title: lesioned-3

value: GFP+ cells ( mysopetal and perivascular cells)

value: 4 day post-fertilzation


title: unlesioned-2

status: Public on Dec 23 2020

type: SRA

city: Erlangen

first: Daniel

last: Wehner

address: Staudtsraße 2

department: Division Biological Optomechanics

country: Germany

institute: Max Planck Institut for the Science of Light

library_source: transcriptomic

data_processing:
bcl2fastq 2.19.1
alignment with GSNAP (2018-07-04) aligner and Ensembl 92 zebrafish annotation to zebrafish (GRCz11) reference
featureCounts (1.6.2) to detect reads and used the Ensembl 92 zebrafish annotation
Genome_build: GRCz11
Supplementary_files_format_and_content: tab separated file from featureCounts; the first columns describing the gene (ID, Start, End, Strand, Length) followed by the 8 sequenced samples

molecule: total RNA

organism: Danio rerio

source_name: pdgfrb+ cells

growth_protocol: Zebrafish embryos were raised in E3 medium at 28.5°C

extract_protocol:
Total RNA Purification Plus Micro Kit (Norgen Biotek)
Library construction followed the instruction from the SMARTSeq 2 manual

treatment_protocol: mechanical lesion to the spinal cord; enzymatic tisue dissociation using Trypsin, FACS

tag: transgenic line

tag: cell type

tag: protocol

value: unlesioned

tag: age


title: J15900_TCR

city: Kiel

first: Daniela

last: Esser

address: Arnold-Heller-Str. 3

department: Institute of Clinical Chemistry

institute: University Hospital Schleswig-Holstein

data_processing:
Bcl2fastq2/2.20.0.422
Cellranger-3.1.0 (count, VDJ)
Seurat v3.2.0
Genome_build: GRCh38 v3.0.0 (scRNA),  GRCh38 v2.0.0 (TCR)
Supplementary_files_format_and_content: tab-delimited text files with expression data
raw matrix files (Cellranger)
filtered matrix files (Cellranger)
TCR clonotypes
tab-delimited text file with Seurat metadata

organism: Homo sapiens

source_name: blood

extract_protocol:
CD154+ cells were isolated by MACS and further purified by FACS sorting on a MACSQuant Tyto (Miltenyi Biotec) based on dual expression of CD154 and CD69. Sorted CD154+ T cells were removed from the sorting chamber into pre-coated low-bind collection tubes, 1ml RPMI-1640 medium supplemented with 5% AB Serum was added, and cells were centrifuged for 5 min at 400 x g, 4°C. The supernatant was carefully removed leaving 10-30μl to reach a maximum concentration of 1000 cells /μl.
Single-cell suspensions were loaded on a ChromiumChip G (10x Genomics) according to the manufacturer’s instructions for processing with the Chromium Next GEM Single Cell 5′ Library and  Gel  Bead  Kit  v1.1. TCR  single-cell  libraries  were subsequently prepared from the same cells with the Chromium Single Cell V(D)J Enrichment Kit, Human T Cell.
Chromium Next GEM Single Cell 5′ Library

treatment_protocol: PBMCs were stimulated for 7h with peptide pools of SARS-CoV-2 and reactive CD154+CD4+ T cells were isolated

tag: individual

value: control

tag: who class

value: healthy

tag: severity

tag: tissue

value: blood

value: CD154+ T cells


title: Primitive tumor [JB08]

type: RNA

city: Milan

first: Marco

last: Silvestri

state: ITALY

address: Via Amadeo 42

department: Department of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

description: Gene expression data from Primitive Breast Cancer Tumor

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: Data were processed using RMA algorithm implemented in oligo Bioconductor package (McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics,    11(2):242-253.)

label: Biotin

source_name: Primitve Breast Cancer Tumor

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Affymetrix).

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: type

value: Primitive

value: FFPE

tag: grade


title: lesioned-2

value: 1 day post-lesion


title: SET1-NBAT1SH3-NUT10

city: Gothenburg

first: Subazini

last: TK

address: Medicineragatan 9A

country: Sweden

institute: Gothenburg university

description:
NBAT1 Knockdown Replicate1 nutlin treated
NUT_tmt_FPKM.txt.gz

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Picard tools is used to determine the average insert size and standard deviation
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample analyzed (Genesymbol,GeneID,SET1-CSH-NUT10,SET2-CSH-NUT10,SET1-NBAT1SH3-NUT10,SET2-NBAT1SH3-NUT10)

growth_protocol: SH-SY5Y cell lines were maintained at 37°C with 5% carbon dioxide in  DMEM supplemented with 10% FBS and antibiotics.

extract_protocol:
Total RNA was isolated from NBAT1 knockdown and its respective control (Csh) SH-SY5Y cells were isolated 24 hours after nutlin-3a (10 μM) or DMSO treatement
Using Relia RNA miniprep system from Promega and mRNA enrichment was performed by rRNA depletion. Following steps were followed before running the library in BGI seqplatform.  1) RNA fragment and reverse transcription. 3) End repair, add A and adaptor ligation. 4) RCR amplification. 5) Single strand separation and cyclization. 6) DNA nanoball synthesis. 7) Sequencing on BGISEQ platform

treatment_protocol: Nutilin  treatment

tag: genotype/variation

value: knock down of lncRNA NBAT1 in SHSY-5Y cells

tag: treatment

value: nutlin


title: SET2-NBAT1SH3-NUT10

description:
NBAT1 Knockdown Replicate2 nutlin treated
NUT_tmt_FPKM.txt.gz


title: S1-Nut

description:
Replicate1 nutlin treated
NUT_Sel_FPKM.txt.gz

data_processing:
Sequenced reads were mapped to hg38 whole genome using hisat2 with default parameters
The reads are quantified using featureCounts from Subread package
Picard tools is used to determine the average insert size and standard deviation
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample analyzed (Genesymbol,GeneID,SET1-CSH-NUT10,SET2-CSH-NUT10,SET1-NBAT1SH3-NUT10,SET2-NBAT1SH3-NUT10)
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample analyzed (Genesymbol,Geneid,S1.NT,S2.NT,S1.Nut,S2.Nut,S1.Nut.sel,S2.Nut.sel,S1.Sel,S2.Sel)

extract_protocol: Total RNA after drug treatment was extracted using SV total RNA isolation system from Promega.

treatment_protocol: Nut and Sel  treatment

tag: cell line


title: J15899_TCR


title: Primitive tumor [JB14]


title: J15891_TCR


title: SET2-CSH-NUT10

description:
Control Replicate2 nutlin treated
NUT_tmt_FPKM.txt.gz


title: SET1-CSH-NUT10

description:
Control Replicate1 nutlin treated
NUT_tmt_FPKM.txt.gz


title: lesioned-1


title: J15890_TCR

value: COVID-19 patient

value: WHO 2

value: non-hospitalized


title: Primitive tumor [JB00]


title: 2D duodenum organoids with flow day4

city: Tokyo

first: Shinya

last: Sugimoto

address: 35 Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

data_processing:
Adaptors were removed from raw fastq files with cutadapt (version 1.18).
Reads were aligned to hg38 using STAR (version 2.6.1b) and gene expression levels were estimated using RSEM (version 1.3.3).
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

source_name: Normal duodenum organoid

growth_protocol: Organoids were maintained in a medium containing Afamin/Wnt-3A, EGF, Noggin, R-spondin1, A83-01, IGF-1 and FGF-2. For monolayer organoid culture, human duodenum organoids were pre-cultured in Matrigel for 7 days before dissociation and then seeded onto 0.4-um pore ThinCert 24-well plates (Greiner) coated with 20% Matrigel.

extract_protocol:
Total RNA from monolayer-cultured human duodenum organoids was extracted using the Direct-zol RNA MicroPrep Kit (Zymo Research) according to the manufacturer's instructions. RNA was collected from organoids with or without a four-day medium rotation, and after 0, 1, 2 or 4 days of medium rotation. Three wells were prepared for each condition.
Sequence library was prepared with TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: At confluence (3 days post-seeding), luminal flow was generated on a rotary shaker at 150 rpm.

value: Normal 2D duodenum organoid

value: with flow day4 (medium rotation)


title: J14205_TCR

value: WHO 5

value: mild-moderate


title: Primitive tumor [JA96]


title: Primitive tumor [JA98]


title: 2D duodenum organoids with flow day2

value: with flow day2 (medium rotation)


title: latent_HV02

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

country: USA

institute: Washington University in St.Louis

data_processing:
The Cell Ranger Single-Cell Software 3.0 available at 10X website was used to perform sample demultiplexing. We aligned resulting fastq files on mmul10 genome (Genebank, https://www.ncbi.nlm.nih.gov/assembly/GCF_003339765.1/, with addition of Ensembl mmul8 mitochondrial genes for GTF file) with cellranger count. For each sample the recovered-cells parameter was set to 10,000 cells that we expected to recover for each individual library. We used R package Seurat 3 for downstream analysis of count matrixes that we got as output from cellranger count. We filtered cells that (1) had more than 12.5% (samples KP77, KR71), 20% (samples KM67, KN08, LD09, LE99, 33935, KP87), 25% (samples GP50, HV02), 30% (samples KN21, 31810) of mitochondrial gene content, (2) had less than 725 detected genes. We chose different thresholds for mitochondrial gene content due to different distributions between samples. Data was log-normalized with a scale factor of 104. The most variable genes were detected by the FindVariableFeatures function and used for subsequent analysis. Latent variables (number of UMI’s and mitochondrial content) were regressed out using a negative binomial model (function ScaleData). Principle component analysis (PCA) was performed with RunPCA function. A UMAP dimensionality reduction was performed on the scaled matrix (with most variable genes only) using the first 20 PCA components to obtain a two-dimensional representation of the cell states. For clustering, we used the functions FindNeighbors (20 PCA) and FindClusters (resolution 0.25).
Genome_build: mmul10

organism: Macaca mulatta

source_name: dematricized lung cells

extract_protocol:
At necropsy lung tissues were collected and digested with DNase I and Liberase at 37ºC for 30-45 mins. Digested lung tissue was gently dispersed by passage through a 70 μm pore size nylon tissue strainer (Falcon; BD Biosciences); the resultant single-cell suspension was treated with ACK lysis buffer to remove any residual RBC, washed twice, and counted, as previously described (Foreman et al., 2016; Gautam et al., 2018; Kaushal et al., 2015; Kuroda et al., 2018; Mehra et al., 2015). Cells prepared in this way were stored at -70ºC and then used for downstream processing of scRNA-seq.
scRNA-seq was done according to the manufacturer instructions (10X genomics). Briefly, after quickly thawing the frozen lung single cell suspension in water bath, 2X106 cells were taken for downstream processing. Cell suspensions were enriched for CD45 by using NHP CD45-microbeads according to the manufacturer instruction (Milteny Biotec). After then, CD45+ enriched lung single cell suspensions were subjected to droplet-based massively parallel single-cell RNA sequencing using Chromium Single Cell 3’ (v3) Reagent Kit in the BSL-3 level laboratory as per manufacturer’s instructions (10x Genomics). Briefly, cell suspensions were loaded at 1,000 cells/μL with the aim to capture 10,000 cells/lane. The 10x Chromium Controller generated GEM droplets, where each cell was labeled with a specific barcode, and each transcript labeled with a unique molecular identifier (UMI) during reverse transcription. The barcoded cDNA was isolated and removed from the BSL-3 space for library generation. The cDNA underwent 11 cycles of amplification, followed by fragmentation, end repair, A-tailing, adapter ligation, and sample index PCR as per the manufacturer’s instructions. Libraries were sequenced on a NovaSeq S4 (200 cycle) flow cell, targeting 50,000 read pairs/cell.

treatment_protocol: All animal procedures were approved by the Tulane National Primate Research Center (TNPRC) Institutional Animal Care and Use Committee and performed in strict accordance with the NIH, USDA and AALAAC guidelines. Specific-pathogen-free, retrovirus-free, mycobacteria-naive, adult rhesus macaques were bred and housed at the TNPRC and they were assigned into three groups. One group of macaques (n=4) remained uninfected. The second (~ 10 CFU) (n=4) (LTBI) and third (~1000 CFU) group (n=6) (PTB) of animals were aerosol-challenged with Mtb CDC1551 using a custom head-only dynamic inhalation system housed within a class III biological safety cabinet as described extensively before (Bucsan et al., 2019a; Foreman et al., 2020; Foreman et al., 2016; Kaushal et al., 2015; Mehra et al., 2015). Humane endpoints were predefined in the animal use protocol and applied as a measure of reduction of discomfort. Criteria for euthanasia included presentation of four or more of the following conditions: (i) body temperatures consistently greater than 2°F compared to pre-infection values for 3 or more weeks in a row; (ii) loss of body weight for 15% or more; (iii) serum CRP values higher than 10 mg/mL for 3 or more consecutive weeks, since CRP is a marker for systemic inflammation and exhibits a high degree of correlation with active TB in macaques; (iv) Thoracic radiographs (CXR) values higher than 2 on a scale of 0–4; with a score of 0 denoting normal lung and a score of 4 denoting severe tuberculous pneumonia and pathology. (v) respiratory discomfort leading to vocalization; (vi) significant or complete loss of appetite; and (vii) detectable bacilli in BAL samples. At necropsy, lung, spleen, and liver tissues were collected and processed, as previously described, using two sections of pulmonary tissue that represented every lung lobe in at least one sample; CFU were determined per gram of tissue. We also evaluated CFU from individual lung granulomas isolated at necropsy, as described earlier.

tag: disease

value: latent tuberculosis

tag: infection strain

tag: cfu delivered

tag: celll type

value: dematricized lung cells


title: 2D duodenum organoids with flow day1

value: with flow day1 (medium rotation)


title: J14204_TCR

value: WHO 7

value: severe

value: blood

value: CD154+ T cells


title: control_LE99

value: uninfected


title: Primitive tumor [JB06]

value: Primitive

value: FFPE


title: Primitive tumor [JA92]


title: Primitive tumor [JA94]


title: control_LD09


title: Primitive tumor [JA90]


title: control_31810


title: J11689_TCR

value: COVID-19 patient

value: WHO 2


title: 2D duodenum organoids without flow

value: Normal 2D duodenum organoid

value: without flow


title: J10888_TCR

value: WHO 4


title: J10887_TCR

value: WHO 6


title: Primitive tumor [JA84]


title: Primitive tumor [JA88]


title: 2D duodenum organoids with flow

value: with flow (a four-day medium rotation)


title: J10886_TCR

value: WHO 5

value: mild-moderate


title: rebral organoid, mt

city: Shanghai

first: Zikai

last: Zhou

state: Shanghai

address: 600 Wan Ping Nan Road

department: Research Center

country: China

institute: Shanghai Mental Health Center

data_processing:
Cell Ranger was used to base-calling, alignment, filtering and generation of normalized abundance measurements
read1: contains the 16bp 10X barcode and the 10bp UMI (bases 17-26), Index contains the sample barcode, Read2 contains the cDNA information
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files include normalized median scaling values for each cell

source_name: cerebral organoid

growth_protocol: Cerebral organoid differentiation was generated based on the previously established protocol with several modifications. Briefly, hNPCs were detached with Dispase (1 U/ml, Gibco) to form embryoid bodies (EBs) in suspension in neural induction medium (NIM) consisting of DMEM/F12 (Gibco), N2 supplement (1:100; Gibco) and NEAA (1:100; Gibco) for 7 days. Half of the media was changed every 2–3 days and primitive neuroepithelial was induced. To generate organoids, neuroepithelial tissues were transferred to Matrigel (Corning) droplets. After 1 month, organoids were seen to begin to exhibit neuronal differentiation.

extract_protocol:
The cerebral organoids were digested into single-cell suspension then processed to prepare single-cell master mix following the manufacturer’s instructions (Chromium™ Single Cell 3’ Library & Gel Bead Kit v2).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Human cerebral organoids were treated with ALK inhibitor or vehicle at 23 day in vitro

value: human embryonic stem cells derived neural progenitors and neurons

tag: passages

value: ALK inhibitor


title: active_KP87

value: active tuberculosis

value: dematricized lung cells


title: active_KR71


title: Primitive tumor [JA80]


title: J10625_TCR

value: non-hospitalized

value: blood

tag: cell type

value: CD154+ T cells


title: 2D duodenum organoids with flow day0

value: with flow day0 (medium rotation)


title: Primitive tumor [JA82]

value: Primitive

value: FFPE


title: cerebral organoid, mc

value: control


title: J10624_TCR

value: COVID-19 patient

value: WHO 2


title: J10535_TCR

value: WHO 4


title: Primitive tumor [JA78]


title: active_KN21


title: J09836_TCR

value: WHO 1


title: active_KM67


title: Mx1-Jak2VF-Ldlr-/- 4

city: New York

first: David

middle: G

last: Thomas

state: NY

department: Medicine

institute: Columbia University

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
vf_ldlr_4

data_processing:
Nextseq 500 lanes were merged using gunzip/cat
Adaptor contamination was removed using cutadapt
Reads were aligned to mouse genome mm10 using HISAT2
Feature assignment was performed using Subread-featureCounts
Statistical comparison of read counts was performed using DESeq2
Differentially expressed gene lists were prepared by filtering for q<0.05 (5% FDR)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with counts for each gene; comma-delimited text file with differentially expressed gene lists

molecule: polyA RNA

organism: Mus musculus

source_name: CD11b+ cells from spleen

growth_protocol: WT or Ldlr-/- reciprient were irradiated with 9.5gly, then transplanted from bone marrow with and Mx1-Cre drivin Jak2V617F mutation or littermate control, 4 weeks later ldlr-/- mice were subjected to western type diet (Teklad TD88137) for 7 weeks.

extract_protocol:
Spleens were harvested from mice then passed through a 0.45um cell filter, washed and incubated with CD11b beads. CD11b positive cells were isoalted using a magnetic field, then washed and collected fro RNA isolation.
RNA with RIN > 8 was subjected to poly-dT pulldown using magnetic beads (NEB) before preparation for RNA-seq using RNA Ultra kits (NEB).

treatment_protocol: CD11b cells were then harvested from spleens using CD11b magentic beads (Militenyi Biotec 130-126-725)

value: CD11b+ cells from spleen

tag: strain

tag: diet

value: Western type diet 7 weeks (Teklad TD 88137)

tag: Sex

value: Female


title: Mx1-Jak2VF-Ldlr-/- 2

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
vf_ldlr_2


title: active_KP77


title: active_KN08


title: AML127.1 C

city: Boston

first: Andrew

middle: M

last: Lippa

state: MA

address: 300 Longwood Ave

department: Pediatrics, Division of Infectious Diseases

institute: Boston Children's Hospital

description:
Sample 7 C
PAO1 ΔmvaU ΔmvaT ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_C_background_normalized.profile.wig.gz
RpoD-V_delUT_C_normalized.profile.wig.gz

library_source: genomic

data_processing:
Paired ChIP-Seq reads corresponding to fragment sizes of 200 bp were aligned to the PAO1 genome using bowtie2 (version 2.3.5.1) allowing 1 mismatch in a 28 bp seed region with no discordant or unpaired alignments.
The program samtools (version 1.9) was used to extract read 1 from each mapped read pair.
For MvaT-V and MvaU-V ChIP experiments (samples 2 and 3, respectively): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from wild-type PAO1 cells (sample 1) with the following settings: KDE = 45, seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.
For PAO1 ∆pilY1 RpoD-V ChIP experiments (sample 5): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from ∆pilY1-parental cells (sample 4) with the following settings: KDE = 30, seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.
For PAO1 ∆pilY1 ∆mvaU ∆mvaT RpoD-V ChIP experiments (sample 7): Peaks were identified using QuEST (version 2.4; Valouev et al., 2008) using control data from PAO1 ∆pilY ∆mvaU ∆mvaT-parental cells (sample 6) with the following settings: KDE = 30, seeding fold enrichment = 1.25, extension fold enrichment = 1.5, ChIP to background fold enrichment = 2.
Bed files for each experimental replicate were created by QuEST and the final processed bed files were generated by identifying the largest overlapping peak region which satisfy the following conditions: (1) peak regions must have a positive peak shift, (2) peak regions must have a positive strand correlation, (3) peak regions must have a q-value of less than 0.01, and (4) peak regions must be shared by two or more experimental replicates.
Genome_build: NC_002516.2
Supplementary_files_format_and_content: Wig files were generated using QuEST; Scores represent normalized smoothed read density.
Supplementary_files_format_and_content: Bed intervals reflect regions with significant (as defined above in data processing steps) enrichment of reads in the experimental condition in comparison to the mock control condition.

molecule: genomic DNA

organism: Pseudomonas aeruginosa PAO1

source_name: Bacterial cells grown to OD 0.35

growth_protocol: Bacterial cultures were started from single colonies, grown overnight to saturation, and back-diluted in LB media to an OD600~0.01 and cultures were grown with aeration at 250 rpm at 37°C to a final OD600 ~0.35. For RpoD-V ChIP samples, 15 mL of culture was also reserved and processed for RNA-seq.

extract_protocol:
DNA associated with proteins of interest were immunoprecipitated from lysates with anti-VSVG monoclonal antibody.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) following manufacturer’s instructions. Size selection of DNA fragments was not used.

treatment_protocol: Samples were crosslinked with formaldehyde at 1% final concentration for 30 minutes, then the reaction was quenched with addition of glycine to a final concentration of 250 mM. Cell pellets were washed 3 times with PBS and frozen at -80°C for further processing/extraction.

tag: genotype

value: PAO1 <delta>mvaU <delta>mvaT <delta>pilY1 rpoD-vsvG

tag: growth phase

value: mid-logarithmic phase culture

tag: chip antibody

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: J21856_RNA

tag: individual

tag: who class

value: healthy

tag: severity

tag: tissue


title: Mx1-Jak2VF-Ldlr-/- 3

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
vf_ldlr_3


title: Mx1-Jak2VF-Ldlr-/- 1

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
vf_ldlr_1


title: AML127.1 B

description:
Sample 7 B
PAO1 ΔmvaU ΔmvaT ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_B_background_normalized.profile.wig.gz
RpoD-V_delUT_B_normalized.profile.wig.gz


title: Control-Ldlr-/- 6

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_6


title: J21855_RNA

value: blood


title: Primitive tumor [JA74]

tag: type

tag: grade


title: AML127.1 A

description:
Sample 7 A
PAO1 ΔmvaU ΔmvaT ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_A_background_normalized.profile.wig.gz
RpoD-V_delUT_A_normalized.profile.wig.gz


title: Primitive tumor [JA76]


title: Primitive tumor [JA68]


title: Primitive tumor [JA72]


title: Primitive tumor [JA70]


title: Control-Ldlr-/- 5

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_5


title: Primitive tumor [JA66]


title: J21854_RNA

value: WHO 7

value: severe

value: CD154+ T cells


title: Primitive tumor [JA64]

value: Primitive

value: FFPE


title: Control-Ldlr-/- 4

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_4


title: AML85.1.1 C

description:
Sample 6 C
PAO1 ΔmvaU ΔmvaT ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_C_background_normalized.profile.wig.gz
RpoD-V_delUT_C_normalized.profile.wig.gz

value: PAO1 <delta>mvaU <delta>mvaT <delta>pilY1


title: J15893_RNA

value: COVID-19 patient

value: WHO 5

value: mild-moderate


title: AML85.1.1 B

description:
Sample 6 B
PAO1 ΔmvaU ΔmvaT ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_B_background_normalized.profile.wig.gz
RpoD-V_delUT_B_normalized.profile.wig.gz


title: Control-Ldlr-/- 2

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_2

value: CD11b+ cells from spleen


title: Control-Ldlr-/- 3

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_3

value: Western type diet 7 weeks (Teklad TD 88137)


title: J15900_RNA

value: control


title: AML85.1.1 A

description:
Sample 6 A
PAO1 ΔmvaU ΔmvaT ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_delUT_AllPeaks.bed
RpoD-V_delUT_A_background_normalized.profile.wig.gz
RpoD-V_delUT_A_normalized.profile.wig.gz


title: Primitive tumor [JA62]

description: Gene expression data from Primitive Breast Cancer Tumor


title: Control-Ldlr-/- 1

description:
jak2_raw_counts.txt
vf-effect_hld_2F.csv
wt_ldlr_1

value: Female


title: AML121 C

description:
Sample 5 C
PAO1 ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_C_normalized.profile.wig.gz
RpoD-V_Parental_C_background_normalized.profile.wig.gz

value: PAO1 <delta>pilY1 rpoD-vsvG

value: mid-logarithmic phase culture


title: J15892_RNA

value: healthy


title: AML121 B

description:
Sample 5 B
PAO1 ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_B_normalized.profile.wig.gz
RpoD-V_Parental_B_background_normalized.profile.wig.gz

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: Mx1-Jak2VF-WT 7

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_7

value: Chow Diet


title: Mx1-Jak2VF-WT 6

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_6


title: J15891_RNA

value: blood


title: AML121 A

description:
Sample 5 A
PAO1 ΔpilY1 rpoD-vsvG
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_A_normalized.profile.wig.gz
RpoD-V_Parental_A_background_normalized.profile.wig.gz


title: Primitive tumor [JA60]


title: J15890_RNA

value: WHO 2

value: non-hospitalized

value: CD154+ T cells


title: Primitive tumor [JA54]

value: Primitive

value: FFPE


title: Primitive tumor [JA56]


title: AML91 C

description:
Sample 4 C
PAO1 ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_C_normalized.profile.wig.gz
RpoD-V_Parental_C_background_normalized.profile.wig.gz

value: PAO1 <delta>pilY1


title: Mx1-Jak2VF-WT 5

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_5


title: J15899_RNA


title: AML91 B

description:
Sample 4 B
PAO1 ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_B_normalized.profile.wig.gz
RpoD-V_Parental_B_background_normalized.profile.wig.gz


title: J14205_RNA

value: COVID-19 patient

value: WHO 5

value: mild-moderate


title: Mx1-Jak2VF-WT 4

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_4

value: CD11b+ cells from spleen


title: AML91 A

description:
Sample 4 A
PAO1 ΔpilY1
Immunoprecipitated DNA was not size-selected during library construction.
RpoD-V_Parental_AllPeaks.bed
RpoD-V_Parental_A_normalized.profile.wig.gz
RpoD-V_Parental_A_background_normalized.profile.wig.gz


title: Primitive tumor [JA48]


title: J09835_TCR

value: WHO 1


title: J11689_RNA


title: J14204_RNA

value: WHO 7

value: severe


title: latent_GP50

tag: disease

value: latent tuberculosis

tag: infection strain

value: dematricized lung cells


title: Mx1-Jak2VF-WT 2

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_2

value: Chow Diet

value: Female


title: AML87 C

description:
Sample 3 C
Immunoprecipitated DNA was not size-selected during library construction.
MvaT_AllPeaks.bed
MvaT-V_C_normalized.profile.wig.gz
MvaT-V_C_background_normalized.profile.wig.gz

value: mvaT-vsvG

value: mid-logarithmic phase culture

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: J10888_RNA

value: WHO 4

value: blood

value: CD154+ T cells


title: AML87 B

description:
Sample 3 B
Immunoprecipitated DNA was not size-selected during library construction.
MvaT_AllPeaks.bed
MvaT-V_B_normalized.profile.wig.gz
MvaT-V_B_background_normalized.profile.wig.gz


title: Mx1-Jak2VF-WT 1

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_1


title: Control-WT 6

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_6


title: J10886_RNA

value: COVID-19 patient


title: J10887_RNA

value: WHO 6


title: Primitive tumor [JA52]

description: Gene expression data from Primitive Breast Cancer Tumor

value: Primitive

value: FFPE


title: Control-WT 5

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_5

value: CD11b+ cells from spleen


title: Primitive tumor [JA46]


title: J10625_RNA

value: WHO 2

value: non-hospitalized


title: AML86 C

description:
Sample 2 C
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaU-V_C_normalized.profile.wig.gz
MvaU-V_C_background_normalized.profile.wig.gz

value: mvaU-vsvG


title: Mx1-Jak2VF-WT 3

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
vf_wt_3


title: J10624_RNA


title: AML87 A

description:
Sample 3 A
Immunoprecipitated DNA was not size-selected during library construction.
MvaT_AllPeaks.bed
MvaT-V_A_normalized.profile.wig.gz
MvaT-V_A_background_normalized.profile.wig.gz


title: Control-WT 4

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_4


title: Control-WT 3

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_3


title: Primitive tumor [JA42]


title: Control-WT 2

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_2


title: PAO1 C

description:
Sample 1 C
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaT_AllPeaks.bed
MvaU-V_C_normalized.profile.wig.gz
MvaU-V_C_background_normalized.profile.wig.gz
MvaT-V_C_normalized.profile.wig.gz
MvaT-V_C_background_normalized.profile.wig.gz

value: wild-type


title: Primitive tumor [JA44]


title: Primitive tumor [JA50]


title: Primitive tumor [JA36]


title: J09836_RNA

value: WHO 1


title: Primitive tumor [JA32]


title: Primitive tumor [JA34]


title: PAO1 B

description:
Sample 1 B
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaT_AllPeaks.bed
MvaU-V_B_normalized.profile.wig.gz
MvaU-V_B_background_normalized.profile.wig.gz
MvaT-V_B_normalized.profile.wig.gz
MvaT-V_B_background_normalized.profile.wig.gz


title: Control-WT 1

description:
jak2_raw_counts.txt
vf-effect_nl_2F.csv
wt_wt_1

value: Chow Diet

value: Female


title: J09835_RNA


title: PAO1 A

description:
Sample 1 A
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaT_AllPeaks.bed
MvaU-V_A_normalized.profile.wig.gz
MvaU-V_A_background_normalized.profile.wig.gz
MvaT-V_A_normalized.profile.wig.gz
MvaT-V_A_background_normalized.profile.wig.gz

value: mid-logarithmic phase culture


title: Primitive tumor [JA40]


title: AML86 A

description:
Sample 2 A
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaU-V_A_normalized.profile.wig.gz
MvaU-V_A_background_normalized.profile.wig.gz

value: Agarose-immobilized anti-VSVG antibody (Sigma-Aldrich, catalog number A1970, monoclonal antibody clone P5D4)


title: J10535_RNA

value: WHO 4

value: mild-moderate


title: Infection_3_RNAseq_salivary_glands_paired

status: Public on Dec 22 2020

city: Granada

first: Jose

middle: Luis

last: Ruiz Rodriguez

state: Granada

address: Avda. del Conocimiento 17. P. T. Ciencias de la Salud

country: Spain

institute: IPBLN-CSIC

description:
Infection_3_RNAseq_sgs_paired
Sequencing approach: paired-end

data_processing:
First, raw ATAC-seq reads were trimmed 20 bases from the 3′ end of each read (-3 20), and aligned to the An. gambiae PEST genome (AgamP4) with Bowtie2 (v2.4.1) using default parameters, except for –no-unal –no-mixed -X 2000.
We applied a MAPQ score threshold (10) and sorted and deduplicated the reads using SAMtools (v1.10).
To adjust the known bias and ensure the mapping of Tn5 cutting sites, we shifted aligned reads +4 bp for + strands and −5 bp for – strands with ATACSeqQC (v1.10).
We removed not properly-paired reads and extracted nucleosome-free fragments with a size threshold of 130 bp (SAMtools).
We performed peak-calling on nucleosome-free reads with MACS2 (v.2.1.2) callpeak module and the following parameters: -f BAMPE -g 273109044 -q 0.01 -B --keep-dup all --nomodel --nolambda
To identify THSs unique or common across samples, we used BEDTools intersect requiring a minimum overlap of 51% (-f/-F 0.51).
We annotated THSs to genomic features combining HOMER (v4.11) and ChIPseeker (v1.22). We used the AgamP4.12 gene set and considered the first coordinate of the 5’ UTRs as the TSSs. For genes without an annotated 5’ UTR we took the translation start site (ATG codon) as the reference point. In either case, the 1 Kb upstream window was considered as the putative promoter region.
To quantify the ATAC-seq nucleosome-free signal enrichment at genomic regions of interest, we used BEDTools intersect -c. The read counts were normalized (RPKM) and we added a pseudocount (0.1) when required to get finite values.
We trimmed adapters from the RNA-seq raw reads using BBDuk (v38.79) with -tbo -tpe -minlength=35 parameters and removed rRNA contamination using SortMeRNA (v4.2) with default parameters. Apart from the default rRNA databases, we used additional large and small subunit An. gambiae and P. falciparum rRNA sequences from the SILVA database (LSU r132/SSU r138).
Cleaned directional RNA-seq reads were mapped against the AgamP4 v2.00 reference genome using STAR (v2.7.3a). Two different sets of reads were available, 2x150 bp and 1x75bp, which were processed in parallel until we combined the raw counts. We took unique mapping reads using SAMtools.
Raw counts at the gene level were obtained using CoCo (v.0.2.2) and then provided to DESeq2 (v1.26) for normalization.
Genome_build: AgamP4.12 (VectorBase)
Supplementary_files_format_and_content: *bw: Tracks of the aligned ATAC-seq and RNA-seq signal (bigWig, bw, files obtained using bamCompare).
Supplementary_files_format_and_content: Table_S3_ATAC_seq_THSs.xlsx: Excel table with full results of MACS2 peak-calling process.

organism: Anopheles gambiae

source_name: mosquito salivary glands

growth_protocol: Five-day-old female An. gambiae Kisumu mosquitoes from a genetically outbred laboratory colony in the University of Glasgow were used for experimental infections. Mosquitoes were maintained under standard insectary conditions (27 ± 2 °C, 80 ± 5% relative humidity, 12:12 LD).

extract_protocol:
We performed dissection of midguts on adults at 7 days post-infection and of salivary glands at 14 days post-blood meal.
Total RNA was extracted from fresh mosquito tissues (~30 midguts and ~60 salivary glands). Immediately after dissection, tissues were stored in TRIzol (Invitrogen) and frozen at -80ºC until subsequent processing. We used the Ovation® Universal RNA-seq System (Nugen Technologies) for strand specific RNA-seq library construction following the manufacturer’s instructions. Custom primers specific to mosquito ribosomal sequences were designed to reduce the percentage of ribosomal reads in the sample and the ribo-depletion step was incorporated into the standard workflow. RNA concentration was quantified using a Qubit® 2.0 Fluorometer, and RNA integrity was determined with an Agilent 2100 Bioanalyzer. Illumina libraries were prepared and sequenced at the Cabimer, using an Illumina NextSeq500 sequencer, 75 bp single-end reads.

treatment_protocol: Females were fed through membrane feeders on blood containing gametocytes of P. falciparum clone 3D7, prepared according to standard protocols. Thereafter the mosquitoes were given access to a solution of 5% glucose/ 0.05% 4-aminobenzoic acid ad libitum. Three independent experimental infections (Infections 1, 2 and 3) were carried out.

value: Kisumu

value: Salivary glands

tag: infection status

value: Infected with P. falciparum

tag: time point

value: 14 days

tag: replicate


title: Infection_2_RNAseq_salivary_glands_paired

description:
Infection_2_RNAseq_sgs_paired
Sequencing approach: paired-end

tag: strain


title: Primitive tumor [JA28]

value: Primitive

value: FFPE


title: Infection_3_RNAseq_midguts_paired

description:
Infection_3_RNAseq_mgs_paired
Sequencing approach: paired-end

source_name: mosquito midgut

value: Midguts

value: 7 days


title: Infection_2_RNAseq_midguts_paired

description:
Infection_2_RNAseq_mgs_paired
Sequencing approach: paired-end


title: Infection_3_RNAseq_salivary_glands_single

description:
Infection_3_RNAseq_sgs_single
Sequencing approach: single-end


title: AML86 B

description:
Sample 2 B
Immunoprecipitated DNA was not size-selected during library construction.
MvaU_AllPeaks.bed
MvaU-V_B_normalized.profile.wig.gz
MvaU-V_B_background_normalized.profile.wig.gz

value: mvaU-vsvG


title: unlesioned-1

tag: transgenic line

tag: cell type

value: GFP+ cells ( mysopetal and perivascular cells)

tag: protocol

value: unlesioned

tag: age

value: 4 day post-fertilzation


title: human bladder cancer cell line

city: Nanning

first: Aruo

state: Guangxi

address: Guangxi Medical University, Nanning 530021, Guangxi, China

institute: Guangxi Medical University

description: super-enhancer expression profile in human bladder cancer cell line

hyb_protocol: The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA.

scan_protocol: 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Scanned images were imported into Agilent Feature Extraction software for raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software limma package. After quantile normalization of the raw data, low intensity filtering was performed.

source_name: human bladder cancer cell line, UM-UC-3 cell

label_protocol: Briefly, total RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Quick Amp Labeling Kit, One-Color (Agilent p/n 5190-0442)). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen p/n 74104).

extract_protocol: Total RNA was isolated from the cells manually using TRIzol reagent (Invitrogen, Grand Island, NY, USA) following the manufacturer's recommendations.

treatment_protocol: The SV-HUC-1 cells were cultured in F-12K (21127-022, Gibco, USA) supplemented with 10% fetal bovine serum (FBS; 1750114, Gibco). The UM-UC-3 cells were cultured in DMEM (11995-065, Gibco, USA) containing 10% FBS. All cells were cultured in a humid environment (5% CO2 and 95% O2) at 37°C.

value: human bladder cancer cell line

tag: cell line


title: Infection_2_RNAseq_midguts_single

description:
Infection_2_RNAseq_mgs_single
Sequencing approach: single-end

tag: Sex

value: Female


title: J15892_TCR

tag: individual

value: control

tag: who class

value: healthy

value: blood

value: CD154+ T cells


title: Infection_3_RNAseq_midguts_single

description:
Infection_3_RNAseq_mgs_single
Sequencing approach: single-end

value: Kisumu

tag: tissue


title: Primitive tumor [JA26]

description: Gene expression data from Primitive Breast Cancer Tumor

tag: type


title: human urothelial immortalized cell line

description: super-enhancer expression profile  in human urothelial immortalized cell line

source_name: human urothelial immortalized cell line, SV-HUC-1 cell

value: human urothelial immortalized cell line


title: Primitive tumor [JA30]

tag: grade


title: Infection_2_RNAseq_salivary_glands_single

description:
Infection_2_RNAseq_sgs_single
Sequencing approach: single-end

value: Salivary glands

value: Infected with P. falciparum

value: 14 days


title: N2_5

city: Wuhan

first: Jingxuan

last: Li

state: Hubei

address: Shizishan Street NO.1

department: Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education

institute: Huazhong Agricultural University

data_processing:
Each base sequencing error rate is determined by sequencing Phred score (Qphred).The Phred value is calculated by using a prediction error probability model during Base Calling.
Tophat2(Kim et al., 2013) was used to compare and analyze the reference genome of the filtered sequencing sequence
Transcript splicing was performed by cufflinks(Trapnell et al.,2010) and scripture(Guttman, M., et al.,2010)
HTSeq software was used for quantitative analysis
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: txt files include FPKM values for each samples

organism: Sus scrofa

source_name: 48h of differentiation

extract_protocol:
Total RNA was extracted from the endometrium using the Trizol reagent
RNA libraries were prepared for sequencing using standard protocols

tag: breed

value: Yorkshire

value: skeletal muscle

value: satellite cells

tag: treatment

value: 48h of differentiation


title: N2_4


title: N1_6

source_name: 24h of differentiation

value: 24h of differentiation


title: N2_6


title: N1_4


title: Group B

city: Frederiksberg C

first: knud

middle: arnbjerg

last: christensen

address: Grønnegårdsvej 3,

department: Department of Veterinary Clinical Sciences, Animal Genetics, Bioinformatics and Breeding,

country: Denmark

institute: University of copenhagen

data_processing:
bowtie producing bam file for 97 group A animals
bowtie producing bam file for 97 group B animals
bowtie mpileup produsing genotypes  A animals and B animals
counting numbers of genotypes for group A and for group B animals
and joining the two group by means of the mink genome location
Genome_build: NNQGG.v01

organism: Neogale vison

source_name: B

extract_protocol: none provided by the submitter

tag: phenotype

value: ADS resistant


title: Group A

source_name: A

value: ADS susceptible


title: Input_DNA

first: Huairui

last: Yuan

address: 320 Yueyang Road

department: Shanghai Institutes for Biological Sciences

institute: Chinese Academy of Sciences

data_processing:
For RNA-Seq, transcriptome reads from Hiseq RNA-Seq experiments were mapped to the reference genome (mm10) by using Bowtie tool. Gene expression levels were quantified by a software package called RSEM. The list of significance was operated by setting fold changes threshold at level of 1.5 and p value < 0.05.
For ChIP-Seq, the 75-nt sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm with default settings. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis.tags are extended in silico (using Active Motif software) at their 3´-ends to a length of 150-250 bp, depending on the average fragment length in the size selected library (normally 200 bp).To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined.The two main peak callers used at Active Motif are MACS (Zhang et al., Genome Biology 2008, 9:R137) and SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig for ChIP-Seq and count/rpkm for RNA-seq

source_name: organoid cells

growth_protocol: The mouse prostatic organoid cells generation and organoids formation assay were according to previously reported protocol (Drost et al., 2016).

extract_protocol:
For RNA-seq, total RNA was extracted from the prostatic organoid cells derived from 3-month-old PtenPC+/- and PtenPC+/-; Setd2PC-/- mice with or without Ezh2 deletion, and then subjected to PE150 Hiseq. The chromatin was prepared and followed by ChIP-Seq analysis by Active Motif, Inc. using the antibody against H3K27me3 ( Active Motif 39155).
Libraries were prepared according to standard Illumina protocols.

value: Prostate epithelial cells

tag: chip antibody

tag: genotype/variation

value: PtenPC+/-


title: Sample_neuron_P74

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

data_processing:
basecalling: bcl2fastq2 v2.17
Basecalling was done with bcl2fastq versions 1.8.4 and 2.17. Included as a column of the SAMPLES section above, labelled "protocol: basecalling". Reads were trimmed for adapter, low quality base calls, and poly-A sequence using in-house software and then mapped to the mouse genome (mm10) using STAR v2.4.0 (Dobin et al. 2013).
Uniquely mapped reads were used for gene quantification using VERSE v0.1.4 with parameters “-s 1 -z 3 --nonemptyModified” (Zhu et al. 2016, doi:https://doi.org/10.1101/053306)
Genome_build: mm10
Supplementary_files_format_and_content: comma delimited text files containing raw gene counts

source_name: neuron

growth_protocol: Not Applicable

extract_protocol:
We used standard brain slice preparation technology. Briefly, mice were quickly anesthetized in 2% isoflurane, and decapitated. Brains were removed and laced into ice cold artificial cerebrospinal fluid (ACSF). Slices were cut by vibratome (Leica VT1000 S, Leica Biosystems, Wetzlar, Germany) under ice cold ACSF supplied with Carbogen (5% CO2 in 95% oxygen), then were stored in storage ACSF on room temperature in a chamber and permanently supplied by Carbogen for 1 hour before recording. Three hundred µm slices were cut from a mouse brain so that we were able to collect cells from different layers from the prefrontal cortex (PFC). Individual cells were collected by patch-clamp pipette.
libraries made with Illumina TruSeq Stranded kit (RS-122-2101/2)

treatment_protocol: No Treatment

tag: strain

tag: source region

value: cortex

tag: source type

value: acute slice

tag: basecalling

value: bcl2fastq2 v2.17


title: CTRL_H3K27me3_chipseq

tag: cell type

value: H3K27me3 ( Active Motif 39155)


title: Sample_neuron_P75


title: CS2_CER [CS2]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

hyb_protocol: Standard Illumina protocol. In short, a total of 0.75 μg of biotin-labeled cRNA was hybridized at 58°C for 16 hours to Illumina Human HT12v4 Expression Bead Chips (Illumina, San Diego, CA). The arrays were then rinsed, blocked and the biotin-labeled cRNA was detected by staining with streptavidin-conjugated Cy3.

scan_protocol: Arrays were scanned at a resolution of 0.54 μm using the Illumina iScan scanner.

data_processing:
Data was extracted using the Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0. Any spots at or below the background were filtered out using an Illumina detection Pvalue of 0.02 and above. The natural log of all remaining scores were used to find the avg and std of each array and the z-score normalization was calculated and presented below.  Z-score = (raw value - avg)/std.  Complete data including detection scores is supplied.
Z_VALUE = Z transformation of the natural log of the raw intensity values
Detection_Pval = Detection Pvalue from Illumina GenomeStudio software V2011.1, Gene expression module 1.9.0.

label_protocol: Standard Illumina protocol using Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, cat # IL1791) In short, 0.5 μg of total RNA was first converted into single-stranded cDNA with reverse transcriptase using an oligo-dT primer containing the T7 RNA polymerase promoter site and then copied to produce double-stranded cDNA molecules. The double stranded cDNA was cleaned and concentrated with the supplied columns and used in an overnight in-vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporation of biotin-16-UTP.

extract_protocol:
Postmortem samples of Cockayne syndrome (CS) and control (WT) cerebellum was obtained  from the NIH NeuroBioBank’s Brain and Tissue repository at the University of Maryland, Baltimore.
RNA was extracted from cerebellum samples from Cockayne patients and age- and gender-matched healthy individuals using the Nucleospin RNA isolation kit (catalog no. 740955.250; Macherey-Nagel, Bethlehem, PA) according to the manufacturer’s instructions.  RNA quantity and integrity was evaluated by Nanodrop and Agilent Bioanalyzer RNA 6000 Chip (Agilent, Santa Clara, CA).

tag: subject status/condition

value: Cockayne syndrome (CS)

tag: gender

value: F

tag: age (yrs)

value: Brain

tag: region

value: Cerebellum


title: Sample_neuron_P71


title: CS6_CER [CS6]

tag: tissue


title: SETD2 KO_H3K27me3_chipseq


title: Sample_neuron_P72


title: CS1_CER [CS1]

value: M


title: CS3_CER [CS3]


title: CS7_CER [CS7x]


title: WT5_CER [WT5]

value: control (WT)


title: WT1_CER [WT1]


title: CS8_CER [CS8]


title: WT3_CER [WT3]


title: WT4_CER [WT4]


title: WT6_CER [WT6]


title: CS4_CER [CS4R]


title: Sample_neuron_P73


title: N1_5

value: Yorkshire

value: skeletal muscle

value: satellite cells


title: Sample_neuron_P66


title: Sample_neuron_P67


title: Sample_neuron_P69


title: Sample_neuron_P68


title: Sample_neuron_P63


title: Sample_neuron_P64


title: Sample_neuron_P65


title: Sample_neuron_P70


title: Sample_neuron_P60


title: Sample_neuron_P57


title: Sample_neuron_P59


title: Sample_neuron_P56


title: Sample_neuron_P55


title: Sample_neuron_P62


title: Sample_neuron_P54


title: Sample_neuron_P58


title: Sample_neuron_P53


title: Sample_neuron_P42


title: Sample_neuron_P44


title: Sample_neuron_P52


title: Sample_neuron_P45


title: Sample_neuron_P40


title: Sample_neuron_P39


title: Sample_neuron_P38


title: Sample_neuron_P41


title: Sample_neuron_P61


title: Sample_neuron_P43


title: Sample_neuron_P36


title: Sample_neuron_P37


title: Sample_neuron_P32


title: Sample_neuron_P33


title: Sample_neuron_P31


title: Sample_neuron_P34


title: Sample_neuron_P29


title: Sample_neuron_P30


title: Sample_neuron_P27


title: Sample_neuron_P25


title: Sample_neuron_P24


title: Sample_neuron_P26


title: Sample_neuron_P21


title: Sample_neuron_P22


title: Sample_neuron_P19


title: Sample_neuron_P18


title: Sample_neuron_P15


title: Sample_neuron_P16


title: Sample_neuron_F27


title: Sample_neuron_F8


title: Sample_neuron_F28


title: Sample_neuron_F30


title: Sample_neuron_F5


title: Sample_neuron_F26


title: Sample_neuron_P35


title: Sample_neuron_P17


title: Sample_neuron_F25


title: Sample_neuron_F24


title: Sample_neuron_F23


title: Sample_neuron_F22


title: Sample_neuron_F20


title: Sample_neuron_F21


title: Sample_neuron_P20


title: Sample_neuron_F16


title: Sample_neuron_F17


title: Sample_neuron_F18


title: Sample_neuron_F13


title: Sample_neuron_F15


title: Sample_neuron_F14


title: Sample_neuron_F12


title: Sample_neuron_F7


title: Sample_neuron_F11


title: PE_ZNF593-AS_rep2

first: rong

last: xie

address: Jiefang Ave.

institute: Huazhong university of science and technology

data_processing:
Illumina Casava software was used for basecalling.
Cutadapt (Version 1.2.1) (Martin M, 2011) was used to remove 3' end joints, at least 10 bp Overlap (AGATCGGAAG), and 20% base error rate was allowed.
QC of sequenced reads were done by FASTQC.
Reads were than aligned to the GRCh38 genome assembly using Bowtie2 and Tophat2.
Genome_build: GRCh38
Supplementary_files_format_and_content: xlsx files include RPKM values for each Sample

source_name: human-derived primary cardiomyocytes

growth_protocol: Human-derived primary cardiomyocytes ( ScienCell research laboratories, Carlsbad, CA) were from a single fetal donor, not pooled, and were maintained in cardiac myocyte medium (CMM, ScienCell research laboratories, Cat. #6201), according to the instruction manual. CMM consists of basal medium, foetal bovine serum (FBS), cardiac myocyte growth supplement, and penicillin/streptomycin solution.

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen Life Technologies).
Sequencing libraries were prepared according to Illumina’s protocols.

tag: cell

value: human-derived primary cardiomyocytes

value: phenylephrine

tag: transfection


title: PE_pcDNA3.1_rep3


title: PE_ZNF593-AS_rep3


title: PE_pcDNA3.1_rep2


title: PE_ZNF593-AS_rep1


title: PE_pcDNA3.1_rep1


title: GlyandChitinLEP1

city: Cork

first: Miguel

last: Villoria Recio

address: Gaol walk

department: Alimentary Pharmabiotic Centre

country: Ireland

institute: University College Cork

description:
processed data file: Raw_counts_of_sequenced_reads.xlsx
processed data file: DESeq2_output.xlsx

data_processing:
Reads were mapped to the complete sequenced genome of reference strains EGDe (ENSEMBL ASM19603v1) using Bowtie 2 v 2.2.4 with standard parameters and --sensitive-local (Langmead and Salzberg 2012).
BAM alignment files were used as input for read counting using htseq-count (HTSeq version 0.6.0) (Anders et al. 2015).
Differential expression analyses were performed using DESeq2 in R v 3.2.2 (Love et al. 2014). The differential expression was reported as log2 fold changes, with p-values adjusted by the DESeq2 default Benjamini-Hochberg (BH) adjustment method and genes with a >2-fold change in expression and a p-value < 0.05 were considered as DE.
Genome_build: NC_003210.1
Supplementary_files_format_and_content: Raw_counts_of_sequenced_reads.xlsx: Excel table with raw counts of sequenced reads for each replicate in every gene.
Supplementary_files_format_and_content: DESeq2_output.xlsx: Excel file includes normalised, log2 fold change and p-value for each gene.

organism: Listeria monocytogenes

source_name: bacterial pellets

growth_protocol: Bacterial cells were grown in a chemically defined media, 25mM glycerol until O.D600 = 1.

extract_protocol:
Samples were stabilised in RNAlater and RNA was extracted using RNeasy mini prep kit (Qiagen).
The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (Illumina) was used to prepare the cDNA fragment libraries.

treatment_protocol: Addition of 0.2% chitin.

value: EGD-e

value: 0.2% chitin

tag: growth phase

value: Late exponential phase


title: GlyandChitinLEP3

tag: treatment


title: GlyandChitinLEP2


title: GlyLEP3

value: No chitin


title: GlyLEP2


title: GlyLEP1


title: Sample_neuron_F19

value: cortex

value: acute slice

value: bcl2fastq2 v2.17


title: Primitive tumor [JA58]

data_processing: Data were processed using RMA algorithm implemented in oligo Bioconductor package (McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics,    11(2):242-253.)

source_name: Primitve Breast Cancer Tumor

extract_protocol: RNA was extracted with miRNeasy FFPE kit (Qiagen) in accordance with the manufacture's protocol.

tag: type

value: Primitive

value: FFPE

tag: grade


title: Control_04

city: Montreal

first: Bruno

last: Larrivée

state: Quebec

address: 5415 Boul. L'Assomption

country: Canada

institute: Hôpital Maisonneuve-Rosemont

data_processing:
Analysis was performed using the Torrent Suite software v5.12 (Thermo Fisher) and the AmpliSeqRNA plugin (Thermo Fisher)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited csv file include raw read counts for each sample

source_name: HUVEC Controls

growth_protocol: EndoGRO-MV-VEGF Complete Culture Media Kit  (SCME003 Sigma-Aldrich)

extract_protocol:
RNeasy plus mini kit ( Qiagen, Cat No./ID: 74134)
Transcriptomic analysis using Ion AmpliSeq Transcriptome Human Gene Expression Kit (Thermo Fisher Scientific) according to manufacturer's instructions.
Transcriptome profiling by Ampliseq using the Human Gene Expression Core Panel simultaneously targeting over 20 000 RefSeq genes

treatment_protocol: HUVEC cells treated with PBS or with COCO (60ng/ml) for 16 hours

value: HUVEC

value: control


title: Control_03


title: Control_02


title: COCO_04

source_name: HUVEC COCO treated

value: COCO


title: COCO_02


title: COCO_01


title: At Col-0 AG-7

city: Springfield

first: Laszlo

last: Kovacs

state: Missouri

address: 901 S  National Avenue

institute: Missouri State University

data_processing:
Raw sequences were uploded and filtered by length (between 15 and 1,000 nt) and quality (limit 0.05) using deault settings implemented by CLC Genomics Workbench 7.0.4 (Qiagen).
To remove remaining adapter sequences, 15 nucleotides were deleted from the 5-end of all reads using CLC Genomics Workbench 7.0.4 (Qiagen).
Filtered sequences were mapped to Arabidopsis TAIR10 reference genome sequence (downloaded from ENSEMBL) using gene and mRNA annotations on the default settings in the forward direction (CLC Genomics Workbench 7.0.4).
Mapped reads were normalized as RPKMs, and differential transcipt abundance analysis was performed between treatment and control with replicates using the "EDGE" test on default settings (CLC Genomics Workbench 7.0.4).
The resulting EDGE test results were subjected to both FDR and Bonferroni corrections (CLC Genomics Workbench 7.0.4).
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: Format: CSV; Content: AgNP vs Control fold-change values, p-value, tagwise dispersions fold-change, weighted difference, Bonferroni-corrected p-value, FDR-corrected p-value, Read counts, RPKM, exon-exon reads, intron reads, and chromosomal coordinates of genes.

organism: Arabidopsis thaliana

source_name: silver nanoparticles 20nm length @ 4µg/mL

growth_protocol: Plants were seeded and grown in 1/2 MS, 2.5% MOPS and 08% agar media. After3 days of stratification at 4°C , plants were transferred to a Conviron Adaptis A1000-AR Growth Chamber for 14 days at 21°C and a 10h light/14h dark cycle.

extract_protocol:
Thirty seedlings (entire ornisms) from each replicate were harvested and flash frozen using liquid nitrogen, then pulvarized using a mortar and a pestle. RNA extraction was performed using the standard Trizol method. RNA was purified using RNeasy RNA-Extraction Kit (Qiagen) following rhe manufacturer's protocols. 1 µg of RNA was used to construct libraries using the TruSeq  Stranded mRNA Sample Preparation Kit (Illumina).
RNA libraries were constructed with TruSeq Stranded mRNA Sample Preparation Kit (Illumina) following the protocol provided by Illumina.
RNA-seq libraries were purified, amplified and sigle-end sequenced (100-nt length) on two flow cells of Illuimna HiSeq2500 Sequencer at the Genome Sequencing Facility of the University of Kansas Medical Center.

treatment_protocol: Treated seedlings were grown for 14 days on 1/2 MS agar-solidified medium containing silver nanoparticles of 20 nm diameter at concentration of 4 µg/mL.  Control seedlings were grown for 14 days on 1/2 MS agar-solidified medium without nanomaterials. Plants were seeded directly on the treatment or control media.

tag: ecotype

value: Columbia

value: whole plant

tag: age

value: 14 days


title: At Col-0 AG-4

value: silver nanoparticles 20nm length @ 4µg/mL


title: At Col-0 CO-4B

source_name: water (control)

value: water (control)


title: At Col-0 CO-7


title: At Col-0 CO-5


title: NFYA_CUTRUN_CD34_AAVS32_rep1

last: Liu

address: 300 Longwood Avenue

department: Hematology/Oncology

data_processing:
Library strategy: CUT&RUN
Data was processed with CUT&RUNTools, which incorporates the following softwares
Reads were trimmed with trimmomatic 0.36 to remove low quality reads and adapter sequences. (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Bowtie2 (v2.2.9) was used to align reads to reference genome
Aligned reads were marked for duplicates with Picard 2.8.0 MarkDuplicates function.
Samtools 1.3.1 was used to remove duplicate reads, sort and index alignment files. DNA fragments larger than 120 bp were removed
MACS2 v2.1 was used to call peaks based on alignment file
bigwig was generated using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads

source_name: CD34+ HSPC derived erythroid precursors

extract_protocol:
Briefly, 1 million cells were collected and frozen in 10% DMSO in FBS, as necessary. Frozen cells were thawed, pelleted, and washed once with PBS, and  processed according to the following steps: 1) addition of 0.5 mL of NE buffer (20 mM HEPES-KOH, pH 7.9, 10 mM KCl, 0.5 mM Spermidine, 0.1% Triton X-100, 20% Glycerol and 1x protease inhibitor cocktails from Sigma) for nuclei isolation. Nuclei were pelleted at 600 x g for 3 min, resuspended with 0.4 mL of NE buffer. 2) 25 uL BioMagPlus Concanavalin A beads slurry was washed twice and resuspended in 200uL Binding Buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2), and   Binding Buffer is added to the nuclei suspension. The mixture was thoroughly mixed on a rocker for 10 min to allow binding to nuclei to the beads. 3) The nuclei were pelleted with a magnet stand and blocked with Wash Buffer (20 mM HEPES-NaOH pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.1% BSA and 1x protease inhibitor cocktails from Sigma) supplemented with 2 mM EDTA. After washing once with Wash Buffer, nuclei were resuspended in 200 uL Wash buffer containing 2 ug of antibody, and incubated overnight to allow antibody binding. 4) The next day, wash the nuclei twice on a magnet stand with wash buffer and incubate with 1:1000 pA-MN in 200 uL Wash Buffer. After 1 hr, wash twice to remove unbound pA-MN. 5) Resuspend the nuclei in 150 uL Wash Buffer, chill on a 0°C metal block that sits in water-ice mixture. Add 3 uL 100 mM CaCl2 to activate pA-MN, and incubate at 0°C for 60 min. 6) The reaction was stopped by adding 150 uL 2XSTOP buffer (200 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/mL RNase A and 40 mg/mL glycogen). The protein-DNA complex was released by centrifugation and then digested by proteinase K at 50°C overnight. DNA was extracted by ethanol precipitation, followed by Qubit fluorometer and bioanalyzer quality control.
Library preparation of CUT&RUN was performed using NEB Ultra II library preparation kit with important modifications. Briefly, less than 30 ng DNA is used as input. End prep was performed at 20°C for 30 min and then 50°C for 60min (instead of 65°C for 30 min in the manual). The reduced temperature prevents melting of short DNA fragments. 5 pmol adaptor was added and ligated to end prep products at 20°C for 15 min. USER enzyme was then used to cleave the uracil in the loop. 1.7x volume of AMPure beads were used to purify the ligation product. The use of 1.7x beads is essential for recovery of short fragments. To amplify the library, the ligation product was mixed with 2x Ultra II Q5 mix, universal primer and index primers. PCR was carried out as follows: 98°C 30 s, 12 cycles of 98°C 10s and 65°C 10s, and final extension 65°C 5 min. The PCR product was subjected twice to double size selection  with 0.8x and then 1.2x AMPure beads. The purified library was quantified with Qubit and Tapestation. Libraries were pooled at similar molar amount and sequenced using Nextseq500 platform. Paired-end sequencing, read length 42 bp x 2, 6 bp index was performed. For detailed protocol please see: dx.doi.org/10.17504/protocols.io.wvgfe3w

value: CD34+ HSPC derived erythroid precursors (Primary cells, adult)

tag: genotype

value: AAVS1 KO

tag: antibody

value: NFYA


title: NFYA_CUTRUN_CD34_KO32_rep1

value: BCL11A KO


title: NFYA_CUTRUN_CD34_shNFYA

value: Knockdown NFYA


title: NFYA_CUTRUN_BCLKOdCas9_208_rep2

source_name: HUDEP-2 cells

tag: cell line

value: HUDEP-2 cells

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor, Immortalized

value: BCL11A KO;dCas9/sgRNA_208


title: TBP_CUTRUN_CD34_KO32_rep1

tag: cell type

value: TBP


title: NFYA_CUTRUN_BCLKOdCas9_197_rep2

value: BCL11A KO;dCas9/sgRNA_197


title: NFYA_CUTRUN_CD34_shCtr

value: Knockdown control


title: NFYA_CUTRUN_BCLKOdCas9_158_rep2

value: BCL11A KO;dCas9/sgRNA_158


title: COCO_03

value: HUVEC

value: COCO


title: NFYA_CUTRUN_BCLKOdCas9_139_rep2

value: BCL11A KO;dCas9/sgRNA_139


title: Control_01

value: control


title: NFYA_CUTRUN_BCLKOdCas9_124_rep2

value: BCL11A KO;dCas9/sgRNA_124


title: NFYA_CUTRUN_BCLKOdCas9_115_rep2

value: BCL11A KO;dCas9/sgRNA_115


title: At Col-0 AG-5

value: Columbia

value: whole plant

value: silver nanoparticles 20nm length @ 4µg/mL

value: 14 days


title: NFYA_CUTRUN_BCLKOdCas9_102_rep2

value: HUDEP-2 cells

value: BCL11A KO;dCas9/sgRNA_102

value: NFYA


title: NFYA_CUTRUN_BCLKOdCas9_62_rep2

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor, Immortalized

value: BCL11A KO;dCas9/sgRNA_62


title: NFYA_CUTRUN_BCLKOdCas9_208_rep1

value: BCL11A KO;dCas9/sgRNA_208


title: NFYA_CUTRUN_BCLKOdCas9_AAVS_rep2

value: BCL11A KO;dCas9/sgRNA_AAVS1


title: NFYA_CUTRUN_BCLKOdCas9_158_rep1

value: BCL11A KO;dCas9/sgRNA_158


title: NFYA_CUTRUN_BCLKOdCas9_197_rep1

value: BCL11A KO;dCas9/sgRNA_197


title: NFYA_CUTRUN_BCLKOdCas9_139_rep1

value: BCL11A KO;dCas9/sgRNA_139


title: NFYA_CUTRUN_BCLKOdCas9_124_rep1


title: NFYA_CUTRUN_CD34_shBCL

value: CD34+ HSPC derived erythroid precursors (Primary cells, adult)

value: Knockdown BCL11A


title: NFYA_CUTRUN_BCLKOdCas9_102_rep1


title: NFYA_CUTRUN_BCLKOdCas9_115_rep1

value: BCL11A KO;dCas9/sgRNA_115


title: NFYA_CUTRUN_BCLKOdCas9_62_rep1


title: NFYA_CUTRUN_Cord_CD34

value: Cord Blood CD34+ HSPC derived erythroid precursors (Primary cells, fetal)

value: wild-type


title: NFYA_CUTRUN_BCLKOdCas9_AAVS_rep1


title: NFYA_CUTRUN_cloneF11d

value: BCL11A motif editing


title: TBP_CUTRUN_CD34_AAVS32_rep1

value: AAVS1 KO

value: TBP


title: NFYA_CUTRUN_cloneE11p

value: HUDEP-2 cells

value: BCL11A KO;NF-Y motif editing


title: NFYA_CUTRUN_cloneE1d

value: Human Umbilical Cord Blood-Derived Erythroid Progenitor, Immortalized

value: NFYA


title: NFYA_CUTRUN_cloneC4p


title: NFYA_CUTRUN_cloneD10d


title: NFYA_CUTRUN_cloneB7p


title: NFYA_CUTRUN_cloneB7d


title: NFYA_CUTRUN_cloneA9d


title: NFYA_CUTRUN_cloneB6p


title: NFYA_CUTRUN_cloneB2p


title: NFYA_CUTRUN_HDP2_rep2


title: NFYA_CUTRUN_HDP1_rep2

source_name: HUDEP-1 cells

value: HUDEP-1 cells


title: NFYA_CUTRUN_BCLKOHDP2_rep2

value: BCL11A KO


title: NFYA_CUTRUN_HDP1_rep1


title: NFYA_CUTRUN_BCLKOHDP2_rep1


title: NFYA_CUTRUN_HDP2_rep1


title: PROseq_CD34_BCLKO_72hr_rep2

description: nascent RNA

data_processing:
FASTQ read pairs were trimmed to 40bp per mate, and read pairs with a minimum average base quality score of 20 were retained. Read pairs were then further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10).
R1 reads were then aligned to the spike genome index using Bowtie 1.2.2 (-v 2 --best --un), with those reads failing to map serving as input to the primary genome alignment step(s) (using Bowtie options -v 2 --best).
Reads mapping to the reference genome were sorted via samtools 1.3.1 (-n), and subsequently converted to bedGraph format. Because PRO-seq reveals the position of the RNA 3’ end, the “+” and “-” strands were swapped to generate bedGraphs representing 3’ end positions.
Tags on each gene were summed and normalized. A table containing the TPM (Tags per Million reads) of each gene was generated.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph contains location/count of  3' end of mapped reads; csv file is a table containing the TPM (Tags per million reads) of each gene.

growth_protocol: The cells were thawed and recovered to EDM (IMDM (Corning, 15-016-CV)  supplemented with 330 μg/mL Holo-Human Transferrin, 10 μg/mL Recombinant Human Insulin, 2 IU/mL Heparin, 5% Inactivated Plasma, 3 IU/mL Erythropoietin, 2 mM L-Glutamine) with three supplements (10-6 M hydrocortisone, 100 ng/mL SCF, 5 ng/mL IL-3) for 7 days to allow erythroid differentiation, then further differentiated in EDM with one supplement (100 ng/mL SCF).

extract_protocol:
Ten million CD34+ cells undergoing erythroid differentiation were harvested on ice, and washed with cold PBS. Cells were resuspended in 2 mL cold Buffer W (10 mM Tris-Cl, pH 8.0, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 0.5 mM DTT, 10% glycerol, 0.5% BSA) using wide-bore P1000 tip and transferred to a 2 mL low binding tube, and strained through a 35 micron nylon mesh cell strainer. Immediately add 18 mL Chilled Buffer P (Buffer W supplemented with 0.05% Igepal CA-630) to cell suspension and mix gently for 2 min. Cells were centrifuged at 400xg for 8 min and resuspended in 1 mL Buffer F (50 mM Tris-HCl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT, 0.5% BSA), and centrifuged again at 400xg for 8 min. The pellets were resuspended in 400 uL Buffer F, counted using a hemocytometer to ensure that >95% cells were permeabilized. The cell density was adjusted to 1 x 106/100 uL, and the suspension was snap-frozen and stored at -80°C.An aliquot of frozen cells were thawed on ice and counted. For each sample, take 1 million cells and spike in 50,000 permeabilized Drosophila S2 cells, and add the same volume of 2x Nuclear Run-On buffer (10 mM Tris-HCl pH 8.0, 300 mM KCl, 1% Sarkosyl, 5 mM MgCl2, 1 mM DTT, 200 uM biotin-11-A/C/G/UTP (Perkin-Elmer), 0.8 u/mL SUPERaseIN inhibitor [Ambion]) and then incubate at 30°C for 5 min. Total RNA was isolated and fragmented by base hydrolysis with 0.25 N NaOH on ince for 10 min, and neutralized with 1x volume of Tris-HCl pH 6.8. Biotinylated RNA was bound to 30 uL Streptavidin M-280 beads (Thermo Fisher Scientific) in Binding Buffer (300 mM NaCl, 10 mM Tris-HCl pH 7.4, 0.1% Triton X-100). Beads were washed twice with High salt buffer (2 M NaCl, 50 mM Tris- HCl pH 7.4, 0.5% Triton X-100), twice in Binding Buffer, and twice in Low salt buffer (5 mM Tris-HCl pH 7.4, 0.1% Triton X-100). Bound RNA was extracted using Trizol (Invitrogen), precipitated using ethanol and dissolved in H2O.
Nascent RNA was ligated with 10 pmol of 3’ RNA adaptor (5’p-rNrNrNrNrNrNrGrArUrCrGrUrCrGrGrArCrUrGrUrArGrArArCrUrCrUrGrArArC-/3’InvdT/) and T4 RNA ligase I (NEB) at 20°C for 2hrs. Ligated RNA was enriched with another round of streptavidin beads purification with one additional round of washing with 1x ThermoPol Buffer (NEB). RNA products were treated with RNA 5’ Pyrophosphohydrolase (RppH, NEB) at 37°C for 30 min followed by one wash of High, Low and T4 PNK Buffer. 5’ ends were repaired with Polynucleotide Kinase (PNK, NEB) at 37°C for 30 min. RNA was ligated to 5’ RNA adaptor 5’-rCrCrUrUrGrGrCrArCrCrCrGrArGrArArUrUrCrCrA-3’ with T4 RNA ligate I (NEB) for 2 hrs at 20 °C, and enriched with streptavidin beads with additional wash using 1x SuperScript IV buffer (Thermo Fisher Scientific) and reverse transcribed using 25 pmol RT primer AATGATACGGCGACCACC GAGATCTACACGTTCAGAGTTCTACAGTCCGA. 12.5 pmol RPI index primers and RT pimer were added to the RT product for library amplification.

treatment_protocol: Cells were nucleofected with indicated sgRNA 32 or 72 hrs before permeabilization.

value: Erythroid

value: CD34+ HSPC derived erythroid precursors

tag: sgrna target

value: BCL11A exon2

value: BCL11A knockout

tag: time (after genome editing)

value: 72 hrs

tag: time  (erythroid differentiation stage)

value: Day 8.5


title: PROseq_CD34_AAVS1_72hr_rep2

description: nascent RNA

value: control


title: PROseq_CD34_BCLKO_72hr_rep1

description: nascent RNA


title: NFYA_CUTRUN_cloneG8d


title: NFYA_CUTRUN_cloneE6p


title: NFYA_CUTRUN_cloneG10p


title: PROseq_CD34_AAVS1_72hr_rep1

description: nascent RNA


title: NFYA_ChIP_HDP2_shNFYA

data_processing:
Data was processed with CUT&RUNTools using default settings unless specified below.
Reads were trimmed with trimmomatic 0.36 to remove low quality reads and adapter sequences. (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Bowtie2 (v2.2.9) was used to align reads to reference genome
Aligned reads were marked for duplicates with Picard 2.8.0 MarkDuplicates function.
Samtools 1.3.1 was used to remove duplicate reads, sort and index alignment files. DNA fragments between 150 bp and 500 bp were selected for peak calling.
MACS2 v2.1 was used to call peaks based on alignment file
bigwig was generated using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads

growth_protocol: HUDEP-2 cells were maintained in expansion medium: StemSpan™ SFEM (STEMCELL Technologies, 09650) with SCF (50 ng/ml), EPO (3 IU/ml), Dexamethasone (10-6 M), Doxycycline (1 μg/ml), and passaged every three days. The cell density was maintained within 20 thousand to 500 thousand cells/mL. Erythroid differentiation was carried out by replacing the medium to EDM (Erythroid Differentiation Media: IMDM (Corning, 15-016-CV) supplemented with 330 μg/mL Holo-Human Transferrin, 10 μg/mL Recombinant Human Insulin, 2 IU/mL Heparin, 5% Inactivated Plasma, 3 IU/mL Erythropoietin, 2 mM L-Glutamine) with two supplements (100 ng/mL SCF, 1 μg/mL doxycycline). Cells were collected for downstream assays after 5 days differentiation.

extract_protocol:
Five million differentiated HUDEP cells were collected and fixed with1% formaldehyde for 5 minutes at room temperature, and quenched with 125 mM glycine. Cells were washed with ice-cold PBS twice and resuspended in 0.13 mL lysis buffer (50 mM Tris-HCl 8.0, 10 mM EDTA, 0.5% SDS) and sonicated in a microtube (Covaris, 520045) with Covaris E220 ultrasonicator (Covaris) to an average of 300-500 bp. Sonicated chromatin was diluted with 1 mL ChIP dilution buffer (20 mM Tris-HCl 8.0, 2 mM EDTA, 1% Triton X-100, 300 mM NaCl, protease inhibitor), followed by adding 20 uL Dynabeads protein G (Thermo Fisher Scientific) and 3 ug antibody (NFYA, ab139402, Abcam). The mixture was incubated on a rotator overnight and washed with the following buffers: twice with RIPA150 (20 mM Tris-HCl 8.0, 1 mM EDTA, 1% Triton X-100,150 mM NaCl, 0.1% Sodium Deoxycholate, 0.1% SDS), twice with RIPA500 (20 mM Tris-HCl 8.0, 1 mM EDTA, 1% Triton X-100, 500 mM NaCl, 0.1% Sodium Deoxycholate, 0.1% SDS), twice with LiCl buffer (10 mM Tris-HCl 8.0, 1 mM EDTA, 0.5% NP-40, 250 mM LiCl, 0.5% Sodium Deoxycholate), twice with TE buffer (10 mM Tris-HCl 8.0, 1 mM EDTA). The washed chromatin was eluted using 300 uL Elution buffer (50 mM Tris-HCl 8.0, 10 mM EDTA, 1% SDS, 150 mM NaCl, 0.1 mg/mL Proteinase K) and decrosslinked at 65°C overnight. DNA was extracted with phenol-chloroform, and precipitated by adding 2.5x volume of absolute ethanol followed by centrifuging at 14,000 rpm for 15 minutes. The pellet was washed once with 75% ethanol, then dried and dissolved with 50 uL TE buffer.
Library was prepared with NEBNext Ultra II DNA Library Prep Kit (NEB) according to manufacturer’s protocol.

value: Knockdown NFYA

tag: chip antibody

value: NFYA (ab139402, Abcam)


title: NFYA_ChIP_HDP1_shNFYA

tag: tissue


title: PROseq_CD34_AAVS1_32hr_rep2

description: nascent RNA

value: 32 hrs

value: Day 7


title: PROseq_CD34_AAVS1_32hr_rep1

description: nascent RNA


title: NFYA_CUTRUN_cloneB8p

value: HUDEP-2 cells


title: NFYA_ChIP_BCLKOHDP2_shNFYA


title: PROseq_CD34_BCLKO_32hr_rep1

description: nascent RNA


title: NFYA_ChIP_BCLKOHDP2_ctr

value: Knockdown control


title: NFYA_ChIP_HDP2_ctr


title: NFYA_ChIP_HDP1_ctr


title: ATAC_CD34_BCLKO72_rep2

data_processing:
Data was processed with CUT&RUNTools, which incorporates the following softwares. All the settings were default as in CUT&RUNTools.
Reads were trimmed with trimmomatic 0.36 to remove low quality reads and adapter sequences. (ILLUMINACLIP:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25)
Bowtie2 (v2.2.9) was used to align reads to reference genome
Aligned reads were marked for duplicates with Picard 2.8.0 MarkDuplicates function.
Samtools 1.3.1 was used to remove duplicate reads, sort and index alignment files. DNA fragments larger than 120 bp were removed
MACS2 v2.1 was used to call peaks based on alignment file
bigwig was generated using bedGraphToBigWig
Genome_build: hg19
Supplementary_files_format_and_content: BigWig file is a binary format of Wig file, value represents pile-up signal of mapped reads

extract_protocol:
Omni-ATAC was performed with 50,000 fresh cells or frozen pellets. Cells were first permeabilized with 50 uL RSB buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) with 0.1% NP40, 0.1 Tween-20 and 0.01% Digitonin for 3 minutes. 1 mL of cold RSB containing 0.1% Tween-20 was added before cells were pelleted again. The pellets were then resuspended with 50 uL transposition mixture (25uL 2xTD buffer from ATACseq kit, 2.5 uL transposase, 16.5 uL PBS, 0.5 ul 1% digitonin, and 0.5 ul 10% Tween-20), and reaction was carried out at 37 °C for 60 minutes. Genomic DNA was extracted with Qiagen minElute PCR purification kit according to manufacturer’s manual. Total DNA was used as template for amplification, mixed with 15 uL of 2x Ultra II Q5 mix, 1 uL of 10 uM i7 primer (AATGATACGGCGACCACCGAGATCTACAC-TCGTCGGCAGCGTCAGATGTG) and 1 uL of 10 uM i5 primer (CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGT) where N represent barcodes. PCR amplification was performed as follow: 65°C 5 min, 98°C 30 s, 98°C 10 s, 63°C 30 s, repeat step 3-4 for 9 times, and 63°C 5min. PCR products were purified with AMPure beads and quantified using Qubit and Tapestation before pooling and sequencing.
Total tagmentated genomic DNAwas  mixed with 15 uL of 2x Ultra II Q5 mix, 1 uL of 10 uM i7 primer (AATGATACGGCGACCACCGAGATCTACAC-TCGTCGGCAGCGTCAGATGTG) and 1 uL of 10 uM i5 primer (CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTCTCGTGGGCTCGGAGATGT) where N represent barcodes. PCR amplification was performed as follow: 65°C 5 min, 98°C 30 s, 98°C 10 s, 63°C 30 s, repeat step 3-4 for 9 times, and 63°C 5min. PCR products were purified with AMPure beads and quantified using Qubit and Tapestation before pooling and sequencing.
Tn-seq

tag: time

value: 72 hrs KO time

tag: differentiation stage


title: ATAC_CD34_aavs72_rep2


title: ATAC_CD34_BCLKO72_rep1


title: ATAC_CD34_aavs32_rep1

value: 32 hrs KO time


title: PROseq_CD34_BCLKO_32hr_rep2

description: nascent RNA


title: PFOS20_598_t4_S22_R1_001

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

data_processing:
bcl files were processed into fastq files with bcl2fastq v.2.17.1.14
Fastq files were processed with the manufacturer's script generate_reference.R and pete.star.script_3.0.R where tables of feature counts were generated for each samples.
Genome_build: Human TempO-Seq® Tox+ Surrogate (S1500+) custom probe annotation
Supplementary_files_format_and_content: table of probe counts for each sample, grouped by exposure length

source_name: human liver spheroids Insphero

growth_protocol: 14 day in minimal media

extract_protocol:
not extracted, tempoSeq lysis buffer used to lyse cells, which were then frozen and 2ul used for TempO-Seq library building
Assay Principle
The TempO-Seq assay utilizes a detector oligo (DO) pool specific to the RNA targets to be monitored. BioSpyder offers fixed content and custom DO pools to measure focused sets of transcripts, up to whole transcriptomes. The assay can utilize purified RNA, cell lysates, tissue lysates, or FFPE tissue lysates (FFPE kit available separately). In addition, both positive and negative control samples can be included.
Samples are annealed to a matched pair of detector oligos (DOs), with each pair targeting a single gene. The DO pool targets up to tens of thousands of RNA sequences, depending on the targeted gene content of the assay, but all share the same pair of primer binding sequences (indicated in Fig 1. by the red and yellow sections of each DO). The DOs hybridize to sequences of the targeted RNA molecule such that their respective 3’ and 5’ ends are adjacent. Each UDO has an additional target-specific sequence at their 3’ end that hybridizes to the targeted RNA.
After DO annealing, excess oligos and mis-hybridized or weakly hybridized DOs are removed by nuclease digestion, and the annealed oligos are ligated to form amplifiable templates. The ligated DOs are amplified with one pair of primers (making each PCR reaction single-plex regardless of the number of genes measured), with a different combination of sample index/tag sequences assigned to each sample. The PCR products are pooled together into a sequencing library, which is then purified and run on an Illumina NGS to count the number of ligated detector oligo sequences per sample (ThermoFisher-compatible kit under development). Because TempO-Seq includes an end-point PCR reaction, quantitation of the amplified products before library pooling is not needed. Very low concentration and negative control samples are expected to show low reads in the sequencing data.
BioSyder -TempO-Seq protocol v2.1 sept 6,2017
Human S1500, index E,F,H,G were used for indexing

treatment_protocol: PFAS replenished every 3rd day with media change

tag: chemical

value: PFOS

tag: dose(um)

tag: time point (days)


title: PFOS2_710_t4_S134_R1_001


title: PFOS20_690_t4_S114_R1_001


title: PFOS20_694_t4_S118_R1_001


title: PFOS20_594_t4_S18_R1_001


title: PFOS2_706_t4_S130_R1_001


title: PFOS2_610_t4_S34_R1_001


title: PFOS2_614_t4_S38_R1_001


title: PFOS10_702_t4_S126_R1_001


title: PFOS10_606_t4_S30_R1_001


title: PFOS10_602_t4_S26_R1_001


title: PFOS10_698_t4_S122_R1_001


title: PFOS1_622_t4_S46_R1_001


title: PFOS0.2_630_t4_S54_R1_001


title: PFOS1_618_t4_S42_R1_001


title: PFOS0.2_626_t4_S50_R1_001


title: PFOS0.1_638_t4_S62_R1_001


title: PFOS0.02_742_t4_S166_R1_001


title: PFOS0.1_634_t4_S58_R1_001


title: PFOS0.2_726_t4_S150_R1_001


title: PFOS0.02_642_t4_S66_R1_001


title: PFOS0.02_646_t4_S70_R1_001


title: PFOA20_599_t4_S23_R1_001

value: PFOA


title: ATAC_CD34_BCLKO32_rep1

value: Erythroid

value: BCL11A KO


title: PFOA2_707_t4_S131_R1_001


title: PFOA20_595_t4_S19_R1_001


title: PFOA2_711_t4_S135_R1_001


title: PFOA2_615_t4_S39_R1_001


title: PFOA10_703_t4_S127_R1_001


title: PFOA10_603_t4_S27_R1_001


title: PFOA1_715_t4_S139_R1_001


title: PFOA0.2_723_t4_S147_R1_001


title: PFOA0.2_627_t4_S51_R1_001


title: PFOA1_719_t4_S143_R1_001


title: PFOA1_623_t4_S47_R1_001


title: PFOA0.2_727_t4_S151_R1_001


title: PFOA0.2_631_t4_S55_R1_001


title: PFOA0.1_735_t4_S159_R1_001


title: PFOA1_619_t4_S43_R1_001


title: PFOS1_718_t4_S142_R1_001


title: PFOA10_699_t4_S123_R1_001


title: PFOA20_691_t4_S115_R1_001


title: PFOA0.1_639_t4_S63_R1_001


title: PFOA0.02_743_t4_S167_R1_001


title: PFOA0.02_643_t4_S67_R1_001


title: PFOA0.02_647_t4_S71_R1_001


title: PFDS50D0.17_685_t4_S109_R1_001

value: PFDS


title: PFDS50D0.17_589_t4_S13_R1_001


title: PFDS20_593_t4_S17_R1_001


title: PFDS20_693_t4_S117_R1_001


title: PFDS20_597_t4_S21_R1_001


title: PFDS2_613_t4_S37_R1_001


title: PFDS50D0.17_585_t4_S9_R1_001


title: PFDS2_705_t4_S129_R1_001


title: PFDS2_609_t4_S33_R1_001


title: PFDS2_709_t4_S133_R1_001


title: PFDS100D0.3_673_t4_S97_R1_001


title: PFDS100D0.3_677_t4_S101_R1_001


title: PFDS10_697_t4_S121_R1_001


title: PFDS10_605_t4_S29_R1_001


title: PFDS10_701_t4_S125_R1_001


title: PFOA0.1_635_t4_S59_R1_001


title: PFDS10_601_t4_S25_R1_001


title: PFDS0.2_721_t4_S145_R1_001


title: PFDS1_713_t4_S137_R1_001


title: PFDS1_617_t4_S41_R1_001


title: PFDS100D0.3_577_t4_S1_R1_001


title: PFDS0.2_625_t4_S49_R1_001


title: PFDS0.2_725_t4_S149_R1_001


title: PFDS0.1_729_t4_S153_R1_001


title: PFDS0.1_637_t4_S61_R1_001


title: PFDS0.02_737_t4_S161_R1_001


title: PFDS0.1_633_t4_S57_R1_001


title: PFDS0.02_741_t4_S165_R1_001


title: PFDS0.2_629_t4_S53_R1_001


title: PFBS50D0.17_688_t4_S112_R1_001

value: PFBS


title: PFDS0.02_641_t4_S65_R1_001


title: PFDS0.02_645_t4_S69_R1_001


title: PFBS50D0.17_684_t4_S108_R1_001


title: PFBS50D0.17_588_t4_S12_R1_001


title: PFBS20_696_t4_S120_R1_001


title: PFBS20_692_t4_S116_R1_001


title: PFBS20_600_t4_S24_R1_001


title: PFBS20_596_t4_S20_R1_001


title: PFDS1_621_t4_S45_R1_001


title: PFBS2_712_t4_S136_R1_001


title: PFBS2_616_t4_S40_R1_001


title: PFBS2_612_t4_S36_R1_001


title: PFBS10_604_t4_S28_R1_001


title: PFBS100D0.3_676_t4_S100_R1_001


title: PFBS10_608_t4_S32_R1_001


title: PFBS1_720_t4_S144_R1_001


title: PFBS100D0.3_580_t4_S4_R1_001


title: PFBS10_704_t4_S128_R1_001


title: PFBS10_700_t4_S124_R1_001


title: PFBS100D0.3_680_t4_S104_R1_001


title: PFBS1_716_t4_S140_R1_001


title: PFBS1_620_t4_S44_R1_001


title: PFBS1_624_t4_S48_R1_001


title: PFBS50D0.17_592_t4_S16_R1_001


title: PFBS0.2_728_t4_S152_R1_001


title: PFBS0.2_724_t4_S148_R1_001


title: PFBS0.1_732_t4_S156_R1_001


title: PFBS0.2_632_t4_S56_R1_001


title: PFBS0.1_736_t4_S160_R1_001


title: PFBS0.02_744_t4_S168_R1_001


title: PFBS0.02_648_t4_S72_R1_001


title: PFBS0.02_644_t4_S68_R1_001


title: DMSO0_659_t4_S83_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_659

value: DMSO


title: DMSO0_660_t4_S84_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_660


title: DMSO0_658_t4_S82_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_658


title: PFOS20_502_t3_S118_R1_001


title: PFBS2_708_t4_S132_R1_001


title: PFBS0.1_640_t4_S64_R1_001


title: PFOS20_498_t3_S114_R1_001


title: PFBS100D0.3_584_t4_S8_R1_001


title: PFOS1_430_t3_S46_R1_001


title: PFOS0.2_534_t3_S150_R1_001


title: PFOS2_518_t3_S134_R1_001


title: PFOS10_510_t3_S126_R1_001


title: PFOS0.2_530_t3_S146_R1_001


title: PFOS10_414_t3_S30_R1_001


title: PFOS20_402_t3_S18_R1_001


title: PFOS2_422_t3_S38_R1_001


title: PFOS1_526_t3_S142_R1_001


title: PFOS10_410_t3_S26_R1_001


title: PFOS20_406_t3_S22_R1_001


title: PFOS1_426_t3_S42_R1_001


title: PFOS0.2_438_t3_S54_R1_001


title: PFOS0.2_434_t3_S50_R1_001


title: PFBS0.1_636_t4_S60_R1_001


title: PFOS0.1_442_t3_S58_R1_001


title: PFOS0.1_446_t3_S62_R1_001


title: PFOS0.1_538_t3_S154_R1_001


title: PFBS0.02_740_t4_S164_R1_001


title: PFOS0.02_550_t3_S166_R1_001


title: PFOS0.02_546_t3_S162_R1_001


title: PFOS0.02_454_t3_S70_R1_001


title: DMSO0_657_t4_S81_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_657


title: PFOS2_418_t3_S34_R1_001


title: PFOS0.02_450_t3_S66_R1_001


title: PFOA50D0.17_495_t3_S111_R1_001


title: PFOA50D0.17_491_t3_S107_R1_001


title: PFOA50D0.17_395_t3_S11_R1_001


title: PFOA20_503_t3_S119_R1_001


title: PFOA20_407_t3_S23_R1_001


title: PFOS0.1_542_t3_S158_R1_001


title: PFOA2_519_t3_S135_R1_001


title: PFOA20_403_t3_S19_R1_001


title: PFOA10_507_t3_S123_R1_001


title: PFOA1_527_t3_S143_R1_001


title: PFOA10_411_t3_S27_R1_001


title: PFOA1_523_t3_S139_R1_001


title: PFOA2_423_t3_S39_R1_001


title: PFOA0.2_531_t3_S147_R1_001


title: PFOA0.1_539_t3_S155_R1_001


title: PFOA0.2_435_t3_S51_R1_001


title: PFOA1_427_t3_S43_R1_001


title: PFOA0.1_443_t3_S59_R1_001


title: PFOA20_499_t3_S115_R1_001


title: PFOA10_415_t3_S31_R1_001


title: PFOA0.1_543_t3_S159_R1_001


title: PFOA2_419_t3_S35_R1_001


title: PFOA0.02_547_t3_S163_R1_001


title: PFOA1_431_t3_S47_R1_001


title: PFOA0.1_447_t3_S63_R1_001


title: PFOA0.02_551_t3_S167_R1_001


title: PFOA0.02_451_t3_S67_R1_001


title: PFDS50D0.17_493_t3_S109_R1_001


title: PFOA50D0.17_399_t3_S15_R1_001


title: PFOA0.2_439_t3_S55_R1_001


title: PFOA10_511_t3_S127_R1_001


title: PFDS50D0.17_489_t3_S105_R1_001


title: PFOA0.2_535_t3_S151_R1_001


title: PFDS50D0.17_397_t3_S13_R1_001


title: PFDS50D0.17_393_t3_S9_R1_001


title: PFDS20_501_t3_S117_R1_001


title: PFDS20_497_t3_S113_R1_001


title: PFDS2_417_t3_S33_R1_001


title: PFDS2_517_t3_S133_R1_001


title: PFDS2_421_t3_S37_R1_001


title: PFDS2_513_t3_S129_R1_001


title: PFDS20_401_t3_S17_R1_001


title: PFDS10_509_t3_S125_R1_001


title: PFDS10_505_t3_S121_R1_001


title: PFDS10_413_t3_S29_R1_001


title: PFDS1_525_t3_S141_R1_001


title: PFDS100D0.3_385_t3_S1_R1_001


title: PFDS100D0.3_389_t3_S5_R1_001


title: PFDS1_429_t3_S45_R1_001


title: PFDS1_521_t3_S137_R1_001


title: PFDS0.2_529_t3_S145_R1_001


title: PFDS1_425_t3_S41_R1_001


title: PFDS0.1_541_t3_S157_R1_001


title: PFDS0.1_537_t3_S153_R1_001


title: PFDS10_409_t3_S25_R1_001


title: PFDS0.2_433_t3_S49_R1_001


title: PFDS0.2_437_t3_S53_R1_001


title: PFDS0.1_441_t3_S57_R1_001


title: PFDS0.1_445_t3_S61_R1_001


title: PFDS0.02_549_t3_S165_R1_001


title: PFDS0.02_453_t3_S69_R1_001


title: PFBS50D0.17_496_t3_S112_R1_001


title: PFBS50D0.17_492_t3_S108_R1_001


title: PFBS50D0.17_396_t3_S12_R1_001


title: PFBS20_500_t3_S116_R1_001


title: PFBS20_408_t3_S24_R1_001


title: PFDS0.2_533_t3_S149_R1_001


title: PFBS2_516_t3_S132_R1_001


title: PFBS20_404_t3_S20_R1_001


title: PFBS2_424_t3_S40_R1_001


title: PFBS100D0.3_488_t3_S104_R1_001


title: PFBS50D0.17_400_t3_S16_R1_001


title: PFBS100D0.3_388_t3_S4_R1_001


title: DMSO0_572_t3_S188_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_572


title: PFBS1_524_t3_S140_R1_001


title: PFBS0.02_456_t3_S72_R1_001


title: PFBS1_528_t3_S144_R1_001


title: PFBS0.1_444_t3_S60_R1_001


title: PFBS0.02_552_t3_S168_R1_001


title: PFBS10_508_t3_S124_R1_001


title: PFBS0.02_452_t3_S68_R1_001


title: PFBS0.2_532_t3_S148_R1_001


title: PFBS0.2_440_t3_S56_R1_001


title: DMSO0_566_t3_S182_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_566


title: PFBS0.2_436_t3_S52_R1_001


title: PFBS10_512_t3_S128_R1_001


title: DMSO0_568_t3_S184_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_568


title: DMSO0_564_t3_S180_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_564


title: PFBS0.1_448_t3_S64_R1_001


title: PFBS0.2_536_t3_S152_R1_001


title: PFBS100D0.3_392_t3_S8_R1_001


title: PFBS10_412_t3_S28_R1_001


title: PFBS0.1_540_t3_S156_R1_001


title: DMSO0_567_t3_S183_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_567


title: DMSO0_565_t3_S181_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_565


title: PFBS10_416_t3_S32_R1_001


title: PFBS1_432_t3_S48_R1_001


title: DMSO0_563_t3_S179_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_563


title: DMSO0_562_t3_S178_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_562


title: PFBS0.02_548_t3_S164_R1_001


title: DMSO0_561_t3_S177_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_561


title: DMSO0_472_t3_S88_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_472


title: PFOS10_606_S30_R1_001


title: DMSO0_469_t3_S85_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_469


title: PFOS2_706_S130_R1_001


title: PFOS0.2_630_S54_R1_001


title: DMSO0_468_t3_S84_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_468


title: PFOS20_594_S18_R1_001


title: PFOS20_690_S114_R1_001


title: DMSO0_467_t3_S83_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_467


title: PFOS10_698_S122_R1_001


title: PFOS20_598_S22_R1_001


title: PFOS10_702_S126_R1_001


title: PFOS0.2_722_S146_R1_001


title: DMSO0_471_t3_S87_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_471


title: DMSO0_476_t3_S92_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_476


title: DMSO0_470_t3_S86_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_470


title: PFOS20_694_S118_R1_001


title: PFOS2_710_S134_R1_001


title: PFOS0.2_626_S50_R1_001


title: PFOS1_622_S46_R1_001


title: PFOS0.1_734_S158_R1_001


title: PFBS2_420_t3_S36_R1_001


title: PFOS1_618_S42_R1_001


title: DMSO0_466_t3_S82_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_466


title: PFOS1_714_S138_R1_001


title: PFOS2_614_S38_R1_001


title: PFOS1_718_S142_R1_001


title: PFOS0.1_730_S154_R1_001


title: PFOS0.1_638_S62_R1_001


title: PFOS2_610_S34_R1_001


title: PFOS0.02_642_S66_R1_001


title: PFOS0.2_726_S150_R1_001


title: PFOA50D0.17_687_S111_R1_001


title: PFOA50D0.17_591_S15_R1_001


title: PFOA20_599_S23_R1_001


title: DMSO0_465_t3_S81_R1_001

description:
controls for doses 0.02, 0.1,1,2,10,20
DMSO_0_465


title: PFOA2_711_S135_R1_001


title: PFOA50D0.17_587_S11_R1_001


title: PFOA2_707_S131_R1_001


title: PFOA100D0.3_583_S7_R1_001


title: PFOA2_611_S35_R1_001


title: PFOS0.02_646_S70_R1_001


title: PFOA100D0.3_679_S103_R1_001


title: PFOA100D0.3_579_S3_R1_001


title: PFOA20_595_S19_R1_001


title: PFOS0.02_742_S166_R1_001


title: PFOA50D0.17_683_S107_R1_001


title: PFOA10_703_S127_R1_001


title: PFOA2_615_S39_R1_001


title: PFOA10_699_S123_R1_001


title: PFOA1_719_S143_R1_001


title: PFOA1_623_S47_R1_001


title: PFOA1_715_S139_R1_001


title: PFOA0.2_727_S151_R1_001


title: PFOA1_619_S43_R1_001


title: PFOA20_695_S119_R1_001


title: PFOS0.02_738_S162_R1_001


title: PFOA0.2_723_S147_R1_001


title: PFOA0.2_627_S51_R1_001


title: PFOA0.2_631_S55_R1_001


title: PFOA0.02_743_S167_R1_001


title: PFOA0.1_731_S155_R1_001


title: PFOA0.02_739_S163_R1_001


title: PFOA0.02_647_S71_R1_001


title: PFOA0.1_735_S159_R1_001


title: PFOA0.1_639_S63_R1_001


title: PFOA0.02_643_S67_R1_001


title: PFDS50D0.17_585_S9_R1_001


title: PFDS50D0.17_685_S109_R1_001


title: PFDS50D0.17_681_S105_R1_001


title: PFDS50D0.17_589_S13_R1_001


title: PFDS20_597_S21_R1_001


title: PFDS2_709_S133_R1_001


title: PFDS2_705_S129_R1_001


title: PFDS20_689_S113_R1_001


title: PFDS2_613_S37_R1_001


title: PFDS20_593_S17_R1_001


title: PFDS2_609_S33_R1_001


title: PFDS100D0.3_673_S97_R1_001


title: PFDS100D0.3_577_S1_R1_001


title: PFDS100D0.3_677_S101_R1_001


title: PFDS10_605_S29_R1_001


title: PFDS100D0.3_581_S5_R1_001


title: PFDS10_697_S121_R1_001


title: PFDS10_601_S25_R1_001


title: PFDS1_713_S137_R1_001


title: PFDS1_717_S141_R1_001


title: PFDS20_693_S117_R1_001


title: PFDS0.2_725_S149_R1_001


title: PFDS1_621_S45_R1_001


title: PFDS0.2_721_S145_R1_001


title: PFDS1_617_S41_R1_001


title: PFDS0.1_733_S157_R1_001


title: PFDS0.2_625_S49_R1_001


title: PFDS0.1_637_S61_R1_001


title: PFDS0.1_729_S153_R1_001


title: PFDS0.02_737_S161_R1_001


title: PFDS0.02_645_S69_R1_001


title: PFDS0.02_641_S65_R1_001