title: ChIP-Seq_DnaJ3-HA_Caulobacter_crescentus_UG22107_PYE+Nal20


title: CB cells, efnA5-FC, Rep 4

status: Public on Nov 09 2023

type: genomic

city: Aachen

first: Geraldine

middle: Marion

last: Zimmer-Bensch

state: NRW

address: Worringer Weg 3

department: Neuroepigenetic

country: Germany

institute: RWTH Aachen

description: 1200 ng gDNA bisulfite converted using the Zymo EZ-96 DNA Methylation kit (Zymo Research, Irine, CA, USA)

hyb_protocol: according to instructions

scan_protocol: Illumina iScan System

data_processing: Differentially methylated regions (DMRs) were detected using the R packages Enmix (Xu et al., 2016), sva (Leek, 2007) and minfi (Aryee et al., 2014). The raw idat files were loaded by Enmix::readidat() together with Illumina’s Infinium mouse-methylation manifest file (v.1.0). For background correction, dye bias correction, inter-array normalization and probe type bias correction we applied Enmix::mpreprocess() on the raw idat data setting the parameters qc and impute to TRUE. It returns a matrix of preprocessed methylation beta values. As a second preprocessing step we used sva::ComBat() to mitigate the batch effect contained in these beta values which was introduced by different experiment runs under inevitably different conditions. The experiment run ID was set as the batch variable. Eventually, DMRs were identified by calling minfi::dmpFinder() on the preprocessed beta values. The parameter pheno was set to the respective cell conditions (for each sample either ctrl-Fc or efnA5-Fc) and the parameter type to =”categorical”. CpGs for which the dmpFinder result indicates a p-value of 0.05 or smaller were considered significant DMRs. If not indicated otherwise, default parameters have been passed to the applied R functions.

label: Cy5 and Cy3

molecule: genomic DNA

organism: Mus musculus

source_name: cell culture 24 post treatment

label_protocol: according to instructions

growth_protocol: Cerebellar granule (CB) cells (Fossale et al., 2004) were cultured as previously described (Pensold et al., 2021). Briefly, CB cells were incubated in Dulbecco’s modified Eagle medium (DMEM) with high glucose (#11965084, Gibco), supplemented with 10% fetal bovine serum (FBS) (#S1810, Biowest), 1× GlutaMAX™ (#35050038, Thermo Scientific) and 24 mM KCl at 33℃, 5% CO2 and 95% relative humidity. Upon thawing, the medium was additionally supplemented with 100 U/mL penicillin and 100 µg/mL streptomycin until the first passage.

extract_protocol: 24 h after ephrinA5-Fc or control Fc stimulation, CB cells were harvested and their DNA was extracted using the PureLink® Genomic DNA Mini Kit (#K1820, Invitrogen). The samples were then treated with proteinase K and RNase A supplied in the kit.

treatment_protocol: Cells were stimulated with 5 µg/mL of either the recombinant ephrinA5-Fc (#374-EA, Biotechne) or Fc protein (#109-1103, Rockland) as control, both pre-clustered with 10 µg/mL Alexa488-conjugated anti-human IgG (#A11013, Invitrogen) for 30 min at RT.

tag: cell type

value: cerebellar granule (CB) cells

tag: treatment

value: 5 ug/mL efnA5-FC


title: YAP1_0min_1; TGFb 0min; YAP1 Knock-down

type: SRA

city: Cheongju

first: Jung-Won

last: Lee

address: 1, Chungdae-ro

department: Department of Biochemistry, School of Medicine

country: South Korea

institute: Institute for Tumor Research

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to hg19 whole genome using Tophat
FPKM calculation using Cufflink
Assembly: hg19
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Kidney; Embryo

growth_protocol: HEK293 cells (ATCC, Manassas, VA, USA) were maintained in Dulbecco’s modiﬁed Eagle’s medium (Gibco BRL, Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal bovine serum (Gibco BRL) and 1% penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA). Cells were incubated at 37°C with 5% CO2

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using the NEBNext Ultra II Directional RNA-Seq Kit standard protocols.

treatment_protocol: Cells were cultured at low cell density. Before TGFb1 treatment, cells were cultured under serum-free conditions for 1 h and then, treated with 1 ng/ml TGFb1 (Cat# 100-21C, PeproTech, Rocky Hill, USA).

tag: tissue

value: Kidney; Embryo

tag: cell line

value: HEK 293 cells

value: immortalized human embryonic kidney cells

tag: genotype

value: YAP1 Knock-down

value: TGFb 1ng/ml

tag: time


title: CB cells, ctrl-FC, Rep 4

value: 5 ug/mLFC


title: CB cells, efnA5-FC, Rep 3

description: 1200 ng gNDa bisulfite converted using the Zymo EZ-96 DNA Methylation kit (Zymo Research, Irine, CA, USA)


title: Totalinput_DjlA-HA_Caulobacter_crescentus_UG22388(tipR::Tn)_PYE+Nal20

city: Geneva 4

first: Patrick

middle: H.

last: Viollier

address: Rue Michel Servet 1

department: Dept.  Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva, Faculty of Medicine / CMU

library_source: genomic

data_processing:
Base calling: NextSeq Control Software 4.0.2.7, RTA2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.73+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.2+galaxy0)
Peak calling: MACS2 (Galaxy Version 2.1.1.20160309.6 , No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
Motif-based sequence analysis: http://meme-suite.org/
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Assembly: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary files format and content: The xlsx file reporting DjlA-HA, DnaJ12345-HA and ClpX-HA ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature Type; column 5: Feature Name; column 6: Description; column 7 to 18: DjlA-HA, DnaJ12345-HA and ClpX-HA ChIP-Seq profiles (normalized Read Per Million unit, RPM)

organism: Caulobacter vibrioides

growth_protocol: Overnight cultures in PYE of C. crescentus were freshly restarted (starting O.D.660nm~0.05) in 80ml of PYE supplemented with Xylose 0,3% and incubated at 30°C under agitation. Nalidixic acid treated culture was supplemented with 20 μg/mL of antibiotic 30 minutes before being fixed.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 seconds to shear DNA fragments to an average length of 0.2-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 5% of each pre-cleared lysate were reserved as total input samples (negative control samples). The pre-cleared lysates were then incubated overnight at 4°C with monoclonal rabbit antibodies Anti-HA (1:250 dilution) (Clone 114-2C-7, Merck Millipore). The immuno-complexes were captured after incubation with Protein-A agarose beads (pre-saturated with BSA) during a 4 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A agarose beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 hours at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μL of DNAse/RNAse free water.
Immunoprecipitated chromatins were used to prepare sample libraries used for deep sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions. Single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles were performed and yielded several million reads per sequenced samples.

treatment_protocol: Cultures of exponentially growing cells (O.D.660nm of 0.5) were supplemented with 10 μM sodium phosphate buffer (pH 7.6) and then treated with formaldehyde (1% final concentration) at RT for 10 minutes to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 minutes on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were stored at -80°C.

tag: strain

value: {delta}bla (CCNA_02223) tipR::Tn xyl::Pxyl-djlA-HA

value: Medium supplemented with 0,3% Xylose and treated with Nalidixic acid (20µg/ml) 30 min prior fixation


title: ChIP-Seq_DjlA-HA_Caulobacter_crescentus_UG22103_PYE+Nal20

tag: chip antibody

value: Anti-HA (Merck Millipore, Clone114-2C-7)


title: ChIP-Seq_DnaJ-HA_Caulobacter_crescentus_UG22105_PYE+Nal20


title: RUNX3_0min_3; TGFb 0min; RUNX3 Knock-down

value: RUNX3 Knock-down


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)+Nal_rep2

data_processing:
Base calling: NextSeq Control Software 2.2.0.4, RTA 2.4.11, bcl2fastq2.17 v2.17.1.14
Read sequencing quality control: FastQC, Galaxy Version 0.72
Alignment: Bowtie2, Galaxy Version 2.3.4.3
Raw counts: htseq-count, Galaxy Version 0.9.1
Normalized counts and differential expression analysis: DESeq2, Galaxy Version 2.11.40.6
Assembly: Caulobacter crescentus : NC_011916.1
Supplementary files format and content: The xlsx file reporting the RNA-Seq analysis (Raw counts, Normalized counts and differential expression analysis) is organized as follows: Raw_counts: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(WT)+Nal_rep1; column 5: NA1000(WT)+Nal_rep2; Normalized_counts: column 1: geneID; column 2: NA1000(WT)_rep1; column 3: NA1000(WT)_rep2; column 4: NA1000(WT)+Nal_rep1; column 5: NA1000(WT)+Nal_rep2; Diff_expression_analysis : column 1: Start; column 2: End; column 3: Orientation; column 4: Gene ID; column 5: Name;column 6: Description; column 7: Mean normalised counts; column 8: Log2(Fold change); column 9: SEM Log2(Fold change); column 10: p-value; column 11: -Log10(p-value); column 12: Fold change.

growth_protocol: Overnight cultures in PYE of C. crescentus NA1000(WT) (two independent biological replicates per conditions) were freshly restarted in 10ml of PYE (starting O.D.660nm~0.05) and incubated at 30°C under agitation to reach an O.D.660nm~0,5. Nalidixic acid treated cultures were supplemented with 20 μg/mL of antibiotic 30 minutes before being collected.

extract_protocol:
Cells were lysed in a Ready-Lyse lysozyme solution (Epicentre Technologies) according to manufacturer’s instructions and lysates were homogenized through QiaShredder columns (Qiagen, Switzerland). The RNeasy Mini Kit (Qiagen, Switzerland) was used for total RNA extraction according to the manufacturer’s protocol which included a first DNase treatment using the On-column DNase I digestion kit (Qiagen, Switzerland). Extracted total RNA was subjected to a second DNase treatment using Promega RQ1 at 1 unit/μg of RNA. Another total RNA cleanup was performed after the DNase treatment. The RNA concentration was measured using a Nanodrop 1000 spectrophotometer (ThermoScientific, USA) and RNA quality was assessed using a 2100 Bioanalyzer Instrument (Agilent Technologies, USA).
RNA-Seq library preparation and sequencing was performed at Fasteris SA (Geneva, Switzerland). Bacterial rRNA were removed from each total RNA samples and RNA-Seq libraries were prepared using the Ovation Complete Prokaryotic RNA-Seq library system kit according to the manufacturer’s instructions. Single-end runs were performed on an Illumina NextSeq 500 instrument (50 cycles), yielding several million reads (stored as fastq files).

treatment_protocol: To provide immediate stabilization of RNA, each cell cultures (4ml) are treated with 2 volumes of RNA Protect Bacteria reagent (Qiagen, Switzerland) according to the manufacturer’s protocol.

value: WT

value: Treated with Nalidixic acid (20µg/ml) 30 min prior RNA extraction


title: ChIP-Seq_Control-HA_Caulobacter_crescentus_NA1000_PYE+Nal20


title: RUNX3_0min_1; TGFb 0min; RUNX3 Knock-down


title: CB cells, efnA5-FC, Rep 2


title: ChIP-Seq_DjlA-HA_Caulobacter_crescentus_UG14074_PYE+Nal20.


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)_rep1


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)+Nal_rep1


title: RNA-Seq_Caulobacter_crescentus_NA1000(WT)_rep2


title: CB cells, ctrl-FC, Rep 2


title: Totalinput_Caulobacter_crescentus_UG14074_PYE_Richmedium

data_processing:
Base calling: NextSeq Control Software 4.0.2.7, RTA2.11.3, bcl2fastq2.17 v2.17.1.14
Read Quality: FastQC (Galaxy Version 0.73+galaxy0), FASTQ Trimmer (Galaxy Version 1.1.5)
Alignment: Bowtie2 (Galaxy Version 2.4.2+galaxy0)
Peak calling: MACS2 (Galaxy Version 2.1.1.20160309.6 , No broad regions option) relative to the total input DNA samples. The q-value (false discovery rate, FDR) cut-off for called peaks was 0.05.
Motif-based sequence analysis: http://meme-suite.org/
ChIP-Seq profiles RPM normalized and annotation: SeqMonk Software v1.47.2 (Braham Bionformatics Institute)
Assembly: Caulobacter crescentus NA1000 (NC_011916.1)
Supplementary files format and content: The xlsx file reporting TipR and DjlA-HA ChIP-Seq RPM normalized profiles was generated by SeqMonk software. The sheet is organized in columns as follows: column 1: Start (bp); column 2: End (bp); column 3: Feature strand; column 4: Feature Type; column 5: Feature Name; column 6: Description; column 7 to 10: TipR ChIP-Seq profiles (normalized Read Per Million unit, RPM); column 11 to 14: DjlA-HA ChIP-Seq profiles (normalized Read Per Million unit, RPM)

growth_protocol: Overnight cultures in PYE of C. crescentus NA1000(WT) and UG14074 were freshly restarted (starting O.D.660nm~0.05) in 80ml of PYE or 80ml of PYE supplemented with Xylose 0,3%, respectively, and incubated at 30°C under agitation. Nalidixic acid treated culture was supplemented with 20 μg/mL of antibiotic 30 minutes before being fixed.

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, the cell resuspensions were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 seconds to shear DNA fragments to an average length of 0.2-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 mL using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of Protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 5% of each pre-cleared lysate were reserved as total input samples (negative control samples). The pre-cleared lysates were then incubated overnight at 4°C with polyclonal rabbit antibodies Anti-TipR (1:400 dilution) (Kirkpatrick and Viollier, 2014) or monoclonal rabbit antibodies Anti-HA (1:250 dilution) (Clone 114-2C-7, Merck Millipore). The immuno-complexes were captured after incubation with Protein-A agarose beads (pre-saturated with BSA) during a 4 h incubation at 4°C and then, washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The immuno-complexes were eluted from the Protein-A agarose beads with two times 250 μL elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 hours at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μL of DNAse/RNAse free water.
Immunoprecipitated chromatins were used to prepare sample libraries used for deep sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions. Single-end run was performed on an Illumina Next-Generation DNA sequencing instruments (NextSeq High), 50 cycles were performed and yielded several million reads per sequenced samples.

value: delt_bla (CCNA_02223) PxylX::djlA_HA

value: Medium supplemented with 0,3% Xylose

value: none (input)


title: Totalinput_Caulobacter_crescentus_UG14074_PYE+Nal20


title: CB cells, efnA5-FC, Rep 1

value: cerebellar granule (CB) cells


title: ChIP-Seq_DjlA-HA_Caulobacter_crescentus_UG14074_PYE+Nal20


title: ChIP-Seq_DjlA-HA_Caulobacter_crescentus_UG14074_PYE_Richmedium


title: SJWLM069401_D2

city: Birmingham

first: Changde

last: Cheng

state: AL

address: 1824 6th Ave S, Wallace Tumor Institute 520A

department: Medicine

country: USA

institute: University of Alabama at Birmingham

data_processing:
RNAseq reads were mapping using St. Jude standard pipeline. RNA-seq gene level read counts and FPKM were generated using HTseq-count based on transcript models in GENCODE v19.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include counts for each Sample

source_name: Tumor

extract_protocol:
Trizol
Libraries were prepared from 250 ng to 1000 ng of total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina P/N 20020613)

value: Tumor

tag: disease

value: Wilms tumor


title: SJWLM069399_D4


title: Totalinput_Caulobacter_crescentus_NA1000_PYE+Nal20

value: Treated with Nalidixic acid (20µg/ml) 30 min prior fixation


title: SJWLM069399_D3


title: ChIP-Seq_DnaJ2-HA_Caulobacter_crescentus_UG22109_PYE+Nal20


title: CB cells, ctrl-FC, Rep 1


title: Totalinput_Caulobacter_crescentus_NA1000_PYE_Richmedium


title: CB cells, ctrl-FC, Rep 3


title: A549, input

city: University Park

first: Lu

last: Bai

state: PA

address: 406 South Frear Building

institute: Penn State University

data_processing:
Basecalls were performed using DRAGEN BCL Convert (v3.8.4).
Paired-end reads were filtered using fastp (Version 0.23.2) according to default settings.
Filtered reads were aligned to the human reference genome (hg38) using BWA-MEM2 (Version 2.2.1)
Resulting BAM files were filtered for MAPQ scores > 20 using SAMtools (Version 1.8)
Read coverage (bigwig file) was obtained separately for input and ChIP samples using deepTools “bamCoverage”, with a bin size of 10 bp (Version 3.5.1). In this step, blacklisted regions were removed (hg38 Version 2, https://doi.org/10.1038/s41598-019-45839-z)
ChIP peaks were called using MACS2 callpeak with the default settings (Version 2.1.1.20160309).
Assembly: hg38
Supplementary files format and content: bigwig for ChIP and input samples
Supplementary files format and content: bed only for ChIP samples

growth_protocol: Ham's F-12K (Kaighn's), 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with formaldehyde (1% final concentration) for 10 minutes at room temperature. Crosslinking was quenched with glycine (0.125M final concentration) for 5 minutes ar room temperature. After cell and nuclei lysis, chromatin was fragmented in Diagenode Pico with a circulating water bath at 4°C using the Shear and Go Easy Mode setting for 3 cycles (30 seconds on followed by 30 seconds off).
Sequencing library was constructed by NEBNext ultra II DNA library prep kit (NEB E7103L). 50 million paired-end 50bp reads were obtained for each ChIP and input sample using a NextSeq 2000 instrument.

treatment_protocol: For doxycyline treated cells, doxycyline was added to cell medium a final concentration of 1 μg/mL. Cells were fixed with formaldehyde 48 hours after doxycycline induction.

value: Human lung carcinoma

tag: antibody


title: A549, FOXA1, ChIP, Biol Rep 2

value: FOXA1 (GeneTex, GTX100308)


title: SJWLM069397_D2


title: ChIP-Seq_TipR_Caulobacter_crescentus_NA1000_PYE+Nal20

value: Anti-TipR (Kirkpatrick and Viollier, 2014 ; PMID:24726830)


title: SJWLM069396_D4


title: yeast, control group, biol rep 2

city: Cheng Du

first: Yan

last: Pan

address: Northern Jianshe Road

country: China

institute: University of Electronic Science and Technology of China

description:
WT4741-2
WT4741 gene expression.txt

data_processing:
SOAPnuke v1.5.6
Sequence reads for adaptor sequence/low-quality sequence/unknown base ('N' base) using SOAPnuke software. Low-Quality limit (base quality less than or equal to 15):20%, unknown base limit: 5%.
Clean sequence reads analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com)
The clean data were aligned to the reference genome using HISAT2 (v2.1.0) and  aligned to the gene set using Bowtie2.
Expression level of gene was calculated by RSEM (v1.3.1). The differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
Assembly: R64
Supplementary files format and content: tab-delimited text file includes  FPKM values for each sample

organism: Saccharomyces cerevisiae

source_name: yeast cell

growth_protocol: The yeast strains were cultivated in YPD complete medium containing 2% glucose, 2% peptone, 1% yeast extract

extract_protocol:
RNA was harvested following the Microbial RNA BGI-NGS-TQ-RNA-002 protocol of Beijing Genomics institution
RNA libriaries for RNA-seq were prepared following the BGI-NGS-JK-RNA-001 protocol of Beijing Genomics institution

value: yeast cell

value: YPD at 30℃


title: RUNX3_0min_2; TGFb 0min; RUNX3 Knock-down

value: Kidney; Embryo

value: HEK 293 cells

value: immortalized human embryonic kidney cells

value: TGFb 1ng/ml


title: ChIP-Seq_TipR_Caulobacter_crescentus_NA1000_PYE_Richmedium

value: WT


title: A549, FOXA1, ChIP, Biol Rep 1


title: SJWLM069396_D3


title: SJWLM069400_D2


title: yeast, control group, biol rep 1

description:
WT4741-1
WT4741 gene expression.txt


title: yeast cells, BY4741, SUL1 mutant, OD600(0.6), biol rep3

description:
SUL1_3
SUL1 gene expression.txt

value: SUL1 knockout


title: SJWLM069394_D3


title: yeast cells, BY4741, SUL1 mutant, OD600(0.6), biol rep1

description:
SUL1_1
SUL1 gene expression.txt


title: yeast cells, BY4741, SUL1 mutant, OD600(0.6), biol rep2

description:
SUL1_2
SUL1 gene expression.txt


title: young_p21_1 [g5_17_P21_9861_S17]

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Fastq files were QC'd using fastQC
QC'd fastq files were aligned to the GRCm39 mouse reference genome using the Rsubread align function
Gene counts were quantified using featureCounts in R
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes gene count information for each sample

source_name: Lung

extract_protocol:
Lungs were homogenised using pellet pestles and RNA extraction was performed using the Isolate II RNA mini kit according to manufacturer’s instruction
An input of 100 ng of total RNA was prepared and indexed for illumina sequencing using the TruSeq RNA sample Prep Kit with RiboGlobin depletion as per manufacturer’s instruction. The indexed libraries were pooled and diluted to 1.5 pM for paired end sequencing (2 x 81 cycles) on a NextSeq 500 instrument using the v2 150 cycle High Output kit as per manufacturer’s instructions.

value: Lung

tag: age

value: young

tag: treatment/passsage


title: SJWLM069394_D4


title: young_p2_1 [h3_27_P2_9871_S26]


title: old_p21_2 [f8_8_P21_610_S8]

value: old


title: old_mock_4 [g4_16_MOCK_618_S16]

value: mock


title: SJWLM069393_D2

value: Tumor

value: Wilms tumor


title: SJWLM069392_D2


title: Kidney_CLP_24h_Rep1

type: RNA

city: Zhanjiang

first: Tongtong

last: Ma

state: Guangdong

address: No. 57 South Renmin Avenue

department: Affiliated hospital of Guangdong Medical University

institute: Guangdong Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Array V2 (Aksomics), containing 14,236 circRNA probes.

scan_protocol: The arrays were captured by a Scanner (G2505C, Agilent).

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze the acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package.
Expression changes greater than twofold of circRNAs in SAKI mice were screened out and identified by Volcano Plot filtering.

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA with Arraystar Super RNA Labeling Kit (Aksomics, Shanghai, China).

extract_protocol: Briefly, Total RNA from renal cortex sample was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. The quantity and quality of the RNA samples were determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific, MA, USA). The RNA integrity was examined by 1.5% agarose gel electrophoresis and quantified with a QubitTM RNA Broad Range Assay kit (Q10210, Life Technologies). Total RNAs (2 μg) were used for stranded RNA sequencing library preparation by using KCTM Stranded mRNA Library Prep Kit for Illumina® (DR08402, Seqhealth Technology) following the manufacturer’s instruction.

treatment_protocol: The mouse sepsis model was established with the classic CLP method. Briefly, mice were anesthetized by the intraperitoneal injection of 2% sodium pentobartital. The cecum was ligated below the ileocecal valve by using 4-0 silk ligatures. Then the cecum was perforated at 2 positions with a 21-gauge needle and gently compressed to extrude the feces. The guts were then returned to the abdomen and the incision was closed. For the control mice, they were subjected to the same surgical procedures without ligating the puncturing the cecum. After the surgery, all mice received fluid resuscitation with saline solution (50 mL/kg) by subcutaneous injection.

tag: Sex

value: Male

value: CLP

value: renal cortex


title: Kidney_CLP_24h_Rep2


title: Kidney_CLP_24h_Rep3


title: young_p21_5 [h1_25_P21_9869_S25]


title: SJWLM069391_D4


title: Kidney_control_24h_Rep2

value: control


title: young_p2_6 [h8_32_P2_9876_S31]


title: Kidney_control_24h_Rep1


title: oviduct, E2h_Isth

city: Columbia

first: Wipawee

last: Winuthayanon

state: Missouri

address: 1030 Hitt Street

department: OB/GYN & Women's Health

institute: University of Missouri

description: 10x Chemistry: Single Cell 3’ v3

library_source: transcriptomic single cell

data_processing:
Processing of the raw sequencing data (mkfastq files) was carried out using Cell Ranger v6.0.1 to generate fastq files with default settings.
Fastq files were then processed through Velocyto v0.1.24 to produce loom files with spliced and unspliced mRNA information. Velocyto was run using the command run10x with default setting and a repeat masker gtf file from UCSC Genome Browser for mouse with an assembly for GRCm38/mm10-r-102 to mask expressed repeated elements. Generated loom files were then read in scanpy v1.6.0 using JupyterLab for analyses and saved in an h5ad format for downstream analyses.
Assembly: GRCm38/mm10-r-102
Supplementary files format and content: .tar.gz files

source_name: ovariectomized females

extract_protocol:
Oviducts were pooled and collected in Leibovitz-15 media supplement with 1% fetal bovine serum (L15+1%FBS) and placed on ice. For Veh and E2-treated samples, the oviduct was dissected into distal (infundibulum with ampulla, referred to as InfAmp) or proximal (isthmus with UTJ, referred to as IsthUTJ) regions. To isolate oviductal cells, oviducts were quickly uncoiled by trimming the mesosalpinx in order to locate the ampulla-isthmus junction (AIJ). Then, the tissues were dissected at the AIJ region for subsequent InfAmp and IsthUTJ cell isolation. For estrus samples, the entire length of the oviduct was used. After dissection, 0.25% trypsin-EDTA was injected into the oviduct using a blunted 30-gauge needle until the trypsin was visibly flushed out from the other end of the oviduct. The tissues were then placed in a tube containing 500 µL of trypsin and incubated on ice for 30 min and at 37°C for another 30 min. After the incubation, 500 uL of FBS was added to stop the enzymatic activity of trypsin. Oviductal cells were then flushed out from oviductal tubes with 4°C L15+10%FBS. At this stage, the epithelial, stromal, and parts of muscle cell layers were visibly flushed out. Only translucent longitudinal muscle cells were left intact. Cell clumps and tissue debris were strained twice through 40-µm cell strainers. Cells were then spun down and resuspended in 0.04% bovine serum albumin in phosphate-buffered saline. The final cell concentration was targeted for 8,000 cells/run.
10x library was constructed according to manufacturer's protocol using Chromium Single Cell 3’ v3 reagents.
libraries generated were sequenced using an Illumina NovaSeq600, targeting 1 billion reads/lane, paired-end, and 100bp read length.

treatment_protocol: Adult (8- to 12-week-old) C57B6/J female mice (n=4 mice per treatment) were ovariectomized and left for 14 days to recover and eliminate endogenous steroid hormones. Sesame oil (100 µL) was used as a negative (Vehicle or Veh) control group. 17beta-estradiol (E2) at a dose of 0.25 µg was diluted in 100 µL of 10% ethanol and sesame oil. Ovariectomized females were subcutaneously injected with Veh or E2. Two hrs after injection, the oviduct was collected for scRNA-seq analysis.

value: oviduct

tag: region

value: isthmus and uterotubal junction

value: wild-type

value: 17b-estradiol 2 hrs


title: old_mock_3 [g3_15_MOCK_617_S15]


title: oviduct, E2h_Amp

description: 10x Chemistry: Single Cell 3’ v3

value: infundibulum and ampulla


title: SJWLM069391_D3


title: oviduct, V2h_Isth

description: 10x Chemistry: Single Cell 3’ v3

value: vehicle 2 hrs


title: young_mock_4 [g9_21_MOCK_9865_S21]


title: oviduct, V2h_Amp

description: 10x Chemistry: Single Cell 3’ v3


title: old_p2_6 [f6_6_P2_608_S6]


title: Kidney_control_24h_Rep3


title: young_mock_3 [g8_20_MOCK_9864_S20]


title: SJWLM069389_D2


title: SJWLM069388_D2


title: NAc-projecting cells 5

city: Austin

first: Jennifer

last: Donegan

state: TX

address: 1701 Trinity

department: Psychiatry

institute: UT Austin

data_processing:
To analyze the data, Cutadapt and perl scripts were used to remove reads containing adaptor contamination, low quality bases, or undetermined bases. Then sequence quality was verified using FastQC.
HISAT2 was used to map reads to the mouse genome and mapped reads were assembled using StringTie.
Next, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the final transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all the transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM.
The differentially expressed mRNAs were selected with log2 (fold change)>1 or log2 (fold change) <-1 and with statistical significance (p<0.05) by R package edgeR.
Assembly: Mus musculus genome assembly GRCm38.p6
Supplementary files format and content: xlxs file that includes raw counts for each sample

source_name: Brain (vHipp)

extract_protocol:
RNA was prepared using Qiagen RNEasy Micro kit and sent to LC Biosciences for low input RNA sequencing.
Briefly, a Poly (A) RNA sequencing library was prepared using Illumina’s TruSeq-stranded-mRNA preparation protocol. RNA integrity was determined using Agilent Technologies 2100 bioanalyzer. Poly (A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification, followed by fragmentation using divalent cation buffer in elevated temperature. After DNA library construction, quality control analysis was performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA chip.

treatment_protocol: Briefly, a retrograde virus (pAAV[Exp]-EF1A>{myrmScarlet-1}:{P2A}:{yellow pre-eGRASP(p32)}:WPRE, 4.29x1013GC/ml, Vector Builder) was injected into the mPFC or NAc to express myrScarlet in vHipp projection neurons of wild-type animals. After 6 weeks, vHipp tissue was dissected and minced, placed in Hibernate A (Gibco), and spun for 2 min at 425 x g. Supernatant was replaced with accutase (Thermo Fisher) and tubes were placed on a shaking platform at 4⁰C for 30 minutes. Tissue homogenates were spun for 2 min at 425 x g and the pellet was resuspended in Hibernate A. Cells were dissociated by trituration with fire polished glass pipettes. Supernatant containing cells were combined and filtered through a 75 μm strainer, then stored on ice. Cells were sorted using a BD FACSAria III (Franklin Lakes, NJ, USA, 70µm nozzle, 50 psi) and analyzed using FACS Diva 6.1.3 software (BD). After excluding doublets, Scarlet-positive cells were collected in RNALater (Invitrogen).

value: Brain (vHipp)

value: Pyramidal

value: Viral-mediated fluorescent label


title: NAc-projecting cells 6


title: young_p2_4 [h6_30_P2_9874_S29]

value: Lung

value: young


title: old_p21_1 [f7_7_P21_609_S7]

value: old


title: old_p2_5 [f5_5_P2_607_S5]


title: NAc-projecting cells 3


title: old_mock_1 [g1_13_MOCK_615_S13]

value: mock


title: NAc-projecting cells 4


title: young_mock_2 [g7_19_MOCK_9863_S19]


title: SJWLM069386_D2

value: Tumor

value: Wilms tumor


title: NAc-projecting cells 2


title: old_p2_4 [f4_4_P2_606_S4]


title: young_p21_3 [g11_23_P21_9867_S23]


title: young_p2_3 [h5_29_P2_9873_S28]


title: young_mock_1 [g6_18_MOCK_9862_S18]


title: NAc-projecting cells 1


title: SJWLM069385_D2


title: young_p2_5 [h7_31_P2_9875_S30]


title: young_p2_2 [h4_28_P2_9872_S27]


title: old_p2_3 [f3_3_P2_605_S3]


title: SJWLM069384_D2


title: old_mock_2 [g2_14_MOCK_616_S14]


title: mPFC-projecting cells 5


title: SJWLM069390_D2


title: old_p21_3 [f9_9_P21_611_S9]


title: old_p2_2 [f2_2_P2_604_S2]


title: SJWLM069383_D2


title: old_p21_6 [f12_12_P21_614_S12]


title: SJWLM069387_D2


title: SJWLM069382_D2


title: mPFC-projecting cells 3


title: old_p2_1 [f1_1_P2_603_S1]


title: old_p21_5 [f11_11_P21_613_S11]


title: SJWLM069381_D2


title: old_p21_4 [f10_10_P21_612_S10]


title: mPFC-projecting cells 2


title: young_p21_2 [D10_22_P21_9866_S22]


title: SJWLM069380_D2


title: young_p21_4 [D12_24_P21_9868_S24]


title: SJWLM069378_D2


title: Liver, 7dpci, rep2

first: Andrew

last: Cox

state: Victoria

address: 305 Grattan St

institute: PeterMacCallum Cancer Centre

data_processing:
Sequencing files were convereted to FastQ files using Galaxy
Reads were trimmed using Cutadapt (v1.16)
Reads were mapped to zebrafish genome (Ensembl danrer10) using HISAT (v2.1.0)
Counting was performed using featurecounts (v1.6.0)
Differentially expressed genes were identified using Degust (Limma-Voom v3.40.6)
Assembly: Genome_build: Reads were mapped to zebrafish genome (Ensembl danrer10)
Supplementary files format and content: Supplementary_files_format_and_content: csv file containing the counts for all samples in the study (sham, 1, 3 and 7 dpci )

molecule: polyA RNA

organism: Danio rerio

source_name: Liver

extract_protocol:
Adult zebrafish livers were dissected and transferred into TRIzol solution. RNA was extracted using an Direct-zol RNA miniPREP kit. RNA quality was confirmed a Tapestation system before sequencing
Libraries were prepared in accordance to SMARTer Stranded Total RNA-seq Kit V2 Pico Input
Libraries were sequeced using an Illumina NextSeq 500, 75bp reads to a depth of 15M per sample

value: Liver

value: CI


title: Liver, 7dpci, rep3


title: mPFC-projecting cells 4


title: Sample 7

city: Frederick

first: Yongmei

last: Zhao

state: MD

address: Post Office Box B

department: Biomedical Informatics and Data Science (BIDS) Directorate

institute: Frederick National Labroatory for Cancer Research

data_processing:
Bcl2fastq v2.20 was used for sample demultiplexing
Adapters from the samples were trimmed using Trimmomatic
Genome mapping and transcript annotation were using STAR v2.5.1 with mouse reference genome mm10
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: gene count matrix in csv format

source_name: E17 TECs

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA Library Prep kit for Illumina following manufacturer's protocols.

value: E17 TECs

value: thymic epithelial cells

value: Ccl21a+Rank- #2

value: sorted thymic epithelial cell subpopulations from RANK-Venus/CCL21a-tdTomato mouse embryos


title: Liver, 7dpci, rep4


title: Liver, 7dpci, rep1


title: Sample 9

value: Ccl21a-Rank- #2


title: SJWLM066792_D4


title: Liver, 3dpci, rep1


title: Liver, 3dpci, rep2


title: Liver, 3dpci, rep4


title: Sample 8

value: Ccl21a-Rank+ #2


title: Sample 5

value: Ccl21a-Rank- #1


title: Liver, 3dpci, rep3


title: SJWLM066797_D2


title: Liver, 1dpci, rep2


title: Liver, 1dpci, rep3


title: Sample 4

value: Ccl21a-Rank+ #1


title: SJWLM066792_D2


title: mPFC-projecting cells 1

value: Brain (vHipp)

value: Pyramidal

value: Viral-mediated fluorescent label


title: Liver, 1dpci, rep4


title: SJWLM069379_D2


title: SJWLM066791_D2


title: Liver, 1dpci, rep1


title: Liver, sham, rep5

value: sham


title: Sample 3

value: Ccl21a+Rank- #1


title: Liver, sham, rep4


title: SJWLM066790_D2

value: Tumor


title: Sample 12

value: Ccl21a-Rank+ #3


title: Liver, sham, rep3

value: Liver


title: SJWLM066789_D4

value: Wilms tumor


title: WT control organoids, 10 nM IL17a treatment, 72 hours (IL17A-72h_3)

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
RNA-seq was performed with the Illumina sequencing platform, and the quality assessment was done by Fast-QC (version 0.11.9).
Then, the data were uniquely mapped to the mm10 genome by STAR (version 2.5.3) and the normalized gene counts were performed by DESeq2 (version 1.28.1).
The analysis of differentially expressed genes (DEGs) and expression values was performed by DESeq2 (version 1.28.1) software.
Genes with absolute log2-transformed fold changes ≥1 were regarded as differentially expressed genes, and a threshold of P value < 0.05 was used.
The counts value after each sample is normalized additional according to the different processing of each group.
Assembly: mm10
Supplementary files format and content: Excel files in CSV format include each Sample counts values after DESeq2 normalized.

source_name: intestine

growth_protocol: Colonic organoids cultured in ENR medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX-I, N2, B27, and N-acetylcysteine (Sigma-Aldrich)) containing EGF (50 ng ml  1, Invitrogen), Noggin (100 ng ml  1, R&D) , R-spondin1 (500 ng ml  1, R&D), 30% Wnt3a contitional mecium and CHIR (2.5 μM; Selleck) was added and refreshed every 3 days.

extract_protocol:
RNA was purified using the RNeasy Kit 9 (mf167-01; Mei5 Biotech).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
20 mg/ml tamoxifen was subcutaneously injected for five consecutive days (100 μl/day).
10nM IL-1a/1b or IL-17a were added in the cultured medium for 12 or 72 hours.

value: intestinal epithelium

value: Colonic organoids

value: WT

value: 10 nM IL17a treatment, 72 hours

value: 72 hours


title: Liver, sham, rep1


title: SJWLM066789_D3


title: Sample 11

value: E17 TECs

value: thymic epithelial cells

value: Ccl21a+Rank- #3

value: sorted thymic epithelial cell subpopulations from RANK-Venus/CCL21a-tdTomato mouse embryos


title: SJWLM066787_D2


title: WT control organoids, 10 nM IL17a treatment, 72 hours (IL17A-72h_2)


title: SJWLM066786_D2


title: Her1-YFP, anti-H2AZ

city: Lausanne

middle: Charles

last: Oates

address: Station 19

department: SV IBI

institute: EPFL

data_processing:
library strategy: Cut&Tag
Paired reads were quality checked by FastQC (version 0.11.9) and aligned to the zebrafish genome assembly (GRCz.11 toplevel, Ensembl release 109) using Bowtie2 (version 2.5.1)
The resulting sam files were then converted into bam files, sorted and indexed using samtools (version 1.17) and visualized with the Integrated Genomics Viewer (IGV version 2.16.0).
Overlapping peak between the biological replicates was done using bedtools intersect (version 2.31.0)
The peak calling was performed, on the intersection between both replicates, using macs2 callpeak (version 2.2.7) with the following parameters: -g 1.5e+9 -f BAMPE -q 0.01 --keep-dup all.
Assembly: GRCz.11 toplevel, Ensembl release 109
Supplementary files format and content: bigWig, narrowPeak

source_name: whole embryo

extract_protocol:
The dissociated single cells were then washed three times and bound to activated Concanavalin A-coated magnetic beads. Cells were resuspended into 100 µl of antibody buffer (wash buffer containing 0.05% (wt/vol) digitonin (Dig), 2 mM EDTA and 0.1 % BSA). Antibody at 1mg.ml was added to a final concentration of 1:50 and cells were incubated overnight at 4°C on a nutator. The next day, cells were resuspended in 100 µl of Dig wash buffer (wash buffer containing 0.05% (wt/vol) Dig) containing the secondary antibody at a final concentration of 1:100 and incubated for 60min at room temperature. After incubation, beads/cells were washed three times with Dig-wash buffer to remove unbound antibody, followed by resuspension and incubation of beads/cells in 100 µl Dig-300 wash buffer (Dig wash buffer at 300 mM NaCl) with pA-Tn5 adapter complex (1:200 dilution), at room temperature for 1 h on a nutator. After two washes with Dig-300 wash buffer, beads/cells were resuspended in 100 µl tagmentation buffer (Dig-300 buffer containing 10mM Mgcl2) and incubated at 37°C for 1 hour. Tagmentation reaction was stopped by adding exactly 3.3µl 0.5M EDTA, 1µl 10% SDS and 1µl 20mg.ml Proteinase K followed by 60 min incubation at 55°C shaking at full speed (1300 rpm) to solubilize DNA fragments. Beads/cells were placed on a magnetic stand and the supernatant containing DNA fragments was transferred into a new tube for DNA purification (MinElute Qiagen, 28004).
Cut&Tag libraries for next generation sequencing were prepared by PCR reaction using the NEBnext HIFI 2x PCR master mix and indexed i5 and i7 10µM primers as previously described48. Samples were then cleaned up using the DNA Clean and concentrator-5 kit from Zymo. Libraries were pooled together and paired-end 76bp sequencing was done using the Illumina NextSeq 500 instrument for Tg(her1:her1-YFP) samples and the MiSeq instrument for Tg(her1:nls-mkate2,Her7:her7-YFP) samples.

value: whole embryo


title: Her1-YFP, negative control


title: WT control organoids, 10 nM IL17a treatment, 72 hours (IL17A-72h_1)


title: Her1-YFP, anti-GFPpoly

value: anti-GFPpoly


title: SJWLM066785_D2


title: Her1-YFP, anti-Venus

value: anti-Venus


title: SJWLM066784_D4


title: WT control organoids, 10 nM IL1a+IL1b treatment, 72 hours (IL1α+IL1β-72h_2)

value: 10 nM IL1a+IL1b treatment, 72 hours


title: WT control organoids, 10 nM IL1a+IL1b treatment, 72 hours (IL1α+IL1β-72h_1)


title: Liver, sham, rep2

value: sham


title: Whole fly, 37 degrees, polyA-selected, biol rep 3

city: Burlington

first: Seth

last: Frietze

state: Vermont

address: 111 Colchester Ave

institute: University of Vermont

data_processing:
polyA (NovaSeq) reads were trimmed to 85 bp to match rRNA (HiSeq) reads.
Paired-end reads were aligned to dm6 chromosomes using STAR (v 2.7.7a) using indexes built using ensemble genes. Dm6 fasta and gtf files were dowloaded from UCSC, ensembl gtf version 101. STAR parameters included "--quantMode TranscriptomeSAM" and "--twopassMode Basic".
Post alignment, polyA reads were downsampled (samtools view -s, v 1.11) such that rRNA and polyA libraries had equalized numbers of uniquely aligned reads.
Salmon quant (v 1.4.0) was used following STAR transcriptomic alignment to quantify transcripts.
suppa2 was run for psiPerIsoform and psiPerEvent for all event types.
In R (v 4.2.2), tximport::tximport (v 1.26.1) and DESeq2::DESeqDataSetFromTximport (v 1.38.3) were used to load quant.sf files into final count matrices.
Assembly: dm6
Supplementary files format and content: raw_counts_from_full.csv.gz contains count data from polyA and rRNA with no equalization. Counts from polyA and present pre- (150bp) and post-trimming (85bp).
Supplementary files format and content: raw_counts_from_equalized.csv.gz contains count data from polyA and rRNA after trimming equalization procedure.

organism: Drosophila melanogaster

source_name: Whole animal, 6 flies

growth_protocol: Flies were reared at 25C at L:D 12:12 at a density of 30-50 flies per vial. Flies were fed a standard cornmeal and soy flour diet.

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Kit (Zymo Research, Inc). 0.8 ug of total RNA was used for the construction of polyA-selected sequencing libraries and 0.3 ug of total RNA was used for the construction of rRNA-depleted sequencing libraries.
RNA libraries for RNA-seq were prepared using either a stranded polyA+ Library Prep Kit or a rRNA-depletion Library Prep Kit (Tecan), per manufacturer's protocols.

treatment_protocol: Adult female flies were sealed in glass vials (n = 6 per vial) and submerged in a water bath that was programmed to heat or cool at a rate of 0.25C/min to one of four temps: 4C, 10C, 34C, or 37C. Flies were removed immediately after the bath reached either 4C or 10C, and held for 5 min at 34C or 37C. Flies were frozen in liqued nitrogen immediately after being removed from the water bath.

value: Whole animal, 6 flies

tag: developmental stage

value: Adult

value: Female

value: heat shock at 37 degrees

tag: library prep

value: polyA-selected


title: WT control organoids, 10 nM IL1a+IL1b treatment, 72 hours (IL1α+IL1β-72h_3)

value: intestinal epithelium

value: Colonic organoids

value: WT


title: Total-Input_PhoB_Caulobacter_crescentus_ΔpstS_GHA-542

description:
PhoB purification and antibody production :
His6-(SUMO-)PhoB protein was expressed from pCWR350 in E. coli Rosetta (DE3)/pLysS (Novagen, Madison, WI) and purified under native conditions using Ni2+ chelate chromatography. Briefly, cells were pelleted, resuspended in 25 mL of lysis buffer (10 mM Tris HCl pH8, 0.1 M NaCl, 1.0 mM   -mercaptoethanol, 5% glycerol, 0.5 mM imidazole triton 0.02%). Cells were sonicated (Sonifier Cell Disruptor B-30; Branson Sonic Power. Co., Danbury, CT) on ice using 12 bursts of 20 sec at output level 4.5. After centrifugation at 6   000 rpm for 20 min, the supernatant was loaded onto a column containing 5 ml of Ni-NTA agarose resin. The column was rinsed with lysis buffer, 400 mM NaCl and 10 mM imidazole, both prepared in lysis buffer. The eluted His6-(SUMO-)PhoB was used as antigen for the production of polyclonal antibodies in New Zealand white rabbits (Josman LLC, Napa, CA).

data_processing:
Base calling: HiSeq Control Software 2.2.58, RTA 1.18.64.0, CASAVA-1.8.2
Alignment: Map with Bowtie for Illumina (Galaxy Version 1.1.2), SAM-to-BAM (Galaxy Version 2.1.1)
Peak calling and refinement: MACS2 Callpeak (Galaxy Version 2.1.1.20160309.6)
Peak annotation: SeqMonk Software v1.45.4 (Braham Bionformatics Institute)
Genome_build: Caulobacter crescentus : NC_011916.1
Supplementary_files_format_and_content: The xls file reporting PhoB ChIP-Seq peaks in WT and ΔpstS mutant during exponential growth phase (as described in the paper) was generated by MACS2 software. The sheet is organized in columns as follows: column 1: Peak # (order on chromosome); column 2: Peak start coordinates (bp); column 3: Peak end coordinates (bp); column 4: Peak length (bp); column 5: Peak summit coordinates (bp); column 6: Peak pileup; column 7: -LOG10(pvalue); column 8: Fold enrichment; column 9: -LOG10(qvalue).

source_name: Caulobacter crescentus culture

growth_protocol: Overnight saturated cultures of Caulobacter crescentus strains were freshly diluted in PYE media and cultures were grown at 30°C to mid-log phase (O.D.660nm~0.5).

extract_protocol:
After resuspension of the cells in TES buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 100 mM NaCl) containing 10 mM of DTT, they were incubated in the presence of Ready-Lyse lysozyme solution (Epicentre, Madison, WI) for 10 minutes at 37°C, according to the manufacturer's instructions. Lysates were sonicated (Bioruptor® Pico) at 4°C using 15 bursts of 30 sec to shear DNA fragments to an average length of 0.3-0.5 kbp and cleared by centrifugation at 14,000 rpm for 2 min at 4°C. The volume of the lysates was then adjusted (relative to the protein concentration) to 1 ml using ChIP buffer (0.01% SDS, 1.1% Triton X-84 100, 1.2 mM EDTA, 16.7 mM Tris-HCl [pH 8.1], 167 mM NaCl) containing protease inhibitors (Roche) and pre-cleared with 80 μl of protein-A agarose (Roche, www.roche.com) and 100 μg BSA. 2% of each pre-cleared lysate was kept as total input samples (negative control samples). The rest of the pre-cleared lysates was incubated overnight at 4°C with rabbit polyclonal antibodies targeting PhoB (1:1,000 dilution). The immuno-complexes were captured after incubation with Protein-A agarose (pre-saturated with BSA) during a 2 h incubation at 4°C and they were washed subsequently with low salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 150 mM NaCl), with high salt washing buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, 500 mM NaCl), with LiCl washing buffer (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris-HCl pH 8.1) and finally twice with TE buffer (10 mM Tris-HCl pH 8.1, 1 mM EDTA). The complexes were eluted from the Protein-A agarose beads with two times 250 μl elution buffer (SDS 1%, 0.1 M NaHCO3, freshly prepared) and then, just like total input samples, incubated overnight with 300 mM NaCl at 65°C to reverse the crosslinks. The samples were then treated with 2 μg of Proteinase K for 2 h at 45°C in 40 mM EDTA and 40 mM Tris-HCl (pH 6.5). DNA was extracted using phenol:chloroform:isoamyl alcohol (25:24:1), ethanol-precipitated using 20 μg of glycogen as a carrier and resuspended in 50 μl of DNAse/RNAse free water.
Immunoprecipitated chromatin was used to prepare sample libraries used for deep-sequencing at Fasteris SA (Geneva, Switzerland). ChIP-Seq libraries were prepared using the DNA Sample Prep Kit (Illumina) following manufacturer instructions.

treatment_protocol: C. crescentus wildtype and ΔpstS cells were treated with formaldehyde (1% final concentration) in 1 uM sodium phosphate buffer (pH 7.6) at RT for 10 min to achieve crosslinking. Subsequently, the cultures were incubated for an additional 30 min on ice and washed three times in phosphate buffered saline (PBS, pH 7.4). The resulting cell pellets were frozen in liquid nitrogen and stored at -80°C.

value: [delta]pstS


title: ChIP-Seq_PhoB_Caulobacter_crescentus_NA1000(WT)_GHA-531

value: Wild type


title: ChIP-Seq_PhoB_Caulobacter_crescentus_ΔpstS_GHA-536


title: Total-Input_PhoB_Caulobacter_crescentus_NA1000(WT)_GHA-541


title: Whole fly, 37 degrees, polyA-selected, biol rep 2


title: SJWLM066788_D2

value: Tumor

value: Wilms tumor


title: SJWLM066784_D2


title: Whole fly, 34 degrees, polyA-selected, biol rep 2

value: heat shock at 34 degrees


title: WT control organoids, 72 hours (Control-72h_2)

description:
Control-IL1a+IL1b-72h.csv
Control-IL17a-72h.csv

value: Control, no treatment

value: 72 hours


title: WT control organoids, 72 hours (Control-72h_1)


title: Whole fly, 34 degrees, polyA-selected, biol rep 1


title: Whole fly, 37 degrees, polyA-selected, biol rep 1


title: Whole fly, 25 degrees, polyA-selected, biol rep 2

value: control, 25 degrees


title: Whole fly, 25 degrees, polyA-selected, biol rep 1


title: Whole fly, 25 degrees, polyA-selected, biol rep 3


title: WT control organoids, 72 hours (Control-72h_4)


title: Whole fly, 10 degrees, polyA-selected, biol rep 3

value: cold shock at 10 degrees


title: WT control organoids, 10 nM IL17a treatment, 12 hours (IL17A-12h_4)

value: 10 nM IL17a treatment, 12 hours

value: 12 hours


title: Whole fly, 4 degrees, polyA-selected, biol rep 2

value: Whole animal, 6 flies

value: Adult

value: Female

value: cold shock at 4 degrees


title: SJWLM066780_D3


title: Whole fly, 10 degrees, polyA-selected, biol rep 2

value: polyA-selected


title: WT control organoids, 10 nM IL17a treatment, 12 hours (IL17A-12h_3)

value: intestinal epithelium

value: Colonic organoids

value: WT


title: Whole fly, 10 degrees, polyA-selected, biol rep 1


title: Whole fly, 4 degrees, polyA-selected, biol rep 1


title: SJWLM066782_D2

value: Tumor


title: Whole fly, 4 degrees, polyA-selected, biol rep 3


title: WT control organoids, 10 nM IL17a treatment, 12 hours (IL17A-12h_1)


title: SJWLM066779_D4

value: Wilms tumor


title: SJWLM066780_D4


title: SJWLM066781_D2


title: 3dpi, SG200ΔUMAG_11060-UMAG_11060 with mutations infected, rep2

city: Köln

first: Gunther

last: Doehlemann

address: Zülpicher Straße 47a

institute: University of Cologne/ Universität zu Köln

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060-UMAG_11060  with 58-61aa and 92-97aa mutation with alanine, 3dpi,rep2
C2

data_processing:
TrimGalore(0.6.5) was used for quality filtering of the paired-end reads.
STAR (2.5.1a) was used for the mapping of the quality-filtered reads to the reference genome of maize.
StringTie (2.2.0)was used for assembly of RNA-Seq alignments into potential transcripts.
FeatureCounts (2.0.3) was used to count the mapped reads.
edgeR_3.42.0 and DESeq2_1.36.0 were used for the differential gene expression analysis.
Assembly: Zea mays reference genome Zm-B73-REFERENCE-NAM-5.0
Supplementary files format and content: txt files containing transcript counts for each sample.

organism: Zea mays

source_name: leaf

extract_protocol:
RNA was harvested from frozen and homogenized samples using TRIzol reagent (Invitrogen, Darmstadt, Germany). The Turbo DNA-Free Kit from Ambion (Ambion Life TechnologiesTM, Carlsbad, USA) was used to exclude DNA contamination.
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 ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: leaf

value: Golden Bantam

value: infected by fungal Ustilago maydis SG200ΔUMAG_11060_UMAG_11060

tag: time point


title: 3dpi, SG200ΔUMAG_11060-UMAG_11060 with mutations infected, rep1

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060-UMAG_11060  with 58-61aa and 92-97aa mutation with alanine, 3dpi,rep1
C1


title: 3dpi, SG200ΔUMAG_11060-UMAG_11060 with mutations infected, rep3

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060-UMAG_11060  with 58-61aa and 92-97aa mutation with alanine, 3dpi,rep3
C3


title: WT control organoids, 10 nM IL1a+IL1b treatment, 12 hours (IL1α+IL1β-12h_4)

tag: cell type

value: 10 nM IL1a+IL1b treatment, 12 hours


title: SJWLM066783_D2


title: SJWLM066779_D3


title: 3dpi, SG200ΔUMAG_11060 infected, rep3

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060, 3dpi,rep3
K3

tag: treatment

value: infected by fungal Ustilago maydis SG200ΔUMAG_11060


title: WT control organoids, 10 nM IL1a+IL1b treatment, 12 hours (IL1α+IL1β-12h_3)

tag: tissue


title: 3dpi, SG200ΔUMAG_11060 infected, rep2

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060, 3dpi,rep2
K2


title: SJWLM066778_D4


title: 3dpi, SG200ΔUMAG_11060 infected, rep1

description:
maize_leaf, infected by Ustilago maydis SG200ΔUMAG_11060, 3dpi,rep1
K1


title: WT control organoids, 10 nM IL1a+IL1b treatment, 12 hours (IL1α+IL1β-12h_1)


title: 3dpi, SG200 infected, rep3

description:
maize_leaf, infected by Ustilago maydis SG200, 3dpi,rep3
S3

value: infected by fungal Ustilago maydis SG200


title: Whole fly, 34 degrees, polyA-selected, biol rep 3

value: heat shock at 34 degrees


title: 3dpi, SG200 infected, rep1

description:
maize_leaf, infected by Ustilago maydis SG200, 3dpi,rep1
S1


title: WT control organoids, 12 hours (Control-12h_4)

description:
Control-IL1a+IL1b-12h.csv
Control-IL17a-12h.csv

value: Control, no treatment

value: 12 hours


title: SJWLM066777_D4


title: Clec16a_TNF/IL1 [4KMQ.TCGACGTC_TCGCATAA]

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCh38 reference genome and quantified using Kallisto
Genome_build: GRCh38
Supplementary_files_format_and_content: gzipped tsv files from kallisto

source_name: Astrocytes

extract_protocol: Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

value: hESC astrocytes


title: WT control organoids, 12 hours (Control-12h_2)


title: SJWLM066777_D3


title: Clec16a_Vehicle [4KMQ.CCTAAGAC_TCGCATAA]

value: Vehicle


title: Clec16a_TNF/IL1 [4KMQ.CGATCAGT_TCGCATAA]


title: WT control organoids, 12 hours (Control-12h_1)


title: Clec16a_Vehicle [4KMQ.TAGCGCTC_TCGCATAA]


title: Gli1CreERT2-Smad4-loxp mice, tdTomato cells, Proximal colon (GS4T-Proximal_1)

value: Gli1CreERT2-tdTomato positive cells

value: Smad4 knockout in Gli1+ cells

value: Tamoxifen subcutaneous injection

value: Day 30


title: Gli1CreERT2-Smad4-loxp mice, tdTomato cells, Proximal colon (GS4T-Proximal_2)

value: intestinal epithelium


title: SJWLM066776_D4

value: Tumor

value: Wilms tumor


title: Control_TNF/IL1 [4KMQ.ATGCGCAG_TCGCATAA]


title: Control_TNF/IL1 [4KMQ.CGGAGCCT_TCGCATAA]


title: Gli1CreERT2-Smad4-loxp mice, tdTomato cells, Distal colon (GS4T-Distal_2)


title: SJWLM066775_D2


title: Control_Vehicle [4KMQ.GCGTAGTA_TCGCATAA]


title: SJWLM066774_D2


title: Control_Vehicle [4KMQ.GGAGCTAC_TCGCATAA]


title: SJWLM066778_D2


title: Gli1CreERT2-Smad4-loxp mice, tdTomato cells, Distal colon (GS4T-Distal_1)


title: 3dpi, SG200 infected, rep2

description:
maize_leaf, infected by Ustilago maydis SG200, 3dpi,rep2
S2

value: leaf

value: Golden Bantam


title: Control_Vehicle [4KMQ.ACTCGCTA_TCGCATAA]


title: Clec16a_TNF/IL1 [4KMQ.TGCAGCTA_TCGCATAA]


title: Clec16a_Vehicle [4KMQ.ACTGAGCG_TCGCATAA]


title: Gli1CreERT2-Alk3-loxp mice, tdTomato cells, Proximal colon (GA3T-Proximal_2)

value: Alk3 knockout in Gli1+ cells


title: Clec16a_TNF/IL1 [4KMQ.TCGACGTC_TAAGGCTC]


title: SJWLM066773_D3


title: Clec16a_TNF/IL1 [4KMQ.TGCAGCTA_TAAGGCTC]


title: SJWLM066776_D2


title: SJWLM066772_D2


title: Clec16a_TNF/IL1 [4KMQ.CGATCAGT_TAAGGCTC]


title: Control_TNF/IL1 [4KMQ.CCTAAGAC_TAAGGCTC]


title: Gli1CreERT2-Alk3-loxp mice, tdTomato cells, Distal colon (GA3T-Distal_2)


title: Control_TNF/IL1 [4KMQ.ACTGAGCG_TAAGGCTC]


title: Gli1CreERT2-Alk3-loxp mice, tdTomato cells, Distal colon (GA3T-Distal_1)


title: Gli1CreERT2-Alk3-loxp mice, tdTomato cells, Proximal colon (GA3T-Proximal_1)


title: Clec16a_Vehicle [4KMQ.TACGCTGC_TAAGGCTC]


title: Clec16a_Vehicle [4KMQ.ATGCGCAG_TAAGGCTC]


title: SJWLM066771_D4


title: Clec16a_Vehicle [4KMQ.CGGAGCCT_TAAGGCTC]


title: Control_TNF/IL1 [4KMQ.TAGCGCTC_TAAGGCTC]


title: SJWLM066771_D3


title: Gli1CreERT2 mice, tdTomato cells, Proximal colon (GWTT-Proximal_2)

description:
GWTT-GA3T-Proximal.csv
GWTT-GS4T-Proximal.csv

value: WT


title: Control_Vehicle [4KMQ.GCGTAGTA_TAAGGCTC]


title: SJWLM066773_D4


title: Control_Vehicle [4KMQ.GGAGCTAC_TAAGGCTC]


title: Gli1CreERT2 mice, tdTomato cells, Proximal colon (GWTT-Proximal_1)


title: Control_Vehicle [4KMQ.ACTCGCTA_TAAGGCTC]


title: LDHAi-2

city: CHICAGO

first: Peiwen

state: IL

address: 303 East Superior Street, Suite 6-512

institute: Northwestern University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: CT2A were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

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

treatment_protocol: CT2A cells were treated with or without 8 uM LDHA inhibitor FX11.

tag: cell line

value: Glioma cells

value: KDM4D knockdown

value: LDHA inhibitor


title: LDHAi-1

tag: genotype


title: Control-2

value: control


title: Gli1CreERT2 mice, tdTomato cells, Distal colon (GWTT-Distal_2)

description:
GWTT-GA3T-Distal.csv
GWTT-GS4T-Distal.csv

tag: time


title: SJWLM066770_D3


title: Sample 65-Naïve CD8 T cells

first: Wang

last: Yao

address: No. 28, fuxing street

institute: Chinese general PLA hospital

data_processing:
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA).
The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
cutadapt-1.9 [1] (cutadapt.readthedocs.io/en/stable/)was used to remove the reads that contained adapter contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC v0.10.1 [2] (www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used hisat2-2.0.4 [3](ccb.jhu.edu/software/hisat2/)to map reads to the genome of Homo sapiens two rounds of purification.
transcripts that overlapped with known mRNAs and transcripts shorter than 200 bp were discarded. Then we utilized CPC0.9-r2 [6] (cpc2.cbi.pku.edu.cn/) with default parameters(cpc2 -i novel.fa -o cpc2.out) and CNCI2.0 [7] (wwww.bioinfo.org/software/cnci) with default parameters (CNCI.py -f novel.fa -o CNCI.result -p 1 -m ve -g novel.gtf -d genome.fa) to predict transcripts with coding potential. All transcripts with CPC score <-1 and CNCI score <0 were removed and remained transcripts were considered as lncRNAs.
Assembly: hisat2-2.0.4
Supplementary files format and content: tab-delimited text file includes fpkm values for each Sample

source_name: apheresis cells of DLBCL patient

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

tag: patient id

value: PBMC

tag: cell subtype

value: Naïve CD8 T cells

value: Day 0

tag: disease state

value: PD patient


title: Control-1


title: SJWLM066770_D4

data_processing:
RNAseq reads were mapping using St. Jude standard pipeline. RNA-seq gene level read counts and FPKM were generated using HTseq-count based on transcript models in GENCODE v19.
Assembly: GRCh37
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
Trizol
Libraries were prepared from 250 ng to 1000 ng of total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina P/N 20020613)

tag: disease


title: Sample 63-Naïve CD8 T cells


title: Gli1CreERT2 mice, tdTomato cells, Distal colon (GWTT-Distal_1)

value: Gli1CreERT2-tdTomato positive cells

value: Tamoxifen subcutaneous injection


title: Gli1CreERT2-Smad4-loxp mice, Muc2-mCherry cells, Proximal colon (GS4M2-Proximal_1)

value: intestinal epithelium

value: Muc2-mCherry positive cells

value: Smad4 knockout in Gli1+ cells

value: Day 30


title: Pre-manufacture T cells [HX_CART]

description:
10x Genomics
The raw data were submitted as single-end because the forward read file (R1) was corrupted.

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: pre-manufacture T cells

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: DLBCL

value: T cells

value: pre-manufacture T cells

value: pre-manufacture T cells of DLBCL patient

tag: response

value: Progression of disease (PD) after CAR-T cell therapy


title: Gli1CreERT2-Smad4-loxp mice, Muc2-mCherry cells, Proximal colon (GS4M2-Proximal_2)


title: Pre-manufacture T cells [Y_PB]

description: 10x Genomics


title: Pre-manufacture T cells [X_PB]

description: 10x Genomics

value: Complete remission (CR) after CAR-T cell therapy


title: Pre-manufacture T cells [BYX_PBMC]

description: 10x Genomics


title: Sample 64-Naïve CD8 T cells

value: Day 5


title: Sample 62-Naïve CD8 T cells

value: PBMC


title: CAR-T cell products [Y_CART]

description: 10x Genomics

source_name: CAR T

value: CAR T

value: CAR T of DLBCL patient


title: Sample 61-Naïve CD8 T cells

value: Naïve CD8 T cells

value: PD patient


title: Pre-manufacture T cells [HB_PB]

description: 10x Genomics


title: Gli1CreERT2-Smad4-loxp mice, Muc2-mCherry cells, Distal colon (GS4M2-Distal_1)

value: Tamoxifen subcutaneous injection


title: Gli1CreERT2-Smad4-loxp mice, Muc2-mCherry cells, Distal colon (GS4M2-Distal_2)

value: intestinal epithelium


title: Sample 60-Naïve CD8 T cells

value: CR patient


title: Gli1CreERT2-Alk3-loxp mice, Muc2-mCherry cells, Proximal colon (GA3M2-Proximal_2)

value: Muc2-mCherry positive cells

value: Alk3 knockout in Gli1+ cells


title: CAR-T cell products [X_CART]

description: 10x Genomics

value: DLBCL


title: Sample 59-Naïve CD8 T cells


title: CAR-T cell products [HB_CART]

description: 10x Genomics

value: T cells


title: CAR-T cell products [BYX_CART]

description: 10x Genomics


title: Gli1CreERT2-Alk3-loxp mice, Muc2-mCherry cells, Proximal colon (GA3M2-Proximal_1)

value: Day 30


title: Sample 58-Naïve CD8 T cells


title: Gli1CreERT2-Alk3-loxp mice, Muc2-mCherry cells, Distal colon (GA3M2-Distal_2)


title: IDC50X_RNA

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
RNA-seq data was initially aligned to both human hg19 and mouse mm10 genomes. Two-pass mapping was performed using the STAR RNA-seq aligner version STAR_2.5.1b {Dobin, 2013, PMID: 23104886} (--outSAMDstrandField intronMotif, --outFilterMultimapNmax 20, -- alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, -- outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, -- alignMatesGapMax 1000000, --outFilterType BySJout, --outFilterScoreMinOverLread 0.33, -- outFilterMatchNminOverLread 0.33, --limitSjdbInsertNsj 1200000, --chimSegmentMin 15, -- chimJunctionOverhangMin 15, --twopassMode Basic).
Reads uniquely mapped only to the hg19 genome were kept, along with uniquely mapped reads that had significantly better alignment scores in the h19 genome compared to the mm10 genome.
Filtered RNA-seq reads were aligned to version hg19 of the human genome and gene count and FPKM values were obtained using the VIPER pipeline {Cornwell, 2018, PMID: 29649993}, with parameters (stranded: true, library_type: ‘fr-firststrand’, filter_mirna: true).
Assembly: hg19
Supplementary files format and content: counts table and FPKM table

source_name: breast cancer cells

growth_protocol: Tumors were induced by bilateral orthotopic mammary fat pad injection of 2 × 10^6 PDX cells suspended in 50 μl total volume of 50% DMEM media and 50% of Matrigel

extract_protocol:
RNA was extracted and purified from samples using Qiagen ALLPrep according to standard instructions
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.

tag: pdx model id


title: HCI002_RNA


title: Pre-manufacture T cells [L_PB]

description: 10x Genomics

value: pre-manufacture T cells

value: pre-manufacture T cells of DLBCL patient


title: Sample 57-Naïve CD8 T cells


title: Gli1CreERT2 mice, Muc2-mCherry cells, Proximal colon (GWTM2-Proximal_2)

description:
GWTM2-GA3M2-Proximal.csv
GWTM2-GS4M2-Proximal.csv

value: WT


title: Sample 55-Naïve CD4 T cells

value: Naïve CD4 T cells


title: 2147TG5_RNA


title: Gli1CreERT2-Alk3-loxp mice, Muc2-mCherry cells, Distal colon (GA3M2-Distal_1)


title: 4195TG5_RNA


title: Sample 56-Naïve CD8 T cells

value: PBMC


title: HCI001_RNA


title: 4013TG6_RNA


title: 3936TG5_RNA


title: CAR-T cell products [HX_PB_P]

description: 10x Genomics

value: CAR T

value: Progression of disease (PD) after CAR-T cell therapy


title: BCM2665_RNA


title: Sample 54-Naïve CD4 T cells


title: T272X_RNA


title: CAR-T cell products [L_CART]

description: 10x Genomics

value: CAR T of DLBCL patient

value: Complete remission (CR) after CAR-T cell therapy


title: Gli1CreERT2 mice, Muc2-mCherry cells, Distal colon (GWTM2-Distal_2)

description:
GWTM2-GA3M2-Distal.csv
GWTM2-GS4M2-Distal.csv

value: Tamoxifen subcutaneous injection


title: HCI009_RNA


title: BCM3611_RNA


title: Sample 53-Naïve CD4 T cells

value: PD patient


title: BCM3107_RNA


title: Gli1CreERT2 mice, Muc2-mCherry cells, Distal colon (GWTM2-Distal_1)

value: intestinal epithelium


title: Sample 52-Naïve CD4 T cells


title: 5998TG5_RNA


title: 4272TG5_RNA


title: HCI010_RNA


title: Day7 periodontitis

city: Los Angeles

first: Takeru

last: Kondo

state: California

address: 10824 Lindbrook Dr. #304

institute: UCLA School of Dentistry

data_processing: The Cell Ranger output of single cell RNA sequencing data were analyzed using R-program (Seurat, https://satijalab.org/seurat/).

source_name: Palatal gingiva

extract_protocol:
At 1, 4, and 7 days after ligature placement, the gingival tissue from the ligature side of the palate was harvested (n=4).  The gingival tissue without ligature placement was used as helthy gingiva. Gingival tissues were cut into 1-mm pieces and placed in digestion buffer containing 1 mg/ml collagenase II (Life Technologies, Grand Island, NY), 10 units/ml DNase I (Sigma-Aldrich) and 1% bovine serum albumin (BSA; Sigma-Aldrich) in Dulbecco’s modified Eagle’s medium (DMEM; Life Technologies) for 20 min at 37°C on a 150 rpm shaker. The tissues were passed through a 70µm cell strainer. The collected cells were pelleted at 1,500 rpm for 10 min at 4°C and resuspended in phosphate buffered saline (PBS; Life Technologies) that was supplemented with 0.04% BSA (Cell suspension A).  The remaining tissues were further incubated in 0.25% trypsin (Life Technologies) and 10 units/ml DNase I for 30 min at 37 ℃ on a 150 rpm shaker.
The combined trypsin-released cells and collagenase II-released cells were counted and the equal number of cells (2,000~3,000) from each animal were combined in the group for single cell RNA sequencing (10X Genomics, San Francisco, CA).

treatment_protocol: A silk thread (ligature) was gently tied around the left maxillary second molar of female C57BL6/J wild type mice.

tag: strain

value: Gingiva

tag: age

value: 8-12 weeks old


title: Gli1CreERT2 mice, Muc2-mCherry cells, Proximal colon (GWTM2-Proximal_1)

value: Muc2-mCherry positive cells


title: Control_TNF/IL1 [4KMQ.TACGCTGC_TCGCATAA]

value: hESC astrocytes

tag: Sex


title: Day1 periodontitis


title: Day4 periodontitis


title: HCI-002_H3K27ac_ChIP_Input

data_processing:
Reads were aligned to hg19 with BWA-mem v0.7.17 (http://bio-bwa.sourceforge.net).
Duplicates were removed using Picard MarkDuplicates v2.18.17 (http://broadinstitute.github.io/picard/), with parameters (REMOVE_DUPLICATES=TRUE, VALIDATION_STRINGENCY=LENIENT).
ChIP-signal was quantified and peaks were called using MACS2 v2.1.2 {Zhang, 2008, PMID:18798982}, with parameters (--SPMR -B --keep-dup=1 --extsize=146 --nomodel, -q 0.05).
Assembly: hg19
Supplementary files format and content: bigwig of signals & bed files of called peaks

extract_protocol:
tissues were pulverized and then crosslinked with 1% paraformaldehyde for 10 min at room temperature.  Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.]
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

tag: antibody


title: Sample 48-Naïve CD4 T cells

value: CR patient


title: 4013-TG6_H3K27ac_ChIP_Input


title: 2147-TG5_H3K27ac_ChIP_Input


title: HCI-001_H3K27ac_ChIP_Input


title: Sample 50-Naïve CD4 T cells


title: Sample 49-Naïve CD4 T cells


title: BCM-2665_H3K27ac_ChIP_Input


title: T272X_H3K27ac_ChIP_Input


title: 4195-TG5_H3K27ac_ChIP_Input


title: Sample 47-Naïve CD4 T cells


title: Sample 46-Naïve CD4 T cells


title: BCM-3107_H3K27ac_ChIP_Input


title: 5998-TG5_H3K27ac_ChIP_Input


title: iN WT day10

city: Minneapolis

first: Nobuaki

last: Kikyo

state: MN

address: University of Minnesota, MTRF, Room 2-216, 2001 6th St SE

institute: University of Minnesota

data_processing:
Barcoded processing, gene counting, and aggregation were made using the Cell Ranger software v7.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: induced neurons

extract_protocol:
Total RNA was prepared with a Quick RNA Microprep (Zymo Research, R1051).
Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Chromium, PN-1000268) was used.

value: induced neurons

value: Transduced BAM genes


title: iN Per1-/- day10


title: Sample 51-Naïve CD4 T cells


title: Sample 45-Non-Naïve CD8 T cells

value: Non-Naïve CD8 T cells


title: 4272-TG5_H3K27ac_ChIP_Input


title: iN Per2-/- day7


title: IDC50X_H3K27ac_ChIP_Input


title: IDC50X_H3K27ac_ChIP

value: anti-H3K27ac (Diagenode, C15410196)


title: Sample 44-Non-Naïve CD8 T cells

value: PBMC


title: HCI-002_H3K27ac_ChIP


title: Healthy gingiva


title: iN Per1-/- day7


title: Sample 43-Non-Naïve CD8 T cells


title: iN Per2-/- day10


title: Sample 42-Non-Naïve CD8 T cells


title: iN WT day7

value: WT


title: HCI-001_H3K27ac_ChIP


title: 4013-TG6_H3K27ac_ChIP


title: 2147-TG5_H3K27ac_ChIP


title: HCI-009_H3K27ac_ChIP_Input


title: BCM-2665_H3K27ac_ChIP


title: Sample 41-Non-Naïve CD8 T cells


title: 4195-TG5_H3K27ac_ChIP


title: T272X_H3K27ac_ChIP


title: HCI-009_H3K27ac_ChIP


title: Sample 40-Non-Naïve CD8 T cells


title: BCM-3107_H3K27ac_ChIP


title: iN Per1-/- day4


title: Sample 39-Non-Naïve CD8 T cells


title: 5998-TG5_H3K27ac_ChIP


title: SUM159_RNA

data_processing:
Raw RNA-seq reads were aligned to version hg19 of the human genome and gene count and FPKM values were obtained using the VIPER pipeline {Cornwell, 2018, PMID: 29649993}, with parameters (stranded: true, library_type: ‘fr-firststrand’, filter_mirna: true).
Assembly: hg19
Supplementary files format and content: counts table and FPKM table

growth_protocol: Cells were grown in their respective media prepared per provider's guidelines, at 37 degree C, 5% CO2.

extract_protocol:
Total RNA was extracted using the Qiagen RNeasy Mini Kit.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kits from 500 ng of purified total RNA according to the manufacturer’s protocol. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to the manufacturer’s protocols.


title: 4272-TG5_H3K27ac_ChIP


title: Sample 38-Non-Naïve CD8 T cells


title: SUM149_RNA


title: SUM1315_RNA


title: iN Per2-/- day4, biol rep 2

data_processing:
Raw reads of fastq format were first processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter or ploy-N and low quality reads. At the same time, Q20, Q30 and GC contents in the clean data were calculated. All the downstream analyses were based on the clean data.
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 read numbers mapped to each gene and calculate FPKM based on the length of the gene and read counts mapped to the gene.
Differential expression analysis of two groups (three biological replicates per condition) was performed using the DESeq2Rpackage (1.20.0).
Assembly: mm10
Supplementary files format and content: Tab-delimited file "gene_fpkm" contains fpkm values of all samples.

extract_protocol:
Total RNA wad prepared with a Quick RNA Microprep (Zymo Research, R1051).
NEB Next Ultra II RNA Library Prep by Illumina following manufacturer's protocols.


title: iN Per2-/- day4, biol rep 1


title: iN Per2-/- day4


title: iN Per2-/- day4, biol rep 3


title: MDAMB157_RNA


title: Sample 35-Non-Naïve CD4 T cells

value: Non-Naïve CD4 T cells


title: HDQP1_RNA


title: Hs578_RNA


title: iN Per1-/- day4, biol rep 2


title: MDAMB436_RNA


title: MFM223_RNA


title: iN Per1-/- day4, biol rep 1


title: Sample 37-Non-Naïve CD8 T cells


title: Sample 34-Non-Naïve CD4 T cells


title: HCC2185_RNA


title: HCC38_RNA


title: HCC70_RNA


title: Sample 36-Non-Naïve CD8 T cells


title: iN WT day4


title: Sample 32-Non-Naïve CD4 T cells


title: iN WT day4, biol rep 3


title: HCC1569_RNA


title: Sample 33-Non-Naïve CD4 T cells


title: HCC1937_RNA


title: iN WT day4, biol rep 2


title: HCC1395_RNA


title: Sample 31-Non-Naïve CD4 T cells


title: iN WT day4, biol rep 1


title: CAL148_RNA


title: HCC1143_RNA


title: iN Per1-/- day4, biol rep 3


title: Sample 30-Non-Naïve CD4 T cells


title: CAL120_RNA


title: BT549_RNA


title: SUM229_RNA


title: Sample 29-Non-Naïve CD4 T cells


title: UACC3199_RNA


title: SUM185_RNA


title: iN Per2-/- day2, biol rep 2


title: Sample 28-Non-Naïve CD4 T cells


title: Sample 27-Non-Naïve CD4 T cells


title: Sample 26-Non-Naïve CD4 T cells


title: iN Per2-/- day2, biol rep 1


title: iN Per1-/- day2, biol rep 3


title: MDAMB468_RNA


title: HCC3153_RNA


title: Sample 25-Non-Naïve CD4 T cells


title: iN Per1-/- day2, biol rep 2


title: iN Per1-/- day2, biol rep 1


title: MDAMB231_RNA


title: HCC1187_RNA


title: HCC2157_RNA


title: Whole fly, 37 degrees, rRNA-depleted, biol rep 3

value: Whole animal, 6 flies

tag: developmental stage

value: Adult

value: Female

value: heat shock at 37 degrees

tag: library prep

value: rRNA-depletion


title: Sample 24-Non-Naïve CD4 T cells

tag: cell type


title: iN WT day2, biol rep 3

tag: treatment


title: Whole fly, 37 degrees, rRNA-depleted, biol rep 2

tag: tissue


title: Sample 23-CD4+CAR T cells

source_name: CAR T of DLBCL patient

value: CAR T cells

value: CD4+CAR T cells

value: Day 10

value: PD patient


title: FCIBC02_RNA

tag: cell line


title: iN Per2-/- day2, biol rep 3

tag: genotype

tag: time


title: iN WT day2, biol rep 2


title: SUM102_RNA


title: PMC42_RNA


title: Whole fly, 37 degrees, rRNA-depleted, biol rep 1


title: EMG3_RNA


title: Sample 22-CD4+CAR T cells

tag: patient id

tag: cell subtype


title: Sample 21-CD4+CAR T cells

tag: disease state


title: DU4475_RNA


title: Whole fly, 34 degrees, rRNA-depleted, biol rep 3

value: heat shock at 34 degrees


title: iN Per2-/- day0, biol rep 3

value: induced neurons


title: Whole fly, 34 degrees, rRNA-depleted, biol rep 2


title: CAL851_RNA


title: Sample 20-CD4+CAR T cells


title: iN Per2-/- day0, biol rep 2

value: Transduced BAM genes


title: Sample 19-CD4+CAR T cells


title: CAL51_RNA


title: HCC1806_RNA


title: iN Per2-/- day0, biol rep 1


title: Sample 18-CD4+CAR T cells


title: Whole fly, 25 degrees, rRNA-depleted, biol rep 3

value: control, 25 degrees


title: iN Per1-/- day0, biol rep 3


title: TT642_shPRRX1_3_DOX_RNA

source_name: rhabdoid tumor cells

treatment_protocol: cells were treated with 3ug/ml doxycycline to induce shRNA expression

tag: parental cell line

tag: shRNA

tag: condition

value: doxycycline


title: Sample 17-CD4+CAR T cells

value: CR patient


title: iN Per1-/- day0, biol rep 2


title: Sample 16CD4+CAR T cells


title: Whole fly, 25 degrees, rRNA-depleted, biol rep 2


title: Whole fly, 25 degrees, rRNA-depleted, biol rep 1


title: TT642_shPRRX1_2_DOX_RNA


title: TT642_shPRRX1_3_no_DOX_RNA

value: no doxycycline


title: iN WT day2, biol rep 1

value: WT


title: iN Per1-/- day0, biol rep 1


title: iN WT day0, biol rep 3


title: Sample 14-CD4+CAR T cells


title: Whole fly, 10 degrees, rRNA-depleted, biol rep 3

value: Whole animal, 6 flies

value: cold shock at 10 degrees


title: Whole fly, 34 degrees, rRNA-depleted, biol rep 1

value: Adult

value: Female


title: TT642_shPRRX1_1_DOX_RNA


title: Whole fly, 10 degrees, rRNA-depleted, biol rep 2

value: rRNA-depletion


title: iN WT day0, biol rep 2


title: TT642_shPRRX1_1_no_DOX_RNA


title: Whole fly, 10 degrees, rRNA-depleted, biol rep 1


title: Sample 15-CD4+CAR T cells

value: CAR T cells


title: iN WT day0, biol rep 1


title: Whole fly, 4 degrees, rRNA-depleted, biol rep 3

value: cold shock at 4 degrees


title: Sample 12-CD4+CAR T cells

value: CD4+CAR T cells

value: Day 10


title: TT642_no_sh_DOX_RNA


title: Whole fly, 4 degrees, rRNA-depleted, biol rep 2


title: Renal cortex_CLP1 repeat 3

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed
Clean data were mapped to the reference genome of mouse from GRCm38/mm10 using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1).
Assembly: A p-value cutoff of 0.05 and fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Supplementary files format and content: GRCm38/mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: kidney

extract_protocol:
Briefly, Total RNA from renal cortex sample was extracted using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s instructions. The quantity and quality of the RNA samples were determined with a NanoDrop spectrophotometer (Thermo Fisher Scientific, MA, USA). The RNA integrity was examined by 1.5% agarose gel electrophoresis and quantified with a QubitTM RNA Broad Range Assay kit (Q10210, Life Technologies). Total RNAs (2 μg) were used for stranded RNA sequencing library preparation by using KCTM Stranded mRNA Library Prep Kit for Illumina® (DR08402, Seqhealth Technology) following the manufacturer’s instruction.
Total RNAs (2 μg) were used for stranded RNA sequencing library preparation by using KCTM Stranded mRNA Library Prep Kit for Illumina® (DR08402, Seqhealth Technology) following the manufacturer’s instruction.

value: kidney

value: tissue

value: cecal ligation and punture

value: 24 hours


title: TT642_no_sh_no_DOX_RNA


title: Whole fly, 4 degrees, rRNA-depleted, biol rep 1


title: Renal cortex_CLP1 repeat 2


title: Sample 10-CD8+CAR T cells

value: CD8+CAR T cells

value: PD patient


title: Hs578_shPRRX1_3_DOX_RNA

value: doxycycline


title: Renal cortex_CLP1 repeat 1

value: WT


title: hTSC, undifferentiated, clone CT27, Input

city: Sendai

first: Eri

middle: H

last: Kobayashi

state: Miyagi

address: 2-1 Seiryo-machi, Aobaku

department: Medical Biochemistry

country: Japan

institute: Tohoku University Graduate School of Medicine

data_processing:
ChIP-Seq reads were trimmed for quality control using TrimGalore v0.6.7 and mapped to the reference genome (UCSC hg38) using Bowtie 2 v2.2.5.
Assembly: UCSC hg38
Supplementary files format and content: BigWig

growth_protocol: hTSCs were maintained in hTSC medium [DMEM/F12 (FUJIFILM Wako #048-29785) supplemented with 1% knockout serum replacement (KSR) (Thermo Fisher Scientific #10828028), 0.5% penicillin-streptomycin (Thermo Fisher Scientific #15140122), 0.15% bovine serum albumin (BSA) (FUJIFILM Wako #017-22231), 1% ITS-X supplement (FUJIFILM Wako #094-06761), 200 µM L-ascorbic acid (FUJIFILM Wako #013-12061), 25 ng/ml EGF (FUJIFILM Wako #053-07871), 2 μM CHIR99021 (FUJIFILM Wako #038-23101), 5 μM A83-01 (FUJIFILM Wako #035-24113), 0.8 mM valproic acid (FUJIFILM Wako #227-01071), and 2.5 μM Y27632 (FUJIFILM Wako #257-00511)] at 37°C in 95% air and 5% CO2. When hTSCs reached sub-confluence, they were dissociated with TrypLE Express (Thermo Fisher Scientific #12604021) diluted with PBS at a 1:1 ratio for 10-15 min at 37°C. Dissociated cells were seeded in hTSC medium supplemented with 0.5 µg/ml iMatrix-511 (Nippi #892011). hTSCs were typically passaged every two days at a split ratio of 1:4 to 1:8. For CRISPR screening and gene KO, 10 ng/ml BMP4 (R&D Systems #314-BP) was added to the hTSC medium to ameliorate the toxicity of gene transfection and antibiotic selection.

extract_protocol:
Cells were fixed with 1% PFA for 10 min. After quenching and cell lysis, chromatin was sonicated.
ChIP-Seq libraries of TFs were constructed using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB # E7645) with two custom adaptors: Adapter-T and Adapter-C. Adapter-T with a 3′-T overhang was prepared by annealing (5′-CTA CAC GAC GCT CTT CCG ATC TT-3′) and (5′-AGA TCG GAA GAG CAC ACG TCT GAA-3′; 5′ phosphorylated). Adapter-C with a 3′-C overhang was prepared by annealing (5′- CTA CAC GAC GCT CTT CCG ATC TC-3′) and (5′-AGA TCG GAA GAG CAC ACG TCT GAA-3′; 5′ phosphorylated). Adapter-C was added to increase the ligation efficiency.

treatment_protocol: To induce EVT differentiation, hTSCs were cultured in EVT medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 50 ng/ml NRG1 (Cell Signaling #5218SC or #26941), 7.5 μM A83-01, 2.5 μM Y-27632, and 4% KSR] supplemented with 2% Matrigel (Corning #354263) for three days. The culture medium was then replaced with EVT medium without NRG1. Fro ST diffirentiation, hTSCs were cultured on plates coated with 1 µg/ml Col IV (Corning #354233) using ST medium [DMEM/F12 supplemented with 0.5% penicillin-streptomycin, 0.15% BSA, 1% ITS-X supplement, 2.5 μM Y-27632, 2 μM forskolin, and 4% KSR].

value: trophoblast stem cells

value: undifferentiated


title: Sample 9-CD8+CAR T cells


title: Hs578_shPRRX1_3_no_DOX_RNA

value: no doxycycline


title: Renal cortex_control repeat 3

value: control


title: TT642_shPRRX1_2_no_DOX_RNA


title: Sample 8-CD8+CAR T cells


title: hTSC, EVT, GCM1, clone CT27, ChIP

value: EVT differentiation


title: Hs578_shPRRX1_2_DOX_RNA


title: Renal cortex_control repeat 2


title: Sample 13-CD4+CAR T cells

value: CAR T cells

value: CR patient


title: Sample 7-CD8+CAR T cells


title: CnR_IgG_NPC_rep2

city: New York

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Library strategy: CUT&RUN
Sequencing reads were trimmed and filtered using version 0.4.5 of TrimGalore
Reads were aligned to human assembly hg19 with version 2.3.4.1 of bowtie2
Read density profiles were made using BEDTools and normalized to a depth of 10 million mapped fragments
Global peak atlas was made using version 1.6.1 of featureCounts
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to a depth of 10 million mapped fragments

source_name: hPSC-derived neural progenitor cells

growth_protocol: WA09 (H9 ) human pluripotent stem cell (hPSC) line was cultured in Essential 8 on Vitronectin coated dishes and expanded by dissociation with 0.5mM EDTA. Neural induction was completed using the dual SMAD inhibition protocol and WNT inhibition on Matrigel coated dishes. hPSC for differentiation and neuronal progenitors were dissociated using Accutase. Neurons were maintained on poly-L-ornithine and Laminin/ Fibronectin coated plates in Neurobasal medium supplemented with B27, L-glutamine, BDNF, GDNF, cAMP, AA. DAPT was added to the neuronal maintenance medium from day20 to day30 of differentiation.

extract_protocol:
50,000 cells were freshly harvested and bound to concanavalin A-coated magnetic beads after an 8min incubation at RT on a rotator. Cell membranes were permeabilized with digitonin and the different antibodies were incubated overnight at 4°C on a rotator. Beads were washed and incubated with pA-MN. Ca2+-induced digestion occurred on ice for 30min and stopped by chelation. DNA was finally isolated using an extraction method with phenol and chloroform as described in Skene et al., 2018
Libraries were prepared for sequencing using standard Illumina protocols

value: neural progenitor cells

value: wild type

value: IgG (ab6709, abcam)


title: CnR_IgG_NPC_rep1


title: Hs578_shPRRX1_2_no_DOX_RNA


title: Hs578_shPRRX1_1_DOX_RNA


title: Sample 6-CD8+CAR T cells

value: Day 10


title: Sample 11-CD8+CAR T cells


title: Sample 5-CD8+CAR T cells


title: CnR_IgG_D53_rep2

source_name: hPSC-derived neurons

value: neurons


title: Hs578_shPRRX1_1_no_DOX_RNA


title: Lungs, ISM1-KO, 2 months, Rep2

city: Singapore

first: Jong

middle: Huat

last: Tee

state: Singapore

address: 14 Science Drive 4

department: Department of Biological Sciences

country: Singapore

institute: National University of Singapore

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling).
Sequence reads were trimmed for adaptor sequence, low-quality sequence and uncertain nucleotides constitute more than 10% of either read (N>10%).
Trimmed sequence reads were mapped to GrCM38/mm10 using STAR software which precisely and effectively performs positioning junction reads for RNA sequencing data analysis.
Mapped results (BAM files) were visualised using the Integrative Genomics Viewer (IGV) software.
Gene expression level is then calculated based on the number of mapped reads.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: Lung tissue

extract_protocol:
Lungs were perfused with chilled PBS to remove the blood. Lung tissues were then homogenised into cell suspension in  Trizol reagent using gentleMACS dissociator. After a series of washing, RNA pellet was dissolved in RNase free water. 1.5 ug of total RNA was used for the construction of sequencing libraries.
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina PE150 technology is employed to sequence the sample and the final stage involves the bioinformatics analysis.

value: Lung tissue

value: Untreated


title: Lungs, ISM1-KO, 2 months, Rep3


title: CnR_IgG_D53_rep1


title: Hs578_no_sh_DOX_RNA


title: Lungs, ISM1-KO, 2 months, Rep1


title: Sample 3-CD8+CAR T cells

value: CD8+CAR T cells


title: CnR_H3K9me3_NPC_rep2

value: rabbit anti-H3K9me3 (ab8898, abcam)


title: Lungs, Wildtype, 2 months, Rep3

value: WT


title: Hs578_no_sh_no_DOX_RNA


title: CnR_H3K9me3_NPC_rep1


title: Sample 2-CD8+CAR T cells


title: LS_PRRX1_ChIP_Input_cond2

source_name: neuroblastoma cells

extract_protocol:
Cells (1 × 10^7) were fixed with 1% paraformaldehyde for 10 min at room temperature. DSG was then removed and replaced with fixing buffer (50 mM HEPES-NaOH (pH 7.5), 100 mM NaCl, 1mM EDTA) containing 1% paraformaldehyde (Electron Microscopy Sciences, 15714) and cross-linked for 10 min at 37 °C. Crosslinking was quenched by adding glycine to a final concentration of 0.125 M. The cells were washed with ice-cold PBS, harvested in PBS. The nuclear fraction was extracted by first resuspending the pellet in 1 ml of lysis buffer (50 mM HEPES-NaOH (pH 8.0), 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, and 0.25% Triton X-100) for 10 min at 4 °C. Cells were pelleted and washed in 1 ml of wash buffer (10 mM Tris-HCL (pH 8.0), 200 mM NaCl, 1 mM EDTA) for 10 min at 4 °C. Cells were then pelleted and resuspended in 1 ml of shearing buffer (10 mM Tris-HCl (pH 8), 1 mM EDTA, 0.1% SDS) and sonicated in a Covaris sonicator. Lysate was centrifuged for 5 min at 14,000 rpm to purify the debris. Then 100 µl of 10% Triton X-100 and 30 µl of 5M NaCl were added. The sample was then incubated with 20 µl of Dynabeads Protein G (LifeTechnologies,10003D) for 1 h at 4 °C. Primary antibodies were added to each tube, and immunoprecipitation (IP) was conducted overnight at 4 °C. Cross-linked complexes were precipitated with Dynabeads Protein G for 2 hr at 4 °C. The beads were then washed in low salt wash buffer (20 mM Tris-HCl pH 8, 150 mM NaCl, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C, high salt wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C and LiCl wash buffer (50 mM Tris-HCl pH 8, 10 mM EDTA, and 1% SDS) for 5 min at 4 °C. DNA was eluted in elution buffer (100 mM sodium bicarbonate and 1% SDS). Cross-links were reversed overnight at 65 °C. RNA and protein were digested with 0.2 mg ml−1 RNase A for 30 min at 37 °C followed by 0.2 mg ml−1 Proteinase K for 1 h at 55 °C. DNA was purified with phenol-chloroform extraction and isopropanol precipitation.
ChIP-seq libraries were prepared using the Rubicon ThruPLEX DNA-seq Kit from 1 ng of purified ChIP DNA or input DNA according to the manufacturer’s protocol.

value: LS

tag: sonication condition


title: Lungs, Wildtype, 2 months, Rep2


title: Renal cortex_control repeat 1

first: Tongtong

last: Ma

address: No. 57 South Renmin Avenue

institute: Guangdong Medical University

value: kidney

value: tissue

value: 24 hours


title: Lungs, Wildtype, 2 months, Rep1


title: CnR_H3K9me3_D53_rep1


title: Sample 1-CD8+CAR T cells


title: CnR_H3K9me3_D53_rep2