title: HCECs, PM3

first: Danni

last: Lyu

address: 88 Jiefang Rd.

department: Eye Center

institute: 2nd Affiliated Hospital of Zhejiang University School of Medicine

data_processing:
Quality control was performed for each sample using FastQC.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were mapped to the reference genome using Hisat2 v2.0.5.
The expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced (FPKM) of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.16.1).
Genome_build: hg19
Supplementary_files_format_and_content: FPKMs

source_name: human corneal epithelial cells

growth_protocol: HCECs were grown in 50:50 DMEM/F-12 medium containing 15% FBS, supplemented with penicillin (50 units/ml) and streptomycin (100 mg/ml).

extract_protocol:
Total RNAs were extracted using the Trizol reagent.
Sequencing cDNA libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following the manufacturer’s instruction. The clustering of the samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS. Then the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

treatment_protocol: The unexposed control HCECs were cultured without any other treatment. The HCECs of the PM2.5-exposed group were incubated at 37°C in 5% CO2 and grown to 80-90% confluence before addition of PM2.5 (50 μg/mL) to cell culture medium.

value: Human Corneal Epithelial Cells

tag: passage


title: sdg33_plusN_Shoot_3

status: Public on Aug 01 2022

type: SRA

city: New York

first: Ying

last: Li

state: NY

address: 12 Waverly Place

department: Biology

country: USA

institute: New York University

library_source: transcriptomic

data_processing:
The raw sequencing reads were trimmed by the Purdue Genomics Core to remove adaptors and low-quality reads.
trimmed reads were mapped against the tomato genome (build 3.0, assessed on June 5, 2019) using BBmap
mapped reads were used to generate a count for each gene feature in the genome, using the tomato gene models ITAG3.2 and the annotated miRNA loci based on miRbase using FeatureCounts
differentially expressed genes were detected using DESeq2 (Love et al., 2014) with the design (~Genotype+Treatment+Genotype:Treatment), for sdg33 and sdg34, separately.
Genome_build: tomato genome (build 3.0, assessed on June 5, 2019)
Supplementary_files_format_and_content: normalized expression level of genes in txt format

molecule: total RNA

organism: Solanum lycopersicum

source_name: shoot tissues

growth_protocol: Seeds were surface sterilized with 20% sodium hypochlorite for 20 minutes and rinsed with distilled water. The seeds were then germinated on filter paper in the dark until the radicle emerged and transferred into black sand for the seedlings to be established for one week. Seedlings were then grown hydroponically in foil tapped plastic containers with one litre nutrient medium, which consisted of 1.2 mM KNO3, 0.8mM Ca(NO3)2, 0.2mM NH4H2PO4, 0.2mM MgSO4, 50μM KCl, 12.5 μM H3BO3, 1 μM MnSO4, 1 μMZnSO4, 0.5 μMCuSO4, 0.1 μM H2MoO4, 0.1 μM NiSO4 and 10 μM Fe-EDDHA. Plants were grown in the greenhouse with a photoperiod of 16-h light and 8-h dark at 24 °C. Two plants were grown in one container and aeration was provided for one hour daily to increase the oxygen content of the nutrient medium. The nutrient medium was refreshed every three days.

extract_protocol:
Three independent plants were pooled to make one replication and three replications per treatment per genotype were used for RNA extraction. RNA for transcriptome profiling was extracted from the root and shoot samples harvested five hours after N treatments. Total RNA was extracted from the shoots and roots using Trizol (Invitrogen) according to the manufacturer’s instructions.  After extraction, total RNA was treated with DNase (New England Biolabs) according to the manufacturer’s instructions. RNA was then precipitated with 3M sodium acetate and three-times volume of 100% ethanol and resuspended in DEPC treated water. RNA was then concentrated using ZYMO RNA clean and concentrator kit (ZYMO Research) according to the manufacturer’s instructions.  The integrity of RNA was accessed by the Agilent Bioanalyzer (Agilent technologies).
RNA samples were submitted to the Purdue Genomics Core for RNA-Seq library preparation and sequencing on an Illumina Novaseq platform with paired-end 50bp format.

treatment_protocol: After two weeks of growth in the nutrient medium, plants were transferred into starvation medium, which is identical to the nutrient medium except for that 1.2 mM KNO3, 0.8mM Ca(NO3)2, 0.2mM NH4H2PO4 were replaced by 0.6mM K2SO4, 0.8mM CaSO4, 0.2mM KH2PO4 respectively. After two days in the starvation medium, plants were transferred into two treatment media: (1) with N (+N); and (2) with control (-N). The +N treatments medium was the same as the growth medium and the -N treatment medium was the same as the starvation solution.

tag: genotype

tag: condition

value: plusN

tag: organ

value: Shoot


title: Mf_16wpf_MS173_175

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: cDNAs amiplified from 1 ng total RNA extracted from cells using SC3-seq technology

data_processing:
The processing of the 3-prime-sequencing data for calculating the gene-expression levels was performed as described previously (Nakamura et al., 2015).  In brief, all reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences.
The reads of 30-bp or longer were mapped onto a mouse transcript reference, ref_macFas5, annotation 101, with 3'-end of transcripts, extended by up to 10kb, using Tophat v2.0.11/Bowtie2 v2.2.7.  Read counts per gene were calculated using HTSeq v0.9.1 with the default settings.  Read counts were converted to read counts per million mapped reads (RPM) and used for the analysis.
Genome_build: macFas5
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each sample.

molecule: polyA RNA

organism: Macaca fascicularis

source_name: An oocyte from 16 wpf fetal ovary

extract_protocol:
Fetal ovaries collected from cy fetuses at 8-18 wpf were carefully dissected out in chilled PBS.  Fetal ovaries at 8-14 wpf were minced with scissors in 0.05% trypsin/EDTA/PBS solution (GIBCO, 15400-054), then incubated for 15 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium [DMEM (GIBCO, 10313021) containing 10% FBS, 2mM L-glutamine (GIBCO, 25030081), 1X penicillin/streptomycin (GIBCO, 15070063), and 100μg/mL DNaseI (MERCK, DN25)] was added for further dissociation. For fetal ovaries at 16 and 18 wpf, minced tissues were incubated in Accumax (Innovative Cell Technologies, AM105) for 40 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium was added for further dissociation.  For SC3-seq analysis, cells were picked under the inverted microscope (OLYMPUS, IX71) to exclude multiplet cells.   For dissociating cy rOvaries, tissues were incubated with TryPLE Express (1X) (GIBCO, 12604021) for 5 min.  After adding dissociation medium, cells were processed for single-cell analyses. Dissociated germ cells from in vivo monkey fetal ovaries and monkey rOvaries were manually picked using glass capillaries under the stereo microscope (Leica, S8 APO).  Following cDNA synthesis and amplification methods were previously described (Nakamura et al., 2015).
The cDNA synthesis was performed according to the single-cell 3 prime RNA-seq (SC3-seq) method described previously (Nakamura et al., 2015).  The cDNA libraries for Nextseq500 (Illumina) were constructed as described previously (Ishikura et al., 2016).The sequencing was performed on an Illumina Nextseq500/550 platform with a Nextseq500/550 Hiqh output kit (Illumina).

tag: developmental stage

value: 16 wpf

tag: xenotransplantation period

tag: in vitro culture period

tag: cell type

value: Germ cell


title: Mf_16wpf_MS173_176


title: HCECs, PM2

city: Hangzhou

country: China

organism: Homo sapiens

tag: treatment


title: sdg33_plusN_Shoot_2


title: T47D_LTED9M_shcjun_Input_ChIPseq

city: Miami

first: Liliana

last: Garcia-Martinez

state: Florida

address: 1501 NW 10th Avenue

department: Human Genetics

institute: University of Miami

library_source: genomic

data_processing:
ChIP-seq: Single-end ChIP-seq fastq files were processed using the ENCODE Transcription Factor and Histone ChIP-Seq processing pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2). Reads were trimmed using cutadapt v2.5. Reads were aligned to the hg19 genome using Bowtie2 v2.3.4.3, and the SAMtools v1.9 was used to convert the output file to the BAM format. Duplicates were removed using Picard Tools v2.20.7. Peaks were called/signal tracks were generated using MACS2 v2.2.4, and peaks with fold change > 3.5 compared to input and a FDR < 0.05 were used for subsequent analysis. Only default parameters were used.
RNA-seq: Single-end RNA-seq fastq files were processed using the LSF-RNAseq Pipeline from Diderote (https://github.com/diderote/LSF-RNAseq). Reads were trimmed using cutadapt v2.3 with the following parameters: -j 4 --netseq-trim=20 -m 18. Reads were aligned to the hg19 genome using STAR v2.6.1a along default parameters, and RSEM v1.3.0 was used to obtain the expected gene counts against the human refseq also along default parameters.
RNA-seq differential expression was determined using DESeq2 v1.18.1 and R (version 3.4.1) with q-value <0.05. Ruvseq v1.12.0 was used for factor analysis to remove count based on ERCC spike-in. GSEA analysis was performed using gsea-3.0.jar. These additional analysis steps were included in the Diderote LSF-RNAseq Pipeline.
Bedtools v2.29.0 intersect was used to determine peak overlaps and assign target genes.
Homer v4.11 was used for peak annotation and motif analysis (http://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip)
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in bigWig format containing the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

molecule: genomic DNA

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 9 months.After transduction with pLKO-shcjun, cells were selected and maintained in media containing 2 ug/ml puromycin.Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL)

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 11% solution containing formaldehyde (Thermo Fisher #28908), 50mM HEPES-KOH(pH 7.5), 100mM Nacl, 0.5M EDTA, 0.5M EGTA for 10 min. 1/20 of the plates volume equivalent of freshly prepared Glycine 2.5M(stock) was added to quench the reaction for 5min . The supernatant was aspirated, and the cells were washed twice with 5 ml PBS and harvested on ice using cell scrapers . Cells were pelleted at 2950 x g for 10 min at 4°C, washed 1x with 10 ml cold PBS, and pelleted once more. Cell pellets were flash freeze in liquid nitrogen and store at -80°C until processing day. Cell pellet collected from 6 plates of cells was resuspended in 5 ml of Lysis Buffer 1 (50 mM HEPES-KOH, pH 7.5; 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), allowed to rotate for 10 min at 4°C, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 5 ml of Lysis Buffer 2 (10 mM Tris-HCL pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), allowed to rotate for 10 min at room temperature, and pelleted at 2950 x g for 10 min at 4°C. Cells were then resuspended in 3 ml of Lysis Buffer 3 (10 mM Tris-HCl pH 8, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) and then transfer to 15ml sonication tubes (Diagenode cat# C01020031). Cells were sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles with 1.2 g of sonication beads. After sonication, samples were transferred to 2 separate 1.5 ml microtube and centrifuged at 20,000 x g for 15 minutes at 4°C. The supernatant was transferred to new 15 ml tubes. To check sonication efficiency, 50µl of sonicated samples was transferred to a new microtube with 50µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H20. 1 ug of decrosslinked chromatin from each sample were run in a 1% agarose gel at 100V for 45min and imaged on a Bio-rad ChemiDoc XRS+. DNA concentration in the sonicated decrosslinked samples were measured via qubit, and this concentration was then used to estimate the concentration of chromatin in the un-decrosslinked samples.  10ug of Antibody (see Key Resources table for list of antibodies) along with 2ug of Spike-in antibodies (Active Motif 61686) were bound to 50 ul of Dynabeads Protein G (Thermo Fisher 10004D), previously washed with 1 ml of 0.5% BSA in 1x PBS three times, and rotated end-to-end overnight at 4°C (Eppendorf cat# 0030108051). After binding of the antibodies , beads were washed with 1 ml of 0.5% BSA in 1x PBS three times. 30ug of chromatin and 50 ng of Spike-in chromatin (Active Motif 53083) were added to 1.5ml LoBind tube (Eppendorf cat# 0030108051) containing pre-bound antibodies beads and brought up to 500µl final volume with Lysis Buffer and rotated end-to-end overnight at 4°C.  5 µl was removed as input material (1%) and placed in a separate microtube at 4°C completing the volume to 50uL with Lysis Buffer 3.  Beads were washed 6 times with 1 ml Wash Buffer (50 mM Hepes-KOH, pH 7.6; 500 mM LiCl, 1 mM EDTA, 1% NP-40; 0.5% Na-Deoxycholate) and once with 1 ml TE containing 50 mM NaCl. Beads were dried after the last wash by removing as much TE as possible. 210 ul of Elution Buffer (50 mM Tris-HCl, pH 8; 10 mM EDTA, 1% SDS) was added to each sample and  150 ul elution buffer were added to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 15 minutes on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 960xg at RT and 200µl of supernatant was transferred to a new tube and reverse crosslinked overnight at 65°C. Next day, 200 ul of TE was added to each decrosslinked sample and input, and the samples were treated sequentially with 0.2 mg/ml RNAse A (Sigma R5503) at 37°C and 0.2 ug/ml Proteinase K (NEB P8107S) at 55°C for two hours each. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 50µl of H2O and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: Parental estrogen deprived for 9 months, plko-shcjun estable SHCLNG-NM_002228 (TRCN0000010366) Sigma Aldrich

tag: chip antibody


title: HCECs, PM1


title: Mf_16wpf_MS173_174


title: T47D_LTED9M_shcjun_LSD1_ChIPseq

value: Anti-KDM1 / LSD1 antibody - ChIP Grade (ab17721)


title: Mf_16wpf_MS173_180


title: T47D_LTED9M_Input_ChIPseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 9 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL

value: Parental estrogen deprived for 9 months


title: HCECs, CTRL3

value: unexposed


title: Mf_16wpf_MS173_173


title: WT_minusN_Shoot_3

value: WT

value: minusN


title: Mf_16wpf_MS173_172


title: HCECs, CTRL2


title: WT_minusN_Shoot_2


title: HCECs, CTRL1


title: sdg33_plusN_Shoot_1


title: T47D_FM_Input_ChIPseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061).

value: Parental


title: T47D_FM_LSD1_ChIPseq


title: WT_minusN_Shoot_1


title: T47D_LTED9M_LSD1_ChIPseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 9 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL)


title: T47D_LTED8m_72h_Corin_Rep1_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 8 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were treated for 72h with 500nM of compound Corin (MedChem Express HY-111048)

extract_protocol:
Total RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity and quality was measured on a nanodrop.2 ug of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) to remove DNA contamination and later on DNAse and divalent cations from the sample. 1ug of the treated RNA was used for library preparation. Quality was checked using a Bioanalyzer
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.

value: Parental estrogen deprived for 8 months


title: Mf_16wpf_MS238_218


title: T47D_LTED8m_72h_Corin_Rep2_RNAseq

extract_protocol:
Total RNA was isolated from frozen cell pellets using the TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions. RNA quantity and quality was measured on a nanodrop. 2 ug of RNA were treated using the TURBO DNA-free Kit (Thermo Fisher AM1907) to remove DNA contamination and later on DNAse and divalent cations from the sample. 1ug of the treated RNA was used for library preparation. Quality was checked using a Bioanalyzer
Library preparation was perfromed on Dnase-treated RNA using the Illumina TruSeq Stranded Total RNA Library Prep Gold (Illumina 20020598). TruSeq RNA UD Indexes (Illumina 20022371) were used for the adapter ligation step. Samples were normalized to a concentration of ranging from 100-250ng for input, and 1 ul of ERCC spike-in Mix 1 (Thermo Fisher 4456740) diluted 1:200 was added to the samples.


title: Mf_16wpf_MS173_171


title: Mf_16wpf_MS238_217


title: sdg34_minusN_Shoot_2


title: Mf_16wpf_MS238_216


title: sdg34_minusN_Shoot_1


title: T47D_LTED8m_72h_SP2509_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 8 ,months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were treated for 72h with 500nM of compound SP2509 (Cayman Chemical Company 15487)


title: T47D_LTED8m_72h_SP2509_Rep1_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 8 months. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL). Cells were treated for 72h with 500nM of compound SP2509 (Cayman Chemical Company 15487)


title: Mf_12wpf_MS238_211

source_name: An oocyte from 12 wpf fetal ovary

value: 12 wpf


title: sdg33_minusN_Shoot_3


title: sdg33_minusN_Shoot_2


title: Mf_12wpf_MS238_210


title: Mf_12wpf_MS236_209


title: sdg33_minusN_Shoot_1


title: sdg34_minusN_Shoot_3


title: T47D_FM_Corin_72h_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ). Cells were treated for 72h with 500nM of compound Corin (MedChem Express  HY-111048)


title: WT_plusN_Root_3

source_name: root tissues

value: Root


title: Mf_12wpf_MS236_208


title: WT_plusN_Root_2


title: T47D_FM_Corin_72h_Rep1_RNAseq


title: Mf_12wpf_MS236_204


title: Mf_12wpf_MS236_206


title: T47D_FM_SP2509_72h_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ). Cells were treated for 72h with 500nM of compound SP2509 (Cayman Chemical Company 15487)


title: K9-DFX-d4

city: Los Angeles

first: William

last: Lowry

state: CA

address: 621 Charles Young Drive South

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with DFX for 4 days

data_processing:
Read ends adapter- and quality-trimmed using cutadapt and sickle
Alignment to hg38 with Bowtie2 in very sensitive mode
Discarded alignments using samtools with flag 2820, or MAPQ < 30, or mapped to chrM
Removed duplicates with Picard
Called peaks with MACS2
Generated BigWig files using bamCoverage from deepTools package
Genome_build: hg38
Supplementary_files_format_and_content: Genome Browser Tracks (BigWig format); for narrow peak histone ChIP (K27ac), peak coordinates (BED format)

source_name: pluripotent derived neural progenitor cells

growth_protocol: hiPSCs were cultured as described previously (Xie et al., 2014) in accordance with UCLA Embryonic Stem Cell Research Oversight committee. Briefly, feeder-free hESC or hiPSC lines were maintained with mTeSR1 (Stem Cell Technologies) and passaged mechanically. Neural rosette derivation, NPC purification, and differentiation into neurons and glia were performed as described (Patterson et al., 2011). Rosettes were generated by growing PSCs for at least 7 days in Dulbecco’s modified Eagle’s medium (DMEM)/F12 with N2 and B27 supplements (Invitrogen), 20 ng/ml basic fibroblast growth factor (FGF) (R&D Systems), 1 mM retinoic acid (RA) (Sigma), and 1 mM Sonic Hedgehog Agonist (Calbiochem). Once the rosettes were picked, NPCs were expanded in Poly-L-ornithine (Sigma) and laminin (Sigma) coated 6-well plates with medium containing DMEM/F12, N2 and B27, 20 ng/ml basic FGF, and 50 ng/ml EGF (GIBCO). NPCs were passaged weekly in 20% oxygen unless specified.

extract_protocol:
ChIP-sequencing was performed as described previously with modifications (Sridharan et al., 2013). Briefly, NPCs were crosslinked by 1% formaldehyde (final concentration) for 10 minutes at room temperature, and quenched with 125mM glycine (final concentration). Cells were re-suspend in sonication buffer containing 50 mM Hepes-KOH (pH=7.9), 140 mM NaCl, 1mM EDTA (pH=8), 1% Triton X-100, 0.1% sodium Deoxycholate, 1% SDS and protease inhibitor, and sonicated with Misonix sonicator S-4000. Cell extracts were incubated with 5µg antibodies against H3K27Ac (Abcam, ab4729) or H3K9Me3 (Abcam, ab8898) overnight at 4 °C. Immunoprecipitates were collected with magnetic beads, and washed twice with PBS, low-salt buffer, high-salt buffer and LiCl buffer as described before (Sridharan et al., 2013). Reverse crosslinking was preformed by addition of 1% SDS and proteinase K with gentle shaking overnight at 56°C. DNA was precipitated using phenol-chloroform-isoamyl alcohol mixture (Sigma, P2069) and Phase Lock Gel (5 Prime) according to manufacturer’s protocol.
ChIP-seq library preparation was performed using Ovation Ultralow System V2 1-16 (NuGEN) following the user’s guide. The sequencing was performed on HiSeq 2000 platform with single-end 50bp run.

treatment_protocol: For day 4 samples, 20% oxygen, 2% oxygen, DFX (Sigma, D9533) (50 mM), or DMOG (Sigma, D3695) (200 mM) were added to the NPCs for 4 days. For day 9 samples, after 4 days of treatment with 20% oxygen, 2% oxygen, DFX, or DMOG, low oxygen and drugs were withdrawn from the cells, and the cells were grown at 20% oxygen for additional 5 days before they were collected for ChIP at day 9.

value: hiPSCs derived NPCs

value: H3K9Me3 (Abcam, ab8898)


title: K9-DMOG-d4

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with DMOG for 4 days


title: K9-2-d9

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with 2% oxygen for 4 days and stoped treatment for additional 5 days


title: K9-DMOG-d9

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with DMOG for 4 days and stoped treatment for additional 5 days


title: K9-20-d4

description:
Immunoprecipitated DNA
H3K9me3 data for control NPCs grown in 20% oxygen for 4 days


title: sdg34_plusN_Root_3

value: plusN


title: K9-2-d4

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with 2% oxygen for 4 days


title: K9-20-d9

description:
Immunoprecipitated DNA
H3K9me3 data for control NPCs grown in 20% oxygen for 9 days


title: T47D_FM_SP2509_72h_Rep1_RNAseq


title: WT_plusN_Root_1


title: K9-DFX-d9

description:
Immunoprecipitated DNA
H3K9me3 data for NPCs treated with DFX for 4 days and stoped treatment for additional 5 days


title: T47D_FM_DMSO_72h_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061). Cells were culture in  72h in the presence of DMSO.


title: K27-DFX-d9

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with DFX for 4 days and stoped treatment for additional 5 days

value: H3K27Ac (Abcam, ab4729)


title: Mf_12wpf_MS236_203

value: Germ cell


title: K27-DMOG-d4

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with DMOG for 4 days


title: K27-DFX-d4

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with DFX for 4 days


title: TKO scRNAseq

city: Chicago

first: Peng

last: Ji

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The prepared libraries were sequenced with DNBseq PE 100 platform. The sequencing data were processed (including alignment and quantification) using Cell Ranger  pipeline. The joint analysis of three single-cell datasets were performed by Seurat v4. The percentage of mitochondrial and ribosomal genes per cell were calculated and added to the metadata. The proportion of hemoglobin genes were examined to eliminate the red blood cell contamination. Filtering criteria “min. cells = 3, min. features = 200” was applied to filter the preliminary data. Single cells with less than 500 detected genes or more than 4000 detected genes or more than 15% reads aligned to mitochondrial genes were excluded further. For cell clustering analysis, “IntegrateData” function in the Seurat package were used for data combination with resolution value = 0.5 and 30 principal components.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: RBC depleted bone marrow from femur and tibia

extract_protocol:
Red blood cells from freshly collected total bone marrow cells using RBA lysis buffer. The remaining bone marrow cells were resuspended in PBS with 0.5% BSA.
An estimated 10,000 cells were loaded into the 10X Chromium system per sample. RNA was converted to cDNA and libraries were generated using the Chromium Single Cell 3’ v3 Kit. Bioanalyzer confirmed the main peak size of cDNA were generally between 450-490 bp.

tag: tissue

value: bone marrow cells

tag: age

value: 12 month old


title: sdg34_plusN_Root_2


title: sdg34_plusN_Root_1


title: K27-DMOG-d9

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with DMOG for 4 days and stoped treatment for additional 5 days


title: sdg33_plusN_Root_3


title: Mf_12wpf_MS236_201


title: DKO scRNAseq

description: 10x Genomics

value: RBC depleted bone marrow from femur and tibia


title: IL6 KO scRNAseq

description: 10x Genomics


title: sdg33_plusN_Root_2


title: WT_minusN_Root_3


title: WT_minusN_Root_2


title: sdg33_plusN_Root_1


title: 12wks_ivc

description: Single cell transcriptome of monkey cultured rOvary

data_processing:
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v5.0.1) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger with default setting to map to the reference genome for Macaca fascicularis genome, macFas5.0.
Cell Ranger count command were also performed with "--include-intron" option (data with "_include_intron" marked) and with transcript reference including long non-coding RNAs (data marked with "_include_lncRNA").
Genome_build: macFas5.0
Supplementary_files_format_and_content: Cell Ranger output

source_name: xrOvary

extract_protocol:
Fetal ovaries collected from monkey fetuses at 8-18 wpf were carefully dissected out in chilled PBS.  Fetal ovaries at 8-14 wpf were minced with scissors in 0.05% trypsin/EDTA/PBS solution (GIBCO, 15400-054), then incubated for 15 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium [DMEM (GIBCO, 10313021) containing 10% FBS, 2mM L-glutamine (GIBCO, 25030081), 1X penicillin/streptomycin (GIBCO, 15070063), and 100μg/mL DNaseI (MERCK, DN25)] was added for further dissociation.  For fetal ovaries at 16 and 18 wpf, minced tissues were incubated in Accumax (Innovative Cell Technologies, AM105) for 40 min at 37℃ with gentle pipetting every 5 min.  Dissociation medium was added for further dissociation.  Cell suspensions were further treated with TryPLE Express (1X) (GIBCO, 12604021) for 5min at 37℃ to make the single-cell suspension. Dissociated cells from monkey fetal ovaries and cultured monkey rOvaries were stained with DRAQ7 to distinguish dead cells.  All DRAQ7(-) live cells were collected by using FACS (BD Biosciences, FACS Aria III).
The cDNA library for NGS was conducted with Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 (Single Index) or Next GEM single cell 3' Library & Gel beads kit ver 3.1 (Single Index) according to the manufacturer’s instructions.
scRNA-seq

value: fetal

value: cultured rOvaries

value: 12 weeks

tag: scrna-seq protocol

value: Chromium Next GEM single cell 3' Library & Gel beads kit ver 3.1 (Single Index)


title: T47D_LTED_Rep1_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 1 year. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin (Thermo Fisher Scientific 15140-12, 10000U/mL)

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133

value: Parental long term estrogen deprived


title: 15wks_ivc

value: 15 weeks


title: T47D_FM_DMSO_72h_Rep1_RNAseq

value: Parental


title: K27-2-d4

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with 2% oxygen for 4 days

value: hiPSCs derived NPCs


title: K27-2-d9

description:
Immunoprecipitated DNA
H3K27ac data for NPCs treated with 2% oxygen for 4 days and stoped treatment for additional 5 days


title: T47D_LTED_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations. Cells were culture in  estrogen deprived conditions for 1 year. Cell culture media: IMEM with no phenol red (Corning 10-026-CV supplemented with 10% charcoal stripped FBS(Gemini 100-119) and Penicillyn/Streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL)


title: T47D_LTED_LSD1_KO_2E10_Rep1_RNAseq

value: LSD1 KO long term estrogen deprived cells generated with CRISPR/Cas9


title: T47D_LTED_LSD1_KO_2E10_Rep2_RNAseq


title: Input-20-d4

description: genomic DNA


title: 18wpf

description: Single cell transcriptome of monkey fetal ovary in vivo

source_name: fetal ovary

value: 18 wpf

value: ovary in vivo


title: WT_minusN_Root_1

value: WT

value: minusN

value: Root


title: sdg34_minusN_Root_3


title: Input-DMOG-d4

description: genomic DNA


title: T47D_FM_Rep2_RNAseq

growth_protocol: T47D were maintained at 37°C with 5% CO2 according to ATCC recommendations and split 1:3 every 3 days. Culture media: RPMI-1640(Lonza 12-167Q) supplemented with 10% FBS(Gemini 100-106), 1x penicillin/streptomycin(Thermo Fisher Scientific 15140-12, 10000U/mL), and 1x glutamax( Life Technologies 35050-061 ).


title: Input-2-d4

description: genomic DNA


title: K27-20-d4

description:
Immunoprecipitated DNA
H3K27ac data for control NPCs grown in 20% oxygen for 4 days

value: H3K27Ac (Abcam, ab4729)


title: T47D_FM_Rep1_RNAseq


title: K27-20-d9

description:
Immunoprecipitated DNA
H3K27ac data for control NPCs grown in 20% oxygen for 9 days


title: sdg34_minusN_Root_2


title: Hek + Hela Input

city: London

first: David

middle: Jonathan

last: Fear

address: 5th Floor, Tower Wing, Great Maze Pond

department: Respiratory Medicine and Allergy

country: United Kingdom

institute: Kings College London

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the hg19 genome build using Bowtie2 (Galaxy)
PCR duplicates, non-uniquely mapped sequences and prro quality reads were removed
peaks were called using MACS and SICER peak callers (Galaxy)
Following peak calling, regions with >2x average input read depth were removed. Peaks falling in known blacklisted regions (Duke blacklist) and regions of high input depth (top 0.1 of genome - UCSC) were excluded. Only peaks >4.5 fold enriched (3 fold for SICER) were used in subsequent analyses
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated by MACS

source_name: HEK and HeLa_input

growth_protocol: Primary Human B cells were isolated from the tonsils of donors undergoing routine tonsilectomy and culture in the presence of anti-CD40 antibody and rhIL-4 for 48 hours

extract_protocol:
Lysates were clarified from Micrococcal treated and sonicated nuclei and histone-DNA complexes isolated with an antibody.
Libraries were prepared according to Illumina's instructions accompanying the CHIP-Seq sample prep kit. Libraries were sequenced on the Genome Analyzer II or HiSEq2000 following the manufacturer's protocols.

treatment_protocol: After 48hours B cells were crosslinked and nuclei collected

tag: cell line

value: HEK and Hela


title: 16wpf_#2

value: fetal

value: 16 wpf

value: Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (Single Index)


title: TWT scRNAseq

description: 10x Genomics

value: RBC depleted bone marrow from femur and tibia

value: bone marrow cells

value: 12 month old


title: CBD treated EAE IECs biological replicates 6-10

type: RNA

city: COLUMBIA

first: Nicholas

last: Dopkins

state: SC

address: 1825 Saint Julian Pl 18A

institute: University of South Carolina

description: mRNA expression profile of IECs from Cannabidiol treated EAE mice 6-10

hyb_protocol: Microarray experiment performed in-house in the Nagarkatti lab at the University of South Carolina School of Medicine.

scan_protocol: Hybridized Clariom  D assay chips were washed in accordance with manufacturer s recommended fluidics protocol FS450_0001 using GeneChip  Fluidics Station 450. After completion of the fluidics protocol, the assay chips were analyzed using a GeneChip  Scanner.

data_processing: Downstream transcriptomic analysis was conducted using Applied Biosystems  Transcriptomic Analysis Console version 4.0.

label: biotin

source_name: IEC CBD 6-10

label_protocol: Protocol outlined in GeneChip™ WT Pico Reagent Kit

growth_protocol: Housed in SPF housing at the USC SOM Animal Resourse Facility

extract_protocol: Qiazol extraction of total RNA from PE selected IECs

treatment_protocol: CBD = 20mg/kg CBD in 90% PBS / 10% ETOH; VEH = 90%PBS / 10% ETOH

value: intestinal IECs

value: Cannabidiol 6-10

tag: strain

value: EAE


title: T47D_FM_LSD1_KO_2E8_Rep2_RNAseq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133

value: LSD1 KO parental cells generated with CRISPR/Cas9


title: sdg34_minusN_Root_1

growth_protocol: Seeds were surface sterilized with 20% sodium hypochlorite for 20 minutes and rinsed with distilled water. The seeds were then germinated on filter paper in the dark until the radicle emerged and transferred into black sand for the seedlings to be established for one week. Seedlings were then grown hydroponically in foil tapped plastic containers with one litre nutrient medium, which consisted of 1.2 mM KNO3, 0.8mM Ca(NO3)2, 0.2mM NH4H2PO4, 0.2mM MgSO4, 50μM KCl, 12.5 μM H3BO3, 1 μM MnSO4, 1 μMZnSO4, 0.5 μMCuSO4, 0.1 μM H2MoO4, 0.1 μM NiSO4 and 10 μM Fe-EDDHA. Plants were grown in the greenhouse with a photoperiod of 16-h light and 8-h dark at 24 °C. Two plants were grown in one container and aeration was provided for one hour daily to increase the oxygen content of the nutrient medium. The nutrient medium was refreshed every three days.


title: T47D_FM_LSD1_KO_2E8_Rep1_RNAseq


title: 12wpf

value: 12 wpf

value: ovary in vivo


title: 16wpf_#1

value: Chromium Next GEM single cell 3' Library & Gel beads kit ver 3.1 (Single Index)


title: VEH treated EAE IECs biological replicates 6-10

description: mRNA expression profile of IECs from Vehicle treated EAE mice 6-10

source_name: IEC vehicle 6-10

value: Vehicle 6-10


title: sdg33_minusN_Root_2

value: minusN

value: Root


title: 10wpf

value: fetal

value: 10 wpf


title: rep 2 AID ChIP

source_name: total (CD20+) B cells_AID ChIP

tag: subject status

value: donors undergoing routine tonsilectomy

tag: donor id

value: donor 2

value: tonsil

value: Primary Human B cells

value: AID (Abcam, ab5197)


title: VEH treated EAE IECs biological replicates 1-5

description: mRNA expression profile of IECs from Vehicle treated EAE mice 1-5

source_name: IEC vehicle 1-5

value: intestinal IECs

value: Vehicle 1-5

value: EAE


title: sdg33_minusN_Root_3

tag: genotype

tag: condition


title: CBD treated EAE IECs biological replicates 1-5

description: mRNA expression profile of IECs from Cannabidiol treated EAE mice 1-5

source_name: IEC CBD 1-5

value: Cannabidiol 1-5


title: rep 2 Input

source_name: total (CD20+) B cells_input


title: sdg33_minusN_Root_1

tag: organ


title: Hek + Hela AID ChIP

source_name: HEK and HeLa_AID ChIP

value: HEK and Hela


title: 8wpf_#2

tag: developmental stage

value: 8 wpf

value: ovary in vivo

value: Chromium Single Cell 3' GEM, Library & Gel Bead Kit v3 (Single Index)


title: rep 1 Input

value: donor 1


title: B16 melanoma cells, IFNγR1KO 12

status: Public on Jul 31 2022

city: Birmingham

first: Min

last: Gao

state: AL

address: 1900 University Blvd, THT Building Suite #130G

institute: University of Alabama at Birmingham

data_processing:
Sequencing reads were mapped to GrCM38/mm10 using STAR v2.7.5a
Read counts were counted using htseq-count of Htseq package v0.11.2
Normalization and differential expression analysis were performed using DEseq2 v1.34.0
Assembly: mm10
Supplementary files format and content: read counts for each Sample
Supplementary files format and content: tab-delimited text files include normalized read counts for all samples

growth_protocol: B16 melanoma cells were maintained in MEM supplemented with 10% fetal bovine serum (FBS) 2mM L-glutamine, 1mM sodium pyruvate, 1% non-essential amino acids, 1% vitamin, 100 units/mL of penicillin and 100 µg/mL of streptomycin in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Melanoma cell


title: B16 melanoma cells, IFNγR1KO 10


title: B16 melanoma cells, control 2

value: WT


title: B16 melanoma cells, control 3


title: B16 melanoma cells, control 1


title: B16 melanoma cells, IFNγR1KO 11


title: 8wpf_#1

value: fetal

tag: in vitro culture period


title: rep 1 AID Chip

value: donors undergoing routine tonsilectomy

tag: cell type


title: Wild type cells + pS2 antibody replicate 1

city: Lebanon

first: Diwakar

last: Pattabiraman

state: New Hampshire

address: 1 Medical Center Drive

department: Molecular systems biology

institute: Geisel School of Medicine at Dartmouth

description: CUT&RUN fragments

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using Bowtie (v2.2.6) in “--local” mode with parameters ““--local --no-mixed --no-discordant”
Raligned reads were filtered for unmapped or multi-mapping reads using sambamba (v0.6.8)
Duplicate reads were identified and removed using MarkDuplicates (Picard Tools) to create filtered BAMs
For MYC peaks were called using the MACS2 (v2.2.7.1) callpeak command in narrowpeak mode, using IgG IP samples as controls with parameters “-f BAMPE --keep-dup all -g 2913022398 -q 0.05”
For H4Ac and pS2, peaks were identified using MACS2 callpeak command in broadpeak mode again using IgG IP samples as controls and with identical parameters as above, as well as additional parameters “--broad --broad-cutoff 0.05”
Called peaks were filtered against the ENCODE human blacklist (dataset: ENCFF356LFX) and further restricted to peaks demonstrating a 2-fold or greater signal increase relative to control (IgG) samples
BEDTools (v 2.29.2) command “intersect” with parameters “-a” was used to compare replicates and identify a set of reproducible overlapping peaks for each sample group
Matricies of raw read counts (used for differential binding analyses) were generated using the featureCounts() function (Rsubread package) with options “isPairedEnd=TRUE, countMultiMappingReads=FALSE”
Genome_build: hg38
Supplementary_files_format_and_content: matrix of raw read counts in txt format
Supplementary_files_format_and_content: CPM normalized signal tracks in BigWig format
Supplementary_files_format_and_content: peak files in BED format

source_name: Human cell line

growth_protocol: MCF10A cells were cultured in 50:50 DMEM/F12 (Corning) supplemented with 5% horse serum (HS) (Gibco), 6mM L-glutamine (Corning), 0.5µg/mL hydrocortisone (Sigma), 20ng/mL hEGF (PeproTech), 10µg/mL insulin (Sigma), 100ng/mL cholera toxin (Sigma), 1% penicillin/streptomycin, and prophylactic plasmocin (InvivoGen).

extract_protocol:
Resuspended CUT&RUN fragments were prepared for next generation sequencing using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® and NEBNext® Multiplex Oligos for Illumina® (Dual Index Primers Set 1). Library preparation was performed using 15 cycles of amplification PCR. Size selection was performed using ProNex beads (Promega #NG2001) to collect library fragments ~150bp to ~750bp.
CUT&RUN Assay Kit #86652

treatment_protocol: No treatment

value: Breat epithelial non-tumorigenic

tag: cell line origin

tag: antibody

value: pS2 antibody


title: Wild type cells + H4Ac antibody replicate 2

description: CUT&RUN fragments

value: H4Ac antibody


title: S146L cells + H4Ac antibody replicate 1

description: CUT&RUN fragments


title: S146L cells + MYC antibody replicate 2

description: CUT&RUN fragments

value: MYC antibody


title: S146L cells + Isotype control replicate 2

description: CUT&RUN fragments

value: Isotype control


title: S146L cells + H4Ac antibody replicate 2

description: CUT&RUN fragments


title: S146L cells + pS2 antibody replicate 2

description: CUT&RUN fragments


title: Wild type cells + H4Ac antibody replicate 1

description: CUT&RUN fragments


title: Wild type cells + MYC antibody replicate 1

description: CUT&RUN fragments


title: Wild type cells + Isotype control replicate 2

description: CUT&RUN fragments


title: S146L cells + Isotype control replicate 1

description: CUT&RUN fragments


title: S146L cells + MYC antibody replicate 1

description: CUT&RUN fragments


title: S146L MYC replicate 3

data_processing:
FASTQ files were generated using bcl2fastq v2.20.0.422 from Illumina Inc.
Raw reads were trimmed with Cutadapt (v2.4) and aligned to hg38 using STAR (2.7.2b) with parameters “--outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1”
Gene-level abundance estimates were generated using HTSeq (v0.11.2) with “--stranded yes” and default options.
Genome_build: hg38
Supplementary_files_format_and_content: txt files, Htseq-count output for each sample. Gene Identifers are from ENSEMBL v97

extract_protocol:
RNA was isolated from sub-confluent cultures using a Qiagen RNeasy Mini Kit (Qiagen # 74104). The subsequent procedure was performed as recommended by the manufacturer, including the optional on-column DNase digest using Qiagen RNase-free DNase (Qiagen #79256).
QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen Inc., #015.96)


title: S146L MYC replicate 1


title: Wild type cells + MYC antibody replicate 2

description: CUT&RUN fragments


title: Wild type cells + Isotype control replicate 1

description: CUT&RUN fragments


title: W135E MYC replicate 3


title: S146L MYC replicate 2


title: W135E MYC replicate 2


title: W135E MYC replicate 1


title: S146L cells + pS2 antibody replicate 1

description: CUT&RUN fragments


title: Wild-type MYC replicate 3


title: Wild type cells + pS2 antibody replicate 2

description: CUT&RUN fragments


title: Wild-type MYC replicate 2


title: Wild-type MYC replicate 1


title: Empty vector replicate 1


title: Empty vector replicate 3


title: Empty vector replicate 2


title: Patient 5 GF200 005_normal urethral

status: Public on Jul 30 2022

city: Changsha

first: Bin

last: Ye

address: Renmin Middle Road

institute: Second Xiangya Hospital, Central South University

scan_protocol: standard protocol The circRNAs expression difference and statistical significance P value were calculated by GeneSpring GX software. Cluster analysis and graphical display were performed with Cluster3.0 software.

data_processing: Kyoto encyclopedia of genes and genomes (KEGG) Pathway analysis was performed on the linear mRNA transcripts corresponding to different circRNA. The miRNA that circRNA might bind to was predicted by bioinformatics.

source_name: urethral stricture

label_protocol: The extracted RNAs were amplified and had reverse transcription into cDNA, then labeled with Cy3-dCTP. After purification, the labeled DNAs were hybridized into a microarray (CapitalBio Technology Human CircRNA Array v2).

extract_protocol:
The urethral scar tissue or normal urethral tissue was repeatedly rinsed in PBS containing antibiotics to remove redundant epithelial tissue. The tissues were divided into small pieces of 5 mm×5 mm in size and dropped the culture medium was onto the tissue to keep it moist. The tissues were put into a centrifuge tube, added 0.25% trypsin digestive juice -EDTA and collagenase, digested in a constant temperature water bath at 37℃ for 4 ~ 5 hours, and shaken once every hour. Filter the suspension with a filter screen, take the filtered suspension for centrifugation, discard the supernatant, add 6 mL of fresh culture solution, and culture in a cell incubator at 37℃ and 5% CO2. The next day, most of the fibroblasts adhered to the wall, the cell culture medium was changed, and the cells were changed every 2 ~ 3 days. Finally, urethral scar fibroblasts and normal urethral fibroblasts were successfully separated and cultured. The α-smooth muscle actin (α-SMA) was selected as a marker of fibroblasts for detection.
The circRNA expression profile of the urethral scar and normal urethral tissue was detected using CapitalBio Technology Human CircRNA Array v2 (CapitalBio Technology, China). The total RNA of three urethral scar tissue and three normal urethral tissue were extracted. The purity and concentration of the RNA were determined by a NanoDrop ND-1000 instrument (Thermo Scientific, USA).

tag: tissue type

value: normal urethral


title: Patient 1 GF200 001_urethral scar

hyb_protocol: After purification, the labeled DNAs were hybridized into a microarray (CapitalBio Technology Human CircRNA Array v2).

value: urethral scar


title: Patient 3 GF200 003_urethral scar


title: Patient 2 GF200 002_urethral scar


title: Patient 4 GF200 004_normal urethral


title: LLC tumour

status: Public on Jul 29 2022

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: comma-delimited text files including raw UMI counts and metadata with information per cell

source_name: tumour

extract_protocol: All methods listed in Murgaski et al. Efficacy of CD40 agonists is mediated by distinct cDC subsets and subverted by suppressive macrophages. 2022.

value: F11r fl/fl LysM-Cre-

value: LLC tumour

tag: platform

value: 10x Genomics


title: DAC, WGBS

status: Public on Jul 28 2022

city: Beijing

first: Jing

last: Nie

state: Beijing

address: No.28, Fuxing Road

institute: Chinese PLA General Hospital

data_processing:
The scRNA-seq reads were aligned to the mm10 reference genome and quantified using cellranger count (10x Genomics, v6.0.1).
TCR reads were aligned to the mm10 reference genome and consensus TCR annotation was performed using cellranger vdj (10x Genomics, v6.0.1).
The quality control of ATAC-seq  data was performed by FastQC (v0.11.9). Raw reads were trimmed using trim_galore (v0.6.6) and aligned to the mouse reference genome (mm10) using Bowtie2 (v2.3.5.1). Duplicate reads were removed using picard MarkDuplicates(v2.25.5) and only primary alignments with mapping quality greater than 30 were retained. ATAC-seq peaks were called using MACS2 (v 2.2.7.1) on each individual sample. Peaks that present in both replicates are preserved for downstream analysis.
The quality control of WGBS (Whole Genome Bisulfite Sequencing) was performed by FastQC (v0.11.9) . Raw reads were trimmed using trim_galore (v0.6.6) and aligned to the mouse reference genome (mm10) using bsmap (v2.90). Duplicate reads were removed using sambamba (v.0.6.8).
Assembly: mm10

source_name: spleen

extract_protocol:
The tumor tissues were minced and dissociated into single-cell suspensions using a tissue dissociation kit (Miltenyi Biotec). Cells were washed and re-suspended in PBS and stained with a Viability Dye, CD45 and CD3, the alive CD45+CD3+ TILs were sorted on a BD Bioscience cell sorter. Sorted cells were collected into cold PBS plus 2% FBS, and used for the scRNA-seq or ATAC-seq. For the ACT assay, the alive CD45.2+CD45.1-CD8+ transfered T cells were sorted and used for the scRNA-seq. For the WGBS assay, CD8+ naive T cells were treated with PBS or decitabine (10nM) in vitro.
(scRNA-seq with paired scTCR-seq) Cells were loaded between 10,000 and 15,000 cells/chip position using the 10x Chromium Single Cell V(D)J Reagent Kits v1.1. Library was performed according to the manufacter's instructions (single cell 5' v1+TCR protocol).
(ATAC-seq)  ATAC-seq DNA library was constructed using TruePrepTM DNA Library Prep Kit V2 for Illumina.
(WGBS) The C-T transformation was Bisufile processed according to EZ DNA Methylation-GoldTM Kit (D5006) process, and then WGBS library was constructed.

treatment_protocol: MC38-OVA tumor-bearing mice were treated with either PBS (Control group), decitabine (0.2 mg/kg/day) intraperitoneally for three consecutive days (DAC group), anti-PD-1 (200 μg per mouse) every three days (anti-P group), or decitabine-plus-anti-PD-1 (DP group). For the ACT assay, PBS or decitabine (10nM)-pretreated CD45.2+CD8+ T cells were transfered into MC38-OVA tumor-bearing CD45.1+ mice, followed by anti-PD-1 treatment 12 days after T cell transfer.

tag: tissue

value: spleen

value: CD8+ T cells

tag: treatment

value: decitabine treatment


title: Con, WGBS

value: Control


title: Patient 6 GF200 006_normal urethral


title: DAC, ACT, scTCR-seq

description: 10x Genomics

source_name: colon tumor

value: colon tumor

value: CD45.2+CD45.1-CD8+ transfered T cells


title: Con, ACT, scRNA-seq

description: 10x Genomics


title: DAC, ACT, scRNA-seq

description: 10x Genomics


title: DP, ACT, scTCR-seq

description: 10x Genomics

value: decitabine-plus-anti-PD-1 treatment


title: Con, ACT, scTCR-seq

description: 10x Genomics


title: PD1, ACT, scTCR-seq

description: 10x Genomics

value: anti-PD-1 treatment


title: DP, ACT, scRNA-seq

description: 10x Genomics


title: DP, scTCR-seq

description: 10x Genomics

value: CD3+ TILs


title: PD1, ACT, scRNA-seq

description: 10x Genomics


title: PD1, scTCR-seq

description: 10x Genomics


title: PD1, scRNA-seq

description: 10x Genomics


title: DP, replicate1, ATAC-seq


title: DAC, scRNA-seq

description: 10x Genomics


title: Con, scRNA-seq

description: 10x Genomics


title: Con, scTCR-seq

description: 10x Genomics


title: DP, replicate2, ATAC-seq


title: PD1, replicate2, ATAC-seq


title: Con, replicate1, ATAC-seq


title: PD1, replicate1, ATAC-seq


title: Opto_600_min

city: Santa Barbara

first: Siddharth

last: Dey

address: 3008 BioEngineering Bldg. University of California, Santa Barbara

institute: University of California, Santa Barbara

description: CEL-Seq based library

data_processing:
Reads were mapped to the transcriptome (RefSeq gene model based on the human genome release hg19, with the addition of the set of 92 ERCC spike-in molecules) using the Burrows-Wheeler Aligner (BWA) and filtered for uniquely mapping reads to the genome. Custom scripts written in Perl were used to demultiplex the data, identify strand information, and remove PCR duplicates.
Paired-end sequencing of the libraries was performed on an Illumina NextSeq 500, and hits were quantified and z-score normalized per gene. Transcriptomic data was then analyzed through custom pipeline on python packages “numpy” and “pandas”. As data preparation, all genes that were missing entry at any time were removed from data matrix. We then applied SVD function from “numpy” to gene matrix, where rows were distinct genes and columns were duration of stimulation in increasing order, then sorted the data based on U matrix of SVD decomposition. We also applied centroid clustering on the gene matrix through clustermap function of “seaborn” package.
Assembly: hg19
Supplementary files format and content: tab-delimited text files

growth_protocol: H4 adherent cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
H4 cells carrying Cry2Olig-PKR cells were plated on fibronectin treated 96-well glass-bottom plate. Cells were illuminated according to experimental set-up using the optoPlate device set to continuous illumination intensity of 7.5 mcd as mentioned in Optogenetic stimulation. Cells were immediately lysed using 120 µL Trizol (Gibco, 15596026) per well, under red light, and incubation for lysis for 5 min at room temperature. RNA was extracted according to the manufacturer’s protocol.
RNAseq libraries were prepared following an adaptation of the single-cell method “CEL-Seq2” where we treated every illumination duration as a single cell (Hashimshony et al., 2016; Wangsanuwat et al., 2020). Briefly, sample RNA was reverse transcribed with Cel-Seq2 primer #4 (25 ng) using Superscript II reverse transcriptase. Second Strand Synthesis (SSS) was carried out via E. coli ligase (Invitrogen, Cat. # 18052–019) and DNA polymerase I (Invitrogen, Cat. # 18010–025) in SS buffer for 2 hours at 16°C. Next, cDNA was purified with 1:1 AMPure XP DNA beads (Beckman Coulter, Cat. # A63881), and washed with 80% ethanol twice, before elution into nuclease-free water and vacufuge concentrated. In vitro transcription was then carried out using MEGAscript T7 kit (Thermo Fisher Scientific, AMB13345) for 13 hours at 37°C, followed by RNA treatment using EXO-SAP (Thermo Fisher Scientific, 78200.200.UL) for 15 min at 37°C, and finally the samples were fragmented (200 mM Tris-acetate (pH 8.1), 500 mM KOAc, 150 mM MgOAc) at 94°C for 3 min before being quenched by 0.5 M EDTA. The fragmented RNA was size selected with 0.8x AMPure RNA beads (RNAClean XP Kit, Beckman Coulter, Cat. # A63987) and eluted in nuclease-free water.

treatment_protocol: Light treatment of cells through custom blue light array, at 60-90% confluency in glass bottom 96 well plate

value: neuroglioma

value: 600 minutes of blue light illumination


title: DP, scRNA-seq

description: 10x Genomics


title: Opto_0_min

description: CEL-Seq based library

value: 0 minutes of blue light illumination


title: Opto_240_min

description: CEL-Seq based library

value: 240 minutes of blue light illumination


title: Opto_120_min

description: CEL-Seq based library

value: 120 minutes of blue light illumination


title: Opto_720_min

description: CEL-Seq based library

value: 720 minutes of blue light illumination


title: Opto_480_min

description: CEL-Seq based library

value: 480 minutes of blue light illumination


title: Opto_60_min

description: CEL-Seq based library

value: 60 minutes of blue light illumination


title: DAC, scTCR-seq

description: 10x Genomics


title: 3hr il10ra mut (homozygous/mutant)

status: Public on Jul 27 2022

city: kansas city

first: Tatjana

last: Piotrowski

state: MO

address: 1000 East 50th street

institute: Stowers institute for medical research

data_processing:
Raw reads were demultiplexed and aligned to version 10 of the zebrafish genome (GRCz10), ensembl release 91, using the Cell Ranger (version 2.1.1) pipeline from 10x genomics using the default settings.
Assembly: danRer10
Supplementary files format and content: h5 files contain the UMI counts for each cell.

organism: Danio rerio

source_name: macrophage

extract_protocol:
Presumptive macrophages (GFP+) were isolated by FACS.
Standard 10x genomics scRNA-seq protocol using v3 chemistry

tag: age

value: macrophage

value: 3hr il10ra mut (homozygous/mutant)


title: 5hr post-neomycin

value: 5hr post-neomycin


title: 1hr il10ra mut (homozygous/mutant)

value: 1hr il10ra mut (homozygous/mutant)


title: 3hr post-neomycin

value: 3hr post-neomycin


title: 1hr il10ra sib (heterozygous/sibling)

value: 1hr il10ra sib (heterozygous/sibling)


title: homeo il10ra sib (heterozygous/sibling)

value: homeo il10ra sib (heterozygous/sibling)


title: 1hr post-neomycin

value: 1hr post-neomycin


title: 8861_hpNPC_Tbr2

status: Public on Jul 26 2022

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

data_processing:
ChIP-seq and ATAC-seq data were aligned to hg19 or panTro5 as appropriate using BWA-mem
RNA-seq data were analyzed with kallisto using hg19 or panTro5 as appropriate
scRNAseq data were mapped with cellranger using hg19 or panTro5 as appropriate, then analyzed in the R Package Seurat
ATAC-seq peaks were called with MACS2.
RNA-seq gene expression was quantified using Kallisto
For input bigwig was made with Deeptools
Assembly: hg19 for Homo sapiens samples and panTro5 for Pan troglodytes samples.
Supplementary files format and content: peak text files (ChIP-seq, ATAC-seq), Kallisto quantification (spreadsheet) for RNA-seq. Bigwig for input of Chip-seq, matrix + features + barcode files for scRNAseq

organism: Pan troglodytes

source_name: PT Rep 3 (8861 line)

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 or the NextSeq500 producing 80x80 PE reads

tag: antibodies

value: TBR2/EOMES Abcam ab216870


title: human_iPSC_scRNAseq

source_name: HS Rep 1 (SV20 line)

extract_protocol: Cells were treated with hpIPC media (Yu et al 2014) in five wells representing each day of differentiation, with an additional untreated iPSC well. Six well from both species were collected on the same day and resuspened in 10%FBS prior to treatment with the Cell Multiplexing Oligos in accordance with the 10X Cell Multiplexing Oligos Protocol.


title: 15min post-neomycin

value: 15min post-neomycin

tag: strain


title: 21792_hpNPC_H3K27Ac

source_name: HS Rep 3 (21792 line)


title: 3hr il10ra sib (heterozygous/sibling)

value: 3hr il10ra sib (heterozygous/sibling)


title: human_d5_scRNA_seq


title: human_d4_scRNAseq


title: homeo il10ra mut (homozygous/mutant)

value: homeo il10ra mut (homozygous/mutant)


title: 8861_hpNPC_H3K27Ac


title: Con, replicate2, ATAC-seq

value: colon tumor

value: CD3+ TILs

value: Control


title: human_d3_scRNAseq


title: 40280_input_R1_May2021 (Control for ChIP)

source_name: PT Rep 2 (40280 line)


title: human_d1_scRNAseq


title: chimp_d4_scRNAseq


title: chimp_d5_scRNAseq


title: homeo

value: homeo


title: chimp_d2_scRNAseq


title: chimp_d3_scRNAseq


title: chimp_d1_scRNAseq


title: chimp_iPSC_scRNAseq


title: B11-10ug-B [S17]

status: Public on Jul 25 2022

city: Minneapolis

first: Zohar

last: Sachs

state: MN

address: 420 Delaware Street SE MMC 480

department: Department of Medicine, Division of Hematology, Oncology and Transplantation

institute: University of Minnesota Twin Cities

data_processing:
rnaseq-pipeline of Gopher-pipelines (https://bitbucket.org/jgarbe/gopher-pipelines), running HISAT2 and Cuffnorm
Genome_build: Ensembl version GRCh38.84
Supplementary_files_format_and_content: Tab delimited text file includes FPKM values for all samples

growth_protocol: THP1 and B-11 clone were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum .

extract_protocol:
RNA samples were prepared using the RNeasy Mini kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols for RNA-seq

treatment_protocol: THP1 and B-11 clone were treated with 0 ug/ml, 1 ug/ml, 10 ug/ml of Doxycyclin for five days.

tag: cell line background

value: acute myeloid leukemia (AML) cells

tag: clone id

tag: nras mutation

value: heterozygous NRAS-G12V

tag: dox treatment

value: 10 ug/ml


title: THP1-10ug-C [S9]

value: heterozygous NRAS-G12D


title: B11-1ug-C [S15]

value: 1 ug/ml


title: B11-0ug-C [S12]

value: 0 ug/ml


title: THP1-10ug-A [S7]


title: B11-1ug-A [S13]


title: B11-10ug-A [S16]


title: B11-0ug-A [S10]


title: THP1-10ug-B [S8]


title: THP1-1ug-C [S6]


title: B11-1ug-B [S14]


title: B11-10ug-C [S18]


title: human_d2_scRNAseq


title: B11-0ug-B [S11]


title: THP1-0ug-B [S2]


title: THP1-1ug-A [S4]


title: THP1-0ug-A [S1]


title: Covid_006329D58

status: Public on Jul 24 2022

city: Pozzuoli

first: Francesco

last: Panariello

state: Napoli

address: Via Campi Flegrei 34

country: Italy

institute: TIGEM

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1

source_name: Oronasopharingeal swab

extract_protocol:
RNA extraction was performed by using either the Maelstrom 9600 (TANBead) or GeneQuality X120 (AbAnalitica) automatic platforms according to manufacturer's specifications.
40-60uL unquantified swab RNA extract (1-5 ng/ul estimate) was treated with DNAse I (Life Technologies), purified and concentrated to a final volume of 5uL. Libraries were prepared using 3'DGE mRNA-seq clinical-grade sequencing service (Next Generation Diagnostic srl).

value: Heterogeneous cell types from the oronasopharingeal tract

tag: disease state


title: Covid_006462D58


title: Covid_007165D58


title: Covid_002845D54


title: Covid_007167D58


title: Covid_0000137485


title: Covid_0000116723


title: Covid_005601D58

value: SARS-CoV-2 positive


title: Covid_0000116710


title: THP1-1ug-B [S5]


title: Covid_005521D58


title: THP1-0ug-C [S3]


title: Covid_005687D58


title: Covid_007161D58


title: Covid_0000137486


title: Covid_005540D58


title: Covid_006720D58


title: Covid_003751D55


title: Covid_004589D34


title: Covid_003852D55


title: Covid_005525D58


title: Covid_005542D58


title: Covid_004616D34


title: Covid_004712D34


title: Covid_006822D58


title: Covid_007406D58


title: Covid_005524D58


title: Covid_005674D58


title: Covid_007009D58


title: Covid_006557D58


title: Covid_007413D58


title: Covid_005654D58


title: Covid_005602D58


title: Covid_006576D58


title: Covid_007390D58


title: Covid_005938D58


title: Covid_004268D34


title: Covid_004331D58


title: Covid_003406D34


title: Covid_005661D58


title: Covid_006802D58


title: Covid_0000101431


title: Covid_007493D58


title: Covid_004484D58


title: Covid_004770D58


title: Covid_006769D58


title: Covid_006674D53


title: Covid_0000164311


title: Covid_006633D53


title: Covid_006918D58


title: Covid_004690D58


title: Covid_006582D53


title: Covid_006295D53


title: Covid_006847D58


title: Covid_004860D58


title: Covid_008581D58


title: Covid_006721D53


title: Covid_004677D58


title: Covid_007842D57


title: Covid_006645D53


title: Covid_005562D53


title: Covid_005638D53


title: Covid_006714D53


title: Covid_005639D53


title: Covid_006673D53


title: Covid_006857D53


title: Covid_006648D53


title: Covid_005628D53


title: Covid_006266D53


title: Covid_006340D53


title: Covid_005913D53


title: Covid_005275D58


title: Covid_005475D53


title: Covid_005607D53


title: Covid_005143D53


title: Covid_006220D58


title: Covid_006455D53


title: Covid_005416D53


title: Covid_005916D53


title: Covid_006241D53


title: Covid_005914D53


title: Covid_006593D53


title: Covid_006563D53


title: Covid_005473D53


title: Covid_006568D53


title: Covid_006355D53


title: Covid_004400D58


title: Covid_006456D53


title: Covid_006134D53


title: Covid_006675D53


title: Covid_005087D53


title: Covid_005955D53


title: Covid_008951D58


title: Covid_0000164324


title: Covid_004635D34


title: Covid_0000164323


title: Covid_005793D57


title: Covid_0000164322


title: Covid_004175D34


title: Covid_0000098412


title: Covid_0000135479


title: Covid_0000089471


title: Covid_0000089468


title: Covid_004636D34


title: Covid_0000135480


title: Covid_0000089469


title: Covid_0000098413


title: Covid_003147D34


title: Covid_005690D58


title: Covid_006252D53


title: Covid_003217D34


title: Covid_004369D34


title: Covid_0000116722


title: Covid_003214D34


title: Covid_002516D55


title: Covid_0000116721


title: Covid_0000116715


title: Covid_0000116716


title: Covid_004568D34


title: Covid_002490D55


title: Covid_20700920867


title: Covid_20700920870


title: Covid_20200112288


title: Covid_20700920847


title: Covid_20700920840


title: Covid_20700920816


title: Covid_20200112291


title: Covid_20700920818


title: Covid_20700920860


title: Covid_20700920854


title: Covid_20700920864


title: Covid_20700920873


title: Covid_20700920852


title: Covid_20700920845


title: Covid_20700920848


title: Covid_20700920957


title: Covid_20700920869


title: Covid_20700920931


title: Covid_20700920992


title: Covid_20700920985


title: Covid_20700920967


title: Covid_20700921011


title: Covid_20700920888


title: Covid_20700920980


title: Covid_20700920949


title: Covid_20700920971


title: Covid_20700920968


title: Covid_20700920919


title: Covid_20700920943


title: Covid_20700920861


title: Covid_20700920907


title: Covid_20700920984


title: Covid_20700920891


title: Covid_20700920969


title: Covid_66502


title: Covid_002729D55


title: Covid_20700920920


title: Covid_004321D34


title: Covid_20700920921


title: Covid_20700920915


title: Covid_20700920922


title: Covid_20200112388


title: Covid_20200112374


title: Covid_20700920881


title: Covid_20700920874


title: Covid_106333


title: Covid_145472


title: Covid_20700920926


title: Covid_20200112379


title: Covid_66499


title: Covid_20200112342


title: Covid_20200112339


title: Covid_20200112404


title: Covid_20700920923


title: Covid_20200112373


title: Covid_20200112403


title: Covid_20200112371


title: Covid_20200112392


title: Covid_20200112340


title: Covid_20700920851


title: Covid_0000116711


title: Covid_0000137487


title: Covid_0000116709


title: Covid_0000116718


title: Covid_002816D54


title: Covid_20200112399


title: Covid_0000116717


title: Covid_004674D54


title: Covid_0000116776


title: Covid_005538D58


title: Covid_004647D58


title: Covid_20200112395


title: Covid_20200112336


title: Covid_20200112365


title: Covid_0000116720


title: Covid_20200112370


title: Covid_20200112376


title: Covid_20200112405


title: Covid_20200112328


title: Covid_20200112369


title: Covid_106335


title: Covid_20200112363


title: Covid_20200112316


title: Covid_20200394096


title: Covid_20200112346


title: APC Mutant small intestine organoid 11T rep3 [SAM24363804]

status: Public on Jul 21 2022

city: South San Francisco

first: Matthew

middle: R

last: Grimmer

address: 1 DNA Way

department: Discovery Oncology

institute: Genentech

data_processing:
RNA-seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads. The remaining reads were aligned to the mouse reference genome (NCBI Build 38; GRCm38; mm10) using GSNAP37 version 2013-10-10, allowing a maximum of two mismatches per 50-base sequence (parameters: -M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1–pairmax-rna = 200000–clip-overlap). Transcript annotation was based on the RefSeq database (NCBI Annotation Release 104). To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated. Read counts were scaled by library size, quantile normalized and precision weights were calculated using the voom R package. Subsequently, differential expression analysis on the normalized count data was performed using the limma R package.
Assembly: GRCm38 / mm10
Supplementary files format and content: counts_release.txt is a tab-delimited matrix table containing the raw count data for all samples across all GRCm38 genes

source_name: Small intestine

growth_protocol: Colon from adult C57BL/6 mice was removed, flushed, opened lengthwise and washed in cold PBS to remove all luminal contents. The colon was cut into 0.5-1 cm pieces in cold PBS, vortexed, washed for 3 times and placed into 25 ml 2.5mM EDTA-PBS for 5 minutes at 37°C. The supernatant was then removed and the colon pieces were washed with PBS followed by the incubation in 25 ml 5mM EDTA-PBS for 15 minutes at 37°C. After being vigorously vortexed, supernatant was collected and was filtered through 100μm filters, spinned at 500 g for 5 min, washed with cold PBS and then resuspended with 1:1 in Intesticult media (StemCell # 06005) and Matrigel (Corning # 356231). Intesticult media was changed on organoids every two-three days and they were passaged by mechanical disruption every 7-10 days. To generate AKPS organoids mutations in Apc, KrasG12D, Trp53 and Smad4 were introduced by CRISPR-Cas9 technology. The following gene-specific sgRNAs were used: Apc CAGGACTGCATTCTCCTGAA, AATGCAGTCCTGTCCCCATG, TTCTTGGGAATGACCCCATG, Kras CTGAATTAGCTGTATCGTCA and G12D donor sequence, Trp53 GGAGCTCCTGACACTCGGAG and Smad4 GATGTGTCATAGACAAGGTG. Organoids were dissociated into a single-cell suspension using accutase (Sigma-Aldrich) for 5 min at 37 °C and then electroporated with 2 μl of Cas9 and 3 μl of sgRNA using the P1 buffer and CM137 program (Lonza). After electroporation cells were embedded in Matrigel and DMEM advanced (GIBCO) media supplemented with 10 mM Hepes (Sigma-Aldrich), 2 mM GlutaMAX (Life Technologies), 1x Penicillin/Streptomycin (Life Technologies), 1x N2 (GIBCO), 1x B27 (GIBCO), 1mM N-acetysteine (Sigma Aldrich), 50 ng/ml EGF (Life Technologies), 100 ng/ml Noggin (Peprotech), and R-spondin-1 (R&D systems). Selection for mutated cells was performed using growth factor depletion from the culture medium (R-spondin depletion to select for Apc deficient cells, EGF depletion to select for Kras+/G12D cells, presence of 10 μ M Nutlin-3 (Sigma-Aldrich) to select for Trp53 mutants, and Noggin depletion with presence of TGF-β (Peprotech, 10 ng/ml) to select for cells with Smad4 deficiency. Normal colon organoids were obtained from donor west and were cultured in Intesticult Organoid Growth Medium (Stem cell, Cat # 06010). Patient derived organoids colorectal cancer organoids PDM95, PDM96 and PDM2674 were purchased from ATCC, Cat # HCM-CSHL-0142-C18, HCM-CSHL-0143-C20 and HCM-CSHL-0382-C19).  Established CRC organoids were cultured in ATCC organoid media #1. Organoid media #1 consists of Advanced DMEM:F12 (Thermo Fisher, Cat # 12634028), 10mM HEPES (Genentech), 2mM L-Glutamine (ATCC, Cat # 30-2214), 1x B27 (Thermo Fisher, Cat # 17504-044), 100ng/mL Noggin (Bio-techne, Cat # 6057-NG), 50ng/mL EGF (Bio-techne, Cat # 236-EG), 10nM Gastrin (Bio-techne, Cat # 3006), 10uM SB202190 (Bio-techne, Cat # 1264), 500nM A83-01 (Bio-techne, Cat # 2939), 10mM Nicotinamide (LKT Labs, Cat # N3310) and 1.25mM N-Acetyl Cysteine (LKT Labs, Cat # A0918). All human colon organoids were grown in 50% matrigel plugs (Corning, Cat #356231). At confluency, media was aspirated from well and organoid plugs were resuspended in PBS with pipetting to dissociate extracellular matrix. Cells were centrifuged at 500g for 5 minutes at 4°C before aspiration of PBS and resuspension of cells in TrypLE Express (Gibco, Cat# 12604013). Organoids were dissociated by incubation at 37°C for 3-5 minutes with intermittent pipetting to aid dissociation. After enzymatic and mechanical dissociation, cold basal media was added to organoids and cells were centrifuged at 500g for 5 minutes at 4°C. Media was carefully aspirated, and subsequently organoids were washed 1x with cold PBS and centrifuged at 500g for 5 minutes at 4°C. PBS was carefully aspirated and organoids were resuspended in 50:50 mix of complete media and matrigel. Organoids were seeded in 3D domes on pre-warmed plates and allowed to solidify for 5 minutes at 37°C before plate inversion and 15 minutes before addition of media.

extract_protocol: RNA-sequencing (RNA-seq) libraries were prepared with the TruSeq RNA Sample Preparation kit (Illumina, CA). The libraries were sequenced on Illumina HiSeq 2500 sequencers to obtain on average 34 million 50-bp single-end reads per sample.

value: Small intestine

value: primary organoid

tag: genotype

value: APC mutation 11T


title: hCS at day 257 of differentation

status: Public on Jul 23 2022

city: Stanford

first: Kevin

last: Kelley

address: 318 Campus Drive

institute: Stanford University

data_processing:
Gene expression levels were quantified for each putative nuclei barcode using the 10x Genomics CellRanger analysis software suite (version 6.1.2).
CellRanger count command with –include-introns=TRUE to include reads mapping to intronic regions.
For t-hCS samples, human nuclei were identified based on a conservative requirement of at least 95% of total mapped reads aligning to the human genome.
Raw count matrices outputted from CellRanger were further processed using the R  (version 4.1.2) package Seurat (version 4.1.1) (Stuart et al., 2019). Low quality nuclei with less than 1,000 unique genes detected and with mitochondrial counts accounting for greater than 20% of the total counts were identified and removed. Gene normalization (sctransform), PCA anaylsis (top 30 PCs), clustering (FindNeighbors/FindClusters, dataset dimension = 30, resolution=0.5) were performed using Seurat with default paramaters.
An initial round of clustering was performed with a high-resolution parameter (resolution = 2) to identify subpopulations of low-quality cells based on outlier low gene count detection, predominantly mitochondrial marker genes , and/or high proportions of putative doublets using the DoubletFinder package (McGinnis et al., 2019). Following low quality nuclei removal, each sample was reanalyzed using the above Seurat workflow with a clustering resolution = 0.5. We identified and categorized major cell classes through marker gene expression and comparisons with published literature.
Assembly: human (GRCh38, Ensemble release 98) and rat (Rnor_6.0, Ensemble release 100)
Supplementary files format and content: tsv files with feature  and nuclei barcode  information corresponding to row and column indices of gene count data for each sample
Supplementary files format and content: matrix exchange format for sparse matrices of gene count data for each sample
Supplementary files format and content: csv file with annotated cell classes of high-quality nuclei for each sample
Supplementary_files_format_and_content: rds files are processed seurat objects in RDS format

source_name: hCS day 257

growth_protocol: To initiate the generation of hCS from hiPS cells cultured on feeders, intact hiPS cell colonies were lifted from the plates using dispase (0.35 mg ml−1) and transferred to ultra-low-attachment plastic dishes (Corning) in hiPS cell medium supplemented with the two SMAD inhibitors dorsomorphin (5 μM, Sigma-Aldrich, P5499) and SB-431542 (10 μM, Tocris, 1614) and the ROCK inhibitor Y-27632 (10 μM, Selleckchem, S1049). For the first five days, the hiPS cell medium was changed every day and supplemented with dorsomorphin and SB-431542. On the sixth day in suspension, neural spheroids were transferred to neural medium containing neurobasal-A (Life Technologies, 10888), B-27 supplement without vitamin A (Life Technologies, 12587), GlutaMax (1:100, Life Technologies), penicillin and streptomycin (1:100, Life Technologies) and supplemented with the epidermal growth factor (EGF, 20 ng ml−1; R&D Systems) and fibroblast growth factor 2 (FGF2, 20 ng ml−1; R&D Systems) until day 24. From day 25 to day 42, the medium was supplemented with brain-derived neurotrophic factor (BDNF, 20 ng ml−1, Peprotech) and neurotrophin 3 (NT3, 20 ng ml−1, Peprotech) with medium changes every other day. From day 43 onward, hCSs were maintained in unsupplemented neurobasal-A medium (NM, Thermo Fisher, 1088022) with medium changes every 4–6 days.

extract_protocol:
Nuclei isolation was performed as described in (Matson et al., 2018) with some modifications. Briefly, t-hCS and hCS were disrupted using the detergent-mechanical cell lysis method with a 2 ml glass tissue grinder (Sigma-Aldrich/KIMBLE, D8938). Crude nuclei were then filtered using a 40 μm filter and centrifuged at 320 x g for 10 minutes at 4°C before performing a sucrose density gradient to separate them from cellular debris. After a centrifugation step (320 x g, 20 minutes at 4°C), samples were resuspended in 0.04% BSA/PBS supplemented with 0.2 U/μl RNAse inhibitor (Ambion 40U/μl, AM2682) and passed through a 40 μm flowmi filter.
Dissociated nuclei were then resuspended in PBS containing 0.02% BSA and loaded onto a Chromium Single cell 3’ chip (with an estimated recovery of 10,000 cells per channel). snRNA-seq libraries were prepared with the Chromium Single cell 3’ GEM, Library & Gel Bead Kit v3 (10x Genomics).

value: cell type:hiPS-derived cortical spheroids (hCS)

tag: differentiation day

tag: cell line

value: in vitro


title: Covid_0000116724

tag: cell type


title: APC Mutant small intestine organoid 11T rep1 [SAM24363802]


title: transplanted hCS at day 227 of differentiation

source_name: t-hCS day 227

value: transplanted into rat


title: APC Mutant small intestine organoid 5T rep1 [SAM24363796]

value: APC mutation 5T


title: Normal small intestine organoid rep2 [SAM24363794]

value: WT


title: D6_PMNs_WT (phagocyte infection)

status: Public on Jul 20 2022

city: New York City

first: Ze

last: Chen

state: New York

address: 430 East 29th Street

institute: NYU Grossman School of Medicine

data_processing:
Libraries were generated for each donor using the CelSeq2 protocol and were sequenced on Illumina HiSeq (phagocyte infection) and Illumina NovaSeq (whole blood). Reads were mapped by Bowtie2.3.1 to the hg38 reference genome, and uniquely mapped indices were determined by HTSeq-counts.Before normazlization, we removed genes which express among less than 25% of samples, removed genes whose average values are lowest 10 percent and removed genes whose coefficient of variation are lowest 10 percent. Normalized count tables were generated in R (v3.5.1) using DESeq2 (v1.30.1)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include normalized count values for each Sample

source_name: Neutrophils

extract_protocol:
Cells were washed with PBS. Cells were resuspended in RLT buffer (Qiagen) and vortexed for 1 min before being placed at −80°C. RNA for each donor was then isolated with the RNeasy Plus Mini Kit (Qiagen) following the protocol with on column DNAse Digestion (Qiagen).
Libraries were generated for each donor using the CelSeq2 protocol (Hashimshony et al. Genome Biol 2016) and were sequenced on  Illumina NovaSeq.

tag: experiment name

value: phagocyte infection

tag: individual

value: donor 3

value: Lac

tag: moi

value: Neutrophils


title: APC Mutant small intestine organoid 5T rep2 [SAM24363797]

tag: tissue


title: transplanted hCS at day 224 of differentiation

data_processing:
Gene expression levels were quantified for each putative nuclei barcode using the 10x Genomics CellRanger analysis software suite (version 6.1.2).
CellRanger count command with –include-introns=TRUE to include reads mapping to intronic regions.
For t-hCS samples, human nuclei were identified based on a conservative requirement of at least 95% of total mapped reads aligning to the human genome.
Raw count matrices outputted from CellRanger were further processed using the R  (version 4.1.2) package Seurat (version 4.1.1) (Stuart et al., 2019). Low quality nuclei with less than 1,000 unique genes detected and with mitochondrial counts accounting for greater than 20% of the total counts were identified and removed. Gene normalization (sctransform), PCA anaylsis (top 30 PCs), clustering (FindNeighbors/FindClusters, dataset dimension = 30, resolution=0.5) were performed using Seurat with default paramaters.
An initial round of clustering was performed with a high-resolution parameter (resolution = 2) to identify subpopulations of low-quality cells based on outlier low gene count detection, predominantly mitochondrial marker genes , and/or high proportions of putative doublets using the DoubletFinder package (McGinnis et al., 2019). Following low quality nuclei removal, each sample was reanalyzed using the above Seurat workflow with a clustering resolution = 0.5. We identified and categorized major cell classes through marker gene expression and comparisons with published literature.
Genome_build: human (GRCh38, Ensemble release 98) and rat (Rnor_6.0, Ensemble release 100)
Supplementary_files_format_and_content: tsv files with feature  and nuclei barcode  information corresponding to row and column indices of gene count data for each sample
Supplementary_files_format_and_content: matrix exchange format for sparse matrices of gene count data for each sample
Supplementary_files_format_and_content: csv file with annotated cell classes of high-quality nuclei for each sample
Supplementary_files_format_and_content: rds files are processed seurat objects in RDS format

source_name: t-hCS day 224

value: hiPS-derived cortical spheroids (hCS)

tag: treatment


title: APC Mutant small intestine organoid 8T rep3 [SAM24363801]

value: APC mutation 8T


title: APC Mutant small intestine organoid 11T rep2 [SAM24363803]


title: APC Mutant small intestine organoid 8T rep1 [SAM24363799]


title: APC Mutant small intestine organoid 5T rep3 [SAM24363798]


title: D6_DCs_WT (phagocyte infection)

source_name: dendritic cell

value: dendritic cell


title: transplanted hCS at day 276 of differentiation

source_name: t-hCS day 276


title: D6_Macs_WT (phagocyte infection)

value: macrophage


title: hCS at day 227 of differentation

source_name: hCS day 227


title: D6_Monos_WT (phagocyte infection)

source_name: monocytes

value: monocytes


title: D4_PMNs_WT (phagocyte infection)

value: donor 1


title: D5_DCs_WT (phagocyte infection)

value: donor 2


title: APC Mutant small intestine organoid 8T rep2 [SAM24363800]

value: Small intestine

value: primary organoid


title: D5_Monos_WT (phagocyte infection)


title: hCS at day 236-251 of differentation

value: in vitro


title: D4_Monos_WT (phagocyte infection)


title: D5_PMNs_WT (phagocyte infection)


title: D4_Macs_WT (phagocyte infection)


title: Normal small intestine organoid rep3 [SAM24363795]


title: D6_DCs_Buffer (phagocyte infection)

value: Buffer


title: D6_Macs_Buffer (phagocyte infection)


title: D6_Monos_Buffer (phagocyte infection)


title: D4_DCs_WT (phagocyte infection)


title: D5_Macs_Buffer (phagocyte infection)


title: Normal small intestine organoid rep1 [SAM24363793]


title: D5_PMNs_Buffer (phagocyte infection)


title: D5_Monos_Buffer (phagocyte infection)


title: D5_DCs_Buffer (phagocyte infection)


title: D3_HK100 (whole blood infection)

source_name: whole blood

extract_protocol:
Tubes were spun for 10 min at 450 × g without break. The pellets were resuspended in 2 ml of PAXgene reagent. Tubes were incubated at room temperature for 2 h and placed at 4°C overnight. RNA was then isolated using the PAXGene protocol.
Libraries were generated for each donor using the CelSeq2 protocol (Hashimshony et al. Genome Biol 2016) and were sequenced on  Illumina NovaSeq.

value: whole blood infection

value: 1E8 of Heat Killed at 95 ℃

value: whole blood


title: D5_Macs_WT (phagocyte infection)

value: phagocyte infection


title: D4_PMNs_Buffer (phagocyte infection)


title: D4_Monos_Buffer (phagocyte infection)


title: D3_HK1 (whole blood infection)

value: donor 3

value: 1E6 of Heat Killed at 95 ℃


title: D3_Live100 (whole blood infection)

value: 1E8 of Live bacteria


title: D1R_Live100 (whole blood infection)

value: donor 1 repeated


title: D3_Buffer (whole blood infection)


title: D4_Macs_Buffer (phagocyte infection)


title: D1R_HK1 (whole blood infection)


title: D1R_Buffer (whole blood infection)


title: D4_DCs_Buffer (phagocyte infection)

value: dendritic cell


title: D2_HK100 (whole blood infection)


title: D6_PMNs_Buffer (phagocyte infection)

value: Neutrophils


title: D2_Live1 (whole blood infection)

value: 1E6 of Live bacteria


title: D1R_Live1 (whole blood infection)


title: D2_HK1 (whole blood infection)


title: D2_Live100 (whole blood infection)


title: D1_HK100 (whole blood infection)

value: donor 1


title: D1_Buffer (whole blood infection)


title: D1_HK1 (whole blood infection)


title: D2_Buffer (whole blood infection)

value: donor 2


title: D4_HK65 (Bacterial strains)

value: Bacterial strains

value: donor 4

value: Heat Killed at 65 ℃


title: D1_Live1 (whole blood infection)


title: D4_03928 (Bacterial strains)


title: D4_Boiled (Bacterial strains)

value: Heat Killed at 95 ℃


title: D1_Live100 (whole blood infection)

value: whole blood infection


title: D4_04929 (Bacterial strains)


title: D4_00994 (Bacterial strains)


title: D4_03710 (Bacterial strains)


title: D4_00573 (Bacterial strains)


title: D4_02094 (Bacterial strains)


title: D4_FPR (Bacterial strains)

value: FPR


title: D4_epidermidis (Bacterial strains)

value: S. epidermidis

value: whole blood


title: D4_MUZ211 (Bacterial strains)


title: D4_DsrtA (Bacterial strains)

value: ΔsrtA


title: D4_Dagr (Bacterial strains)

value: Δagr


title: D4_Dcoa (Bacterial strains)

value: ΔcoaΔvWbp


title: D4_Toxinless (Bacterial strains)

value: Toxinless


title: D3_04929 (Bacterial strains)

value: donor 3


title: D4_DsaeQRS (Bacterial strains)

value: ΔsaeQRS


title: D3_HK65 (Bacterial strains)


title: D4_LAC (Bacterial strains)

value: Lac


title: D3_Boiled (Bacterial strains)


title: D3_03928 (Bacterial strains)


title: D3_00994 (Bacterial strains)


title: D3_02094 (Bacterial strains)


title: D3_03710 (Bacterial strains)


title: D4_Buffer (Bacterial strains)

value: Buffer


title: D3_FPR (Bacterial strains)


title: D3_Buffer (Bacterial strains)


title: D3_Dagr (Bacterial strains)


title: D3_LAC (Bacterial strains)


title: D3_epidermidis (Bacterial strains)


title: D3_Toxinless (Bacterial strains)


title: D2_Boiled (Bacterial strains)

value: donor 2


title: D3_00573 (Bacterial strains)

value: Bacterial strains


title: D3_Dcoa (Bacterial strains)


title: D3_MUZ211 (Bacterial strains)


title: D3_DsrtA (Bacterial strains)


title: D2_HK65 (Bacterial strains)


title: D2_04929 (Bacterial strains)


title: D2_03710 (Bacterial strains)


title: D2_00994 (Bacterial strains)


title: D2_MUZ211 (Bacterial strains)


title: D2_02094 (Bacterial strains)


title: D2_epidermidis (Bacterial strains)


title: D2_FPR (Bacterial strains)


title: D2_DsrtA (Bacterial strains)


title: D2_Dcoa (Bacterial strains)


title: D2_Dagr (Bacterial strains)


title: D2_LAC (Bacterial strains)


title: D2_Toxinless (Bacterial strains)


title: D2_00573 (Bacterial strains)


title: D3_DsaeQRS (Bacterial strains)


title: D2_Buffer (Bacterial strains)


title: D1_Boiled (Bacterial strains)

value: donor 1


title: D1_HK65 (Bacterial strains)

value: Heat Killed at 65 ℃


title: D1_02094 (Bacterial strains)


title: D1_03928 (Bacterial strains)


title: D1_00573 (Bacterial strains)


title: D2_DsaeQRS (Bacterial strains)


title: D1_epidermidis (Bacterial strains)


title: D1_04929 (Bacterial strains)


title: D1_FPR (Bacterial strains)


title: D1_MUZ211 (Bacterial strains)


title: D1_DsaeQRS (Bacterial strains)


title: D1_Dcoa (Bacterial strains)


title: D2_03928 (Bacterial strains)


title: D1_03710 (Bacterial strains)


title: D1_Dagr (Bacterial strains)


title: D1_Toxinless (Bacterial strains)


title: D1_LAC (Bacterial strains)


title: 96_noHBV_RO21_100nM_24h

status: Public on Jul 15 2022

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

description: Data contained no reads mapped to HBV genome, thus no raw data are provided for this sample

data_processing:
Linker tags were removed from RNA sequencing by the FASTX Toolkit, v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads mapped to the human genome are removed. The STAR aligner (version 2.6.1d) and the human reference genome GRch38.p12 is used.
The remaining reads were analyzed with HBVouroboros.
Assembly: HBV genomes in HBVdb are used as part of the HBVouroboros
Supplementary files format and content: infref_genome_depth.tsvthe contains values that arethe number of reads at each genomic position of the automatically inferred HBV genotype.

organism: Hepatitis B virus

source_name: HBV-infected hepatocytes Veh RO21 24h

extract_protocol:
Cell were harvested 3h, 6h, 12h, and 24h after test compound addition by removing the culture medium. Cell lysates in 50 µl RLT buffer (QIAGEN, Hombrechtikon, Switzerland) were immediately frozen and stored at -80°C.
For ribosomal RNA depletion the RiboZero magnetic Gold kit (Illumina) was used. Quality of amplified libraries was accessed by capillary electrophoresis with a high sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and quantified by quantitative PCR with a sequencing library quantification kit (KAPA Biosystems) on a Roche Light Cycler 480. Multiplexed libraries with 1 % spiked in PhiX control were sequenced on a HiSeq2500 instrument for 50 cycles using version 4 chemistry reagents (Illumina).

tag: cell type_used_for_viral_infection

value: Hepatocyte

tag: cell genotype

value: WT

tag: time


title: 95_noHBV_RO21_100nM_24h


title: 94_noHBV_RO22_100nM_24h

source_name: HBV-infected hepatocytes Veh RO22 24h


title: 91_noHBV_Veh_0nM_24h

source_name: HBV-infected hepatocytes Veh 24h

value: Veh


title: 90_noHBV_RO21_100nM_24h


title: 92_noHBV_Veh_0nM_24h


title: 93_noHBV_RO22_100nM_24h


title: D1_00994 (Bacterial strains)


title: D1_Buffer (Bacterial strains)


title: D1_DsrtA (Bacterial strains)


title: 88_noHBV_RO22_100nM_24h


title: 86_noHBV_Veh_0nM_24h


title: 80_HBV_Veh_0nM_24h


title: 83_HBV_RO21_100nM_24h


title: 81_HBV_RO22_100nM_24h


title: 82_HBV_RO22_100nM_24h


title: 85_noHBV_Veh_0nM_24h


title: 79_HBV_Veh_0nM_24h


title: 84_HBV_RO21_100nM_24h


title: 78_HBV_RO21_100nM_24h


title: 89_noHBV_RO21_100nM_24h


title: 77_HBV_RO21_100nM_24h


title: 76_HBV_RO22_100nM_24h


title: 74_HBV_Veh_0nM_24h


title: 87_noHBV_RO22_100nM_24h


title: 73_HBV_Veh_0nM_24h


title: 71_noHBV_RO21_100nM_12h

source_name: HBV-infected hepatocytes Veh RO21 12h


title: 72_noHBV_RO21_100nM_12h


title: 70_noHBV_RO22_100nM_12h

source_name: HBV-infected hepatocytes Veh RO22 12h


title: 69_noHBV_RO22_100nM_12h


title: 68_noHBV_Veh_0nM_12h

source_name: HBV-infected hepatocytes Veh 12h


title: 65_noHBV_RO21_100nM_12h


title: 63_noHBV_RO22_100nM_12h


title: 66_noHBV_RO21_100nM_12h


title: 67_noHBV_Veh_0nM_12h


title: 64_noHBV_RO22_100nM_12h


title: 60_HBV_RO21_100nM_12h


title: 62_noHBV_Veh_0nM_12h


title: 59_HBV_RO21_100nM_12h


title: 58_HBV_RO22_100nM_12h


title: 75_HBV_RO22_100nM_24h


title: 54_HBV_RO21_100nM_12h


title: 57_HBV_RO22_100nM_12h


title: 52_HBV_RO22_100nM_12h


title: 53_HBV_RO21_100nM_12h


title: 55_HBV_Veh_0nM_12h


title: 51_HBV_RO22_100nM_12h


title: 46_noHBV_RO22_100nM_6h

source_name: HBV-infected hepatocytes Veh RO22 6h


title: 49_HBV_Veh_0nM_12h


title: 45_noHBV_RO22_100nM_6h


title: 44_noHBV_Veh_0nM_6h

source_name: HBV-infected hepatocytes Veh 6h


title: 43_noHBV_Veh_0nM_6h


title: 61_noHBV_Veh_0nM_12h


title: 42_noHBV_RO21_100nM_6h

source_name: HBV-infected hepatocytes Veh RO21 6h


title: 40_noHBV_RO22_100nM_6h


title: 37_noHBV_Veh_0nM_6h


title: 36_HBV_RO21_100nM_6h


title: 35_HBV_RO21_100nM_6h


title: 34_HBV_RO22_100nM_6h


title: 32_HBV_Veh_0nM_6h


title: 33_HBV_RO22_100nM_6h


title: 50_HBV_Veh_0nM_12h


title: 31_HBV_Veh_0nM_6h


title: 30_HBV_RO21_100nM_6h


title: 29_HBV_RO21_100nM_6h


title: 48_noHBV_RO21_100nM_6h


title: 27_HBV_RO22_100nM_6h


title: 22_noHBV_RO22_100nM_3h

source_name: HBV-infected hepatocytes Veh RO22 3h


title: 47_noHBV_RO21_100nM_6h


title: 28_HBV_RO22_100nM_6h


title: 20_noHBV_Veh_0nM_3h

source_name: HBV-infected hepatocytes Veh 3h


title: 18_noHBV_RO21_100nM_3h

source_name: HBV-infected hepatocytes Veh RO21 3h


title: 26_HBV_Veh_0nM_6h


title: 24_noHBV_RO21_100nM_3h


title: 23_noHBV_RO21_100nM_3h


title: 15_noHBV_RO22_100nM_3h


title: 25_HBV_Veh_0nM_6h


title: 41_noHBV_RO21_100nM_6h


title: 39_noHBV_RO22_100nM_6h


title: 21_noHBV_RO22_100nM_3h


title: 38_noHBV_Veh_0nM_6h


title: 11_HBV_RO21_100nM_3h


title: 09_HBV_RO22_100nM_3h


title: 13_noHBV_Veh_0nM_3h


title: 17_noHBV_RO21_100nM_3h


title: 14_noHBV_Veh_0nM_3h


title: 08_HBV_Veh_0nM_3h


title: 04_HBV_RO22_100nM_3h


title: 16_noHBV_RO22_100nM_3h


title: 19_noHBV_Veh_0nM_3h


title: 03_HBV_RO22_100nM_3h


title: 56_HBV_Veh_0nM_12h


title: 12_HBV_RO21_100nM_3h


title: 10_HBV_RO22_100nM_3h


title: 05_HBV_RO21_100nM_3h


title: 06_HBV_RO21_100nM_3h


title: 02_HBV_Veh_0nM_3h


title: 07_HBV_Veh_0nM_3h


title: 01_HBV_Veh_0nM_3h


title: 3-6-KO1

status: Public on Jul 13 2022

city: Houston

first: Chang-Jiun

last: Wu

state: TX

address: 1515 Holcombe Blvd

department: Genomic Medicine

institute: University of Texas, MD Anderson Cancer Center

data_processing:
The NextSeq RTA (version 2.4.11.0) was used for base calling and bcl2fastq (version 2.20.0) was used to convert the .bcl files into .fastq files.
Fastq files were aligned to the mouse reference genome (mm9) using HISAT2 software and assembled using StringTie.
Comparisons between groups were hampered by low input of total RNA isolated from tumor macrophages manifesting as inconsistent raw/normalized read counts for housekeeping genes in the different groups.
To enable comparisons between APC-WT and APC-KO tumors, we re-normalized the read counts of multiple M2 macrophage markers with housekeeping gene read counts (GAPDH and ACTB)
Assembly: mm9
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Tumor infiltrated macrophage from MC38 orthotopic tumors implanted in C57BL/6J mice.

growth_protocol: APC-WT and APC-KO MC38 orthotopic tumors implanted in C57BL/6J mice were digested with Liberase DL (Roche #5401160001) and Liberase TL (Roche #05401020001).

extract_protocol:
Stained cells were sorted as CD45+, CD11b+, and F4/80+.
Total RNA was isolated from sorted cells and were sequenced by Ultra low Input RAN sequencing (Illumina NexteraXT) with six replicates of each sample.

treatment_protocol: After RBC lysis, cells were blocked with CD16/CD32 blocking antibody (BD Biosciences Cat# 553142, RRID:AB_394657) for 30 min and stained with antibodies: CD45 APC 30-F11 (BioLegend Cat# 103111, RRID:AB_312976), CD11b eFluor 605 M1/70 (Thermo Fisher Scientific Cat# 69-0112-82, RRID:AB_2637406), F4/80 PerCp-Cy5.5 BM8 (BioLegend Cat# 123127, RRID:AB_893496), and SYTOX green (ThermoFisher Cat# R37168).

value: TAM from APC-KO MC38 tumor 1

tag: sample type

value: TAM from APC-KO MC38 tumor 1 replicate 6


title: 3-3-KO1

value: TAM from APC-KO MC38 tumor 1 replicate 3


title: 4-5-KO2

value: TAM from APC-KO MC38 tumor 2

value: TAM from APC-KO MC38 tumor 2 replicate 5