole body

tag: chip antibody

value: anti-FLAG (Sigma, polyclonal)


title: Liver_S2_8


title: 2014-674_M2-3_Dyak_Caf_in_Dmel


title: 2014-636_M2-INPUT_Dyak_Caf_in_Dmel

value: NONE (Input Control)


title: Liver_S2_4


title: 2014-673_M2-2_Dyak_Caf_in_Dmel


title: Liver_S2_10


title: Liver_S2_9


title: Liver_S2_2


title: 2014-672_M2-1_Dyak_Caf_in_Dmel


title: 2014-1008_A1_INPUT_Dsim_Zeus


title: 2014-633_G1-1_Dmel_Zeus_in_Dmel


title: 2014-670_G1-2_Dmel_Zeus_in_Dmel


title: Liver_S2_1


title: Liver_S2_3


title: 2014-671_G1-INPUT_Dmel_Zeus_in_Dmel


title: 2014-1006_A1_Dsim_Zeus_in_Dmel


title: 2014-1005_A1_Dsim_Zeus_in_Dmel


title: Liver_FREE_BLANCO_1

description:
Liver_Raw_Counts.txt
Liver_CPMnormalized_Counts.txt
DEG_Results_Liver_TruSeq_slick_vs_free.txt

tag: sire

value: BLANCO

value: FREE

value: TruSeq Stranded mRNA Sample Preparation


title: Liver_S1_1


title: Liver_FREE_RANGER_5

value: RANGER


title: Liver_SLICK_BLANCO_4

value: SLICK


title: RNA-seq Auixn+ rep6

city: Seoul

first: Hyoung-Pyo

last: Kim

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

description:
Auxin Inducible Degron cell
M_IAA3

data_processing:
sequnced using Illumina HiSeq2500 platform
Paired-end sequenciong reads were trimmed using TrimGalore v0.6.4 with default parameters (version 0.6.4).
Reads were mapped to the hg19 human reference genome using STAR v2.6.0a with parameters --sjdbOverhang 100 --chimSegMin 20 --quantMode TranscriptomeSAM --twopassMode Basic.
Gene expressions were quantified using RSEM v1.2.31 with parameters --paired-end --estimated-rspd.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM gene count

source_name: HCT116 cells

growth_protocol: CTCF degron cells were cultured in RPMI1640 medium supplemented with 10% FBS, 100U/ml Penicillin and 100μg/ml Streptomycin.

extract_protocol:
RNA was harvested using Trizol reagent. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA.
RNA libraries were prepared for sequencing using NEBNext RNA Library prep kit protocols. Libraries were amplified using NEBNext Multiplex Oligos and were purified using SPRI AMPureXP beads.

treatment_protocol: For inducing auxin-inducible degron system, 500μM 3-indole acetic acid was treated for 6 hours.

value: human colorectal cancer cells

value: Auxin


title: RNA-seq Auixn+ rep5

description:
Auxin Inducible Degron cell
M_IAA2


title: Liver_S2_6


title: 2014-1004-A1_Dsim_Zeus_in_Dmel


title: Liver_SLICK_BLANCO_3


title: Liver_FREE_RANGER_4


title: RNA-seq Auixn+ rep4

description:
Auxin Inducible Degron cell
M_IAA1


title: Liver_SLICK_RANGER_5


title: RNA-seq Auixn- rep6

description:
Auxin Inducible Degron cell
M_Con3

value: untreated


title: Liver_SLICK_BLANCO_5


title: Liver_FREE_RANGER_7


title: 2014-1007_A1_Dsim_Zeus_in_Dmel


title: Liver_FREE_RANGER_6


title: Liver_SLICK_RANGER_4


title: RNA-seq Auixn- rep5

description:
Auxin Inducible Degron cell
M_Con2


title: Liver_FREE_RANGER_3


title: Liver_SLICK_RANGER_3


title: RNA-seq Auixn- rep4

description:
Auxin Inducible Degron cell
M_Con1


title: RNA-seq Auixn+ rep2

description:
Auxin Inducible Degron cell
I_IAA2


title: RNA-seq Auixn+ rep1

description:
Auxin Inducible Degron cell
I_IAA1


title: Liver_FREE_RANGER_1


title: Liver_FREE_RANGER_2


title: RNA-seq Auixn- rep3

description:
Auxin Inducible Degron cell
I_Con3


title: Liver_SLICK_BLANCO_2


title: RNA-seq Auixn- rep2

description:
Auxin Inducible Degron cell
I_Con2


title: Liver_SLICK_RANGER_1


title: RNA-seq Auixn- rep1

description:
Auxin Inducible Degron cell
I_Con1


title: Liver_SLICK_BLANCO_1


title: RNA Pol. II HiChIP Auxin+ rep2

description: Auxin Inducible Degron cell

data_processing:
sequnced using Illumina HiSeq2500 platform
Raw reads were processed using HiC-Pro pipeline v2.11.4
Genome_build: hg19
Supplementary_files_format_and_content: hic contaning validpairs

extract_protocol:
Fixed chromatin was digested using DpnⅡ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, DNA was sonicated and immunoprecipitated with antibody. Reverse-crosslinked DNA was captured with Streptavidin C-1 beads.
Libraries were prepared using Nextera DNA library preparation kit according to manufacturer's instructions. DNA was amplified using Nextera PCR primers. Libraries were purified using SPRI AMPureXP beads and were paired-end sequenced on Illumina HiSeq2500 platform
hic contaning validpairs

value: Phospho-Rpb1 CTD (CST, Cat# 13523)


title: Well-paired-seq_ drug_treated_cells_1_uM_2

description:
the gene expression matirx and sample annotation (txt file)
Well-paired-seq_drug_treated_cells_raw_dge.txt.gz
drug_treatment_sample_annotation.txt.gz

source_name: lung adenocarcinoma cells

value: exposed to vorinostat at 1 µM for 36 hours


title: RNA Pol. II HiChIP Auxin- rep2

description: Auxin Inducible Degron cell


title: Well-paired-seq_ drug_treated_cells_10_uM_2

value: exposed to vorinostat at 10 µM for 36 hours


title: Well-paired-seq_ drug_treated_cells_0.1_uM_2

value: exposed to vorinostat at 0.1 µM for 36 hours


title: RNA Pol. II HiChIP Auxin+ rep1

description: Auxin Inducible Degron cell


title: RNA Pol. II HiChIP Auxin- rep1

description: Auxin Inducible Degron cell


title: Well-paired-seq_ drug_treated_cells_0_uM_2

value: exposed to vorinostat at 0 µM for 36 hours


title: HiC Auxin+ rep2

description: Auxin Inducible Degron cell

extract_protocol:
Fixed chromatin was digested using DpnⅡ enzyme, followed by biotin incorporation with Biotin-14-dATP. After DNA ligation, DNA was sonicated and captured with Streptavidin C-1 beads.
Libraries were prepared using Nextera DNA library preparation kit according to manufacturer's instructions. DNA was amplified using Nextera PCR primers. Libraries were purified using SPRI AMPureXP beads and were paired-end sequenced on Illumina HiSeq2500 platform


title: HiC Auxin- rep2

description: Auxin Inducible Degron cell


title: Well-paired-seq_ drug_treated_cells_10_uM_1


title: Well-paired-seq_ drug_treated_cells_1_uM_1


title: HiC Auxin- rep1

description: Auxin Inducible Degron cell


title: HiC Auxin+ rep1

description: Auxin Inducible Degron cell


title: Well-paired-seq_ drug_treated_cells_0.1_uM_1


title: Input DNA Auxin+ rep2

description: Auxin Inducible Degron cell

data_processing:
sequnced using Illumina HiSeq2500 platform
Raw ChIP-seq reads were trimmed for adaptor sequence, and aligned to the hg19 genome assembly using bwa mem v0.7.17 with default parameters
aligned files were filtered for MAPQ > 30 and sorting, deduplication were processed using PICARD  v2.18.23
peaks were called using macs2 v2.2.7.1 with the following setting: -g hs --nomodel -c $INPUT_BAM
normalized enrichment file, bigwig files were generated applying CPM normalization using deeptools v3.4.3
Genome_build: hg19
Supplementary_files_format_and_content: Peak, CPM normalized bigwig

extract_protocol:
Fixed chromatin was sonicated and immunoprecipitated with antibody.
Libraries were prepared using Nextera DNA library preparation kit according to manufacturer's instructions. DNA was amplified using Nextera PCR primers. Libraries were purified using SPRI AMPureXP beads and were paired-end sequenced on Illumina HiSeq2500 platform


title: Well-paired-seq_ drug_treated_cells_0_uM_1


title: Well-paired-seq_ PBMC_2

description:
the gene expression matirx and sample annotation (txt file)
Well-paired-seq_PBMC_raw_dge.txt.gz
PBMC_sample_annotation.txt.gz

source_name: PBMC


title: RNA-seq Auixn+ rep3

description:
Auxin Inducible Degron cell
I_IAA3


title: Input DNA Auxin- rep1

description: Auxin Inducible Degron cell


title: Well-paired-seq_ PBMC_1


title: Input DNA Auxin+ rep1

description: Auxin Inducible Degron cell


title: Well-paired-seq_ five human lung adenocarcinoma cell lines_1

description:
the gene expression matirx and sample annotation (txt file)
Well-paired-seq_five_human_lung_adenocarcinoma_cell_lines_raw_dge.txt.gz
human_lung_cell_lines_sample_annotation.txt.gz


title: Input DNA Auxin- rep2

description: Auxin Inducible Degron cell


title: mixed-sample (non-demultiplexed)

city: Memphis

first: Jeremy

middle: Chase

last: Crawford

state: TN

address: MS 221, 262 Danny Thomas Place

department: Department of Host-Microbe Interactions

institute: St. Jude Children's Research Hospital

data_processing:
Bulk TCR repertoire data were demultiplexed and assembled into the UMI consensuses with migec (v. 1.2.7; with collision filter and force-overseq parameters set to 1).
V and J-segment alignment, CDR3 identification, and assembly of reads into clonotypes were performed with MiXCR (v. 3.0.3) with default parameters.
MiXCR outputs were converted to VDJtools format using the VDJtools Convert routine.
Genome_build: NOT PROVIDED
Supplementary_files_format_and_content: clonotype frequency estimates

source_name: lymph node fine needle aspirate

extract_protocol:
RNA was isolated using Trizol reagent (Invitrogen) according to the manufacturer's protocol. All RNA was used for cDNA synthesis with SmartScribe kit (Takara), using template switch oligonucleotide and primers specific for TCRalpha and TCRbeta constant segments. cDNA was amplified in two rounds of PCR using Q5 high-fidelity polymerase (NEB).
KAPA HyperPrep kit (Roche)

value: lymph node

value: T follicular helper cells

tag: cell markers

tag: timepoint (days after vaccination)


title: H3K27Ac Auxin+ rep1

description: Auxin Inducible Degron cell

value: H3K27Ac (Abcam, Cat# ab4729)


title: H3K27Ac Auxin- rep2

description: Auxin Inducible Degron cell


title: Liver_SLICK_RANGER_2

value: Liver

value: Senepol


title: Pinkie Strain normal cornea-F4

city: Houston

first: JEHAN

last: ALAM

state: TEXAS

address: Baylor One Plaza

institute: Baylor College of Medicine

hyb_protocol: One hundred nanograms of total RNA were hybridized with the Nanostring Technologies nCounter Mouse Immunology Panel and Nanostring Technologies nCounter Gene Expression Mouse Myeloid Innate Immunity Panel codeset (NS_MM_Myeloid_V2.0+Pls) containing 770 Unique pairs of 35-50bp reporter probes, 12 custom probe pairs and biotin-labeled capture probes, including internal refereance controls. overnight hybridization occured for 20hours at 65C.

scan_protocol: The cartridge containing immobilized sample was transferred to the nCounter Digital Analyzer (Software v3.0.1.4) and scanned at 555 field of view (FOV).

data_processing:
Data was processed using ROSALIND (https://app.rosalind.bio)
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library3, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro4, NCBI5, MSigDB6,7, REACTOME8, WikiPathways9. Enrichment was calculated relative to a set of background genes relevant for the experiment.

source_name: whole cornea

label_protocol: The samples were labeled according to the condition

growth_protocol: C57B/6 Mice were purchased from Jackson lab AND Pinkie mice were inhouse breed and maintained at BCM animal facilities until use

extract_protocol:
Whole cornea was dissolved into RNA lysis buffer
Whole cornea was surgically removed or the in vitro cultured Immune cells were spun down and the RNA was extracted using the standard protocol provided by the manufacturer, we use the Qiagen RNA preparation kit

treatment_protocol: Mice colonies were maintained at Baylor college of Medicne vivarium under the standard protocol

value: Pinkie

tag: experimental group

value: Pinkie Mouse Normal cornea

tag: Sex

value: Female

value: whole cornea


title: Pinkie Strain ulcerated cornea-F2

value: Pinkie Mouse Ulcerated cornea


title: Pinkie Strain ulcerated cornea-F3


title: Pinkie Strain ulcerated cornea-F1


title: SW480_CD44v6_2

city: Rotterdam

first: Mathijs

last: Verhagen

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus Medical Center

description: Sample 12_SW480_CD44v6 OE_2

data_processing:
Paired-end reads of 100 bases were trimmed by removing adapter sequences, and quality check was performed using Fastp (v.0.21.0).
The reads were mapped to the human reference genome (hg19) with the RNA-seq aligner STAR (v2.7.9a).
Duplicates reads were marked with sambamba (v0.8.0).
Reads were counted with subread (v2.0.3) featureCounts using the GENCODE v35 annotation.
Downstream analysis was done with DESeq2 (v1.30.1), and counts were processed with a variance stabilizing transformation (VST)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Ensemble Gene Ids, VST values and Hgnc symbols

source_name: colon cancer cell line

growth_protocol: HCT116 and SW480 colon cancer cell lines were grown in standard culture medium.

extract_protocol:
RNA was harvested using Trizol reagent.
Paired end RNA-Seq was performed at the BGI (Shenzhen, China) according to manufacturer’s DNBSEQ protcol. Samples were sequenced to a depth of 50-60M reads.

treatment_protocol: Cells were transfected with pcDNA-CD44s/CD44v6 plasmids, and selected was done with Geneticin

value: colon

tag: cell line

value: CD44v6 OE


title: H3K27Ac Auxin- rep1

description: Auxin Inducible Degron cell

value: human colorectal cancer cells

value: untreated


title: Pinkie Strain normal cornea-F3


title: RNA Pol. II Auxin+ rep2

description: Auxin Inducible Degron cell

value: Auxin

value: Phospho-Rpb1 CTD (CST, Cat# 13523)


title: SW480_CD44v6_1

description: Sample 11_SW480_CD44v6 OE_1


title: E18.5 ureters, Rbpj-cKO vs control, rep2

city: Hannover

first: Andreas

last: Kispert

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies).

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).

data_processing: Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates were averaged using the geometric mean of ProcessedSignal (PS) values (for each channel independently) to retrieve one resulting value per non-control probe, sample, and channel. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed at 10 normalized PS units. All of those measurements that fell below this intensity cutoff were substituted by the respective surrogate value of 10.

source_name: control

label_protocol: Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E18.5 embryos.

value: NMRI

value: Rbpj(fl/?)

tag: gender

value: female

tag: developmental stage

value: ureter

source_name: Rbpj-cKO


title: Pinkie Strain normal cornea-F2


title: SW480_CD44std_2

description: Sample 10_SW480_CD44s OE_2

tag: treatment

value: CD44s OE


title: RNA Pol. II Auxin+ rep1

description: Auxin Inducible Degron cell


title: RNA Pol. II Auxin- rep2

description: Auxin Inducible Degron cell


title: E18.5 ureters, Rbpj-cKO vs control, rep1

value: male


title: H3K27Ac Auxin+ rep2

description: Auxin Inducible Degron cell

value: H3K27Ac (Abcam, Cat# ab4729)


title: C57B/6 normal cornea-F4

value: C57B/6 Mouse Normal cornea

tag: age


title: C57B/6 normal cornea-F3

value: Female


title: SW480_CD44std_1

description: Sample 9_SW480_CD44s OE_1


title: Pinkie Strain normal cornea-F1

value: Pinkie

value: Pinkie Mouse Normal cornea

value: whole cornea


title: C57B/6 normal cornea-F2


title: SW480_Parental_2

description: Sample 8_SW480_Parental_2

value: colon

value: parental


title: C57B/6 normal cornea-F1


title: RNA Pol. II Auxin- rep1

description: Auxin Inducible Degron cell

tag: cell type

value: human colorectal cancer cells

value: untreated


title: SW480_Parental_1

description: Sample 7_SW480_Parental_1

tag: tissue


title: SMC1 Auxin+ rep2

description: Auxin Inducible Degron cell

value: Auxin

value: SMC1 (Bethyl lab, Cat# A300-055A)


title: HCT116_CD44v6_2

description: Sample 6_HCT116_CD44v6 OE_2

value: CD44v6 OE


title: SMC1 Auxin- rep2

description: Auxin Inducible Degron cell


title: HCT116_CD44v6_1

description: Sample 5_HCT116_CD44v6 OE_1


title: SMC1 Auxin+ rep1

description: Auxin Inducible Degron cell


title: IRTC2

city: Barcelona

first: Antoni

last: Celià-Terrassa

address: Carrer Dr.Aiguader 88

country: Spain

institute: IMIM

data_processing:
Mapping of raw reads with STAR to mm10 genome (gencode release M24 annotation)
Count of reads per gene and per sample with STAR option --quantMode TranscriptomeSAM GeneCounts (keep 4th column as the data is reverse stranded)
DESeq2 used for normalization and differential expression analysis.
Genome_build: GRMm38/mm10
Supplementary_files_format_and_content: Tab-separated file containing the DESeq2-normalized STAR read counts per gene and per sample.

source_name: control tumor sample 2

growth_protocol: Tumors were mechanically and enzymatically digested at 37ºC for 2 hours in Mammary Epithelial Cell Growth Medium (MEGM)4 (see Supplementary Table 1) supplemented with murine Hyaluronidase (Merck, CAS 37326-33-3) and type I Collagenase (Merck, C2674-500mg), followed by a short incubation with 5 mg/mL dispase (Merck, D4693) and 0,1 mg/mL DNase I (Merck, D5025-150). Cells were harvested in regular DMEM media previous to the RNA obtention

extract_protocol:
RNA was extracted using  Qiagen RNA extraction Kit following the manufacturer's instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Anti-PD-L1 in vivo

value: Balb/c

value: 4TO7 from control tumors

value: Untreated


title: HCT116_CD44std_2

description: Sample 4_HCT116_CD44s OE_2

value: CD44s OE


title: IRT2

source_name: resistant to immunotherapy tumor sample 2

value: 4TO7 from resistant to immunotherapy tumors


title: HCT116_CD44std_1

description: Sample 3_HCT116_CD44s OE_1


title: SMC1 Auxin- rep1

description: Auxin Inducible Degron cell


title: IRT1

source_name: resistant to immunotherapy tumor sample 1


title: HCT116_Parental_2

description: Sample 2_HCT116_Parental_2


title: P4 Ureter,  Rbpj-cKO vs control, rep2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended for 4-plex Microarray-Slides in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent Technologies), except that 2500ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing:
Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.
Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.
For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:
normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)
Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.
Fold change values always represent Rbpj-cKO / control. Measurements of control features were removed.

source_name: control 2

label_protocol: 1000ng of total RNA were used as input. Synthesis of AlexaFluor555- or AlexaFluor647- (Invitrogen) labeled cRNA was performed with the ‘Amino Allyl MessageAmp™ II aRNA Amplification Kit’ (#AM1753, Life Technologies) according to the manufacturer’s recommendations, except that the proportion of aminoallyl-UTP/UTP was adjusted to 1+11 (instead of 1+1) and that reaction volumes were halved.

value: NMRI

value: male

value: Ureter

source_name: Rbpj-cKO 2


title: E13.5 ureters, Fgfr2cKO vs control, rep2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2500ng of labeled cRNA were used for hybridization.

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file ‘GE2_107_Sep09.xml’.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

label_protocol: 150ng of total RNA were used as input. Synthesis of Cy3- or Cy5-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit, Two Color’ (#5190-2944, Agilent Technologies) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E13.5 embryos.


title: CTCF Auxin- rep2

description: Auxin Inducible Degron cell

value: CTCF (CST, Cat# 2899)


title: P4 Ureter,  Rbpj-cKO vs control, rep1

source_name: control 1

value: female

source_name: Rbpj-cKO 1


title: HICHIP_DOX_rep1

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

data_processing:
Library strategy: HiChIP-seq
ChIP-seq data was aligned to hg19 using BWA-mem
HiChIP data processed via HiChIP Loop Calling and FitHiChIP
RNA-seq data were analyzed with kallisto using hg19
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples
Supplementary_files_format_and_content: peak text files (ChIP-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for Chip-seq. Bed for HiChIP

source_name: SCi-NCCIT (+doxy)

growth_protocol:
A dCas9-KRAB fusion piggyBac transposon and two sgRNAs, cloned into a piggyBac transposon, targeting ~80% of all SVAs were subsequently transfected into NCCIT cells using Fugene (Promega) 6:1 ratio (SCi-NCCITs).
The SCi-NCCITs were maintained in ATCC-formulated RPMI media supplemented with 10% tet-free FBS, 1% L-glutamine, 1ug/mL puromycin, and 400ug/mL
The SCi-NCCITs were treated with 2ug/mL doxycycline for 72 hours for repressive dCas9-KRAB induction

extract_protocol: Barcoded libraries were made with Illumina Nextera Library Prep Kit and AMPure XP beads were used for a double size selection. The DNA was sequenced on an Illumina NextSeq500 producing 100 bp paired-end reads.

tag: cell-type/cell line

tag: antibodies

value: YY1 Cell Signaling Technology D5D9Z/46395S

tag: doxycycline treatment

value: doxy+


title: NCCIT_SVA_YY1_NO_DOXY_rep2

data_processing:
ChIP-seq data was aligned to hg19 using BWA-mem
HiChIP data processed via HiChIP Loop Calling and FitHiChIP
RNA-seq data were analyzed with kallisto using hg19
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Genome_build: hg19 for Homo sapiens samples
Supplementary_files_format_and_content: peak text files (ChIP-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for Chip-seq. Bed for HiChIP

source_name: SCi-NCCIT (- doxy)

extract_protocol: Barcoded libraries were made with NEB ULTRA II DNA Library Prep Kit for Illumina, and sequenced on Illumina NovaSeq6000, producing 100x100 PE reads

value: doxy-


title: NCCIT_SVA_YY1_DOXY_rep2


title: M6583: E14.5 ureters, Gata6cKO vs control, rep1

treatment_protocol: Ureters were mechanically dissected from E14.5 embryos.

tag: strain

tag: genotype

value: ureter

source_name: Gata6cKO 1


title: E13.5 ureters, Fgfr2cKO vs control, rep1


title: M6584: E14.5 ureters, Gata6cKO vs control, rep2

source_name: Gata6cKO 2


title: CTCF Auxin+ rep1

description: Auxin Inducible Degron cell

source_name: HCT116 cells

value: human colorectal cancer cells

value: Auxin

tag: chip antibody


title: E14.5 ureters, Rbpj-cKO vs control, rep2

value: Rbpj(fl/?)


title: NCCIT_SVA_plusDoxy_Rep2

extract_protocol:
Cells were lysed in Tri-reagent (Zymo research) and total RNA was extracted using Quick-RNA Miniprep kit (Zymo research).
RNA libraries were prepared using NEBNext® Poly(A) mRNA Magnetic Isolation Module, NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® according to the manufacturer’s instructions (New England Biolabs). 1 μg of total RNA input was used for each library


title: HICHIP_no_DOX_rep3


title: E14.5 ureters, Rbpj-cKO vs control, rep1


title: NCCIT_SVA_plusDoxy_Rep3


title: NCCIT_SVA_plusDoxy_Rep1


title: IRTC1

source_name: control tumor sample 1

value: Balb/c


title: CTCF Auxin+ rep2

description: Auxin Inducible Degron cell


title: HICHIP_no_DOX_rep2


title: NCCIT_SVA_OCT4_NO_DOXY

value: OCT4 Abcam ab181557


title: Pinkie Strain ulcerated cornea-F4

source_name: whole cornea

value: Pinkie

value: Pinkie Mouse Ulcerated cornea

value: Female

value: whole cornea


title: NCCIT_SVA_OCT4_DOXY


title: Input_rep2

first: Cristina

middle: Lopez

last: Rodriguez

address: Carrer Dr. Aiguader, 88

institute: UPF

data_processing:
Reads were aligned with the bowtie2 mapper v. 2.3.2 to release 27 of the Homo sapiens Gencode version of the genome (GRCh38/hg38 assembly)
The quality of the mapped files (BAM format) was checked with QualiMap v.2.2.1.
Peaks on individual samples were identified using the MACS2 program v.2.1.1.20160309 (narrow peaks with q-value < 0.1 were initially selected).
The overlap of peaks across biological replicates was retrieved using the bedtools v.2.26.0 suite of tools.
Genome_build: GRCh38

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

growth_protocol: Cells were grown in a 150 mm2 plates in optimal conditions up to 80% of confluence. Cells were culture in normal regular media (DMEM supplemented with 10% FBS, glutamine, pen/strepto)

extract_protocol:
Crosslink of proteins-chromatin was performed with formaldehyde solution. Crosslink reaction was stopped with glycine. Cells were lysated and sonicated for 7 cycles of 30'' on 30'' off in a Bioruptor Sonicator. Chromating was co-immunoprecipitated using anti-HA antibody (abcam, AB9110).
Libraries were prepared according to Illumina's instructions accompanying and were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

tag: antibody


title: HICHIP_no_DOX_rep1


title: HCT116_Parental_1

description: Sample 1_HCT116_Parental_1

source_name: colon cancer cell line

value: colon

value: parental


title: NCCIT_SVA_minusDoxy_Rep2


title: HICHIP_DOX_rep3


title: NCCIT_SVA_minusDoxy_Rep1


title: Well-paired-seq_ five human lung adenocarcinoma cell lines_2

data_processing:
Well-paired-seq sequencing libraries produced paired-end reads: read 1 contains a cell barcode (12 bases) and a UMI (8 bases); read 2 contains the sequence of the transcript.
Data preprocessing and read alignment were implemented by using the Drop-seq core computational program (https://github.com/broadinstitute/Drop-seq/releases/tag/v2.3.0).
Briefly, the program extracted cell barcodes and UMIs from raw reads, filtered out low-quality reads, trimmed unusable read 2 sequences, performed the read alignment, added gene tags, repaired cell barcodes, and generated a digital gene expression matrix.
Reads filtration aimed to remove reads where the cell barcode or UMI had at least 1 base with quality lower than 10. At least five contiguous bases of the adapter and at least six contiguous bases of A with no mismatch were hard clipped off the read 2. After trimming, the reads were aligned to the hg19 or hg19_mm10 reference genome using STAR version 2.7.1a33 with default parameters. Thus, a gene tag “GE” was added to each read and multi-mapping reads were discarded.
Cell barcodes correlation, including detection and repairing of substitution errors and indel synthesis errors, were then carried out. UMIs for a gene with one edit distance were merged together. The total number of unique UMIs for each gene were counted as the number of transcripts of that gene for a given cell to generate digital gene expression.
Genome_build: hg19, mm10
Supplementary_files_format_and_content: digital gene expression and sample annotation in text file

source_name: lung adenocarcinoma cells

extract_protocol:
Cells were lyzed and mRNA captured on barcoded beads were reverse transcripted and amplified using PCR.
RNA libraries were prepared for sequencing using standard TruePrep® DNA Library Prep Kit V2 for Illumina® (Vazyme, cat#TD502) according to the manufacturer’s protocols


title: Input_rep1


title: NCCIT_SVA_H3K9me3_NO_DOXY_rep2

value: H3K9 Tri-methyl Abcam ab8898


title: NCCIT_SVA_H3K9me3_DOXY_rep2


title: NCCIT_SVAgRNA_noDoxy_YY1ChIP


title: ΔHTH_rep1

value: anti-HA (abcam, AB9110)


title: NCCIT_SVAgRNA_noDoxy_H3K9


title: PEO23 R 24Hr rep3

city: Seattle

first: Amanda

last: Paulovich

state: WA

address: 1100 Fairview Ave. N.

institute: Fred Hutchinson Cancer Research Center

data_processing:
Illumina Bcl2fastq v2.18
Genome_build: UCSC hg19
Supplementary_files_format_and_content: .csv

source_name: Human Ovarian Cancer cell line (platinum resistant)

growth_protocol: Cells were grown in RPMI1640 (Corning 10-040-CV) medium supplemented with L-glutamine and 10% fetal bovine serum (heat Inactivated FBS, Atlanta Biologicals S10250)

extract_protocol:
Total RNA was extracted from cell pellets with the miRNeasy Kit (Qiagen, cat#217504).
Purified total RNA samples were evaluated for quality and quantity by Agilent Bioanalzyer using RNA 6000 Nano chip and reagents (cat#5067-1511). Sequencing libraries were prepared using Illumina TruSeq stranded Total RNA sample preparation kit (cat# 20020597) from 200ng of RNA according to manufacturer’s protocol. The finished libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200 D1000 screentape (cat#5067-5582), and RT-qPCR using the Roche Kapa Biosystems library quantification kit (cat#KK4854) according to manufacturer’s protocols. Whole genome libraries for copy number analysis were sequenced with >25M 75bp read pairs and RNAseq libraries were sequenced with >50M 75bp read pairs by the Molecular Biology Core Facilities at Dana-Farber Cancer Institute.

treatment_protocol: Cells were plated in 150-mM tissue culture plates and cultured for 48 hours, at which point they were approximately 50% confluent. The cultures were then treated with vehicle or 80 µM carboplatin (S1215, Selleckchem US) for 8 or 24 hours

value: 80uM carboplatin

tag: time of treatment

tag: cell line and catalog #

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: H3K9_NCCIT

source_name: NCCIT


title: NCCIT_SVAgRNA_Doxy_H3K9

value: doxy+


title: NCCIT_SVAgRNA_Doxy_YY1ChIP

value: YY1 Cell Signaling Technology D5D9Z/46395S


title: LSKAA_rep2


title: LSKAA_rep1


title: PEO14 S 24Hr rep3

source_name: Human Ovarian Cancer cell line (platinum sensitive)

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: CTCF Auxin- rep1

description: Auxin Inducible Degron cell

value: human colorectal cancer cells

value: untreated

value: CTCF (CST, Cat# 2899)


title: RKO cells, shCHD7-2-1

city: tianjin

first: zhenyu

last: shi

state: 天津

address: West Huan-Hu Rd, Ti Yuan Bei, Hexi District  Tianjin, 300060, P.R.China

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
ATAC-seq reads were aligned to the hg19 human genome using Bowtie2 version 2.2.5(default parameters, paired-end mode)
Duplicate reads ,mitochondrial reads and low mapping quality reads were removed using SAMTools version 1.9
Peak calling was performed using macs2 version 2.1.2 with the following parameters; --nomodel --shift  -100 --extsize 200
Bam files were transformed to Bigwig tracks using bamcoverage version 3.3.0 for visualization
Peaks annoted by ChIPpeakAnno version 3.20.1 to find the nearest gene, exon, miRNA or custom features
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files contented the coverage of each region of the reference genome, sequencing depth
Supplementary_files_format_and_content: Narrow peak files called by macs2

source_name: colon

growth_protocol: RKO cells were cultured in Eagle’s Minimum Essential Medium supplemented with 10% fetal bovine serum at 37 ℃ in a humidified atmosphere with 5% CO2.

extract_protocol:
100,000 cell nuclei were extracted using NPB buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, and 0.1% Triton X-100) at 4 °C for 10 minutes. Tagmentation was performed in a reaction buffer (Vazyme) containing Tn5 transposase (#TD501, Vazyme, Nanjing, China) at 37 °C for 30 minutes. DNA was then extracted using a PCR purification kit (#28106, Qiagen, Hilden, Germany)
DNA libraries were generated by PCR for sequencing using standard Illumina protocols.

treatment_protocol: The lentiviruses expressing control or shCHD7 shRNA were employed to infect RKO cells to obtain stable expression cells.

value: human colon cancer cell

value: RKO

value: CHD7 shRNA2

value: CHD7 knockdown


title: NCCIT_SVA_minusDoxy_Rep3

value: doxy-


title: PEO4 R 24Hr rep3

value: PEO4 MilliporeSigma 10032309-1VL/ ECACC 10032309


title: RKO cells, shCHD7-2-2

value: colon


title: LCOR-HA_rep2


title: RKO cells, control-2

value: control


title: RKO cells, control-1


title: PEO1 S 24Hr rep3

value: PEO1 MilliporeSigma 10032308-1VL/ ECACC 10032308


title: PEA2 R 24Hr rep3

description: PEA2 p27

value: 80uM carboplatin

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: ΔHTH_rep2

value: anti-HA (abcam, AB9110)


title: PEA1 S 24Hr rep3

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: Control_rep2


title: LCOR-HA_rep1


title: HICHIP_DOX_rep2

value: YY1 Cell Signaling Technology D5D9Z/46395S

value: doxy+


title: small_RNA_HLTE_A23_uninfected

first: Frank

last: Pessler

address: Feodor-Lynen-Str. 7-9

department: Experimental Infection Research

institute: Center for Experimental and Clinical Infection Research GmbH

data_processing:
Large sets of high‐throughput sequencing reads were mapped against the Homo sapiens hg38 reference genome via Oasis 2.0 tool.
Oasis2.0 was used to normalize the counts of each gene to account for differences in sequencing depth and low count variability. The DESeq2 normalization metric is based on the median of ratios method.
Following normalization, DESeq2 was run in a pairwise manner, identifying significantly differentially expressed genes with higher levels of expression in the uninfected group in comparison to the infectiojn group.
Genome_build: human reference genome (hg19, GRCh38)
Supplementary_files_format_and_content: normalized count txt files

source_name: Human lung

growth_protocol: HLTEs were cultured in RPMI medium without any supplement at 37°C, 5% CO2 for overnight

extract_protocol:
HLTE tissue were snap frozen in liquid nitrogen and stored at -80C. Qiagen miRNeasy kit was used to extract total RNA.
Quality and integrity of total RNA was controlled on Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany).
The RNA sequencing library was generated from 200 ng total RNA using NEBNext® Single Cell/Low Input RNA Library to manufacture´s protocols. The libraries were sequenced on Illumina NovaSeq 6000 using NovaSeq 6000 S1 Reagent Kit (100 cycles, paired end run 2x 50 bp) with an average of 5 x107 reads per RNA sample.

treatment_protocol: For IAV, infection medium containing 2.0 x 105 ffu/ml in RPMI medium was added to a 24 well plate, placing one HLTE piece per well. For BCG, Infection medium containing 5X106 CFU/ml was prepared and HLTEs were subjected to infection in a 24 well plate. For PA, infection medium was prepared containing 1x108 CFU/ml in RPMI medium. HLTEs were incubated in 24 well plates for 2 h at 37°C. After infection, HLTEs were washed and incubated in RPMI medium containing 50 μg/ml gentamycin.

tag: infection group

value: Uninfected

tag: patient number

value: lung tissue explants

tag: molecule subtype

value: small non-coding RNA


title: Control_rep1

tag: cell line


title: small_RNA_HLTE_A23_BCG infection

value: Mycobacterium bovis (BCG)


title: PEO23 R 08Hr rep3

tag: treatment

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: small_RNA_HLTE_A22_IAV infection

value: Influenza A virus (IAV)


title: small_RNA_HLTE_A22_PA infection

value: Pseudomonas aeruginosa (PA)


title: PEO14 S 08Hr rep3

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: postZGA_Jarid2_ChIP_rep2

city: Salt Lake City

first: Graham

middle: James McGuire

last: Hickey

state: UT

address: 2000 Circle of Hope Drive

department: Oncological Sciences

institute: University of Utah

description:
Jarid2_4.3hpf_ChIP.bw
Jarid2_4.3hpf_ChIP.narrowPeak

data_processing:
ChIP-seq Fastq files were aligned to Zv10 using Novocraft Novoalign (v3.8) with the following settings: -o SAM -r Random.
SAM files were processed to BAM format, sorted, and indexed using Samtools (v1.8).
MACS2 (v2.2.5) was utilized for peak calling with the following settings: -B -q 0.01 --SPMR. BAM files of ChIP replicates and input were provided to MACS2 in a single execution under the -t and -c flags, respectively.
Bedgraph output files from MACS2 were used to produce bigwig files with UCSC bedGraphToBigWig (v4).
Genome_build: zv10
Supplementary_files_format_and_content: narrowPeak and bigwig file formats. The narrowPeak files contain peaks that were called by MACS2 with a q value cutoff of 0.01. The bigwig files are the treatment fragment pileups produced by MACS2 and are normalized by signal per million reads.

organism: Danio rerio

source_name: WT Tubingen

growth_protocol: Standard zebrafish growth conditions.

extract_protocol:
Approximately 1.5 million cells were used for each ChIP replicate. Embryos were allowed to progress to the desired developmental stage and then transferred to 1.5 ml microcentrifuge tubes (~200 embryos per tube). Chorions were removed enzymatically by treatment with pronase 1.25mg/ml in PBS). Dechorionated embryos were gently washed twice with PBS to remove pronase. Samples were fixed with 1% formaldehyde (Electron Microscopy Sciences, Cat# 15712) for 10 minutes at room temperature with end over end rotation. Fixation was quenched with 130 mM glycine for five minutes at room temperature. Samples were centrifuged for five minutes at 500 x g at 4oC. Supernatant was discarded and cell pellets were washed twice with ice cold PBS. Cell pellets were frozen with liquid nitrogen and stored at -80ºC. 1 ml of Mild Cell Lysis Buffer (10 mM Tris-HCl pH 8.1, 10 mM NaCl, 0.5 NP-40, 2X proteinase inhibitors) was applied to cell pellets from 1000 embryos and rotated at 4ºC for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC. Supernatant was discarded and nuclei pellets were resuspended in 1 ml Nuclei Wash Buffer (50 mM Tris-HCl pH 8.0, 100 mM NaCl, 10 mM EDTA, 1% SDS, 2X protease inhibitors) and rotated at room temperature for 10 minutes. Samples were centrifuged at 1300 X g for 5 minutes at 4ºC to pellet nuclei. Supernatant was discarded and nuclei pellets were resuspended in 100 µl of Nuclei Lysis Buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS, 2X proteinase inhibitors). Samples were incubated on ice for 10 minutes. 900 µl of IP Dilution Buffer (16.7mM Tris-HCl pH 8.1, 167mM NaCl, 1.2mM EDTA, 0.01% SDS, 1.1% Triton X-100, 2X proteinase inhibitors) was added to samples. Nuclear lysates were sonicated with a Branson Digital Sonifier with the following settings: 10 second duration (0.9 seconds ON, 0.1 seconds OFF), 30% amplitude. 7 sonication cycles were performed. Samples were placed in an ice bath for at least 1 minute between each sonication cycle. Sonicated samples were centrifuged at 14,000 rpm, 4ºC, for 10 minutes to pellet insoluble material. Supernatants were transferred to new tubes. A portion of the sample was set aside to confirm optimal chromatin shearing by agarose gel electrophoresis. 20 µl of Dynabeads (Invitrogen) were blocked with 0.5mg/ml BSA in PBS. Blocked Dynabeads were subsequently applied to each sonicated sample and rotated for 1 hour at 4ºC. Samples were placed on a magnet stand for 1 minute and precleared supernatant was transferred to a new tube. 5% of the sample was removed and stored at -80ºC as input. Antibody and fresh 1X protease inhibitors were added to each sample. Samples were rotated overnight at 4ºC. Samples were centrifuged at 14,000 rpm, 4ºC, for 5 minutes to pellet insoluble material. Supernatants were transferred to new tubes. 50 µl of Dynabeads (Invitrogen) were blocked with BSA 5mg/ml in PBS. Blocked Dynabeads were subsequently applied to each sample and rotated for 6 hours at 4ºC. All wash buffers were kept ice cold during stringency washes. Samples were washed 8 times with RIPA Buffer (10 mM Tris-HCl pH 7.5, 140 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, 2X protease inhibitors), 2 times with LiCl Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% sodium deoxycholate, 2X protease inhibitors), 2 times with TE Buffer (10mM Tris-HCl pH 8.0, 1 mM EDTA, 2X protease inhibitors). 100 µl of Elution Buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1% SDS) was added to beads. 2ul of RNase A (Thermo Fisher, Cat #EN531) was added to each ChIP and input sample and incubated at 37ºC for 30 minutes with gentle agitation. 10 µl of Proteinase K (Thermo Fisher, Cat # 25530049) was added to each sample and incubated at 37ºC for 1 hour with gentle agitation. Crosslinks were reversed overnight at 65ºC with gentle agitation. ChIP DNA was purified with a Qiagen MinElute PCR Purification kit (Cat #28004).
ChIP seq libraries were prepared using NEBNext ChIP-Seq Library Prep Reagent Set for Illumina (New England BioLabs, Cat # E6240).

treatment_protocol: Untreated or embryo media was supplemented with 150 μM PRT4165 (or DMSO) from when the embryos were at the 1-cell stage until the embryos were harvested.

value: Tubingen

value: WT

tag: developmental stage

value: 4.3 hpf

value: Whole body (embryo)

value: Untreated


title: PEO4 R 08Hr rep3

value: 80uM carboplatin

value: PEO4 MilliporeSigma 10032309-1VL/ ECACC 10032309


title: small_RNA_HLTE_A22_BCG infection


title: small_RNA_HLTE_A21_uninfected


title: small_RNA_HLTE_A21_IAV infection


title: small_RNA_HLTE_A23_IAV infection


title: small_RNA_HLTE_A21_PA infection


title: 3.5hpf_PRT4165_RNAseq_rep3

description:
19057X12
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_PRT4165_RNAseq_RPKM.bw

data_processing:
RNA-seq fastq files were aligned to Zv10 using STAR (v2.5.4a) with the following settings: --runMode alignReads --twopassMode Basic --alignIntronMax 50000 --outSAMtype BAM SortedByCoordinate --outWigType bedGraph --outWigStrand Unstranded.
BAM files were subsequently indexed using Samtools (v1.8).
FeatureCounts (v1.5.1) was utilized to collect count data for zv10 Ensemble v90 genes via the following command: -T 16 -s 2 –largestOverlap.
Count data for all replicates across experimental conditions were combined into a single count matrix in R. The count matrix was subsequently used to identify differentially expressed genes with the R package DESeq2 (v1.18).
For generation of bigwig files, Bam files for a given condition were merged, sorted, and indexed with samtools. Subsequently deepTools bamCoverage (v2.5.4) was used with the --normlizeUsingRPKM option to produce bigwig files.
Genome_build: zv10
Supplementary_files_format_and_content: Text file and bigwig files. The count matrix contains data regarding the number of counts each experimental replicate has across zv10 Ensembl v90 transcripts. The bigwig files contain RNA-seq signal normalized by RPKM.

extract_protocol:
Total RNA was harvested from zebrafish embryos with a Qiagen Allprep kit (Cat #80204). The Invitrogen DNA-free DNA removal kit (Cat # AM1906 ) was subsequently used to remove contaminating DNA from RNA samples.
Intact poly(A) RNA was purified from total RNA samples (100-500 ng) with oligo(dT) magnetic beads and stranded mRNA sequencing libraries were prepared as described using the Illumina TruSeq Stranded mRNA Library Preparation Kit (RS-122-2101, RS-122-2102).

treatment_protocol: Embryo media was supplemented with 150 μM PRT4165 (or DMSO) from when the embryos were at the 1-cell stage until the embryos were harvested.


title: postZGA_Jarid2_ChIP_rep1


title: PEO1 S 08Hr rep3

value: PEO1 MilliporeSigma 10032308-1VL/ ECACC 10032308


title: PEA2 R 08Hr rep3

description: PEA2 p27

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: small_RNA_HLTE_A21_BCG infection


title: small_RNA_HLTE_A20_uninfected

value: Uninfected


title: 3.5hpf_PRT4165_RNAseq_rep2

description:
19057X11
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_PRT4165_RNAseq_RPKM.bw


title: small_RNA_HLTE_A20_BCG infection

value: lung tissue explants


title: small_RNA_HLTE_A23_PA infection

value: small non-coding RNA


title: small_RNA_HLTE_A20_PA infection


title: small_RNA_HLTE_A19_uninfected


title: PEO23 R 24Hr rep2


title: small_RNA_HLTE_A22_uninfected


title: PEA1 S 08Hr rep3

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: small_RNA_HLTE_A19_IAV infection


title: 3.5hpf_DMSO_RNAseq_rep3

description:
19057X9
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_DMSO_RNAseq_RPKM.bw

value: DMSO


title: small_RNA_HLTE_A19_BCG infection

value: Mycobacterium bovis (BCG)


title: 3.5hpf_DMSO_RNAseq_rep2

description:
19057X8
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_DMSO_RNAseq_RPKM.bw


title: OMM2.3-rep2

city: Shanghai

first: gu

last: xiang

address: No.833 Zhizaoju Road

institute: Shanghai Jiao Tong University school of medicine

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low qualityreads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All thedownstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene wascalculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number ofFragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect ofsequencing depth and gene length for the reads count at the same time, and is currently the most commonlyused method for estimating gene expression levels.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05
GO and KEGG enrichment analysis of differentially expressed genes
Genome_build: hg38
Supplementary_files_format_and_content: bigwig

source_name: Uveal melanoma cell

growth_protocol: Uveal melanoma cells were extracted from uveal melanoma and cultured in a 6 cm culture dish with 1640.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: Uveal melanoma

value: untreated


title: PEO4 R 24Hr rep2


title: PIG1-rep1

source_name: normal melanocyte cell


title: PEO1 S 24Hr rep2


title: PIG1-rep2


title: 3.5hpf_DMSO_RNAseq_rep1

description:
19057X7
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_DMSO_RNAseq_RPKM.bw

value: Tubingen

tag: tissue


title: small_RNA_HLTE_A20_IAV infection

value: Influenza A virus (IAV)


title: OMM2.3-rep1


title: 2.5hpf_PRT4165_RNAseq_rep2

description:
19057X5
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_PRT4165_RNAseq_RPKM.bw

value: WT


title: OMM2.3-H3K79me2-IgG-rep1

data_processing:
Library strategy: CUT&Tag
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads  from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream  analyses were based on the clean data with high quality.
Reads mapping to the reference genome
Reads mapping to the reference genome
The HOMER's findMotifsGenome.pl tool was used for Motif analysis. The input file is the peak file and the genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
genome fasta file. The DNA sequence is extracted according to the peak file, and the sequence is compared with the Motif database to obtain the Motif.
GO and KEGG enrichment analysis
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using Macs2
Supplementary_files_format_and_content: peak text files

growth_protocol: Uveal melanoma cells were extracted from uveal melanoma and cultured in a 15 cm culture dish with 1640.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: IgG(12-370, Millipore)


title: 2.5hpf_PRT4165_RNAseq_rep3

description:
19057X6
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_PRT4165_RNAseq_RPKM.bw

value: Whole body (embryo)


title: PEA2 R 24Hr rep2

description: PEA2 p26

value: 80uM carboplatin


title: 3.5hpf_PRT4165_RNAseq_rep1

description:
19057X10
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
ZGA_PRT4165_RNAseq_RPKM.bw


title: OMM2.3-H3K79me2-IgG-rep2

value: IgG(12-371, Millipore)


title: PEA1 S 24Hr rep2


title: 2.5hpf_PRT4165_RNAseq_rep1

description:
19057X4
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_PRT4165_RNAseq_RPKM.bw


title: OMM2.3-H3K79me2-rep2

value: H3K79me2(ab3595, Abcam)


title: C27-N9

city: Toronto

first: Amro

last: Zayed

state: Ontario

address: 4700 Keele Street

department: Biology

country: Canada

institute: York University

description:
HI.4193.008.Index_9.C27-N9
processed data file: Apiary_Nurses_Logcpm.txt

data_processing:
We used Trimmomatic v0.36 to remove removes adapters, low quality bases (leading and trailing 20), and low quality reads (reads shorter than 50 bases and when the average quality per base drops below 25 for a 20 base window).
Field and Apiary data were analyzed seperatly
The RNA sequences were aligned and gene expression quantified with the amel 4.5 Apis mellifera genome assembly and Official Gene Set v3.2 using Spliced Transcripts Alignment to a Reference (STAR) v2.7
The gene expression counts were then processed using EdgeR in R version 3.6.3
Any genes that had an expression count lower than 1 count per million (cpm) in less than two samples were filtered out
The remaining counts were normalized using the default trimmed mean of M-values (TMM) method
Genome_build: Amel_4.5
Supplementary_files_format_and_content: Matrix tables with normalized gene counts in log(cpm) for every gene in Apiary Foragers, Apiary Nurses, Field Foragers, or Field Nurses

organism: Apis mellifera

extract_protocol:
RNeasy Mini Kit (Qiagen) following manufacturer instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: caste

value: Nurse

tag: experiment

value: Apiary

value: Unexposed

value: Brain


title: OMM2.3-H3K79me2-rep1

value: H3K79me2(ab3594, Abcam)


title: C28-F1

description:
HI.4193.008.Index_8.C28-F1
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager

value: Exposed


title: PEO23 R 08Hr rep2

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: C27-F5

description:
HI.4193.008.Index_5.C27-F5
processed data file: Apiary_Foragers_Logcpm.txt


title: 2.5hpf_DMSO_RNAseq_rep3

description:
19057X3
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_DMSO_RNAseq_RPKM.bw

value: DMSO


title: C27-F3

description:
HI.4193.008.Index_4.C27-F3
processed data file: Apiary_Foragers_Logcpm.txt


title: PEO14 S 08Hr rep2

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: 2.5hpf_DMSO_RNAseq_rep2

description:
19057X2
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_DMSO_RNAseq_RPKM.bw

value: Tubingen


title: C27-N7

description:
HI.4193.008.Index_3.C27-N7
processed data file: Apiary_Nurses_Logcpm.txt


title: PEO14 S 24Hr rep2


title: small_RNA_HLTE_A19_PA infection

value: Pseudomonas aeruginosa (PA)

value: lung tissue explants

value: small non-coding RNA


title: 2.5hpf_DMSO_RNAseq_rep1

description:
19057X1
2.5hpf_3.5hpf_PRT4165_vs__DMSO_RNaseq_counts.txt
preZGA_DMSO_RNAseq_RPKM.bw

value: WT

value: Whole body (embryo)


title: C27-N1

description:
HI.4193.008.Index_19.C27-N1
processed data file: Apiary_Nurses_Logcpm.txt


title: C27-F6

description:
HI.4193.008.Index_12.C27-F6
processed data file: Apiary_Foragers_Logcpm.txt


title: PEO4 R 08Hr rep2

value: 80uM carboplatin

value: PEO4 MilliporeSigma 10032309-1VL/ ECACC 10032309


title: C26-N5

description:
HI.4193.007.Index_7.C26-N5
processed data file: Apiary_Nurses_Logcpm.txt

value: Nurse

value: Apiary


title: C27-N4

description:
HI.4193.008.Index_1.C27-N4
processed data file: Apiary_Nurses_Logcpm.txt

value: Unexposed

value: Brain


title: PEA2 R 08Hr rep2

description: PEA2 p26

value: PEA2 MilliporeSigma 10032307-1VL/ ECACC 10032307


title: PEA1 S 08Hr rep2

value: PEA1 MilliporeSigma 10032306-1VL/ ECACC 10032306


title: PEO23 R 24Hr rep1

value: PEO23 MilliporeSigma 10032313-1VL/ ECACC 1003213


title: C26-F5

description:
HI.4193.007.Index_2.C26-F5
processed data file: Apiary_Foragers_Logcpm.txt

value: Forager


title: 4hpf PRT4165_Aebp2_ChIP_rep_2

description:
15987X27
Zebrafish
Aebp2_PRT4165_4hpf_ChIP.narrowPeak
Aebp2_PRT4165_4hpf_ChIP.bw

data_processing:
ChIP-seq Fastq files were aligned to Zv10 using Novocraft Novoalign (v3.8) with the following settings: -o SAM -r Random.
SAM files were processed to BAM format, sorted, and indexed using Samtools (v1.8).
MACS2 (v2.2.5) was utilized for peak calling with the following settings: -B -q 0.01 --SPMR. BAM files of ChIP replicates and input were provided to MACS2 in a single execution under the -t and -c flags, respectively.
Bedgraph output files from MACS2 were used to produce bigwig files with UCSC bedGraphToBigWig (v4).
Genome_build: zv10
Supplementary_files_format_and_content: *.narrowPeak: The narrowPeak files contain peaks that were called by MACS2 with a q value cutoff of 0.01.
Supplementary_files_format_and_content: *bw: The bigwig files are the treatment fragment pileups produced by MACS2 and are normalized by signal per million reads.


title: 4hpf PRT4165_Aebp2_ChIP_rep_3

description:
15987X28
Zebrafish
Aebp2_PRT4165_4hpf_ChIP.narrowPeak
Aebp2_PRT4165_4hpf_ChIP.bw


title: C26-N2

description:
HI.4193.007.Index_6.C26-N2
processed data file: Apiary_Nurses_Logcpm.txt


title: Monocytes+LPS (0.5ug/ml)+9CISRA(100nM)_3

data_processing:
Data was processed using ROSALIND (https://app.rosalind.bio)
Data was analyzed by ROSALIND® (https://rosalind.bio/), with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Read Distribution percentages, violin plots, identity heatmaps, and sample MDS plots were generated as part of the QC step. Normalization, fold changes and p-values were calculated using criteria provided by Nanostring. ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library1. Abundance of various cell populations is calculated on ROSALIND using the Nanostring Cell Type Profiling Module. ROSALIND performs a filtering of Cell Type Profiling results to include results that have scores with a p-Value greater than or equal to 0.05. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual. P-value adjustment is performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR). Clustering of genes for the final heatmap of differentially expressed genes was done using the PAM (Partitioning Around Medoids) method using the fpc R library2 that takes into consideration the direction and type of all signals on a pathway, the position, role and type of every gene, etc. Hypergeometric distribution was used to analyze the enrichment of pathways, gene ontology, domain structure, and other ontologies. The topGO R library3, was used to determine local similarities and dependencies between GO terms in order to perform Elim pruning correction. Several database sources were referenced for enrichment analysis, including Interpro4, NCBI5, MSigDB6,7, REACTOME8, WikiPathways9. Enrichment was calculated relative to a set of background genes relevant for the experiment.

source_name: in vitro cultured Purified Monocytes

extract_protocol:
RNA was extracted from cultured cells
Whole cornea was surgically removed or the in vitro cultured Immune cells were spun down and the RNA was extracted using the standard protocol provided by the manufacturer, we use the Qiagen RNA preparation kit

tag: experimental group

value: Monocytes +LPS (0.5ug/ml)+9CISRA(100nM)

tag: Sex

value: Female

tag: age

tag: cell type

value: in vitro cultured Purified Monocytes


title: 4hpf PRT4165_Aebp2_ChIP_rep_1

description:
15987X26
Zebrafish
Aebp2_PRT4165_4hpf_ChIP.narrowPeak
Aebp2_PRT4165_4hpf_ChIP.bw

tag: strain

value: Tubingen

tag: genotype

tag: chip antibody


title: 4hpf PRT4165_Aebp2_input_3

description:
15987X25
Zebrafish


title: Monocytes+LPS (0.5ug/ml)+9CISRA(100nM)_2


title: PEO14 S 24Hr rep1

tag: time of treatment

tag: cell line and catalog #

value: PEO14 MilliporeSigma 10032311-1VL/ ECACC 10032311


title: Monocytes+LPS (0.5ug/ml)+9CISRA(100nM)_1


title: C26-N7

description:
HI.4193.007.Index_18.C26-N7
processed data file: Apiary_Nurses_Logcpm.txt


title: PEO4 R 24Hr rep1


title: 4hpf PRT4165_Aebp2_input_2

description:
15987X24
Zebrafish

value: WT


title: C27-F2

description:
HI.4193.007.Index_16.C27-F2
processed data file: Apiary_Foragers_Logcpm.txt


title: PEO1 S 08Hr rep2

value: PEO1 MilliporeSigma 10032308-1VL/ ECACC 10032308


title: Monocytes+LPS (0.5ug/ml)_3

value: Monocytes +LPS (0.5ug/ml)

value: LPS (0.5ug/ml)


title: PEO1 S 24Hr rep1

value: 80uM carboplatin


title: 4hpf PRT4165_Aebp2_input_1

description:
15987X23
Zebrafish

value: Whole body (embryo)