title: RAW264.7, [O] HMGB1 + IL1β, XG-4-3

city: Chicago

first: Xiaodong

last: Ge

state: IL

address: 909 South Wolcott Ave, COMRB 6140

institute: The University of Illinois at Chicago

description: RAW264.7 with Complex or BSA.txt

data_processing:
Data were aligned using RNA-Seq Alignment v.2.0.1 in basespace
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count for each sample

extract_protocol:
Total liver RNA was isolated with illustra™ RNAspin Mini RNA Isolation Kit; RAW264.7 RNA was isolated with Qiagen miRNeasy micro kit.
RNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA library prep

treatment_protocol: Mice were fed with control diet or alcoholic  diet for 6 weeks. RAW264.7 cells were treated with BSA or complex ([O] HMGB1 + IL1β) for 6 hours

value: Monocyte/macropahe-like cells

value: WT

tag: time

value: 6 hours

value: [O] HMGB1 + IL1β

tag: gender

value: Male


title: Input_ChIPseq

status: Public on Feb 21 2024

type: SRA

city: Aurora

first: Elena

last: Abarinov

state: Colorado

address: 1775 Aurora Ct

country: USA

institute: University of Colorado at Denver

description:
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
n/a

library_source: genomic

data_processing:
RNA-seq files
Reads were mapped to the mouse genome (mm10) using the RNA-seq alignment algorithm in the STAR (Spliced Transcripts Alignment to a Reference) software package (version 2.3.1) (Dobin et al., 2013).
To estimate the relative abundances of transcripts, Cufflinks software was used (version 2.2.1) (Trapnell et al., 2013). FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) were calculated per individual gene.
Differential RNA expression across cohorts was assessed using DESeq2 (Love et al., 2014) for E15.5 samples. All other samples were analyzed using EdgeR (version 3.20.9) and limma (version 3.34.9) software (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010).
Assembly: mm10
Supplementary files format and content: raw readcount text file used as input into DESeq2/EdgeR/limma
Supplementary files format and content: text files of results of DESeq2/EdgeR/limma analysis
Supplementary files format and content: text file of abundance measurements (FPKM values)
ChIP-seq files
Peak calling of Nkx2.2 ChIP-seq carried out using the GEM algorithm (Guo et al., 2012).
Read-count intensity was obtained within +/- 500bp of all GEM identified peaks. Read counts of individual replicates were then normalized to their respective sequencing library size, and only loci above a given threshold in both replicates were used for subsequent analysis.
GEM peaks were then further processed as follows. If multiple peaks resided within 500bp of each other, they were merged into one peak using Bedtools (version 2.17.0) (Quinlan, 2010). The locus with the highest read density (+/- 100bp) was identified using Tidyverse (version 1.2.1) (Wickham H., 2019) and utilized as the center of the occupied region. Read counts for replicates were then obtained within +/- 500bp from the center of these merged peaks. The new 500bp readcount dataset was then imported into the EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010).
Final readcounts for all peaks were converted to counts per million (CPM), quantile-normalized, log2 transformed (logCPM), and then averaged. The average logCPM value for each peak was used as a measurement of the level of Nkx2.2 occupancy in that region.
Supplementary files format and content: peak text files generated by GEM software
Supplementary files format and content: raw readcount text files for peaks used as input into EdgeR/limma software and to make logCPM files
Supplementary files format and content: logCPM text files for all peaks used in EdgeR/limma analysis

molecule: genomic DNA

organism: Mus musculus

source_name: MIN6 cells

growth_protocol: Inducible ESC lines were cultured and generated as previously described (Mazzoni et al., 2011). Inducible lines created in this study include wildtype NKX2.2 (iNKX2.2) and SD-mutant NKX2.2 (iSDmut), which harbors the same mutations as the Nkx2.2SDmut mice described above. iNKX2.2 and iSDmut ESC lines were differentiated into MNs as previously described (Wichterle et al., 2002). The first day of the differentiation protocol was referred to as Day 0. To induce expression of the transgenes in OLIG2+ pMN, DOX (1µg/ml) was added on late Day 3 for ~16hrs.

extract_protocol:
See Gutierrez et al, 2017
See Gutierrez et al, 2017

treatment_protocol: Selected samples were treated with doxycycline (DOX) for 14-16hrs prior to collection. See SAMPLES section.

tag: tissue

value: MIN6 cells


title: ARM1_B

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

library_source: transcriptomic

data_processing:
Sequencing was performed on Illumina MiSeq (150) 75 P.E at 2M reads/ sample.
Fastq files were generated using bcl2fastq version 2.19 using the default thresholds.
Reads were aligned to the human genome and analysed using the miRNA Quant tool on the QIAGEN portal using default thresholds (IPA Target Filters are listed among the processed data).
Raw counts were used as input for differential expression analysis using DESeq2, grouping samples in the same ARM compared to the Vehicles.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Gene sets were filtered to contain genes upregulated after treatment (FC >1) and downregulated (FC <0.5).

molecule: total RNA

organism: Homo sapiens

source_name: Prostate Cancer cells

growth_protocol: Cells were injected subcute in nude-nude mice (2x106 in matrigel). When the tumours were visible, the mice were treated as described above. The tumours were harvasted at maximum size of 1000 mm3 or after 21 days of daily treatment.

extract_protocol:
The RNA was extracted from the cells and collected utilizing the column-based method through the miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
The miRNA library preparations were performed with the QIAseq miRNA library prep kit (QIAGEN, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: To obtain single cells, the tumours were dissociated  through mechanical and enzymatic digestion with Collagenase IV (1%) at 37˚C.

tag: cell line

tag: treatments

value: Mycophenolate mofetil (100 mg/kg) – delivered daily by OG in a 0.9% saline solution

tag: experiment

value: in vivo (xenograft)

tag: strain

value: nude-nude

value: tumour explant


title: ARM1_A


title: ARM1_C


title: ARM2_A

value: Abiraterone at 0.5mmol/kg/d in vehicle - delivered by IP in 5% benzyl alcohol, 95% safflower oil together with


title: ARM4_C

value: Mycophenolate mofetil (100mg/kg) and ARN-509 (30mg/kg)


title: RAW264.7, [O] HMGB1 + IL1β, XG-4-1

department: Pathology

description: RAW264.7 with Complex or BSA.txt

tag: cell type

tag: genotype

tag: treatment


title: RAW264.7, [O] HMGB1 + IL1β, XG-4-2

description: RAW264.7 with Complex or BSA.txt


title: ARM3_A

value: ARN-509 at 30mg/kg- delivered daily by OG in a formulation solution consisting of 15% Vitamin E-TPGS and 65% of a 0.5% w/v CMC solution in 20 mM citrate buffer (pH 4.0)


title: Nkx2.2_ChIPseq_rep1 [Nkx2_rep1]

description:
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
n/a
Nkx2_rep1


title: RAW264.7, BSA, XG-1-3

description: RAW264.7 with Complex or BSA.txt

value: BSA


title: Nkx2.2_ChIPseq_rep2 [Nkx2_rep2]

description:
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
n/a
Nkx2_rep2


title: betaKO_rep2 [beta_KO_2]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
beta_KO_2

source_name: 4wk islets

value: 4wk islets


title: 4wk_CTRL_rep2 [4wk_ctrl2]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
4wk_ctrl2


title: Total liver, Rage{delta}Mye, Alcohol diet, XG3-4-2

description: Liver, WT and Rage^mye, CD or EtOH.txt

source_name: Total liver

value: Total liver

value: Liver tissue lysate

value: Rage{delta}Mye

value: 6 weeks

value: Alcohol diet


title: betaKO_rep1 [beta_KO_1]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
beta_KO_1


title: AP_betaSD8 [beta_SD_3]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
beta_SD_3

source_name: 8wk islets

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using Illumina Trueseq RNA Prep Kit.

value: 8wk islets


title: Total liver, Rage{delta}Mye, Alcohol diet, XG3-4-3

description: Liver, WT and Rage^mye, CD or EtOH.txt

value: Male


title: RAW264.7, BSA, XG-1-1

description: RAW264.7 with Complex or BSA.txt

value: Monocyte/macropahe-like cells

value: WT

value: 6 hours


title: AP_betaSD7 [beta_SD_2]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
beta_SD_2


title: Total liver, Rage{delta}Mye, Alcohol diet, XG3-4-1

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: AP_betaSD6 [beta_SD_1]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
beta_SD_1


title: Total liver, Rage{delta}Mye, Control diet, XG3-3-2

description: Liver, WT and Rage^mye, CD or EtOH.txt

value: Control diet


title: AP_ctrl10_8wks [8wk_ctrl2]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
8wk_ctrl2


title: Total liver, Rage{delta}Mye, Control diet, XG3-3-3

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: Total liver, Rage{delta}Mye, Control diet, XG3-3-1

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: iSDmut_EA8_TTAGGC_L003_R1_001 [SD_DOX_2]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
SD_DOX_2

source_name: motor neuron progenitor cells

extract_protocol:
RNA was extracted using Trizol Reagent (Life Technologies, SC: 15596-018) in combination with RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using Illumina Trueseq RNA Prep Kit.

value: ES-derived neuron progenitors

value: mES iSDmut

value: treated with DOX ~16hrs

tag: differentiation stage


title: AP_ctrl9_8wks [8wk_ctrl1]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
8wk_ctrl1


title: RAW264.7, BSA, XG-1-2

description: RAW264.7 with Complex or BSA.txt


title: iNkx2.2_EA14_ATTCCT_L004_R1_001 [WT_DOX_3]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
WT_DOX_3

value: mES iNkx2.2


title: Total liver, WT, Alcohol diet, SD1-29

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: Total liver, WT, Alcohol diet, SD1-28

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: Total liver, WT, Control diet, SD1-39

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: Total liver, WT, Alcohol diet, SD1-31

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: Total liver, WT, Control diet, SD1-37

description: Liver, WT and Rage^mye, CD or EtOH.txt


title: iNkx2.2_EA2_CGTACG_L002_R1_001 [WT_DOX_1]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
WT_DOX_1


title: SAS-HPLM

city: Chuo-ku

first: Jun

last: Nakayama

state: Osaka-shi / Osaka

address: Otemae 3-1-69

country: Japan

institute: Osaka International Cancer Institute

data_processing:
Single-end sequenced reads were checked by FastQC.
Estimation of transcripts was performed using Kallisto.
The expression matrix was constructed and normlized by Tximport in R
Assembly: hg38
Supplementary files format and content: tsv

molecule: polyA RNA

source_name: Human oral cancer cell line

growth_protocol: DMEM or HPLM, 10% heat-inactivated fetal bovine serum, 1% (v/v) Antibiotic-Antimycotic. Cells were cultured in a humidified incubator containing 5% CO2 at 37℃.

extract_protocol:
Total RNA was extracted using QIAzol and the miRNeasy Mini Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocols. RNA quantity and quality were evaluated with a Nanodrop ND-1000 spectrophotometer (Thermo Fisher Scientific) and an Agilent Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
cDNA libraries for RNA sequencing were established from total RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) for selecting poly-A mRNA followed by strand-specific library preparation using MGIEasy RNA Directional Library Prep Set V2.0 (MGI tech). The resulting double-stranded library fragments were further processed into single-stranded circular DNA (sscDNA), which is the final form of MGI library. The sscDNA libraries were quantified by Qubit ssDNA Assay Kit and used for generating DNA nanoballs (DNBs) by rolling circle replication reaction. DNBs were then loaded into a flow cell for sequencing on DNBSEQ-G400 platform (MGI tech), according to the manufacturer’s instructions.

value: Human oral cancer cell line

value: HPLM


title: mESC-Input-Rep2-ConditionL

city: Clayton

first: Evan

last: Healy

state: VIC

address: 23 Innovation Way, Building 77,, Monash University

country: Australia

institute: Monash University

data_processing:
Reads were aligned to the mouse (mm10) or human (hg38) reference genome using bowtie2. Bigwig files were generated using bamCoverage at a resolution of 10bp and number of reads per bin were normalised using CPM (counts per million mapped reads).
Assembly: mm10 and hg38
Supplementary files format and content: bigWig

source_name: mESC

growth_protocol: Mouse embryonic stem cells (mESCs) were grown on gelatinised culture dishes in DMEM supplemented with 10 % FBS (Scientifix; FBSAU-2007A), 1 % (v/v) penicillin-streptomycin (Thermo Scientific #15140122), 50 µM beta-mercaptoethanol (Millipore; ES-007-E), 1:100 non-essential amino acids, 1:100 sodium pyruvate, 1:100 GlutaMax (all GIBCO) and ESGRO leukemia inhibitory factor (LIF) (Millipore; ESG1107; 10,000x). K562 cells were cultured in RPMI-1640 (Merck #R8758) growth medium supplemented with 10 % FBS (Cellsera AU-FBS/SF) and 1 % (v/v) penicillin-streptomycin (Thermo Scientific #15140122),and were incubated at 37 °C with 5 % CO2. K562 cells were acquired from ATCC. Human induced pluripotent stem cells (iPS) were maintained in a feeder-free system on vitronectin (VTN-N; Gibco; A31804) coated tissue culture plastics in Essential 8 Flex medium (Gibco; A2858501). Cells were incubated at 37 ºC and 5 % CO2, and passaged every 2-3 days using 0.5mM EDTA. Human iPS cells were obtained from the Jose Polo Lab. All cell lines were tested periodically for mycoplasma contamination.

extract_protocol:
Mouse ESC, K562 or human iPS cells were collected, counted and washed once with PBS before crosslinking for 10 minutes with PBS containing 1 % formaldehyde (Sigma). Cells were crosslinked in 15 mL falcon tubes at a density of ~5x106 cells/mL. Crosslinking was quenched with 0.125 M Glycine prior to two PBS washes. Crosslinked cells were then snap-frozen on liquid nitrogen and stored at -80ºC before proceeding with the rest of the ChIP assay. rChIP Condition L - ChIP conditions resulting in RNase-dependent loss of PRC2. ChIP assay with RNAse A treatment was performed based on a previous study [Long et al 2020]. Specifically, crosslinked cells were thawed on ice, lysed in 2 mL lysis buffer (50 mM Tris-Cl pH 8.1, 10 mM EDTA, 0.5-1.0 % SDS, plus 1X protease inhibitor cocktail [Sigma; P8340]) and incubated on ice for 10 mins. Chromatin was sheared to approximately 200bp-500bp fragments by sonication using a Bioruptor Plus (Diagenode) at high power. Total sonication time (e.g. total “on” time) was 20 mins with 30 sec on/off pulses. After sonication, the lysate was cleared by centrifugation at 16,300 g for 10 min at 4 ºC. The supernatant was stored at -80ºC or used directly in the ChIP assay. Lysate was diluted 1:5 in IP buffer (16.7 mM Tris-HCl pH 8.1, 1.2 mM EDTA, 167 mM NaCl, 1% Triton X-100 and 1X protease inhibitor cocktail [Sigma; P8340]) and pre-cleared with 50 µL protein G Dynabeads (ThermoFisher; 10004D) for 1 hour at 4 ºC. The sonicated lysate was incubated overnight with antibody while rotating at 4 ºC. Prior to overnight incubation with the antibodies, an input sample was taken (1%). RNase A (DNase and protease-free Thermo Fisher Scientific; #EN0531) was added along with the antibody to the plus RNase A samples at a final concentration of 50 µg/mL. Extracts from 2.5x106 cells were used per ChIP (+/- RNase A). The Next morning, Protein G Dynabeads were equilibrated in IP buffer: 25 µL beads were added to each ChIP and incubated for 1 hour at 4ºC. After incubation, beads were washed twice in low salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 150 mM NaCl, 0.1 % SDS, 1 % Triton x-100), twice with high salt buffer (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 0.1 % SDS, 1% Triton x-100), twice in LiCl buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% Sodium Deoxycholate (w/v), 1% NP-40 substitute) followed by one final wash in TE buffer (10 mM Tris pH 8.0, 1 mM EDTA). All the washes were performed at 4 ºC. Immunoprecipitated material was eluted from the beads with 120 µL elution buffer (0.1 M NaHCO3, 1% SDS) for 20 min at room temperature. The supernatant was retained and 200 mM NaCl was added and incubated along with input samples overnight at 65 ºC while shaking to reverse the crosslinks. The eluted material was then subjected to RNase A (DNase and protease-free Thermo Fisher Scientific; #EN0531) and Proteinase K (ThermoFisher; #EO0491) treatments prior to DNA clean up (QIAGEN MinElute PCR Purification Kit Cat#28004). ChIP enrichments were analysed by qPCR using the QuantiNova SYBR Green PCR kit (Qiagen; 208054). rChIP Condition M - ChIP conditions resulting in no changes to the PRC2 occupancy following RNase A treatment. Crosslinked cells were thawed on ice and lysed in 5 mL of SDS-Lysis buffer (100 mM NaCl, 50 mM Tris pH 8.1, 5 mM EDTA pH 8.0, 0.5 % SDS, 1X protease inhibitor cocktail [Sigma; P8340]). Nuclei and chromatin were pelleted by centrifugation at 1200 rpm for 6 min at room temperature. The supernatant was then discarded, and the pellet was resuspended in 2 mL of ChIP buffer (33 mM Tris-HCl pH 8, 100 mM NaCl, 5 mM EDTA, 0.33% SDS, 1.67% Triton X-100, 1X protease inhibitor cocktail [Sigma; P8340]). Chromatin was sheared to approximately 200 bp to 500 bp fragments by sonication using a Bioruptor Plus (Diagenode) at high power. Total sonication time (i.e. cumulative “on” time) was 15min with 30 sec on/off pulses. Sonicated chromatin was incubated overnight with antibody while rotating at 4 ºC. Prior to overnight incubation with antibodies, an input sample was taken (1 %). RNase A (DNase and protease-free Thermo Fisher Scientific; #EN0531) was added along with the antibody to the plus RNase A samples at a final concentration of 50 µg/mL. Extract from 2.5x106 cells were used per ChIP (+/- RNase A). The following morning, samples were clarified by centrifugation at 20,000 g for 20 min at 4 ºC. Following clarification, the chromatin was incubated for 3 hours with Protein G Dynabeads (ThermoFisher; 10004D; 50 µL beads were used per ChIP). After incubation, the beads were washed three times in Mixed Micelle Buffer (150 mM NaCl, 20 mM Tris pH 8.1, 5 mM EDTA pH 8.0, 5.2 % Sucrose, 1 % Triton X-100, 0.2 % SDS), twice with Buffer 500 (0.1 % Sodium Deoxycholate, 1 mM EDTA pH 8.0, 50 mM HEPES pH 7.5, 1 % TritonX-100), twice with LiCl detergent wash (0.5 % Sodium Deoxycholate, 1 mM EDTA pH 8.0, 250 mM LiCl, 0.5 % NP-40,10 mM Tris pH 8.0) and finally, one wash with TE. All the washes were performed at 4ºC. Immunoprecipitated material was eluted from the beads with 100 µL elution buffer (0.1 M NaHCO3, 1 % SDS) while shaking for 1 hour at 65 ºC. The supernatant was retained and incubated overnight at 65 ºC while shaking to reverse the crosslinks. The eluted material was then subjected to RNase A (DNase and protease-free Thermo Fisher Scientific; #EN0531) and Proteinase K (ThermoFisher; #EO0491) treatments prior to DNA clean up (QIAGEN MinElute PCR Purification Kit Cat#28004). ChIP enrichments were analysed by qPCR using the QuantiNova SYBR Green PCR kit (Qiagen; 208054).
Following ChIP (+/- RNase A) experiments, the precipitated DNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Q32854). A total of 1-10 ng of DNA from each ChIP experiment was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) and NEBNext Multiplex Oligos for Illumina (Set#1 & #2; E7335 & E7500). Following adaptor ligation, DNA was PCR amplified for 4-10 cycles, depending on the amount of the input DNA. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality and size distributions of DNA libraries were ascertained on a TapeStation (Agilent) using High Sensitivity D1000 ScreenTape assay reagents (Agilent; 5067-5585). The resulting libraries were then used for cluster generation and sequencing on an Illumina-based platform with a 150 bp paired-end read format (2-3x107 reads per sample) (GeneWiz/Azenta)

treatment_protocol: RNase A (5-50 ug/mL)

value: mESC

tag: chip antibody


title: Total liver, WT, Alcohol diet, SD1-30

description: Liver, WT and Rage^mye, CD or EtOH.txt

value: Total liver

value: Liver tissue lysate


title: SAS

value: DMEM


title: H3K27me3-neg-Rep2-mESC-ConditionL

value: anti-H3K27me3 (CST - C36B11)


title: H3K27me3-RNaseA-Rep1-mESC-ConditionL

value: RNase A


title: H3K27me3-RNaseA-Rep2-mESC-ConditionL


title: iSDmut_EA4_ACTGAT_L002_R1_001 [SD_DOX_1]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
SD_DOX_1


title: H3K27me3-neg-Rep1-mESC-ConditionL


title: HSC3


title: iNkx2.2_EA6_ATCACG_L002_R1_001 [WT_DOX_2]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
WT_DOX_2


title: Total liver, WT, Control diet, SD1-38

description: Liver, WT and Rage^mye, CD or EtOH.txt

value: 6 weeks

value: Male


title: pMN_EA5_ATTCCT_L002_R1_001 [pMN_CTRL_2]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
pMN_CTRL_2

value: untreated


title: EZH2-neg-Rep1-mESC-ConditionL

value: anti-EZH2 (CST - D2C9)

value: WT


title: Total liver, WT, Control diet, SD1-36

description: Liver, WT and Rage^mye, CD or EtOH.txt

value: Control diet


title: SUZ12-1-pos-RNAse-ConditionM

value: anti-SUZ12 (CST - D39F6)


title: pMN_EA1_GTTTCG_L002_R1_001 [pMN_CTRL_1]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
pMN_CTRL_1

value: ES-derived neuron progenitors


title: 4wk_CTRL_rep1 [4wk_ctrl1]

description:
Adult_pancreas_RNAseq_readcounts.txt
Adult_pancreas_FPKM.txt
Adult_pancreas_RNAseq_SDmut_vs_CTRL_SigGenes.txt
betaSDmut_vs_betaKO_Nkx2.2_bound_SigGenes.txt
Nkx2.2_logCPM_final_sites.txt
RawCounts_Nkx2.2_all_GEM_events.txt
betaSDmut_vs_betaKO_vs_CTRL_SigGenes.txt
4wk_ctrl1

value: 4wk islets


title: mESC-Input-Rep1-ConditionL


title: HSC4-HPLM

value: Human oral cancer cell line


title: EZH2-RNaseA-Rep2-mESC-ConditionL


title: Ctrl 4 mRNA

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

institute: Cincinnati Children's Hospital Medical Center

description: Transcriptome of liver tissue obtained from control subject

data_processing:
HISAT2 was used for mapping trimmed reads to HG19. StringTie was used for the assembly of transcripts.
Trimmed reads were mapped on miRNA precursors using SHiMPS aligner/miRbase and the reads associated with mature miRNAs were counted.
Data were log2-transformed and baselined to the median of all samples. All detected transcripts and miRNAs were tested for differential expression using a moderated t-test (significance cutoff false discovery rate <0.05). Hierarchical clustering and principal component analyses were performed for the identification of sample cluster patterns and transcript/miRNA clusters
Assembly: HG19
Supplementary files format and content: mRNA samples are in .txt format with transcript ID, gene symbol, and FPKM.
Supplementary files format and content: miRNAs are presented in .txt format with miRNA ID and RPM.

source_name: Liver

growth_protocol: Tumors from patients with HCC, corresponding nontumorous liver tissues, and livers from subjects without liver disease as diagnosed by the institutional pathologists were analyzed.

extract_protocol:
For gene expression profiling, total RNA extracted from frozen tissues was processed using Illumina TruSeq Stranded Total RNA. For miRNA sequencing, small RNAs purified from 2 μg of total RNA using a 15% denaturing polyacrylamide gel were barcoded using adapters, and ligated small RNAs were purified, reverse transcribed and amplified by polymerase chain reaction using the following primers: forward, AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA; reverse, CAAGCAGAAGACGGCATACGA.
Ribo-Zero Library Prep per manufacturer’s standard protocol and sequenced using Illumina NovaSeq6000 S (150bp paired-end).

value: Liver

tag: subjectid

tag: diagnosis

value: No liver disease control

tag: tumor type

value: not applicable

tag: tissue location

value: control liver

tag: patient age

value: pediatric


title: HSC4

value: DMEM


title: SUZ12-1-neg-ConditionM

value: mESC


title: Ctrl 1 mRNA


title: HCC Tumor C14 mRNA

description: Transcriptome of non-fibrolamellar hepatocellular carcinoma tumor

value: Hepatocellular carcinoma

value: Non-fibrolamellar

value: tumor


title: RBP1-2-neg-ConditionM

value: anti-RPB1-NTD (CST - D8L4Y)


title: HCC Tumor C13 mRNA

description: Transcriptome of fibrolamellar hepatocellular carcinoma tumor

value: Fibrolamellar


title: INPUT-1-neg-ConditionM

value: WT


title: HCC Tumor C10 mRNA


title: H3K27me3-1-pos-RNase-ConditionM

value: anti-H3K27me3 (CST - C36B11)

value: RNase A


title: HCC Background C10 mRNA

description: Transcriptome of non-fibrolamellar hepatocellular carcinoma background liver tissue

value: background liver


title: EZH2-RNaseA-Rep1-mESC-ConditionL

value: anti-EZH2 (CST - D2C9)


title: EZH2-neg-Rep2-mESC-ConditionL


title: Ctrl 3 mRNA

value: Liver


title: pMN_EA13_ACTGAT_L004_R1_001 [pMN_CTRL_3]

description:
Neural_progenitors_RNAseq_FPKM.txt
Neural_progenitors_RNAseq_readcounts.txt
Neural_progenitors_RNAseq_SigGenes.txt
pMN_CTRL_3

value: ES-derived neuron progenitors

value: mES iNkx2.2

value: untreated


title: HSC3-HPLM

value: Human oral cancer cell line

value: HPLM


title: Ctrl 2 mRNA

value: No liver disease control

value: not applicable

value: control liver

value: pediatric


title: RBP1-2-pos-RNAse-ConditionM

value: mESC

value: anti-RPB1-NTD (CST - D8L4Y)


title: HCC Background C14 mRNA

value: Hepatocellular carcinoma

value: Non-fibrolamellar


title: H3K27me3-1-neg-ConditionM

value: anti-H3K27me3 (CST - C36B11)

value: WT


title: HCC Background C2 mRNA

value: background liver


title: H3K27Ac-1-pos-RNase-ConditionM

value: anti-H3K27Ac (abcam - ab4729)

value: RNase A


title: HCC Tumor C2 mRNA

value: Liver

value: tumor


title: H3K27Ac-1-neg-ConditionM


title: Back epidermis KO3

city: Hangzhou

first: Yingzhe

last: Cui

address: Jiefang road

country: China

institute: Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
(1)Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence; (2) paired-end clean reads were aligned to the Mus Musculus(GRCm38/mm10) using hisat2 (v2.0.5)；(3)featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: Back epidermis

extract_protocol:
RNA was harvested using Trizol reagent. 0.4 ug of total RNA was used for the construction of sequencing libraries；
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Tamoxifen (MCE) treatment was performed by oral gavage of tamoxifen 4 times/week within 4 weeks (0.1 mg/g body weight) of a 20 mg/ml solution in corn oil.

value: Back epidermis

value: Spry1flox/flox K14-Cre-ERT2

value: Tamoxifen


title: HCC Background C1 mRNA

description: Transcriptome of fibrolamellar hepatocellular carcinoma background liver tissue

value: Fibrolamellar


title: Back epidermis KO2


title: Back epidermis KO1


title: HCC Tumor C1 mRNA


title: EZH2-pos-iPS-ConditionL

source_name: iPS

value: iPS

value: anti-EZH2 (CST - D2C9)


title: Back epidermis Ctrl2


title: SUZ12-pos-iPS-ConditionL

value: anti-SUZ12 (CST - D39F6)


title: EZH2-neg-iPS-ConditionL

molecule: cytoplasmic RNA


title: Back epidermis Ctrl3


title: VDJ_pool_4

city: Freising

first: Gustavo

middle: P.

last: de Almeida

state: Bavaria

address: Liesel-Beckmann-Str. 1

department: Division of Animal Physiology and Immunology

country: Germany

institute: Technical University of Munich

description: scRNA-Seq + TCR + Hashing (10x Genomics): The whole dataset consists of the following treatment groups and were demultiplexed using the indicated antibodies: BRAFV600E melanoma in Ptger2-/-Ptger4fl/fl (TotalSeq™-C 0302 anti-mouse Hashtag 2, clone: M1/42;30-F11, Biolegend # 155863), CD4CrePtger2-/-Ptger4fl/fl (TotalSeq™-C 0303 anti-mouse Hashtag 3, clone: M1/42;30-F11, Biolegend # 155865), GzmBCrePtger2-/-Ptger4fl/fl (TotalSeq™-C 0304 anti-mouse Hashtag 4, clone: M1/42;30-F11, Biolegend # 155867) and Wildtype (TotalSeq™-C 0301 anti-mouse Hashtag 1, clone: M1/42;30-F11, Biolegend # 155861) mice.

library_source: transcriptomic single cell

data_processing:
Read alignment, read counting and clonotype call: Performed with 10x Genomics Cell Ranger v6.1.1, using the pre-built mouse reference v2020-A (10x Genomics, Inc) based on mm10 - GENCODE vM23/Ensembl 98. The pipeline was modified according to manufacture instructions to enable compatibility between 5' Chromium Next GEM Single Cell Immune Profiling and cell hashing. At first, only the gene expression libraries were demultiplexed through sample tags with cellranger multi, setting the expected cell number to 21,000. The BAM files were converted to FASTQ files using the tool bamtofastq with the argument --reads-per-fastq set to the total number of reads in the BAM file plus ten thousand. After that, gene expression and TCR analysis were combined by running cellranger multi separately for each demultiplexed sample, disabling library concordance reinforcement. The algorithm was forced to find the number of cells identified in the first step of demultiplexing and sample-specific FASTQ files were used as input for the gene expression analysis pipeline. The pre-built Ensembl GRCm38 Mouse V(D)J Reference v5.0.0 was used for TCR analysis.
[Individual analysis of each group]
Filtering: Only cells with more than 2000 genes detected, less than 10% of mitochondrial genes and with UMI counts less than 3 standard deviations above the mean were kept for downstream analysis. Only data for genes detected in at least 3 cells in each sample were kept. Contaminating cells were identified based on the cluster expression of the marker genes Cd14, Lyz2, Fcgr3, Ms4a7, Fcer1g, Cst3, H2-Aa, Ly6d, Ms4a1 and Ly6d. Cycling cells were identified based on expression of Cdk1, Mcm2, Pclaf, H2afz, Birc5 and Mki67.
Normalization: Filtered read counts from each sample were normalized independently with sctransform v0.3.2 with glmGamPoi method.
Integration: Anchors between cells from different replicates were identified on top 1000 highly variable genes using Canonical correlation analysis and 30 canonical vectors. Data integration was performed on first 20 PCA dimensions.
Dimensional reduction: PCA was calculated for the integrated data on the top 1000 highly variable genes and both KNN graph and UMAP were computed on the 30 nearest neighbors and first 20 PCA dimensions.
Clustering: Louvain clusters were identified using the Shared nearest neighbor (SNN) modularity optimization-based algorithm at resolutions 0.9, 0.65 and 0.9 for the groups Ptger2-/-Ptger4fl/fl, CD4CrePtger2-/-Ptger4fl/fl and GzmBCrePtger2-/-Ptger4fl/fl, respectively.
[Integrative analysis between groups]
Filtering: Data was filtered as mentioned above along with the removal of contaminating cells and cycling cells.
Normalization: Filtered read counts from each sample were normalized independently with sctransform v0.3.2 with glmGamPoi method.
Integration: Anchors between cells from all groups and all their replicates were identified using a more conservative approach that resulted in a weaker integration. For that purpose, reciprocal PCA was applied on top 1000 highly variable genes and anchors were picked using the first 20 dimensions and one neighbor only.
Dimensional reduction: PCA was performed on the integrated data on the top 1000 highly variable genes. KNN graph and UMAP (spread 0.4, min. distance 0.01) were computed on first 20 PCs and 30 nearest neighbors.
Clustering: A resolution of 0.6 was used for Louvain clusters identification using the Shared nearest neighbor (SNN) modularity optimization-based algorithm.
Differential expression: Differentially expressed genes between two groups were identified using the Wilcoxon Rank Sum test and Bonferroni correction.
Trajectory: Transcriptional trajectories were inferred using the R package slingshot v2.4.0 over the UMAP calculated on the integrated data, approximating the curves by 150 points. The pseudotime was calculated as a weighted average across lineages, weighted by the assignment weight.
RNA velocity: Read splicing annotation was performed with velocyto v0.17 using the gene annotation from the pre-built mouse reference v2020-A (10x Genomics, Inc). Expressed repetitive elements were masked based on the genome annotation from UCSC assembly GRCm38/mm10. RNA velocity was estimated using the R package velocyto.R v0.6 with gene-relative model. Gamma fit was performed on the 2% quantile from both extremes and 30 nearest neighbors were used on slope calculation smoothing. For the calculation of cell distances, filtered read counts from all samples were merged and normalized together with sctransform v0.3.2 with glmGamPoi method. PCA was calculated for the merged data on the top 1000 highly variable genes and both KNN graph and UMAP (spread 0.4, min. distance 0.01) were computed on the 30 nearest neighbors and first 20 PCA dimensions. RNA velocities were visualized using correlation-based transition probability matrix within the kNN graph with square root scaling on the UMAP calculated on the integrated data.
TCR repertoire: TCR analysis of clonotype was performed using the R package scRepertoire v1.6.0. Clonotypes were called based on a combination of VDJC genes comprising the TCR and the nucleotide sequence of the CDR3 region.
Assembly: GRCm38.p6 (release 98) - GENCODE Release M23
Supplementary files format and content: Compressed files contain the filtered UMI counts matrix (Market Exchange Format for sparse matrices), TSV files with genes and barcode sequences (corresponding to row and column indices respectively), the filtered VDJ contig annotations as output by Cell Ranger and the .loom file as output from velocyto.R.
Supplementary files format and content: The supplementary metadata file contains annotations for each cell in the whole experiment, with rows being cells and columns being annotated features. It also contains the normalized expression data for each gene (column) in each cell (row).

source_name: BRAFV600E melanoma

extract_protocol:
Tumous were digested with DNase I (100 µg/mL) and Collagenase IV (200 U/mL) for 40 minutes at 37°C and subsequently mashed through a 70 µm and  a 30 µm cell strainer. Cells were labelled with TotalSeq-C Hashtag antibodies (Hashtags 1-4, Biolegend) and stained for surface markers and viability. Intratumoural CD8+ T cells were then sorted (live CD8a+ CD3+ CD45+ cells).
Library construction was carried out by using the following kit and protocol: Chromium Next GEM Single Cell 5' Reagent Kits v2 User Guide with Feature Barcode technology for Cell Surface Protein, Rev D. For sequencing, libraries were pooled fulfilling the minimum criteria: 2x10^4 reads/cell for gene expression libraries and 5x10^3 reads/cell for TCR libraries. Pooled libraries were sent to Novogene for sequencing.

treatment_protocol: Tumours were harvested from mice 11 days post tumour cell inoculation.

value: BRAFV600E melanoma

tag: surface marker

value: CD45, CD8, CD3

value: Tumour infiltrating CD8+ T cells

tag: condition

value: BRAFV600E in Ptger2-/-Ptger4fl/fl, CD4CrePtger2-/-Ptger4fl/fl, GzmBCrePtger2-/-Ptger4fl/fl and Wildtype (C57BL/6J background)

tag: Sex

value: female

tag: replicate


title: HCC Tumor C5 mRNA

tag: tissue

value: Hepatocellular carcinoma

value: pediatric


title: Back epidermis Ctrl1


title: SUZ12-neg-iPS-ConditionL

tag: cell line


title: BGC-823 cells, PCDH9-Cter-Flag-2

city: Shanghai

first: Yajuan

last: Zhang

address: 320 Yueyang Road

institute: Shanghai Institute of Biochemistry and Cell Biology

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine calf serum (HyClone, Logan, UT, USA)

extract_protocol:
1 μg of total RNA was subjected to library synthesis using the TruSeq V2 RNA-Seq kit. 1 μg of total RNA was enriched for the Poly-A mRNA and reverse transcribed to double-stranded cDNA. The cDNA was end repaired, adenylated, and ligated with Illumina indexes prior to 12 cycles of PCR. Sequencing was performed using 12pM hybridization to a 2x150 paired end flow cell.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PCDH9-Cter overexpression


title: BGC-823 cells, PCDH9-Cter-Flag-1


title: BGC-823 cells, Flag-2

value: control


title: VDJ_pool_1


title: VDJ_pool_2


title: BGC-823 cells, Flag-3


title: SP_pool_4


title: SP_pool_2


title: SP_pool_1


title: HMEC-1 rep 4

city: Ljubljana

first: Tim

last: Bozic

address: Zaloška cesta 2

department: Department of Experimental Oncology

country: Slovenia

institute: Institute of Oncology Ljubljana

description: column J in genes.readcount.txt

data_processing:
quality control: fastp
mapping to reference genome: HISAT2
quantification: featurecounts
differential expression analysis: DESeq2
Assembly: GRCh38
Supplementary files format and content: genes.readcount.xls includes counts for each sample

source_name: cell line

growth_protocol: EA.hy926 cells were cultured in Advanced DMEM medium (Gibco) supplemented with 5% FBS. HMEC-1 cells were cultured in MCDB 131 medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), 10 ng/mL epidermal growth factor and 1 μg/mL hydrocortisone. All media were supplemented with 10 mM L-glutamine, 50 mg/mL gentamicin and 100 U/mL penicillin. Both cell lines were purchased from American Type Culture Collection (ATCC) and routinely tested for mycoplasma using MycoAlert™ Plus Mycoplasma Detection Kit (Lonza).

extract_protocol:
Cells were trypsinized with 0.25 % trypsin and the RNA was extracted using the peqGOLD Total RNA Kit (VWR, West Chester, PA, USA) following the manufacturer’s instructions. The purity of the isolated RNA was assessed spectrophotometrically using the A260/A280 and A260/A230 ratios. The quality of the RNA was assessed using the RNA Assay for LabChip® GX Touch (PerkinElmer, Waltham, Massachusetts, ZDA) according to the manufacturer’s instructions. Samples with an RNA Quality Score higher than 6.8 were used for transcriptome sequencing
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.

value: cell line

value: endothelial cells

value: WT


title: BGC-823 cells, Flag-1


title: HMEC-1 rep 3

description: column I in genes.readcount.txt


title: HMEC-1 rep 5

description: column K in genes.readcount.txt


title: SP_pool_3


title: HMEC-1 rep 2

description: column H in genes.readcount.txt


title: GEX_pool_4


title: HMEC-1 rep 1

description: column G in genes.readcount.txt


title: GEX_pool_3


title: GEX_pool_2


title: EA.hy926 rep 5

description: column F in genes.readcount.txt


title: BGC-823 cells, PCDH9-Cter-Flag-3


title: EA.hy926 rep 4

description: column E in genes.readcount.txt


title: GEX_pool_1


title: EA.hy926 rep 3

description: column D in genes.readcount.txt


title: VDJ_pool_3


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep3

data_processing:
Quality control: Reads containing adapter, poly-N, and low quality reads were removed from raw reads using an in-inhouse perl script by Novogene. Q20, Q30, and GC contet of the clean data were calculated. All further data analyses were based on the clean data set.
Clean reads (paired-end) were aligned to the reference genome (Mus Musculus(GRCm38/mm10)) using Hisat2 v2.0.5.
For the quantification of gene espression levels, featureCounts v1.5.0-p3 was used. FPKM of each gene was calculated based on the length and reads count.
Differential expression analysis was performed using DESeq2 R package (1.20.0). The obtained p-values were adjusted using the Benjamini and Hochberg´s apporach for controlling the FDR. Genes were assigned as differentitally expressed when adjusted p-value reached <=0.05 (found by DESeq2).
Assembly: GRCm38/mm10
Supplementary files format and content: The feature_counts.xls files is a Microsoft Excel Binary File containing gene counts as rows and samples and gene features as columns. The gene_fpkm.xls is a Microsoft Excel Binary File containing gene FPKM as rows and samples and gene features as columns.

source_name: spleen

growth_protocol: Naive mouse CD8+ T cells were isolated from mouse spleens and then differentiated into TCF1+CD8+ T cells over 4 days.

extract_protocol:
RNA was isolated using Total RNA Miniprep (Monarch)
Isolated RNA was sent to Novogene for library preparation. Libraries were prepared using mRNA Library preparation Poly A enrichment and The NEB Next® Ultra™ RNA Library Prep Kit (i7 index read, 8bp; i5 index read, 8bp).

treatment_protocol: In vitro differentiated and repetitively stimulated antigen-experienced TCF1+CD8+ T cells were pre-incubated with or without PGE2 (100 ng/mL) for 1 hour at 37°C. Subsequently, the cells were stimulated for an additional 4 hours with low dose IL-2 (85 U/ml) or the combination of low dose IL-2 and aCD3/CD28 beads (1 bead/cell).

value: spleen

tag: developmental stage

value: Naive CD8 T cells isolated from mouse spleen and then differentiated into TCF1+CD8+T cells

value: Murine in vitro differentiated TCF1+CD8+ T cells

value: aCD3/CD28 Beads + IL-2, PGE2


title: EA.hy926 rep 2

description: column C in genes.readcount.txt

tag: cell type


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep2

tag: genotype


title: EA.hy926 rep 1

description: column B in genes.readcount.txt


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep1

tag: treatment


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, no PGE2, rep3

value: aCD3/CD28 Beads + IL-2, Control


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, no PGE2, rep4


title: D30_CHIR

city: Toronto

first: De Hua Andy

last: Yang

state: Ontario

address: 160 College St

department: CCBR

country: Canada

institute: University of Toronto

description: 10xGenomics 3'CellPlex per-sample data output

data_processing:
Data from D11 and D30 were processed, demultiplexed and aligned using 10X Genomics Cell Ranger pipeline (version 6.0.0) to the Human reference (GRCh38)-2020-A
Assembly: Human reference (GRCh38)-2020-A
Supplementary files format and content: tab-seperated vaule files and matrix files

source_name: H1 hESC

extract_protocol:
VM patterning was induced from H1 hESC using CHIR99021 or F5L6.13 and continued differentiation to day 11 and day 30. At the time of harvest, live cells were harvested using Accutase and washed three times before filtering for single cells with 40 µm cell strainers. The cells were then processed following the 10X CellPlex pipeline at Princess Margaret Genomic Sequencing Center (Toronto, Canada)
The CMO labeling was done according to the 10X protocol (https://support.10xgenomics.com/single-cell-gene-expression/overview/doc/demonstrated-protocol-cell-multiplexing-oligo-labeling-for-single-cell-rna-sequencing-protocols), Libraries were prepped according to standard 10X protocol workflow (https://support.10xgenomics.com/single-cell-gene-expression/library-prep/doc/user-guide-chromium-single-cell-3-reagent-kits-user-guide-v31-chemistry).

tag: time point

value: H1 hESC

value: Differentiated with CHIR


title: D11_F5L6.13

value: Differentiated with F5L6.13


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, no PGE2, rep2


title: D11_CHIR


title: Sb3

city: Tianjin

first: Rui

last: Wang

address: Pingjiang Road 23

department: Urology

institute: The Second Hospital of Tianjin Medical University

data_processing:
Paired-end reads were harvested from Illumina NovaSeq 6000 sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3), the high quality clean reads were aligned to the reference genome (UCSC HG19) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (part of cufflinks) was used to get the gene level FPKM as the expression profiles of mRNA
Fold change and p-value were calculated based on FPKM, differentially expressed mRNA were identified
GO and Pathway enrichment analysis were performed based on the differentially expressed mRNAs
Assembly: HG19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

growth_protocol: HK-2 cells were maintained in DMEM-F12 medium supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Qiagen 74134 RNeasy Plus Mini Kit wasused for RNA extracted
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions.RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions.

treatment_protocol: HK-2 cells treated with palmitic acid for 24 h

value: Renal proximal tubular cells

value: BSA+palmitic acid


title: TCF1+CD8+ T cells, no beads, IL-2, PGE2, rep4

value: IL-2, PGE2


title: TCF1+CD8+ T cells, no beads, IL-2, PGE2, rep3


title: TCF1+CD8+ T cells, no beads, IL-2, PGE2, rep2


title: Sb1


title: C3

value: BSA


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep4


title: Sb2


title: C2


title: TCF1+CD8+ T cells, no beads, IL-2, PGE2, rep1


title: TCF1+CD8+ T cells, no beads, IL-2, no PGE2, rep4

value: IL-2, Control


title: TCF1+CD8+ T cells, no beads, IL-2, no PGE2, rep3


title: Input-K562-ConditionL

tag: chip antibody


title: TCF1+CD8+ T cells, no beads, IL-2, no PGE2, rep1


title: C1


title: H3K27me3-RNaseA-ConditionL

value: anti-H3K27me3 (CST - C36B11)

value: RNase A


title: H3K27me3-neg-K562-ConditionL


title: D30_F5L6.13


title: RPB1-pos-Rep2-ConditionL

value: iPS

value: anti-RPB1-NTD (CST - D8L4Y)


title: VSMCs - Hashtag

city: Brooklyn

first: Ngoc

last: Luu

state: NY

address: 6 Metrotech Center

institute: New York University

description: 10x Genomics

library_source: other

data_processing:
Cell Ranger Single Cell Software was used to perform de-multiplexing, barcode and UMI processing, and single-cell 3′ gene counting, Seurat package was used for quality control, data filtering, dimensionality reduction, differential gene expression analysis, and uniform manifold approximation.
Supplementary files format and content: Tab-separated values files and matrix files

molecule: protein

source_name: Vascular smooth muscle cells

extract_protocol:
Four groups of vascular smooth muscle cells  cultured on 6-well plate different conditions (Young, Old, Young + Angiotensin II, Old + siPiezo1) were harvested by 0.25% Trypsin-EDTA (Gibco) and cell viability was confirmed using an automated cell counter (Biorad, TC20).
Cell hashing with anti-mouse oligo-tagged antibodies (TotalSeq A, Biolegend) were performed according to the manufacturer’s protocol before mixing them in single-cell suspension. The libraries were prepared using Chromium Single Cell 3′ Library & Gel Bead Kit v3.1, PN-1000268, the Chromium Next GEM Chip G Single Cell Kit PN-1000120 and theDual Index Kit TT, Set A PN-1000215,(10x Genomics). Amplified cDNA was evaluated on a Agilent BioAnalyzer 2100 using a High Sensitivity DNA Kit (Agilent Technologies) and final libraries on a Agilent TapeStation 4200 using High Sensitivity D1000 ScreenTape (Agilent Technologies).

treatment_protocol:
Young vascular smooth muscle cells were treated with 10-7 M Angiotensin II (AngII) for 48 hours in Young + AngII group
Knockdown of Piezo1 was performed by siRNA transfection with 20 nM of either ON-TARGETplus Piezo1 siRNA Reagents (L-061455-00-0005, Horizon Discovery) or ON-TARGETplus non-targeting control pool (D-001810-10-05, Horizon Discovery) using Lipofectamine™ 3000 Transfection Reagent (L3000001, Invitrogen).

value: Vascular smooth muscle cells

value: two control and two experimental group

tag: age

value: 12-78 weeks old


title: VSMCs - GEX

description: 10x Genomics


title: RPB1-neg-Rep2-ConditionL

value: WT


title: TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, no PGE2, rep1

value: spleen

value: Naive CD8 T cells isolated from mouse spleen and then differentiated into TCF1+CD8+T cells

value: Murine in vitro differentiated TCF1+CD8+ T cells

value: aCD3/CD28 Beads + IL-2, Control


title: Mid-Aged, Infected

city: Sapporo

first: Kyoko

last: Hida

address: Kita-ku, N13W7

institute: Hokkaido University

data_processing:
NovaSeq Control Software v 1.7.5
Real Time Analysis (RTA) v 3.4.4
bcl2fastq2 v 2.20
DRAGEN Bio-IT Platform v.3.7.5
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited text files include TPM values and read counts for each Sample.

source_name: lung endothelial cells

extract_protocol:
RNA was harvested using ReliaPrep™ RNA Miniprep Systems (Promega).
RNA libraries for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing following manufacturer's protocols.

value: lung endothelial cells

value: mid-aged


title: Young, Infected

value: young


title: iPS-INPUT-neg-ConditionL


title: Young, Uninfected

value: PBS


title: Mid-Aged, Uninfected


title: RPB1-pos-Rep1-ConditionL


title: Sitag

city: Beijing

first: Haidong

last: Tang

address: Shuangqing Road

institute: Tsinghua University

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the SeekOne tools software v1.2.0 (https://www.seekgene.com/fxrj).
Assembly: NOT PROVIDED
Supplementary files format and content: NOT PROVIDED

source_name: Tumor

extract_protocol:
Single cell suspensions were prepared from mouse tumor tissues. CD45+ cells were sorted by MACS.
Library was performed according to the manufacter’s instructions (SeekOne® DD Single Cell 5’ library preparation kit, SeekOne).

value: Tumor

tag: strain

value: MC38-OVA tumor-bearing mice

value: Sitagliptin


title: Ctrl

value: Control


title: E15.5_Mut_8351_D [Mutant_8351_D]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Mutant_8351_D

source_name: E15.5 whole pancreas

value: E15.5 whole pancreas


title: H3K27me3-pos-Rep1-ConditionL

value: iPS

value: anti-H3K27me3 (CST - C36B11)

value: RNase A


title: H3K27me3-neg-Rep1-ConditionL

value: WT


title: TCF1+CD8+ T cells, no beads, IL-2, no PGE2, rep2

value: spleen

value: IL-2, Control


title: E15.5_Mut_8627_F [Mutant_8627_F]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Mutant_8627_F


title: H3K27me3-pos-Rep2-ConditionL


title: H3K27Ac-pos-Rep1-ConditionL

value: anti-H3K27Ac (abcam - ab4729)


title: E15.5_Mut_8640_F [Mutant_8640_F]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Mutant_8640_F


title: E15.5_Mut_8640_G [Mutant_8640_G]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Mutant_8640_G


title: E15.5_Ctrl_8627_D [Control_8627_D]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Control_8627_D


title: RBP Perturb-seq

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Department of Biochemistry and Biophysics

institute: UCSF

description: 10x Genomics Chromium v3 Chemistry. Sample was sequenced twice, (10X_* file names indicate first sequencing run, JY*_ file names indicate second sequencing run). Mu_matrix.tsv is the embeddings matrix

data_processing:
Cell Ranger (version 3.0.1, 10X Genomics) with default parameters was used to align reads and generate digital expression matrices from single-cell sequencing data. To assign cell genotypes, a bwa reference (H. Li and Durbin 2009) database was created containing all guide sequences present in the library using bwa index command. The barcode-enrichment libraries were mapped to this database to establish the guide identities; to detect the cell barcodes, the barcode correction scheme used in Cell Ranger was used (the mapping of uncorrected to corrected barcodes was extracted from Cell Ranger analysis run of the whole transcriptome libraries; this mapping was then applied to the reads of barcode-enrichment libraries). UMI correction was performed by merging the UMIs within the hamming distance of 1 from each other. For each UMI, the guide assignment was done by choosing the guide sequence most represented among the reads containing the given UMI. To make the final assignment of a guide to cell barcodes, we only considered the barcodes that were represented by at least 5 different UMIs, with >80% UMIs representing the same guide.  Data filtering was performed using scanpy package (F. A. Wolf, Angerer, and Theis 2018). Data were denoised using a modification of scvi autoencoder (Gayoso et al. 2022) with loss function penalizing for the similarity between cells having different RBPs knocked down. The distance between transcriptome profiles of individual RBP knockdowns was calculated by applying the t-test to individual gene counts across the cells that were assigned the respective guide sequence.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files.
Supplementary files format and content: Cell barcode to sgRNA comma-separated mapping file

growth_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. The 293T cells (ATCC CRL-3216) were cultured in DMEM high-glucose medium supplemented with 10% FBS, glucose (4.5 g/L), L-glutamine (4 mM), sodium pyruvate (1 mM), penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). The K562 cell line was cultured in RPMI-1640 medium supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). All cell lines were routinely screened for mycoplasma with a PCR-based assay.

extract_protocol: 68 RBPs were chosen for Perturb-seq analysis based on the clustering analysis of ENCODE eCLIP dataset and DeepBind dataset (Alipanahi et al. 2015). Perturb-seq experiment was performed as previously described (Datlinger et al. 2017). Briefly, a library of 205 sgRNAs (5 non-targeting sgRNAs and 200 sgRNAs targeting 100 genes, 2 sgRNAs per gene) was ordered as a pooled oligonucleotide library from Twist Bioscience with the following design:  [ATCTTGTGGAAAGGACGAAACACCG]-[Protospacer Sequence]-[GTTTTAGAGCTAGAAATAGCAAGTTAAAATAAGGC]  The library was PCR-amplified using Q5 Hot Start High-Fidelity 2X Master Mix (NEB) with the primers with the following sequences: 5’-ATCTTGTGGAAAGGAC-3’ and 5’-GCCTTATTTTAACTTGCTA-3’. To clone libraries into CROPseq-Guide-Puro vector (Addgene 86708), the starting vector was digested with BsmBI following the protocol outlined in (Sanjana, Shalem, and Zhang 2014). The library was cloned into the digested backbone using Gibson Assembly method (Thomas, Maynard, and Gill 2015). The reaction product was transformed into Takara Stellar competent cells according to manufacturer recommendations, grown overnight in 100 mL LB with ampicilin and purified using ZymoPURE II Plasmid Midiprep Kit. K562 cells were infected with the plasmid library at a low multiplicity of infection to minimize double infection. The infected cells were selected with 2 µg/mL puromycin for 3 days. Live cells were isolated on a flow cytometer (FACSAria II) by propidium iodide staining. Approximately 5000 live cells were captured by 10X Chromium Controller using Chromium Single Cell 3’ Reagent Kits v2. Sample preparation was performed according to the manufacturer’s protocol. Samples were sequenced on a NovaSeq 6000 using the following configuration: Read 1: 28, i7 index: 8, i5 index: 0, Read 2: 98.  To facilitate sgRNA assignment, sgRNA-containing transcripts were additionally amplified by PCR reactions by modifying a previously published approach (Hill et al. 2018). The following primers were used for amplification: 5'-AATGATACGGCGACCACCGAGATCTACAC-3' and 5'-CAAGCAGAAGACGGCATACGAGATTACGACAGGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCTggactatcatatgcttaccgtaacttgaaag-3'. PCR product was cleaned up by 1.0x SPRI beads (SPRIselect; BECKMAN COULTER; Cat. No. B23317). Samples were sequenced using paired-end 150 bp sequencing on an Illumina MiSeq sequencer.

treatment_protocol: K562 cells expressing dCas9-KRAB fusion protein were constructed by lentiviral delivery of pMH0006 (Addgene #135448) and FACS isolation of BFP-positive cells.  The lentiviral constructs were co-transfected with pCMV-dR8.91 and pMD2.D plasmids using TransIT-Lenti (Mirus) into 293T cells, following the manufacturer’s protocol. The virus was harvested 48 hours post-transfection and passed through a 0.45 µm filter. Target cells were then transduced overnight with the filtered virus in the presence of 8 µg/mL polybrene (Millipore).  Guide RNA sequences for CRISPRi-mediated gene knockdown were cloned into pCRISPRia-v2 (Addgene #84832) via BstXI-BlpI sites. After transduction with sgRNA lentivirus, K562 cells were selected with 2 µg/mL puromycin (Gibco). Knockdown of target genes was assessed by RT-qPCR using PerfeCTa SYBR Green SuperMix (QuantaBio) per the manufacturer’s instructions. HPRT1 was used as endogenous control.


title: H3K27Ac-neg-Rep1-ConditionL


title: E15.5_Ctrl_8640_A [Control_8640_A]

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Control_8640_A


title: ACMs, KDM5B_sgRNA1-3

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing:
All RNA-seq libraries were sequenced on an Illumina NovaSeq Sequenced reads were aligned to the human genome (GRCh38) using STAR (279a) Differential expression analysis was performed with DESeq2 (1301) Pathway enrichment analysis was carried out with Metascapeorg
Assembly: hg38
Supplementary files format and content: GeneCounts_RNAseq_KDM5B.csv

source_name: Differentiated HPS

extract_protocol:
Total RNAs from ACMs were extracted with the QIAGEN RNeasy Mini Kit (74106) according to the manufacturer’s instructions
KAPA HyperPrep RNA-seq with RiboErase (KK8560) followed according to manufacturers instructions
Total RNA-seq libraries

value: Differentiated HPS

value: atrial cardiomyocyte

value: KDM5B LentiCrispr 1


title: ACMs, KDM5B_sgRNA2-2

value: KDM5B LentiCrispr 2


title: ACMs, KDM5B_sgRNA2-3


title: onc+msc.ev 2w

city: Guangzhou

first: xialin

last: liu

address: Jinsui Road

institute: Zhongshan Opythalmic Center, Sun yat-sen University

description: 10x Genomics

data_processing:
10X Genomics Cellranger 3.0.2
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Retina

extract_protocol:
Retinas from 6 mice per group were pooled together and cut into small pieces to be digested in Ames’ Medium containing 15 U/mL papain (Worthington) and 0.1 mg/mL DNase I (Sigma) at 34 ℃for fifteen minutes. After centrifugation in 300 g for 8 min at 4 ℃, cell pellets were resuspended and incubated with 10 µL of CD45 Microbeads (Miltenyi Biotec) in 90 µl MACS buffer (0.5% BSA in PBS) per 107 total cells at 4 ℃ for 15 min according to the manufacture instruction. After washed with MACS buffer, single cell suspension was applied onto the column (Miltenyi Biotec), which was placed in the magnetic field of a MACS Separator (Miltenyi Biotec).Magnetically labeled CD45+ cells were immediately flushed out into the collection tube by firmly pushing the plunger into the column with 1 ml MACS buffer.
ScRNA-seq libraries were prepared using the Chromium Single Cell 30 Reagent Kits v3 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer’s instructions. Briefly, single cells were partitioned with Gel beads in EMulsion (GEMs) using the Chromium instrument. Then, cells lysis, reverse transcription, cDNA amplification, enzymatic fragmentation, adaptor attachment, and sample indexing were performed sequentially. Generated libraries were sequenced on an Illumina NovaSeq 6000, at a sequencing depth of 50K-100K reads per cell and followed by de-multiplexing and mapping to the mouse genome (build mm10) using CellRanger (10x Genomics, version 3.0.2) with default parameter.

value: Retina immune cells

value: Retina

value: 6-8 weeks old

value: MSC-sEV


title: ACMs, KDM5B_sgRNA2-1


title: ACMs, KDM5B_sgRNA1-2


title: H3K27me3-neg-Rep2-ConditionL


title: ACMs, KDM5B_sgRNA1-1


title: brain microvascular pericytes P4 msc.ev treated 2

data_processing:
The quality of all datasets was checked by FastQC (v 0.11.8), and low-quality reads were removed.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. The output matrix was utilized as input into BIOMEX software.
Identification of differentially expressed genes between experimental group and control group was performed by the default module of differential analysis based on LIMMA methods in BIOMEX. Pathway enrichment was performed by the GSEA module.
Supplementary files format and content: 10mm
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: brain microvascular pericytes

extract_protocol:
Cells and retinas were resuspended in 1 ml of Trizol buffer (Cat. No. 9109, TAKARA) for RNA extraction. Total RNA was purified, and the RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Libraries were constructed using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: brain microvascular pericytes

value: treated with MSC.sEV

tag: time

value: 12 hour


title: RPB1-neg-Rep1-ConditionL

value: iPS

value: anti-RPB1-NTD (CST - D8L4Y)


title: brain microvascular pericytes P4 msc.ev treated 3

value: WT


title: onc 2w

description: 10x Genomics

value: PBS


title: ACMs, Ctrl_sgRNA_3

value: ctrl

value: ctrl LentiCrispr


title: ACMs, Ctrl_sgRNA_2

value: Differentiated HPS


title: brain microvascular pericytes P4  replicate 2

value: treated with PBS


title: brain microvascular pericytes P4  replicate 3


title: ACMs, Ctrl_sgRNA_1

value: atrial cardiomyocyte


title: Sample_1000

city: Chicago

first: Gayatry

last: Mohapatra

address: 840 S Wood Street

institute: University of Illinois at Chicago

data_processing:
FASTQ files corresponding to the forward and reverse reads for 189 samples in total, 96 FM and 93 control were obtained from Basespace and used for analysis. The files were processed using the Trim Galore (Babraham Bioinformatics) and Cutadapt (DOI:10.14806/ej.17.1.200) tools to perform a quality trimming by removing short, low quality reads and the adapters. RNA-seq reads were mapped to the reference genome (Gencode.v38) and aligned using STAR aligner. Duplicate reads were removed and uniquely mapped transcripts were selected using Samtools. The TPMs (Transcripts per million) were computed using StringTie corrected by IsoformSwitchAnalyzeR and normalized using TMM (Trimmed Means of M value). Differential expression analysis was performed using DESeq2, using all annotated genes. Ontological analysis of gene expression was carried out using the Qiagen Ingenuity Pathway Analysis (IPA), and Gene Set Enrichment Analysis (GSEA). The Interactome analysis was carried out by Pearson Correlation clustering using the 914 most differentially expressed genes for FM1 and the 361 most differentially expressed genes for FM2 using Cytoscape,  the clusters were determined by AlegroMcode (AllegroViva Corporation, 2011) using default parameters.
Assembly: HG38
Supplementary files format and content: Log of normalized transcripts per million

source_name: Blood

extract_protocol:
Total RNA was extracted using QIAamp RNA blood mini kit
RNA libraries were prepared using Agilent SureSelectXT RNA Direct workflow following manufacturer’s instructions.
Hybridization capture method, paired-end sequencing

value: Blood

value: Blood cells from Healthy patient (CONTROL)

value: Female

tag: disease state

value: Healthy patient (CONTROL)


title: onc+msc.ev treated replicate 3

source_name: Retina cells

value: Retina cells

value: Day 1


title: brain microvascular pericytes P4  replicate 1

value: brain microvascular pericytes


title: E15.5_Ctrl_8640_C [Control_8640_C]

city: Aurora

first: Elena

last: Abarinov

address: 1775 Aurora Ct

institute: University of Colorado at Denver

description:
E15.5_pancreas_RNAseq_readcounts.txt
E15.5_pancreas_RNAseq_SigGenes.txt
E15.5_pancreas_RNAseq_Normalized_readcounts.txt
Control_8640_C

data_processing:
RNA-seq files
Reads were mapped to the mouse genome (mm10) using the RNA-seq alignment algorithm in the STAR (Spliced Transcripts Alignment to a Reference) software package (version 2.3.1) (Dobin et al., 2013).
To estimate the relative abundances of transcripts, Cufflinks software was used (version 2.2.1) (Trapnell et al., 2013). FPKM values (Fragments Per Kilobase of exon per Million fragments mapped) were calculated per individual gene.
Differential RNA expression across cohorts was assessed using DESeq2 (Love et al., 2014) for E15.5 samples. All other samples were analyzed using EdgeR (version 3.20.9) and limma (version 3.34.9) software (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010).
Assembly: mm10
Supplementary files format and content: raw readcount text file used as input into DESeq2/EdgeR/limma
Supplementary files format and content: text files of results of DESeq2/EdgeR/limma analysis
Supplementary files format and content: text file of abundance measurements (FPKM values)
ChIP-seq files
Peak calling of Nkx2.2 ChIP-seq carried out using the GEM algorithm (Guo et al., 2012).
Read-count intensity was obtained within +/- 500bp of all GEM identified peaks. Read counts of individual replicates were then normalized to their respective sequencing library size, and only loci above a given threshold in both replicates were used for subsequent analysis.
GEM peaks were then further processed as follows. If multiple peaks resided within 500bp of each other, they were merged into one peak using Bedtools (version 2.17.0) (Quinlan, 2010). The locus with the highest read density (+/- 100bp) was identified using Tidyverse (version 1.2.1) (Wickham H., 2019) and utilized as the center of the occupied region. Read counts for replicates were then obtained within +/- 500bp from the center of these merged peaks. The new 500bp readcount dataset was then imported into the EdgeR (version 3.20.9) and limma (version 3.34.9) software packages (Phipson et al., 2016; Ritchie et al., 2015; Robinson et al., 2010).
Final readcounts for all peaks were converted to counts per million (CPM), quantile-normalized, log2 transformed (logCPM), and then averaged. The average logCPM value for each peak was used as a measurement of the level of Nkx2.2 occupancy in that region.
Supplementary files format and content: peak text files generated by GEM software
Supplementary files format and content: raw readcount text files for peaks used as input into EdgeR/limma software and to make logCPM files
Supplementary files format and content: logCPM text files for all peaks used in EdgeR/limma analysis

extract_protocol:
RNA was extracted with the RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using Illumina Trueseq RNA Prep Kit.

value: E15.5 whole pancreas


title: onc+msc.ev treated replicate 2


title: Sample_996

value: Blood cells from Fibromylagia patient (FMA)

value: Male

value: Fibromylagia patient (FMA)


title: onc treated replicate 3

value: WT

value: ONC+PBS


title: onc treated replicate 2


title: Sample_988


title: Sample_994


title: Sample_992


title: Naïve CD4 T cell, KO_S1PR1_H

city: New York

first: Dhaval

last: Dixit

address: 550 First Avenue

institute: NYU School of Medicine

data_processing:
For the RNA sequencing analysis, sequencing reads were mapped to the mouse reference genome (GRCm38.85/mm10) using the STAR aligner (v2.5.0c).
Alignments were guided by a Gene Transfer Format file. The mean read insert sizes and their standard deviations were calculated using Picard tools (v.1.126)
The read count tables were generated using HTSeq (v0.6.0), normalized based on their library size factors using DEseq2, and differential expression analysis was performed.
The read per million normalized BigWig files were generated using BEDTools (v2.17.0) and bedGraphToBigWig tool (v4).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

source_name: lymph nodes

extract_protocol:
RNA was isolated from FACS-sorted naïve CD4+ T cells using TRIzol LS (Invitrogen) followed by DNase I (QIAGEN) treatment and cleanup with an Rneasy Plus Micro kit (QIAGEN), and quantified on a 2100 BioAnalyzer instrument (Agilent technologies, Inc.).
The RNASeq library prep and sequencing were performed at the NYU Langone Genome Technology Center. 5-20 ngs of total RNA was used to prepare libraries using Trio RNA-Seq library prep kit (Tecan Genomics, Inc.) following manufacturer’s instructions. The protocol contains the following steps: DNase treatment to remove any DNA in the sample, first strand and second stand cDNA synthesis from the input RNA, single primer isothermal amplification (SPIA) of the resultant cDNAs, enzymatic fragmentation and construction of unique barcoded libraries, PCR library amplification (4 cycles were used) and an AnyDeplete step to remove rRNA transcripts. The Agencourt AMPure XP bead (Beckman Coulter) purified libraries were quantified using by qPCR and the size distribution was checked using Agilent TapeStation 2200 system.

value: lymph nodes

value: naive CD4 T cell

tag: strain background


title: onc treated replicate 1


title: brain microvascular pericytes P4 msc.ev treated 1

value: treated with MSC.sEV

value: 12 hour


title: Sample_944

value: Blood


title: Naïve CD4 T cell, KO_S1PR1_D


title: Sample_986


title: Naïve CD4 T cell, KO_S1PR1_B


title: Naïve CD4 T cell, KO_S1PR1_J


title: Sample_938

value: Blood cells from Healthy patient (CONTROL)


title: Sample_950

value: Female


title: onc+msc.ev treated replicate 1


title: Naïve CD4 T cell, Ctrl_S1PR1_I

value: littermate S1pr1 ctrl


title: Naïve CD4 T cell, Ctrl_S1PR1_E


title: Sample_713


title: Sample_942

value: Healthy patient (CONTROL)


title: Naïve CD4 T cell, Ctrl_S1PR1_C


title: Naïve CD4 T cell, Ctrl_S1PR1_A


title: Sample_940


title: Sample_998


title: Sample_936


title: Naïve CD4 T cell, Ctrl_S1PR1_G


title: Sample_990


title: Sample_709


title: Sample_715


title: Naïve CD4 T cell, KO_S1PR1_F


title: Naïve CD4 T cell, KO_SPNS2_7


title: Naïve CD4 T cell, KO_SPNS2_1


title: Sample_701


title: Naïve CD4 T cell, Ctrl_SPNS2_4

value: littermate Spns2 ctrl


title: Sample_707


title: Sample_705


title: Naïve CD4 T cell, KO_SPNS2_3


title: Sample_695


title: Sample_699


title: Naïve CD4 T cell, Ctrl_SPNS2_6


title: Sample_697


title: Sample_691


title: Sample_711


title: cDC2 EGFP+ rep2 [M_14_2_P]

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.39).
Trimmed sequence reads were mapped to mm10 using STAR (2.7.5c).
Read count extraction was performed using cufflinks (v2.2.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

extract_protocol:
RNA was extracted and reverse transcription was carried out following a previous study (Picelli et al. Nature Protocols, 2014, 9: 171-181).
RNA libraries for RNA-seq were prepared using KAPA Hyper Prep Kits following manufacturer's protocols.

value: Tumor

value: Colon cancer


title: Sample_693

value: Blood cells from Fibromylagia patient (FMA)


title: cDC2 EGFP- rep1 [M_13_2_M]


title: Sample_658


title: Naïve CD4 T cell, KO_SPNS2_5


title: cDC1 EGFP- rep2 [M_14_1_M]


title: Sample_703


title: cDC2 EGFP+ rep1 [M_13_2_P]


title: cDC2 EGFP- rep2 [M_14_2_M]


title: cDC1 EGFP+ rep2 [M_14_1_P]


title: cDC1 EGFP+ rep1 [M_13_1_P]


title: Sample_644


title: Sample_654


title: Sample_656


title: Sample_652

value: Male


title: Sample_650

value: Fibromylagia patient (FMA)


title: cDC1 EGFP- rep1 [M_13_1_M]

value: WT


title: SH9-3

city: Shijiazhuang

first: Kun-ang

last: Liu

state: Hebei

address: No. 46, Friendship South Street, Qiaoxi District

department: Institute of Biology

institute: Hebei Academy of Sciences

description:
X9ck-3
processed data file: gene_expression.txt

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads, sequencing adapters, short-fragment reads and other low-quality reads.
We used Hisat2 (version:2.0.4) to map the cleaned reads to the Fv1.0 reference genome with two mismatches.
Cufflinks v2.1.1 was run with a reference annotation to generate FPKM values for known gene models.
Genome_build: Fv1.0
Supplementary_files_format_and_content: gene_expression.txt: Tab-delimited text file includes counts and FPKM values for each Sample.

organism: Flammulina velutipes

source_name: mycelium

growth_protocol: Mycelia were harvested after 10 days of cultivation on PDA medium at 25 ° C.

extract_protocol:
Total RNA was extracted by using mirVana miRNA Isolation kit and treated with RNase-free DNase Set to remove potential genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain/background

tag: phenotype

value: parent

value: mycelium


title: JK502-2

description:
X502-2
processed data file: gene_expression.txt

value: anti-disease


title: SH9-2

description:
X9ck-2
processed data file: gene_expression.txt


title: Naïve CD4 T cell, Ctrl_SPNS2_2

value: lymph nodes

value: naive CD4 T cell


title: JK502-1

description:
X502-1
processed data file: gene_expression.txt


title: Sample_636

value: Blood

tag: Sex


title: SH9-1

description:
X9ck-1
processed data file: gene_expression.txt


title: Sample_632


title: Sample_642


title: Sample_646


title: JK502-3

description:
X502-3
processed data file: gene_expression.txt


title: Sample_640


title: Sample_634


title: JK501-3

description:
X501-3
processed data file: gene_expression.txt

value: early fruiting


title: Sample_638

value: Female


title: Ribo-seq bam,hs-bam 38hr AHS rep2

first: Tamsin

middle: Joy

last: Samuels

address: Downing Street

department: Department of Genetics

institute: University of Cambridge

description:
38h_Ribo
Ribo_seq_fpkm.csv

data_processing:
*library strategy: Ribo-Seq
Trimmed reads were aligned to non-coding RNA reference sequences (flybase, dmel_r6.39) using Bowtie
non rRNA reads were mapped to the Drosophila melanogaster reference genome dm6 using STAR
Ribo-seq reads quantified and differentially translated genes were identified using Cuffdiff v2.2.1
Assembly: dm6
Supplementary files format and content: .bw and .bigWig files are bigWig files for each sample
Supplementary files format and content: RNA_Seq_fpkm.csv contains FPKM values for every gene at each time point in the RNA-seq
Supplementary files format and content: Ribo_Seq_fpkm.csv contains FPKM values for every gene at each time point in the Ribo-seq

organism: Drosophila melanogaster

source_name: whole adult ovary

growth_protocol: Adult females were heatshocked at 37C for 1 hour then 34C for 2 hours, then returned to 25C. Samples were collected with no heat shock, or at different times after heat shock (AHS)

extract_protocol:
Ovaries were dissected for each sample in cold Dissection buffer (PBS 1X, 0.01% Tween 20, 100 μg/ml cycloheximide) and stored at -80°C. Frozen samples were homogenised with an electrical pestle in Polysome extraction buffer (50 mM Tris pH 7.5, 5 mM MgCl2, 150 mM NaCl, 0.5% Triton x-100, 1 mM DTT, 100 μg/ml cycloheximide, protease inhibitor, 25 u/ml Turbo DNAse), then passed 20 times through a 26-gauge needle. The lysate was centrifuged at 20,000g for 10 min at 4°C to pellet tissue debris. 100-140 μg of total RNA was used for Ribo-seq. Total RNA was treated with 1.25 units of RNase I (Ambion) per μg RNA, and the quenched with SuperaseIn (0.8 units per μg RNA). The sample was brought to 1 ml by adding Polysome extraction buffer and subjected to a 3 ml 34% sucrose cushion, by centrifugation at 70,000 rpm for 5.5 hr at 4°C. The resulting pellet was resuspended in nuclease free water with 1% SDS. RNA was extracted with hot phenol-chloroform and purified by Zymo RNA Clean & Concentrator kit.
rRNA was depleted as for the RNA-seq through binding of complementary oligos and treatment with RNase H. Size selection was performed on a 15% Urea PAGE Gel, cutting the band corresponding to 28 to 34 bp. RNA was purified by ZYMO small-RNA PAGE recovery kit. RNA was treated with 1 ul of T4 PNK for end repair and libraries were produced with the NEBNext Small RNA Library Kit, according to manufacturer9s instructions. Libraries were size selected at 148-154 nucleotides, corresponding to ligated constructs from 28 to 34 nt RNA fragments.

value: whole adult ovary

value: after heat shock 38hr


title: Sample_626


title: Sample_648


title: Sample_630


title: JK501-1

description:
X501-1
processed data file: gene_expression.txt


title: Ribo-seq bam,hs-bam 18hr AHS rep2

description:
18h_Ribo
Ribo_seq_fpkm.csv

value: after heat shock 18hr


title: JK501-2

description:
X501-2
processed data file: gene_expression.txt


title: Sample_628


title: Ribo-seq bam,hs-bam 38hr AHS rep1

description:
38h_Ribo
Ribo_seq_fpkm.csv


title: Ribo-seq bam,hs-bam 18hr AHS rep1

description:
18h_Ribo
Ribo_seq_fpkm.csv


title: Sample_616


title: Sample_624


title: Sample_618


title: Sample_622


title: Ribo-seq bam,hs-bam 28hr AHS rep2

description:
28h_Ribo
Ribo_seq_fpkm.csv

value: after heat shock 28hr


title: Ribo-seq bam,hs-bam 28hr AHS rep1

description:
28h_Ribo
Ribo_seq_fpkm.csv


title: Sample_620


title: Sample_614


title: Ribo-seq bam,hs-bam 5hr AHS rep2

description:
5h_Ribo
Ribo_seq_fpkm.csv

value: after heat shock 5hr


title: Ribo-seq bam,hs-bam 9hr AHS rep1

description:
9h_Ribo
Ribo_seq_fpkm.csv

value: after heat shock 9hr


title: Sample_612

value: Blood cells from Healthy patient (CONTROL)

value: Male

value: Healthy patient (CONTROL)


title: Sample_610

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: Ribo-seq bam,hs-bam 9hr AHS rep2

description:
9h_Ribo
Ribo_seq_fpkm.csv


title: Sample_608


title: Ribo-seq bam,hs-bam 5hr AHS rep1

description:
5h_Ribo
Ribo_seq_fpkm.csv


title: Sample_604


title: Sample_606


title: Ribo-seq bam,hs-bam no HS rep2

description:
0h_Ribo
Ribo_seq_fpkm.csv

value: no heat shock


title: Sample_600


title: Ribo-seq bam,hs-bam 0.5hr AHS rep2

description:
0_5h_Ribo
Ribo_seq_fpkm.csv

value: after heat shock 0.5hr


title: Ribo-seq bam,hs-bam no HS rep1

description:
0h_Ribo
Ribo_seq_fpkm.csv


title: Sample_602


title: Sample_598


title: Sample_596


title: Sample_592


title: Sample_594


title: Sample_590


title: Sample_588


title: Sample_586


title: Ribo-seq bam,hs-bam 0.5hr AHS rep1

description:
0_5h_Ribo
Ribo_seq_fpkm.csv


title: Sample_584


title: Sample_582


title: Sample_578


title: Sample_576


title: Sample_574


title: A699-80

type: RNA

city: Graz

first: Silvia

last: Groiss

address: Neue Stiftingtalstraße 6

department: Institute of Pathology

country: Austria

institute: Medical University of Graz

description:
Pat21 <5% HCC t3
cDNA, from amplified total RNA

hyb_protocol: Affymetrix GeneChip Human Genome U219 Array Plate (Cat No. ???); Affymetrix GeneChip® HT hybridization, Wash and Stain Kit (Cat No. 900720); Affymetrix Genechip®  fluidics station 450: protocol FS450_0001 for Cartridge Arrays

scan_protocol: Affymetrix Scanner: GCS3000

data_processing: Affymetrix Geneexpression Console (Expression Console EC1.2.1.20) using Affymetrix default analysis settings for generation of CEL-files. Data Pre-Processing and Filtering (Partek Software, v.6.6): RMA  (background correction, quantile normalization across all chips in the experiment, log2 transformation, median polish summarization); paired t-test

label: Biotin

source_name: liver

label_protocol: Affymetrix GeneChip® 3’ IVT Express Kit (P/N 702646 Rev. ; Cat.No. 901228

extract_protocol: not provided

value: liver

tag: patient

value: pat 21

tag: disease

value: HCC

tag: steatosis


title: A699-81

description:
Pat21 <5% HCC t0
cDNA, from amplified total RNA

tag: tissue


title: A699-83

description:
Pat21 <5% HCC t2
cDNA, from amplified total RNA


title: A699-74

description:
Pat19 >20% CRC Met t1
cDNA, from amplified total RNA

value: pat 19

value: CRC Met


title: A699-77

description:
Pat20 >20% CRC Met t0
cDNA, from amplified total RNA

value: pat 20


title: A699-82

description:
Pat21 <5% HCC t1
cDNA, from amplified total RNA


title: A699-70

description:
Pat18 >20% HCC t1
cDNA, from amplified total RNA

value: pat 18


title: Sample_570

value: Blood

tag: cell type

value: Female


title: A699-75

description:
Pat19 >20% CRC Met t2
cDNA, from amplified total RNA


title: Sample_572


title: Sample_568


title: A699-71

description:
Pat18 >20% HCC t2
cDNA, from amplified total RNA


title: A699-78

description:
Pat20 >20% CRC Met t1
cDNA, from amplified total RNA


title: Sample_564


title: A699-79

description:
Pat20 >20% CRC Met t2
cDNA, from amplified total RNA


title: A699-73

description:
Pat19 >20% CRC Met t0
cDNA, from amplified total RNA


title: A699-72

description:
Pat19 >20% CRC Met t3
cDNA, from amplified total RNA


title: Sample_566


title: Sample_531


title: Sample_580


title: Sample_529


title: A699-76

description:
Pat20 >20% CRC Met t3
cDNA, from amplified total RNA


title: A699-66

description:
Pat17 <5% other t1
cDNA, from amplified total RNA

value: pat 17

value: other


title: A699-69

description:
Pat18 >20% HCC t0
cDNA, from amplified total RNA


title: Sample_527

value: Blood cells from Healthy patient (CONTROL)

value: Male


title: A699-68

description:
Pat18 >20% HCC t3
cDNA, from amplified total RNA


title: A699-67

description:
Pat17 <5% other t2
cDNA, from amplified total RNA


title: A699-62

description:
Pat16 <5% CRC Met t1
cDNA, from amplified total RNA

value: pat 16


title: A699-63

description:
Pat16 <5% CRC Met t2
cDNA, from amplified total RNA


title: Sample_525

value: Healthy patient (CONTROL)


title: A699-64

description:
Pat17 <5% other t3
cDNA, from amplified total RNA


title: Sample_523


title: Sample_517

value: Blood cells from Fibromylagia patient (FMA)

value: Fibromylagia patient (FMA)


title: Sample_521


title: Sample_519


title: Sample_509


title: Sample_505


title: Sample_515


title: Sample_511


title: Sample_507


title: Sample_503


title: Sample_501


title: Sample_497


title: A699-59

description:
Pat15 <5% CRC Met t2
cDNA, from amplified total RNA

value: liver

value: pat 15


title: S1-36_Con3

city: Jinju-si

first: Hyun-Eui

last: Park

state: Gyeongsangnam-do

address: 15, Jinju-daero 816beon-gil

department: College of Medicine

country: South Korea

institute: Gyeongsang National University

data_processing:
FastQC v0.11.7 was conducted to assess the quality of sequences, and only sequences with a Phred quality score ≥ 30 were retained for further analysis
Trimmomatic 0.38 was used to trim and crop Illumina (FASTQ) data as well as to remove adapters.
Bowtie 1.1.2 was used to aligned to the reference genome
HTseq version 0.10.0 was used for initial quality assessment of sequencing runs
Assembly: Mycobacterium intracellulare ATCC 13950
Supplementary files format and content: Expression_Profile.ASM27712v1.gene.txt file includes raw counts for each sample

organism: Mycobacterium intracellulare

source_name: Bacteria

growth_protocol: M. intracellulare were incubated in 7H9 broth supplemented with 0.5% glycerol and 10% OADC at 37℃ and 250 rpm

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.0 µg of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Library Prep Gold Kit

treatment_protocol: For oxidative stress, 10 mM of hydrogen peroxide was treated for 16h. For acidic stress, bacterial cells were treated with pH 4.5 Sauton's media for 16h.

value: Bacteria

tag: genotype

value: Untreated (control)


title: A699-58

description:
Pat15 <5% CRC Met t1
cDNA, from amplified total RNA

value: CRC Met


title: Sample_499


title: A699-60

description:
Pat16 <5% CRC Met t3
cDNA, from amplified total RNA


title: A699-52

description:
Pat14 <5% CRC Met t3
cDNA, from amplified total RNA

value: pat 14


title: A699-61

description:
Pat16 <5% CRC Met t0
cDNA, from amplified total RNA


title: A699-55

description:
Pat14 <5% CRC Met t2
cDNA, from amplified total RNA


title: A699-53

description:
Pat14 <5% CRC Met t0
cDNA, from amplified total RNA


title: A699-57

description:
Pat15 <5% CRC Met t0
cDNA, from amplified total RNA


title: Sample_495


title: S1-36_Con2

tag: treatment


title: S1-36_Con1


title: A699-54

description:
Pat14 <5% CRC Met t1
cDNA, from amplified total RNA

tag: time point


title: Sample_493


title: S1-36_O3

value: 10 mM of hydrogen peroxide


title: Sample_491

value: Blood


title: S1-36_O1


title: A699-56

description:
Pat15 <5% CRC Met t3
cDNA, from amplified total RNA


title: A699-50

description:
Pat13 >20% CRC Met t1
cDNA, from amplified total RNA

value: pat 13


title: A699-49

description:
Pat13 >20% CRC Met t0
cDNA, from amplified total RNA


title: A699-51

description:
Pat13 >20% CRC Met t2
cDNA, from amplified total RNA


title: A699-48

description:
Pat13 >20% CRC Met t3
cDNA, from amplified total RNA


title: A699-47

description:
Pat12 <5% CRC Met t2
cDNA, from amplified total RNA

value: pat 12


title: A699-45

description:
Pat12 <5% CRC Met t0
cDNA, from amplified total RNA


title: S1-36_A2

value: pH 4.5 Sauton's media


title: A699-46

description:
Pat12 <5% CRC Met t1
cDNA, from amplified total RNA


title: S1-36_A1


title: Sample_487

value: Blood cells from Healthy patient (CONTROL)


title: Sample_489

value: Female


title: A699-65

description:
Pat17 <5% other t0
cDNA, from amplified total RNA

value: pat 17

value: other


title: ileum, KO CME(+), rep2

city: Lebanon

first: Mark

last: Sundrud

state: NH

address: Dartmouth Hitchcock Medical Center One Medical Center Drive

department: Microbiology and Immunology

institute: Dartmouth Hitchcock Medical center

description: processed data in countsmatrix.csv column 23, named ‘177212_16’

data_processing:
Quality control performed on reads using FastQC
Reads trimmed using cutadapt. max-n parameter set to 0.8
Aligned to genome using HISAT2 aligner
Sequence metrics and rRNA identified using Picard
Duplicate marking using Picard
Assembly: Gencode GRCm39
Supplementary files format and content: A counts matrix stored as a gz compressed csv. Each row represents a gene, and each column represents a sample. The first row and column contain the name of each of the genes and samples respectively.

source_name: ileum

extract_protocol:
Total RNAs were harvested using TRIzol (Invitrogen) and Rneasy Mini Kit (Qiagen) with Dnase I treatment (Qiagen). 100 ng of total RNAs was used for the construction of sequencing libraries.
cDNA libraries were prepared using QuantSeq 3' mRNA-seq V2 Library Prep Kit with UDI (Lexogen)

treatment_protocol:
Ileal fragments were treated with DMSO, tauroCDCA, or bile acid extraction with or without bile acid depletion for 8 hours.
Medium is Advanced DMEM/F12 (Gibco) containing 100 U/ml penicilin, 100 ug/ml streptomycin, 10 mM HEPES, 2 mM GlutaMAX (Gibco)

value: ileum

value: wild-type

value: male

value: 8 hours


title: S1-36_O2

value: Bacteria


title: ileum, KO CME(+), rep3

description: processed data in countsmatrix.csv column 24, named ‘177212_17’


title: ileum, WT CME(+), rep4

description: processed data in countsmatrix.csv column 22, named ‘177212_15’


title: Sample_483

value: Male

value: Healthy patient (CONTROL)


title: ileum, KO CME(+), rep4

description: processed data in countsmatrix.csv column 25, named ‘177212_18’


title: A699-44

description:
Pat12 <5% CRC Met t3
cDNA, from amplified total RNA

value: liver

value: CRC Met


title: ileum, WT CME(+), rep2

description: processed data in countsmatrix.csv column 20, named ‘177212_13’, removed from analysis for having poor read mapping


title: ileum, KO CME(-), rep4

description: processed data in countsmatrix.csv column 19, named ‘177212_12’


title: A699-42

description:
Pat11 <5% CRC Met t1
cDNA, from amplified total RNA

value: pat 11


title: ileum, KO CME(-), rep3

description: processed data in countsmatrix.csv column 18, named ‘177212_11’, removed from analysis for having poor read mapping


title: Sample_485

value: Blood


title: S1-36_A3


title: A699-40

description:
Pat11 <5% CRC Met t3
cDNA, from amplified total RNA


title: A699-41

description:
Pat11 <5% CRC Met t0
cDNA, from amplified total RNA


title: ileum, KO CME(-), rep2

description: processed data in countsmatrix.csv column 17, named ‘177212_10’


title: Sample_481


title: ileum, WT CME(-), rep4

description: processed data in countsmatrix.csv column 16, named ‘177212_09’

value: 200 uM WT_2278N_silc_extraction_CME(-)


title: Sample_479


title: ileum, WT CME(+), rep3

description: processed data in countsmatrix.csv column 21, named ‘177212_14’


title: ileum, tCDCA, rep4

description: processed data in countsmatrix.csv column 13, named ‘177212_06’

value: 200 uM tauroCDCA


title: ileum, WT CME(-), rep3

description: processed data in countsmatrix.csv column 15, named ‘177212_08’

value: 200 uM WT_2277N_silc_extraction_CME(-)


title: A699-39

description:
Pat10 <5% CRC Met t2
cDNA, from amplified total RNA

value: pat 10


title: ileum, WT CME(-), rep2

description: processed data in countsmatrix.csv column 14, named ‘177212_07’

value: 200 uM WT_2276N_silc_extraction_CME(-)


title: ileum, tCDCA, rep3

description: processed data in countsmatrix.csv column 12, named ‘177212_05’


title: Sample_473

value: Blood cells from Healthy patient (CONTROL)


title: Sample_477


title: A699-43

description:
Pat11 <5% CRC Met t2
cDNA, from amplified total RNA


title: Sample_471

value: Blood cells from Fibromylagia patient (FMA)

value: Female

value: Fibromylagia patient (FMA)


title: ileum, tCDCA, rep2

description: processed data in countsmatrix.csv column 11, named ‘177212_04’

value: ileum

value: wild-type

value: male

value: 8 hours


title: Sample_475

value: Healthy patient (CONTROL)


title: ileum, DMSO, rep4

description: processed data in countsmatrix.csv column 10, named ‘177212_03’

value: 0.6% DMSO


title: ileum, DMSO, rep3

description: processed data in countsmatrix.csv column 9, named ‘177212_02’


title: Sample_469


title: ileum, KO CME(+), rep1

description: processed data in countsmatrix.csv column 7, named ‘170987_0006’

value: Asbt-/-silcextractCME+


title: A699-38

description:
Pat10 <5% CRC Met t1
cDNA, from amplified total RNA

value: liver

value: CRC Met


title: ileum, DMSO, rep2

description: processed data in countsmatrix.csv column 8, named ‘177212_01’


title: Sample_467

value: Blood


title: ileum, KO CME(-), rep1

description: processed data in countsmatrix.csv column 6, named ‘170987_0005’

value: Asbt-/-silcextraxtCME-


title: ileum, WT CME(+), rep1

description: processed data in countsmatrix.csv column 5, named ‘170987_0004’

value: WTsilcextractCME+


title: Sample_465


title: ileum, tCDCA, rep1

description: processed data in countsmatrix.csv column 3, named ‘170987_0002’

value: tauroCDCA


title: A699-36

description:
Pat10 <5% CRC Met t3
cDNA, from amplified total RNA

value: pat 10


title: HSC3, DMEM, rep2

city: Chuo-ku

first: Jun

last: Nakayama

address: Otemae 3-1-69

institute: Osaka International Cancer Institute

data_processing:
Fastq files were trimmed to remove Illumina Nextera adapter sequence using Skewer with “-f sanger -t 20 -m pe -x” options
For removing reads from chrM or repeat sequences, pre-alignments to eliminate reads that would map to these regions using Bowtie2 with “-k 1 -D 20 -R 3 -N 1 -L 20 -I S,1,0.50 -X 2000 --no-mixed --no-discordant” options.
Filtered reads were aligned to the hg38 human reference genome using Bowtie2 with “--very-sensitive -X 2000 -no-mixed --no-discordant” options.
For removing duplicates, Picard (http://broadinstitute.github.io/picard/) MarkDuplicates tool was used with “VALIDATION_STRINGENCY = LENIENT REMOVE_DUPLICATES = true” options.
Peak calling on the Tn5-corrected single-base insertions was conducted using MACS2 with “--shift -75 --extsize 150 --nomodel --call-summits --nolambda --keep-dup all -p 0.01”.
Assembly: hg38
Supplementary files format and content: narrowPeak

source_name: OSCC

extract_protocol:
Cells were detached with trypsin and collected by centrifugation at 1,000 rpm, 5 min, at room temperature.
ATAC-seq libraries were prepared according to the Omni-ATAC protocol (PMID: 28846090).

value: OSCC

tag: cell line

value: Human oral squamous carcinoma

value: DMEM


title: A699-33

description:
Pat9 >20% other t0
cDNA, from amplified total RNA

value: pat 9

value: other


title: HSC3, HPLM1, rep1

value: HPLM


title: HSC3, DMEM, rep1


title: Sample_459

value: Blood cells from Healthy patient (CONTROL)

value: Male


title: A699-37

description:
Pat10 <5% CRC Met t0
cDNA, from amplified total RNA


title: Sample_461

value: Female

value: Healthy patient (CONTROL)


title: ileum, WT CME(-), rep1

description: processed data in countsmatrix.csv column 4, named ‘170987_0003’

value: ileum

value: wild-type

value: male

value: WTsilcextractCME-

value: 8 hours


title: A699-35

description:
Pat9 >20% other t2
cDNA, from amplified total RNA

value: liver


title: A699-34

description:
Pat9 >20% other t1
cDNA, from amplified total RNA


title: HSC3, HPLM1, rep2