title: HT-29-ING3 KO subclone #2 replicate 2

city: St. Louis

first: Gaopeng

last: Hou

state: MO

address: McDonnell Pediatric Research Building, Rm 9220

department: molecular microbiology

institute: Washinton University inSt. Louis

data_processing:
DNBseq
SE 50bp
20 M Clean reads per sample
The SE reads were aligned to the hg19 build using Bowtie2 to map clean reads to reference gene and using HISAT2 to reference genome with the following parameters: --phred64 --sensitive -I 1 -X 1000. Reads were counted using Subread and differential gene expression analysis was performed using DESeq2BGI data was analyzed using DESeq2.
Genome_build: Homo_sapiens GCF_0000001405.38_GRCh38.p12
Supplementary_files_format_and_content: AllSamples.GeneExpression.FPKM

source_name: HT-29-ING3 KO #2

extract_protocol:
Trizol extraction and RNA quality control by Agilent 2100 Bioanalyzer
DNBseq RNA-Seq Quantification Library
Libraries were sequenced on the BGISEQ-500 RNASeq platform

tag: cell line

value: colonic epithelial cell line HT-29

value: ING3 KO #2


title: 713-FB: WT_forebrain rep2

status: Public on Aug 04 2021

type: SRA

city: Edinburgh

first: Graeme

middle: Richard

last: Grimes

address: Western General Hospital, Crewe Road

department: Human Genetics Unit

country: United Kingdom

institute: University of Edinburgh, The Institute of Genetics and Cancer

library_source: transcriptomic

data_processing:
RNA-Seq read level data was processed using the bcbio-nextgen (v1.1.5-b pipeline). Using salmon (v0.14.0, options(  -l SR   --seqBias  --validateMappings --numBootstraps 30) )  against mm10 transcriptome
Gene level quantification carried out in R (3.6.0) bioconductor package bcbioRNASeq  ( 0.3.25) and tximport (1.12.3)
Raw read counts transformed using variance stabilizing transformation (VST)  using the DESeq2 Bioconductor package (1.30.1)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Matrix table with vst transformed gene counts for every gene and every sample
Supplementary_files_format_and_content: salmon quant tab delimited output files

molecule: polyA RNA

organism: Mus musculus

source_name: forebrain

extract_protocol:
Total RNA was extracted from dissected fore brain, mid brain and hind brain of 3 biological replicates P-25 wild type and Fmr1CRE knockin mutant mice from same litter using the RNeasy kit (QIAGEN) combined with QIAshredder (QIAGEN), following the manufacturer’s instructions.
Random primed cDNA from poly(A) selected RNA was converted into an Illumina sequencing library using RNA Library Prep Kit from Illumina (E7420, NEB, USA) in conjunction with NEBNext® Multiplex Oligos for Illumina (E7335/E7500, NEB, USA).
Single-end 50-base pair (bp) reads were generated using a NextSeq 500 (Illumina Inc, SY-415-1002)

tag: tissue

value: forebrain

tag: genotype

value: wildtype


title: 11-baseline-BK [miRNA-seq]

city: Duarte

first: Xiwei

last: Wu

state: CA

address: 1500 E. Duarte Rd.

department: Computational and Quantitative Medicine

country: USA

institute: City of Hope National Medical Center

description:
28841_11-baseline-BK_S18_L999
BK_baseline_miRNA

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to hg19 genome assembly using Tophat2 with default settings
gene expression levels of Refseq genes were counted with Htseq-count
For miRNA, reads were trimmed to remove adapter and aligned to hg19 using Bowtie
miRNAs in miRBase v21 were counted using customized R scripts
Genome_build: hg19
Supplementary_files_format_and_content: tab delimited text file containing the raw count

molecule: total RNA

organism: Homo sapiens

source_name: CTCL patient_Skin_Baseline

extract_protocol:
QIAGEN RNAeasy FFPE
Kappa mRNA Hyperprep kit for mRNA-seq, and Illumina TruSeq miRNA for miRNA-seq

treatment_protocol: Cobomarsen given via intralesional injection (75 mg/dose), subcutaneous (SC), IV rapid bolus injection, or 2-hour IV infusion (300, 600 or 900 mg/dose)

tag: subject status

value: CTCL patient

value: Skin

tag: timepoint

value: Baseline


title: 702-FB: WT_forebrain rep1


title: 711-FB: Fmr1CRE_forebrain rep2

value: Fmr1 Mut


title: S15.4786.A1 [11435_S15.4786.A1_GTCCGC]

data_processing:
Base calling was done using Illumina RTA and bcl2fastq v2.18.0.12
reads were aligned to hg19 genome assembly using Tophat2 with default settings
gene expression levels of Refseq genes were counted with Htseq-count
For miRNA, reads were trimmed to remove adapter and aligned to hg19 using Bowtie
miRNAs in miRBase v21 were counted using customized R scripts
Genome_build: hg19
Supplementary_files_format_and_content: CSV file containing the raw count

extract_protocol: RNAseq libraries were prepared from Illumina TruSeq miRNA for miRNA-seq

tag: disease/tissue type

value: Plaque


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [VDJ]

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s002_Tcells_capture2_VDJ_S32

data_processing:
cellranger v4
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger barcodes, features, and matrix files

source_name: tumor and healthy donor blood

extract_protocol:
Single cell suspensions were generated from human brain metastases
10X single cell gene expression, CITE-seq, and VDJ libraries were created.

tag: primary tumor

value: 16:melanoma; 26:breast carcinoma; 27:lung adenocarcinoma

tag: hashing antibodies

value: patient 16:C0251; patient 26:C0252; patient 27:C0253; healthy donor:C0254; CD8:C0046; CD4:C0045; PD-1/streptavidin:C0961


title: HT-29WT #1 replicate 2

value: WT


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s002_Tcells_capture2_CITE_S13


title: HT-29-ING3 KO subclone #1 replicate 2

source_name: HT-29-ING3 KO #1

value: ING3 KO #1


title: HT-29-ING3 KO subclone #2 replicate 1


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 2 [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s002_Tcells_capture2_GEX_S2


title: 7-baseline-WS [miRNA-seq]

description:
28837_7-baseline-WS_S14_L999
WS_baseline_miRNA

source_name: CTCL patient_Skin_Treated

value: Treated


title: 8-treatment-WS [miRNA-seq]

description:
28838_8-treatment-WS_S15_L999
WS_treated_miRNA


title: Propyzamide_Colon_Sample_3

city: Boston

first: Zhaorong

last: Li

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

data_processing:
The sample is aligned to GRCm38 transcriptome using RSEM.
Genome_build: GRCm38
Supplementary_files_format_and_content: Zipped Kallisto alignment/quantification software output including txt format with transcripts ID and abundance

source_name: Propyzamide-treated mouse during TNBS-induced colitis

extract_protocol:
A piece of colon was flash frozen and later disrupted in Trizol (Invitrogen). RNA was extracted following manufacturer’s instructions and eluted in water.
Libraries were prepared by the Broad Institute according to the SMARTseq 2 protocol as described (Trombetta et al 2014).

treatment_protocol: Colon was isolated from vehicle or propyzamide treated mice, 3 days after TNBS-induction.

tag: strain

tag: Sex

value: Male

tag: age

value: 11 weeks old

tag: treatment

value: propyzamide


title: 9-baseline-CH [miRNA-seq]

description:
28839_9-baseline-CH_S16_L999
CH_baseline_miRNA


title: 5-baseline-HK [miRNA-seq]

description:
28835_5-baseline-HK_S12_L999
HK_baseline_miRNA


title: 701-FB: Fmr1CRE_forebrain rep1


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s001_Tcells_capture1_CITE_S12


title: Propyzamide_Colon_Sample_1


title: 10-treatment-CH [miRNA-seq]

description:
28840_10-treatment-CH_S17_L999
CH_treated_miRNA


title: HT-29WT #1 replicate 1

value: colonic epithelial cell line HT-29


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s001_Tcells_capture1_VDJ_S31


title: 6-treatment-HK [miRNA-seq]

description:
28836_6-treatment-HK_S13_L999
HK_treated_miRNA


title: Mutant rep 2

city: Orsay

first: Olivier

last: Namy

address: Rue Gregor Mendel, bat 400

country: France

institute: CNRS, Université Paris-Sud

description: polysome extraction

data_processing:
RiboDoc package
Sequenced reads were trimmed for adaptor sequence, and size filtered to keep only reads between 25-35nts
Reads are mapped using bowtie2 on Saccer3
Differential expression is obtained using DESeq2 package
Genome_build: Saccer3
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: All strains were grown to mid-exponential growth phase in a synthetic medium,

extract_protocol:
the extraction is performed as previously published Baudin-Baillieu A et al. Methods Mol. Biol. 2016, 1361:105-24. briefly: Pellet cells by centrifugation at 4 °C, 4000×g for 10 min. resuspend pellet in 10 ml cold Lysis Buffer containing 50 μg/ml cycloheximide. Pulverize Cells by adding glass beads and vortexing the mix- ture for 10 min at 4 °C. Remove cells debris by centrifugation at 4 °C, 5000×g for 5 min and transfer the supernatant to chilled 1.5 ml microfuge tubes on ice. The supernatant is clarified by centrifugation at 4 °C, 15,000×g for 15 min. Recover supernatant.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA preparation kits

treatment_protocol: Cycloheximide is added to the medium at 50 µg/mL

value: CHX

tag: genotype/variation

value: mutant


title: TNBS_Colon_Sample_2

source_name: Vehicle-treated mouse during TNBS-induced colitis

value: vehicle


title: Propyzamide_Colon_Sample_2


title: 4-treatment-JS [miRNA-seq]

description:
28834_4-treatment-JS_S11_L999
JS_treated_miRNA

value: CTCL patient


title: HT-29-ING3 KO subclone #1 replicate 1


title: All tumor-infiltrating T cells from brain metastases (patients 16,26,27); pooled_capture 1 [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. Tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. Cells from the interface were frozen. For this sample, naïve T cells from a healthy donor (hashtag: Biolegend C0254) were mixed with tumor-infiltrating T cells from three brain metastasis samples: patient 16 (hashtag: Biolegend C0251), patient 26 (hashtag: Biolegend C0252) and patient 27 (hashtag: Biolegend C0253) and sequenced.
p21066_s001_Tcells_capture1_GEX_S1


title: TNBS_Colon_Sample_1


title: 3-baseline-JS [miRNA-seq]

description:
28833_3-baseline-JS_S10_L999
JS_baselin_miRNA

value: Skin


title: 2-treatment-RL [miRNA-seq]

description:
28832_2-treatment-RL_S9_L999
RL_treated_miRNA


title: 2526_cerebellum_female_ethanol

city: Bryan

first: Rajesh

last: Miranda

state: Texas

address: 8441 Riverside Pkwy

department: Neuroscience and Experimental Therapeutics

institute: Texas A&M University School of Medicine

description: 2526 cbl

data_processing:
Trimmomatic read trimmer was used to evaluate and trim all adapter sequences and low quality bases. Reads were scanned with a sliding window of 5, cutting when the average quality per base drops below 20, then trimming reads at the beginning and end if base quality drops below 25, and then if the read length is less than 35.
HISAT2 was used for read mapping
HTSeq generated transcript-wise counts
DESeq2 was used for normalizing counts, calculating fold change, and initial differential analysis. In order to perform sex x treatment analysis, we used the DESeq2 normalized counts and ran multiple 2-way ANOVAs with subsequent FDR correction.
Genome_build: mm10
Supplementary_files_format_and_content: htseq-count_refGene_on_*tabular: raw counts

source_name: Brain

growth_protocol: Adult C57BL/6J mice were purchased from The Jackson Laboratory and a breeding colony was established to produce neonates for experiments.

extract_protocol:
On P10, 24 hours following the final E or V treatment, animals were anesthized using isoflurane vapor, transcardially perfused with phosphate buffered saline containing 5 U/mL heparin, brains were removed, and the hippocampus and cerebellum were microdissected, flash frozen in liquid nitrogen, and stored at -80 degrees Celcius. Hippocampus and cerebellum were homogenized according to manufacturer specification using a Next Advance BBX24B Bullet Blender homogenizer and 0.5 mm glass beads.  RNA was isolated using the Qiagen RNeasy Mini Kit plus on-column DNase Removal Kit.
RNA quantity was assessed using the Qubit 3.0 fluorometer with the Qubit Broad-Range RNA Assay Kit and an Agilent Fragment Analyzer with the Standard Sensitivity RNA Gel Kit was used to assess RNA quality.  All samples had an RNA Quality No. ≥ 8.9 (Mean 9.7, Median 10.0).  RNA-seq libraries were prepared using the Illumina TruSeq mRNA Library Prep Kit with TruSeq Unique Dual Indexed adapters and were quantified with the Qubit 1X dsDNA High-Sensitivity NGS Gel Kit.  Libraries were further characterized for functionality with the KAPA Library Quantification Kit and for fragment size using the Agilent Fragment Analyzer with the High-Sensitivity NGS Gel Kit.  Library molarities were calculated followed by dilution and denaturation all according to manufacturer’s specification for clustering.  An initial set of n = 5V and 5E were clustered on a cBot and paired-end sequenced on a HiSeq 3000 with a 150-cycle SBS kit for 2X75 reads.  A supplemental set of n = 2V and 2E were clustered on a high-output NextSeq 500 flow cell and paired-end sequenced with a 150-cycle SBS kit for 2X75 reads.

treatment_protocol: Experimental neonates were distributed between treatment groups, ethanol (E) or vehicle control (V) and were separated according to sex as evenly as possible over multiple litters. On P4-9 intragastric gavage was utilized to administer ethanol at 4g/kg/day in 20% Intralipid  or 20% Intralipid vehicle equivalent alone.

value: Cerebellum

value: Postnatal Day 10

value: Ethanol

value: female


title: WT rep 1

description: polysome extraction

value: wild type


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s002_Pt16_VDJ_S7

source_name: tumor

value: melanoma

value: circulating naive:C0251; tumor-infiltrating C0252


title: 11-baseline-BK [RNA-seq]

description:
28817_11-baseline-BK_S5_L999
BK_baseline_RNA

value: Baseline


title: 2437_hippocampus_male_ethanol

description: 2437 hip

value: Hippocampus

value: male


title: 10-treatment-CH [RNA-seq]

description:
28816_10-treatment-CH_S4_L999
CH_treated_RNA


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s002_Pt16_GEX_S3


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s003_Pt17_CITE_S12


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s001_Pt15_VDJ_S6

value: lung adenocarcinoma


title: 1-baseline-RL [miRNA-seq]

description:
28831_1-baseline-RL_S8_L999
RL_baseline_miRNA


title: 9-baseline-CH [RNA-seq]

description:
28815_9-baseline-CH_S3_L999
CH_baseline_RNA


title: S15.3475.A1 [11431_S15.3475_A1_AGTTCC]

value: Plaque


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s003_Pt17_VDJ_S8


title: 2437_cerebellum_male_ethanol

description: 2437 cbl


title: 2471_cerebellum_male_vehicle

description: 2471 cbl

value: Vehicle


title: 2526_hippocampus_female_ethanol

description: 2526 hip


title: Mutant rep 1

description: polysome extraction

value: CHX

value: mutant


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 17) [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s003_Pt17_GEX_S4


title: 12-treatment-BK [RNA-seq]

description:
28818_12-treatment-BK_S6_L999
BK_treated_RNA

value: CTCL patient


title: WT rep 2

description: polysome extraction


title: 6-treatment-HK [RNA-seq]

description:
28812_6-treatment-HK_S6_L999
HK_treated_RNA

value: Skin

value: Treated


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s001_Pt15_CITE_S10


title: 5-baseline-HK [RNA-seq]

description:
28811_5-baseline-HK_S5_L999
HK_baseline_RNA


title: DOX+ REP4 [17_Wap_myc_pIND21_HPN_DOX_pos_S9]

city: Helsinki

first: Juho

last: Väänänen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCm38 whole genome using STAR aligner (2.6.0c) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.vM23.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCm38 from GENCODE Mus musculus Release M23
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

extract_protocol:
Whole tumor tissue RNA was extracted by using Precellys hard-tissue beads and TRIzol (Ambion by Life Technologies, #15596026). RNA was then DNase treated and purified using RNeasy Mini Kit from Qiagen.
Before the library preparation for sequencing, 1 μg  of total RNA was treated with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) that removes the ribosomal RNA from the total RNA. The ribosomal depleted RNA was purified with RNeasy mini Elute columns (Qiagen). The absence of rRNA and the quantity of mRNA was measured with Agilent TapeStation 4200. Samples were sequenced with Illumina NextSeq500  (Illumina, San Diego, CA, USA) at the Biomedicum Functional Genomics Unit, University of Helsinki using NEBNext Ultra Directional RNA Library Prep kit. The sequencing was performed as single-end sequencing for read length 75 bp

treatment_protocol: Isolated Wap-Myc mammary epithelial cells from virgin Wap-Myc mice. Cells were transduced with concentrated pIND21-HPN lentivirus (MOI=10) o/n on the day of cell isolation. Cells were transplanted the next day into the fat pads of recipient mice (105 cells/gland, 3 weeks old). Doxycycline (DOX) was administered in drinking water (2mg/ml 5% sucrose) three days after transplantation. Wap-Myc expression was induced when the mice were 8 weeks old by 2 consecutive pregnancies. Tumor development was monitored once-twice a week after pregnancy. Mice were sacrificed when tumor size reached 1 cm

tag: strain bacground

value: FVB

value: transduced with lentiviral construct pIND21-HPN

value: received sugar water +DOX

tag: tumor stage

value: 1cm diameter


title: 4-treatment-JS [RNA-seq]

description:
28810_4-treatment-JS_S4_L999
JS_treated_RNA


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 15) [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s001_Pt15_GEX_S2


title: 2444_cerebellum_female_vehicle

description: 2444 cbl

value: Cerebellum

value: Postnatal Day 10

value: female


title: 8-treatment-WS [RNA-seq]

description:
28814_8-treatment-WS_S2_L999
WS_treated_RNA

value: Baseline


title: 7-baseline-WS [RNA-seq]

description:
28813_7-baseline-WS_S1_L999
WS_baseline_RNA


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
P20103-s001_Brain_met_14_GEX_S1

value: circulating naive:C0251; tumor-infiltrating C0252


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
P20103-s001_Brain_met_14_CITE_S9

value: lung adenocarcinoma


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 16) [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
p20126-s002_Pt16_CITE_S11

value: melanoma


title: 2444_hippocampus_female_vehicle

description: 2444 hip

value: Hippocampus

value: Vehicle


title: DOX+ REP3 [16_Wap_myc_pIND21_HPN_DOX_pos_S8]


title: DOX+ REP2 [15_Wap_myc_pIND21_HPN_DOX_pos_S7]


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
1_BrainMetTILs_VDJ_S2

value: lung squamous cell carcinoma


title: 2-treatment-RL [RNA-seq]

description:
28808_2-treatment-RL_S2_L999
RL_treated_RNA

value: CTCL patient


title: DOX+ REP1 [14_Wap_myc_pIND21_HPN_DOX_pos_S6]


title: DOX- REP5 [10_Wap_myc_pIND21_HPN_DOX_neg_S5]

value: received sugar water


title: 1-baseline-RL [RNA-seq]

description:
28807_1-baseline-RL_S1_L999
RL_baseline_RNA

value: Skin


title: whole blood, TD_131012

type: genomic

first: Oxana

middle: Yu.

last: Naumova

address: 4849 Calhoun Rd, TIMES, Rm 373

department: Psychology

institute: University of Houston

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to the Illumina Infinium HumanMethylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iScan using standard recommended Illumina scanner setting

data_processing: The Minfi Bioconductor package (Aryee, et al., 2014; Bioinformatics, 30:13631369); the stratified quantile normalization of beta-values (Wu & Aryee, 2010; Comput Biol, 17:13851395)

label: Cy5 and Cy3

molecule: genomic DNA

source_name: whole blood IC23

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Male

value: 15 mos.

value: whole blood

tag: disease state

value: normal


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [GEX]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
1_BrainMetTILs_GEX_S1


title: whole blood, TD_191011

source_name: whole blood IC26

value: Female

value: 27 mos.


title: miRNA-Seq HuT78 cell line

description:
HuT78 cell line
HuT78 cell line

source_name: Cell line

growth_protocol: MyLa (MF-derived cell line), H9 (SS-derived cell line), HH (MF-derived cell line), and HuT78 (SS-derived cell line) were cultured in RPMI-1640 or Dulbecco’s medium (IMDM) medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin. All cell lines utilized for the experiments herein were maintained at 37°C, 5% CO2 and were tested negative for mycoplasma contamination.

extract_protocol:
QIAGEN RNAeasy
Kappa mRNA Hyperprep kit

tag: sample type

value: Tumor


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 5) [CITE]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
1_BrainMetTILs_CITE_S3


title: Tumor infiltrating PD-1+ CD8 T cells from brain metastasis (patient 14) [VDJ]

description:
Surgically resected brain metastases were processed as soon as possible after surgery. A piece was cut, embedded into OCT, and flash-frozen for spatial transcriptomics. Remaining tumor was chopped into fine pieces, digested with shaking at 37 °C for 1 hour with a mixture of elastase, DNase, and collagenases I, II, and IV, and forced through a cell strainer. This single-cell suspension was washed and subjected to a 44%/67% Percoll gradient. The interface was collected, washed, and either subjected directly to flow sorting for scRNA-seq or frozen for later scRNA-seq.
P20103-s001_Brain_met_14_VDJ_S5


title: ABCB1-50-4

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

description: HMECs with adenovirus transduced ABCB1, replicate 4

data_processing:
Quality was checked with FastQC before and after trimming with trimmomatic (v0.38).
Reads were aligned to the humen reference genome assembly hg19 with STAR v2.2.1.
A GTF based on RefSeq protein-coding RNAs was used.
Transcripts per million (TPM) was estimated using RSEM v1.3.1.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with TPM.

source_name: human mammary epithelial cell

growth_protocol: HMECs were cultured in Mammary Epithelial Cell Basal Medium supplemented with Mammary Epithelial Cell Growth Medium SingleQuot supplements (Lonza).

extract_protocol:
RNA was extracted using the RNEasy Plus mini kit with on-column Dnase I digestion (Qiagen).
cDNA libraries were generated using NEBNext ultra directional RNA prep kit and sequenced on an Illumina NovaSeq 6000 instrument with 150 cycles of paired end reads.

treatment_protocol: HMECs were starved in basal media without supplement for 36 hours, followed by adenovirus transduction at 50 MOI for 12 hours.

tag: transgene

tag: moi

tag: replicate


title: DOX- REP4 [9_Wap_myc_pIND21_HPN_DOX_neg_S4]

value: FVB

value: transduced with lentiviral construct pIND21-HPN

value: 1cm diameter


title: 2471_hippocampus_male_vehicle

description: 2471 hip

tag: tissue

value: Postnatal Day 10

value: male


title: whole blood, DS_91017

source_name: whole blood IC04

value: 10 mos.

value: Down syndrome (Trisomy 21)


title: DOX- REP3 [7_Wap_myc_pIND21_HPN_DOX_neg_S3]


title: ABCB1-50-3

description: HMECs with adenovirus transduced ABCB1, replicate 3


title: whole blood, DS_131028

source_name: whole blood IC10

value: 39 mos.


title: miRNA-Seq MyLa cell line

description:
MyLa cell line
MyLa cell line


title: DOX- REP2 [6_Wap_myc_pIND21_HPN_DOX_neg_S2]

value: received sugar water


title: miRNA-Seq H9 cell line

description:
H9 cell line
H9 cell line


title: DOX+ REP5 [18_Wap_myc_pIND21_HPN_DOX_pos_S10]

value: received sugar water +DOX


title: ABCB1-50-2

description: HMECs with adenovirus transduced ABCB1, replicate 2


title: ABCB1-50-1

description: HMECs with adenovirus transduced ABCB1, replicate 1


title: whole blood, DS_131023

source_name: whole blood IC09

value: 54 mos.


title: miRNA-Seq HH cell line

description:
HH cell line
HH cell line


title: DOX- REP1 [5_Wap_myc_pIND21_HPN_DOX_neg_S1]


title: whole blood, DS_131038

source_name: whole blood IC12

value: 30 mos.


title: miRNA-Seq Healthy CD4

description:
Healthy CD4
Healthy CD4

source_name: CD4 T cell

value: Healthy


title: whole blood, DS_131015

source_name: whole blood IC06

value: Male

value: 53 mos.

value: whole blood


title: Hpn-/-2 [HPNQ2160_neg]

data_processing:
bcl2fastq2 Conversion Software was used to convert BCL files to FASTQ file format and demultiplex samples.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using Trimmomatic. Parameters used: :2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to GRCm38 whole genome using STAR aligner (2.6.0c) with parameters  --runThreadN 20 --chimSegmentMin 12 --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJstitchMismatchNmax 5 -1 5 5 --outFilterType BySJout --outFilterMismatchNmax 999 --outSAMattributes NH HI NM MD AS nM jM jI XS --outSAMtype BAM SortedByCoordinate --outSAMmapqUnique 60 --quantMode GeneCounts --twopassMode Basic
Counts per gene were calculated using featureCounts software. Parameters used: -s 2 -T 20 -t exon -g gene_id -a gencode.vM21.annotation.gtf
Differential expression analysis used the DESeq2 software in R environment. Procedures included: Normalization of count values between samples using a geometric mean, estimation of sample-wise factors to correct for library size variability (for example), estimation of dispersion (i.e. variance, scatter) of gene-wise values between conditions, negative binomial linear model and Wald test to produce p-values, removal of low-expression outliers (using Cook's distance) results to optimize for p-value adjustment and finally, multiple testing adjustment of p-values with Benjamini-Hochberg procedure.
Genome_build: GRCm38 from GENCODE Mus musculus Release M21
Supplementary_files_format_and_content: Raw count matrix of sequencing reads (featureCounts meta-feature level) as .xlsx

extract_protocol:
Whole tissue RNA was extracted from up to 6 weeks old mouse mammary glands using Precellys hard-tissue beads and TRIzol. RNA was then DNase treated and purified using RNeasy Mini Kit from Qiagen.
Before the library preparation for sequencing, 1 μg  of total RNA was treated with NEBNext rRNA Depletion Kit (Human/Mouse/Rat) that removes the ribosomal RNA from the total RNA. The ribosomal depleted RNA was purified with RNeasy mini Elute columns (Qiagen). The absence of rRNA and the quantity of mRNA was measured with Agilent TapeStation 4200. Samples were sequenced with Illumina NextSeq500  (Illumina, San Diego, CA, USA) at the Biomedicum Functional Genomics Unit, University of Helsinki using NEBNext Ultra Directional RNA Library Prep kit. The sequencing was performed as single-end sequencing for read length 75 bp

tag: strain background

value: 6 weeks

value: Hpn-/-

value: mammary glands


title: GFP-50-3

description: HMECs with adenovirus transduced GFP, replicate 3

value: GFP


title: RNA-Seq HuT78 cell line

description:
HuT78 cell line
HuT78 cell line

value: Tumor


title: Hpn-/-1 [HPNQ2130_neg]

value: FVB


title: whole blood, TD_191002

source_name: whole blood IC24

value: 41 mos.

value: normal


title: GFP-50-4

description: HMECs with adenovirus transduced GFP, replicate 4


title: GFP-50-2

description: HMECs with adenovirus transduced GFP, replicate 2


title: whole blood, TD_131006

source_name: whole blood IC21

value: Female

value: 39 mos.


title: WT3 [HPNQ2188wt]

value: 5 weeks

value: WT


title: Hpn-/-3 [HPNQ2189_neg]


title: RNA-Seq H9 cell line

description:
H9 cell line
H9 cell line


title: WT2 [HPNQ2181wt]


title: GFP-50-1

description: HMECs with adenovirus transduced GFP, replicate 1


title: RNA-Seq MyLa cell line

description:
MyLa cell line
MyLa cell line


title: 3-baseline-JS [RNA-seq]

description:
28809_3-baseline-JS_S3_L999
JS_baselin_RNA

source_name: CTCL patient_Skin_Treated

tag: subject status

value: CTCL patient

value: Skin

tag: timepoint

value: Treated


title: whole blood, TD_131007

source_name: whole blood IC22

value: Male

value: 21 mos.


title: RNA-Seq HH cell line

description:
HH cell line
HH cell line


title: whole blood, TD_131004

source_name: whole blood BFC04

value: 40 mos.

value: whole blood


title: WT1 [HPNQ2198wt]

value: 2 weeks

value: mammary glands


title: 221_D4_control

city: Hamilton

first: Craig

last: Martens

state: MT

address: 903 S. 4th St

department: DIR

institute: NIAID

data_processing:
Illumina Casava1.8.2 software was used for basecalling
Raw fastq reads were trimmed of Illumina adapter sequences using cutadapt version 1.12 and then trimmed and filtered for quality using the FASTX-Toolkit (Hannon Lab).
Remaining reads were aligned to the hamster genome using Hisat2.
Reads mapping to genes were counted using htseq-count, version 0.9.1
Gene normalization and differential expression analysis were performed using Deseq2, version 1.16.1
Genome_build: MesAur1.0 (GCF_000349665)
Supplementary_files_format_and_content: deseq2 normalized reads counts

organism: Mesocricetus auratus

source_name: lung tissue

growth_protocol: SARS-CoV-2 strain nCoV-WA1-2020 (MN985325.1) was provided by CDC, Atlanta, USA. Virus propagation was performed in VeroE6 cells in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 2% foetal bovine serum (FBS), 2 mM L-glutamine, 100 U/mL penicillin and 100 ?g/mL streptomycin. Cells were cultured in DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 ?g/mL streptomycin

extract_protocol:
Frozen tissues were pulverized in 1 mL of Trizol (Thermofisher Scientific, Waltham, MA), 200 µL of 1-Bromo-3-chloropropane (MilliporeSigma, St. Louis, MO) was added, samples mixed, and centrifuged at 16,000 x g for 15 min at 4°C.  RNA containing aqueous phase of 600 µL was collected from each sample and passed through Qiashredder column (Qiagen, Valencia, CA) at 21,000 x g for 2 minutes to homogenize any remaining genomic DNA in the aqueous phase. Aqueous phase was combined with 600uL of RLT lysis buffer (Qiagen, Valencia, CA) with 1% beta mercaptoethanol (MilliporeSigma, St. Louis, MO) and RNA was extracted using Qiagen AllPrep DNA/RNA 96-well system (Valencia, CA). An additional on-column DNase 1 treatment was performed during RNA extraction.
Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus workflow (Illumina, San Diego, CA).

treatment_protocol: Three groups of 12, 4-6-week-old, female hamsters were inoculated with SARS-CoV-2 via the intranasal (I.N.; 8x104 TCID50), aerosol (1.5x103 TCID50) or fomite (8x104 TCID50) routes (Fig 1 a). An unexposed control was included (N = 12) as comparison. For each group, 4 animals were euthanized on 1 day post inoculation (DPI) and 4 DPI, the remaining 4 animals were monitored until 14 DPI

tag: agent

value: female

tag: infection route


title: picloram treatment 96 hours replicate 3

city: Dresden

first: Jutta

last: Ludwig-Müller

address: Zellescher Weg 20b

department: Biology

country: Germany

institute: Technische Universität Dresden

data_processing:
Original image data file from high-throughput sequencing platforms (like Illumina) is transformed to sequenced reads (called Raw Data or Raw Reads) by CASAVA base recognition (Base Calling). Raw data are stored in FASTQ(fq) format files, which contain sequences of reads and corresponding base quality.
Raw data filtering: (1)Remove reads with adaptor contamination. (2)Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%). (3)Remove reads when low quality nucleotides (Base Quality less than 5) constitute more than 50 percent of the read.
Algorithm for mapping sequences: HISAT2 is selected to map the filtered sequenced reads to the reference genome. In general, HISAT2 supports genomes of any size, including those larger than 4 billion bases and most of the parameters are set to default.Spliced reads of RNA Seq data can be effictively aligned using HISAT2, which is the fastest system currently available, with equal or better accuracy than any other method.
The Stringtie was used to assemble the set of transcript isoforms of each bam file obtained in the mapping step. gffcompare can compare Stringtie assemblies to reference annotation files and help sort out new genes from known ones. Gene expression level is calculated by the number of mapped reads. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Software used: Mapping, hisat2; Novel Gene prediction, StringTie; Assemble transcripts, GffCompare; Compare transcriptomes; QuantificationFeatureCounts; Differential Analysis, DESeq2, EdgeR; Enrichment Analysis, ClusterProfiler; GSEA Analysis, gsea; Protein-Protein Interaction Analysis, NCBI BLAST; Alternative splicing, rMATS; SNP/InDel Analysis, GATK4, SNPEff
Correlation of the gene expression levels between samples plays an important role to verify reliability and sample selection, which can not only demonstrate the repeatability of the experiment but estimate the differential gene expression analysis as well.
Genome_build: GCA_000751015
Supplementary_files_format_and_content: FPKM

organism: Brassica napus

source_name: leaf

growth_protocol: Brassica napus was grown on standard soil in pots with 4 plants per pot in a controlled environment at a constant temperature of 15°C, an approximate humidity of 60% and with 12 hours light exposure to developmental stage BBCH11.

extract_protocol:
RNA was extracted using NucleoZOL according to the manufacturer's instructions. Samples were checked for quality with a Bioanalyzer.
Sequencing libraries were generated by Novogene using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The treatment was performed by pipetting the control and herbicide solutions to one leaf consisting of 5 drops. The tissue was inubated for 2, 48 and 96 hours and then directly frozen for RNA isolation. Three replicates were performed from different plant materials. Herbicide concentrations were for halauxifen 0.5 ug/leaf and for picloram 2.4 ug/leaf, which represents the concentratons used in the field applications for the different compounds.

tag: cultivar

value: Visby

value: leaf stage BBCH11

value: treatment with picloram

tag: time


title: 220_D4_control

tag: Sex


title: 222_D4_control


title: HDE Z-REX

first: Jesse

last: Poganik

state: MA

address: 77 Avenue Louis Pasteur

department: Medicine/Genetics

institute: Brigham and Women's Hospital, Harvard Medical School

description:
Poganik-Long_FPKM_table.txt
Poganik-Long_RawCount_table.txt

data_processing:
Reads were trimmed for low quality and adaptor sequences with cutadapt v1.8 [parameters: –m 50 –q 20 –a AGATCGGAAGAGCACACGTCTGAACTCCAGTC –match-read-wildcards] (Martin, M. EMBnet.journal 2011, 17, 10-12)
Reads were mapped to the reference genome/transcriptome (D. rerio GRCz10 [Ensembl]) using tophat v2.1 [parameters: –library-type=fr-firststrand –no-novel-juncs –G <ref_genes.gtf>] (Kim, D. et al., Genome Biology 2013, 14, R36)
Cufflinks v2.2 (cuffnorm/cuffdiff) was used to generate FPKM values and statistical analysis of differential gene expression. (Trapnell, C. et al. Nat Biotechnol 2013, 31, 46-53)
Genome_build: D. rerio GRCz10 [Ensembl]
Supplementary_files_format_and_content: Matrix tables of raw counts and FPKMs

organism: Danio rerio

source_name: Zebrafish embryos expressing Halo-TEV-Keap3

growth_protocol: Embryos were produced by natural mating in breeding tanks. The yolk sack of embryos at the 1–4-cell stage was microinjected with approximately 2 nl of mRNA encoding Halo-TEV-Keap1 (1.4–1.6 mg/ml, mMessage mMachine kit used according to manufacturer’s protocol). Fish were grown at 28.5°C with a 14 h light/ 10 h dark cycle in 10% Hank’s Balanced Salt Solution (HBSS). All procedures at Cornell University were approved by the Institutional Animal Care and Use Committee (IACUC) and performed in accordance with the guidelines of the NIH. All procedures at EPFL were performed in accordance with the Swiss regulations on animal experimentation (Animal Welfare Act SR 455 and Animal Welfare Ordinance SR 455.1), in the EPFL zebrafish unit, cantonal veterinary authorization VD-H23.

extract_protocol:
Euthanized embryos were lysed in Trizol using ceramic hard tissue homogenizing mix (VWR), and RNA was isolated following the manufacturer’s protocol.  The quality of the RNA was assessed by Nanodrop spectrophotometry (A260/A280 ratio ~2) and fragment analysis using a Bioanalyzer (Agilent).
Library construction and sequencing were performed by the RNA sequencing core (RSC) service at Cornell University. Briefly, from 500 ng total RNA input, polyadenylated RNA was isolated with the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). TruSeq-barcoded RNAseq libraries were generated with the NEBNext Ultra Directional RNA Library Prep Kit (New England Biolabs). Each library was quantified with a Qubit 2.0 (dsDNA HS kit; Thermo Fisher) and the size distribution was determined with a Fragment Analyzer (Advanced Analytical) prior to pooling. Libraries were sequenced on a NextSeq500 instrument (Illumina). At least 20M single-end 81nt reads were generated per library.

treatment_protocol: Z-REX was performed as previously reported (Long et al. Nat Chem Biol, 2017, 13, 333-338). Embryos injected with mRNA encoding Halo-TEV-Keap1 as described above were treated with Ht-preHNE(alkyne) (1 μM) in 10% HBSS containing penicillin-streptomycin (Gibco) and grown in the dark for 30 h. Embryos were then rinsed with 10% HBSS 3 times for 30 minutes each in a red-light room, and exposed to UV light (365 nm, 0.5 mW/cm2) for 3 minutes with gentle agitation of the plate every minute. After 1.5 h of incubation post-Z-REX, embryos were euthanized and total RNA was isolated.

tag: treatment condition

value: HDE Z-REX

value: embryos


title: HNE Z-REX

source_name: Zebrafish embryos expressing Halo-TEV-Keap2

value: HNE Z-REX


title: whole blood, DS_131020

source_name: whole blood IC08

value: Female

tag: age

value: 29 mos.

value: Down syndrome (Trisomy 21)


title: picloram treatment 96 hours replicate 2

tag: treatment


title: RNA-Seq Healthy CD4

description:
Healthy CD4
Healthy CD4

value: Healthy


title: non-treated

source_name: Zebrafish embryos expressing Halo-TEV-Keap1

value: non-treated


title: whole blood, DS_111018

source_name: whole blood IC13

tag: gender

value: 20 mos.

tag: disease state


title: picloram treatment 48 hours replicate 3


title: 217_D1_control


title: V4

city: Tübingen

first: Omelyan

last: Trompak

state: BW

address: Otfried-Müller-Straße 14

department: Internal Medicine VIII

institute: University Hospital of Tübingen

description: raw_counts.tsv, Column 7

data_processing:
Base calling was done with Illumina NextSeq RTA v2.4.11, followed by FASTQ conversion with bcl2fastq v2.20.0.422.
FastQC to assess read quality, and Cutadapt v1.6 to trim sequencing reads, eliminate Illumina adaptor remains, and to discard reads <30 base pairs.
The reads were mapped to the GRCh38 reference genome (gencode, release 31) using STAR v2.6.2h.
Raw counts per gene were converted to the log values of counts per million (LogCPM) and genes with no counts in more than two-thirds of the samples within the same experimental group were disregarded for the following steps.
Differential expression analysis was performed using the edge R package and an experimental based design matrix comparing the VHL samples against the Control group. Further, differentially expressed genes were identified at FDR of <0.05 and log2 fold change > 1.
Genome_build: GRCh38 - R31
Supplementary_files_format_and_content: raw_counts.tsv: Tab-delimited text file containing the raw counts for all the mapped genes distributed along the sequenced samples.

source_name: blood outgrowth endothelial cells (BOEC)

growth_protocol: For the growth and expansion of BOECs, 50 mL of periphery blood were extracted from volunteers after reading and signing written consent. Blood samples were subjected to a Ficoll density gradient, for which samples were first diluted 1:1 in HBSS and then carefully transferred to 50 mL Falcon tubes containing 25 mL of LymphoprepTM (PromoCell, Heidelberg, Germany).

extract_protocol:
RNA extraction and library preparation were completed following the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).
Illumina NextSeq 550 system was used for mRNA sequencing.

tag: cell type

value: blood outgrowth endothelial cells

tag: genotype

value: VHL c.463,+2A>C, Sp intron 2


title: V5

description: raw_counts.tsv, Column 8

value: VHL c.191G>C, p.R64P, exon 1


title: whole blood, DS_91015

source_name: whole blood IC02

value: 28 mos.

value: whole blood


title: 218_D1_control

value: female


title: picloram treatment 48 hours replicate 2

value: Visby

value: leaf stage BBCH11


title: picloram treatment 96 hours replicate 1

value: treatment with picloram


title: 219_D4_control


title: 215_D1_control


title: V3

description: raw_counts.tsv, Column 6

value: VHL c.525C>A, p.Y175X, exon 3


title: V2

description: raw_counts.tsv, Column 5

value: VHL c.485G>A, p.C162Y, exon 3


title: 198_D4_IN

value: intranasal


title: whole blood, TD_131002

source_name: whole blood IC19

value: Female

value: 27 mos.

value: normal


title: whole blood, TD_131003

source_name: whole blood IC20


title: picloram treatment 48 hours replicate 1


title: picloram treatment 2 hours replicate 3


title: picloram treatment 2 hours replicate 2


title: C3

description: raw_counts.tsv, Column 3

value: wt VHL


title: 197_D4_IN


title: whole blood, DS_131014

source_name: whole blood IC05

value: Male

value: 55 mos.

value: Down syndrome (Trisomy 21)


title: 196_D4_IN


title: V1

description: raw_counts.tsv, Column 4

value: blood outgrowth endothelial cells

value: VHL c.500G>A, p.R167Q, exon 3


title: whole blood, TD_191005

source_name: whole blood IC25

value: 6 mos.

value: whole blood


title: whole blood, TD_191001

source_name: whole blood BFC03

value: 30 mos.


title: 195_D4_IN

value: female


title: whole blood, DS_131037

source_name: whole blood IC11

value: 56 mos.


title: picloram treatment 2 hours replicate 1

value: Visby

value: leaf stage BBCH11

value: treatment with picloram


title: whole blood, TD_111005

source_name: whole blood IC18

value: Female

value: 46 mos.


title: halauxifen treatment 96 hours replicate 3

value: treatment with halauxifen


title: C2

description: raw_counts.tsv, Column 2

value: wt VHL


title: whole blood, DS_91014

source_name: whole blood IC01

value: Male

value: 33 mos.


title: halauxifen treatment 96 hours replicate 2


title: WT_CPC_SMC

city: Ann Arbor

first: Dogukan

last: Mizrak

state: MI

address: NCRC Building 26, 263S

department: Cardiac Surgery

institute: University of Michigan

data_processing:
12-nt cell barcodes (CBs) and 8-nt unique molecular identifiers (UMIs) were extracted from read 1. Degenerate CBs containing either 'N's or more than four consecutive 'G's were discarded. Synthesis errors, which can result in truncated 11-nt cell barcodes, were corrected.
Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Any resulting fragment shorter than 24 nucleotides were discarded.
Trimmed reads were aligned to the human genome and transcriptome annotation (GRCh38) using STAR v.2.5 with parameters --sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted. Only reads with unique, strand-specific alignments to exons were kept for further analysis.
All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix.txt files contain the gene expression profiles in each sample.
Supplementary_files_format_and_content: Cell_barcodes.txt files contain the ordered cell barcodes for each cell in the gene expression matrix.

source_name: CPC-SMC

extract_protocol:
mRNA molecules were captured using bead-bound oligo dT(30).
Captured mRNA molecules were reverse transcribed with template switching to obtain cDNA. cDNA was amplified by PCR reactions (12 cycles). Aliquots of amplified cDNA from each sample were pooled, and purified with AMPure XP beads. The purified PCR products were used as input for the Nextera XT reactions to generate the sequencing libraries.

value: CPC-SMC

value: TGFBR1 +/+

tag: number of cells


title: halauxifen treatment 96 hours replicate 1

source_name: leaf

tag: tissue


title: WT

city: Seoul

first: Donghwan

last: YUN

state: Jongno-gu

address: 103 Daehakro

country: South Korea

institute: Seoul National University Hospital

data_processing:
The purified libraries were quantified using qPCR according to the protocol (Sigma Aldrich, St. Louis, MO, USA) and qualified using the Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, USA), and sequenced using the HiSeqX (Illumina, San Diego, CA, USA) with a read length of 28 bp for read 1 (cell barcode and UMI), 8 bp index read (sample barcode), and 91 bp for read 2 (RNA read). The Cell Ranger pipeline (version 3.1.0; 10× Genomics) was used to process the raw dataset.
Genes expressed in >=5 cells, cells with >=200 UMI counts, and cells with <=10% mitochondrial gene were selected.
R (version 4.0.3; The Comprehensive R Archive Network: http://cran.r-project.org) and Seurat (version 3.2.3) packages were used in analyses, as follows: SCTransform, merging data with adjusting batch-effects; FindNeighbors and FindClusters, finding clusters.
Genome_build: mm9
Supplementary_files_format_and_content: The pooled scRNA data of WT and Vsir-/- cells (file names: barcodes, features, matrix, metadata) only includes the immune clusters with high Ptprc expressions.

source_name: CD45+ cells were flow cytometrically sorted

extract_protocol:
Kidneys were digested with 0.2 mg/ml of liberase (Roche, Basel, Switzerland) at 37°C for 30 min.
Libraries were prepared using the Chromium controller according to the 10× chromium Next GEM Single Cell 3’ protocol (version 3.1; 10× Genomics, Pleasanton, CA, USA).

treatment_protocol: For the nephrotoxic nephritis model, mice were pre-immunized with 200 μg of sheep immunoglobulin G in Freund's complete adjuvant via intraperitoneal route, followed by 2 μl/g of sheep nephrotoxic serum (Probetex, Inc., San Antonio, TX, USA) via intravenous injection 4 days later.

tag: strain

tag: genotype/variation

value: WT

value: 8 weeks

value: kidney


title: TGFBR1HOM_CPC_SMC

value: TGFBR1 A230T/A230T


title: 212_D4_fomite

source_name: lung tissue

value: female

value: fomite


title: 214_D4_fomite


title: whole blood, DS_111007

source_name: whole blood IC14

value: whole blood

value: Down syndrome (Trisomy 21)


title: halauxifen treatment 48 hours replicate 3

value: Visby

value: leaf stage BBCH11


title: WT_NCSC_SMC

source_name: NCSC-SMC

value: NCSC-SMC


title: 211_D4_fomite


title: TGFBR1HET_CPC_SMC

value: TGFBR1 A230T/+


title: 190_D4_aerosol

value: aerosol


title: PatientCorrect_CPC_SMC

value: Female


title: whole blood, TD_301060

source_name: whole blood BFC02

value: Male

value: 42 mos.

value: normal


title: halauxifen treatment 2 hours replicate 3

value: treatment with halauxifen


title: halauxifen treatment 48 hours replicate 2


title: whole blood, DS_111009

source_name: whole blood IC17

value: 23 mos.


title: SI ILC2

city: Shanghai

first: Ju

last: Qiu

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Quality control was performed using Scater package. ScRNA-seq analysis was performed using Seurat package (version 2 and 3) in R (version 3.6.1). Counts were normalized using LogNormalize function. Then, FindViariableGenes, RunPCA and JackStraw functions were used to perform linear dimensional reduction based on statistically significant principal components. FindClusters, RunTSNE and FindAllMarkers were used to identify the cell clusters, visualize cluster and look for differentially expressed genes. Contaminated clusters with representative signature genes for non-ILC2s were filtered from analysis. MergeSeurat was used to aggregate quality-filtered ILC2 single-cell data from all tissues. Differentially expressed genes in clusters were identified using "1 versus 1" comparison between all clusters as one strategy and "1 versus all (other clusters as a bulk population)" as another strategy.
Genome_build: mm10
Supplementary_files_format_and_content: compressed mtx and tsv files processed by Cell Ranger
Supplementary_files_format_and_content: Tissue_ILC2_sub-cluster_signature_genes.xlsx

source_name: small intestine ILC2

extract_protocol:
Bone marrow cells were processed by flushing femur and tibia using a syringe.   For isolation of mononuclear cells from lung or pancreas, tissues were dissected and blood clots, fat tissues and bronchus were discarded. Lung or pancreas tissues were cut into pieces and digested with 10 ml RPMI 1640 medium (Thermo Fisher Scientific) containing DNase I (50 U/ml for digestion of lung, 250U/ml for digestion of pancreas, Sigma-Aldrich) and collagenase VIII (250 U/ml, Sigma-Aldrich) at 37°C for 1h (for digestion of lung) or 30 minutes (for digestion of pancreas). The digested tissues were homogenized by vigorous shaking and passed through a 70-μm cell strainer. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll (GE Healthcare) gradient after a spin at 2500 rpm for 20 minutes at room temperature.   For isolation of large and small intestine lamina propria lymphocytes, tissues were dissected. Fat tissues and peyer’s patches in the small intestine were removed. The intestines were then cut into pieces, washed, and shaken in PBS containing 1mM dithiothreitol for 10 minutes at room temperature. Intestines were incubated with shaking at 220 rpm in PBS containing 30 mM ethylenediaminetetraacetic acid (EDTA) at 37°C for 10 minutes for 2 cycles. The tissues were then digested in RPMI 1640 medium containing DNase I (150 ug/ml) and collagenase VIII (150 U/ml) at 37°C in an incubator with 5% CO2 for 1.5h. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll gradient after a spin at 2500 rpm for 20 minutes at room temperature.
Viability of cells was more than 95% before cells were loaded on the Chromium Single Cell Controller (10XGenomics). Libraries were generated using the Chromium Single Cell 3′ Reagents Kits (v2 chemistry; 10X Genomics) following manufacturer’s protocol. The obtained libraries were sequenced on Illumina Hiseq X Ten system. Libraries of ILC2s from lung, large intestine and small intestine were generated together in one batch of experiment from 10 mice pooled together, and libraries of ILC2s from bone marrow, pancreas were generated in another batch of experiment from 10 mice pooled together. Two rounds of sequencing were performed on the each library of ILC2s from every tissue to obtain abundant reads and pooled for subsequent analysis.

value: 6 weeks old

value: male

value: small intestine

value: Group 2 innate lymphoid cells


title: halauxifen treatment 48 hours replicate 1


title: whole blood, DS_111001

source_name: whole blood IC15

value: 25 mos.

value: whole blood


title: 187_D4_aerosol

value: female


title: Pancreas ILC2

source_name: pancreas ILC2

value: pancreas


title: whole blood, TD_301050

source_name: whole blood BFC01

value: 30 mos.


title: BM ILC2

source_name: bone marrow ILC2

value: bone marrow


title: halauxifen treatment 2 hours replicate 1

value: Visby

value: leaf stage BBCH11


title: Lung ILC2

source_name: lung ILC2

value: lung


title: 188_D4_aerosol

value: aerosol


title: 189_D4_aerosol


title: Patient_CPC_SMC

value: CPC-SMC

value: Female

value: TGFBR1 A230T/+


title: LI ILC2

source_name: large intestine ILC2

value: 6 weeks old

value: large intestine


title: whole blood, DS_131018

source_name: whole blood IC07

value: Male

value: 56 mos.

value: Down syndrome (Trisomy 21)


title: H4-3

city: Corbeil-Essonnes

first: Hélène

last: Polvèche

address: 28, Rue Henri Desbruères

institute: I-Stem

description: replicate 3

data_processing:
For each sample, 100ng of total RNA was used. mRNAs were purified using poly-T oligo from TruSeq Stranded kit (Illumina®) and were fragmented and retro-transcribed using the TruSeq Stranded kit following the protocol of the manufacturer. Final library was quantified using Agilent High Sensitivity DNA kit before the samples were pooled in sets of six for sequencing. 2nM of pooled libraries were denatured and the quantity of 1.8pM was used for cluster generation before paired-end sequencing on an Illumina Nextseq550 (Hight output 2*150pb run).
For the Alternative splicing the raw reads was annotated on GRCh37.75 EnsEMBL reference annotation by Tophat2 (v2.0.13) and analyzed using only reads on exonics junctions with FaRLine pipeline (36 FasterDB database
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing raw counting reads

source_name: Myotube

growth_protocol: hiPSCs were dissociated with StemPro Accutase Cell Dissociation Reagent (Gibco®) and plated at 3000 cells per cm2 onto collagen I-coated plates (Gibco®) and maintained for 10 days in skeletal muscle induction medium (SKM01). At day 10, cells were dissociated with Trypsin-EDTA 0,05% (Gibco®), plated at 5000 cells per cm2 onto collagen I-coated plates and maintained for 6 days in skeletal myoblast medium (SKM02). At day 16, myoblasts were dissociated and cryopreserved. For terminal differentiation, cells were thawed at 10.000 cells per cm2 in SKM02 and after 2-3 days, when cells reached confluence, the medium was replaced by the myotube medium (SKM03). Cells were then maintained for 5 to 6 days in SKM03.

extract_protocol:
Total RNA was extracted using the RNeasy Micro/Mini kit (Qiagen®)
For each sample, 100ng of total RNA was used. mRNAs were purified using poly-T oligo from TruSeq Stranded kit (Illumina®) and were fragmented and retro-transcribed using the TruSeq Stranded kit following the protocol of the manufacturer. Final library was quantified using Agilent High Sensitivity DNA kit before the samples were pooled in sets of six for sequencing. 2nM of pooled libraries were denatured and the quantity of 1.8pM was used for cluster generation before paired-end sequencing on an Illumina Nextseq550 (Hight output 2*150pb run). Samples were sequenced with an average of 89 532 366 reads (paired-end) per sample.

tag: cell line

value: MBNL1 -/- MBNL2 -/-

tag: extract

value: Total cells


title: H4-1

description: replicate 1


title: control treatment 96 hours replicate 3

value: no treatment


title: E3n3

description: replicate 3

value: MBNL1 -/- MBNL2 +/+


title: SI2

library_source: genomic

data_processing:
ATAC-seq raw sequence reads were initially processed by FastQC (version 0.11.9) for quality control, and then adapter sequences and poor quality reads were removed. Quality filtered reads were then mapped to mouse genome (mm10) using Bowtie2 (version 2.2.9), and only uniquely mapped reads were kept. Sam files were converted to Bam format using Samtools (version 1.8). Peak calling was done using MACS (2.1.1) with an initial threshold q-value of 0.01 as cutoff. Differentially expressed peaks were analyzed using DESeq2. Differentially peaks significantly higher or lower (p<0.05) in one tissue ILC2s compared to other tissue ILC2s through a 1 versus 1 comparison mode were overlapped and were defined as "ILC2 tissue specific open chromatin regions (ILC2 TS OCRs)" or "commonly decreased peaks". To look for large and small intestine ILC2 common OCRs, differentially expressed peaks were firstly identified in large intestine or small intestine ILC2s compared to each of the other 3 tissue ILC2s respectively, and then overlapped peaks were intestine ILC2 specific OCRs.
Genome_build: mm10
Supplementary_files_format_and_content: Visualization of read count data was performed by converting raw bam files to bigwig files using IGV tools.
Supplementary_files_format_and_content: ILC2_tissue_differential_ATACseq_peaks.xlsx

source_name: Small intestine ILC2

extract_protocol:
Bone marrow cells were processed by flushing femur and tibia using a syringe.   For isolation of mononuclear cells from lung or pancreas, tissues were dissected and blood clots, fat tissues and bronchus were discarded. Lung or pancreas tissues were cut into pieces and digested with 10 ml RPMI 1640 medium (Thermo Fisher Scientific) containing DNase I (50 U/ml for digestion of lung, 250U/ml for digestion of pancreas, Sigma-Aldrich) and collagenase VIII (250 U/ml, Sigma-Aldrich) at 37°C for 1h (for digestion of lung) or 30 minutes (for digestion of pancreas). The digested tissues were homogenized by vigorous shaking and passed through a 70-μm cell strainer. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll (GE Healthcare) gradient after a spin at 2500 rpm for 20 minutes at room temperature.   For isolation of large and small intestine lamina propria lymphocytes, tissues were dissected. Fat tissues and peyer’s patches in the small intestine were removed. The intestines were then cut into pieces, washed, and shaken in PBS containing 1mM dithiothreitol for 10 minutes at room temperature. Intestines were incubated with shaking at 220 rpm in PBS containing 30 mM ethylenediaminetetraacetic acid (EDTA) at 37°C for 10 minutes for 2 cycles. The tissues were then digested in RPMI 1640 medium containing DNase I (150 ug/ml) and collagenase VIII (150 U/ml) at 37°C in an incubator with 5% CO2 for 1.5h. Mononuclear cells were then harvested from the interphase of a 40% and 80% Percoll gradient after a spin at 2500 rpm for 20 minutes at room temperature.
Library preparation was performed using TruePrepTM DNA Library Prep Kit V2 for Illumina® kit from Vanzyme (Nanjing, China). 1.2×Agencourt AMPure XP beads (Beckman Coulter) were used to purify libraries for sequencing.

value: male

value: Small intestine

value: Group 2 innate lymphoid cells


title: whole blood, TD_301041

source_name: whole blood IC28

value: 38 mos.

value: whole blood

value: normal


title: H4-2

description: replicate 2


title: halauxifen treatment 2 hours replicate 2

source_name: leaf

value: Visby

value: leaf stage BBCH11

value: treatment with halauxifen


title: control treatment 96 hours replicate 2


title: 194_D1_IN

source_name: lung tissue

tag: agent

value: female

tag: infection route

value: intranasal


title: 191_D1_IN


title: E3n1

description: replicate 1


title: whole blood, TD_331013

source_name: whole blood BFC05

value: Male

value: 39 mos.


title: 210_D1_fomite

value: fomite


title: control treatment 48 hours replicate 3

tag: cultivar

tag: time


title: 193_D1_IN

tag: Sex


title: control treatment 48 hours replicate 2


title: E3n2

description: replicate 2

value: Total cells


title: whole blood, DS_111025

source_name: whole blood IC16

tag: age

value: Down syndrome (Trisomy 21)


title: 56c2-2

description: replicate 2

value: WT


title: P1

source_name: Pancreas ILC2

value: 6 weeks old

value: male

value: Pancreas


title: 56c2-3

description: replicate 3


title: whole blood, TD_301048

source_name: whole blood IC29

value: 38 mos.


title: P2

value: Group 2 innate lymphoid cells


title: 56c2-1

description: replicate 1


title: 207_D1_fomite


title: LI2

source_name: Large intestine ILC2

value: Large intestine


title: L1

source_name: Lung ILC2

value: Lung


title: SI1

value: Small intestine


title: 192_D1_IN


title: L2


title: 209_D1_fomite


title: whole blood, TD_301040

source_name: whole blood IC27

value: 37 mos.

value: whole blood

value: normal


title: 61c7n2

description: replicate 2


title: whole blood, DS_91016

source_name: whole blood IC03

value: Male

value: 6 mos.


title: control treatment 96 hours replicate 1

value: Visby

value: leaf stage BBCH11

tag: treatment

value: no treatment


title: 183_D1_aerosol

value: female

value: aerosol


title: control treatment 48 hours replicate 1


title: pfap2-g5_dDBD_3D7_S_rep2_RNA-seq

status: Public on Aug 03 2021

first: Shijun

last: Shen

state: Shanghai

address: 1239 Siping Road, Shanghai, P.R. China

department: Bioninformatics

institute: Tongji University

description: WT_vs_pfap2-g5_dDBD_3D7_rep2_FPKM_sense_and_antisense_RNA.xlsx

data_processing:
Low-quality and adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 75 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Hisat2 strand-specific mode (v2.1.0)  with parameters: --rna-strandness RF --dta --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Mapped reads were subsequently assembled into transcripts guided by the PlasmoDB gff annotation files (Pf 3D7 v32) using featureCounts (v1.6.1)  with parameters: -M -p -B -C for all; -s 2 for sense transcripts; -s 1 for antisense transcripts.
The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The raw counts were calculated by featureCounts as described above. Then FPKM of each gene was calculated in R.

organism: Plasmodium falciparum

growth_protocol: Parasites were cultured in medium containing 0.5% Albumax II with O type fresh red blood cells, and a gas phase with 5% O2, 5 % CO2 at 37 °C.

extract_protocol:
Total RNA was isolated from parasites with a combination of TRIzol (Invitrogen) treatment and using a Direct-zol RNA Kit (Zymo Research) as manufacturer’s instructions.
Library preparation for strand-specific RNA-seq was carried out by poly(A) selection with the KAPA mRNA Capture Beads (KAPA), and fragmented to about 300–400 nucleotides (nt) in length, then all subsequent steps were performed according to a KAPA Stranded mRNA-Seq Kit Illumina platform (KK8421).

treatment_protocol: Parasite lines were  synchronized twice in two continuous intraerythrocytic cycles by 5% sorbitol solution followed by a percoll treatment in the cycle to obtain asexual ring (10-15 hpi), trophozoite (25-30 hpi), schizont (40-45 hpi) at continuous timepoints.

tag: development stage

value: Schizont

value: Pf 3D7

tag: host

value: Homo sapiens


title: control treatment 2 hours replicate 3


title: pfap2-g5_dDBD::pfap2-g_ko_3D7_R_rep1_RNA-seq

description: pfap2-g5_dDBD&pfap2-g_ko_3D7_rep1_FPKM_sense_and_antisense_RNA.xlsx

value: Trophozoite


title: pfap2-g5_dDBD_3D7_T_rep2_RNA-seq


title: pfap2-g5_dDBD_3D7_R_rep2_RNA-seq

value: Ring


title: 61c7n3

description: replicate 3

value: Total cells


title: 185_D1_aerosol


title: control treatment 2 hours replicate 2


title: BM2

source_name: Bone marrow ILC2

value: 6 weeks old

tag: gender

value: male

value: Bone marrow

tag: cell type

value: Group 2 innate lymphoid cells


title: pfap2-g5_dDBD_3D7_S_rep1_RNA-seq

description: WT_vs_pfap2-g5_dDBD_3D7_rep1_FPKM_sense_and_antisense_RNA.xlsx

tag: genotype


title: LI1

tag: tissue

value: Large intestine


title: control treatment 2 hours replicate 1


title: 184_D1_aerosol


title: BM1

tag: strain


title: pfap2-g5_dDBD_3D7_T_rep1_RNA-seq


title: pfap2-g5_dDBD_3D7_R_rep1_RNA-seq


title: 213_D4_fomite

value: fomite


title: pfap2-g5_trun_H3K9Ac_T_rep2_HM_ChIP-seq

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

extract_protocol:
Synchronized WT and pfap2-g5_trun::WT  parasites at trophozoite  stage were harvested and cross-linked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 min at 37 ℃, then quenched with 0.125 M glycine for 5 min. The culture was resuspended with 1 x PBS and parasites were released from iRBC with 0.15% saponin for 10- 15 min on ice. The washed nuclei were isolated by incubation with 2 ml of Lysis Buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1 mM EDTA pH8.0, 0.1mM EGTA pH8.0, 1mM DTT, 0.25% NP40, 1 x protease inhibitors cocktail) for 30 min on ice, and followed by dounce homogenization for 100 strokes. Afterwards the nuclei were resuspended in 200 μl of SDS Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH8.0) for sonication to generate 200–500 bp fragments in length on the highest power setting for 10-20 min at 30-s intervals with Bioruptor (BioruptorTM UCD-200). The sonicated chromatin was diluted ten-fold with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 150 mM NaCl, 1 x protease inhibitors cocktail) and precleared with Protein A/G magnetic beads (Pierce) for two hours. The precleared chromatin supernatant was incubated with 3μg  anti-H3K9ac (Millipore, 07-352)  or anti-H3K9me3 (Abcam, ab8898) and Protein A/G magnetic beads at 4 ℃ overnight with a small volume of non-immunoprecipitated input material kept separately. After extensive washes, protein-DNA complexes were eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3). Crosslinking was reversed by incubating overnight at 45°C and DNA was treated with RNase A at 37°C for 30 min and Proteinase K at 45°C for two hours. ChIP-DNA was extracted using MinElute PCR purification kit (Qiagen, 28006).
ChIP-DNA was end-repaired  (Epicentre No.ER81050), adding protruding 3’ A base (NEB No.M0212L), adapter ligation(NEB No.M2200L), size selection and amplification of libraries(KAPA Biosystems, KB2500) with a PCR program: 1 min at 98 ℃, 12 cycles of 10 s at 98 ℃, 1 min at 65 ℃; finally extended 5 min at 65 ℃.

treatment_protocol: WT and pfap2-g5_trun::WT parasite lines were  synchronized twice in two continuous intraerythrocytic cycles by 5% sorbitol solution to harvest  trophozoite stage parasites.

value: Trophozoite (30-40hpi)

tag: chip antibody

value: H3K9ac, Millipore, 07-352


title: Vsir-/-

source_name: All kinds of kidney cells were included

tag: genotype/variation

value: Vsir-/-

value: 8 weeks

value: kidney


title: DS_3

city: Hohhot

first: Rui

last: Shi

address: No.306, Zhaowuda Road, Saihan District, Hohhot

institute: Inner Mongolia Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Genome_build: Transcripts assembled with Trinity; FASTA file available on series record.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Medicago ruthenica

source_name: drought stress

growth_protocol: Medicago ruthenica seeds were obtained from the Institute of Grassland Research, Chinese Academy of Agricultural Sciences at the Inner Mongolia Autonomous Region, China. This cultivar grows well in Inner Mongolia, with higher drought and cold resistance. The sanded Medicago ruthenica seeds were sterilized in concentrated sulfuric acid for 10 min, and then washed thoroughly with sterile water. After incubating for three days at 4   C in dark conditions, the seeds were placed on soaked filter paper in Petri dishes, and incubated in an artificial climate chamber (temperature, 25    2  C; photoperiod, 16 h light/8 h dark cycle; relative humidity, 50%). Two days later, the germinated seeds were transferred to pots (13 cm in diameter and 10 cm deep) with vermiculite and quartz sand. There were eight plants in each pot.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 1000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an IlluminaHiseq4000 instrument (LC Sciences, USA) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Four-week-old seedlings were randomly divided into three groups: the control group (CK), the drought stress treatment group (DS), and the re-watering group (RW). The drought treatment period lasted for 15 days. During the experiment, CK plants were watered every three days, maintaining a relative soil moisture content of more than 80%, while DS and RW plants were subjected to water deprivation for 15 days, resulting in a relative soil moisture content of 20% on the 15th day. The RW plants were rehydrated to full soil saturation on the 15th day. To avoid any interference, no nutrients were added. Other growth conditions were maintained. Each treatment group had three biological replicates. Leaf samples of CK and DS were collected on the 15th day, and leaves of RW were collected 2 days after rewatering. Samples were immediately frozen in liquid nitrogen, and stored at -80   C for later use.

value: Leaves

tag: developmental stage

value: Four-week-old seedlings


title: RW_2

source_name: rewatered after drought stress


title: pfap2-g5_trun_H3K9me3_T_rep2_HM_ChIP-seq

value: Pf 3D7

value: H3K9me3, abcam, ab8898

value: Homo sapiens


title: 61c7n1

description: replicate 1

source_name: Myotube

tag: cell line

tag: extract

value: Total cells


title: RW_3


title: pfap2-g5_trun_input_T_rep2_HM_ChIP-seq


title: WT_H3K9Ac_T_rep2_HM_ChIP-seq

value: wild type


title: WT_input_T_rep2_HM_ChIP-seq


title: WT_H3K9me3_T_rep2_HM_ChIP-seq


title: RW_1


title: CK_3

source_name: control


title: DS_1


title: WT_H3K9Ac_T_rep1_HM_ChIP-seq


title: DS_2


title: WT_H3K9me3_T_rep1_HM_ChIP-seq


title: WT_input_T_rep1_HM_ChIP-seq


title: pfap2-g5_dDBD_NF54_WGS-seq

data_processing:
Library strategy: WGS-seq
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using BWA (v0.7.17)  with parameters: mem -k 32 -M.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
The Samtools (v1.9)  was used to perform SNP/InDel calling with parameters: mpileup -q 1  -C 50 -m 2 -F 0.002 -d 1000.Then we filtered this sets using the following criteria: the mapping quality >20 and the depth of the variate position >4.
ANNOVAR was used for functional annotation of variants. Vcftools (v0.1.16) was used for set comparison between samples.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The final SNP/InDel sets of each sample were uploaded as supp.

extract_protocol:
Genomic DNA was extracted according to the DNeasy  Blood and Tissue Kit (QIAGEN) manufacturer's requirements.
Genomic DNA samples were randomly broken into fragments of 350 bp length by Covaris ultrasonic disruptor. TruSeq Library Construction Kit was used for library construction. The entire library preparation was completed by end repair, addition of ployA tails, addition of adaptors, purification, and PCR amplification. The libraries were sequenced by illumina.

treatment_protocol: The medium was changed every other day until parasitaemia rose to 5%.

value: Pf NF54


title: CK_2


title: RNA-seq-SARS2-highMOI-6hpi-CHX-rep3

city: Saint Louis

first: Sebla

middle: Bulent

last: Kutluay

address: 660 S. Euclid Avenue, Campus Box 8230

institute: Washington University School of Medicine

data_processing:
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots. Read counts per read are shown in the processed files
Supplementary_files_format_and_content: *hpi.txt: counts files for reads mapping to host cell genome/transcriptome
Supplementary_files_format_and_content: *repaired.txt: mpileup files of reads that map to the viral genomes

organism: Chlorocebus sabaeus

source_name: Vero E6

growth_protocol: Vero E6 cells were grown in DMEM-10%FBS media. Isolation and growth of primary human bronchial epithelial cells is explained elsewhere. Primary CD4+ T-cells were isolated from PBMCs of deidentified blood donors using negative selection kit from StemCell Technologies and grown in RPMI media supplemented with 10%FBS, IL-2 and activated with CD3/CD28 conjugated Dynabeads.

extract_protocol:
Cytosolic extracts were either subjected to ribo-seq or RNA-seq as in published protocols
Infected cells were lysed and two aliquots were processed in parallel for ribo-seq and RNA-seq. For RNA-seq, total RNA was isolated using ZymoClean RNA-Clean and Concentrator kit and subjected to Illumina stranded mRNA prep. Ribo-seq libraries were prepared in house following published protocols. Both libraries were sequenced using Illumina NextSeq following the manufacturer's protocols.

treatment_protocol: Cells were infected with SARS-CoV-2 at an MOI of 0.1 pfu/cell (low MOI) and 2 pfu/cell (high MOI) for Vero E6 cells, or MOI of 0.5 pfu/cell (low) and 1 pfu/cell (high) for primary human bronchial epithelial cells. Primary activated CD4+ T-cells were infected with HIV-1 at an MOI of 2

value: Cycloheximide

tag: agent

tag: time point


title: pfap2-g5_dDBD_3D7_WGS-seq


title: pfap2-g5_trun_input_T_rep1_HM_ChIP-seq


title: PfAP2-G_GFP_pfap2-g5_trun_T_rep2_INPUT_ChIP-seq

data_processing:
Low-quality and the adaptor sequences were trimmed from the reads using cutadapt (v1.16)  with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20,20.
Then, the reads were mapped to the Plasmodium falciparum 3D7 genome (Pf 3D7 v32, obtained from PlasmoDB) using Bowtie2 (v2.3.4.3)  with parameters: -N 0 --no-discordant --no-mixed --no-unal.
The Samtools (v1.9) was used to filter low mapping quality reads and transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8) .
MACS2 (v2.1.1) was used to perform peak calling with the p-value cutoff of 0.01.
Genome_build: Pf 3D7 v32
Supplementary_files_format_and_content: The bam files were converted to bigwig files using bamCoverage from the deeptools suite  (v3.1.3) with parameters: --normalizeUsing RPKM --binSize 10 --smoothLength 30 -ignore Pf3D7_API_v3 Pf_M76611.

extract_protocol:
Synchronized PfAP2-G5-GFP::WT, PfAP2-G-GFP::WT, PfAP2-G-GFP::pfap2-g5_trun parasites at different stages were harvested and cross-linked immediately with 1% paraformaldehyde (Sigma) by rotating for 10 min at 37 ℃, then quenched with 0.125 M glycine for 5 min. The culture was resuspended with 1 x PBS and parasites were released from iRBC with 0.15% saponin for 10- 15 min on ice. The washed nuclei were isolated by incubation with 2 ml of Lysis Buffer (10 mM HEPES pH 7.9, 10 mM KCl, 0.1 mM EDTA pH8.0, 0.1mM EGTA pH8.0, 1mM DTT, 0.25% NP40, 1 x protease inhibitors cocktail) for 30 min on ice, and followed by dounce homogenization for 100 strokes. Afterwards the nuclei were resuspended in 200 μl of SDS Lysis Buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH8.0) for sonication to generate 200–500 bp fragments in length. The sonicated chromatin was diluted ten-fold with dilution buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH8.0, 150 mM NaCl, 1 x protease inhibitors cocktail) and precleared with Protein A/G magnetic beads (Pierce) for two hours. The precleared chromatin supernatant was incubated with 1 μg rabbit anti-GFP (Abcam, ab290) or rabbit IgG (Abcam) as control and Protein A/G magnetic beads at 4 ℃ overnight with a small volume of non-immunoprecipitated input material kept separately. After extensive washes, protein-DNA complexes were eluted with Elution Buffer (1% SDS, 0.1 M NaHCO3). Crosslinking was reversed by incubating overnight at 45°C and DNA was treated with RNase A at 37°C for 30 min and Proteinase K at 45°C for two hours. ChIP-DNA was extracted using MinElute PCR purification kit (Qiagen, 28006).
ChIP-DNA was end-repaired (Epicentre No.ER81050), adding protruding 3’ A base (NEB No.M0212L), adapter ligation(NEB No.M2200L), size selection and amplification of libraries(KAPA Biosystems, KB2500) with a PCR program: 1 min at 98 ℃, 12 cycles of 10 s at 98 ℃, 1 min at 65 ℃; finally extended 5 min at 65 ℃.

treatment_protocol: PfAP2-G5-GFP::WT, PfAP2-G-GFP::WT, PfAP2-G-GFP::pfap2-g5_trun parasite lines were  synchronized twice in two continuous intraerythrocytic cycles by 5% sorbitol solution to harvest  trophozoite stage parasites. PfAP2-G5-GFP::WT line was synchronized twice with 5% sorbitol solution followed by a percoll treatment in the cycle before the cultures were set up for gametocytogenesis assay. Then the highly synchronized ring-stage parasites were set up at 2% parasitemia (4% haematocrit). After re-invasion, 50 mM N-acetyl-D-glucosamine was added into the cultures to kill the asexual replicating forms after sexual commitment to harvest G0-G1 stage parasites.


title: CK_1


title: Ribo-seq-SARS2-highMOI-12hpi-CHX-rep3

data_processing:
Library strategy: Ribo-seq
Reads were cleared off of adapters and demiltiplexed using BBDuk.
Ribo-seq reads were cleared off of rRNAs.
Reads were mapped to SARS-CoV-2/HIV-1 genomes and the unmapped reads were mapped to Vero/human genomes/transcriptomes using STAR.
Reads were annotated and counts files generated.
Reads mapping to viral genomes were processed by samtools pileup function to generate read density plots. Read counts per read are shown in the processed files
Supplementary_files_format_and_content: *hpi.txt: counts files for reads mapping to host cell genome/transcriptome
Supplementary_files_format_and_content: *repaired.txt: mpileup files of reads that map to the viral genomes


title: IgG_rep1_ChIP-seq

value: IgG, abcam, ab171870


title: pfap2-g5_trun_H3K9Ac_T_rep1_HM_ChIP-seq


title: IgG_rep2_ChIP-seq


title: pfap2-g5_trun_3D7_WGS-seq


title: pfap2-g5_trun_NF54_WGS-seq


title: Ribo-seq-SARS2-highMOI-24hpi-CHX-rep3


title: Ribo-seq-SARS2-highMOI-6hpi-CHX-rep3


title: RNA-seq-SARS2-highMOI-12hpi-CHX-rep3


title: PfAP2-G_GFP_pfap2-g5_trun_T_rep1_INPUT_ChIP-seq


title: pfap2-g5_trun_H3K9me3_T_rep1_HM_ChIP-seq


title: RNA-seq-SARS2-highMOI-24hpi-CHX-rep3


title: Ribo-seq-SARS2-highMOI-2hpi-CHX-rep3


title: RNA-seq-SARS2-highMOI-2hpi-CHX-rep3


title: PfAP2-G_GFP_pfap2-g5_trun_T_rep2_TF_ChIP-seq

value: GFP, abcam, ab290


title: Ribo-seq-mock-highMOI-CHX-rep3

value: mock-highMOI


title: PfAP2-G_GFP_WT_T_rep1_INPUT_ChIP-seq

value: Trophozoite (30-40hpi)


title: H2A.X KO Rep2 - D0

city: Rochester

first: Cameron

last: Baker

state: NY

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
FastP version 0.20.0 with the following parameters: "--length_required 35 --cut_front_window_size 1 --cut_front_mean_quality 13 --cut_front --cut_tail_window_size 1 --cut_tail_mean_quality 13 --cut_tail -y -r"
STAR_2.7.0f with the following parameters: "—twopass Mode Basic --runMode alignReads --outSAMtype BAM SortedByCoordinate – outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical –outReads UnmappedFastx"
subread-1.6.4 package (featureCounts) with the following parameters: "-s 2 -t exon -g gene_name"
Differential expression analysis was performed using DESeq2-1.22.1
Genome_build: GRCh39/hg38 + Gencode 31
Supplementary_files_format_and_content: raw gene counts

growth_protocol: Cells were grown in expansion media and the cells were allowed to mature in differentiation media. Cells were taken at D0 and D6 of differentiation.

extract_protocol: The total RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA). The TruSeq RNA Sample Preparation Kit V2 (Illumina, San Diego, CA) was used for next generation sequencing library construction per manufacturer’s protocols. Briefly, mRNA was purified from 100ng total RNA with oligo-dT magnetic beads and fragmented. First-strand cDNA synthesis was performed with random hexamer priming followed by second-strand cDNA synthesis. End repair and 3` adenylation was then performed on the double stranded cDNA. Illumina adaptors were ligated to both ends of the cDNA, purified by gel electrophoresis and amplified with PCR primers specific to the adaptor sequences to generate amplicons of approximately 200-500bp in size. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA) at a concentration of 8pM per lane. Single end reads of 100nt are generated for each sample and aligned to the organism specific reference genome.

tag: differentiation day

value: H2A.X KO


title: H2A.X KO Rep1 - D6


title: RNA-seq-mock-highMOI-CHX-rep3


title: PfAP2-G5_GFP_WT_D5_rep1_TF_ChIP-seq


title: H2A.X WT Rep2 - D0

value: H2A.X WT


title: PfAP2-G5_GFP_WT_T_rep2_TF_ChIP-seq


title: PfAP2-G5_GFP_WT_T_rep2_INPUT_ChIP-seq


title: PfAP2-G5_GFP_WT_D5_rep1_INPUT_ChIP-seq


title: PfAP2-G_GFP_WT_T_rep2_INPUT_ChIP-seq


title: PfAP2-G_GFP_pfap2-g5_trun_T_rep1_TF_ChIP-seq


title: H2A.X WT Rep1 - D0


title: H2A.X WT Rep2 - D6


title: H2A.X KO Rep3 - D0


title: PfAP2-G_GFP_WT_T_rep2_TF_ChIP-seq


title: PfAP2-G5_GFP_WT_D5_rep2_INPUT_ChIP-seq


title: H2A.X KO Rep1 - D0


title: PfAP2-G5_GFP_WT_T_rep1_INPUT_ChIP-seq


title: H2A.X KO Rep3 - D6


title: PfAP2-G5_GFP_WT_T_rep1_TF_ChIP-seq