title: Fridge4 [4_9]

city: Shanghai

first: Cenxi

last: Liu

address: Songhu Road 2005

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for  low-quality sequence, then mapped to mm10 whole genome using Hisat2
Stringtie was used to quantify
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: liver

extract_protocol:
Total RNA was extracted from tissues by using TRIzol reagent (Invitrogen). Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: liver

tag: condition

value: Fridge

value: mice fed by HFD stored in the fridge (HFDfri)


title: RNA-seq of non-targeting siRNA-treated primary RPTEC, rep 2

status: Public on Dec 31 2022

type: SRA

city: Saint Louis

first: Nicolas

last: Ledru

state: MO

address: 660. S Euclid Ave., CB 8118

country: USA

institute: Washington University in St. Louis

library_source: transcriptomic

data_processing:
Illumina bcl files were demultiplexed and processed to generate fastq files.
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read. Reads were aligned to the Ensembl release 101 assembly with STAR v2.7.9a. Sequencing performance was assessed for the total number of aligned reads and uniquely aligned reads, as well as features detected. Gene counts were calculated from uniquely aligned unambiguous reads by Subread:featureCount v2.0.3. Gene counts were then adjusted for differences in library size with TMM normalization size factors.
Assembly: hg38
Supplementary files format and content: The rnaseq_gene_counts.tsv file contains gene counts for each of the 6 samples sequenced.

molecule: total RNA

organism: Homo sapiens

source_name: primary human renal proximal epithelial cells

extract_protocol:
RNA was extracted from the proximal tubule cell cultures with the RNeasy Mini Kit (Qiagen, 74104) following manufacturer instructions.
Total RNA integrity was determined by Agilent 4200 Tapestation. Library preparation was performed with 0.5-1 ug of total RNA. Ribosomal RNA was removed by RNase-H method using RiboErase kits (Kapa Biosystems). mRNA was fragmented in reverse transcriptase buffer and heated to 94 degrees for 8 minutes. mRNA was then reverse transcribed using SuperScript III RT enzyme (Life Technologies, per manufacturer’s instructions) and random hexamers to produce cDNA. cDNA was blunt ended, had an A base added to the 3’ ends, and had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using a 2x150bp configuration.

treatment_protocol: Non-targeting or NFAT5-targeting siRNA transfection was performed with RNAiMAX (Thermo Fisher, 13778075). At 48 hours following transfection, cells were harvested.

tag: cell line

value: Human renal proximal tubule epithelial cells (Lonza, CC-2553)

tag: treatment

value: Non-targeting siRNA (Horizon Discovery, D-001810-10)


title: Fridge3 [4_8]

country: China

organism: Mus musculus

tag: strain

tag: tissue


title: 21-1A,HCC Tumor tissue,Tu_M replicate 1

city: Guangzhou

first: Shi-Ting

last: Feng

state: Guangdong

address: The Second Zhongshan Road

institute: The first affiliated hospital of Sun Yat-sen University

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Ericscript (v0.5.5) [4] and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively.
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database for this organism built by BGI (Beijing Genomic Institute in ShenZhen), which known and novel, coding transcripts were included, then expression level of gene was calculated by RSEM (v1.2.12).
The heatmap was drawn by pheatmap (v1.0.8) according to the gene expression in different samples.
Differential expression analysis was performed using the DESeq2(v1.4.5) with Q value ≤ 0.05.
GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper (https://en.wikipedia.org/wiki/Hypergeometric_distribution) based on Hypergeometric test . The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) by Bonferroni.
Assembly: GCF_000001635.26
Supplementary files format and content: core_table_gene xls file includes fpkm, tpm, read count values and analysis for each sample.

source_name: HCC Tumor tissue

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and productswere purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and pair end 100 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

value: HCC Tumor tissue

tag: genotype

value: c-Myc/Alb-cre transgenic


title: F2_D1 individual, grown at 4C [T4_P2.B10_F2_D1]

city: Vienna

first: Rahul

last: Pisupati

address: Dr. Bohrgasse 3

country: Austria

institute: Gregor Mendel Institute

library_source: genomic

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: leaf

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf

tag: developmental stage

value: 7-10 leave rosette

tag: cell type


title: Fridge2 [4_10]


title: 15-2A,HCC Peritumor tissue,Pe_F replicate 1

source_name: HCC Peritumor tissue

value: HCC Peritumor tissue


title: 15-1A,HCC Tumor tissue,Tu_F replicate 1


title: F2_D2 individual, grown at 4C [T4_P2.A9_F2_D2]


title: Freezer5 [20_9]

value: Freezer

value: mice fed by HFD stored in the freezer (HFDfre)


title: M4

first: Hang

last: Su

state: Other (Non U.S.)

address: 上海市杨浦区政民路507号上海市肺科医院

institute: Shanghai pulmonary hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
The raw data contained low quality reads, contaminated joints, and unspecified high N base reads. These reads need to be removed by using SOAPnuke v1.5.2 solfware with parameters -l 15 -q 0.2 -n 0.1 (BGI Platform: https://github.com/BGI-flexlab/SOAPnuke) before data analysis to ensure the reliability of the results (QC).
After we got clean reads, we used HISAT(Hierarchical Indexing for Spliced Alignment of Transcripts) (Kim, Langmead et al. 2015) v2.0.4 software with parameters -p 8 --phred64 --sensitive -I 1 -X 1000 (http://www.ccb.jhu.edu/software/hisat) to compare clean reads to the reference genome sequence (May need to QC of alignment).
Clean reads were aligned to the reference sequence by using Bowtie2 (Langmead and Salzberg 2012) v2.2.5 software with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200 (http://bowtie-bio.sourceforge.net/ Bowtie2 /index.shtml), and then RSEM (Li and Dewey 2011) v1.2.12 software with the default parameters (http://deweylab.biostat.wisc.edu/ RSEM) was used to calculate the expression levels of genes and transcripts.
We used DEGseq algorithm with parameters Fold Change >= 2 and Adjusted Pvalue <= 0.001  for differential gene analysis a protocol from (Wang, Feng et al. 2010).
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: mouse tumor

growth_protocol: C57BL/6 female, 6-8-week-old mice were divided into 4 groups (with 6 animals per group) for vehicle treatment (N), cisplatin alone (C), brivanib alone )B), and cisplatin and brivanib combination (M)  treatments. Three million LLC cells mixed in Matrigel (Corning) were injected into each ﬂank of the 6 mice to generate 10-12 xenograft tumors per treatment group.

extract_protocol:
Total RNA of each sample was extracted using Trizol Reagen(Invitrogen) or RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After the tumors grew to a total tumor volume of at least 100 mm3, the drugs (cisplatin alone, brivanib alone, and cisplatin and brivanib combination) with a total volume of 100 μL per treatment were injected directly into the peritoneal. Treatments were carried out twice per week for 4 weeks. On the dosing day, tumors were ﬁrst measured with calipers, body weights were recorded, and then the drugs would be were injected directly into the peritoneal. The mice were sedated with isoﬂuorane prior to measurements and treatments.

value: Lewis Lung Cancer cell

tag: mouse host strain

tag: culture method

value: xenografted

value: cisplatin and brivanib combination

tag: age

value: 6-8 weeks

tag: Sex

value: female


title: M3

address: 上海市杨浦区政民路507号上海市肺科医院


title: Control11

first: Yingyue

last: Zhou

state: Missouri

address: 425 South Euclid Ave, 8107, 8th floor BJCIH,, Pathology and Immunology

department: Pathology and Immunology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sample demultiplexing, barcode processing and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (5.0.0, 10x Genomics). Cellranger count was used to align samples to the reference genome provided by 10X Genomics (GRCh38-2020-A for human) with “include introns = TRUE”.
Assembly: GRCh38-2020-A
Supplementary files format and content: Comma-separated values files and count matrix of processed Seurat object
Supplementary files format and content: Tab-separated values files and metadata of processed Seurat object
Supplementary files format and content: H5 files and count matrix from 10X CellRanger of each sample

source_name: brain

extract_protocol:
Post-mortem frozen brain tissue was homogenized in a Dounce homogenizer in Lysis Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.025% NP-40), and incubated on ice for 15 min. The suspension was filtered through a 30-μm filter to remove debris and pelleted at 500g for 5 min at 4 oC. Nuclei were washed and filtered twice with Nuclei Wash (1% BSA in PBS with 0.2 U μl–1 RNasin (Promega)). Nuclei pellets were resuspended in 500 μl nuclei wash and 900 µl 1.8 M sucrose. This 1,400 μl mixture was carefully layered on top of 500 μl 1.8 M sucrose and centrifuged at 13,000g for 45 min at 4 oC to separate the nuclei from myelin debris. The nuclei pellet was resuspended in nuclei wash at 1,000 nuclei μl–1 and filtered through a 40-μm FlowMi Cell Strainer.
Chromium Single Cell 5′ Reagent Kits (v2)

tag: disease state

value: control

tag: dap12 genotype

value: WT

tag: sample identifier

value: male

value: occipital cortex

tag: batch


title: NHD3

description: 10x Genomics

value: NHD

value: DAP12 c.2T>C


title: Freezer4 [20_8]

value: liver


title: F2_D2 individual, grown at 4C [T4_P2.A7_F2_D2]

value: leaf


title: Freezer3 [20_7]


title: F2_D1 individual, grown at 4C [T4_P2.A6_F2_D1]

value: 7-10 leave rosette


title: M2

address: 上海市杨浦区政民路507号上海市肺科医院


title: Control9

description: 10x Genomics


title: F2_D1 individual, grown at 4C [T4_P2.A5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P2.A8_F2_D1]


title: C3

address: 上海市杨浦区政民路507号上海市肺科医院

value: cisplatin


title: RNA-seq of non-targeting siRNA-treated primary RPTEC, rep 1

value: Human renal proximal tubule epithelial cells (Lonza, CC-2553)

value: Non-targeting siRNA (Horizon Discovery, D-001810-10)


title: Control7

description: 10x Genomics

source_name: occipital cortex


title: F2_D2 individual, grown at 4C [T4_P2.A4_F2_D2]


title: Freezer1 [20_2]

value: Freezer

value: mice fed by HFD stored in the freezer (HFDfre)


title: Control6

description: 10x Genomics


title: Fridge1 [4_1]

value: Fridge

value: mice fed by HFD stored in the fridge (HFDfri)


title: Control10

description: 10x Genomics


title: C1

address: 上海市杨浦区政民路507号上海市肺科医院

value: Lewis Lung Cancer cell

value: xenografted

value: 6-8 weeks

value: female


title: C2

address: 上海市杨浦区政民路507号上海市肺科医院


title: F2_D2 individual, grown at 4C [T4_P2.A2_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P2.A1_F2_D2]


title: KI CA-4948 4

city: St. Louis

first: Kian-Huat

last: Lim

address: 4566 Scott Avenue, Room 502

department: Internal Medicine/Oncology

institute: Washington University School of Medicine

description: Orthotopic KI tumor

data_processing:
Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-seq reads were then aligned to the mouse Ensembl GRCh38.76 primary assembly with STAR aligner version 2.5.1a.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5.
The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in at least four samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma6. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples with the voomWithQualityWeights
Genome_build: mouse Ensembl GRCh38.76 primary assembly
Supplementary_files_format_and_content: gene counts

source_name: Pancreatic cancer

growth_protocol: All cells were cultured in DMEM/10% FBS, 1% Pen/Strep prior to orthotopic inoculation in syngeneic FVBN/J mice

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 100K KI cells were injected orthotopically into the pancreas of FBN/J mice, which were allowed to recover.  Treatment with vehicle or IRAK4 inhibitor (CA-4948) were started when tumors became palpable, for totally 14 days.

value: Pancreatic cancer line from KRAS/INK4A mouse

tag: passages

value: <20 from being generated

value: FVBN/J


title: KI CA-4948 2

description: Orthotopic KI tumor


title: N3

address: 上海市杨浦区政民路507号上海市肺科医院

value: vehicle


title: Control4

description: 10x Genomics

value: control

value: WT

value: male

value: occipital cortex


title: Control5

description: 10x Genomics


title: Control8

description: 10x Genomics


title: N5

address: 上海市杨浦区政民路507号上海市肺科医院


title: Control3

description: 10x Genomics


title: Freezer2 [20_6]

value: liver

tag: condition


title: KI CA-4948 3

description: Orthotopic KI tumor


title: N2

address: 上海市杨浦区政民路507号上海市肺科医院


title: P_6191 individual, grown at 4C [T4_P2.A11_P_6191]

value: leaf

value: 7-10 leave rosette


title: F2_D2 individual, grown at 4C [T4_P2.A12_F2_D2]


title: ΔH, H2/CO2, biol rep 2

city: Tübingen

first: Bastian

last: Molitor

state: Baden Württemberg

address: Schnarrenbergstr. 94-96

department: Center for Applied Geosciences

country: Germany

institute: University of Tübingen

data_processing:
Sequencing reads were quality filtered and trimmed with BBMap version 38.93 and FastX Toolkit version 0.0.14 with specific parameters for paired-end reads.
Reads from each bioreactor culture were mapped to the reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377) using BWA-MEM version 0.7.17.
Mapped reads were assigned to genomic features using the FeatureCounts program from the Subread package version 2.0.1. Additionally, an alignment-free quantification of gene features was performed using Salmon version 1.5.2.
Pairwise differential expression analysis was performed on the Salmon counts using DESeq2 version 1.32.0 with the homologous genes present in the pan-genome database (see manuscript) and ConsensusDE version 1.10.0.
The adjusted P-value cut-off threshold was set to 0.05
Assembly: Reference genomes of M. thermautotrophicus ΔH (CP064324), M. thermautotrophicus Z-245 (CP064336 and CP064337) and M. marburgensis Marburg (CP069376 and CP069377)
Supplementary files format and content: quant.sf = Salmon's quantification file, plain-text, tab-separated file, with the headers: Name, Length, EffectiveLength, TPM, NumReads

organism: Methanothermobacter thermautotrophicus

source_name: prokaryotic

growth_protocol: Briefly: The three microbes were culivated continuously in bioreactors with minimal salts media and fed and 80/20 v/v % gas mixture of H2/CO2. Details on cultivation can be found in manuscript.

extract_protocol:
A hot phenol method was used for RNA extraction. The samples were thawed on ice and centrifuged at 4°C and 4100 × g for 10 min, the supernatant discarded, and the samples resuspended in 800 µL of RNase free water.
The 800 µL were mixed with 950 µL of saturated phenol (Sigma-Aldrich, Merck, Germany) and 115 μL of a lysis solution in Lysing Matrix B (MP Biomedicals Germany GmbH, Eschwege, Germany). The lysis solution contained sodium acetate (20 mM pH 5.2), sodium dodecyl sulfate (SDS; 0.5 % v/v), ethylenediaminetetraacetic acid (EDTA; 1 mM), and DNase/RNase-free distilled water (DI; Invitrogen, Thermo Fischer Scientific, Germany).
The cells were homogenized for one cycle (5 x 40 s at 6 m/s and 20 s off) in a FastPrep-24TM 5G bead-beater (MP Biomedicals Germany GmbH, Eschwege, Germany) and then centrifuged at room temperature and 21130 × g for 10 min (5424 Eppendorf, Hamburg, Germany). The top layer was placed into 600 µL of phenol-chloroform-isoamyl alcohol (ROTI® Aqua-P/C/I, Carl Roth, Karlsruhe, Germany) and centrifuged as in the previous step. This step was repeated twice.
The top layer was added to 1.2 mL of ethanol (undenatured absolute, SERVA Electrophoresis GmbH, Heidelberg, Germany) and left overnight at -80 °C to precipitate the RNA. The following day, the tubes were centrifuged at 4°C and 21130 × g for 10 min, and then the supernatant was removed. The RNA pellet was washed with 1 mL of 75% v/v ethanol solution and centrifuged as in the previous step. The supernatant was pipetted off, and the pellet was resuspended with 53 µL of DNase/RNase-free distilled water.
The RNA was cleaned (which included DNA depletion) and concentrated using the RNA Clean & Concentrator kit (Zymo Research, Irvine, CA, United States), according to the manufacturer’s instructions. The cleaning and concentrating protocols were repeated four times.
RNA libraries for RNA-seq were prepared using 100 ng of RNA and the TruSeq™ Stranded Total RNA Kit with Ribo-Zero™ Plus following manufacturer's protocols.

treatment_protocol: After 7 days of which 2.7 days were at steady state, four-times 9 ml of bioreactor sample was placed in 5 mL of prechilled RNAlater (overnight at 4°C). The samples were stored overnight at 4°C and then frozen at -20°C until RNA isolation.

value: prokaryotic

value: [delta]H

value: exponential growth (continous bioreactors) day 7

tag: reactor id


title: KI CA-4948 1

description: Orthotopic KI tumor

tag: treatment


title: B5

address: 上海市杨浦区政民路507号上海市肺科医院

value: Lewis Lung Cancer cell

value: xenografted

value: brivanib


title: 12-2A,HCC Peritumor tissue,Pe_M replicate 3

value: HCC Peritumor tissue

value: c-Myc/Alb-cre transgenic


title: P_6191 individual, grown at 4C [T4_P2.A3_P_6191]


title: KI Vehicle 4

description: Orthotopic KI tumor

value: Pancreatic cancer line from KRAS/INK4A mouse

value: <20 from being generated

tag: strain

value: FVBN/J


title: P_6046 individual, grown at 4C [T4_P2.B2_P_6046]

tag: tissue


title: B3

address: 上海市杨浦区政民路507号上海市肺科医院

value: 6-8 weeks

value: female


title: F2_D1 individual, grown at 4C [T4_P1.H9_F2_D1]

tag: genotype


title: KI Vehicle 2

description: Orthotopic KI tumor

value: vehicle


title: Vg2/3/4 CD103negative 4

city: London

first: Philip

last: East

address: Midland Road

country: United Kingdom

institute: The Francis Crick Institute

description:
Sorted into lysis buffer and RNA extracted
DAR223A2

data_processing:
bcl2fastq2 v2.2.0
reads trimmed with cutadapt
aligned and quantified with STAR and RSEM
Assembly: GRCh38
Supplementary files format and content: tab delimited RSEM gene-level count matrix

source_name: Colon

extract_protocol:
Biopsies were dissociated according to the Miltenyl Human Tumour Dissociation kit protocol, with the modification that the volume of enzyme R used was reduced to 20% of that specificed in the manufacturers instructions and FACS purified.
For GN096 the single cell suspension was FACS sorted directly into Trizol and frozen and sent to Genewiz for RNA extraction. For GN097, GN099 the single cell suspensions were FACS sorted direclty into PBS and frozen immediately and sent to Genewiz for RNA extraction. For GN142 the single cell suspension was sorted directly into lysis buffer of the PicoPure kit (Thermofisher) and DNA extraction occured immediately. For samples GN096, GN097, GN099 the samples were processed by genewiz using an ultralow input RNAseq library prep. For sample GN142 the RNA was processed by the advanced sequencing facility at the Francis Crick institute using the Nugen Ovation UltraLow RNA-Seq System.

value: Colon


title: Vg2/3/4 CD103positive 3

description:
Sorted into PBS and RNA extracted
GN099-CD103plus

value: Facs sorted CD3+/TCRgd+/Vg2/3/4+/CD103+


title: KI Vehicle 3

description: Orthotopic KI tumor


title: B2

address: 上海市杨浦区政民路507号上海市肺科医院


title: KI Vehicle 1

description: Orthotopic KI tumor


title: F2_D1 individual, grown at 4C [T4_P1.H7_F2_D1]

value: leaf

tag: developmental stage

value: 7-10 leave rosette


title: Vg2/3/4 CD103positive 2

description:
Sorted into PBS and RNA extracted
GN097-CD103plus

tag: cell type


title: F2_D1 individual, grown at 4C [T4_P1.H6_F2_D1]


title: RNAseq_NPC_5084_KO

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

data_processing:
ATACseq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Bowtie2 v2.3.4.3 with --phred33, --sensitive, look for multiple alignments and report best with MAPQ, --maxins 1000.
MACS2 was used for peak calling with --keep-dup 1 --shift -100 --extsize 200 –nomodel
RNA-seq:
Sequenced reads were trimmed for adapter sequence, and masked for low-complexity or low-quality sequence (--quality 20 --phred33 --stringency 1 --length 20 --paired), then mapped to mm10 whole genome using Tophat2 v2.1.1 with parameters --max-multihits 20 --transcriptome-max-hits 60.
The number of reads falling in the exons were counted by FeatureCounts v1.6.3 with GTF file (gencode.vM20.annotation.gtf).
Supplementary_files_format_and_content: Peak text files
Supplementary_files_format_and_content: Raw counts text files

source_name: Neurosphere culture from Ganglionic eminence

extract_protocol:
ATAC-Seq: 50,000 to 100,000 nuclei from GE_NPC were used for ATAC-seq library preparation.
ATAC-seq library preparation using reagents from TruePrep DNA Library Preparation Kit V2 (Vazyme, TD501-02, China) following the manufactory's protocol with modifications.
RNA-seq: Total RNA was extracted from fresh frozen GE_NPCs and GE tissue at E15.5 by Direct-zolTM RNA MicroPrep kit (ZYMO RESEARCH, catalog #R2060) and RNeasy Lipid Tissue Mini Kit (Qiagen, catalog #74804), respectively.
mRNA-seq libraries from GE_NPCs were prepared by BGI Genomics, China. Total RNA-seq libraries from GE tissue were prepared using QIAseq™ Stranded Total RNA Lib Kit (Qiagen, Cat#180745) following the manufacturer’s instructions.

value: Neural progenitor cells

value: Nestin-KO

tag: gender


title: Vg2/3/4 CD103positive 1

description:
Sorted into trizol and library made
GN096-CD103plus


title: Brain, Plxnd1-KO, 4

city: Seoul

first: Jung-Woong

last: Kim

address: 84 Heuksuk-ro Dongjak-ku

department: Life Science

country: South Korea

institute: Chung-Ang University

data_processing:
Illumina Casava software used for basecalling
Sequenced read were trimmed for adaptor sequence, and masked for low-quality sequence using TrimGalore
Alignment to mm10 whole genome with HISAT2 and transcript assembly with StringTie
Genome_build: mm10
Supplementary_files_format_and_content: txt files include raw counts, normalized counts(FPKM)

molecule: polyA RNA

source_name: Brain, Plxnd1-KO

extract_protocol:
Total RNA was extracted using Trizol reagent.  Illumina Truseq RNA kit (cat# 20040534) includes the specific beads to capture poly-A tailed mRNA.
RNA libraries were prepared for sequencing using standard Truseq RNA Illumina protocols.

value: neonatal

value: brain (striatum)


title: Brain, Plxnd1-KO, 2


title: Vg2/3/4 CD103negative 2

description:
Sorted into PBS and RNA extracted
GN097-CD103neg


title: RNAseq_NPC_5088_WT

value: WT


title: Brain, Plxnd1-KO, 3


title: Vg2/3/4 CD103negative 3

description:
Sorted into PBS and RNA extracted
GN099-CD103neg


title: RNAseq_NPC_4643_KO

value: male


title: F2_D1 individual, grown at 4C [T4_P2.A10_F2_D1]


title: Vg2/3/4 CD103positive 4

description:
Sorted into lysis buffer and RNA extracted
DAR223A1


title: Vg2/3/4 CD103negative 1

description:
Sorted into trizol and library made
GN096-CD103neg


title: Brain, Plxnd1-KO, 1


title: RNAseq_NPC_3046_WT


title: RNAseq_NPC_4647_WT


title: F2_D1 individual, grown at 4C [T4_P1.H3_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P1.H4_F2_D2]


title: MDA-MB-231, PFKFB4-KO, biol rep 3

city: Buffalo

first: Subhamoy

last: Dasgupta

state: NY

address: Elm and Carlton Streets

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE (p7) annotation (v25) using Tophat (v2.1.1)
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Assembly: GRCh38.p7 GENCODE v25 (MDA-MB-231)
Assembly: mm10 (EMT6)
Supplementary files format and content: csv file; raw counts

growth_protocol: Both EMT6 and MDA-MB-231 cells were maintained in high-glucose DMEM supplemented with 10%FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
The purification of total RNAs is prepared using the miRNeasy mini kit (Qiagen).
The sequencing libraries are prepared with the mRNA HyperPrep kit (Roche), from 500ng total RNA.

tag: cell line

value: breast cancer cells


title: Brain, Plxnd1-WT, 4

source_name: Brain, Plxnd1-WT

value: wild type


title: F2_D1 individual, grown at 4C [T4_P1.H8_F2_D1]


title: MDA-MB-231, PFKFB4-KO, biol rep 2


title: aged mouse 6 (72 weeks) [Sequel]

city: NORWICH

first: Laura

last: mincarelli

state: County (optional)

address: Norwich Research Park, Colney Lane, Colney

institute: Earlham Institute

description: single cell fulllenght cDNA (10x Genomics)

data_processing:
Illumina data
Raw Illumina sequencing data were analysed with the 10X Genomics CellRanger pipeline (version 3.0.2) to obtain a single-cell expression matrix object.
Using Seurat v3 in R data were normalised using NormalizeData
data from multiple samples were merged using the FindIntegrationAnchors and IntegrateData commands
count matrices produced by short-read sequencing for individual libraries were combined in Seurat using FindIntegrationAnchors and IntegrateData functions
Illumina and PacBio reads were integrated in Seurat using the CreateAssayObject command to add the long-read data to an existing Seurat object already containing the short-read data
Pacbio data
Circular Consensus reads (CCS) were generated using smrtlink-6.0.0.47841 amnd the command "ccs --numThreads=24 --noPolish --minLength=50 --maxLength=15000 --minPasses=1 --minPredictedAccuracy=0.8"
Reads with identified polydA or polydT were demultiplexed using bbduk and the 10X genomics barcodes identified from the short-read analysis
Long-reads were mapped to the mouse genome (mm10) using Minimap 2 (v2.17), and to the gencode (vM19) transcriptome. De novo transcript annotation was performed with TALON  v.5 was used to generate custom transcriptome using gencode v.M24 and GRCm38.p6. Minimum identity threshold 0.9, coverage 0.8. Novel features filtered with N=5 reads in K=3 samples. Transcriptome then filtered for mis-called antisense transcripts. Novel features were merged with v.M24 reference to make custom annotation. Count matrices were generated using HTSeq, the alignments to the genome (GRCm38.p6, Minimap2) and the TALON annotation
Novel exons were identified by investigating the alignment of the reads to the transcriptome
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: gene level counts
Supplementary_files_format_and_content: de novo annotation
Supplementary_files_format_and_content: gene levels counts

source_name: bone marrow cells

extract_protocol:
Bone marrow was isolated from spine, femora, tibiae, and ilia,blood cell depletion was performed with ammonium chloride lysis  and lineage negative cells were isolated using the EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit
3’ end single cell RNA-Seq using the 10X Genomics Chromium (V2 Kit) according to manufacturer’s protocol
Libraries compatible for Illumina platform and for Pacific Biosciences Sequel/Sequel II systems were prepared from input cDNA

value: Lineage negative, cKit (Cd117) positive (LK) cell fraction

tag: age

value: 72 weeks


title: Brain, Plxnd1-WT, 3


title: P_6046 individual, grown at 4C [T4_P1.H5_P_6046]


title: MDA-MB-231, PFKFB4-KO, biol rep 1


title: F2_D2 individual, grown at 4C [T4_P1.H1_F2_D2]


title: young  mouse 5 ( 8 weeks) [Sequel]

tag: Sex

value: 8 weeks


title: F2_D2 individual, grown at 4C [T4_P1.H12_F2_D2]


title: MDA-MB-231, WT, biol rep 3


title: Brain, Plxnd1-WT, 1


title: Brain, Plxnd1-WT, 2


title: MDA-MB-231, WT, biol rep 2


title: P_6191 individual, grown at 4C [T4_P1.H11_P_6191]


title: aged mouse 4 (72 weeks) [Sequel]

value: female


title: MDA-MB-231, WT, biol rep 1


title: 21-2A,HCC Peritumor tissue,Pe_M replicate 1

value: HCC Peritumor tissue

value: c-Myc/Alb-cre transgenic


title: F2_D2 individual, grown at 4C [T4_P1.H10_F2_D2]


title: Cd45neg_Il17_rep4

city: Badalona

first: Elisabetta

last: Mereu

address: Ctra de Can Ruti, Camí de les Escoles, s/n

country: Spain

institute: Josep Carreras Leukemia Research Institute

description: scRNA-seq 3'

data_processing:
Reads were then demultiplexed according to the cell barcodes
Sequenced reads were filtered for low-complexity or low-quality sequence.
High quality reads were mapped according to the Cellranger pipeline
Genome_build: Mouse: Gencode release 21, assembly GRCm38 (mm10)
Supplementary_files_format_and_content: h5 files containing gene expression values as UMI counts

extract_protocol:
CD45+ and CD45–/EpCAM– cells were FACS sorted in a BD Fusion cell sorter separately to enrich for the less abundant CD45+ cells, following the sorting strategy depicted in Suppl. Fig. 1a. Cells were collected in PBS + 0.5% BSA at 4°C in LoBind tubes (Eppendorf) and processed immediately with the microfluidics Chromium platform (10X Genomics)
Single-cell RNA sequencing libraries were prepared using the Chromium 3' protocol

tag: protocol

value: Chromium

value: Dermis


title: young  mouse 3 ( 8 weeks) [Sequel]


title: aged mouse 2 (72 weeks) [Sequel]


title: young  mouse 1 ( 8 weeks) [Sequel]


title: Cd45neg_Il17_rep3

description: scRNA-seq 3'


title: F2_D1 individual, grown at 4C [T4_P1.G8_F2_D1]

value: leaf

value: 7-10 leave rosette


title: Cd45neg_Il17_rep2

description: scRNA-seq 3'


title: ALL blast, macrophage reprogrammed

city: San Francisco

first: Amy

last: Fan

state: CA

address: 769 25th Ave

department: Pathology

institute: UCSF

data_processing:
Raw sequencing data were converted to fastq files using 10X Cellranger Single Cell Software Suite version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome) and aligned to transcriptome assembly hg38
Assembly: hg38

source_name: BM

extract_protocol:
Cells were collected from in vitro culture, washed once with PBS, and resuspended in cold PBS.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics)

value: BM

value: 7d culture M-CSF, IL-3, GM-CSF


title: Cd45neg_Il17_rep1

description: scRNA-seq 3'


title: ALL blast, DC reprogrammed

value: 7d culture IL-4 and GM-CSF


title: F2_D2 individual, grown at 4C [T4_P1.H2_F2_D2]


title: CL3B

city: COLLEGE PARK

first: Xudong

last: Zhu

state: Maryland

address: 10300 Baltimore Ave.

institute: USDA-ARS-BARC-FQL

description: Clemente, day 3, rep2

data_processing:
The RNA-seq library read qualities were assessed using FastQC (Babraham Institute, Cambridge, UK). The remaining sequencing adapters were removed using trim_galore (Babraham Institute, Cambridge, UK). The reads were splice-aligned on the genome using STAR (Dobin et al., 2013) (version 2.4.0i using standard parameters) on the lettuce genome Lactuca sativa (assembly Lsat_Salinas_v7, https://www.ncbi.nlm.nih.gov/genome/352) (Verwaaijen B, et al., 2018; Reyes-Chin-Wo et al., 2017). The expression was quantified using featureCounts (Liao et al., 2014) (version V1.4.5-P1 using standard parameters).
Differential gene expression analyses were performed in R 3.6.1 (R core Team, 2019). The Bioconductor package DESeq2 was used for differential expression analyses with the trimmed mean of p values of log2foldchange normalization between each pair of samples (Robinson and Oshlack, 2010; Robinson et al., 2010; McCarthy et al., 2012). Gene enrichment analysis pathway related analyses was performed with the package clusterProfiler (Yu et al., 2012) based on the Gene Ontology and Kyoto Encyclopdia of Genes and Genomes (KEGG) (Kanehisa Laboratories, Japan) database.
Genome_build: assembly Lsat_Salinas_v7, https://www.ncbi.nlm.nih.gov/genome/352
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Lactuca sativa

source_name: Clemente_day 3_midrib

extract_protocol:
Total RNA was extracted using RNeasy Plant Mini kit, and purified by mini columns following the manufacturer instruction (QIAGEN, USA). RNA quality was checked with a NanoDrop 2000 Spectrophotometers (Thermo Scientific, Waltham, MA, USA).
Next generation sequencing of RNA (RNA-seq) was performed on an Illumina HiSeq3000 using a paired-end read length of 2 × 150 bp with Illumina HiSeq3000 sequencing kits (Novogene, Sacramento, CA, USA).

tag: accessions

value: Clemente

tag: phenotype

value: medium degree of browning

tag: time point

value: day 3

value: Midrib


title: Cd45neg_CTR4

description: scRNA-seq 3'

value: CTRL


title: RNAseq_NPC_3043_KO

value: Neural progenitor cells

value: Nestin-KO

value: male


title: F2_D2 individual, grown at 4C [T4_P1.G9_F2_D2]


title: P_6046 individual, grown at 4C [T4_P1.G7_P_6046]


title: ALL blast, Blasts

value: Freshly isolated


title: CL3A

description: Clemente, day 3, rep1


title: F2_D2 individual, grown at 4C [T4_P1.G5_F2_D2]


title: CL2B

description: Clemente, day 2, rep2

source_name: Clemente_day 2_midrib

value: day 2


title: Cd45neg_CTR2

description: scRNA-seq 3'

value: Chromium


title: F2_D1 individual, grown at 4C [T4_P1.G4_F2_D1]


title: CHS1 CCHS Neurons

city: Memphis

first: Daniel

middle: Lee

last: Johnson

state: Tennessee

address: 71 S Manassas

department: Molecular Informatics Core

institute: UTHSC

data_processing:
QC was performed using FASTQC. Reads were trimmed for phread > 30.
Alignment was performed using STAR 2.7.10 using hg38.
Counts were normalized using CPM.
Assembly: hg38
Supplementary files format and content: CPM normalized count table in tsv format.

source_name: Human Dental Pulp Stem Cells

growth_protocol: DPSC used in this study were isolated and cultured according to our previously described protocol and stored in the DPSC Repository (Goorha and Reiter 2017). Briefly, the dental pulp was removed from inside the tooth cavity and minced. Following removal, the pulp was digested with 3 mg/mL Dispase II and 4 mg/mL Collagenase I for 1 hour. Cells were then seeded on poly-D-Lysine coated 12-well plates with DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS), and 100 U/mL penicillin and 100 ug/mL streptomycin (Pen/Strep) (Fisher Scientific, Waltham, MA). Once confluent (80%) cultures were passaged using TrypLETM Express. Only early passage cells (<passage 4) were used for subsequent neuronal differentiation and molecular studies.

extract_protocol:
Total RNA was extracted using Zymo Directzol RNA extraction kit.
Total RNA was checked for quantity and quality on an Agilent Bioanalyzer 6000 pico chip and determined to have an RNA Integrity Number (RIN) of >9.0. For eukaryotic organisms, mature mRNAs, processed and equipped with a poly(A) tail at the 3’end, are captured via oligo(dT) beads. For prokaryotic samples, rRNAs are removed by specialized kits, maintaining mRNA molecules. According to different demands, the mRNAs can be constructed into regular library and strand specific library.    Construction of regular RNA library (non-stranded, non-directional):  After enrichment, mRNAs are fragmented randomly in fragmentation buffer and the first-strand cDNA is synthesized using random hexamer primers and M-MuLV Reverse Transcriptase (RNase H-). The second strand is subsequently generated by dNTPs, DNA polymerase I and RNase H. Double-stranded cDNA molecules are purified by AMPure XP beads and overhanging ends are repaired to blunt ends by exonuclease/polymerase. After 5’ phosphorylation and 3’ adenylation, the cDNAs are ligated with P5/P7 sequencing adapters to prepare for hybridization(1). In order to select the insert fragment of preferentially 150~200 bp in length, the modified libraries are purified with AMPure XP system (Beckman Coulter, Beverly, USA). The final library is ready after PCR amplification and products purification by AMPure XP beads.

treatment_protocol: DPSC lines were seeded at 20,000 cells/cm2 on poly-D-lysine coated flasks with DMEM/F12 1:1, 10% fetal bovine serum (FBS), 10% newborn calf serum (NCS), with 100 U/mL penicillin and 100 ug/mL streptomycin (Pen/Strep). At 80% confluence, the neuronal differentiation protocol was followed as previously published in Kiraly et al., 2009 (Kiraly et al. 2009) with an extended maturation phase (4 weeks versus 7 days) (Goorha and Reiter 2017). Briefly, DPSC were placed in 10 μM 5-azacytidine (Acros Scientific, Geel, Belgium) in DMEM/F12 containing 2.5% FBS and 10 ng/mL bFGF (Fisher Scientific, Waltham, MA) for 48 hours. Following epigenetic reprogramming, neuronal differentiation was induced by exposing the cells to 250 μM IBMX, 50 μM forskolin, 200 nM TPA, 1mM db-cAMP (Santa Cruz, Dallas, TX), 10 ng/mL bFGF (Invitrogen, Carlsbad, CA), 10 ng/mL NGF (Invitrogen, Carlsbad, CA), 30 ng/mL NT-3 (Peprotech, Rocky Hill, NJ), and 1% insulin-transferrin-sodium selenite premix (ITS) (Fisher Scientific, Waltham, MA) in DMEM/F12 for 3 days. At the end of the neural induction period, neuronal maturation was performed by maintaining the cells in Neurobasal A media (Fisher Scientific, Waltham, MA) with 1mM db-cAMP, 2% B27, 1% N2 supplement, 30 ng/mL NT-3, and 1X Glutamax (Fisher Scientific, Waltham, MA) for 28 days.

value: Human Dental Pulp Stem Cells

tag: derived cell_type

value: Neurons

tag: disease state

value: Congenital Central Hypoventilation syndrome (CCHS)

value: Neuronal differentiation


title: CHS2 CCHS Neurons


title: RHD3 ROHHAD Neurons

value: Rapid-onset obesity with hypothalamic dysfunction, hypoventilation, and autonomic dysfunction (ROHHAD)


title: CL2A

description: Clemente, day 2, rep1


title: CL0B

description: Clemente, day 0, rep2

source_name: Clemente_day 0_midrib

value: day 0


title: F2_D1 individual, grown at 4C [T4_P1.G3_F2_D1]

source_name: leaf

value: leaf

value: 7-10 leave rosette


title: RHD2 ROHHAD Neurons


title: Cd45pos_Il17_rep3

description: scRNA-seq 3'

value: Immune


title: RHD1 ROHHAD Neurons


title: CL0A

description: Clemente, day 0, rep1

value: Clemente

value: medium degree of browning

value: Midrib


title: PC3B

description: Parris Island Cos, day 3, rep2

source_name: Parris Island Cos_day 3_midrib

value: Parris Island Cos

value: low degree of browning

value: day 3


title: Cd45pos_Il17_rep4

description: scRNA-seq 3'


title: CON3 Control Neurons

value: Neurotypical control


title: F2_D1 individual, grown at 4C [T4_P1.G2_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.G1_F2_D1]


title: Cd45pos_Il17_rep2

description: scRNA-seq 3'

value: Chromium


title: F2_D2 individual, grown at 4C [T4_P1.G6_F2_D2]


title: PC3A

description: Parris Island Cos, day 3, rep1


title: F2_D2 individual, grown at 4C [T4_P1.G12_F2_D2]


title: PC2B

description: Parris Island Cos, day 2, rep2

source_name: Parris Island Cos_day 2_midrib

value: day 2


title: CON2 Control Neurons

value: Human Dental Pulp Stem Cells

value: Neurons


title: Cd45neg_CTR3

description: scRNA-seq 3'

value: Dermis

value: CTRL


title: Cd45pos_Il17_rep1

description: scRNA-seq 3'


title: PC2A

description: Parris Island Cos, day 2, rep1


title: F2_D2 individual, grown at 4C [T4_P1.G11_F2_D2]


title: CL6_DE3

city: perth

first: Carlos

middle: A

last: Aya-bonilla

state: WA

address: 32 kinship street

country: Australia

institute: Telethon Kids Institute

data_processing:
Bioinformatic analysis was performed by AGRF following standardised pipelines, which involved demultiplexing (DRAGEN BCL Convert 07.021.609.3.9.3 pipeline).
Quality Control: >87% bases above Q30 across all samples.
Raw data was aligned to the reference human genome build version hg38 using STAR aligner v2.7.10a.
The transcriptome was assembled using the StringTie tool v2.1.4 (Gencode annotation).
Differential expression analysis was performed using the edgeR (version 3.32.1) package and raw counts were normalised using the trimmed mean of M-values (TMM) method.
Assembly: hg38
Supplementary files format and content: tmm_counts.txt

source_name: Cell line

growth_protocol: One million cells per millilitre were seeded into each well of a 24-well cell culture plate containing RPMI 1640 supplemented with 20% heat inactivated fetal calf serum (FCS), L-glutamine (2mM final concentration), 2-mercaptoethanol (50µM final concentration), 1% non-essential amino acid mix (100x) and 1% 100mM sodium pyruvate solution. Cell cultures were incubated in a humidified 37°C atmosphere containing 5% CO2 in air.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The yield and quality of the isolated RNA was assessed using a LabChip GX (PerkinElmer) with all the samples displaying high RNA quality (RIN >7.5).
500ng of purified total RNA per sample was used as input for library preparation using the Illumina Stranded mRNA Prep kit (Illumina), according to manufacturer’s instructions, by the Australian Genome Research Facility (AGRF).

treatment_protocol: For each cell line, hypomethylating drugs were added at a final concentration of 1.5µM azacitidine or 1.5µM decitabine in comparison to vehicle control and cells were incubated for 72 hours at 37°C.

value: KMT2A-rearranged infant ALL

value: Decitabine-treated


title: F2_D2 individual, grown at 4C [T4_P1.G10_F2_D2]

value: leaf

value: 7-10 leave rosette


title: Cd45neg_CTR1

description: scRNA-seq 3'


title: Cd45pos_CTR3

description: scRNA-seq 3'

value: Immune


title: CON1 Control Neurons

value: Neuronal differentiation


title: CL6_DE2


title: PC0B

description: Parris Island Cos, day 0, rep2

source_name: Parris Island Cos_day 0_midrib

value: day 0

value: Midrib


title: PC0A

description: Parris Island Cos, day 0, rep1

value: Parris Island Cos

value: low degree of browning


title: CL6_DE1


title: P_6046 individual, grown at 4C [T4_P1.F8_P_6046]


title: F2_D2 individual, grown at 4C [T4_P1.F9_F2_D2]


title: Cd45pos_CTR2

description: scRNA-seq 3'


title: F2_D1 individual, grown at 4C [T4_P1.F7_F2_D1]


title: CL5_DE3


title: TG3B

description: Tall Guzmaine, day 3, rep2

source_name: Tall Guzmaine_day 3_midrib

value: Tall Guzmaine

value: high degree of browning

value: day 3


title: Cd45pos_CTR1

description: scRNA-seq 3'

value: Chromium


title: TG3A

description: Tall Guzmaine, day 3, rep1


title: F2_D2 individual, grown at 4C [T4_P1.F6_F2_D2]


title: CL5_DE2


title: Cd45pos old dermis rep2

description: scRNA-seq 3'

source_name: old dermis


title: TG2B

description: Tall Guzmaine, day 2, rep2

source_name: Tall Guzmaine_day 2_midrib

value: day 2


title: Cd45pos_CTR4

description: scRNA-seq 3'


title: Cd45pos old dermis rep3

description: scRNA-seq 3'


title: F2_D2 individual, grown at 4C [T4_P1.F5_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P1.F4_F2_D2]


title: TG2A

description: Tall Guzmaine, day 2, rep1


title: CL5_DE1


title: Cd45pos old dermis rep1

description: scRNA-seq 3'


title: Cd45pos young dermis rep3

description: scRNA-seq 3'

source_name: young dermis


title: CL4_DE3


title: F2_D2 individual, grown at 4C [T4_P1.F3_F2_D2]


title: Cd45pos young dermis rep2

description: scRNA-seq 3'


title: TG0A

description: Tall Guzmaine, day 0, rep1

source_name: Tall Guzmaine_day 0_midrib


title: P_6191 individual, grown at 4C [T4_P1.F2_P_6191]


title: CL4_DE2


title: CL4_DE1


title: Cd45pos young dermis rep1

description: scRNA-seq 3'


title: Round 2 Selected Library on Bl6 T-cells

city: durham

first: Jonathan

last: Ark

address: 3 genome ct

institute: Duke University

data_processing:
Find sequences
Translate Sequences
Enumerate Sequencing %
Assembly: NA
Supplementary files format and content: list of sequence representation csv
Library strategy: Amplicon-seq

organism: Dependoparvovirus

source_name: Virus

extract_protocol:
IBI gDNA extraction kit (IB47200)
Custom

value: Virus

tag: infected cell_type

value: T-cell

value: Evolved


title: F2_D1 individual, grown at 4C [T4_P1.F1_F2_D1]

tag: treatment


title: Round 1 Selected Library on Bl6 T-cells


title: F2_D1 individual, grown at 4C [T4_P1.F12_F2_D1]


title: CL3_DE3

value: KMT2A-rearranged infant ALL

value: Decitabine-treated


title: Unselected AAV Library

value: Parent


title: 9 dpp testes

city: Yokohama

first: Takahiro

last: Suzuki

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

data_processing:
Raw paired-end sequence data were converted to FASTQ files and mapped to mouse mm10 genome using Cell Ranger software version 3.0.2(10X Genomics).
Genome_build: mm10

source_name: testis

growth_protocol: Testes extracted from 7 days postpartum(dpp) were decapsulated and were cut into 3-4 fragments and placed onto the 1.5% (w/v) agarose gel which was half-submerged in the culture medium (α -Minimum essential medium (a-MEM; ThermoFisher Scientific, Waltham, MA, USA), supplemented with 40 mg/mL AlbuMAX (ThermoFisher Scientific) with PDMS-ceiling chip ceiling.

extract_protocol:
cells were dissociated enzymatically bycollagenase I for 25 mins and 0.05% Tripsin-EDTA for 10 min at  37°C then harvested by centrifugation.
Single-cell RNA sequencing libraries were prepared from the freshly isolated female mouse gonad tissues and ES-derived gonad cells by using Chromium Single Cell 3ʹ v2 Reagent Kits (10X Genomics) as previously described (Yoshino et al. Science (2021)). Briefly, the dissociated cells were mixed with the Single cell Master Mix and generated gel bead-in-emulsions (GEMs). The RNAs in each GEM were revers-transcribed and the resulting cDNAs were amplified by PCR. Illumina sequencer adapted sequencing libraries were constricted from the amplified cDNAs. Single-cell RNA sequencing libraries were sequenced with paired-end reads on the Illumina HiSeq X Ten platform.

tag: strain

value: Acr-Gfp tg mouse (C57BL/6)

value: testis


title: 14 dpp testes

tag: tissue


title: F1_D1 individual, grown at 4C [T4_P1.F11_F1_D1]

first: Rahul

last: Pisupati

data_processing:
Raw sequencing reads were trimmed using cutadapt
Trimmed reads were mapped to reference TAIR10 genome using Bismark
Assembly: TAIR10
Supplementary files format and content: Files are in bedgraph format with "chromosome position strand context mc_score total_reads methylated"

extract_protocol:
DNA was extracted from leaf tissue and performed bisulfite treatment
Libraries were constructed and sequenced through Illumina HiSeq

value: leaf

value: 7-10 leave rosette

tag: genotype


title: CL3_DE1


title: 7-days cultured testes


title: TG0B

description: Tall Guzmaine, day 0, rep2

value: day 0

value: Midrib


title: F2_D2 individual, grown at 4C [T4_P1.F10_F2_D2]

tag: developmental stage


title: F2_D1 individual, grown at 4C [T4_P1.E9_F2_D1]

tag: cell type


title: CL2_DE2


title: IL-15Tg-Xbp1s cKO 3

city: duarte

first: Shoubao

last: Ma

state: California

address: 1500 East Duarte Road

institute: City of Hope

data_processing:
Sequencing reads were mapped to the mouse genome using HISAT2 (Version: v101)
Transcript counts were generated using HTSeq and differential gene analysis was performed using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: RPKM values

source_name: mouse immune cells

extract_protocol:
Total RNA was isolated from purified splenic NK cells from IL-15Tg-WT and IL-15Tg-Xbp1s cKO mice using a RNeasy Mini Kit (QIAGEN).
The RNA libraries were generated using the KAPA Hyper Prep Kit (KAPA Biosystems). Sequencing was performed on the HiSeq2500.  Sequencing was performed at the City of Hope Genomics Facility on an Illumina HiSeq2500 machine with single read 50 bp mode.

value: mouse NK cells

value: spleen

tag: genotype/variation

value: IL-15Tg-Xbp1s cKO


title: CL2_DE1

tag: cell line


title: IL-15Tg-Xbp1s cKO 2


title: F2_D1 individual, grown at 4C [T4_P1.E8_F2_D1]

address: Dr. Bohrgasse 3


title: 2-days cultured testes


title: CL1_DE3


title: F2_D1 individual, grown at 4C [T4_P1.E7_F2_D1]


title: IL-15Tg-Xbp1s cKO 1


title: CL3_DE2


title: P_6191 individual, grown at 4C [T4_P1.E6_P_6191]


title: IL-15Tg WT 3

value: IL-15Tg WT


title: CL1_DE2


title: F2_D1 individual, grown at 4C [T4_P1.E5_F2_D1]


title: CL1_DE1


title: F2_D2 individual, grown at 4C [T4_P1.E4_F2_D2]


title: CL6_AZ3

value: Azacitidine-treated


title: embryo_day8_rep6

type: RNA

city: Quebec

first: Valerie

middle: S

last: Langlois

state: QC

address: 490 rue de la Courrone

department: Centre Eau Terre Environnement

country: Canada

institute: Intitut national de la recherche scientifique (INRS)

description: transcriptional developmental profile

hyb_protocol: Agilent Gene Expression Hybridization kit

scan_protocol: Agilent SureScan Microarray Scanner with Scan Control software at 5 mm resolution

data_processing: SAS JMP Genomics, R package limma, Elsevier Pathway Studio

organism: Phalacrocorax auritus

source_name: whole embryo, incubation day 8

label_protocol: Agilent One-Color Low-Input Labeling kit

growth_protocol: fresh eggs were articfically inbcubated at 38oC and 57% humidity

extract_protocol: Qiagen Rneasy Mini kit

treatment_protocol: no treatment

value: embryo

tag: incubation day


title: CL2_DE3


title: IL-15Tg WT 1


title: liver_day12_rep6

description: transcriptional developmental profile

source_name: liver, incubation day 12

value: liver


title: embryo_day8_rep5

description: transcriptional developmental profile


title: liver_day12_rep5

description: transcriptional developmental profile


title: F2_D2 individual, grown at 4C [T4_P1.E3_F2_D2]

institute: Gregor Mendel Institute


title: CL6_AZ2


title: liver_day24_rep5

description: transcriptional developmental profile

source_name: liver, incubation day 24


title: TTSlamseq mESC input replicate2 TTslamSeq_45mins_input_rep2

first: Stefan

middle: Ludwig

last: Ameres

address: Dr.-Bohr-Gasse 3

institute: Institute of Molecular Biotechnology

description:
TTSlamseq mESC input replicate2
total RNA

data_processing:
3' end sequencing data were used to creat custom annotations using 3' GAmES
SLAMseq was mapped and counted using SLAMdunk 3.4.1. Reads were alingned to the dr11 genome
Additional SNP filtering was performed using samtools pileup
TTSLAMseq data were sequentially mapped to rRNA sequences, mitochondrial sequences and then the genome.
other RNAseq data were mapped to dr11 using STAR and counted using featureCounts
Genome_build: dr11
Supplementary_files_format_and_content: count files of SLAMseq data were created using custom scripts after SNP filtering
Supplementary_files_format_and_content: bedgraph files were genererated using deeptools
Supplementary_files_format_and_content: Count files of TTSLAmseq data were obtained from SLAMdunk

source_name: mESC

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14 hour light/10 hour dark cycle). TLAB fish were generated by crossing zebrafish AB and the natural variant TL (Tupfel Longfin) stocks, and used for all experiments.

extract_protocol: QuantSeq 3' end sequencing was used to prepare libraries for SLAMseq as well as oocyte samples. TTSLAMseq libraries were generated using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina®. (NEB). Other RNAseq libraries were generated using using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs) and indexed with NEBNext Multiplex Oligos for Illumina (Dual Index Primer Set I) (New England Biolabs).

treatment_protocol: Zebrafish embryos were injected with 4sU or incubated in 4sU

value: mouse ES cells

value: mESCs

tag: chip antibody

value: RNA sequencing

value: Soaked with 4sU and SLAMseq at 45 mins post soaking


title: F2_D2 individual, grown at 4C [T4_P1.E2_F2_D2]

source_name: leaf


title: TTSlamseq mESC input replicate1 TTslamSeq_45mins_input_rep1

description:
TTSlamseq mESC input replicate1
total RNA


title: liver_day20_rep5

description: transcriptional developmental profile

source_name: liver, incubation day 20


title: CL6_AZ1

value: KMT2A-rearranged infant ALL


title: F2_D2 individual, grown at 4C [T4_P1.E1_F2_D2]


title: TTSlamSeq 45mins mESCs pulldown replicate2 TTslamSeq_45mins_pulldown_rep2

description:
TTSlamSeq 45mins mESCs pulldown replicate2
total RNA


title: F2_D2 individual, grown at 4C [T4_P1.E12_F2_D2]


title: IL-15Tg WT 2


title: liver_day16_rep3

description: transcriptional developmental profile

source_name: liver, incubation day 16


title: embryo_day5_rep4

description: transcriptional developmental profile

source_name: whole embryo, incubation day 5


title: liver_day24_rep4

description: transcriptional developmental profile


title: liver_day20_rep4

description: transcriptional developmental profile


title: F2_D1 individual, grown at 4C [T4_P1.E10_F2_D1]


title: CL5_AZ1

source_name: Cell line


title: F2_D2 individual, grown at 4C [T4_P1.D9_F2_D2]


title: CL4_AZ3


title: F2_D1 individual, grown at 4C [T4_P1.E11_F2_D1]


title: G4_late_passage_ESC_Terc-/-_rep2

city: tianjin

first: nannan

last: zhao

state: --- Select a state ---

address: nankai

institute: nankai university

data_processing:
The quality control with the software FastQC v0.11.9
Clean reads were aligned to the mouse mm10 genome with the STAR 2.5.3a software
The normalized FPKM were calculated with the software cufflinks-2.2.1.Linux_x86_64
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized counts

source_name: Embryonic Stem Cell

extract_protocol:
Feeder were removed, flash frozen on dry ice, and RNA was harvested using RNA kit(QIAGEN,74134). Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic Stem Cell

value: Terc-/-


title: CL4_AZ2


title: G4_late_passage_ESC_Terc-/-_rep1


title: embryo_day8_rep4

description: transcriptional developmental profile


title: G4_late_passage_ESC_WT_rep2

value: WT


title: G4_late_passage_ESC_WT_rep1


title: CL4_AZ1


title: CL5_AZ3


title: embryo_day5_rep3

description: transcriptional developmental profile


title: liver_day20_rep3

description: transcriptional developmental profile


title: F2_D2 individual, grown at 4C [T4_P1.D7_F2_D2]

city: Vienna

value: leaf

value: 7-10 leave rosette


title: CL3_AZ3


title: G4_early_passage_ESC_Terc-/-_rep2


title: CL5_AZ2


title: CL3_AZ2


title: F2_D1 individual, grown at 4C [T4_P1.D6_F2_D1]


title: G4_early_passage_ESC_Terc-/-_rep1


title: F2_D1 individual, grown at 4C [T4_P1.D5_F2_D1]


title: CL3_AZ1


title: F2_D2 individual, grown at 4C [T4_P1.D4_F2_D2]


title: G4_early_passage_ESC_WT_rep2


title: liver_day12_rep4

description: transcriptional developmental profile


title: liver_day24_rep3

description: transcriptional developmental profile


title: CL2_AZ3


title: F2_D2 individual, grown at 4C [T4_P1.D8_F2_D2]


title: F2_D2 individual, grown at 4C [T4_P1.D3_F2_D2]


title: TTSlamSeq 45mins mESCs pulldown replicate1 TTslamSeq_45mins_pulldown_rep1

description:
TTSlamSeq 45mins mESCs pulldown replicate1
total RNA


title: CL2_AZ2


title: liver_day14_rep3

description: transcriptional developmental profile

source_name: liver, incubation day 14


title: G4_early_passage_ESC_WT_rep1


title: G3_ASC_Terc-/-_rep2

source_name: Adipose Stem Cell

value: Adipose Stem Cell


title: liver_day12_rep3

description: transcriptional developmental profile


title: G3_ASC_Terc-/-_rep1


title: liver_day24_rep2

description: transcriptional developmental profile


title: CL2_AZ1


title: F2_D2 individual, grown at 4C [T4_P1.D1_F2_D2]


title: embryo_day5_rep2

description: transcriptional developmental profile


title: liver_day20_rep2

description: transcriptional developmental profile


title: CL1_AZ3


title: F2_D2 individual, grown at 4C [T4_P1.D12_F2_D2]


title: CL1_AZ2


title: liver_day12_rep2

description: transcriptional developmental profile


title: G3_ASC_WT_rep1


title: F2_D2 individual, grown at 4C [T4_P1.D11_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P1.D10_F2_D1]


title: G3_TTF_Terc-/-_rep1

source_name: Tail Tip Fibroblast

value: Tail Tip Fibroblast


title: CL1_AZ1


title: CL6_C3

value: Control


title: liver_day14_rep2

description: transcriptional developmental profile


title: G3_TTF_Terc-/-_rep2


title: F2_D1 individual, grown at 4C [T4_P1.D2_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.C8_F2_D1]


title: G3_TTF_WT_rep2


title: embryo_day8_rep2

description: transcriptional developmental profile


title: F2_D2 individual, grown at 4C [T4_P1.C7_F2_D2]


title: embryo_day8_rep3

description: transcriptional developmental profile


title: G3_TTF_WT_rep1


title: liver_day24_rep1

description: transcriptional developmental profile


title: CL6_C2


title: CL5_C3


title: liver_day20_rep1

description: transcriptional developmental profile


title: G3_ASC_WT_rep2


title: G3_testis_Terc-/-_rep2

value: testis


title: CL5_C2


title: G3_testis_Terc-/-_rep1


title: liver_day16_rep2

description: transcriptional developmental profile


title: F2_D1 individual, grown at 4C [T4_P1.C5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.C6_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.C4_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.C9_F2_D1]


title: G3_testis_WT_rep1


title: F2_D1 individual, grown at 4C [T4_P1.C3_F2_D1]


title: CL5_C1


title: CL4_C3


title: G3_testis_WT_rep2


title: CL4_C2


title: F2_D1 individual, grown at 4C [T4_P1.C2_F2_D1]


title: WT-U4

city: Aurora

first: Andrés

last: Vázquez-Torres

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description: Barcode: TGACCA; Mean Q-score: 35.02

data_processing:
i7 Illumina universal adapter trimming from raw paired reads with Cutadapt version 2.10
Read mapping with Bowtie2 version 2.3.2 using CP001363.1 and CP001362.1
Duplicate read removal and sorting with Picard version 2.18.27
Count file generation with HTseq version 0.13.5
Statistical analysis performed with DEseq2 1.30.1 and edgeR 3.32.1 in R Studio running R version 4.0.4 via Fisher's exact test on the tagwise dispersion of counts for loci that had at least 80 reads total across all samples be analyzed
Assembly: CP001362.1, CP001363.1
Supplementary files format and content: Comma-delimited matrix file with raw counts for every loci from every sample

organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

source_name: strain 14028s

growth_protocol: Salmonella strains were cultured overnight in LB broth and the subcultured 1:100 into MOPS media with 0.4% D-glucose until an OD600 of 0.25

extract_protocol:
RNA extration was performed via TRIzol reagent with a sodium acetate, glucogen and isopropyl alcohol precipitation. Extracts were washed twice with 70% ethanol, dried, and resuspended in DEPC-treated water. RNA solutions were treated with DNase I according to supplier's specifications (Promega). Reactions were terminated with phenol-choloroform-isoamyl alcohol and RNA was re-extracted as before. rRNA was removed using the MICROBExpress kit (Life Technologies).
1 µg of purified mRNA was fragmented with NEB Magnesium Fragmentation module and purified as previously stated. Libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for a target insert size of 300 bp. Sampels were barcoded with NEBNext Multiplex Oligos

treatment_protocol: No treatment was included for this data set. 2 mL from each culture was pelleted for extraction.

value: Untreated

tag: culture media

value: MOPS Glucose

value: strain 14028s


title: CL4_C1


title: G3_liver_Terc-/-_rep2

source_name: liver

value: liver


title: G3_liver_Terc-/-_rep1


title: F2_D1 individual, grown at 4C [T4_P1.C1_F2_D1]


title: embryo_day8_rep1

description: transcriptional developmental profile

value: embryo


title: liver_day12_rep1

description: transcriptional developmental profile


title: WT-U3

description: Barcode: TTAGGC; Mean Q-score: 34.88


title: G3_liver_WT_rep2


title: WT-U2

description: Barcode: CGATGT; Mean Q-score: 35.16


title: F2_D1 individual, grown at 4C [T4_P1.C12_F2_D1]


title: embryo_day5_rep1

description: transcriptional developmental profile


title: CL3_C2


title: liver_day16_rep1

description: transcriptional developmental profile


title: WT-U1

description: Barcode: ATCACG; Mean Q-score: 35.07


title: G3_liver_WT_rep1


title: F2_D1 individual, grown at 4C [T4_P1.C11_F2_D1]


title: CL3_C1


title: G3_tail_Terc-/-_rep2

source_name: tail tip

value: tail tip


title: greAB-U4

description: Barcode: CTTGTA; Mean Q-score: 35.03

source_name: strain AV19001 ∆greAB

value: strain AV19001 {delta}greAB

value: greAB


title: F2_D2 individual, grown at 4C [T4_P1.C10_F2_D2]


title: CL2_C3

value: KMT2A-rearranged infant ALL


title: G3_tail_Terc-/-_rep1

value: Terc-/-


title: F2_D2 individual, grown at 4C [T4_P1.B9_F2_D2]


title: CL3_C3


title: G3_tail_WT_rep2

value: WT


title: CL2_C2


title: F2_D1 individual, grown at 4C [T4_P1.B8_F2_D1]

value: leaf


title: greAB-U2

description: Barcode: TAGCTT; Mean Q-score: 35.02


title: greAB-U1

description: Barcode: GATCAG; Mean Q-score: 35.12


title: CL2_C1


title: CL1_C3


title: F2_D2 individual, grown at 4C [T4_P1.B6_F2_D2]

value: 7-10 leave rosette


title: Suscepible Sebring colony biol rep 5

city: College Station

first: Xinyue

last: Huang

state: TX

address: 300 Spruce street, Apt 303

department: Entomology

institute: Texas A&M University

description: From laboratory susceptible Sebring strain

data_processing:
Genome Analysis Toolkit (GATK) Best Practices for RNA sequencing data
Sequence reads were trimmed for adaptor sequence/low-quality sequence using TrimGalore (version 0.6.4_dev)
Trimmed sequence reads were mapped to Culex quinquefasciatus reference genome (downloaded from VectorBase, version CpipJ2.4) using STAR (version 2.7.3a)
Picard tools (version 2.20.1) was used to identify and add Read Group (RG) for BAM files obtained from two-pass alignment. Next, reads were counted using featureCounts (version 1.6.0).
Assembly: CpipJ2.4
Supplementary files format and content: tab-delimited text files include raw count value generated from featureCounts for each sample

organism: Culex quinquefasciatus

source_name: Total tissue

extract_protocol:
Extract protocol used was developed for fatty tissues using QIAzol Lysis Reagent. RNA products were purified with the QIAGEN® RNeasy Mini Kit.
RNA libraries for RNA-seq were prepared using PerkinElmer NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 following manufacturer's protocols.

treatment_protocol: Malathion resistant group and malathion susceptible groups were exposed to malathion at a concentration of 400 μg/bottle for 120 min with CDC standard bottle bioassay following instructions in the CONUS manual.

value: Total tissue

value: laboratory susceptible Sebring strain

tag: group

value: Suscepible Sebring colony


title: CL1_C2

value: Control


title: F2_D1 individual, grown at 4C [T4_P1.B7_F2_D1]


title: Suscepible Sebring colony biol rep 4


title: F2_D1 individual, grown at 4C [T4_P1.B5_F2_D1]


title: CL1_C1


title: ATAC-Seq_WT

data_processing:
The quality control with the software FastQC v0.11.9
The raw reads were trimmed with the software Cutadapt
Clean reads were aligned to the mouse mm10 genome with the Bowtie2 software
The peaks were called with the software MACS2
Genome_build: mm10
Supplementary_files_format_and_content: peak files, bedgraph

source_name: Embryonic Stem Cells

extract_protocol:
Samples were lysed and contrast library using TruePrep® DNA Library Prep Kit V2 for Illumina(Vazyme Biotech, TD502)，library were amplified by PCR and purified with AMPure beads (Backman, A63880).
ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols

value: Embryonic Stem Cells


title: Suscepible Sebring colony biol rep 3


title: PS_Yap1

city: Houston

first: Guocan

last: Wang

address: 1515 Holcombe Blvd, T7.3900

institute: MD Anderson Cancer Center

data_processing:
Raw reads were aligned using bowtie (version 1.1.2) (Langmead B et.al., 2009) to build version mm9 of the mouse genome retaining only uniquely mapped reads.
MACS1.4 (Zhang et al., 2008) was used to call peaks in using Input ChIP-seq as control sample using default p value cut-off of 1e-5.
bamCoverage from deeptools (Ramírez Fet.al., 2016) was used to make RPKM normalized bigwig track extending the reads to 200bp fragment length.
Genome_build: Genome_build: mm9
Supplementary_files_format_and_content: Bigwig

source_name: Pten/Smad4-deficient mouse prostate cancer cells

growth_protocol: Pten/Smad4-deficient prostate cancer cells were grown in DMEM containing 10% FBS.

extract_protocol:
chromatin from formaldehyde-fixed cells (10 x106 cells for Yap1 antibody) were cross-linked using 1% paraformaldehyde for 10 minutes and reactions were quenched by 0.125 M glycine for 5 minutes at room temperature. Cells were lysed with ChIP lysis buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 140 mM NaCl, 1% Triton X-100, 0.2% SDS, 0.1% deoxycholic acid) for 30 minutes on ice. Chromatin fragmentation was performed using a Diagenode Bioruptor®Pico sonicator (30 secs on and 30 secs off for 45 cycles) to achieve a DNA shear length of 200 to 500 basepairs. Solubilized chromatin was then incubated overnight with their respective antibody-Dynabead (Life Technologies) mixture (Yap1 antibody: Novus, #NB110-58358). Immune complexes were then washed 3 times with RIPA buffer, once with RIPA-500 (RIPA with 500 mM NaCl), and once with LiCl wash buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA [pH 8.0], 250 mM LiCl, 0.5% NP-40, 0.5% deoxycholic acid). Elution and reverse crosslinking were performed in direct elution buffer (10 mM Tris-Cl [pH 8.0], 5 mM EDTA, 300 mM NaCl, 0.5% SDS) with proteinase K (20 mg/ml) at 65°C overnight.
Libraries were prepared using NEBNext Ultra DNA Library kit (E7370) from NEB.

tag: disease

value: Prostate cancer

tag: antibody


title: F2_D2 individual, grown at 4C [T4_P1.B4_F2_D2]


title: greAB-U3

description: Barcode: GGCTAC; Mean Q-score: 34.87

value: Untreated

value: MOPS Glucose


title: PS_input

value: Input


title: Suscepible Sebring colony biol rep 2


title: G3_tail_WT_rep1

value: tail tip


title: F2_D2 individual, grown at 4C [T4_P1.B3_F2_D2]


title: F2_D1 individual, grown at 4C [T4_P1.B2_F2_D1]


title: Suscepible Sebring colony biol rep 1


title: D30.FluNP.CD44hi.CD4.mem.Input

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
Sequence reads were aligned to GRCm38/mm10 using Burrows-Wheeler Aligner 0.7.6a and converted to bam format by Sambamba 0.5.5.
Tracks for Input libraries were generated by converting bam files to Wiggle tracks and UCSC Wig2Bigwig was used to convert Wiggle tracks to BigWig for display on the UCSC browser.
Input control normalized tracks ChIPseq libraries were generated using MACS2.
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWig, Input and ChIP libraries tracks

source_name: Lung and mediastinal lymph node

extract_protocol:
Cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. Antibodies, H3K27me3 and H3K4me3 were incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG.
Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol:
naïve samples: Single cell suspensions were prepared from pooled lung and lymph nodes of uninfected C57/BL6 mice. CD4+ T cells were purified by negative selection and live CD4+ CD44lo populations isolated by cell sorting. Cells were pooled from ~2 naïve mice.
D10 samples: Single cell suspensions were prepared from pooled lung and lymph nodes of infected C57/BL6 mice on Day 10 post PR8 infection (primary time point). CD4+ T cells were purified by negative selection and stained with FluNP+ MHC Class II tetramers. Live CD4+ CD44hi Flu NP+ populations were isolated by cell sorting. Cells were pooled from ~30 infected mice.
D30 samples: Single cell suspensions were prepared from pooled lung and lymph nodes of infected C57/BL6 mice on Day 30 (memory time point) post PR8 infection. CD4+ T cells were purified by negative selection and stained with FluNP+ MHC Class II tetramers. Live CD4+ CD44hi Flu NP+ populations were isolated by cell sorting. Cells were pooled from ~75 infected mice.
D6 samples: Single cell suspensions were prepared from pooled lung and lymph nodes of  memory stage C57/BL6 initially infected with x31 and rechallenged with PR8 on Day 6 post rechallenge infection (secondary time point). CD4+ T cells were purified by negative selection and stained with FluNP+ MHC Class II tetramers. Live CD4+ CD44hi Flu NP+ populations were isolated by cell sorting. Cells were pooled from ~30 infected mice.

tag: age

value: post natal day 86

value: wild type


title: ATAC-Seq_Terc-/-


title: D6.FluNP.CD44hi.sec.Input

value: post natal day 92


title: RB1m1/m2 12h

city: Beijing

first: Jia

last: Xu

address: 17 Hougou Lane, Chongnei Street

institute: Beijing Institute of Ophthalmology (BIO)

data_processing:
The data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition
Raw reads (raw data) of fastq format were processed firstly  through in-house perl scripts
Clean reads (clean data) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly
V1.5.0-p3 (featureCounts) was used to count the reads numbers mapped to each gene.
Assembly: GRCh38/hg38
Supplementary files format and content: FPKM of each gene was calculated based on reads count mapped to this gene and the length of the gene.

source_name: pluripotent stem cells

extract_protocol:
These samples RNA were isolated with TRIzol reagent (Invitrogen).
To select cDNA fragments length of 370~420 bp, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained

value: pluripotent stem cells

value: microglia

value: RB1 homozygous mutation

value: LPS stimulation for 12 hours


title: RB1m1/m2 12h biol rep1


title: P_6046 individual, grown at 4C [T4_P1.B1_P_6046]

source_name: leaf

value: leaf

value: 7-10 leave rosette


title: RB1m1/m2 8h biol rep1

value: LPS stimulation for 8 hours


title: D10.FluNP.CD44hi.CD4.pri.Input

value: post natal day 66

value: Control


title: Wild collected group biol rep 5

description: WT not treated with bottle assay

value: Total tissue

value: WT

value: Wild collected group


title: RB1m1/m2 8h


title: F2_D2 individual, grown at 4C [T4_P1.B12_F2_D2]


title: Wild collected group biol rep 3

description: WT not treated with bottle assay


title: F2_D2 individual, grown at 4C [T4_P1.B10_F2_D2]


title: Wild collected group biol rep 4

description: WT not treated with bottle assay


title: F2_D2 individual, grown at 4C [T4_P1.B11_F2_D2]


title: RB1m1/m2 4h

value: LPS stimulation for 4 hours


title: RB1m1/m2 0h biol rep1

value: without LPS stimulation


title: Wild collected group biol rep 2

description: WT not treated with bottle assay


title: Wild collected group biol rep 1

description: WT not treated with bottle assay


title: RB1m1/m2 0h


title: Naïve.B6.CD44lo.CD4.Input

value: post natal day 56


title: D30.FluNP.CD44hi.CD4.mem.H3K27Ac

value: post natal day 86

value: H3K27Ac (Diagenode,  )

value: wild type


title: Malthion susceptible biol rep 5

description: Knockdown during bottle assay

value: malathion exposure using CDC bottle assay

value: Malthion susceptible


title: Naïve.B6.CD44lo.CD4.H3K27Ac

value: H3K27Ac (Diagenode, )


title: D10.FluNP.CD44hi.CD4.pri.H3K27Ac


title: Malthion susceptible biol rep 4

description: Knockdown during bottle assay


title: RB1m1/m2 4h biol rep1

value: pluripotent stem cells

value: microglia

value: RB1 homozygous mutation


title: D6.FluNP.CD44hi.sec.H3K4me1

value: post natal day 92

value: H3K4me1 (Diagenode, Cat# C15410037)


title: F2_D2 individual, grown at 4C [T4_P1.A7_F2_D2]

value: leaf

value: 7-10 leave rosette


title: RB1m1/wt 12h

value: RB1 heterozygous mutation

value: LPS stimulation for 12 hours


title: D6.FluNP.CD44hi.sec.H3K27Ac


title: F2_D1 individual, grown at 4C [T4_P1.A8_F2_D1]


title: F2_D2 individual, grown at 4C [T4_P1.A6_F2_D2]


title: D30.FluNP.CD44hi.CD4.mem.H3K4me1


title: Malthion susceptible biol rep 3

description: Knockdown during bottle assay

value: Total tissue

value: WT


title: RB1m1/wt 8h

value: LPS stimulation for 8 hours


title: F2_D1 individual, grown at 4C [T4_P1.A5_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.A9_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.A4_F2_D1]


title: Malthion susceptible biol rep 1

description: Knockdown during bottle assay


title: RB1m1/wt 4h biol rep1

value: LPS stimulation for 4 hours


title: D10.FluNP.CD44hi.CD4.pri.H3K4me1

value: post natal day 66

value: wild type


title: Naïve.B6.CD44lo.CD4.H3K4me1

value: post natal day 56


title: F2_D2 individual, grown at 4C [T4_P1.A3_F2_D2]


title: Malathion resistant biol rep 5

description: Alive after bottle assay

value: malathion exposure using CDC bottle assay

value: Malathion resistant


title: D6.FluNP.CD44hi.sec.H3K27me3

value: H3K27me3 (Diagenode, Cat# pAb-069-050)


title: RB1m1/wt 4h

value: pluripotent stem cells

value: microglia


title: RB1m1/wt 12h biol rep1


title: Malathion resistant biol rep 4

description: Alive after bottle assay


title: liver_day14_rep1

description: transcriptional developmental profile

value: liver


title: RB1m1/wt 8h biol rep1


title: D30.FluNP.CD44hi.CD4.mem.H3K27me3

value: post natal day 86


title: Malthion susceptible biol rep 2

description: Knockdown during bottle assay

value: Malthion susceptible


title: RB1m1/wt 0h biol rep1

value: RB1 heterozygous mutation

value: without LPS stimulation


title: Malathion resistant biol rep 3

description: Alive after bottle assay

value: Total tissue


title: RB1m1/wt 0h


title: Malathion resistant biol rep 2

description: Alive after bottle assay

value: WT


title: RB1wt/wt 12h biol rep1

value: LPS stimulation for 12 hours


title: F2_D2 individual, grown at 4C [T4_P1.A12_F2_D2]

value: leaf

value: 7-10 leave rosette


title: Naïve.B6.CD44lo.CD4.H3K27me3

value: wild type


title: F2_D1 individual, grown at 4C [T4_P1.A11_F2_D1]


title: RB1wt/wt 12h


title: F2_D1 individual, grown at 4C [T4_P1.A2_F2_D1]


title: F2_D1 individual, grown at 4C [T4_P1.A10_F2_D1]


title: skate_adult_pectoral_fin_MethylCseq

city: Sydney

first: Ksenia

last: Skvortsova

state: NSW

address: 384 Victoria St, Darlinghurst

department: Genomics and Epigenetics

institute: Garvan Institute

data_processing:
Sequenced reads in fastq format were trimmed using Trimmomatic software (ILLUMINACLIP:adapter.fa:2:30:10 SLIDINGWINDOW:5:20 LEADING:3 TRAILING:3 MINLEN:50)
Trimmed reads were mapped to Leri_hhj.fasta genome reference (containing the λ phage genome as chrLambda) using WALT (Chen et al, 2016) with the following settings: -m 10 -t 24 -N 10000000 -L 2000.
Optical and PCR duplicates were removed using Picard Tools’s function MarkDuplicates REMOVE_DUPLICATES=true (http://broadinstitute.github.io/picard/).
The numbers of methylated and unmethylated cytosines at each genomic CpG position were called using the MethylDackel extract genome.fasta input.bam -o output --mergeContext. Genotype and methylation bias correction were performed using MethylDackel (MethylDackel extract Leri_hhj_lambda.fasta $input_bam -o $output --mergeContext --minOppositeDepth 5 --maxVariantFrac 0.5 --OT 10,110,10,110 --OB 40,140,40,140) (https://github.com/dpryan79/MethylDackel). (https://github.com/dpryan79/MethylDackel)
Genome_build: little skate: Leri_hhj.fasta
Supplementary_files_format_and_content: bedGraph / The file contains 1. Chromosome / Scaffold; 2. CpG start coordinate; 3. CpG end coordinate; 4. The methylation percentage rounded to an integer; 5. The number of alignments/pairs reporting hydroxymethylated bases; 6. The number of alignments/pairs reporting unmethylated bases

organism: Leucoraja erinaceus

source_name: little skate adult pectoral fin DNA subjected to MethylC-seq

extract_protocol: MethylC-seq library preparation was performed as described previously (PMID: 25692984). Briefly, 1000 ng of genomic DNA extracted from embryonic and adult skate fins was spiked with unmethylated λ phage DNA (Promega) and sonicated to ~300 bp fragments using M220 focused ultrasonicator (Covaris) with the following parameters: peak incident power, 50W; duty factor, 20%; cycles per burst, 200; treatment time, 75 sec. Sonicated DNA was then purified, end-repaired using End-It™ DNA End-Repair Kit (Lucigen) and A-tailed using Klenow Fragment (3'→5' exo-) (New England Biolabs) followed by the ligation of NEXTFLEX® Bisulfite-Seq Adapters. Bisulfite conversion of adaptor-ligated DNA was performed using EZ DNA Methylation-Gold Kit (Zymo Research). Library amplification (13 PCR cycles) was performed with KAPA HiFi HotStart Uracil+ DNA polymerase (Kapa Biosystems). Library size was determined by the Agilent 4200 Tapestation system. The libraries were quantified using the KAPA library quantification kit (Roche) yielding ~10-20 nM.

value: adult

tag: tissue type

value: pectoral fin


title: D6.FluNP.CD44hi.sec.H3K4me3

value: post natal day 92

value: H3K4me3 (Cell Signaling Technology, Cat# 9751S)


title: F2_D2 individual, grown at 4C [T4_P1.A1_F2_D2]


title: D30.FluNP.CD44hi.CD4.mem.H3K4me3


title: D143F AadB

city: Baltimore

first: Marc

last: Ostermeier

state: MD

address: 3400 N. Charles St.

department: Chemical & Department of Chemical & Biomolecular Engineering

institute: Johns Hopkins University

data_processing:
Reads were analyzed for per base sequence quality using FastQC v0.11.9.
We indexed the genome of NEB 5-alpha F'Iq cells (NCBI Reference Sequence: NZ_CP053607.1) and mapped our paired end reads to the transcriptome using STAR version 2.7.0c
Mapped reads were quantified and tabulated using featureCounts from the Subread package v1.6.4.
Normalized counts per million for the two biological replicates of RNA-Seq were tabulated with edgeR version 3.8.
Calculations for the fold-difference in gene expression and statistical analysis were performed in Microsoft Excel 2016
Assembly: Escherichia coli strain K-12 NEB 5-alpha F'Iq
Supplementary files format and content: The processed data file consists of tabs for raw counts of mapped reads, fold-difference in gene expression, variance in fold-difference, and p-values. Each tab is organized with the sample name listed in columns and genes listed in rows.

organism: Escherichia coli

source_name: NEB 5-alpha F'Iq Competent E. coli

growth_protocol: Frozen stocks of NEB 5-alpha LacIq cells containing single-codon substitutions of either the NDM-1, CAT-I, or aadB antibiotic resistance genes were diluted into 10 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose and incubated overnight at 37 °C. The overnight cultures were diluted to an OD of 0.020 in 100 ml media containing 50 μg/ml spectinomycin and 2% w/v glucose, and incubated at 37 °C with shaking until the OD was about 0.5. The culture was diluted back to an OD of 0.020 in 100 ml of media in a shake flask. At time zero, IPTG was added to a concentration of 1 mM and the flasks were incubated at 37°C with shaking until the OD of the controls was approximately 0.640 (5 generations of growth). The culture was then diluted back to an OD of 0.020 in 100 ml of prewarmed media in a separate shake flask and incubated at 37°C with shaking until 330 minutes had passed since first inducing the cultures.

extract_protocol:
Microcentrifuge tubes that had been chilled on ice were filled with 1.5 ml of bacteria culture and centrifuged at 6000 x g and 4°C for 5 minutes. Supernatant was decanted and the cell pellet resuspended in 200 μl of Max Bacterial Enhancement Reagent (Invitrogen) that had been preheated to 95°C. The tubes were incubated at 95°C for 4 minutes before 1 ml of TRIzol Reagent (Invitrogen) was added. Sample lysis, separation of the RNA aqueous phase, and subsequent precipitation and wash steps were performed according to the TRIzol user manual. The resulting RNA pellet was resuspended in 50 μl of nuclease-free water. A second RNA precipitation was performed to remove residual salt as recommended by the MICROBExpress Bacterial mRNA Enrichment Kit (Invitrogen). RNA was resuspended in 0.1X TE buffer (NEB). Concentration of RNA was measured by NanoDrop spectrophotometer. RNA integrity was examined by native agarose gel electrophoresis with 300 ng of total RNA loaded in each lane of a 1.0% TAE gel containing ethidium bromide. mRNA enrichment was completed using the MICROBExpress Bacterial mRNA Enrichment Kit. The enriched mRNA was treated with DNase using the TURBO DNA-free Kit (Invitrogen).
Double-stranded cDNA was synthesized, purified, and end prepped with the NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (NEB). NEBNext Adaptor for Illumina (NEB) was ligated to the cDNA. The ligation reactions were purified using NEBNext Sample Purification Beads and PCR enriched using a unique index primer from the NEBNext Multiplex Oligos for Illumina Kit (NEB) for each sample. PCR products were cleaned with NEBNext Sample Purification Beads and pooled for Illumina Tru-Seq (2 x 75 bp reads) at the Transcriptomics and Deep Sequencing core at Johns Hopkins University.

treatment_protocol: Monoculture growth at 37°C for 330 minutes.

value: NEB 5-alpha LacIq

value: D143F AadB


title: F2_D1 individual, grown at 16C [T16_P5.H9_F2_D1]


title: RB1wt/wt 4h biol rep1

value: pluripotent stem cells

value: microglia

value: LPS stimulation for 4 hours


title: A102L AadB

value: A102L AadB


title: D10.FluNP.CD44hi.CD4.pri.H3K27me3

value: post natal day 66

value: H3K27me3 (Diagenode, Cat# pAb-069-050)


title: F2_D1 individual, grown at 16C [T16_P5.H8_F2_D1]


title: D10.FluNP.CD44hi.CD4.pri.H3K4me3


title: RB1wt/wt 8h

value: WT

value: LPS stimulation for 8 hours


title: RB1wt/wt 4h


title: F1_D1 individual, grown at 16C [T16_P5.H7_F1_D1]

value: leaf


title: Malathion resistant biol rep 1

description: Alive after bottle assay

value: Total tissue

value: malathion exposure using CDC bottle assay

value: Malathion resistant


title: Delta Gene

value: Delta Gene


title: 4OHT_Control_72h_RNASeq_Rep3

city: London

first: Vlad

middle: Cezar

last: Seitan

address: Guy's Hospital

department: Medical & Molecular Genetics

institute: King's College London

description: total RNA (rRNA-depleted)

data_processing:
ChIP-seq: Reads were trimmed and filtered using Cutadapt applying a Phred quality threshold of 25 and a minimal read length of 25 bases. Filtered reads were aligned to the mouse genome (NCBI37/mm9 assembly) with Bowtie 1.1.2 keeping only uniquely aligned reads while allowing a maximum of 2 mismatches (-v 2 -m 1). MACS2 was set to discard PCR/optical duplicates and was used as peak caller within the Irreproducibility Discovery Rate (IDR) pipeline implemented by the ENCODE consortium. The final set of peaks was considered the conservative set for IDR <0.02. From this set we removed blacklisted sites. Peak overlap analysis was carried out in R and normalised read coverage values were obtained using the DiffBind Bioconductor package.
RNA-seq: Bases with a Phred quality score lower than 25 were trimmed from read ends with Cutadapt, and polyA tails were removed using PRINSEQ. Filtered reads were aligned to the mouse transcriptome with STAR using 2-pass mapping, and gene-level counts were generated with HTSeq. Differential gene expression analysis was carried out using the Bioconductor package EdgeR.
Genome_build: mm9

growth_protocol: Mouse embryonic stem cells were maintained in feeder-free conditions, on gelatin-coated plates, in KO DMEM supplemented with 10% foetal bovine serum, LIF, L-Glutamine, 2-mercaptoethanol, non-essential amino acids, penicillin and streptomycin

extract_protocol:
1μg total RNA was used as starting material for each library. rRNA was depleted using the NEBNext rRNA Depletion Kit (E6310, New England Biolabs)
Directional RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (E7420, New England Biolabs).

treatment_protocol: To induce Zbtb11 KO, growth media was supplemented with 4-hydroxytamoxifen (4OHT) pre-slubilised in ethanol. 4OHT was added to a final concentration of 250nM from a 1000x stock solution. As control, Zbtb11lox/lox Rosa26ERt2-Cre were treated with the carrier ethanol, or Zbtb11WT/WT Rosa26WT were treated with 4OHT.

tag: parental esc line

tag: zbtb11 locus genotype

tag: rosa26 locus genotype

value: 4-hydroxytamoxifen (250nM)


title: Induced WT AadB

tag: strain

value: Induced WT AadB


title: P_6046 individual, grown at 16C [T16_P5.H6_P_6046]

tag: tissue

value: 7-10 leave rosette

tag: genotype

tag: treatment


title: Uninduced WT AadB

value: NEB 5-alpha LacIq

value: Uninduced WT AadB


title: RB1wt/wt 0h biol rep1

value: pluripotent stem cells

tag: cell type

value: microglia

value: without LPS stimulation


title: F2_D1 individual, grown at 16C [T16_P5.H5_F2_D1]

tag: developmental stage


title: Naïve.B6.CD44lo.CD4.H3K4me3

value: post natal day 56

value: H3K4me3 (Cell Signaling Technology, Cat# 9751S)

value: wild type


title: RB1wt/wt 8h biol rep1

tag: cell line

value: WT

value: LPS stimulation for 8 hours


title: RB1wt/wt 0h


title: 4OHT_Control_72h_RNASeq_Rep1

description: total RNA (rRNA-depleted)


title: 4OHT_Control_72h_RNASeq_Rep2

description: total RNA (rRNA-depleted)


title: F2_D1 individual, grown at 16C [T16_P5.H4_F2_D1]

value: leaf


title: 4OHT_Zbtb11KO_72h_RNASeq_Rep3

description: total RNA (rRNA-depleted)


title: CL6_C1

data_processing:
Bioinformatic analysis was performed by AGRF following standardised pipelines, which involved demultiplexing (DRAGEN BCL Convert 07.021.609.3.9.3 pipeline).
Quality Control: >87% bases above Q30 across all samples.
Raw data was aligned to the reference human genome build version hg38 using STAR aligner v2.7.10a.
The transcriptome was assembled using the StringTie tool v2.1.4 (Gencode annotation).
Differential expression analysis was performed using the edgeR (version 3.32.1) package and raw counts were normalised using the trimmed mean of M-values (TMM) method.
Assembly: hg38
Supplementary files format and content: tmm_counts.txt

source_name: Cell line

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. The yield and quality of the isolated RNA was assessed using a LabChip GX (PerkinElmer) with all the samples displaying high RNA quality (RIN >7.5).
500ng of purified total RNA per sample was used as input for library preparation using the Illumina Stranded mRNA Prep kit (Illumina), according to manufacturer’s instructions, by the Australian Genome Research Facility (AGRF).

tag: disease state

value: KMT2A-rearranged infant ALL

value: Control


title: F2_D2 individual, grown at 16C [T16_P5.H3_F2_D2]


title: PANC-1 cells, shMIF, Hypoxia [PshM_Co]

city: Tianjin

first: Jing

last: Mo

state: Tianjin

address: 22 Qixiangtai Road, Heping District

institute: Tianjin medical university

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Pancreatic cancer

growth_protocol: PANC-1 cells were maintained in DMED supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Pancreatic cancer

value: Pancreatic cancer  cell line

value: MIF knockdown

value: Hypoxia


title: PANC-1 cells, shNTC, Hypoxia [Pshc_Co]


title: C26D NDM-1

value: NEB 5-alpha LacIq

value: C26D NDM-1


title: P28A NDM-1

value: P28A NDM-1


title: PANC-1 cells, shMIF, Normoxia [PshM_N]

value: Normoxia


title: F2_D2 individual, grown at 16C [T16_P5.H1_F2_D2]

value: 7-10 leave rosette


title: F2_D2 individual, grown at 16C [T16_P5.H2_F2_D2]


title: PANC-1 cells, shNTC, Normoxia [Pshc_N]


title: 4OHT_Zbtb11KO_72h_RNASeq_Rep1

description: total RNA (rRNA-depleted)

value: 4-hydroxytamoxifen (250nM)


title: EtOH_Control_72h_RNASeq_Rep3

description: total RNA (rRNA-depleted)

value: ethanol


title: F2_D2 individual, grown at 16C [T16_P5.H12_F2_D2]


title: 4OHT_Zbtb11KO_72h_RNASeq_Rep2

description: total RNA (rRNA-depleted)