title: EOC295_rAsc_RNA_seq6a

description:
Internal control of EOC295_rAsc_RNA_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: Neoadjuvant chemotherapy


title: antigen-specific CD8+ T cells Trp2 (Dct) wild-type single cells_day3

status: Public on Apr 30 2021

type: SRA

city: Minneapolis

first: Todd

middle: P

last: Knutson

state: MN

address: 117 Pleasant St SE

department: Minnesota Supercomputing Institute

country: USA

institute: University of Minnesota

description:
single cell polyA RNA
scRNAseq_WT_day3

library_source: transcriptomic

data_processing:
Illumina bcl2fastq (bulk RNAseq) or 10X Genomics Cell Ranger (scRNAseq) software was used to demultiplex samples and generate fastq files.
Read mapping was performed via Hisat2 (Bulk RNAseq) or Cell Ranger count (scRNAseq) using the mouse reference genome (mm10).
Gene level quantification was completed using Subread featureCounts (bulk RNASeq) or Cell Ranger count software.
Raw counts data was imported into R for downstream processing, including normalization, principal components analysis, differential gene expression testing, single cell clustering, etc.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw or normalized read count values for each sample

molecule: polyA RNA

organism: Mus musculus

source_name: antigen-specific CD8+ T cells

growth_protocol: Trp2/Kb-specific cells were isolated from pre-immune WT and Dct-/- mice using tetramer enrichment followed by fluorescence-activated cell sorting on double tetramer positive cells.

extract_protocol:
Bulk RNAseq (samples 1-6): cells were isolated from three separate cohorts, with each cohort comprising eight WT and eight Dct-/- mice; Qiagen RNEasy Plus Mini Kit was used to extract RNA. Single cell RNA-seq (scRNAseq samples 1 and 2): sorted cells were supplied as input to the 10x Genomics single cell protocol.
Bulk: Clontech StrandedRNA Pico Mammalian workflow was used for library preparation; scRNAseq: Chromium Single Cell Immune Profiling was used for library preparation. Samples were prepared for sequencing using standard Illumina protocols.

tag: cell type

value: antigen-specific CD8+ T cells

tag: strain

tag: genotype

value: wildtype

tag: tissue

value: spleen

tag: treatment

value: mice were treated with TriVax (200 ug Trp2) 3 days prior


title: EOC26_rAsc1_RNA2_seq3

city: Helsinki

first: Elina

middle: A

last: Pietilä

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description: The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

data_processing:
Read pairs were trimmed using Trimmomatic (version 0.33)
the first 12 and last 5 bases were cropped due to uneven per base sequence content
leading bases with a quality score lower than 20 and any trailing bases with a quality score lower than 30 were removed
the reads were scanned with a 3-base wide sliding window, cutting when the average quality per base dropped below 20
resulting sequences shorter than 20bp were discarded. Trimmed reads were aligned to the reference genome (GRCh38.d1.vd1) using STAR (version 2.5.2b), allowing up to 10 mismatches, and all alignments for a read were output
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with effective counts

molecule: total RNA

organism: Homo sapiens

source_name: Ascites-derived cells from post-chemotherapy relapse patient

growth_protocol: Cells were not cultured

extract_protocol:
Total RNA was extracted from fresh patient tissues and ascites-derived cells by using RNeasy kit from QIAGEN (Qiagen, Hilden, Germany) with DNase I treatment. RNA quality and concentration were tested with Bioanalyzer 2100 (Agilent CA, USA). All samples fulfilled the criteria of RNA integrity number (RIN) > 7 and concentration > 50 ng/µl.
Sequencing libraries were constructed in Beijing Genomics Institute (Beijing, China) using a modified protocol similar to the TrueSeq Stranded Total RNA with RiboZeroKit (Illumina Inc.)

treatment_protocol: The post-chemotherapy samples were collected from patients after chemotherapy treatment.

tag: disease state

value: high-grade serous ovarian carcinoma

tag: anatomical location

value: Ascites

tag: treatment strategy


title: PA23 Root 7dpt rep 3 [7dpi_PA23_root_1-3]

city: Winnipeg

first: Ayooluwa

last: Bolaji

address: 50 Sifton Road

department: Biological Sciences

country: Canada

institute: University of Manitoba

description: NS.1522.001.NEBNext_dual_i7_229---NEBNext_dual_i5_277.7dpi_PA23_root_1-3

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to b. Napus whole genome using hisat2
FeartureCounts was used to obtain read counts by  mapping the reads obtained to the raw counts.  DeSeq2 was used in R to calculate  differential egne expressions
Genome_build: hisat2 was used to index and build the B. napus genome
Supplementary_files_format_and_content: Count matrix table with raw gene counts for every gene and every sample

organism: Brassica napus

source_name: PA23 Root 7dpt

growth_protocol: Plant were grown for 14 days. 7 days post planting, half the plants were treated with LB broth and the other half were treated with Pseudomonas chlororaphis PA23.

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

treatment_protocol: Plants were treated with 15mL of Pseudomonas chlororaphis PA23 grown to a concentration of 10^9 CFU/mL

value: plant root

value: Pseudomonas chlororaphis PA23

tag: time of harvest

value: 7 days post treatment


title: PA23 Root 7dpt rep 2 [7dpi_PA23_root_1-2]

description: NS.1522.002.NEBNext_dual_i7_228---NEBNext_dual_i5_276.7dpi_PA23_root_1-2


title: MG_scRNA-seq

city: Pittsburgh

first: Iliya

last: Lefterov

state: PA

address: 130 De Soto Street

department: Enviromantal and Occupational health

institute: University of Pittsburgh

data_processing:
FASTQ TO BAM
Cell Ranger
Seurat
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file is in excel and is CPM data for all genes in all samples; batch corrected counts from featureCounts

source_name: microglia

growth_protocol: All animal experiments were performed in accordance with the NIH Guide for Care and Use of Animals and approved by the University of Pittsburgh Institutional Animal Care and Use Committee.

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and transcardially perfused with 25 mL of cold 0.1 M PBS, pH 7.4. For Cx3cr1GFP and Trem2ko mice used for FACS, flow cytometry and single cell RNAseq the infusion sites in both hemispheres were excised for cellular isolation as described below. For WT mice, one hemisphere was drop fixed in 4% phosphate-buffered paraformaldehyde at 4 °C for 48 h before storage in 30% sucrose. The other hemisphere was used for cellular isolation as described below. Fixed hemibrains were mounted in O.C.T. and cut in the coronal plane at 30 µm sections using a frozen cryotome (Thermo Scientific) and stored in glycol-based cryoprotectant at -20 °C until histological staining. Prior to staining, sections containing the infusion site were selected under a dissection microscope (Olympus). In a separate cohort of APP/E3 and APP/E4 mice (14 mo.) CSF was collected prior to perfusion. Once anesthetized a small incision was made exposing the foramen magnum, a 28g 1/2" needle was used to puncture a hole at the base of the skull and a capillary tube was applied for CSF withdraw.
scRNA libraries were generated with Chromium single cell 3’ chip kit v3 for scRNA-seq (10x Genomics) according to the manufacturer’s instructions and then the quality assessed using Agilent Bioanalyzer 2100. Sequencing was performed using NovaSeq (Illumina) by MedGenome Inc. with a custom sequencing setting (28bp for Read1 and 91bp for Read2) to obtain an average sequencing depth of 45K reads/cell.

treatment_protocol: The following mouse lines were bred to generated experimental mice: Wild-type C57BL/6J (WT; JAX), human APOE3 and APOE4 targeted replacement mice (E3 & E4; Taconic), Trem2em2ADiuj/J mice (Trem2ko; JAX) and 129P2(Cg)-Cx3cr1tm1Litt/J (Cx3cr1GFP; JAX). Human APOE3 and APOE4 targeted replacement mice were bred to Abca1tm1Jdm/J mice (Abca1ko; JAX) to generate APOE3/Abca1het and APOE4/Abca1het (E3het & E4het). Likewise, human APOE3 and APOE4 targeted replacement mice were bred to Trem2em2ADiuj/J mice (Trem2ko; JAX) to generate APOE3/Trem2ko and APOE4/Trem2ko (E3/Trem2ko & E4/Trem2ko). Furthermore, APP/PS1dE9 mice expressing mutant familial variants of human amyloid precursor protein (APP) with Swedish mutation, and human presenilin 1 carrying the exon-9-deleted variant (PSEN1dE9) were crossed to human APOE3 and APOE4 targeted replacement mice.

tag: Sex

value: Male

tag: tissue/cell type

value: microglia


title: PA23 Root 7dpt rep 1 [7dpi_PA23_root_1-1]

description: NS.1522.001.NEBNext_dual_i7_227---NEBNext_dual_i5_275.7dpi_PA23_root_1-1


title: EOC167_r2Asc_RNA1_seq4


title: EOC167_r1Asc_RNA1_seq3


title: EOC742_pOva_RNA1_seq6

source_name: Tumor tissue from treatment-naïve patient

value: Primary

value: Primary debulking surgery


title: mPTC/Tbx3 KO-1

city: Tianjin

first: Peitao

last: Zhang

address: Qixiangtai Road 22

country: China

institute: Tianjin Medical University

description:
knock out TBX3
all compare_mouse

data_processing:
We use  Bowtie2  to map clean reads to reference gene and use  HISAT to reference genome.Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using   Bowtie2  parameters for SE reads: -q --phred64 --sensitive --dpad 0 --gbar,HISTA parameters for SE reads: -p 8 --phred64 --sensitive -I 1 -X 1000
The FPKM is calculated by RSEM, which is the quantification tool that computed Maximum likelihood abundance estimates using the Expectation Maximization (EM) algorithm for its statistical model, including the modeling of paired-end (PE) and variable-length reads, fragment length distributions, and quality scores, to determine which transcripts are isoforms of the same gene.
Genome_build: hg38 for Homo sapiens and mm10 for Mus musculus
Supplementary_files_format_and_content: tab-delimited text files include FPKM, count values for each Sample

source_name: mPTC/Tbx3 KO-1

growth_protocol: K1 cells were cultured in DMEM with 10% FBS

extract_protocol:
RNA was harvested using Trizol reagent. First Strand cDNA Synthesis Kit (04 896 866 001, Roche) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: K1cells were transfected with control and shRNA targeting TBX3

value: mouse papillary thyroid carcinoma tissue

value: knock out TBX3


title: EOC737_pOvaR1_RNA1_seq5


title: mPTC/Tbx3 KO-2

description:
knock out TBX3
all compare_mouse

source_name: mPTC/Tbx3 KO-2


title: mPTC/Tbx3 KO-3

description:
knock out TBX3
all compare_mouse

source_name: mPTC/Tbx3 KO-3


title: PA23 Root 24hpt rep 3 [24hpi_PA23_root_1-3]

description: NS.1522.001.NEBNext_dual_i7_241---NEBNext_dual_i5_289.24hpi_PA23_root_1-3

source_name: PA23 Root 24hpt

value: 24Hours post treatment


title: PA23 Root 24hpt rep 2 [24hpi_PA23_root_1-2]

description: NS.1522.001.NEBNext_dual_i7_240---NEBNext_dual_i5_288.24hpi_PA23_root_1-2


title: EOC606_pOvaR1_RNA1_seq5


title: mPTC-1

description:
control
all compare_mouse


title: Negative Control Root  7dpt rep 2 [7dpi_neg_root_1-2]

description: NS.1522.001.NEBNext_dual_i7_222---NEBNext_dual_i5_270.7dpi_neg_root_1-2

source_name: Negative Control Root  7dpt

value: Negative


title: EOC933_pOvaL1_RNA1_seq6

value: Neoadjuvant chemotherapy


title: EOC566_pOvaR_RNA1_seq4


title: Negative Control Root  7dpt rep 3 [7dpi_neg_root_1-3]

description: NS.1514.001.NEBNext_dual_i7_223---NEBNext_dual_i5_271.7dpi_neg_root_1-3


title: PTX-Vehicle-red-color-Lid-9

city: Berlin

first: Christian

last: Schinke

state: Berlin

address: Charitéplatz 1

country: Germany

institute: Charité Universitätsmedizin Berlin

description: Reference: (1) Schwartzentruber J, Foskolou S, Kilpinen H, Rodrigues J, Alasoo K, Knights AJ, Patel M, Goncalves A, Ferreira R, Benn CL et al: Molecular and functional variation in iPSC-derived sensory neurons. Nature genetics 2018, 50(1):54-61.

data_processing:
RNA Seq reads were mapped to human genome (GRCh38.p7) with STAR-version 2.7.3a (1) using the default parameters
Reads were assigned to genes with featureCounts (2) with the following parameters: '-t exon -g gene_id, gene annotation - Gencode GRCh38/v25.
The differential expression analysis was carried out with DESeq2-version 1.22.1 (3) using the default parameters.
We kept genes that have at least 5 reads in at least 2 samples. Gene set enrichment analysis was carried out with R/tmod package (4).
References: (1) Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR: STAR: ultrafast universal RNA-seq aligner. Bioinformatics 2013, 29(1):15-21. (2) Liao Y, Smyth GK, Shi W: featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 2014, 30(7):923-930. (3) Love MI, Huber W, Anders S: Moderated estimation of fold change and dispersion for RNA_x0002_seq data with DESeq2. Genome Biology 2014, 15(12). (4) Zyla J, Marczyk M, Domaszewska T, Kaufmann SHE, Polanska J, Weiner J: Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. Bioinformatics 2019, 35(24):5146-5154.

source_name: DMSO - iPSC-DSN

growth_protocol: The s.c. P2 protocol by Schwartzentruber et al. (1) was applied for hiPSC differentiation.

extract_protocol: iPSC-DSN were maintained in geltrex coated 6-well plates at 106 cells/well as described above. After maturation until d44 - d49, three wells were either treated with DMSO at 1/6000 or Paclitaxel at 1 µM for 24h, and RNA was harvested with the Aurum™ Total RNA Mini Kit according to manufacturers’ instructions, with a total RNA amount between 1.49 and 2.97 µg. RNA sequencing was performed by Brooks Life Sciences Genewiz® with PolyA selection for RNA removal, 2x150bp sequencing configuration and 20-30 million reads per sample. 5 samples were analyzed (n = 3 DMSO-treated [batches of 2 directly differentiated neurons and 1 thawed batch] vs. n=2 paclitaxel-treated [1 directly differentiated, 1 thawed).

value: Induced pluripotent stem cell derived sensory neurons (iPSC-DSN)

tag: maturation day

value: DMSO


title: Negative Control Root  7dpt rep 1 [7dpi_neg_root_1-1]

description: NS.1514.001.NEBNext_dual_i7_221---NEBNext_dual_i5_269.7dpi_neg_root_1-1


title: mPTC-3

description:
control
all compare_mouse

value: wildtype


title: EOC568_pTubL1_RNA1_seq5

value: high-grade serous ovarian carcinoma


title: PA23 Root 24hpt rep 1 [24hpi_PA23_root_2-1]

description: NS.1514.001.NEBNext_dual_i7_239---NEBNext_dual_i5_287.24hpi_PA23_root_2-1


title: T0348

description: scRNA-seq

data_processing:
FASTQ TO BAM
bulk: FEATURECOUNTS
bulk: EDGER
single-cell: Cell Ranger
single-cell: Seurat
Genome_build: mm10
Supplementary_files_format_and_content: batch corrected counts from featureCounts
Supplementary_files_format_and_content: Processed data file is in excel and is CPM data for all genes in all samples.

growth_protocol: All animal experiments were approved by the University of Pittsburgh Institutional Animal Care and Use Committee. All procedures were carried out in accordance with the approved guidelines. APP23 transgenic mice (C57Bl6 background) expressing human APP751 familial Swedish AD mutation (APPK670N, M671L) were crossed to wild-type C57BL/6 mice to generate APP23 hemizygous mice

extract_protocol:
Mice were anesthetized with Avertin (250 mg/kg of body weight, i.p.) and perfused transcardially with cold 0.1 M PBS, pH 7.4: left hemisphere fixed in 4% paraformaldehyde for histology. The cortex was dissected from the other and snap frozen on dry ice for RNA and protein isolation
RNA was isolated from cortex and purified using RNeasy mini kit (Qiagen) per the manufacturer’s protocol. RNA quality was assessed using 2100 Bioanalyzer (Agilent Technologies) and samples with RIN > 8 were further used for sequencing. Sequencing libraries were generated by Novogene.
scRNA libraries were generated with Chromium single cell 3’ chip kit v3 for scRNA-seq (10x Genomics) according to the manufacturer’s instructions and then the quality assessed using Agilent Bioanalyzer 2100. Sequencing was performed using NovaSeq (Illumina) by MedGenome Inc. with a custom sequencing setting (28bp for Read1 and 91bp for Read2) to obtain an average sequencing depth of 45K reads/cell.

treatment_protocol: The following mouse lines were bred to generated experimental mice: Wild-type C57BL/6J (WT; JAX), human APOE3 and APOE4 targeted replacement mice (E3 & E4; Taconic), Trem2em2ADiuj/J mice (Trem2ko; JAX) and 129P2(Cg)-Cx3cr1tm1Litt/J (Cx3cr1GFP; JAX). Human APOE3 and APOE4 targeted replacement mice were bred to Abca1tm1Jdm/J mice (Abca1ko; JAX) to generate APOE3/Abca1het and APOE4/Abca1het (E3het & E4het). Likewise, human APOE3 and APOE4 targeted replacement mice were bred to Trem2em2ADiuj/J mice (Trem2ko; JAX) to generate APOE3/Trem2ko and APOE4/Trem2ko (E3/Trem2ko & E4/Trem2ko).

tag: infusion

tag: single/dual

tag: time


title: Negative Control Root  24hpt rep 3 [24hpi_neg_root_1-3]

description: NS.1514.001.NEBNext_dual_i7_235---NEBNext_dual_i5_283.24hpi_neg_root_1-3

source_name: Negative Control Root  24hpt


title: PTX-1uM-red-color-Lid-10

source_name: Paclitaxel - iPSC-DSN

value: Paclitaxel


title: T0343

description: scRNA-seq

value: Female


title: EOC495_pOvaR1_RNA2_seq4


title: T0347

description: scRNA-seq


title: PA23 Shoot 7dpt rep 3 [7dpi_PA23_shoot_1-3]

description: NS.1514.001.NEBNext_dual_i7_226---NEBNext_dual_i5_274.7dpi_PA23_shoot_1-3

source_name: PA23 Shoot 7dpt

value: plant shoot

value: Pseudomonas chlororaphis PA23


title: 1b-PTX-1-RNA-Lid-5


title: F2053

description: scRNA-seq

value: Male


title: 1a-PTX-1-RNA-Lid-1


title: PA23 Shoot 7dpt rep 2 [7dpi_PA23_shoot_1-2]

description: NS.1514.001.NEBNext_dual_i7_225---NEBNext_dual_i5_273.7dpi_PA23_shoot_1-2

value: 7 days post treatment


title: EOC50_pOvaR1_RNA1_seq5

value: Primary


title: Negative Control Root  24hpt rep 2 [24hpi_neg_root_1-1]

description: NS.1522.001.NEBNext_dual_i7_233---NEBNext_dual_i5_281.24hpi_neg_root_1-1

value: plant root


title: EOC44_pOvaR5_RNA1_seq3

value: Primary debulking surgery


title: 1b-PTX-3-RNA-Lid-7


title: PA23 Shoot 7dpt rep 1 [7dpi_PA23_shoot_2-3]

description: NS.1514.001.NEBNext_dual_i7_224---NEBNext_dual_i5_272.7dpi_PA23_shoot_2-3


title: mPTC-2

description:
control
all compare_mouse

value: mouse papillary thyroid carcinoma tissue


title: T0342

description: scRNA-seq

value: microglia


title: EOC495_pOvaL6_RNA1_seq4


title: Negative Control Shoot  7dpt rep 3 [7dpi_neg_shoot_1-3]

description: NS.1514.001.NEBNext_dual_i7_220---NEBNext_dual_i5_268.7dpi_neg_shoot_1-3

source_name: Negative Control Shoot  7dpt

value: Negative


title: F2032

description: scRNA-seq


title: EOC44_pOvaR4_RNA1_seq3

description: The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: Epithelial progenitors E18.5

city: Kobe

first: Hirofumi

last: Kiyokawa

state: Hyogo

address: 2-2-3 Minatojima-minamimachi, Chuo-ku

department: Center for Biosystems Dynamics Research

country: Japan

institute: Riken

data_processing:
Basecalls performed using Illumina RTA 1.18.64 and the fastq files were generated by Cellranger v2.2.0 and bcl2fastq 2.19.0.316
signle cell RNA-seq reads were aligned to the mm10 genome reference using Cellranger v2.2.0 with default parameters
Seurat v2.3.4: the cells meeting any of the following criteria were omitted from further analyses for the quality control; <1,000 or >5,000 UMIs, > 7.5% of reads mapping to mitochondria genes, or EpCAM negative cells. For clustering, principal-component analysis was performed for dimension reduction. Top 15 principal components (PCs) were selected by using a permutation-based test implemented in Seurat and passed to t-Distributed Stochastic Neighbor Embedding (tSNE) for clustering visualization. To maintain a standard procedure for clustering, a value of 0.8 for the resolution was used
Genome_build: mm10
Supplementary_files_format_and_content: Filtered gene-barcode matrix of CellRanger output including sparse matrix (MEX), cellular barcodes (TSV), and gene list (TSV). Processed data with Seurat (Robj)

source_name: Trachea epithelial progenitors

extract_protocol:
To prepare single-cell suspensions of epithelial cells in 7 time points (E12.5, E13.5, E14.5, E16.5, E18.5, and 2months), the epithelial sheet was peeled off from mesenchymal tissue in developing trachea with a tungsten needle after the incubation with 175U/ml collagenase typeⅠ (Worthington Biochemical Corporation, CLS1) at 37℃ for 6 - 120 min. Single-cell suspensions were made through the incubation with Trypsin-EDTA (0.25%) (Thermo Fisher Scientific, 25200056) at 37℃ for 15 min, then loaded onto Chromium Single Cell A Chips (10X Genomics, PN-1000009) for the Chromium Single Cell 3′ Library v2 (10X Genomics, PN-120233) according to the manufacturer’s recommendations (10X Genomics)
Signle-cell suspensions were loaded onto Chromium Single Cell A Chips (10X Genomics, PN-1000009) for the Chromium Single Cell 3′ Library v2 (10X Genomics, PN-120233) according to the manufacturer’s recommendations (10X Genomics). Briefly, single-cell gel bead-in-emulsions (GEMs) were generated from loaded cell suspensions by a Chromium Controller instrument (10X Genomics). After performing GEM-reverse transcriptions (GEM-RTs), GEMs were harvested and the cDNAs were amplified and cleaned up with SPRIselect Reagent Kit (Beckman Coulter, B23318). Indexed sequencing libraries were constructed using Chromium Single Cell 3′ Library v2 (10X Genomics, PN-120233) for enzymatic fragmentation, end-repair, A-tailing, adaptor ligation, ligation cleanup, sample index PCR, and PCR cleanup. Libraries were sequenced on a HiSeq1500 (Illumina) to obtain a sequencing depth of around 50,000 reads per cells.
single cell RNA-seq using Chromium system (PolyA+ RNA)

tag: developmental stage


title: EOC44_pOvaR2_RNA1_seq3


title: F2030

description: scRNA-seq


title: Neutrophil untreated baseline donor 4 rep 2

city: Cambridge

first: Charlotte

last: Summers

address: Box 157, Cambridge Biomedical Campus

department: Department of Medicine

country: United Kingdom

institute: University of Cambridge

data_processing:
Sequences weresamples, trimmed to 36 bases starting fromposition 1, and mapped to 29 reference genomes using Bowtie
Transcripts were assembled
The expression levels of genes were estimated using Cufflinks
Reads were normalised to counts per million (cpm) for all conditions
Differential gene expression was calculated using edgeR (3.26.8)
Differentially expressed genes were selected for pathway analysis using Metascape (www.metascape.org)
Genome_build: hg38
Supplementary_files_format_and_content: Differential gene expression (DGE) excel files of three relevant comparisons

source_name: Neutrophils

growth_protocol: Peripheral venous blood was sampled from healthy volunteers who had provide written informed consent. Blood was anticoagulated with 3.8% sodium citrate (Martindale Pharmaceuticals) and peripheral blood neutrophils were subsequently purified using discontinuous plasma Percoll density gradient centrifugation under sterile conditions

extract_protocol:
Neutrophils were centrifuged for 3 minutes at 300 rpm onto PEN-membrane microscope slides. Laser capture microdissection technique was adapted to our system to identify and isolate populations of neutrophils based on their nuclear morphology. Microdissected neutrophils were lysed in RULT buffer supplemented with 1% of ß-mercaptoethanol (ß-ME), and this was followed by a brief vortex to homogenise the cells before storage at -80 °C for a maximum of three days. RNA extraction was performed according to Qiagen’s RNeasy UCP Micro Kit protocol (Qiagen) including an on-column DNase digest under clean laboratory conditions. The resultant RNA was divided into two equal technical replicates for the cDNA libraries preparation.
cDNA libraries were prepared according to Takara's instructions accompanying the SMART Seq Stranded Micro kit. Each step was optimisied to fit the sample input. Briefly, RNA was reverse-transcribed and converted to cDNA after 4 min of fragmentation. Illumina adapters and barcodes were added through ten cycles of PCR. The PCR products were then purified by immobilisation onto AMPure beads, ribosomal cDNA was depleted using mammalian-specific probes, and the remaining fragments were amplified with 10 additional PCR cycles before a final purification.

treatment_protocol: Human neutrophils were centrifuged and resuspended in 10% autologous serum (AS) in Hank’s Balanced Salt Solution (HBSS) (2.5 x 106 cells /mL) before stimulation with 300 μM captopril for 2h at 37°C in a shaker at 300 rpm for the hypersegmented and captopril conditions,untreated for 2h for age-matched condition or directly cytospinned onto microscope slides for the baseline condition.

tag: sample source

value: Primary Tissue

tag: donor

value: Donor 4

tag: phenotype

value: Not hypersegmented

value: untreated


title: EOC26_pOvaL2_RNA1_seq3

value: high-grade serous ovarian carcinoma

value: Neoadjuvant chemotherapy


title: Negative Control Shoot  7dpt rep 2 [7dpi_neg_shoot_1-2]

description: NS.1514.001.NEBNext_dual_i7_219---NEBNext_dual_i5_267.7dpi_neg_shoot_1-2


title: EOC44_pAdnL_RNA1_seq4


title: F2052

description: scRNA-seq

tag: cell type

tag: genotype


title: Epithelial progenitors E16.5

tag: strain


title: PA23 Shoot 24hpt rep 2 [24hpi_PA23_shoot_1-2]

description: NS.1514.001.NEBNext_dual_i7_237---NEBNext_dual_i5_285.24hpi_PA23_shoot_1-2

source_name: PA23 Shoot 24hpt

tag: tissue

tag: treatment

value: 24Hours post treatment


title: PA23 Shoot 24hpt rep 1 [24hpi_PA23_shoot_1-1]

description: NS.1514.001.NEBNext_dual_i7_236---NEBNext_dual_i5_284.24hpi_PA23_shoot_1-1

value: plant shoot


title: Neutrophil untreated baseline donor 4 rep 1


title: EOC26_pOvaL1_RNA2_seq3

tag: disease state

tag: anatomical location

tag: treatment strategy


title: EOC177_pOvaR2_RNA1_seq3


title: EOC177_pOvaR3_RNA1_seq3


title: Negative Control Shoot 24hpt rep 3 [24hpi_neg_shoot_1-3]

description: NS.1514.001.NEBNext_dual_i7_232---NEBNext_dual_i5_280.24hpi_neg_shoot_1-3

source_name: Negative Control Shoot 24hpt

tag: time of harvest


title: Epithelial progenitors E15.5

description:
E12-E18_barcodes.tsv
E12-E18_matrix.mtx
E12-E18_genes.tsv
E12-18_Seurat_Processed.Robj


title: Neutrophil untreated age-matched donor 4 rep 2

value: untreated, incubated for 2h


title: Negative Control Shoot  7dpt rep 1 [7dpi_neg_shoot_1-1]

description: NS.1514.001.NEBNext_dual_i7_218---NEBNext_dual_i5_266.7dpi_neg_shoot_1-1


title: Mature epithelial cells at 2M

value: Postnatal age 2 months

value: Tracheal epithelium


title: Epithelial progenitors E14.5


title: Neutrophil non-hypersegmented captopril-treated donor 4 rep 2

value: 300 μM captopril for 2h


title: EOC167_pOva1_RNA1_seq3

value: Primary


title: Negative Control Shoot 24hpt rep 2 [24hpi_neg_shoot_1-2]

description: NS.1514.001.NEBNext_dual_i7_231---NEBNext_dual_i5_279.24hpi_neg_shoot_1-2


title: Neutrophil untreated age-matched donor 4 rep 1


title: EOC177_pOvaL1_RNA1_seq3

value: Primary debulking surgery


title: Epithelial progenitors E13.5


title: EOC160_pOva_RNA1_seq6


title: Negative Control Shoot 24hpt rep 1 [24hpi_neg_shoot_1-1]

description: NS.1514.001.NEBNext_dual_i7_230---NEBNext_dual_i5_278.24hpi_neg_shoot_1-1


title: PA23 Shoot 24hpt rep 3 [24hpi_PA23_shoot_1-3]

description: NS.1514.001.NEBNext_dual_i7_238---NEBNext_dual_i5_286.24hpi_PA23_shoot_1-3

value: Pseudomonas chlororaphis PA23


title: EOC148_pOvaL5_RNA1_seq3


title: AGD affected gill biopsy at the lesion biological unmapped host data replicate 1

city: St Lucia

first: Natasha

last: Botwright

state: QLD

address: 306 Carmody Road

department: Agriculture and Food

country: Australia

institute: CSIRO

data_processing:
Illumina Casava1.8 software used for basecalling.
Reads were mapped to the Atlantic salmon genome with HISAT2 v2.1.0.
Reads counts were extracted using HTSeq v 0.7.2
Differential expression was completed with EdgeR
Genome_build: ICSASG_v2 Salmo salar
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each sample

organism:
Salmo salar
Paramoeba perurans

source_name: gill AGD lesion

growth_protocol: Neoparamoeba perurans were grown in a 1x MYB (1 g malt, 1 g yeast in 1 L sterile seawater) at 32 ppm

extract_protocol:
Rneasy mini kit (QIAGEN) with Turbo-DNase treatment
TruSeq RNA Sample Preparation Kit (Illumina)

treatment_protocol: Amoebic gill disease was induced with Neoparamoeba perurans at 100 cells/L

tag: type

value: tissue

value: gill AGD lesion

value: amoebic gill disease


title: AGD affected gill biopsy at the lesion biological unmapped host data replicate 3


title: No-cell environmental control donor 4

value: Primary Tissue

value: Donor 4

value: no cell


title: Epithelial progenitors E12.5


title: Neutrophil hypersegmented donor 4 rep 2

description: hypersegmented_vs_captopril_treated_all_ genes

value: Hypersegmented


title: AGD affected gill biopsy at the lesion biological unmapped host data replicate 2


title: Neutrophil non-hypersegmented captopril-treated donor 4 rep 1

value: Not hypersegmented


title: EOC148_pAdnL1_RNA1_seq3

value: high-grade serous ovarian carcinoma


title: Neutrophil hypersegmented donor 4 rep 1


title: Neutrophil untreated baseline donor 3 rep 1

value: Donor 3

value: untreated


title: pif457_ZT4_lowR:FR_H2AZ_rep3

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

description:
histone variant
Sample 109

library_source: genomic

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare; data extraction using bigWigAverageOverBed
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig; The file processed_data_file_descriptions.txt includes the samples used for bamCompare for each .bw file.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: light-grown seedlings

growth_protocol: light-grown seedlings were grown on Linsmaier and Skoog medium

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: low R:FR exposure

value: low R:FR

tag: chip antibody

value: H2A.Z (Active Motif, 39647)


title: Neutrophil untreated baseline donor 3 rep 2


title: pif457_ZT4_lowR:FR_H2AZ_rep2

description:
histone variant
Sample 108


title: EOC933_pPer1_RNA1_seq6

source_name: Tumor tissue from treatment-naïve patient

value: Peritoneum

value: Neoadjuvant chemotherapy


title: EOC148_pOvaL4_RNA1_seq3

value: Primary

value: Primary debulking surgery


title: EOC148_pAdnL3_RNA1_seq3


title: EOC649_pPer1_RNA_seq6


title: Neutrophil non-hypersegmented captopril-treated donor 3 rep 1

value: 300 μM captopril for 2h


title: pif457_ZT4_WL_H2AZ_rep2

description:
histone variant
Sample 106

value: white light


title: pif457_ZT4_WL_H2AZ_rep3

description:
histone variant
Sample 107


title: EOC495_pPerL_RNA1_seq4


title: een_ZT4_lowR:FR_H2AZ_rep3

description:
histone variant
Sample 105

value: een


title: PAD,exercise,Baseline Jos6119(9)(XP39-B)

type: RNA

city: Boston

first: Grace

last: Daher

address: 1 Joslin Place

institute: Joslin Diabetes Center

hyb_protocol: Following fragmentation, 12 ug of cRNA were hybridized for 16 hr at 45C on Human PrimeView Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Arrays scanned using the Affymetrix GeneChip Scanner

data_processing: RMA normalized using Expression Console from Affymetrix

label: biotin

source_name: skeletal muscle, gastrocnemius

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix 3' IVT protocol from 250 ug total RNA.

extract_protocol: Total RNA was extracted using Trizol

treatment_protocol: PAD patients were randomized into exercise or no exercise groups. The exercise group involved a 12-week training program where subjects walked on a treadmill and allowed to rest as needed for an hour. This treatment was performed three times a week. The no exercise group was left to their usual exercise.

value: PAD

tag: treatment group

value: exercise

tag: visit

value: Baseline

tag: subject


title: Neutrophil non-hypersegmented captopril-treated donor 3 rep 2

tag: sample source

value: Primary Tissue


title: PAD,exercise,Final Jos6122(4c)(XP34-F)

value: Final


title: PAD,no treatment,Baseline Jos5819(23) (XP29-V1)

value: no treatment


title: PAD,no treatment,Baseline Jos6118(8)(XP38-B)


title: PAD,exercise,Final Jos6120(10)(XP39-F)


title: een_ZT4_lowR:FR_H2AZ_rep2

description:
histone variant
Sample 104


title: PAD,exercise,Final Jos6117(7)(XP35-F)


title: Neutrophil untreated age-matched donor 3 rep 2

tag: donor

value: Donor 3

value: Not hypersegmented

value: untreated, incubated for 2h


title: Neutrophil hypersegmented donor 3 rep 1

tag: phenotype

value: Hypersegmented


title: EOC293_pPer1_RNA1_seq6a

description:
Internal control of EOC293_pPer1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: high-grade serous ovarian carcinoma

value: Peritoneum


title: PAD,no exercise,Final Jos6116(6)(XP33-F)

value: no exercise


title: EOC26_pPer2_RNA1_seq3

value: Neoadjuvant chemotherapy


title: WT_ZT4_lowR:FR_H2AZ_rep2

description:
histone variant
Sample 100

value: low R:FR

value: H2A.Z (Active Motif, 39647)


title: Neutrophil untreated age-matched donor 3 rep 1


title: EOC443_pPer2_RNA1_seq6


title: Neutrophil untreated baseline donor 2 rep 2

value: Donor 2

value: untreated


title: Neutrophil untreated baseline donor 2 rep 1


title: PAD,no exercise,Final Jos6114(4)(XP32-F)

value: PAD


title: PAD,no exercise,Baseline Jos6115(5)(XP33-B)

value: Baseline


title: Neutrophil non-hypersegmented captopril-treated donor 2 rep 2

value: Primary Tissue

value: 300 μM captopril for 2h


title: PAD,no treatment,Baseline Jos5820(25) (XP31-V1)

value: no treatment


title: een_ZT4_WL_H2AZ_rep3

description:
histone variant
Sample 103

value: white light

value: een


title: EOC372_pPer1_RNA1_seq5


title: EOC177_pPer1_RNA1_seq3

value: Primary debulking surgery


title: Neutrophil non-hypersegmented captopril-treated donor 2 rep 1

value: Not hypersegmented


title: Neutrophil hypersegmented donor 3 rep 2

value: Donor 3

value: Hypersegmented


title: Neutrophil untreated age-matched donor 2 rep 2

value: untreated, incubated for 2h


title: PAD,no exercise ,Baseline Jos6113(3)(XP32-B)

value: no exercise


title: EOC295_pPer_RNA1_seq6

value: high-grade serous ovarian carcinoma

value: Peritoneum

value: Neoadjuvant chemotherapy


title: een_ZT4_WL_H2AZ_rep2

description:
histone variant
Sample 102

value: H2A.Z (Active Motif, 39647)


title: WT_ZT4_lowR:FR_H3K9ac

description:
histone variant
Sample 95
processed data file is found on GSM4635405

value: low R:FR

value: H3K9ac(Active Motif, 39137)


title: EOC183_pPer_RNA1_seq4


title: WT_ZT4_lowR:FR_H2AZ_rep3

description:
histone variant
Sample 101


title: pif457_ZT4_lowR:FR_H3K9ac

description:
histone variant
Sample 97
processed data file is found on GSM4635407


title: EOC1005_pPer1_RNA_seq6


title: Healthy,no treatment,Baseline Jos5809(18) (XH12)

value: Healthy

value: Baseline


title: EOC742_pOme_RNA_seq6

value: Omentum


title: WT_ZT4_WL_H2AZ_rep3

description:
histone variant
Sample 99

value: white light


title: PAD,no treatment,Baseline Jos5805(14) (XP26)

value: PAD

value: no treatment


title: PAD,no treatment,Baseline Jos5821(26) (XP25-V1)


title: Neutrophil untreated age-matched donor 2 rep 1

value: Primary Tissue

value: Donor 2

value: Not hypersegmented


title: No-cell environmental control donor 3

value: Donor 3

value: no cell


title: EOC26_pPer1_RNA2_seq3

value: high-grade serous ovarian carcinoma


title: PAD,no treatment,Baseline Jos5804(12) (XP24)


title: WT_ZT4_WL_H2AZ_rep2

description:
histone variant
Sample 98


title: PAD,no treatment,Baseline Jos5803(11) (XP17)


title: PAD,no exercise,Baseline Jos5817(21) (XP07-V1)

value: no exercise


title: Healthy,no treatment,Baseline Jos5810(19) (XH13)


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_H3K9ac

description:
histone variant
Sample 92


title: pif457_ZT4_WL_H3K9ac

description:
histone variant
Sample 96


title: EOC167_pPer1_RNA1_seq3

value: Peritoneum

value: Neoadjuvant chemotherapy


title: WT_ZT4_WL_H3K9ac

description:
histone variant
Sample 94


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_H3K9ac

description:
histone variant
Sample 91

value: low R:FR


title: EOC376_pOme1_RNA1_seq5


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_H3K9ac

description:
histone variant
Sample 93

value: H3K9ac(Active Motif, 39137)


title: No-cell environmental control donor 1

value: Donor 1


title: Neutrophil hypersegmented donor 2 rep 1

value: Hypersegmented

value: 300 μM captopril for 2h


title: EOC26_pOme1_RNA1_seq3

value: Omentum


title: Neutrophil hypersegmented donor 2 rep 2


title: pif457_PIF7:PIF7:4xMYC_ZT4_lowR:FR_MYC_rep2_2

description:
transcription factor
P7_new_Cell.GEM_events.txt: PIF7 ChIP-seq peak identifcation with GEM, (PIF7 low R:FR Sample 2,86,87 vs WL Sample 1,88,89)
Sample 88

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare; ChIP-seq peak identification with GEM
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig; The file processed_data_file_descriptions.txt includes the samples used for bamCompare for each .bw file.

value: MYC (Cell Signaling Technology, 2276)


title: EOC44_pOme_RNA1_seq4

value: Primary debulking surgery


title: EOC218_pOme3_RNA1_seq3


title: No-cell environmental control donor 2

value: Primary Tissue


title: EOC423_pOme2_RNA1_seq5


title: pif457_PIF7:PIF7:4xMYC_ZT4_WL_MYC_rep3

description:
transcription factor
P7_new_Cell.GEM_events.txt: PIF7 ChIP-seq peak identifcation with GEM, (PIF7 low R:FR Sample 2,86,87 vs WL Sample 1,88,89)
Sample 87

value: white light


title: PAD,no treatment,Baseline Jos5802(10) (XP14)

value: PAD

value: no treatment

value: Baseline


title: pif457_PIF7:PIF7:4xMYC_WL_H3K9ac

description:
histone variant
Sample 90


title: PAD,no exercise,Final Jos5798_b(3) (XP04-V2)

value: Final


title: PAD,no treatment,Baseline Jos5801(8) (XP20)


title: PAD,no exercise,Final Jos5800(5) (XP27-V2)

value: no exercise


title: Healthy,no treatment,Baseline Jos5660(XH23)

value: Healthy


title: pif457_PIF7:PIF7:4xMYC_ZT4_WL_MYC_rep2

description:
transcription factor
P7_new_Cell.GEM_events.txt: PIF7 ChIP-seq peak identifcation with GEM, (PIF7 low R:FR Sample 2,86,87 vs WL Sample 1,88,89)
Sample 86

data_processing:
base-calling using RTA 2.7.7; alignment using Bowtie2 2.1.0; bam file comparison using deepTools2.0/bamCompare; ChIP-seq peak identification with GEM
Genome_build: TAIR10
Supplementary_files_format_and_content: txt


title: EOC443_pOme1_RNA1_seq5

description: The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: high-grade serous ovarian carcinoma

value: Neoadjuvant chemotherapy


title: EOC177_pOme3_RNA1_seq3


title: Neutrophil untreated baseline donor 1 rep 2

value: Not hypersegmented

value: untreated


title: Neutrophil non-hypersegmented captopril-treated donor 1 rep 2

value: Donor 1


title: Neutrophil non-hypersegmented captopril-treated donor 1 rep 1

value: 300 μM captopril for 2h


title: pif457_PIF7:PIF7:4xMYC_ZT4_lowR:FR_MYC_rep3

description:
transcription factor
P7_new_Cell.GEM_events.txt: PIF7 ChIP-seq peak identifcation with GEM, (PIF7 low R:FR Sample 2,86,87 vs WL Sample 1,88,89)
Sample 89

value: low R:FR


title: pif457_30min lowR:FR_rep1_RNA-seq III

description:
RNA expression
Sample 84
RNAseq_III.tsv

data_processing:
base-calling using RTA 2.7.9
alignment using STAR_2.6.0c
transcript quantification (TPM) using RSEM v1.3.0
Genome_build: TAIR10
Supplementary_files_format_and_content: tsv

extract_protocol:
Qiagen Rneasy Plant Mini kit
Libraries were prepared for sequencing using standard Illumina protocols

value: seedlings

value: 30min low R:FR


title: Neutrophil untreated baseline donor 1 rep 1

value: Primary Tissue


title: PAD,no exercise,Baseline Jos5799(4) (XP27-V1)


title: WT_30min lowR:FR_rep2_RNA-seq III

description:
RNA expression
Sample 83
RNAseq_III.tsv


title: pif457_30min lowR:FR_rep2_RNA-seq III

description:
RNA expression
Sample 85
RNAseq_III.tsv


title: EOC218_pOme1_RNA1_seq3

value: Omentum


title: EOC183_pOme1_RNA1_seq4


title: WT_30min lowR:FR_rep1_RNA-seq III

description:
RNA expression
Sample 82
RNAseq_III.tsv


title: PAD,no exercise,Baseline Jos5797(2) (XP04-V1)

value: PAD


title: pif457_WL_rep2_RNA-seq III

description:
RNA expression
Sample 81
RNAseq_III.tsv

value: white light


title: EOC177_pOme2_RNA1_seq3

value: Primary debulking surgery


title: EOC165_pOme1_RNA1_seq5


title: EOC160_pOme1_RNA1_seq5


title: PAD,no treatment,Baseline Jos5659(XP08-V1)

value: no treatment

value: Baseline


title: EOC839_pMes1_RNA1_seq5

value: Mesentery


title: PAD,no treatment,Baseline Jos5655(XP10-V1)


title: Healthy,no treatment,Baseline Jos5658(XH14)

value: Healthy


title: Neutrophil hypersegmented donor 1 rep 1

value: Hypersegmented


title: WT_WL_rep1_RNA-seq III

description:
RNA expression
Sample 78
RNAseq_III.tsv


title: S10_HelaCAS9_HIF1B_Hx_rep1

city: Oxford

first: David

middle: Robert

last: Mole

address: Roosevelt Drive, Headington

department: Nuffield Department of Medicine

institute: University of Oxford

description: ChIP

data_processing:
Illumina adaptor sequences were trimmed using Trimgalore (0.3.3) and reads were aligned to Genome Reference Consortium GRCh37 (hg19) using BWA (0.7.5a-r405). Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19)
Low quality mapping was removed (MapQ < 15) using SAMtools (0.1.19) and reads mapping to Duke Encode black list regions (http://hgwdev.cse.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeMapability) were excluded using BEDTools (2.17.0)
Duplicate reads were marked for exclusion using Picard tools (1.106) (http://picard.sourceforge.net/).
ChIP-seq peaks were identified using T-PIC (Tree shape Peak Identification for ChIP-Seq) and MACS (Model-based analysis of ChIP-Seq) in control mode
Peaks detected by both peak callers were filtered quantitatively using the total count under the peak to include only peaks that were above the 99.99th percentile of random background regions selected from the ENCODE DNASE II cluster (p-value < 0.0001).
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bigwig and bed files of called peaks

source_name: Hela cells_control_CRISPR

growth_protocol: Wildtype HeLa cells were grown on 15 cm dishes in complete DMEM media

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody for HIF-1alpha, HIF-2alpha or HIF-1beta.
Libraries were constructed according to Illumina protocols
Each sample was sequenced over two lanes, using 150bp paired-end reads

treatment_protocol: Control Hela cells were incubated in 1% oxygen for 6 hr

tag: cell line

value: HeLa

value: Wildtype

tag: ambient o2

tag: treatment time

value: 6 hours


title: Neutrophil untreated age-matched donor 1 rep 1

value: Donor 1

value: Not hypersegmented

value: untreated, incubated for 2h


title: Neutrophil hypersegmented donor 1 rep 2

value: 300 μM captopril for 2h


title: EOC177_pOme1_RNA1_seq3

value: high-grade serous ovarian carcinoma


title: EOC568_pMes1_RNA1_seq6a

description:
Internal control of EOC568_pMes1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: Neoadjuvant chemotherapy


title: S09_HelaCAS9_HIF2A_Hx_rep1

description: ChIP

tag: genotype


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_rep3_RNA-seq II

description:
RNA expression
Sample 77
RNAseq_II.tsv

tag: tissue

value: seedlings

tag: treatment

value: 30min low R:FR


title: S12_HelaCAS9_HIF2A_Hx_rep2

description: ChIP


title: EOC167_pOme1_RNA1_seq3

tag: disease state

tag: anatomical location

value: Omentum


title: pif457_WL_rep1_RNA-seq III

description:
RNA expression
Sample 80
RNAseq_III.tsv

value: white light


title: S13_HelaCAS9_HIF1B_Hx_rep2

description: ChIP


title: S11_HelaCAS9_HIF1A_Hx_rep2

description: ChIP


title: EOC204_pMes1_RNA1_seq5

tag: treatment strategy


title: PAD,exercise,Baseline Jos5656(XP01-V1_2)

value: PAD

value: exercise

value: Baseline


title: WT_WL_rep2_RNA-seq III

description:
RNA expression
Sample 79
RNAseq_III.tsv


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_rep2_RNA-seq II

description:
RNA expression
Sample 76
RNAseq_II.tsv


title: PAD,no treatment,Baseline Jos5657(XP21-V1)

value: no treatment


title: S03_HelaCAS9_HIFinput_Hx_rep1

description: input control

value: HeLa


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_rep1_RNA-seq II

description:
RNA expression
Sample 75
RNAseq_II.tsv


title: EOC742_pAsc_RNA_seq6

source_name: Ascites-derived cells from treatment-naïve patient

value: Ascites

value: Primary debulking surgery


title: PAD,no exercise,Final Jos5629(XP23-V2)

value: no exercise

value: Final


title: EOC566_pAsc_RNA1_seq4


title: Healthy,no treatment,Baseline Jos5653(XH02)

value: Healthy


title: Healthy,no treatment,Baseline Jos5652(XH29)


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_rep3_RNA-seq II

description:
RNA expression
Sample 74
RNAseq_II.tsv

value: 10min low R:FR


title: PAD,no exercise,Baseline Jos5818(22) (XP11-V1)


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_rep2_RNA-seq II

description:
RNA expression
Sample 73
RNAseq_II.tsv


title: PAD,no exercise,Baseline Jos5628(XP23-V1)


title: Healthy,no treatment,Baseline Jos5651(XH28)


title: K1-shctrl-2

description:
control
readcount_fpkm _K1

tag: cell type

value: papillary thyroid carcinoma cells

tag: shRNA

value: shctrl


title: Healthy,no treatment,Baseline Jos5654(XH10)

tag: treatment group


title: K1-shTBX3-2

description:
knock down TBX3 with shRNA
readcount_fpkm _K1


title: K1-shctrl-1

description:
control
readcount_fpkm _K1


title: EOC293_pAsc_RNA1_seq6a

description:
Internal control of EOC293_pAsc_RNA1_seq6b and EOC293_pAsc1_RNA1_seq5
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).

value: high-grade serous ovarian carcinoma


title: S08_HelaCAS9_HIF1A_Hx_rep1

description: ChIP

value: Wildtype

value: 6 hours

tag: chip antibody


title: K1-shTBX3-1


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_rep2_RNA-seq II

description:
RNA expression
Sample 70
RNAseq_II.tsv

value: seedlings

value: 5min low R:FR


title: EOC183_pMes_RNA1_seq4

value: Mesentery

value: Neoadjuvant chemotherapy


title: PAD,no exercise,Final Jos5625(XP12-V2)

value: PAD

tag: visit

tag: subject


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_rep3_RNA-seq II

description:
RNA expression
Sample 71
RNAseq_II.tsv


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_rep1_RNA-seq II

description:
RNA expression
Sample 72
RNAseq_II.tsv


title: EOC177_pAsc1_RNA1_seq3


title: EOC1129_pAsc1_RNA1_seq6a

description:
Internal control of EOC1129_pAsc1_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: EOC293_pAsc1_RNA1_seq5

description:
Internal control of EOC293_pAsc_RNA1_seq6a and EOC293_pAsc_RNA1_seq6b
The raw RNA sequencing data that these effective counts are based on have been deposited in the European Genome-phenome Archive under the accession code (EGAD00001006456, under the study EGAS00001004714).


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_rep1_RNA-seq II

description:
RNA expression
Sample 69
RNAseq_II.tsv


title: PAD,no exercise,Baseline Jos5626(XP18-V1)

value: Baseline


title: EOC1032_pAsc1_RNA1_seq3

value: Ascites


title: Craterostigma plantagineum plant 24H after rehydration replicate 1

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

data_processing:
FASTQ files were uploaded in CLC Genomics Workbench v8.5 discarding reads with poor quality (< Q30). Reads with nucleotide ambiguity were filtered from the remaining sequences. A TrueSeq Illumina adaptor trimming was performed to ensure that no adaptors and indexes remained in the read sequences. Finally, sequences with sizes below 35 bp were removed from the data.
The twelve libraries (sequenced five time each) were then mapped independently on the reference with a maximum hit number of 10, a minimum threshold of 80% length coverage and 80% identity, a mismatch cost of 2 (medium stringency) and a deletion/insertion cost of 3 (the highest stringency).
Expression values were calculated using the Reads per Kilobase transcript per Million reads (RPKM) method (Mortazavi et al. 2008). Contigs/genes, with less than 10 specifically mapped reads and/or with a mean RPKM value of the biological replicates lower than 0.1 in at least one of the libraries, were also removed from the dataset.
Contigs displaying a significant and differential expression were determined using an ANOVA test with 4 groups (i.e. 100%RWC, 60%RWC, 2%RWC and RW). A false discovery rate (FDR) correction was then applied with a stringent cut-off at 0.001 (Benjamini-Hochberg correction). Contigs that displayed a significant difference in expression (FDR p-value < 0.001and fold change > |2|) in, at least, one time-point were retained for the analysis.
Genome_build: Cp_transcriptome_assembly_V2.fa
Supplementary_files_format_and_content: Read count, Relative abundance (RPKM), statistical test, annotation

organism: Craterostigma plantagineum

source_name: Leaf sample

growth_protocol: C. plantagineum plants were grown in the incubators as previously described in Bartels et al. (1990). Briefly, plants were multiplied by vegetative propagation and grown in incubators under 60% relative humidity and a cycle of 14 hr light (60000 lx) at 24 ̊C and 8 hr dark at 20 ̊C.

extract_protocol:
Total RNA was isolated from the fine powder of frozen samples. The extraction was carried out using the RNeasy Plant Mini Kit (Qiagen) according to the manufacturer’s instructions. RNA concentration and quality and were examined using a Nanodrop ND-1000 spectrophotometer (Thermo Scientific) and a 2100 Bioanalyzer (Agilent), respectively.
The RNA integrity number (RIN) values of all extracted RNAs were above 8. SMARTER stranded RNA-Seq Kit was used to prepare libraries according to the manufacturer instructions (Takara). Libraries collected from the time-course experiment were pooled and sequenced to generate 75 bp paired-end reads using five consecutive runs of MiSeq 150 cycles Reagent kit (Illumina, San Diego, CA, USA).

treatment_protocol: For dehydration treatments, untreated/fresh plants (F) were gradually dried in pots until reaching partial dehydration (D1, 3-4 days) or complete desiccation (D2, 15 days). Desiccated plants were rehydrated by submerging the plants in water for 24 hr, then leaves were collected for 24-hr rehydrated samples (R1). For the 48-h rehydrated samples (R2), plants were removed from the water after 24 hr of submersion and left in the incubators under the normal conditions for an additional 24 hr before collecting. The relative water content (RWC) of leaves from partially dehydrated plants was determined as described previously (Bernacchia et al. 1996). Leaves from 6 to 9 untreated, partially dehydrated (approximately 60% relative water content), desiccated, and 24 hr/48 hr rehydrated plants were pooled and ground in liquid nitrogen to obtain experimental samples. Independent leaf pools were prepared and stored at -80 ̊C until use. To enrich the sequence pool used for the assembly of a reference transcriptome, additional leaf, root and flower samples were also collected from plants grown under the same conditions.

value: leaf

tag: water content

value: following rehydration


title: EOC1030_pAsc1_RNA1_seq4

value: Primary debulking surgery


title: Craterostigma plantagineum plant 24H after rehydration replicate 2


title: Craterostigma plantagineum plant 24H after rehydration replicate 3


title: pif457_PIF7:PIF7:4xMYC_WL_rep2_RNA-seq II

description:
RNA expression
Sample 67
RNAseq_II.tsv

value: white light


title: EOC740_iOvaR1_RNA1_seq5

source_name: Tumor tissue from post-chemotherapy patient

value: Primary


title: Craterostigma plantagineum plant at 2% relative water content Biological replicate 3


title: Neutrophil untreated age-matched donor 1 rep 2

tag: sample source

value: Primary Tissue

tag: donor

value: Donor 1

tag: phenotype

value: Not hypersegmented

value: untreated, incubated for 2h


title: Craterostigma plantagineum plant at 2% relative water content Biological replicate 1


title: EOC443_iOvaR1_RNA1_seq6

value: high-grade serous ovarian carcinoma


title: pif457_PIF7:PIF7:4xMYC_WL_rep1_RNA-seq II

description:
RNA expression
Sample 66
RNAseq_II.tsv

value: seedlings


title: EOC649_iOvaL1_RNA1_seq6


title: WT_2h_lowR:FR_2hWLrec_rep3_RNA-seq I

description:
RNA expression
Sample 65
RNAseq_I.tsv

value: 2hours low R:FR + 2h WL


title: pif457_PIF7:PIF7:4xMYC_WL_rep3_RNA-seq II

description:
RNA expression
Sample 68
RNAseq_II.tsv


title: WT_2h_lowR:FR_2hWLrec_rep2_RNA-seq I

description:
RNA expression
Sample 64
RNAseq_I.tsv


title: PAD,no exercise,Baseline Jos5624(XP12-V1)

value: no exercise


title: PAD,no exercise,Final Jos5623(XP11-V2)

value: Final


title: PAD,no exercise,Final Jos5627(XP18-V2)

value: PAD


title: EOC423_iOvaR1_RNA1_seq6

value: Neoadjuvant chemotherapy


title: WT_2h_lowR:FR_2hWLrec_rep1_RNA-seq I

description:
RNA expression
Sample 63
RNAseq_I.tsv


title: Craterostigma plantagineum plant at 60% relative water content Biological replicate 3


title: Craterostigma plantagineum plant at 60% relative water content Biological replicate 2


title: Craterostigma plantagineum plant at 2% relative water content Biological replicate 2


title: PAD,exercise,Final Jos5619(XP19-V2)

value: exercise


title: EOC26_iTubR1_RNA1_seq3


title: PAD,exercise,Baseline Jos5618(XP19-V1)

value: Baseline


title: Craterostigma plantagineum plant at 60% relative water content Biological replicate 1

value: leaf


title: PAD,exercise,Baseline Jos5620(XP06-V1)


title: WT_2h_lowR:FR_rep3_RNA-seq I

description:
RNA expression
Sample 62
RNAseq_I.tsv

value: 2hours low R:FR


title: PAD,exercise,Final Jos5615(XP03-V2)


title: PAD,no exercise,Final Jos5617(XP07-V2)


title: EOC183_iTub_RNA1_seq4


title: Craterostigma plantagineum plant at 100% relative water content Biological replicate 3


title: PAD,exercise,Final Jos5621(XP06-V2)


title: AGD affected spleen biological replicate 4

organism: Salmo salar

source_name: Spleen

tag: type

value: tissue

value: spleen

value: amoebic gill disease


title: PAD,exercise,Baseline Jos5614(XP03-V1)


title: EOC183_iOvaR_RNA1_seq4

value: Primary


title: Craterostigma plantagineum plant at 100% relative water content Biological replicate 2


title: WT_2h_lowR:FR_rep2_RNA-seq I

description:
RNA expression
Sample 61
RNAseq_I.tsv

tag: genotype


title: Craterostigma plantagineum plant at 100% relative water content Biological replicate 1

tag: tissue


title: AGD affected spleen biological replicate 3


title: WT_2h_lowR:FR_rep1_RNA-seq I

description:
RNA expression
Sample 60
RNAseq_I.tsv

tag: treatment


title: WT_WL_rep1_RNA-seq I

description:
RNA expression
Sample 57
RNAseq_I.tsv

value: white light


title: WT_WL_rep3_RNA-seq I

description:
RNA expression
Sample 59
RNAseq_I.tsv


title: Flower florets (FP) repeat3 (RNA-seq)

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

data_processing:
The RNA-seq reads with strand direction were aligned to the moso bamboo genome using tophat(Trapnell et al., 2009) with anchor length more than 8nt for spliced alignments. Only uniquely mapped reads  were retained for subsequent analysis.
Genome_build: P.heterocycla-v1.0; http://202.127.18.221/bamboo/down.php
Supplementary_files_format_and_content: bigwig files were generated using wig2bw program

organism: Phyllostachys edulis

source_name: Flower florets (FP)

growth_protocol: The leaf of flower moso bamboo (P. edulis) were collected from the GUANGXI province

extract_protocol:
Total RNAs were extracted from tissues with the RNAprep Pure Plant Kit (Tiangen, Cat. #DP441, China)
Strand-specific RNA-Seq libraries  were constructed mRNA-Seq library by dUTP method

treatment_protocol: No treatment

tag: developmental stage

value: reproductive growth

value: flower florets


title: EOC26_iOva2_RNA1_seq3

data_processing:
Read pairs were trimmed using Trimmomatic (version 0.33)
the first 12 and last 5 bases were cropped due to uneven per base sequence content
leading bases with a quality score lower than 20 and any trailing bases with a quality score lower than 30 were removed
the reads were scanned with a 3-base wide sliding window, cutting when the average quality per base dropped below 20
resulting sequences shorter than 20bp were discarded. Trimmed reads were aligned to the reference genome (GRCh38.d1.vd1) using STAR (version 2.5.2b), allowing up to 10 mismatches, and all alignments for a read were output
Genome_build: GRCh38.d1.vd1
Supplementary_files_format_and_content: Matrix table with effective counts

tag: disease state

value: high-grade serous ovarian carcinoma

tag: anatomical location


title: WT_WL_rep2_RNA-seq I

description:
RNA expression
Sample 58
RNAseq_I.tsv

value: seedlings


title: EOC530_iPer2_RNA1_seq3

value: Peritoneum

tag: treatment strategy


title: AGD affected spleen biological replicate 1


title: EOC1129_iOvaR1_RNA1_seq6


title: Healthy,no treatment,Baseline Jos5608(XH07)

value: Healthy

value: no treatment


title: EOC372_iPer1_RNA1_seq5

value: Neoadjuvant chemotherapy


title: PAD,exercise,Final Jos5613(XP01-V2)

value: PAD

value: exercise

value: Final


title: Flower florets (FP) repeat2 (RNA-seq)


title: AGD affected spleen biological replicate 2


title: Flower florets (FP) repeat1 (RNA-seq)


title: EOC740_iOme1_RNA1_seq6

value: Omentum


title: WT_IgG_VII

description:
control
Sample 56

data_processing:
base-calling using RTA 2.7.7
alignment using Bowtie2 2.1.0
bam file comparison using deepTools2.0/bamCompare
data extraction using bigWigAverageOverBed
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig; The file processed_data_file_descriptions.txt includes the samples used for bamCompare for each .bw file.

tag: antibodies

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: Naïve spleen biological replicate 3

value: tissue

value: spleen

value: Naive


title: Naïve spleen biological replicate 4


title: Flower leaf (FL) repeat3 (RNA-seq)

source_name: Flower leaf (FL)

value: leaf


title: EOC649_iOme1_RNA2_seq5


title: pif457_ZT4_lowR:FR_H2AZ

description:
histone variant
Sample 55

value: low R:FR

value: H2A.Z (Active Motif, 39647)


title: pif457_ZT4_WL_H2AZ

description:
histone variant
Sample 54

value: white light


title: EOC568_iOme1_RNA2_seq5

value: high-grade serous ovarian carcinoma


title: Naïve spleen biological replicate 2


title: een_ZT4_lowR:FR_H2AZ

description:
histone variant
Sample 53

value: seedlings


title: Flower leaf (FL) repeat2 (RNA-seq)

value: reproductive growth


title: EOC530_iOme4_RNA1_seq3


title: Naïve spleen biological replicate 1


title: Flower leaf (FL) repeat1 (RNA-seq)


title: Flower in the Next year (FLNY) repeat3 (RNA-seq)

source_name: Flower in the Next year (FLNY)


title: een_ZT4_WL_H2AZ

description:
histone variant
Sample 52


title: EOC530_iOme3_RNA1_seq3


title: EOC443_iOme2_RNA1_seq6


title: AGD affected head kidney biological replicate 3

source_name: Head kidney

value: head kidney

value: amoebic gill disease


title: Flower in the Next year (FLNY) repeat1 (RNA-seq)


title: AGD affected head kidney biological replicate 4


title: WT_ZT4_lowR:FR_H2AZ

description:
histone variant
Sample 51


title: WT_ZT4_WL_H2AZ

description:
histone variant
Sample 50


title: One year (OY) repeat3 (RNA-seq)

source_name: One year (OY)

value: vegetative growth


title: AGD affected head kidney biological replicate 1


title: EOC376_iOme1_RNA3_seq5

value: Neoadjuvant chemotherapy


title: One year (OY) repeat2 (RNA-seq)


title: AGD affected head kidney biological replicate 2


title: EOC26_iOme1_RNA1_seq3


title: Flower in the Next year (FLNY) repeat2 (RNA-seq)


title: Naïve head kidney biological replicate 4


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_H2AZ

description:
histone variant
Sample 48

value: 10min low R:FR


title: One year (OY) repeat1 (RNA-seq)


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_H2AZ

description:
histone variant
Sample 47

value: 5min low R:FR


title: EOC218_iOme6_RNA1_seq3

value: Omentum


title: EOC218_iOme4_RNA1_seq3


title: Naïve head kidney biological replicate 3

value: tissue


title: pif457_PIF7:PIF7:4xMYC_WL_H2AZ

description:
histone variant
Sample 46


title: EOC218_iOme2_RNA1_seq3


title: Naïve head kidney biological replicate 2


title: Three week seedling (TW) repeat2 (RNA-seq)

source_name: Three week seedling (TW)


title: Three week seedling (TW) repeat3 (RNA-seq)


title: WT_IgG_VI

description:
control
Sample 45

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: EOC183_iOme1_RNA1_seq4


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_H2AZ

description:
histone variant
Sample 49

value: 30min low R:FR


title: Three week seedling (TW) repeat1 (RNA-seq)

value: leaf


title: EOC218_iMes3_RNA2_seq3

value: Mesentery


title: WT_MYC

description:
control
Sample 44

value: MYC (Cell Signaling Technology, 2276)


title: EOC218_iMes2_RNA1_seq3


title: AGD affected gill biopsy at the lesion biological replicate 2

source_name: Gill

value: gill


title: AGD affected gill biopsy distal to the lesion biological replicate 4


title: AGD affected gill biopsy distal to the lesion biological replicate 3


title: EOC933_iMes1_RNA1_seq5

value: high-grade serous ovarian carcinoma


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_MYC_rep1

description:
transcription factor
Sample 40

value: seedlings


title: pif457_PIF7:PIF7:4xMYC_10min_lowR:FR_MYC_rep2

description:
transcription factor
Sample 41


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_MYC_rep1

description:
transcription factor
Sample 42


title: EOC183_iMes2_RNA1_seq4


title: N2 ech-6+P-80 rep1

city: Lausanne

first: Yasmine

middle: J

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

country: Switzerland

institute: EPFL

description: CPM_s_013_allMerged_N2 ech6+P-80

data_processing:
Reads were subjected to quality control FastQC trimmed using Trimmomatic v0.32
Reads were aligned to the C. elegans genome obtained from Ensembl, wbcel235.v91 using HISAT2 v2.0.4
Counts were obtained using HTSeq (v0.6.1, default parameters) using the corresponding GTF taking into account the directions of the reads.
Statistical analyses were performed using the edgeR and limma/voom R packages.
Genome_build: the C. elegans genome obtained from Ensembl, wbcel235.v91 using HISAT2 v2.0.4
Supplementary_files_format_and_content: CSV files include CPM values for each Sample

organism: Caenorhabditis elegans

source_name: Whole worms

extract_protocol:
Approximately 500 day-1 adult worms were collected in quadruplicates for each treatment and RNA was harvested using Trizol reagent. Samples were processed for Illumina using the NEBNext Ultra Directional RNA Library Prep Kit (NEB #E7420) according to manufacturer’s description. was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared and sequenced with the illumina platform by Genome Scan (Leiden, Netherlands).

tag: strain

value: ech-6 RNAi

tag: agent

value: P-80 supplementation

value: whole worms

tag: age

value: Day1 adult


title: pif457_PIF7:PIF7:4xMYC_30min_lowR:FR_MYC_rep2

description:
transcription factor
Sample 43


title: N2 ech-6+P-80 rep4

description: CPM_s_016_allMerged_N2 ech6+P-80


title: AGD affected gill biopsy at the lesion biological replicate 1

value: amoebic gill disease


title: AGD affected gill biopsy at the lesion biological replicate 3


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_MYC_rep2

description:
transcription factor
Sample 39


title: N2 ech-6 rep4

description: CPM_s_012_allMerged_N2 ech6


title: N2 ech-6+P-80 rep3

description: CPM_s_015_allMerged_N2 ech6+P-80


title: AGD affected gill biopsy distal to the lesion biological replicate 2


title: EOC183_iMes1_RNA1_seq4

value: Neoadjuvant chemotherapy


title: AGD affected gill biopsy distal to the lesion biological replicate 1


title: N2 ech-6 rep3

description: CPM_s_011_allMerged_N2 ech6


title: pif457_PIF7:PIF7:4xMYC_5min_lowR:FR_MYC_rep1

description:
transcription factor
Sample 38

value: 5min low R:FR


title: EOC26_iAsc1_RNA1_seq3

source_name: Ascites-derived cells from post-chemotherapy patient

value: Ascites


title: N2 ech-6 rep2

description: CPM_s_010_allMerged_N2 ech6


title: Naïve head kidney biological replicate 1

value: tissue

value: head kidney

value: Naive


title: N2 ech-6+P-80 rep2

description: CPM_s_014_allMerged_N2 ech6+P-80


title: EOC218_iMes1_RNA1_seq3


title: EOC1129_iAsc1_RNA1_seq6


title: pif457_PIF7:PIF7:4xMYC_WL_MYC_rep2

description:
transcription factor
Sample 37

source_name: light-grown seedlings

value: white light


title: Naïve gill biological replicate 4


title: N2 ech-6 rep1

description: CPM_s_009_allMerged_N2 ech6


title: input shDKC1

city: Guangzhou

first: guangyan

last: kan

address: 651 Dongfeng East Road

institute: Sun Yat-sen University Cancer Center

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36), and the clean reads undergone rRNA deleting through RNAcentral to get effective reads.Genomic alignment (hg19 from UCSC genome browser) was using Tophat(version:2.0.13) to get uniquely mapping reads.
RIPseeker was employed to perform peak calling.Then using Homer(version:4.8) to annotate the Peaks.The nucleotides in Peaks region were used for detection of the consensus motif by DREME (version:4.11.1) and MEME(version:4.11.1). Motif central enrichment was performed by CentriMo (version:4.11.1). Differential peak enrichment was determined by Pyicoenrich(version:2.0.7).
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using DeepTools; Scores represent DKC1 binding level.

source_name: colorectal cancer cells

extract_protocol:
DKC1 binding RNA was isolated with DKC1 antibody from whole cell lysates.
Antibody immunoprecipitation RNA was quality control with Qubit (Thermo Fisher Scientifc,USA) and Agilent 2200 TapeStation (Agilent Technologies, USA). Then, RNA was used for library building following NEBNext® Ultra™ RNA Library Prep Kit protocol for Illumina (NEB, USA). The final library product was assessed with Agilent 2200 TapeStation and Qubit and then sequenced on Illumina platformat pair end reads for 150bp.

treatment_protocol: DLD-1 cells were infected by DKC1 shRNA lentivrirus or shCTL lentivrirus and puromycin selection went for at least 7days to get the stable knockdown cells.

tag: cell line

tag: rip antibody

value: DKC1 knockdown


title: Naïve gill biological replicate 3


title: pif457_PIF7:PIF7:4xMYC_WL_MYC_rep1

description:
transcription factor
Sample 36

value: MYC (Cell Signaling Technology, 2276)


title: input shCTL

value: control


title: Naïve gill biological replicate 2

value: gill


title: N2 EV+P-80 rep2

description: CPM_s_006_allMerged_N2 EV+P-80


title: WT_H2AZ_2h_lowR:FR_2hWLrec_rep1

description:
histone variant
Sample 33

value: seedlings

value: 2hours low R:FR + 1h WL

value: H2A.Z (Active Motif, 39647)


title: pif457_H2AZ_2h_lowR:FR_2hWLrec_rep1

description:
histone variant
Sample 34


title: WT_IgG_V_rep1

description:
control
Sample 35

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: N2 EV+P-80 rep3

description: CPM_s_007_allMerged_N2 EV+P-80

value: P-80 supplementation

value: whole worms

value: Day1 adult


title: DKC1-shDKC1

value: DKC1(santa cruz, sc-373956)


title: pif457_H2AZ_2h_lowR:FR_rep1

description:
histone variant
Sample 32

value: 2hours low R:FR


title: Nf1 KO, Pten KO, EGFRvIII overexpression [WGS]

city: Edinburgh

first: Ben

last: Southgate

address: Little France Dr

institute: University of Edinburgh

description:
BL6_NPE.cnr.txt
CNV_BL6_NPE.vcf
SNV_BL6_NPE.vcf
SV_BL6_NPE.vcf

data_processing:
Library strategy: WGS
Whole genome sequencing (WGS) of BL6 WT, NPE and NPE-IE lines was completed using the best practises WGS paired cancer normal pipeline bcbio (bcbio-nextgen version 1.2.3) (https://github.com/bcbio/bcbio-nextgen).
Adaptors were trimmed with the read trimmer Atropos (version 1.1.25) and aligned to the mm10 genome using the aligner Bowtie2 (version 2.3.5.1).
PCR duplicates were marked with samblaster (version 0.1.25).
GATK base quality score recalibration was completed on the aligned BAM files (gatk version 3.8).
Single nucleotide variant (SNV) calling was completed using an ensemble-based approach using VarDict (version 1.6), Strelka2 (version 2.9.10), and Mutect2 (gatk version 3.8) for somatic calling, and freebayes (version 1.1.0.46), GATK HaplotypeCaller (gatk version 3.8), and Strelka2 (version 2.9.10) for germline calling. Germline calls were used to filter final somatic calls. Variants were combined and included in the final call if present in 2 out of 3 variant callers (bcbio min_allele_fraction: 2).
Variant calls were targeted at exonic regions as defined by the R package TxDb.Mmusculus.UCSC.mm10.knownGene (version 3.4.4).
Structural variants (SVs) were called with Manta (version 1.6.0). Structural variants that did not pass default Manta filters were removed.
Copy number variants (CNVs) were assessed with CNVkit (version 0.9.6) using the “wgs” and "clonal" option, targeted at transcript regions as defined by the R package TxDb.Mmusculus.UCSC.mm10.knownGene. Copy number regions were filtered using confidence interval filtering.
Final SNV and SVs were annotated using the R packages VariantAnnotation (version 1.34.0), TxDb.Mmusculus.UCSC.mm10.knownGene, and BSgenome.Mmusculus.UCSC.mm10.masked (version 1.3.99). Following annotation SNV calls were filtered again to remove those within noncoding regions, those that were synonymous, as well as those with an allele frequency (AF) < 0.25.
Final, filtered, SNV, SV, and CNV calls were overlapped with known cancer driver genes as defined by the COSMIC gene census (https://cancer.sanger.ac.uk/census), converted to mouse homologs via MGI batch query (http://www.informatics.jax.org/batch).
Genome_build: mm10
Supplementary_files_format_and_content: VCF files for copy number variant (CNV), single nucleotide variant (SNV), and structural variant (SV) calls.
Supplementary_files_format_and_content: Copy number ratios from CNVkit for BL6 NPE, and BL6 NPE IE samples

source_name: Mouse Neural Stem Cell

growth_protocol: All cell lines were maintained in standard NSC media: serum-free basal medium supplemented with N2 and B27 (Life Technologies), laminin (Cultrex, 2 mg/ml) and growth factors EGF and FGF2 (Peprotech, 10 ng/ml).

extract_protocol:
DNA was extracted from cells using the Qiagen DNeasy Blood and Tissue kit
Next Generation sequencing libraries were prepared using Illumina SeqLab specific TruSeq PCR-Free High Throughput library preparation kits in conjunction with the Hamilton MicroLab STAR and Clarity LIMS X Edition, following standarad protocols. The gDNA samples are normalised to the concentration and volume required for the Illumina TruSeq PCR-Free library preparation kits then sheared to a 450bp mean insert size using a Covaris LE220 focused-ultrasonicator. The inserts are blunt ended, A-tailed, size selected and the TruSeq adapters are ligated onto the ends.

tag: cell type

value: Mouse Neural Stem Cell

value: Cell line

value: Nf1-/- Pten-/- EGFRvIII


title: N2 EV+P-80 rep1

description: CPM_s_005_allMerged_N2 EV+P-80


title: DKC1-shCTL


title: Nf1 KO, Pten KO, EGFRvIII overexpression, Twice Tumour derived BL6 mouse, Immune evasive [WGS]

description:
BL6_NPE_IE.cnr.txt
CNV_BL6_NPE_IE.vcf
SNV_BL6_NPE_IE.vcf
SV_BL6_NPE_IE.vcf


title: WT_H2AZ_2h_lowR:FR_rep1

description:
histone variant
Sample 31


title: PΔ6 stationary rep P4b

city: Norman

first: Justyna

middle: Weronika

last: Adamiak

state: OK

address: 101 Stephenson Parkway

department: Chemistry and Biochemistry

institute: University of Oklahoma

data_processing:
Raw data for each sample was analyzed using CLC Genomics Workbench version 12.0.1 software (QIAGEN Aarhus, Denmark), with default settings, based on their proprietary algorithms.
Pairwise comparison of the expression results was performed using the total mapping results for deletion mutant vs wild type.
Differential gene lists were created with 2-fold expression cutoff and significant p-values of <0.05 to identify genes that were up- or down-regulated under each condition.
Genome_build: Raw sequence reads were mapped to the Pseudomonas aeruginosa PAO1 genome (Accession# AE004091.2)
Supplementary_files_format_and_content: txt files with RPKM values for each sample
Supplementary_files_format_and_content: fastq raw data for each sample

organism: Pseudomonas aeruginosa

source_name: bacterial cells

growth_protocol: Cells were grown in LB broth until mid-exponential phase (OD600 = 0.5-0.6) and stationary phase (OD600 = 2.0)

extract_protocol:
Total RNA was isolated from cells using hot phenol method. High quality total RNA was further processed by removing 23S and 16S rRNAs using the the Illumina Ribo-Zero Plus rRNA Depletion kit (Illumina, USA). Final concentrations and purity grades of the samples were determined using Bioanalyzer 2100 (Agilent, USA). Samples with the amount at least 0.5-1 µg were used for library construction and RNA sequencing.
Libraries of depleted RNA were prepared using the Illumina TruSeq RNA LT v2 kit according to the manufacturer's instructions. RNA libraries were prepared for sequencing using Illumina protocols

value: knockout mutant


title: N2 EV rep4

description: CPM_s_004_allMerged_N2 EV


title: WT BL6 [WGS]

value: WT


title: PΔ6 stationary rep P4a


title: N2 EV rep3

description: CPM_s_003_allMerged_N2 EV


title: pif457_H2AZ_30min_lowR:FR_rep1

description:
histone variant
Sample 30

value: 30min low R:FR


title: N2 EV+P-80 rep4

description: CPM_s_008_allMerged_N2 EV+P-80


title: Naïve gill biological replicate 1

value: tissue

value: Naive


title: N2 EV rep2

description: CPM_s_002_allMerged_N2 EV


title: WT_H2AZ_30min_lowR:FR_rep1

description:
histone variant
Sample 29

value: seedlings


title: PΔ6 exponential rep P2b


title: PAO1 WT stationary rep P3b

value: parent


title: PAO1 WT stationary rep P3a


title: pif457_H2AZ_15min_lowR:FR_rep1

description:
histone variant
Sample 28

value: 15min low R:FR

value: H2A.Z (Active Motif, 39647)


title: m6A-seq_shNC_input

city: Beijing

first: Dali

last: Han

state: 北京

address: Da-Tun Road

institute: Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences

data_processing:
For RNA-seq, adaptor and low quality bases were trimmed by Trim Galore version 0.6.0 with command "trim_galore -q 20 --three_prime_clip_R1 3 --clip_R2 3 --phred33 --illumina --stringency 3 --paired --length 36". Ribosomal RNA was removed by Bowtie2 version 2.3.5 and reads didn't align concordantly were retained. Clean reads were then aligned to mm10 genome with STAR version 2.7.0f in default setting. Only alignments with mapping quality more than 20 were used for downstream analysis. Aligned reads were converted into bigwig format based on BPM normalization in 1bp bin size with deepTools and visualized with Integrative Genomics Viewer (IGV).
For ATAC-seq, adaptor and low-quality bases were trimmed by Trim Galore version 0.6.0 with command "trim_galore -q 20 --phred33 --nextera --stringency 3 --paired". Clean reads were then aligned to mm10 genome by Bowtie2 version 2.3.5 with parameter "-X 2000 --no-mixed --no-discordant" and alignments with mapping quality more than 20 were retained. Picard toolkit was used to remove duplicates and reads mapped to blacklist regions were discarded. Fragments below 100 bps were considered as originated from nucleosome-free regions and retained for downstream analysis. Reads were then converted into bigwig format based on BPM normalization in 1bp bin size with deepTools and visualized with IGV. MACS2 v2.1.3 was applied to call peak with parameter "-g mm --nomodel --shift -100 --extsize 200 -f BAM --keep-dup all"
For m6A-seq, basic sequencing quality control, sequence alignment, and visualization were performed as described in RNA-seq data analysis. m6A peaks were called by exomePeak v2.16.0.
Genome_build: mm10
Supplementary_files_format_and_content: peaks, gene counts

growth_protocol: B16-OVA-shNC or shFto cells were cultured with complete DMEM medium containing 10% FBS, 1% NEAA, 1% HEPES and 5μg/mL puromycin. Naïve CD8+ OTI T cells were purified using EasySep Mouse CD8+ T Cell Isolation Kit (Stemcell). CD8+ T cells for sequencing were co-cultured with B16-OVA-shNC or shFto tumor cells for 8 hours in RPMI 1640 medium containing 10%FBS, 0.1mM NEAA, 1% HEPES, 2 mM L-glutamine and 50U IL-2.

extract_protocol:
For RNA-seq, total RNAs were extracted using Trizol reagent (invitrogen). For m6A-seq, total RNAs in tumor cells were extracted using Trizol and polyadenylated RNAs were purified using the Dynabeads mRNA Purification Kit (Invitrogen). RNAs were fragmented into ~100-nucleotide-long fragments by using 10X Fragmentation Reagent(Invitrogen) at 94℃ for 45s and stopped by the 10X Stop Solution(Invitrogen). EpiMark N6-methyladenosine enrichment kit (NEB E1610S) was used for m6A immunoprecipitation (m6A-IP) to enrich the m6A marked RNAs followed by RNA extraction by Trizol. For ATAC-seq, 5 × 104 B16-OVA-shNC or shFto cells were first lysed with ATAC RSB buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin on ice for 3 minutes. Then cell lyates were centrifuged to collecte the cell nuclei. After a wash step, the cell nuclei were ready for library construction.
For RNA-seq and m6A-seq, the library construction was performed with SMARTer Stranded Total RNA-Seq Kit (Takara). For ATAC-seq, the libraries were constructed by using TruePrep DNA Library Prep Kit V2 for illumine (Vazyme).

treatment_protocol: For m6A-seq, B16-OVA-shNC or shFto cells were treated with DMSO and shNC cells in Dac51 group were treated with 5μM Dac51 for 48 hours.  CD8+ T cells used for sequencing were co-cultured with B16-OVA-shNC or shFto for 8 hours and then sorted by BD Aria III.

tag: strain background

value: shNC

value: B16-OVA (melanoma)

value: DMSO


title: WT_H2AZ_15min_lowR:FR_rep1

description:
histone variant
Sample 27


title: m6A-seq_shNC_IP


title: pif457_H2AZ_WL_rep1

description:
histone variant
Sample 26

value: white light


title: PΔ6 exponential rep P2a


title: PAO1 WT exponential rep P1b


title: WT_H2AZ_WL_rep1

description:
histone variant
Sample 25


title: N2 EV rep1

description: CPM_s_001_allMerged_N2 EV

value: whole worms

value: Day1 adult


title: PAO1 WT exponential rep P1a


title: m6A-seq_Dac51_IP


title: m6A-seq_Dac51_input


title: m6A-seq_shFto_input

value: shFto


title: WT_IgG_IV

description:
control
Sample 24

value: mouse IgG (Jackson ImmunoResearch, 015-000-003)


title: ATAC-seq_shNC_rep3


title: ATAC-seq_shNC_rep2


title: WT_H2AZ_2h_lowR:FR_1hWLrec

description:
histone variant
Sample 22

value: 2hours low R:FR + 1h WL


title: WT_H2AZ_2h_lowR:FR_2hWLrec

description:
histone variant
Sample 23

value: 2hours low R:FR + 2h WL


title: m6A-seq_shFto_IP


title: WT_H2AZ_30min_lowR:FR

description:
histone variant
Sample 20

value: 30min low R:FR


title: ATAC-seq_shNC_rep1


title: WT_H2AZ_WL

description:
histone variant
Sample 19

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.245
Libraries were prepared for sequencing using standard Illumina protocols


title: ATAC-seq_shFto_rep3


title: ATAC-seq_shFto_rep2


title: WT_IgG_III

description:
control
Sample 18


title: ATAC-seq_shFto_rep1


title: Sbf_20

city: Utrecht

first: Jeroen

last: den Hertog

state: Utrecht

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: See plate_layout_sbf_20 for which cells are double (D) and single (S)

data_processing:
Well numbers (X001-X384) in *.TranscriptCounts.tsv refer to well numbers of the 384-well plate in the following order: A1 to A24 - B1 to B24 - until P24.
The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded.
During sequencing, Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell
The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases. Read 1 was not used for quantification.
cell specific barcodes are specified in the file “cel-seq2_barcodes.csv”
Genome_build: zV9 Danio Rerio
Supplementary_files_format_and_content: transcript counts

organism: Danio rerio

source_name: caudal hematopoietic tissue

extract_protocol:
Cells were sorted into 384 well plates. All wells underwent Cel-Seq2 protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

value: caudal hematopoietic tissue

value: 5 dpf

tag: sort day (see plate layout)

value: day 6

tag: genotype or treatment (see plate layout)

value: wild type


title: Sbf_21

description: See plate_layout_sbf_21 for which cells are double (D) and single (S)


title: WT_H2AZ_2h_lowR:FR

description:
histone variant
Sample 21

value: seedlings

value: 2hours low R:FR

tag: genotype


title: WT_H2AZ_ZT20_lowR:FR

description:
histone variant
Sample 17

tag: tissue

value: low R:FR

value: H2A.Z (Active Motif, 39647)


title: WT_contra_rep3

city: Tucson

first: Danielle

last: Becktel

state: AZ

address: 1656 E Mabel Street, Rm 214

department: Immunobiology

institute: University of Arizona

data_processing:
Sequenced reads were demultiplexed using bcl2fastq v2.19 and trimmed of their indexing adaptors using Trimmomatic v0.32
Trimmed reads were aligned to GRCm38 reference genome using STAR v2.5.2b
Gene expression was calculated using htseq-count function in the HTSeq python tool
Genes were annotated using BioMart database
Differentially expressed genes (>2-fold and FDR-adjusted p-value <0.05) were identified by DESeq2
Genome_build: mouse reference genome GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each gene

source_name: Brain

extract_protocol:
Fresh brain tissue dissected from WT mice was immersed in RNAlater (Invitrogen, Cat. No. AM7020). Samples were assessed for quality with an Advanced Analytics Fragment Analyzer (High Sensitivity RNA Analysis Kit, Cat. No. DNF-491/User Guide DNF-491-2014AUG13) and quantity with a Qubit RNA HS Assay Kit (Cat. No. Q32852).
Given satisfactory quality (RNA integrity number >8) and quantity, samples were used for library construction with the TruSeq Stranded mRNA Library Prep Kit from Illumina (Cat. No. 20020595), as well as the KAPA Dual-Indexed Adapter Kit from Roche (Cat. No. 8278555702).

tag: background strain

value: 3 months

value: Contralateral cortex

tag: time point

value: 7 weeks


title: WT_contra_rep2


title: WT_contra_rep1


title: RNA-seq_shNC_rep2

description: processed data file: RNA-seq_gene_count.csv

value: shNC

value: B16-OVA (melanoma)


title: RNA-seq_shNC_rep3


title: RNA-seq_shNC_rep1


title: yhfW6hBR2

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

data_processing:
mapping of reads was done using: bowtie2  --local using Escherichia coli K12 as template genome
SAM files were converted to BAM files using SAM tools
BAM files were converted to RPKM values using BED-tools
Count values were normalized using the TMM (Trimmed Median Mean) method in T-REx (doi: 10.1186/s12864-015-1834-4)
Genome_build: Bacillus subtilis subsp. subtilis str. 168, circular BCT 15-JAN-2018, AL009126.3
Supplementary_files_format_and_content: Tab delimited text file

organism: Bacillus subtilis

source_name: Δyhfw (bioreplicate 2)

growth_protocol: The following competence medium was used: 18 ml demineralized water, 2 ml 10× competence medium stock [0.615 M K2HPO4•3H2O, 0.385 M KH2PO4, 20% glucose, 10 ml 300 mM Tri‐Na‐citrate, 1 ml 2% ammonium ferric citrate, 1 g casein hydrolysate (oxoid), 2 g potassium glutamate], 100 μl 2 mg ml-1 tryptophan, 67 μl 1 M MgSO4 (Spizizen, 1958; Konkol et al., 2013). Strains were streaked out from -80 stocks on Luria Bertani (LB) agar plates with antibiotics and grown overnight at 37°C. A single colony (sc) was diluted 1000× in PBS or 1× Spizizen solution 100 μl of the sc colony solution was added to 20 ml medium in 100 ml Erlenmeyer flasks and grown at 37°C 220 rpm. Exponential/early stationary overnight cultures were diluted to an OD600 of 0.05 in 20 ml medium without antibiotics. Antibiotic concentrations used were chloramphenicol (cm) 5 μg ml-1, spectinomycin (sp) 50 μg ml-1, erythromicin (ery) 0.5 μg ml-1, and lincomycin 12.5 μg ml-1. Growth conditions in CDSM (Vasantha and Freese, 1980; Hageman et al., 1984) + alanine (10 mM) + tryptophan 1 mM. Strains were grown overnight at 37°C on LB agar + chloramphenicol (control) or chloramphenicol + erythromycin (BFA1698), single colonies were diluted and incubated in 2 ml LB 37°C 220 rpm in test tubes. The diluted cultures were mid‐exponential after overnight growth. The overnight cultures were diluted to OD600 0.05 in 2 ml CDSM + alanine + tryptophan and chloramphenicol (control) or chloramphenicol + erythromycin (BFA1698) in test tubes and grown to mid‐exponential growth at 37°C 220 rpm. Cultures were diluted to OD600 0.1 in 100 μl CDSM + alanine + tryptophan without antibiotics in a 96 wells plate and grown at 37°C, 240 rpm, 10 min measuring interval for 20 h in a Thermo Fisher Varioskan Lux. The remainder of the cultures was grown for 24 h after which the cultures were kept in the dark at 4°C without shaking for 4 days. Spores were harvested by centrifugation at 10 000 g and washed 3× with double distilled water. The spore crops were diluted to the same OD and heated for 10 min at 80°C and dilutions were plated on LB agar with chloramphenicol and grown overnight at 37°C. Colonies were counted and measured with ImageJ. Statistics were done in Sigmaplot using a Rank Sum Test.

extract_protocol:
Cell were lysed using glassbead and totRNA was isolated using phenol/chloroform and ethanol precipitation
Standard library preparation protocol of BGI for Illumina RNA-Seq

treatment_protocol: Bacillus subtilis 168 PcomG‐gfp chloramphenicol resistant variant PcomG‐gfp was grown as described in growth conditions Samples for protein analysis and RNA‐seq analysis were taken at 5.5 and 6.5 h respectively. One hour of sorting through FACS yields approximately 3 × 10^7 GFP‐negative (non‐competent cells) and 1.5 × 10^7 GFP‐positive (competent) cell

value: str 168

tag: genotype/variation

value: {delta}yhfw


title: Healthy,no treatment,Baseline Jos5611(XH19)

data_processing: RMA normalized using Expression Console from Affymetrix

source_name: skeletal muscle, gastrocnemius

tag: phenotype

value: Healthy

tag: treatment group

value: no treatment

tag: visit

value: Baseline

tag: subject


title: WT_H2AZ_ZT16_lowR:FR

description:
histone variant
Sample 15

tag: treatment

tag: antibodies


title: WT_infarct_rep2

tag: age

value: Stroke infarct


title: PB_02

data_processing:
Well numbers (X001-X384) in *.TranscriptCounts.tsv refer to well numbers of the 384-well plate in the following order: A1 to A24 - B1 to B24 - until P24.
The right mate of each read pair was mapped to the ensemble of all gene loci. Reads mapping to multiple loci were discarded.
During sequencing, Read 1 was assigned 26/75* base pairs and was used for identification of the Illumina library barcode, cel barcode and UMI. R2 was assigned 60/75* base pairs and used to map to the reference transcriptome of Zv9 with BWA (Anders and Huber, 2010). Data was demultiplexed as described in Grün et al. 2014. Mapping and generation of count tables was automated using the MapAndGo script1. https://github.com/anna-alemany/transcriptomics/tree/master/mapandgo
Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction. *coutc* files contain number of reads, *coutb* files contain number of observed UMI and *coutt* files contain number of unique UMI-corrected transcripts per gene per cell
The left read contains the barcode information: the first eight bases correspond to a cell specific barcode* followed by a 6bp unique molecular identifier (UMI). The remainder of the left read contains a polyT stretch followed by a number (<40) of transcript derived bases. Read 1 was not used for quantification.
Supplementary_files_format_and_content: cell specific barcodes are specified in the file “cel-seq2_barcodes.csv”
Genome_build: zV9 Danio Rerio

source_name: Whole embryo

tag: developmental stage

value: 5 dpf

tag: sort day

value: Ptpn6 siblings (A-H) and ptpn6 mutants (I-P)


title: PB_03

value: Ptpn6 mutants


title: PB_04

value: Ptpn6 siblings


title: RNA-seq_shFto_rep3

tag: strain background

value: shFto

tag: cell type


title: WT_infarct_rep1

value: wild type


title: WT_infarct_rep3

value: 3 months


title: yhfW6hBR1

source_name: Δyhfw (bioreplicate 1)

tag: strain


title: RNA-seq_shFto_rep2

tag: genotype


title: WT_H2AZ_ZT20_WL

description:
histone variant
Sample 16

tag: tissue

value: seedlings

value: white light

value: H2A.Z (Active Motif, 39647)


title: RNA-seq_shNC_CD8T_rep2

description: processed data file: RNA-seq_CD8T_gene_count.csv

value: OT-I

value: OT-1 CD8+ T cell

value: co-culture with shNC B16-OVA cells


title: BR2_T2_plus

description: IonXpressRNA_014_R_2015_03_12_19_57_34_user_PRI-175-Boonstra_800253_chip3_Auto_user_PRI-175-Boonstra_800253_chip3_253

source_name: compT2 (bioreplicate 2)

value: str 168


title: Co6hBR2

source_name: WT (bioreplicate 2)

value: WT


title: WT_H2AZ_ZT16_WL

description:
histone variant
Sample 14


title: WT_H2AZ_ZT12_lowR:FR

description:
histone variant
Sample 13

value: low R:FR


title: Tim3cko_rep3

city: CAMBRIDGE

first: Meromit

last: Singer

state: MASSACHUSETTS

address: 415 main st, ROOM 6031

institute: Broad Institute of MIT and Harvard

data_processing:
rsem
Genome_build: mm10
Supplementary_files_format_and_content: TPM matrix

source_name: Th1 cells

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: Th1 cells


title: RNA-seq_shFto_rep1

value: B16-OVA (melanoma)


title: Co6hBR1

source_name: WT (bioreplicate 1)


title: WT_H2AZ_ZT12_WL

description:
histone variant
Sample 12


title: WT_H2AZ_ZT4_lowR:FR

description:
histone variant
Sample 9


title: Bat3cko_rep2


title: Tim3cko_rep2


title: RNA-seq_shNC_CD8T_rep1


title: WT_H2AZ_ZT8_lowR:FR

description:
histone variant
Sample 11


title: Tim3cko_rep1


title: BR2_T2_minus

description: IonXpressRNA_015_R_2015_03_12_19_57_34_user_PRI-175-Boonstra_800253_chip3_Auto_user_PRI-175-Boonstra_800253_chip3_253

source_name: nonT2 (bioreplicate 2)


title: LCL161_3 (vivo)

first: Stephanie

last: Dougan

state: MA

address: 1 Jimmy Fund Way

department: Cancer Immunology & Virology

institute: Dana-Farber Cancer Institute

description: CD45+ CD11b+ cells from LCL161-treated mouse pancreatic tumor

data_processing:
FASTQs were aligned using STAR (v2.7.3a) against the GRCm38 genome with ENSEMBL 97 exon annotations.
Gene-level counts were obtained from the alignments using the R package "Rsubread" (v1.32.4).
Count normalization and differential expression analysis was performed with the R package "DESeq2" (v1.26.0)
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated text file of raw (unnormalized) gene-level counts for each sample

source_name: orthotopic 6694c2 pancreatic tumor

extract_protocol:
Pancreatic tumors were excised, minced, digested in RPMI containing collagenase and anti-trypsin, filtered through a 40 um cell strainer, washed with PBS, and sorted by FACS for CD45+ CD11b+ cells. Total RNA was prepared from those cells using a Qiagen RNeasy kit according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: orthotopic 6694c2 pancreatic tumor


title: WT_H2AZ_ZT8_WL

description:
histone variant
Sample 10

extract_protocol:
Kaufmann et al. 2010 DOI:10.1038/nprot.2009.244
Libraries were prepared for sequencing using standard Illumina protocols


title: RNA-seq_shFto-1_CD8T_rep1

value: co-culture with shFto-1 B16-OVA cells


title: RNA-seq_shFto-2_CD8T_rep2

value: co-culture with shFto-2 B16-OVA cells


title: BR2_T1_plus

description:
IonXpressRNA_012_R_2015_03_11_14_20_31_sn247770177_SN2-62-Boonstra_800253_chip2_Auto_sn247770177_SN2-62-Boonstra_800253_chip2_133
IonXpressRNA_012_R_2015_03_12_13_05_40_sn247770177_SN2-63-Boonstra_800253_chip2_Auto_sn247770177_SN2-63-Boonstra_800253_chip2_135

source_name: compT1 (bioreplicate 2)


title: Bat3cko_rep1


title: BR2_T1_minus

description:
IonXpressRNA_013_R_2015_03_11_14_20_31_sn247770177_SN2-62-Boonstra_800253_chip2_Auto_sn247770177_SN2-62-Boonstra_800253_chip2_133
IonXpressRNA_013_R_2015_03_12_13_05_40_sn247770177_SN2-63-Boonstra_800253_chip2_Auto_sn247770177_SN2-63-Boonstra_800253_chip2_135

source_name: nonT1 (bioreplicate 2)


title: WT_H2AZ_ZT4_WL

description:
histone variant
Sample 8

source_name: light-grown seedlings


title: BR1_T2_minus

description:
IonXpressRNA_011_R_2015_03_12_13_05_40_sn247770177_SN2-63-Boonstra_800253_chip2_Auto_sn247770177_SN2-63-Boonstra_800253_chip2_135
IonXpressRNA_011_R_2015_03_11_14_20_31_sn247770177_SN2-62-Boonstra_800253_chip2_Auto_sn247770177_SN2-62-Boonstra_800253_chip2_133

source_name: nonT2 (bioreplicate 1)


title: RD SGI-110 #1

type: genomic

city: Los Angeles

first: Katherine

middle: K

last: Slemmons

address: 4650 Sunset Blvd

department: Hematology/Oncology

institute: Children's Hospital Los Angeles

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to the Illumina Infinium EPIC Beadarrays using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: The raw signal intensities are extracted from the *.IDAT files using the ‘noob’ function in the minfi R package. The ‘noob’ function corrects for background fluorescence intensities and red-green dye-bias as described by Triche et al. The beta value was c

label: Cy5 and Cy3

source_name: RD cell line

label_protocol: Genomic DNA (1000 ng) was bisulfite converted using the Zymo EZ DNA methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s recommendations. The amount of bisulfite-converted DNA as well as the completeness of bisuflite conversion for

growth_protocol: The cell lines were cultured in RPMI-1640, 100_units/ml penicillin and 100__g/ml streptomycin, 2_mM glutamine, and 10% heat inactivated fetal bovine serum at 37ºC in an atmosphere of 5% CO2.

extract_protocol: Total genomic DNA was extracted using the KingFisher (ThermoFisher) per manufacturer’s recommendations.

treatment_protocol: SGI-110 was obtained from AdooQ and resuspended in DMSO at 10mM. Cells were treated with DMSO or 0.5µM SGI-110 for 5 days.

tag: sample type

value: Drug treated

tag: disease

value: embryonal rhabdomyosarcoma


title: RD SGI-110 #3