title: PF2B_ON_Isolate1

value: Isolate from  the overnight culture of the second time fermentation


title: FD2B_Batch1

status: Public on Mar 02 2020

type: SRA

city: Hørsholm

first: Yun

last: Chen

address: Bøge Alle 10

department: Health & Nutrition

country: Denmark

institute: Chr Hansen A/S

library_source: genomic

data_processing:
Eurofins performed basecalling
Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) was used to trim low-quality base pairs (bp) from the reads. The first 5 bps from the 5’end of both paired reads were also trimmed due to the observation of biased quality scores and nucleotide composition.
Spades with the “—careful” setting was used for performing de novo assembly.
Judged by contig coverage distribution, contigs with read coverage lower than 32 folds were removed from downstream analysis
Genome_build: de novo
Supplementary_files_format_and_content: de novo assemblies

molecule: genomic DNA

organism: Lacticaseibacillus rhamnosus

source_name: whole organism

growth_protocol: Freeze-dried product Lactobacillus rhamnosus GG from Chr Hansen were used. Overnight cultures and isolates were grown in MRS pH 6.5-broth and incubated at 37 degrees anaerobically.

extract_protocol:
DNA was extracted  using DNeasy Blood & Tissue Minikit (Qiagen)
Eurofins genomics - 4GLI-000100 shotgun library preparation
Eurofins genomics - 4GLI-000100 final quantification of library pool

treatment_protocol: No further treatment was applied

tag: strain

value: GG

tag: growth

value: Freeze-dried product

tag: second time fermentation batch

tag: freeze-dried batch

tag: growth conditions

value: Non-overnight-culture


title: FD2B_Batch1_ON

value: Overnight culture of freeze-dried product

value: Grown in MRS 6.5 broth


title: RNA-seq_EN_r3

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

country: USA

institute: UC San Diego

description: hESC-derived pancreatic cells

library_source: transcriptomic

data_processing:
For RNA-seq: Sequence fragments were aligned to the hg19 genome build with STAR using the parameters: --runThreadN 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragment per Kilobase of exon per Megabase of library size (FPKM) were calculated using Homer
For ChIP-seq: Sequence fragments were aligned to the hg19 genome build with bowtie2 using the parameters: --very-sensitive -p 16. Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
Fragments were normalized to 1e7 bases of library size using Homer
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated

molecule: total RNA

organism: Homo sapiens

source_name: EN Control replicate 3

growth_protocol: Primary cells were cultured in 1640 RPMI e medium supplemented with 10% FBS, 8.3mM glucose and, antibiotic  at 37˚C and 5% CO2

extract_protocol:
Total RNA was extracted by RNARNeasy Mini Kit
Libraries were prepared using the TruSeq® Stranded mRNA Library Prep Kit (RNA-seq) and the KAPA DNA Library Preparation Kits for Illumina®  KAPA Kit (ChIP-seq)

treatment_protocol: Islets were dissociated and reaggreate, transfected with lentivirus. Total RNA was prepared 72 hours post-transfection.

tag: cell type

value: differentiated hESCs

tag: developmental stage

value: Pancreatic endocrine cells


title: RNA-seq_EN_RA-late_r2

description: hESC-derived pancreatic cells

source_name: Late RA treatment EN replicate 2


title: chcc_source2 rep2

extract_protocol:
DNA was extracted using DNeasy Blood & Tissue Minikit (Qiagen)
Eurofins genomics - 4GLI-000100 shotgun library preparation
Eurofins genomics - 4GLI-000100 final quantification of library pool

value: Original stock


title: FD2A_Batch4


title: PF2B_ON

value: Overnight culture collected from second time fermentation


title: FD2A_Batch4_ON


title: RNA-seq_EN_r2

description: hESC-derived pancreatic cells

source_name: EN Control replicate 2


title: RNA-seq_EN_r1

description: hESC-derived pancreatic cells

source_name: EN Control replicate 1


title: RNA-seq_PP2_RA-early_r2

description: hESC-derived pancreatic cells

source_name: Early RA treatment PP2 replicate 2

value: Late pancreatic progenitor cells


title: FD2A_Batch3


title: FD2A_Batch2_ON


title: Adult_DRG_Sacral_Female_2361

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

data_processing:
Base calls were performed using Real Time Analysis (RTA) v1.18.66.3 on data processed by HiSeq Control Software (HCS) v2.2.68
FASTQ libraries were quality checked using FASTX toolkit version 0.0.14 and were aligned to the mm9 Ensembl 67 genome retaining uniquely mapping reads only. Batch 1 samples aligned with package Subread v1.18 under R v3.2.1 with max indels = 5, max mismatches = 5. Batch 2 samples aligned with package Subread v1.20.6 under R v3.2.2 with same settings.
Raw reads were counted (merged Batch 1 and 2 BAM files as input) and annotated against Ensembl v67 genes using featureCounts function of package Subread v1.20.6 under R v3.2.2
Gene counts were normalized using the “Voom” method of limma package v3.26.9 under R v3.2.2 with additional TMM library size adjustment using edgeR package v3.12.1 and further transformation to produce RPKM log2 abundance measures
An observed technical batch effect between the 2 experimental batches (5 samples from Batch 1 and 19 samples from Batch 2) was corrected on the RPKM log2 expression data using removeBatchEffect function of limma package v3.26.9
Genome_build: mm9 (GRCh37.p7)
Supplementary_files_format_and_content: TAB-separated values, Ensembl Gene v67 annotated TMM RPKM log2 normalized abundance measures

organism: Mus musculus

source_name: dorsal root ganglion

extract_protocol:
Qiagen RNeasy Plus Micro Kit (Qiagen, Australia)
Total RNA was amplified to create double stranded cDNA using the Ovation RNA-Seq System v2 (NuGEN) according to the manufacturer's protocol. cDNA concentrations were measured using the Qubit dsDNA BR assay, with cDNA size determined by using a DNA 1000 Chip. Libraries were then prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies). The purified cDNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq2500 following the manufacturer's protocol. The concentration of the pool is optimized to acquire at least 15-20 million reads per sample.

tag: experimental batch

value: Batch 2

tag: tissue

value: dorsal root ganglion

tag: region

value: sacral

tag: Sex

value: Female

tag: age

value: 6-8 weeks


title: RNA-seq_EN-LSD1-inh-early_r1

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition EN replicate 1


title: FD2B_Batch2_ON


title: RNA-seq_PP2-LSD1-inh-early_r2

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition PP2 replicate 2


title: RNA-seq_PP2_RA-early_r1

description: hESC-derived pancreatic cells

source_name: Early RA treatment PP2 replicate 1


title: FD2A_Batch2


title: RNA-seq_EN_RA-late_r1

description: hESC-derived pancreatic cells

source_name: Late RA treatment EN replicate 1


title: RNA-seq_EN_RA-late_r3

description: hESC-derived pancreatic cells

source_name: Late RA treatment EN replicate 3


title: FD2A_Batch1_ON


title: RNA-seq_PP2-LSD1-inh-early_r1

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition PP2 replicate 1


title: RNA-seq_PP2_r2

description: hESC-derived pancreatic cells

source_name: PP2 Control replicate 2


title: FD2A_Batch1


title: PF2A_ON_Isolate4


title: RNA-seq_PP2_r1

description: hESC-derived pancreatic cells

source_name: PP2 Control replicate 1


title: PF2A_ON_Isolate3


title: RNA-seq_PP1_r3

description: hESC-derived pancreatic cells

source_name: PP1 Control replicate 3

value: Early pancreatic progenitor cells


title: PF2A_ON_Isolate1

value: Isolate from  the overnight culture of the second time fermentation


title: RNA-seq_PP1_r2

description: hESC-derived pancreatic cells

source_name: PP1 Control replicate 2


title: FD2A_Batch3_ON

source_name: whole organism

value: GG


title: PF2A_ON_Isolate2


title: PF2A_ON


title: RNA-seq_PP1_r1

description: hESC-derived pancreatic cells

source_name: PP1 Control replicate 1


title: ChIP-seq_input_pooled

description: hESC-derived pancreatic cells

source_name: Pooled samples from PP1, PP2 and PP2 with LSD1 inhibition

value: Early and late pancreatic progenitor cells (pooled)


title: RNA-seq_PP2_r3

description: hESC-derived pancreatic cells

source_name: PP2 Control replicate 3


title: CRC

city: Shanghai

first: Fangbin

last: Zhou

state: State...

address: Siping Road 1239

country: China

institute: Tongji University School of Medicine

data_processing:
The extracted sequencing reads were stored in file SampleA_RawData.txt and were then used in e standard data analysis
A publicly available software package, CleaveLand3.0, was used to analyze the sequencing data generated
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample

source_name: colorectal cancer

extract_protocol:
Total RNA was extracted using TRK1001 following the manufacturer’s instructions. The total RNA quantity and purity were determined using a Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, Santa Clara, CA, United States) with RIN number > 7.0.
RNA libraries were constructed for sequencing using standard Illumina protocols

value: cancer tissue


title: ChIP-seq_input_PP1

description: hESC-derived pancreatic cells


title: PF1_ON_Isolate1

value: Isolate from  the overnight culture of the first time fermentation


title: ChIP-seq_input_PP2-LSD1-inh

description: hESC-derived pancreatic cells


title: ChIP-seq_input_PP2_r1

description: hESC-derived pancreatic cells


title: PF1_ON

value: Overnight culture collected from first time fermentation

value: Grown in MRS 6.5 broth


title: PF1_ON_Isolate2


title: ChIP-seq_LSD1_PP2-LSD1-inh_r2

description: hESC-derived pancreatic cells

value: differentiated hESCs


title: Ribo-Seq_SRSF7_OE_RepB

city: Frankfurt am Main

first: Michaela

last: Müller-McNicoll

address: Max-von-Laue-Str. 13

department: Institute for Cell Biology and Neuroscience

country: Germany

institute: Goethe University Frankfurt

data_processing:
Library strategy: Ribo-Seq
RNA-Seq: Reads were trimmed with Cutadapt and mapped to the mouse genome mm10 using STAR with default parameters.
Ribo-Seq: RiboSeq reads were trimmed with Cutadapt and reads were mapped to rRNAs using Bowtie2. Unmapped reads were kept and aligned to the mouse genome mm10 using STAR with default parameters.
Genome_build: mm10

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37?C with 5% CO2.

extract_protocol:
Ribosome profiling experiments were performed according to Ingolia et al., 2011. The final RiboSeq libraries were sequenced on an Illumina HiSeq2000 instrument (single end reads).
For RNA-Seq, total RNA was subjected to poly(A)+ selection and Illumina library preparation following standard procedures. RNA-Seq libraries were sequenced on an Illumina NEXTSeq2500 instrument (single-end 75-nt reads; 50 million reads per replicate).

treatment_protocol: For Ribo-Seq, For RiboSeq, cells were pre-treated with 100 µg/ml cycloheximide (Sigma) in culture medium for 1 min at room temperature and washed with ice-cold PBS containing 100 µg/ml cycloheximide. PBS was quickly removed and culture dishes were immediately flash frozen on dry ice.

tag: cell line

tag: genotype/variation

value: SRSF7-GFP OE


title: Ribo-Seq_SRSF7_OE_RepA


title: Ribo-Seq_Ctrl_RepA

value: WT


title: CHCC_Isolate4

value: Isolate from original stock


title: ChIP-seq_LSD1_PP2-LSD1-inh_r1

description: hESC-derived pancreatic cells

value: Late pancreatic progenitor cells


title: ChIP-seq_LSD1_PP2_r2

description: hESC-derived pancreatic cells


title: mSRSF7_RRM_OE_iCLIP_mm9_GGCA_Rep4

data_processing:
Basecalls performed using CASAVA version 1.4
For detail on data processing see: König et al. (2010): iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol PMID:20601959
Genome_build: mm9
Supplementary_files_format_and_content: .bed files containing the genomic coordinates X-links for the replicates and significant X-links (peaks) for the combined replicates.

growth_protocol: Cells were grown in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum and pennicilin/streptomycin antibiotics at 37˚C with 5% CO2.

extract_protocol:
Cells were lysed and treated with RNase I. GFP-tagged proteins were immunoprecipitated with Gamma binding beads coupled to goat anti-EGFP antibody. Endogenous SRSF7 was immunoprecipitated with Gamma binding beads coupled to rabbit anti-SRSF7 antibody.
After stringent washing, RNA was dephosphorylated and ligated to a 3' linker. Protein-RNA complexes were resolved by denaturing gel electrophoresis and transfered to nitrocellulose membrane. A membrane region above the expected size of the protein was cut and RNA was released by Proteinase K treatment. RNA was reverse transcribed using reverse primer containing a barcode sequence. cDNA was size selected by denaturing gel electrophoresis and circularized by ssDNA circligase. A specific oligonucleotide was annealed to create a restriction site for BamHI and cDNA was linearized by digest with BamHI. Linearized cDNA was PCR amplifiied with Solexa sequencing primers to create the final libraries. For more details see: Huppertz et al., (2014): iCLIP: protein-RNA interactions at nucleotide resolution. Methods. PMID:24184352

treatment_protocol: Cells were washed with PBS and irradiated with 254 nm UV light to crosslink proteins to nucleic acids.

tag: genotype

tag: antibody

tag: barcode sequence

value: GGCA

tag: protocol

value: iCLIP


title: mSRSF7-GFP_OE_noUV_iCLIP_mm9_GGTC_Rep1

value: GGTC


title: CHCC_Isolate3

tag: strain

tag: growth


title: mSRSF7-GFP_OE_noAb_iCLIP_mm9_TGGC_Rep1

value: no antibody

value: TGGC


title: CHCC_Isolate2

tag: second time fermentation batch

tag: freeze-dried batch


title: PF1_ON_Isolate4

tag: growth conditions


title: mSRSF7_RRM_OE_iCLIP_mm9_GGCA_Rep3


title: ChIP-seq_LSD1_PP2_r1

description: hESC-derived pancreatic cells

tag: cell type

tag: developmental stage


title: PF1_ON_Isolate3


title: ChIP-seq_input_PP2_r2

description: hESC-derived pancreatic cells


title: CHCC_Isolate1


title: mSRSF7endo_OE_iCLIP_mm9_TTGT_Rep5

value: TTGT


title: mSRSF7endo_WT_iCLIP_mm9_GGTT_Rep1

value: GGTT


title: ChIP-seq_LSD1_PP1_r2

description: hESC-derived pancreatic cells

value: Early pancreatic progenitor cells


title: CHCC_ON

value: GG

value: Original stock


title: mSRSF7endo_OE_iCLIP_mm9_CGGA_Rep4

value: CGGA


title: ChIP-seq_LSD1_PP1_r1

description: hESC-derived pancreatic cells


title: mSRSF7-GFP_OE_iCLIP_mm9_GGTC_Rep4


title: mSRSF7-GFP_OE_iCLIP_mm9_TTGT_Rep3


title: ChIP-seq_H3K4me2_PP2-LSD1-inh_r2

description: hESC-derived pancreatic cells


title: mSRSF7_piCLIP_mm9_poly_IgG_CCAC_Rep1

description:
polysomal fractions
mSRSF7_PiCLIP_mm9_IgG_Poly_Peaks.bed

value: anti-EGFP

value: CCAC

value: piCLIP


title: mSRSF7_piCLIP_mm9_poly_IP_GGCG_Rep2

description:
polysomal fractions
mSRSF7_PiCLIP_mm9_Sum_Mono_Poly_Peaks.bed

value: SRSF7-GFP OE

value: GGCG


title: mSRSF7_piCLIP_mm9_poly_IP_TTGT_Rep1


title: ChIP-seq_H3K4me2_PP2-LSD1-inh_r1

description: hESC-derived pancreatic cells

value: differentiated hESCs

value: Late pancreatic progenitor cells


title: mSRSF7_piCLIP_mm9_mono_IP_GGTT_Rep2

description:
monosomal fractions
mSRSF7_PiCLIP_mm9_Sum_Mono_Poly_Peaks.bed


title: mSRSF7_piCLIP_mm9_mono_IgG_GGTC_Rep1

description:
monosomal fractions
mSRSF7_PiCLIP_mm9_IgG_Mono_Peaks.bed


title: mSRSF7_piCLIP_mm9_mono_IP_CAAT_Rep1

value: CAAT


title: mSRSF7D27aa_noUV_iCLIP_mm9_GGTC_Rep1

value: SRSF7D27aa-GFP noUV

value: GGTC

value: iCLIP


title: ChIP-seq_H3K4me2_PP2_r1

description: hESC-derived pancreatic cells


title: mSRSF7D27aa_iCLIP_mm9_TGGC_Rep2

value: TGGC


title: mSRSF7D27aa_iCLIP_mm9_TGGC_Rep1


title: mSRSF7mutZn_noUV_iCLIP_mm9_GGTT_Rep1

value: SRSF7mutZn-GFP noUV

value: GGTT


title: C57BL/6 MDI Exposed 14

type: RNA

city: New Haven

first: Adam

last: Wisnewski

state: Connecticut

institute: Yale

description: Lung gene expression from sensitized C57BL6 exposed to MDI

hyb_protocol: All reactions and hybridizations were carried out according to the Affymetrix's reccommended protocols

scan_protocol: GeneChips were scanned using a GeneChip Scanner 3000.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using the robubust multiarray averaging module for normalization

label: biotin

source_name: Mouse lung 48hr after exposure to control reaction products

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from250 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: 6-8 week old male Balb/c, C57BL/6, and B cell deficient mice (B6.129S2-Ighmtm1Cgn/J) were fed ad libitum with 12hr light/dark cycle

extract_protocol: Total RNA was extracted using Qiagen RNAeasy mini kit with RLT buffer containing 1% beta-mercaptoethanol

treatment_protocol: All mice were twice exposed to 1% MDI in acetone on shaved back (immune sensitized) and subsequently exposed to MDI-GSH reaction products or control (MDI+GSH seperately reacted) under isoflurane on days 15, 16, 19 and 20 (after 1st skin exposure). Some mice received crofelemer (4mg/kg) intranasally under isoflurane 4 hrs before each respiratory tract exposure to MDI-GSH or control.

tag: drug (crofelemer) treatment

tag: respiratory tract exposure

value: MDI-GSH solution

value: 6-8 weeks

value: male


title: mSRSF7mutZn_iCLIP_mm9_GGCA_Rep4

value: anti-EGFP

value: GGCA


title: ChIP-seq_H3K4me2_PP1_r2

description: hESC-derived pancreatic cells

value: Early pancreatic progenitor cells


title: ChIP-seq_H3K4me2_PP1_r1

description: hESC-derived pancreatic cells


title: C57BL/6 Control + Crofelemer 5

description: Lung gene expression from sensitized C57BL6 exposed to control + crofelemer

value: crofelemer

value: control solution (MDI and GSH reacted seperately)

tag: Sex


title: Male_243_245_L4_L5_15437

data_processing:
Base calls were performed using Off-Line Base Caller (OLB) v1.9.4
FASTQ libraries were quality checked using FASTX toolkit version 0.0.14 and were aligned to the mm9 Ensembl 67 genome retaining uniquely mapping reads only. Samples were aligned with package Subread v1.18 under R v3.2.1 with max indels = 5, max mismatches = 5
Raw reads were counted and annotated against Ensembl v67 genes using featureCounts function of package Subread v1.20.6 under R v3.2.2
Gene counts were normalized using the “Voom” method of limma package v3.26.9 under R v3.2.2 with additional TMM library size adjustment using edgeR package v3.12.1 and further transformation to produce RPKM log2 abundance measures
Genome_build: mm9 (GRCh37.p7)
Supplementary_files_format_and_content: TAB-separated values, Ensembl Gene v67 annotated TMM RPKM log2 normalized abundance measures

source_name: dorsal root ganglion

tag: tissue

value: dorsal root ganglion

tag: region

value: lumbar

tag: age

value: Homozygous Trpv1tm2Bbm

value: Male


title: mSRSF7_iCLIP_mm9_GGTT_Rep4

tag: cell line

tag: genotype

value: SRSF7-GFP OE


title: ChIP-seq_H3K4me2_GT_r1

description: hESC-derived pancreatic cells

source_name: GT Control replicate 1

value: differentiated hESCs

value: Gut tube cells


title: mSRSF7_iCLIP_mm9_TTGT_Rep3

tag: antibody

tag: barcode sequence

value: TTGT

value: iCLIP


title: ChIP-seq_H3K4me1_PP2-LSD1-inh_r2

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition PP2 replicate 2

value: Late pancreatic progenitor cells


title: C57BL/6 Control 5

description: Lung gene expression from sensitized C57BL6 exposed to control

value: 6-8 weeks

tag: strain


title: C57BL/6 MDI Exposed + Crofelemer 4

value: MDI-GSH solution

value: male


title: ChIP-seq_H3K4me2_PP2_r2

description: hESC-derived pancreatic cells


title: ChIP-seq_H3K4me1_PP2-LSD1-inh_r1

description: hESC-derived pancreatic cells


title: Runx3

city: London

first: Gopuraja

last: Dharmalingam

address: Faculty of Medicine, Imperial College, Hammersmith Hospital Campus

department: Epigenetics section

country: United Kingdom

institute: MRC London Institute of Medical Sciences

description: ChIP-Seq data from T cells

data_processing:
Sequencing reads were aligned to Mouse genome mm9 using bowtie version 0.12.8
Reads were extended to fragment length estimated using SISSR
Coverage per base was computed using extended reads and visualised using UCSC genome browser
Genome_build: mm9
Supplementary_files_format_and_content: Bigiwig

source_name: CD4+ T cells

growth_protocol: Sorted naïve CD4+ T cells were activated and spin infeceted with retroviral vectors expressing Runx1 or Runx3 transcription factors, tagged by 2 Flag domains.

extract_protocol:
50x10^6 cells were resuspended in complete media and fixed 1% formaldehyde. Chromatin isolated from fixed nuclei was sonicated and incubate 4ºC overnight with Protein G Dynabeads (Invitrogen) coated with 5ug of anti-Flag antibody (Sigma). Further steps were carried out according to Seitan et al Nature (2011).
Single read high throughput sequencing libraries were prepared from 10ng of ChIP DNA using Illumina ChIP-Seq Sample Prep. Kit and sequenced according to the manufacturer's protocols using Illumina Hiseq 2000

value: anti-Flag antibody (Sigma)


title: Input

description: ChIP-Seq data from T cells

value: anti-HA antibody (invitrogen)


title: Runx1

description: ChIP-Seq data from T cells


title: ChIP-seq_H3K4me1_PP2_r2

description: hESC-derived pancreatic cells


title: C57BL/6 MDI Exposed 13

description: Lung gene expression from sensitized C57BL6 exposed to MDI + crofelemer

value: crofelemer


title: 2CLP+VLP (2CLP + VLP), 24 hrs, replicate 3

city: Jerusalem, ISRAEL

first: Ariella

last: Oppenheim

state: Jerusalem

address: 21 HaAhayot Rd

country: Israel

institute: Hebrew University

data_processing:
Low quality bases were trimmed from both ends with threshold 32, using in house scripts.
Adapter sequences and poly-A tails were removed with cutadapt (version 1.11). Only reads of length 15 and above were kept.
Low quality reads were filtered out with the FASTX package (version 0.0.14), using a threshold of 20 over 90 percent of the read's positions.
Processed reads were aligned using TopHat (v2.0.14), with up to 5 mismatches, using an extended GTF file with longer 3'UTRs, based on Ensembl release 84.
Reads per gene were counted using htseq-count (version 0.6.0). Normalized expression values and differential expression testing were done with DESeq2 (version 1.12.4).
Genome_build: Rnor6
Supplementary_files_format_and_content: An Excel sheet with columns for general gene details, raw counts in each sample, normalized counts, average expression, groups of 5 columns of DESeq2 results for each comparison, columns for significance according to certain thresholds (as indicated). All columns have informative headers.

organism: Rattus norvegicus

source_name: lung

growth_protocol: The rats were housed in a pathogen free (SPF) facility at the maintained on 12-h light and dark cycles with ab libitum food and water at all times.

extract_protocol:
RNA was purified from three frozen lungs for each of the four groups using RNEasy Kit (Qiagen) followed by RNeasy column. RNA quality was evaluated in Tapestation using RNA ScreenTape kit (Agilent Technologies), and quantified using Qubit apparatus (Qubit® DNA HS Assay kit, Invitrogen).
Libraries were prepared by KAPA Stranded mRNA-Seq Kit. The 12 libraries were bar-coded and pooled for multiplex sequencing. The pooled DNA was loaded on NextSeq 500 High Output v2 kit (75 cycles) cartridge (illumine) and sequenced on Illumina NextSeq 500 System, using sequencing conditions of 75 cycles, single-read.

treatment_protocol: The 2CLP operation was performed as followed: Under anesthesia, the abdomen was opened, the cecum ligated above the ileocecal valves and two perforations were made with 14G IV catheter. Rats were resuscitated with normal saline, injected with analgesics and returned to cages with ab libitum food and water.

value: Sprague-Dawley

tag: weight

tag: agent

value: 2CLP+VLP (2CLP + VLP)

tag: harvest time point

value: :24 hrs after the 2CLP insult


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 5

description: Lung gene expression from sensitized B-cell deficient mice exposed to MDI-GSH

source_name: Mouse lung 48hr after exposure to MDI-GSH reaction products

value: MDI solution (MDI and GSH reacted together)


title: mSRSF7mutZn_iCLIP_mm9_GGCA_Rep3

value: anti-EGFP

value: GGCA

tag: protocol


title: 2CLP+VLP (2CLP + VLP), 24 hrs, replicate 2


title: ChIP-seq_H3K4me1_PP2_r1

description: hESC-derived pancreatic cells

tag: cell type

value: differentiated hESCs


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 6


title: ChIP-seq_H3K4me1_PP1_r2

description: hESC-derived pancreatic cells

tag: developmental stage

value: Early pancreatic progenitor cells


title: mSRSF7_iCLIP_mm9_GGTC_Rep2

value: SRSF7-GFP OE

value: GGTC


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 7

tag: drug (crofelemer) treatment


title: VLPs (VLPs only), replicate 3

value: VLPs (VLPs only)


title: 2CLP+VO (2CLP + Vehicle), 24 hrs, replicate 3

value: 2CLP+VO (2CLP + Vehicle)


title: ChIP-seq_H3K4me1_PP1_r1

description: hESC-derived pancreatic cells


title: 2CLP+VO (2CLP + Vehicle), 24 hrs, replicate 1


title: mSRSF7_noUV_iCLIP_mm9_TGGC_Rep1

value: SRSF7-GFP OE noUV

value: TGGC

value: iCLIP


title: VLPs (VLPs only), replicate 2

value: male


title: ChIP-seq_H3K27ac_PP2-LSD1-inh_r2

description: hESC-derived pancreatic cells

value: Late pancreatic progenitor cells


title: B6.129S2-Ighmtm1Cgn/J - Control 6

description: Lung gene expression from sensitized B-cell deficient mice exposed to control

tag: respiratory tract exposure

value: control solution (MDI and GSH reacted seperately)

value: 6-8 weeks


title: B6.129S2-Ighmtm1Cgn/J - Control 7

tag: Sex


title: VLPs (VLPs only), replicate 1

value: Sprague-Dawley


title: VO (Vehicle only), replicate 3

value: VO (Vehicle only)


title: VO (Vehicle only), replicate 2


title: B6.129S2-Ighmtm1Cgn/J - Control 8


title: ChIP-seq_H3K27ac_PP2-LSD1-inh_r1

description: hESC-derived pancreatic cells

source_name: Early LSD1 inhibition PP2 replicate 1


title: 2CLP+VLP (2CLP + VLP), 24 hrs, replicate 1

value: 2CLP+VLP (2CLP + VLP)

value: :24 hrs after the 2CLP insult


title: 2CLP+VLP (2CLP + VLP), rep 3

data_processing:
Raw reads were trimmed off their first 9 bases, using the FASTX package (version 0.0.14)
Low quality bases were trimmed from both ends with threshold 32, using in house scripts.
Adapter sequences were removed with cutadapt (version 1.12)
Low quality reads were filtered out with the FASTX package, using a threshold of 20 over 90 percent of the read's positions. Only reads of length 15 and above were kept.
Processed reads were aligned using TopHat (v2.0.14), with up to 3 mismatches, using an extended GTF file with longer 3'UTRs, based on Ensembl release 84.
Reads per gene were counted using htseq-count (version 0.6.0).
Normalized expression values and differential expression testing were done with DESeq2 (version 1.12.4).
Genome_build: Rnor6
Supplementary_files_format_and_content: An Excel sheet with columns for general gene details, raw counts in each sample, normalized counts, average expression, groups of 5 columns of DESeq2 results for each comparison, columns for significance according to certain thresholds (as indicated). All columns have informative headers.

extract_protocol:
RNA was purified from three frozen lungs for each of the four groups using RNEasy Kit (Qiagen) followed by RNeasy column. RNA quality was evaluated in Tapestation using RNA ScreenTape kit (Agilent Technologies), and quantified using Qubit apparatus (Qubit® DNA HS Assay kit, Invitrogen).
Libraries were prepared by SENSE mRNA-Seq Library Prep Kit The 12 libraries were bar-coded and pooled for multiplex sequencing. The pooled DNA was loaded on NextSeq 500 High Output v2 kit (75 cycles) cartridge (illumine) and sequenced on Illumina NextSeq 500 System, using sequencing conditions of 75 cycles, single-read.

treatment_protocol: Under anesthesia, the abdomen was opened, the cecum ligated above the ileocecal valves and two perforations were made with 14G IV catheter. Rats were resuscitated with normal saline, injected with analgesics and returned to cages with ab libitum food and water.

value: ~200 gram

value: harvested 6 hrs post 2CLP-insult

tag: tissue

value: lung


title: B6.129S2-Ighmtm1Cgn/J - Control 4


title: VO (Vehicle only), replicate 1


title: ChIP-seq_H3K27ac_PP2_r2

description: hESC-derived pancreatic cells

source_name: PP2 Control replicate 2

value: differentiated hESCs


title: ChIP-seq_H3K27ac_PP2_r1

description: hESC-derived pancreatic cells

source_name: PP2 Control replicate 1


title: B6.129S2-Ighmtm1Cgn/J - Control 9


title: 2CLP+VLP (2CLP + VLP), rep 2


title: B6.129S2-Ighmtm1Cgn/J - Control 5


title: B6.129S2-Ighmtm1Cgn/J - Control 2


title: ChIP-seq_H3K27ac_PP1_r1

description: hESC-derived pancreatic cells

value: Early pancreatic progenitor cells


title: 2CLP+VO (2CLP + Vehicle), rep 2


title: 2CLP+VO (2CLP + Vehicle), rep 1


title: 2CLP+VLP (2CLP + VLP), rep 1


title: VLPs (VLPs only), rep 3

value: after 3 days of VLP injection


title: 2CLP+VO (2CLP + Vehicle), 24 hrs, replicate 2

value: 2CLP+VO (2CLP + Vehicle)


title: B6.129S2-Ighmtm1Cgn/J - Control 3


title: genomic DNA at diagnosis from BCP-ALL patient ALL_47

type: genomic

city: Uppsala

first: Yanara

last: Marincevic-Zuniga

address: Husargatan 3, BOX 1432, Biomedicinskt Centrum (BMC)

department: Medical Sciences

country: Sweden

institute: Uppsala University

description: copy number file (".cn") with LogR values for visualization in IGV

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450k Beadchip using standard Illumina protocol

scan_protocol: not provided

data_processing: The raw signal intensities generated from the 450k array were normalized and transformed to “Log R ratio”, which corresponds to the observed intensity signal from the studied sample over the intensity signal obtained from a reference sample (baseline). To determine the reference baseline, 450k data from an in-house panel of CD19+ B-cells and CD3+ T-cells from healthy blood donors representing normal diploid genomes, was used. Log R ratios were analyzed using the CopyNumber450kCancer R package and with the Integrated Genome Viewer (IGV). LogR files  with the extension ".cn" are submitted to GEO and can be visualized in IGV.

label: Cy5 and Cy3

source_name: ALL patient sample

label_protocol: Standard Illumina Protocol

extract_protocol: AllPrep DNA/RNA/miRNA Universal Kit

tag: disease state

value: ALL diagnosis

tag: immunophenotype

value: BCP-ALL

value: primary acute lymphoblastic leukemia


title: VLPs (VLPs only), rep 2

value: male


title: B6.129S2-Ighmtm1Cgn/J - Control 1

value: control solution (MDI and GSH reacted seperately)

tag: age


title: C57BL/6 Control + Crofelemer 3

description: Lung gene expression from sensitized C57Bl/6 mice exposed to crofelemer + control

source_name: Mouse lung 48hr after exposure to control reaction products + crofelemer

value: crofelemer 4mg/kg intranasal under isoflurane

value: crofelemer

value: 6-8 weeks


title: C57BL/6 Control + Crofelemer 4


title: genomic DNA at diagnosis from BCP-ALL patient ALL_707


title: VLPs (VLPs only), rep 1

value: Sprague-Dawley


title: genomic DNA at diagnosis from BCP-ALL patient ALL_689


title: VO (Vehicle only), rep 3

value: after 3 days of VO injection


title: 2CLP+VO (2CLP + Vehicle), rep 3

value: ~200 gram


title: genomic DNA at diagnosis from BCP-ALL patient ALL_604


title: VO (Vehicle only), rep 1


title: genomic DNA at diagnosis from T-ALL patient ALL_559

value: T-ALL


title: VO (Vehicle only), rep 2

value: lung


title: genomic DNA at diagnosis from BCP-ALL patient ALL_501


title: PiCas12a - NT gRNA [Pm3385-NT_S6]

city: Raleigh

first: Chase

last: Beisel

state: NC

address: 840 Main Campus Drive

department: Chemical and Biomolecular Engineering

institute: North Carolina State University

data_processing:
see the following website: https://bitbucket.org/csmaxwell/crispr-txtl-pam-counting-script/overview
Real Time Analysis for basecalling
Supplementary_files_format_and_content: .csv files

organism: synthetic construct

source_name: uncleaved DNA from the randomized protospacer-adjacent motif (PAM) library

extract_protocol:
myTXTL extract purchased from Arbor Biosciences.
The samples were PCR amplified twice. The 1st PCR involved attachment of unique adapters that provided a landing site for the 2nd PCR. The 2nd PCR involved attachment of i5 and i7 Nextera low plex pooling indices.

treatment_protocol: Prior to library construction, the TXTL reaction should be diluted 1:10 for successful amplification using a high-fidelity polymerase.

tag: in vitro environment

value: myTXTL from Arbor Biosciences

tag: lysate origination

value: E. coli

tag: molecule subtype

value: DNA from PCR-amplification


title: C57BL/6 Control + Crofelemer 1

tag: strain


title: PiCas12a - T gRNA [Pm3385_S5]


title: C57BL/6 MDI Exposed + Crofelemer 3

description: Lung gene expression from sensitized C57Bl/6 mice exposed to crofelemer + MDI-GSH

source_name: Mouse lung 48hr after exposure to crofelemer +  MDI-GSH reaction products

value: crofelemer + MDI solution (MDI and GSH reacted together)


title: genomic DNA at diagnosis from BCP-ALL patient ALL_458

value: ALL diagnosis


title: C57BL/6 Control + Crofelemer 2


title: genomic DNA at diagnosis from BCP-ALL patient ALL_613

value: BCP-ALL


title: PdCas12a - NT gRNA [Pd-NT_S4]


title: C57BL/6 MDI Exposed + Crofelemer 1


title: C57BL/6 MDI Exposed + Crofelemer 2


title: MH-S clone 29_ low IL-4Ra activity_ 16h LPS stimulation

city: Sockholm

first: Fredrik

last: Wermeling

state: Stockholm

address: Visionsgatan 18, Center for molecular medicine, Karolinska University Hospital

department: Division of Rheumatology, Department of Medicine, Solna

institute: Karolinska Institute, Stockholm, Sweden

description: Gene expression data from LPS stimulated MH-S cell clones

hyb_protocol: 3ug of ss DNA target was hybridized to a Mouse Gene 2.1 ST Array Plate and washed and stained in the Gene Titan instrument.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Arrays were normalized and expression values determined using Affymetrix Expression Console. The method used to analyse the data is med-polish (rma-bg,quant-norm, sketch=-1, bioc=true, lowprecision=false, usepm=true, target=0, doavg=false).

label: Biotin

source_name: MH-S clone 29, LPS stimulated, 16 h

label_protocol: 150ng of total RNA was used to generate amplified sense strand DNA targets with Ambion WT Expression Kit followed by fragmentation and biotinylation with Affymetrix WT Expression Kit.

growth_protocol: MH-S (mouse alveolar macrophage cell line) were cultured in RPMI-1640 (Sigma-Aldrich) with 10% heat-inactivated bovine serum, 1% penicillin-streptomycin-glutamine and 0.1% β-mercaptoethanol (Gibco).

extract_protocol: TRIzol (Thermo Fisher) and Direct-zol RNA MiniPrep Kit (Zymo Research) were used to isolate RNA from cells, and genomic DNA removed with RNase-free DNase (Zymo Research).

treatment_protocol: Cells were seeded at 250 000 cells/well in 6-well plates, and 50 000 cells/well in 96-well plates, and split every 2-3 days. Cells were stimulated with 0.2 µg/ml LPS (Salmonella Minnesota R595 (Re); Enzo Life Sciences) for 16h.

tag: phenotype

value: low IL-4Ra activity

tag: treatment

value: 16h LPS stimulation

tag: cell line

value: MH-S

value: Alveloar macrophage


title: genomic DNA at diagnosis from BCP-ALL patient ALL_402

value: primary acute lymphoblastic leukemia


title: MH-S clone 69_ high IL-4Ra activity_ 16h LPS stimulation

source_name: MH-S clone 69, LPS stimulated, 16 h

value: high IL-4Ra activity


title: MH-S clone 83_ high IL-4Ra activity_ 16h LPS stimulation

source_name: MH-S clone 83, LPS stimulated, 16 h


title: PdCas12a - T gRNA [Pd-T_S3]


title: MH-S clone 7_ low IL-4Ra activity_ 16h LPS stimulation

source_name: MH-S clone 7, LPS stimulated, 16 h


title: C57BL/6 MDI Exposed 11

description: Lung gene expression from sensitized C57Bl/6 mice exposed to MDI-GSH

value: MDI solution (MDI and GSH reacted together)

value: 6-8 weeks

value: male


title: genomic DNA at diagnosis from BCP-ALL patient ALL_386


title: HkCas12a - NT gRNA [Hk-NT_S2]


title: MH-S clone 75_ low IL-4Ra activity_ 16h LPS stimulation

source_name: MH-S clone 75, LPS stimulated, 16 h


title: C57BL/6 MDI Exposed 10


title: genomic DNA at diagnosis from BCP-ALL patient ALL_390


title: C57BL/6 MDI Exposed 12


title: MH-S clone 69_ high IL-4Ra activity_ unstimulation

description: Gene expression data from MH-S cell clones

source_name: MH-S clone 69, unstimulated, 16 h

value: unstimulated


title: MH-S clone 75_ low IL-4Ra activity_ unstimulation

source_name: MH-S clone 75, unstimulated, 16 h


title: HkCas12a - T gRNA [Hk-T_S3]


title: genomic DNA at diagnosis from BCP-ALL patient ALL_370


title: MH-S clone 73_ high IL-4Ra activity_ 16h LPS stimulation

source_name: MH-S clone 73, LPS stimulated, 16 h


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 4


title: MH-S clone 83_ high IL-4Ra activity_ unstimulation

source_name: MH-S clone 83, unstimulated, 16 h


title: Wheat.root.Hi-C

city: Paris

first: Lorenzo

last: Concia

email: colore@gmail.com, concia@bio.ens.psl.eu

address: 46 Rue d'Ulm

department: Institut de Biologie

country: France

institute: École Normale Supérieure

data_processing:
Short-reads were trimmed with the following command "trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed short-reads were processed with the pipeline HiC-Pro v2.9.0 (Servant N. et al., 2015) with minor modifications. Briefly, reads were aligned to iwgsc_refseq1.0 reference genome assembly using bowtie2 v2.3.3 (60) with default settings, except for the parameter “--score-min L,-0.6,-0.8”. Forward and reverse mapped reads were paired and assigned to MboI restriction fragments. Invalid ligation products (such as dangling ends, fragments ligated on themselves and ligations of juxtaposed fragments) were discarded to identify valid pairs. Valid pairs of each sample were merged and used to produce raw interaction matrixes at various resolution as part of HiC-Pro pipeline. Normalized matrixes were produced by iterative correction using the “ice” utility provided as part of HiC-Pro (Imakaev et al., 2012).
Insulation index was calculated from 25-kb ice-normalized matrixes using tadtool v0.77 with the command "tadtool tads -a ninsulation --write-values MATRIX MATRIX.BED 100000 0.4 > INSULATION_INDEX"
Genome_build: iwgsc_1.0
Supplementary_files_format_and_content: ValidPairs identified by HiC-Pro are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]. Insulation index obtained with TADtool v0.7.7 is stored as bigwig file

organism: Triticum aestivum

source_name: Root

growth_protocol: Seeds were surface sterilized with bayrochlore and ethanol, sown on MS agar plates, placed at 4°C in the dark for 2 days and then grown in a growth chamber for 14 days (long day conditions, 18°C).

extract_protocol:
The experiment was carried out according to the protocol published by Liu et al., 2017 using DpnII enzyme (New England Biolabs) with minor modifications concerning library preparation for which we used NebNext UltraII DNA library preparation kit (New England Biolabs).
For library amplification, nine PCR cycles were performed and Hi-C libraries were purified with SPRI magnetic beads (Beckman Coulter) and eluted in 20 μL of nuclease-free water. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent)

tag: genotype

value: Chinese Spring

value: 14 days old seedlings

value: root


title: WT_rep3

description: Bioreplicate 3

data_processing:
Adapters trimming was performed using the command [java -jar trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20 ]
Pseudo-alignment and estimation of normalized abundance was performed using kallisto [kallisto quant -b 100 --index kallisto_index.iwgsc1.1_HC+LC_peaks trim.Fw.fastq trim.Rv.fastq]
Genome_build: IWGSC_v1.0
Supplementary_files_format_and_content: Supplementary_files_format_and_content: .tsv;  columns represent: transcript name [target_id], transcript lenght [length], effective length [eff_length], estimated counts [est_counts], Transcripts per million (normalized by transcript length) [tpm]

source_name: 12 day-old

growth_protocol: Seeds were surface sterilized with bayrochlore and ethanol, sown on MS agar plates, placed at 4°C in the dark for 2 days and then grown in a growth chamber for 12 days (long day conditions, 18°C).

extract_protocol:
Total RNA were extracted 180 mg of shoots of 12-day-old seedlings with the NucleoSpin RNA kit (Macherey-Nagel), according to the manufacturer’s instructions.
RNA-seq libraries were prepared using 2 μg of total RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs), according to manufacturer’s recommendations. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent).

value: shoot


title: Wheat.shoot.Hi-C

source_name: Shoot


title: MH-S clone 73_ high IL-4Ra activity_ unstimulation

source_name: MH-S clone 73, unstimulated, 16 h

tag: cell type


title: WT_rep2

description: Bioreplicate 2

tag: developmental stage


title: Adurb336Cas12a - NT gRNA [Adurb336-NT_S4]

value: myTXTL from Arbor Biosciences

value: E. coli

value: DNA from PCR-amplification


title: saline [20.ACCATAC]

city: St. Louis

first: Arvind

last: Palanisamy

state: MO

address: 660 S Euclid Ave

department: Anesthesiology

institute: Washington University School of Medicine

description: 20.ACCATAC.run_2398_s_*_withindex_sequence.txt_ACCATAC

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts derived with Subread:featureCount 1.45.  RPKM and CPM calculated from gene counts with custom R scripting.
Genome_build: Ensembl Release 76 Rnor_5.0
Supplementary_files_format_and_content: Gene counts in tab-delimitted text format

source_name: saline_cerebral cortex

extract_protocol:
Total RNA was extracted from the right cerebral cortex using RNAeasy kit (Qiagen). Only RNA with RIN > 9.5 were used for RNA-seq.
oligo-dT

value: Sprague Dawley

value: embryonic day 21

value: maternal administration of saline

value: cerebral cortex


title: oxytocin [19.CTCAATG]

description: 19.CTCAATG.run_2398_s_*_withindex_sequence.txt_CTCAATG

source_name: oxytocin_cerebral cortex

value: maternal administration of oxytocin


title: Adurb336Cas12a - T gRNA [Adurb336_S3]

source_name: uncleaved DNA from the randomized protospacer-adjacent motif (PAM) library


title: Wheat.root.Hi-ChIP

data_processing:
Library strategy: HiChiP
Short-reads were trimmed with the following command "trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed short-reads were processed with the pipeline HiC-Pro v2.9.0 (Servant N. et al., 2015) with default settings. Briefly, reads were aligned to iwgsc_refseq1.0 reference genome assembly using bowtie2 v2.3.3. Forward and reverse mapped reads were paired and assigned to MboI restriction fragments. Invalid ligation products (such as dangling ends, fragments ligated on themselves and ligations of juxtaposed fragments) were discarded to identify valid pairs. Valid pairs of each sample were merged and used to produce raw interaction matrixes at various resolution as part of HiC-Pro pipeline. Normalized matrixes were produced by iterative correction using the “ice” utility provided as part of HiC-Pro (Imakaev et al., 2012).
Genome_build: iwgsc_1.0

extract_protocol:
Nuclei were isolated using the same procedure published by Liu et al., 2017. We then applied the HiChIP protocol of Mumbach et al., 2016 using the DpnII restriction enzyme (New England Biolabs) and anti-Polymerase II antibody (Active Motif, 39097).
The sequencing library was built according to the protocol of Mumbach et al, 2016. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent).


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 3

source_name: Mouse lung 48hr after exposure to MDI-GSH reaction products

tag: drug (crofelemer) treatment


title: Fn3sCas12a - NT gRNA [Fn3-NT_S4]


title: saline [16.TTTCAGA]

description: 16.TTTCAGA.run_2398_s_*_withindex_sequence.txt_TTTCAGA


title: saline [18.CTTGGAA]

description: 18.CTTGGAA.run_2398_s_*_withindex_sequence.txt_CTTGGAA


title: MH-S clone 7_low IL-4Ra activity_unstimulation

source_name: MH-S clone 7, unstimulated, 16 h

value: low IL-4Ra activity

value: MH-S

value: Alveloar macrophage


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 1

tag: respiratory tract exposure

value: MDI solution (MDI and GSH reacted together)

value: 6-8 weeks

value: male


title: KO2

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

country: Spain

institute: CNB-CSIC

description: Peritoneal cavity

data_processing:
Reads from the same sample were concatenated and pre-processed with a pipeline that used Cutadapt v1.7 to remove adapters and FastQC to perform quality controls after each step.
Processed reads were mapped to mm10 whole genome using Bowtie2 v4.1.2 with parameters -X 2000 –very-sensitive
Alignments were filtered using SAMtools (v0.1.18) view to retain only properly paired reads (-f 0x0002) with minimum mapping quality 30 (-q 30) not aligning to unlocalized contigs, unassembled contigs, the mitochondrial genome, and chromosomes X and Y.
ATAC-seq peaks were called using MACS2 v2.1.1 (Zhang et al., 2008) with parameters -nomodel -shift 100 -extsize 200 -keep-dup all -q 0.05
Peaks falling within mouse mm10 ENCODE blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/mm10-mouse) were discarded using bedtools v2.24.0 intersect.
A consensus peak set of peaks detected in at least two samples was generated using function dba.counts from DiffBind R package v2.6.6 (Stark and Brown, 2011; Ross-Innes et al., 2012) and a differential accessibility analysis was performed using EdgeR v3.20.9 (Robinson MD et al., 2010).
Nearest gene annotation and motif discovery were performed using HOMER v4.10.3 (Heinz at al., 2010) package.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ENCODE narrow peak files (extended bed format) including coordinates, score and qvalue for ATACseq PEAKS called for each sample using MACS2.

source_name: Large peritoneal macrophages (LPMs)

extract_protocol:
40,000 sorted LPMs were lysed with lysis buffers (10 mM Tris-HCl pH 7.4, 10mM MgCl2, 0.1% IGEPAL CA-630), and the transposase reaction was performed incubating the isolated nuclei with 2.5 microl per sample of Tn5 (Nextera DNA Library Preparation Kit, Illumina) for 30 min at 37ºC. Transposed DNA was purified with the ChIP DNA Clean & Concentrator kit (Zymo) according to manufacturer´s instructions.
PCR amplification and barcoding were done with the primers described by Buenrostro et al. Each PCR reaction included 11 ml NEB 2× PCR Mix (New England Biolabs), 10 ml of transposed DNA, 0.5 ml of X mM primer Ad_ no Mx (forward) and 0.5 ml of barcoded reverse primer (Ad_2.1 to Ad_2.4). PCR conditions were as follows: 72°C for 5 min, 98 °C for 30 s, 5 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min, followed by 4 ºC next to final 5th cycle. After first PCR DNA was size selected with 0.5X volume SPRI beads (Agencourt AMPure, Beckman Coulter), and cleaned up with 2X SPRI beads. Second PCR with same set of primers was done as follows: 98 °C for 30 s, followed by 6-9 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min. Each sample was amplified for a total of 11 to 14 cycles. Libraries were purified with SPRI beads, and concentration was measured by Qbit dsDNA HS Assay kit (ThermoFischer Scientific) and fragment profiles were analyzed with the Bioanalyzer DNA High Sensitivity Kit (Agilent).

tag: strain/background

tag: genotype/variation

value: LysMCre+RXRabfl/fl

value: 9 weeks

value: Large peritoneal macrophages

tag: library batch


title: Wheat_CS_10-day_shoots_ChIP_RNAPII

data_processing:
Adapters trimming: Sequencing reads were trimmed with trimmomatic with the following command "trimmomatic-0.36.jar PE -phred33 -validatePairs ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Read mapping: Trimmed reads data were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 --very-sensitive" against the genome of Triticum aestivum (iwgsc_1.0).
Filtering step: Mapped reads were sorted with sambamba view v.0.6.6 with the command "sambamba view -F "mapping_quality >= 10"
Duplicate filtering: duplicated reads were removed with sambamba markdup v. 0.6.6 with the command "sambamba markdup --io-buffer-size=8000 --overflow-list-size=1000000 -r"
Peak calling: peaks of read density were called with macs2 2.1.1.20160309 with the command "macs2 callpeak -f BAMPE --nomodel -q 0.001 --broad-cutoff 0.01 -g 17e9 --bw 300"
Bigwig generation: read density was scored over 100-bp non-overlapping bins with deepTools v.3.1.0 with the command "bamCoverage -p 24 -bs 100 -of bigwig --extendReads"
Genome_build: IWGSC_v1.0
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.
Supplementary_files_format_and_content: narrowPeak file from macs2

source_name: Seedlings

extract_protocol:
After fixation with 1% (v/v) formaldehyde, tissues were homogenized, nuclei isolated and lysed. Cross-linked chromatin was sonicated using Covaris S220. Protein/DNA complexes were immunoprecipitated with anti-RNA polymerase II CTD repeat YSPTSPS antibody (abcam ab26721) overnight at 4°C with gentle shaking and incubated for 1h at 4°C with 50 uL of Dynabeads Protein A (Invitrogen, Ref. 100-02D). The beads were washed 2 × 5 min in ChIP Wash Buffer 1 (0.1% SDS, 1% Triton X-100, 20mMTris-HCl pH 8, 2 mM EDTA pH 8, 150 mMNaCl), 2 × 5 min in ChIP Wash Buffer 2 (0.1% SDS, 1% Triton X-100, 20 mMTris-HCl pH 8, 2 mM EDTA pH 8, 500 mMNaCl), 2 × 5 min in ChIP Wash Buffer 3 (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 10 mMTris-HCl pH 8,1 mM EDTA pH 8) and twice in TE (10 mMTris-HCl pH 8, 1 mM EDTA pH 8). ChIPed DNA was eluted by two 15-min incubations at 65°C with 250?L Elution Buffer (1% SDS, 0.1 M NaHCO3). Chromatin was reverse-crosslinked by adding 20?L of NaCl 5M and incubating overnight at 65°C. Reverse-cross-linked DNA was treated with RNase and proteinase K, and extracted with phenol-chloroform. DNA was precipitated with ethanol in the presence of 20?g of glycogen and resuspended in 20?L of nuclease-free water (Ambion) in a DNA low-bind tube.
10 ng of IP or input DNA were used for ChIP-Seq library construction using NEB-Next Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) according to manufacturer's recommendations. For all libraries, ten cycles of PCR were used. The quality of the libraries was assessed with Agilent 2100 Bioanalyzer (Agilent), and the libraries were sequenced using 2x75bp pair-end reads on NextSeq 500 platform (Illumina).

value: Chinese Spring

value: 14 days old seedlings

tag: tissue

value: shoot


title: B6.129S2-Ighmtm1Cgn/J - MDI Exposed 2

tag: age

tag: Sex


title: C57BL/6 MDI Exposed 9


title: Rapeseed.Hi-C_M_18_0819_HiC-3_AD005_L006

data_processing:
Short-reads were trimmed with the following command "trimmomatic-0.36.jar -threads 8 -phred33 -validatePairs ILLUMINACLIP:TruSeq3-SE.fa:2:30:10 LEADING:5 TRAILING:5 MINLEN:20"
Trimmed short-reads were processed with the pipeline HiC-Pro v2.9.0 (Servant N. et al., 2015) with minor modifications. Briefly, reads were aligned to iwgsc_refseq1.0 reference genome assembly using bowtie2 v2.3.3 (60) with default settings, except for the parameter “--score-min L,-0.6,-0.8”. Forward and reverse mapped reads were paired and assigned to MboI restriction fragments. Invalid ligation products (such as dangling ends, fragments ligated on themselves and ligations of juxtaposed fragments) were discarded to identify valid pairs. Valid pairs of each sample were merged and used to produce raw interaction matrixes at various resolution as part of HiC-Pro pipeline. Normalized matrixes were produced by iterative correction using the “ice” utility provided as part of HiC-Pro (Imakaev et al., 2012).
Genome_build: Brassica_napus_v4.1
Supplementary_files_format_and_content: ValidPairs identified by HiC-Pro are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]. Insulation index obtained with TADtool v0.7.7 is stored as bigwig file

organism: Brassica napus

value: Westar

value: Whole seedling


title: C57BL/6 MDI Exposed 6


title: KO1

description: Peritoneal cavity


title: WT_rep1

description: Bioreplicate 1


title: C57BL/6 Control 6

source_name: Mouse lung 48hr after exposure to control reaction products

value: control solution (MDI and GSH reacted seperately)


title: Adurb193Cas12a - T gRNA [Adurb193_S1]

tag: in vitro environment

value: myTXTL from Arbor Biosciences

tag: lysate origination

value: E. coli

value: DNA from PCR-amplification


title: oxytocin [15.TTTTCGG]

description: 15.TTTTCGG.run_2398_s_*_withindex_sequence.txt_TTTTCGG

tag: strain

value: Sprague Dawley

value: embryonic day 21

value: maternal administration of oxytocin

value: cerebral cortex


title: oxytocin [17.TATCTTA]

description: 17.TATCTTA.run_2398_s_*_withindex_sequence.txt_TATCTTA


title: Adurb193Cas12a - NT gRNA [Adurb193-NT_S2]

tag: molecule subtype


title: C57BL/6 MDI Exposed 5

value: MDI solution (MDI and GSH reacted together)

value: 6-8 weeks

value: male


title: WT3

description: Peritoneal cavity

value: RXRabfl/fl

value: 9 weeks

value: Large peritoneal macrophages


title: C57BL/6 MDI Exposed 8


title: oxytocin [14.TCCGGGA]

description: 14.TCCGGGA.run_2398_s_*_withindex_sequence.txt_TCCGGGA

tag: treatment


title: C57BL/6 MDI Exposed 7


title: WT1

description: Peritoneal cavity


title: Wheat_ATAC_S1_001

data_processing:
Adapters trimming: Sequencing reads were trimmed with trim_galore v0.4.4 with the following command "trim_galore --fastqc --paired --nextera --dont_gzip"
Read mapping: Trimmed reads were mapped using bowtie2 v 2.3.3 with the following setting "bowtie2 --very-sensitive" against the genome of Triticum aestivum (iwgsc_1.0).
Filtering step: Mapped reads were sorted with sambamba view v.0.6.6 with the command "sambamba view -F "mapping_quality >= 10 --format bam"
Bigwig generation: read density was scored over 100-bp non-overlapping bins with deepTools v.3.1.0 with the command "bamCoverage --binSize 100 --smoothLength 2100 --centerReads -of bigwig"
peak calling: peaks of read density were called with macs2 2.1.1.20160309 with the command "macs2 callpeak --qvalue 0.01 --format BAMPE --keep-dup all --gsize 1.46e10 --nomodel --shift -100 --extsize 200"
Genome_build: iwgsc_1.0
Supplementary_files_format_and_content: bigwig file, containing Chr, start position, end position.
Supplementary_files_format_and_content: narrowPeak file from macs2

extract_protocol:
100 mg of 14-d-old seedlings were ground and nuclei were isolated with 4°C Buffer (0,25M Sucrose, 10mM Tris-HCl, 10mM MgCL2, 1% Triton, 5mM beta-mercaptoethanol) containing proteinase inhibitor cocktail (Roche) and filtered in 63µm.
DNA libraries were amplified for a total of 8 cycles as described by Buenrostro et al., (2013) and Jégu et al., (2017).
100 mg of 14-d-old seedlings were ground and nuclei were isolated with 4°C Buffer (0,25M Sucrose, 10mM Tris-HCl, 10mM MgCL2, 1% Triton, 5mM beta-mercaptoethanol) containing proteinase inhibitor cocktail (Roche) and filtered in 63µm. Nuclei were resuspended in 1X TD Buffer (Illumina FC-121-1030) and 2.5 μL of Tn5 Transposes (Illumina FC-121-1030) were added. Transposition reaction was performed at 37°C for 30min, and DNA was purified using a Qiagen MinElute Kit. DNA libraries were amplified for a total of 8 cycles as described by Buenrostro et al., (2013) and Jégu et al., (2017).

value: Chinese Spring

value: 14 days old seedlings

value: shoot


title: saline [13.AACGGAG]

description: 13.AACGGAG.run_2398_s_*_withindex_sequence.txt_AACGGAG

value: maternal administration of saline


title: KO-Curdlan-3

city: Wuhan

first: Chenhui

last: Wang

state: Hubei

address: 1037 Luoyu Rd

institute: Huazhong University of Science and Technology

description: RNA sequencing

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
RSEM software was used to calculate gene expression level (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample. Gene IDs are NCBI Gene IDs.

source_name: Bone marrow derived macrophages (BMDMs)

growth_protocol: BMDMs were obtained by differentiating bone marrow progenitors from the tibia and femur of 6–8-week-old male or female mice in Iscove’s Modified Dulbecco’s Media (IMDM) containing 20 ng/ml of M-CSF (Peprotech), 10% heat-inactivated fetal bovine serum (FBS, Invitrogen), 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin (Invitrogen) for 5-7 days.

extract_protocol:
BMDMs were harvested after treatment, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT or TAGAP-KO BMDMs were left untreated or treated with Curdlan (10ug/ml) for 3 hours.

value: Bone marrow derived macrophages (BMDMs)

value: TAGAP-KO

value: Curdlan treated (10ug/ml)


title: MH-S clone 29_ low IL-4Ra activity_ unstimulation

source_name: MH-S clone 29, unstimulated, 16 h

tag: phenotype

value: low IL-4Ra activity

value: unstimulated

tag: cell line

value: MH-S

value: Alveloar macrophage


title: KO-Curdlan-2

description: RNA sequencing

tag: cell type

tag: genotype


title: oxytocin [12.AAACCTT]

description: 12.AAACCTT.run_2398_s_*_withindex_sequence.txt_AAACCTT

value: Sprague Dawley

value: embryonic day 21

value: maternal administration of oxytocin

value: cerebral cortex


title: KO-Curdlan-1

description: RNA sequencing


title: Diversity Sample

city: Berkeley

first: Samuel

middle: Thomas

last: Coradetti

address: 1165 Glen Ave Apt B

department: Bioengineering

institute: UC Berkeley

description: Multiple conditions to sample expression in diverse conditions

data_processing:
Reads mapped to reference transcripts with HiSat2
Transcripts assembled with stringtie1.3
Genome_build: Rhodosporidium toruloides ver 4 (https://genome.jgi.doe.gov/Rhoto_IFO0880_4/Rhoto_IFO0880_4.home.html)
Supplementary_files_format_and_content: Stringtie abuncances (fpkm)

organism: Rhodotorula toruloides

source_name: Microbial Cell Culture

growth_protocol: Microbial Liquid Culture. 30C, 200rpm

extract_protocol:
Ribopure Yeast RNA extraction kit
Illumina TrueSeq

treatment_protocol: Alternate media composition

tag: media

value: YPD, YPD + Salt, or YNB media with alternate carbon sources

tag: hours

tag: replicate


title: saline [11.ACAGATA]

description: 11.ACAGATA.run_2398_s_*_withindex_sequence.txt_ACAGATA


title: C57BL/6 MDI Exposed 1

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using the robubust multiarray averaging module for normalization

tag: drug (crofelemer) treatment

tag: respiratory tract exposure

value: MDI solution (MDI and GSH reacted together)

value: 6-8 weeks

value: male


title: MM-CN120-lateC

description: Low nitrogen, late timepoint

value: Glucose 166 mM, Ammonium Chloride 7 mM, YNB no Amino Acids or Ammonium Sulfphate 1.7 g/L, Sodium phosphate dibasic 25mM, Potassium phosphate monobasic 25mM


title: C57BL/6 MDI Exposed 2


title: WT-Curdlan-3

description: RNA sequencing

value: WT


title: MM-CN120-lateB

description: Low nitrogen, late timepoint


title: MM-CN120-lateA

description: Low nitrogen, late timepoint


title: WT-Curdlan-1

description: RNA sequencing

value: Bone marrow derived macrophages (BMDMs)


title: MM-CN5C

description: High nitrogen, late timepoint

value: Glucose 166 mM, Ammonium Chloride 168 mM, YNB no Amino Acids or Ammonium Sulfphate 1.7 g/L, Sodium phosphate dibasic 25mM, Potassium phosphate monobasic 25mM


title: MM-CN5B

description: High nitrogen, late timepoint


title: KO-untreated-2

description: RNA sequencing

value: TAGAP-KO

value: untreated


title: WT-Curdlan-2

description: RNA sequencing

value: Curdlan treated (10ug/ml)


title: MM-CN5A

description: High nitrogen, late timepoint


title: MM-CN120C

description: Low nitrogen, early timepoint


title: C57BL/6 MDI Exposed 4


title: C57BL/6 Control 3

description: Lung gene expression from sensitized C57Bl/6 mice exposed to control

value: control solution (MDI and GSH reacted seperately)


title: C57BL/6 Control 1


title: WT-untreated-3

description: RNA sequencing


title: C57BL/6 Control 2


title: C57BL/6 Control 4


title: Balb/c MDI Exposed 3

description: Lung gene expression from sensitized Balb/C mice exposed to MDI-GSH

value: Balb/c


title: MM-CN120B

description: Low nitrogen, early timepoint


title: Balb/c MDI Exposed 2


title: WT-untreated-2

description: RNA sequencing


title: RJ Fruit

city: Jammu

first: Archana

last: Koul

state: J&K

address: University of Jammu

department: School of Biotechnology

country: India

institute: University of Jammu

description: Gene Expression_Fruit

hyb_protocol: The purified cRNA (600 ng) was fragmented with fragmentation blocking mix in the presence or absence of formamide (7%) by incubating samples at 60 °C for 30 min. Microarray slides  were prepared in an Agilent Technologies Hybridization Chamber (G2534-90001) and the samples were placed in the hybridization oven (Agilent Technologies, G2505-80085) for incubation at 65 °C for 17 hr. After hybridization, the samples were washed according to the procedure described by Agilent Technologies

scan_protocol: Slides were scanned at a resolution of 5 μm using an Agilent Microarray scanner (G2565CA) with scan control software as per the manufacturer's instructions (G2505-90020)

data_processing: Raw data from the Feature Extraction software were obtained in .txt (Tab delimited) format and were normalized using GeneSpring GX v 12.0

organism: Solanum lycopersicum

source_name: red ripe_ fruit

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1 ug RNA using the One-Color RNA Spike-In Kit (Agilent Technologies, 5188–5282) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN Inc., USA).  Dye incorporation and cRNA yield were checked using Nanodrop 2000c spectrophotometer (Thermo Scientific, USA).

extract_protocol: Total RNA was extracted using TriZol reagent following manufacturer's instructions

tag: tissue

value: Whole fruit


title: Balb/c Control 3

description: Lung gene expression from sensitized Balb/C mice exposed to control

extract_protocol: Total RNA was extracted using Qiagen RNAeasy mini kit with RLT buffer containing 1% beta-mercaptoethanol

tag: age


title: MM-CN120A

description: Low nitrogen, early timepoint


title: SK Fruit

description: Gene Expression_Fruit


title: KO-untreated-1

description: RNA sequencing


title: AV Fruit

description: Gene Expression_Fruit


title: TM Fruit

description: Gene Expression_Fruit


title: PEMV2_3_RNA-seq

status: Public on Mar 01 2020

city: College Park

first: Jared

middle: Paul

last: May

state: MD

address: 4062 Campus Dr.

department: Cell Biology & Molecular Genetics

institute: University of Maryland

data_processing:
Trim Galore! was used to remove illumina adapter sequences and low quality reads (Phred score <20). The first 9 nt from the 5' ends were removed to avoid sequencing artifacts. Reads shorter than 20 nt or orphan reads were excluded from all analyses. FastQC was used to check read quality before and after trimming.
Transcript quantification from cleaned reads was performed using salmon version 0.11.2. The number of reads per transcript were used for downstream analyses
Differentially expressed transcripts were identified using a negative binomial model using MATLAB scripts from the Bioinformatics Toolbox. Read counts were normalized by determining the effective library size from corresponding size factors for each sample, transforming all values to a common scale. Differential expression was determined using a negative binomial model. A locally-regressed, non-parametric smooth function was used to specify the linkage between the variance and the mean. The Bejamini-Hochberg adjustment was used to calculate adjusted P-values to identify transcripts with significant changes in gene expression with a 10% false discovery rate.
Genome_build: Niben.genome.v1.0.1 annotated transcripts
Supplementary_files_format_and_content: .txt processed data files contain the following: transcript id, mean normalized reads for each sample (n=3 for each condition), log2 fold changes (log2FC) for each condition compared to Mock, p-value, adjusted p-value for each condition vs. Mock, 3' UTR sequence, 3' UTR length, 3' UTR GC-content, and presence (= 1) or absence (= 0) of upstream open reading frame (uORF) for each transcript.

molecule: polyA RNA

organism: Nicotiana benthamiana

source_name: Nicotiana benthamiana leaves

growth_protocol: Nicotiana benthamiana seedlings were grown at 24°C with 40–65% relative humidity and a long-day photoperiod (18 h light and 6 h dark). At the 4th to 5th leaf stage, leaves were agroinfiltrated with binary expression constructs.

extract_protocol:
The 4th and 5th true leaves from each plant were pooled for total RNA extraction. Samples were ground in liquid nitrogen and total RNA was extracted using the Total RNA Plant Mini Kit (IBI Scientific), which included an in-column DNAse I digestion.
Library preparation was performed with polyA selection followed by sequencing using Illumina HiSeq with a 2x150 bp paired-end configuration (Genewiz)

treatment_protocol: Binary expression constructs were transformed into agrobacteria (strain C58C1) and cultured for two days (passaged after day 1) in the presence of kanamycin and tetracycline. On day 2, acetosyringone was added at a final concentration of 20 µM. Bacterial cultures were pelleted and resuspended in resuspension buffer [10 mM MgCl2, 10 mM MES-K (pH 5.6)]. All infiltration mixtures contained the p14 silencing suppressor culture at a final OD600 = 0.2. Mock samples received C58C1 bacteria at OD600 = 0.4; U1D samples received the dominant-negative UPF1 mutant construct at final OD600 = 0.4; HA-p26 samples received an HA-tagged p26 construct at final OD600 = 0.4, and PEMV2 samples received the full-length PEMV2 virus at a final OD600 = 0.4. The 4th and 5th true leaves were infiltrated with a syringe (no needle). Infiltrated plants were grown for 3 days before total RNA extraction.

value: 4th and 5th true leaves


title: TM Leaf

description: Gene Expression_Leaf

source_name: mature _leaf

value: Whole leaf


title: HA-p26_2_RNA-seq

value: HA-tagged p26 construct at final OD600 = 0.4


title: Balb/c Control 2

tag: Sex


title: PEMV2_2_RNA-seq

value: full-length PEMV2 virus at a final OD600 = 0.4


title: HA-p26_3_RNA-seq


title: U1D_3_RNA-seq

value: UPF1 mutant construct at final OD600 = 0.4


title: U1D_2_RNA-seq


title: Sk Leaf

description: Gene Expression_Leaf


title: U1D_1_RNA-seq


title: Balb/c Control 1

value: 6-8 weeks


title: Balb/c MDI Exposed 1

value: MDI solution (MDI and GSH reacted together)

value: male


title: HA-p26_1_RNA-seq


title: RJ Leaf

description: Gene Expression_Leaf


title: WT-untreated-1

description: RNA sequencing

value: WT


title: AV Leaf

description: Gene Expression_Leaf


title: Donor A15165 Treatment  Clindamycin Day 14

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

description:
rawCounts.csv
normalizedCounts.csv
S81

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using skewer v0.2.2, then mapped to Mmul_8.0.1 whole genome using Hisat2 v2.0.5
Read summarization was performed by the program featureCounts v1.5.0-p2 as part of the SubRead package using the NCBI Homo sapiens Annotation release 106.
Counts Per Million (CPM) values were generated through the edgeR Library v3.16.5 in R
Genome_build: Mmul_8.0.1
Supplementary_files_format_and_content: rawCounts.csv: counts as generated by featureCounts, rows are gene features, columns are samples
normalizedCounts.csv: remove counts that were all zeroes (across the full set); Perform TMM normalization ; export log2(n+0.25) CPM

organism: Macaca mulatta

source_name: Colon biopsy tissue

growth_protocol: in vivo

extract_protocol:
RNA was extracted from colon biopsies preserved in RNA-Later using RNeasy Micro from Qiagen.
RNA libraries were prepared for sequencing using the Illumina TruSeq Stranded Total RNA - Globin kit.

treatment_protocol: no treament

value: Clindamycin

value: female

tag: timepoint

value: 14 days

value: Colon biopsy tissue


title: PEMV2_1_RNA-seq


title: Mock_1_RNA-seq

value: C58C1 bacteria at OD600 = 0.4


title: Mock_2_RNA-seq


title: Donor A15165 Treatment  Clindamycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S82

value: 28 days


title: Donor A15165 Treatment  Clindamycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S83

value: 63 days


title: Donor A15165 Treatment  Clindamycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S80

value: 3 days


title: Donor A15165 Treatment  Clindamycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S79

value: -21 days


title: Mock_3_RNA-seq

value: 4th and 5th true leaves


title: Donor A15165 Treatment  Clindamycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S78

value: -42 days


title: Wheat.shoot.Hi-ChIP

source_name: Shoot

value: Chinese Spring

tag: developmental stage

value: 14 days old seedlings

value: shoot


title: Donor A15141 Treatment  Clindamycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S77

value: 127 days


title: Donor A15141 Treatment  Clindamycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S75


title: Donor A15141 Treatment  Clindamycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S72


title: Donor A15138 Treatment  Clindamycin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S67


title: Donor A15141 Treatment  Clindamycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S73


title: Donor A15138 Treatment  Clindamycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S68


title: Donor A15138 Treatment  Clindamycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S70


title: Donor A15141 Treatment  Clindamycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S76


title: Donor A15138 Treatment  Clindamycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S69


title: Donor A15141 Treatment  Clindamycin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S74


title: Donor A15138 Treatment  Clindamycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S66


title: Donor A15141 Treatment  Clindamycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S71


title: Donor A15138 Treatment  Clindamycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S65


title: Donor A15165 Treatment  Clindamycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S84


title: Donor A15138 Treatment  Clindamycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S64


title: Donor A15142 Treatment  Paramomycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S63

value: Paramomycin


title: Donor A15142 Treatment  Paramomycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S61


title: Donor A15142 Treatment  Paramomycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S62


title: Donor A15142 Treatment  Paramomycin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S60


title: Donor A15140 Treatment  Paramomycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S56


title: Donor A15142 Treatment  Paramomycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S57


title: Donor A15140 Treatment  Paramomycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S54


title: Donor A15140 Treatment  Paramomycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S55


title: Donor A15142 Treatment  Paramomycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S59


title: Donor A15140 Treatment  Paramomycin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S53


title: Donor A15136 Treatment Cephalexin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S42

value: Cephalexin

value: 119 days


title: Donor A15134 Treatment  Paramomycin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S48

value: female


title: Donor A15134 Treatment  Paramomycin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S46

value: 14 days


title: Donor A15134 Treatment  Paramomycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S45

value: Colon biopsy tissue


title: Donor A15134 Treatment  Paramomycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S43


title: Donor A15134 Treatment  Paramomycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S44


title: Donor A15134 Treatment  Paramomycin Day 127

description:
rawCounts.csv
normalizedCounts.csv
S49


title: Donor A15134 Treatment  Paramomycin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S47


title: Donor A15136 Treatment Cephalexin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S39


title: Donor A15136 Treatment Cephalexin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S38


title: Donor A15136 Treatment Cephalexin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S41


title: Donor A15142 Treatment  Paramomycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S58


title: Donor A15136 Treatment Cephalexin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S37


title: Donor A15135 Treatment Cephalexin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S35


title: Donor A15135 Treatment Cephalexin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S34


title: Donor A15135 Treatment Cephalexin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S30


title: Donor A15135 Treatment Cephalexin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S32


title: Donor A15135 Treatment Cephalexin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S29


title: Donor A15135 Treatment Cephalexin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S33


title: Donor A15132 Treatment Cephalexin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S28


title: Donor A15140 Treatment  Paramomycin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S52


title: Donor A15132 Treatment Cephalexin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S27


title: Donor A15140 Treatment  Paramomycin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S50


title: Donor A15140 Treatment  Paramomycin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S51


title: Donor A15136 Treatment Cephalexin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S40


title: Donor A15139 Treatment Enrofloxacin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S19

value: Enrofloxacin


title: Donor A15132 Treatment Cephalexin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S25


title: Donor A15132 Treatment Cephalexin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S26

value: 28 days


title: Donor A15139 Treatment Enrofloxacin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S16


title: Donor A15132 Treatment Cephalexin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S23


title: Donor A15139 Treatment Enrofloxacin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S20

value: 63 days


title: Donor A15132 Treatment Cephalexin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S24

value: 3 days


title: Donor A15139 Treatment Enrofloxacin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S17


title: Donor A15132 Treatment Cephalexin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S22


title: Fn3sCas12a - T gRNA [Fn3_S3]

tag: in vitro environment

value: myTXTL from Arbor Biosciences

tag: lysate origination

value: E. coli

value: DNA from PCR-amplification


title: Donor A15139 Treatment Enrofloxacin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S21

tag: treatment


title: Donor A15139 Treatment Enrofloxacin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S18


title: Donor A15137 Treatment Enrofloxacin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S14


title: Donor A15135 Treatment Cephalexin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S31


title: Donor A15139 Treatment Enrofloxacin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S15

value: -42 days


title: Donor A15137 Treatment Enrofloxacin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S13


title: Donor A15137 Treatment Enrofloxacin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S11


title: Donor A15133 Treatment Enrofloxacin Day 119

description:
rawCounts.csv
normalizedCounts.csv
S7


title: Donor A15137 Treatment Enrofloxacin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S12


title: Donor A15137 Treatment Enrofloxacin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S10


title: Donor A15137 Treatment Enrofloxacin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S9

value: -21 days


title: Donor A15133 Treatment Enrofloxacin Day 63

description:
rawCounts.csv
normalizedCounts.csv
S6


title: Donor A15133 Treatment Enrofloxacin Day 28

description:
rawCounts.csv
normalizedCounts.csv
S5


title: Donor A15133 Treatment Enrofloxacin Day 14

description:
rawCounts.csv
normalizedCounts.csv
S4


title: C57BL/6 MDI Exposed 3

value: MDI solution (MDI and GSH reacted together)

value: 6-8 weeks

value: male

tag: strain


title: 231-3

city: Beijing

first: Tingting

last: Zhang

address: Nanwei street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
The GO (Gene Ontology, http://geneontology.org/) enrichment of DEGs was implemented by the hypergeometric test, in which p-value is calculated and adjusted as q-value, and data background is genes in the whole genome.
KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) is a database resource containing a collection of manually drawn pathway maps representing our knowledge on the molecular interaction and reaction networks.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: MDA-MB 231

extract_protocol:
cells were collected , flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line background

value: MDA-MB 231

value: breast cancer cell line

tag: genotype/variation

value: control


title: Donor A15133 Treatment Enrofloxacin Day 3

description:
rawCounts.csv
normalizedCounts.csv
S3

value: female


title: Donor A15133 Treatment Enrofloxacin Day -21

description:
rawCounts.csv
normalizedCounts.csv
S2

value: Colon biopsy tissue


title: control_rep1_1

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

description:
Cardiff_CTL18n6_25
18Q
CTL sample single cell RNAseq

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, and then mapped to hg19 whole genome using Cellranger software.
gene counts were quantified using normalized and used for differential stats using Seurat3 software
Genome_build: hg19
Supplementary_files_format_and_content: comma-separated text file includes count values for each cell per a sample

source_name: medium spiny neuron-like

growth_protocol: iPSC were grown and matrigel and in mTESR and then differentiated into medium spiny neuron-like cells using a combination of growth factors, growth medium, and chemical inhibitors

extract_protocol:
Samples for single cell RNA seq were harvested using Dispase (Gibco) for 30 minutes at 37oC, and pipetted off the plate with advanced DMEM/F12 (1:1) with 2% B27 and collected by centrifugation. Cells in 0.1% BSA PBS were filtered through a 70 µm cell strainer and counted. Cells were resuspended at 700 cells/µl in 0.04 % BSA in PBS at >80% viability.
RNA libraries were prepared for sequencing using 10x Genomics single cell platform and standard Illumina protocols

tag: cell type

value: iPSC-derived medium spiny neuron-like

tag: disease state

value: Control


title: HEK293_PKI_C

city: Bethesda

first: Ramiro

last: Iglesias-Bartolome

address: 37 Convent Drive

department: LCMB

institute: NIH/NCI

data_processing:
Reads were trimmed using Cutadapt (version 1.14) to remove sequencing adapters
mapping to the human reference genome, hg19, using STAR (version 2.5.2b) in a two-pass mode.
Expression levels were quantified using RSEM version 1.3.0 with GENCODE annotation version 19.
DESeq2 (version 1.20.0) was used to assess differential expression between conditions.
Genome_build: hg19

growth_protocol: Cells were cultured at 37°C in the presence of 5% CO2. HEK293 cell were obtained from AddexBio and cultured in DMEM (Sigma-Aldrich Inc) containing 10% fetal bovine serum (FBS) (Sigma-Aldrich Inc) and antibiotic/antimycotic solution (Sigma-Aldrich Inc).

extract_protocol:
RNA was isolated and processed using RNeasy Plus Mini Kit (Qiagen) according to manufacturer’s instructions. Cells were lysed using the Precellys lysing kit (Bertin Instruments).
TruSeq mRNA Prep Kit RS-122-2101

treatment_protocol: Cells were transfected one day after plating. DNA constructs were transfected at a concentration of 158 ng/cm^2 using Lipofectamine 3000 (Thermo Fisher Scientific) according to manufacturer instructions.

tag: cell line

value: expressing for GFP fusion proteins for PKI1-24 (PKI)


title: Donor A15133 Treatment Enrofloxacin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S1

value: Enrofloxacin


title: adult_rep1_1

description:
Cardiff_HD53n3_03
53Q
HD sample single cell RNAseq

value: huntington's disease


title: Pep2-E3-2

source_name: MDA-MB 231_Pep2-E3


title: HEK293_inPKI_A

value: expressing for GFP fusion proteins for inPKI1-24 (inPKI) as a control


title: Pep2-E3-1


title: HEK293_inPKI_B


title: 231-2


title: HEK293_PKI_B


title: HEK293_PKI_A


title: 231-1


title: HEK293_inPKI_C


title: Donor A15137 Treatment Enrofloxacin Day -42

description:
rawCounts.csv
normalizedCounts.csv
S8


title: Rosa[1x]_biological rep1

city: Warsaw

first: Barbara

last: Kalenik

address: Pawinskiego 5a

country: Poland

institute: Institute of Biochemistry and Biophysics Polish Academy of Sciences

hyb_protocol: Following fragmentation, 10 ug of cDNA were hybridized for 16 hr at 45 degrees Cent. on Affymetrix ChiGene-1_1-st-v1microarrays, following by washing and staining in the Gene Atlas System following standard manufacturer's instructions.        scan protocol  GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

scan_protocol: The chips were scanned using the Affymetrix Gene Atlas Scanner.

data_processing: The microarray gene expression data was analyzed using Partek Genomic Suite 6.6 beta software (Partek Inc., Louis, MO). Raw data (.cel files) were imported and processed, using Robust Multiarray Averaging (RMA) background correction, quantile normalization, Log2 transformation and median polish summarization.

organism: Gallus gallus

source_name: Rosa 1 chicken (maintained at an experimental poultry house in standard bedding conditions) immunized once with DNA vaccine.

label_protocol: Biotinylated cDNAs were prepared according to the standard Affymetrix protocol from 100 ng total RNA by the sequential use of the Ambion® WT Expression Kit and the Affymetrix GeneChip® WT Terminal Labelling Kit according to the manufacturer’s protocols.

growth_protocol: Rosa 1 chickens were purchased from a commercial brooder on the day of hatching and maintained at an experimental poultry house in standard bedding conditions.

extract_protocol: Whole spleens were homogenised in Buffer RLT Plus (Qiagen) with the ULTRA-TURRAX Tube Disperser (IKA, Germany). According to the manufacturer’s protocol, 700 μl of the lysate was used for RNA isolation with RNeasy Plus Mini Kit (Qiagen) with on-column DNase digestion followed by DNase digestion using TURBO DNase kit (Ambion) to eliminate DNA contamination.

treatment_protocol: Chickens from ‘Rosa[2x]’ group were vaccinated twice with HA DNA vaccine, at 7 and 21 day post hatch (dph). The DNA vaccine was applied with Lipofectin (Invitrogen, Germany) carrier in a final volume of 100 μl via intramuscular injection. The empty pCI vector (Promega, Poland) was used as a negative control. Group ‘Rosa[1x]’ was immunized once at 7 dph with above mentioned vaccine. 7 day post last vaccination dose chickens were sacrificed, their spleens were collected and stored in RNAlater solution (Ambion).

value: Rosa 1

value: spleen

value: DNA vaccine (1x)


title: Pep2-E3-3


title: Rosa[1x]_ctrl_biological rep2

source_name: Rosa 1 chicken (maintained at an experimental poultry house in standard bedding conditions) immunized once with empty vector pCI.

value: empty pCI vector (1x)


title: Rosa[2x]_ctrl_biological rep2

source_name: Rosa 1 chicken (maintained at an experimental poultry house in standard bedding conditions) immunized twice with empty vector pCI.

value: empty pCI vector (2x)


title: Rosa[1x]_ctrl_biological rep3


title: Rosa[2x]_ctrl_biological rep1


title: Rosa[2x]_ctrl_biological rep3


title: 174CS24

city: Cambridge

first: Philip

last: Wigge

address: 47 Bateman street

department: Sainsbury Laboratory

institute: Cambridge University

data_processing:
Library strategy: DAP-seq
Adapters were trimmed off from raw reads with "trim_galore" with default arguments. Raw reads were mapped to the genome "sPta717-v1-1" with "bowtie2" under argument:"--no-mixed --no-discordant --no-unal -k2". Duplicate reads were removed with Picard using default setting.
Genomic binding profile was quantified in RPKM (Reads Per Kilobase per Million mapped reads) using a bin-size of 10bp. "deeptools.bamCoverage" is used.
For each treated ChIP-Seq library, peaks were called against a control None using MACS2 with argument "--keep-dup 1 -p 0.1".
Genome_build: sPta717-v1-1
Supplementary_files_format_and_content: RPKM.bw: RPKM-normalised bigwig track at 10bp resolution
Supplementary_files_format_and_content: .narrowPeak: ENCODE narrowPeak containing MACS2-called peaks.

source_name: IP

extract_protocol:
DAP-seq experiment was done according to O'Malley et al., 2016, Cell 165, 1280-1292; fragmentation method: sonication
The enriched Genomic DNA was sonicated to average length of 450bp and measured using Tapestation. Resulting DNA was size selected and Illumina forked adapter ligated. The resulting DNA was amplified using TruSeq Index Adapters to obtain library with with differing indices. The libraries were sequenced on a NextSeq® 500 (Illumina) using single-end sequencing of 75 bp with a NextSeq® 500/550 High Output v2 Kit for 75 cycles.

tag: dap target protein

value: PtaLHY2 Potri.014G106800

tag: replicate

value: single

tag: chip antibody

value: FLAG M2 agarose affinity gel antibody SIGMA A2220

tag: fragmentation method

value: sonication


title: WL[2x]_ctrl_biological rep2

description: Gene expression data from spleen of chicken immunized twice with empty vector pCI.

source_name: White Leghorn (SPF) chicken immunized twice with empty vector pCI.

growth_protocol: Specific pathogen free (SPF) White Leghorn (WL) chickens were purchased from from VALO Biomedia (Germany) and housed in a biosafety level 3 containment of the National Veterinary Research Institute, Pulawy.

treatment_protocol: Chickens were vaccinated twice with HA DNA vaccine, at 7 and 21 day post hatch (dph). The DNA vaccine was applied with Lipofectin (Invitrogen, Germany) carrier in a final volume of 100 μl via intramuscular injection. The empty pCI vector (Promega, Poland) was used as a negative control.  7 day post booster dose chickens were sacrificed, their spleens were collected and stored in RNAlater solution (Ambion).

value: White Leghorn

tag: tissue


title: Rosa[1x]_biological rep4


title: Rosa[1x]_biological rep3


title: Rosa[1x]_biological rep2


title: WL[2x]_ctrl_biological rep3


title: Rosa[2x]_biological rep2

source_name: Rosa 1 chicken (maintained at an experimental poultry house in standard bedding conditions) immunized twice with DNA vaccine.

value: DNA vaccine (2x)


title: Rosa[2x]_biological rep3


title: WL[2x]_biological rep1

description: Gene expression data from spleen of chicken immunized twice with DNA vaccine.

source_name: White Leghorn (SPF) chicken immunized twice with DNA vaccine.


title: WL[2x]_biological rep2


title: 174CS20

source_name: Input

value: none (input)


title: MP2: Monocyte RFP+ 5

city: Calgary

first: Nathan

last: Peters

state: AB

address: 3330 Hospital Dr NW

department: Microbiology, Immunology and Infectious Diseases

country: Canada

institute: University of Calgary

hyb_protocol: cDNA samples were hybridized to capture the reporter CodeSet and the capture ProbeSet provided by NanoString forming the target-probe complex. The reporter probes are molecular barcodes provided by NanoString. The samples were placed in a pre-heated 65°C thermal cycler and incubated for 20h to allow the hybridization.

scan_protocol: Scanning was conducted using the nCounter Digital Analyser acording to the manufacture's instructions. In general, it collects data by taking images of the immobilized fluorescent reportes in the sample cartridge with a CCD camera trough a microscope objective lens. The images are processed and each lane generates one RRC (Reporter Code Count) file that contains the number of reporters counted.

data_processing: All analysis were done in R version 3.6.0. Raw RCC files were loaded into R and quality analysis was done with NanoStringQCPro1.16.0. For principal component analysis (PCA) and visualization of gene counts the data was normalized with a variance stabilizing transform using NanoStringNorm. PCA was done with the built in R function, prcomp. Differential expression was done with NanoStringDiff 1.14.0, which uses a negative binomial model and includes an empirical Bayes shrinkage procedure to estimate dispersion (Wang et al., 2016). A 2 x 2 factorial model was used and the effect of infection was tested (p < 0.05) on samples.

source_name: infected (RFP+) monocytes

label_protocol: RNA was not labeled. 30ng/ul of RNA was converted to cDNA to follow the NanoString manufacture's protocol for the hybridization

extract_protocol: Monocytes were sorted out of the skin mice using FACSAria II and RNA was extracted using Qiagen Rneasy mini kit according to the manufacture's protocol.

tag: Sex

value: Female

tag: age

value: 8 weeks

tag: time post-infection

value: 2 weeks

tag: parasite

value: Leishmania amazonensis

value: skin


title: 175CS6


title: MN3: Monocyte RFP- 3

source_name: non-infected (RFP-) monocytes


title: MN1: Monocyte RFP- 1


title: MP3: Monocyte RFP+ 6


title: MN2: Monocyte RFP- 2


title: Rosa[2x]_biological rep1

value: Rosa 1


title: WL[2x]_ctrl_biological rep1

value: spleen


title: MP1: Monocyte RFP+ 4


title: Apoe-/-/Treml4-/- macrophages treated 60ug  rep 3

city: Frederick

first: Marieli

last: Gonzalez-Cotto

state: Maryland

department: Cancer & Inflammation Program

institute: National Cancer Institute

data_processing:
BAM files were converted to fastq, followed by Fast QC
Align fastq files to Genecode mouse reference using STAR (with soft trimming)
Post-alignment quality control with RNASeqQC
Subreads counting on aligned BAM files (using RefSeq gtf file)
Genome_build: mm10
Supplementary_files_format_and_content: rpkm

source_name: macrophage treated oxLDL 60

growth_protocol: Total cells from the bone marrow were plated at 7.0 x 10^5 / mL for 5-7 days in complete Dulbecco’s modified eagles media (DMEM) (Gibco #11965) supplemented with 2mM Glutamine, 10% FBS, 100U/mL Penicillin/Streptomicin and 20ng/ml mouse M-CSF allowing for proper BMDM differentiation and growth.

extract_protocol:
Total RNA was isolated using the High-Pure Rna isolation kit (Roche, 11828665001), as per manufacturer's instructions (with the addition that 2-mercaptoethanol (1%v/v) was added to the lysis buffer. RNA quality was checked on Agilent Bioanalyzer.  All samples used have high quality score.
Samples sequence on one Novaseq SP 150bpX2 FC + one Miseq 50bp SR run for barcode normalize
Illumina HiSeq4000, stranded, paired-end, barcoded, read length: 50 bp, reads per sample: 60x10^6

treatment_protocol: After growing BMDM for 6 days in culture, cells were placed in complete culture media and treated with vehicle (PBS) or of LPS (100ng/mL) for  8h or 12h  for proinflammatory activation

tag: genotype

value: Apoe/Treml4 DKO

value: bone marrow derived macrophages

tag: background strain


title: Apoe-/-/Treml4-/- macrophages treated 60ug  rep 2


title: Rosa[1x]_ctrl_biological rep1

tag: strain

tag: treatment

value: empty pCI vector (1x)


title: Apoe-/- macrophages oxLDL treated 60ug  rep 3

value: Apoe KO


title: Apoe-/- macrophages oxLDL treated 60ug  rep 2


title: Apoe-/-/Treml4-/- macrophages treated 10ug  rep 3

source_name: macrophage treated oxLDL 10


title: Apoe-/-/Treml4-/- macrophages treated 10ug  rep 2


title: Apoe-/-/Treml4-/- macrophages treated 10ug  rep 1


title: Apoe-/- macrophages oxLDL treated 10ug  rep 3


title: Apoe-/- macrophages oxLDL treated 10ug  rep 2


title: Apoe-/- macrophages oxLDL treated 10ug  rep 1


title: Apoe-/-/Treml4-/- macrophages untreated rep 2

source_name: macrophage untreated


title: 166CS24

value: PtaLHY2 Potri.014G106800

value: single


title: Apoe-/- macrophages untreated rep 3


title: Apoe-/- macrophages untreated rep 2


title: Apoe-/-/Treml4-/- macrophages treated 60ug  rep 1


title: Apoe-/- macrophages untreated rep 1


title: w1118 FLAG IP control 1

city: Salt Lake City

first: Katherine

last: Beebe

state: UT

address: 15 North 2030 East

department: Molecular Medicine

institute: University of Utah

data_processing: wig files

organism: Drosophila melanogaster

source_name: whole fly

extract_protocol:
ChIP-seq was performed on six-day-old w1118 controls and w1118; dERR-3XFLAG-BACVK22; dERR1/dERR2 adults essentially as described (Barry and Thummel 2016) using FLAG antibodies (Sigma F1804, M2 monoclonal).
ChIP-seq library construction is performed using the Illumina TruSeq ChIP Sample Prep Kit (IP-202-1012 and IP-202-1024) as described below.  Briefly, ChIP DNA is quantitated using an Invitrogen Qubit dsDNA HS Assay (Q32851) and a quantity representing appoximately 10 ng is converted to blunt-ended fragments with 5'-phosphates and 3'-hydroxyl groups using a combination of enzymes that perform fill-in reactions and exhibit exonuclease activity.  An A-base is added to the blunt-ended DNA as a means to prepare the fragments for adapter ligation and to block concatamer formation during the ligation step.  Adapters containing a T-base overhang are ligated to the A-tailed DNA fragments.  Ligated fragments are PCR-amplified (10 cycles) and the amplified library is purified  using Agencourt AMPure XP beads.  The concentration of the amplified library is measured using the Invitrogen Qubit dsDNA HS Assay and an aliquot of the library is resolved on an Agilent 2200 Tape Station using a D1K (cat# 5067-5361 and 5067-5362) or a High Sensitivity D1K (cat# 5067-5363 and 5067-5364) assay to define the size distribution of the sequencing library.  Libraries are adjusted to a concentration of approximately 10 nM and quantitative PCR is performed using the KapaBiosystems Kapa Library Quant Kit (cat# KK4824) to calculate the molarity of adapter ligated library molecules.  The concentration is further adjusted following qPCR to prepare the library for Illumina sequence analysis.

value: whole fly

tag: full genotype

value: male

value: day 6 adults


title: ERR-FLAG IP 1

value: w1118; dERR-3XFLAG-BACVK22; dERR1/dERR2


title: Apoe-/- macrophages oxLDL treated 60ug  rep 1

tag: cell type


title: ERR-FLAG IP 3


title: ERR-FLAG IP 4


title: w1118 FLAG IP control 4


title: ERR-FLAG IP 2


title: w1118 FLAG IP control 3