title: PACs_Aging_Pool_de_2_ech

value: aging mice

value: 16 months


title: AML100

status: Public on Jun 03 2020

type: RNA

city: Nottingham

first: Sergio

last: Rutella

address: Clifton Campus

department: John van Geest Cancer Research Centre

country: United Kingdom

institute: Nottingham Trent University

description: Pan Cancer Immune panel

hyb_protocol: Hybridisation was performed in a PCR for 20 hours at 65°C.

scan_protocol: Scanned with NanoString Digital analyser with 555 FOV

data_processing: Data was normalised using the nSolver software, version 4.0.

label: Nanostring bar coding

molecule: total RNA

organism: Homo sapiens

source_name: AML_bone marrow_Diagnosis

label_protocol: RNA ispecies were identified and counted using the NanoString PanCancer Immune Profiling Panel.

growth_protocol: Human Samples

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.

treatment_protocol: At time of initial diagnosis, achievement of complete remission and relapse.

tag: subject status

value: patient with acute myeloid leukaemia

tag: age (years)

tag: disease stage at sampling

value: Diagnosis

tag: tissue

value: Bone Marrow


title: PolII_NM_15min_R1

type: SRA

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

institute: University of Leicester

library_source: genomic

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg38 genome was performed with Tophat2 v2.1.0 (mNET-seq) or with Bowtie2 v2.2.5 (ChIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq)
Bigwig files were generated with the Deeptools2 bamCoverage tool
Genome_build: hg38 (except HEK293 CDK12as Pol II, Ser2P, and Ser5P ChIP-seq which are mapped on the hg19)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

molecule: genomic DNA

source_name: HEK293 CDK12as

growth_protocol: HEK293 CDK12as cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
DNA were purified from chromatin IP products. Total RNA were purified from immunoprecipitated RNA polymerase II.
For ChIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions. For mNET-seq, libraries were prepared using NEBNext® Small RNA Library Prep Set for Illumina, according to NEB's instructions.

treatment_protocol: Cells were treated with 1-NM-PP1 for 15 minutes.

tag: cell line

value: HEK293 CDK12as

tag: antibody

value: sc-899 X, Santa Cruz Biotechnology (discontinuited antibody)

tag: treatment

value: NM 15 minutes


title: PolII_NM_15min_R2


title: AML99

description: Pan Cancer Immune panel


title: PACs_Apo_Pool_de_4_ech

city: montreal

first: michel

last: desjarlais

state: quebec

address: 5415 Blvd L’Assomption

department: Department of Ophthalmology,

country: Canada

institute: Maisonneuve-Rosemont Hospital Research Center, University of Montréal, Montréal, Québec, Canada.

library_source: transcriptomic

data_processing:
Basecalls performed using Illumina RTA 2.4.11.
Samples demultiplexed using bcl2fastq 2.20 allowing 0 mismatch in the index.
Sequenced fragments were trimmed in for sequencing adapters and candidates longer than 17bp where mapped to the reference genome mm10 using Tophat version 2.0.10.
Known miRNA extracted from miRBase mm10 version 21 were then quantified by counting the number of reads that fall into each of their location on the genome using HTSeq count version 0.5.4, keeping the contribution of ambiguously matched reads.
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited files include columns: A. miRNA identifier, B. readcount and C. readcount per million reads sequenced (RPM).

organism: Mus musculus

source_name: bone marrow-derived PAC

growth_protocol: PACs extraction from bone marrow and cultured in fibronectine coated dish with EGM for 4 days.

extract_protocol:
Ambion mirVana™ miR isolation kit (Life Technologies)
NGS

treatment_protocol: ischemia induced surgically by feroral artery removal

tag: cell type

value: proangiogenic cells (PACs)

tag: genotype/variation

value: APOE-/-

tag: condition

value: hypercholesterolemic mice

tag: age of mice

value: 2 months

tag: pathological aspect

value: hindlimg ischemia

tag: other phenotype

value: NV trigger by ischemia


title: Ser2_NM_15min_R2

value: ab5095:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade. Abcam


title: HIF_LPS_13_male

city: Rehovot

first: Hassan

last: Massalha

address: Herzl St 234

country: Israel

institute: Weizmann Institute of Science

data_processing:
bcl2fastq/2.15.0.4. pool and i7 barcodes was provided for demultiplexing to obtain sample specific reads in two fastq files (read 1 (R1) and read 2 (R2)), barcodes attached in the SAMPLES section.
Genome_build: GRCm38.84
Supplementary_files_format_and_content: tab-delimited text file (expression matrix) includes mRNA molecule count values for each Sample; list of barcods used for demultiplexing the pooled expereiment from the mcSCRBseq (mcSCRBseq_samples_barcodes.txt.gz)

molecule: polyA RNA

growth_protocol: C57bl6 mice were fed regular chow ad libitum

extract_protocol:
Isolation of Bone marrow cells were obtained by flushing long bones with phosphate buffered saline (PBS). Neutrophils were stained for CD45, CD11b and Ly6G (30 min) and sorted by FACS machine.
bulk analysis, mcSCRBseq protocol was used (Bagnoli et al, Nat Commun. 2018)

treatment_protocol: Mice were treated with PBS or LPS and sacrificed 4hr post treatment by cervical dislocation

tag: strain background

value: specific HIF-1 alpha deletion in myeloid lineage

tag: age

value: post natal two months

tag: Sex

value: male

value: FACS sorted neutrophils

value: LPS

tag: barcode

value: CTATAC+TAGCGCTC


title: EV-F10

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

country: USA

institute: Oklahoma Medical Research Foundation

description: Empty Vector

data_processing:
none provided by the submitter
Genome_build: mm10
Supplementary_files_format_and_content: coujnts

source_name: EDL muscle

extract_protocol: Illumina TruSeq v2

value: EDL muscle

value: Female

tag: age in months


title: HIF_LPS_12_male

value: TATAAT+TAGCGCTC


title: Input_SPT6_NM_15min_R1

value: HEK293 CDK12as

value: NM 15 minutes


title: AML97

description: Pan Cancer Immune panel

tag: subject status

value: patient with acute myeloid leukaemia

tag: age (years)

value: Diagnosis

value: Bone Marrow


title: AML98

description: Pan Cancer Immune panel

tag: disease stage at sampling

tag: tissue


title: AML106

description: Pan Cancer Immune panel


title: Input_SPT6_DMSO_R1

tag: cell line

tag: antibody

value: DMSO


title: HIF_PBS_11_female

value: female

tag: cell type

tag: treatment

value: PBS

value: ATTCCT+TACGCTGC


title: Ser2_DMSO_R1

value: ab5095:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade. Abcam


title: HIF_PBS_10_female

tag: genotype/variation

value: specific HIF-1 alpha deletion in myeloid lineage

value: post natal two months

value: CAGATC+TACGCTGC


title: Input_PolII_NM_15min_R2


title: AML95

description: Pan Cancer Immune panel


title: AML96

description: Pan Cancer Immune panel


title: AML101

description: Pan Cancer Immune panel


title: PolII_DMSO_R2

value: sc-899 X, Santa Cruz Biotechnology (discontinuited antibody)


title: HIF_PBS_9_male

value: male

value: FACS sorted neutrophils

value: CCAACA+TACGCTGC


title: HIF_LPS_14_female

value: LPS

value: TCGGCA+TAGCGCTC


title: Input_PolII_NM_15min_R1

value: HEK293 CDK12as

value: NM 15 minutes


title: WT_PBS_8_male

value: wild type

value: ATGAGC+TACGCTGC


title: AML94

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia

value: Diagnosis

value: Bone Marrow


title: Input_PolII_DMSO_R2

value: DMSO


title: AML93

description: Pan Cancer Immune panel


title: WT_LPS_6_female

value: female

value: CTATAC+GCGTAGTA


title: WT_LPS_5_male

value: post natal two months

value: TCGGCA+GGAGCTAC


title: AML91

description: Pan Cancer Immune panel


title: AML90

description: Pan Cancer Immune panel


title: Input_PolII_DMSO_R1


title: Input_CPSF73_NM_15min_R1


title: WT_LPS_4_male

value: male

value: ACTTGA+GGAGCTAC


title: Input_CPSF73_DMSO_R2


title: Input_CPSF73_NM_15min_R2


title: AML89

description: Pan Cancer Immune panel


title: Input_CPSF73_DMSO_R1


title: PolII_DMSO_R1

value: sc-899 X, Santa Cruz Biotechnology (discontinuited antibody)


title: AML88

description: Pan Cancer Immune panel


title: WT_PBS_3_male

value: FACS sorted neutrophils

value: PBS

value: CCGTCC+GGAGCTAC


title: WT_PBS_1_male

value: CGATGT+TAGCGCTC


title: CPSF73_NM_15min_R1

value: HEK293 CDK12as

value: A301-091A, Bethyl Laboratories

value: NM 15 minutes


title: CPSF73_DMSO_R2


title: AML87

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Relapse

value: patient with acute myeloid leukaemia

value: Relapse


title: CPSF73_DMSO_R1

value: DMSO


title: AML84

description: Pan Cancer Immune panel

value: Diagnosis

value: Bone Marrow


title: AML85

description: Pan Cancer Immune panel


title: WT_LPS_7_female

value: wild type

value: post natal two months

value: female

value: LPS

value: ATTCCT+GCGTAGTA


title: AML83

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Complete remission

value: Complete remission


title: iBlast-RUNX1 KD-rep1 [ATAC-seq]

city: New York

first: Hanzhi

last: Luo

state: New York

address: 417 E 68th street

department: Molecular Pharmacology

institute: MSKCC

description: All_peaks_RUNX1 KD.csv

data_processing:
Fastq files were aligned to GRCh37.75 (hg19) using STAR alignment tool
Aligned bam files were filtered for uniquely aligned reads with MAQ > 10
Differential expression analysis was performed using R-package “DESeq2”.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample, log2FC and padj of DESeq2 of A vs S

source_name: human iPSCs

extract_protocol:
nuclei were isolated by washing with ATAC buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2) and lysing with 50 ul of ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). 1ml of ATAC buffer was added to dilute lysis buffer
Cell lysates were spun to obtain nuclear pellets, which were subjected to transposase reaction using the Illumina Nextera DNA Sample Preparation Kit according to the manufacturer’s instructions. The reaction was stopped by adding SDS to a final concentration of 0.2%.

value: RUNX1 KD

tag: differentiation stage

value: Day 18 of hematopoietic differentiation

tag: time post infection

value: 48 hours after transduction


title: iBlast-RUNX1 KD-rep3 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: iBlast-RUNX1 KD-rep2 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: AML92

description: Pan Cancer Immune panel


title: TSCC1

city: New York City

first: Alireza

last: Khodadadi-Jamayran

state: NY

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
Additional cell-level demultiplexing and alignment was performed with 10x Cell Ranger software.
Genome_build: hg19
Supplementary_files_format_and_content: BAM files containing position-sorted reads aligned to the genome and genes-barcodes (tsv file) matrices (matrix file) and vdi contigs (csv file).

extract_protocol:
Patient tumors were obtained on the day of surgery and washed in cold 1X PBS. Any fat was removed from tumor samples using a scalpel. Then, tumors were then cut into small pieces using a razor and resuspended in 10 mL of RPMI [Gibco 11875-093] supplemented with 5% human serum [Sigma H4522-100], 5 mg gentamicin [Sigma H0887], 5 mg/mL collagenase II [Sigma C2674] and 10 U DNase I [Sigma 00453869] for 10 minutes at 37Â°C. After incubation, the suspension was vortexed 1X for 30 sec followed by pipetting sequentially through 25-mL, 10-mL, and 5-mL pipettes for 1 min each. Next, the cell suspension was filtered through a 70-_m filter [Fisher 22363548] and spun at 450 g for 10 minutes. After spinning, the supernatant was removed, and ACK red blood cell lysis was performed according to the manufacturerâ€™s protocol as needed [Gibco a10492-01]. Cells were then stained as described below prior to cell sorting and FACS analysis.
The sorted cellular suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs). Approximately 10-12e3 cells were loaded per channel. Single-cell RNA-Seq libraries were prepared using the following Single Cell 5â€™ Reagent Kits: Chromiumâ„¢ Single Cell 5â€™ Library & Gel Bead Kit, PN-1000006 and Chromium Single Cell VDJ enrichment kit for Human T Cells (PN-100000). Libraries were run on a NovaSeq 6000 SP or S1 flow cell (depending on sample numbers) for both 5â€™ transcriptome data and TCR clonotype determination.
scRNA-seq and scVDJ-seq

tag: condition

value: TSCC


title: TSCC10-4


title: iBlast-control-rep3 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv

value: control


title: WT_LPS_2_male

tag: strain background

value: male

value: FACS sorted neutrophils

value: TGACCA+GGAGCTAC


title: SCC2_102518

value: SCC


title: iBlast-control-rep1 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: AML82

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia

value: Diagnosis


title: iBlast-control-rep2 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: CPSF73_NM_15min_R2

value: HEK293 CDK12as

value: A301-091A, Bethyl Laboratories

value: NM 15 minutes


title: iLSC-RUNX1 KD-rep3 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: AML80

description: Pan Cancer Immune panel

value: Relapse

value: Bone Marrow


title: AML79

description: Pan Cancer Immune panel


title: SCC1_102518


title: hu-Scc3_GE


title: AML78

description: Pan Cancer Immune panel


title: AML81

description: Pan Cancer Immune panel


title: iLSC-RUNX1 KD-rep2 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: CD8T-TSCC_GE


title: AML86

description: Pan Cancer Immune panel


title: iLSC-RUNX1 KD-rep1 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: iLSC-control-rep3 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: CD8-scc2_GE


title: AML77

description: Pan Cancer Immune panel

value: Complete remission


title: iLSC-control-rep2 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: iLSC-control-rep1 [ATAC-seq]

description: All_peaks_RUNX1 KD.csv


title: CD8-scc1_GE


title: AC2


title: AML75

description: Pan Cancer Immune panel


title: AML74

description: Pan Cancer Immune panel


title: iBlast-RUNX1 KD-rep3 [RNA-seq]

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen). PolyA-tailed mRNA was selected with beads from 1µg total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs).
DNAs were generated using random hexamers and ligated to barcoded Illumina adaptors with the NEXTflex Rapid Directional RNA-Seq Library Prep Kit (Bioo Scientific).

value: RUNX1 KD


title: iBlast-RUNX1 KD-rep2 [RNA-seq]

value: Day 18 of hematopoietic differentiation


title: iBlast-RUNX1 KD-rep1 [RNA-seq]

value: 48 hours after transduction


title: AML73

description: Pan Cancer Immune panel


title: AML72

description: Pan Cancer Immune panel


title: 9_12

value: TSCC


title: ChIP-seq 293 Pol II DMSO

data_processing:
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg19 genome was performed with Bowtie2 v2.2.5 (ChIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq)
Bigwig files were generated with the Deeptools2 bamCoverage tool
Genome_build: hg38 (except HEK293 CDK12as Pol II, Ser2P, and Ser5P ChIP-seq which are mapped on the hg19)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: ChIP-seq 293 Pol II DMSO

growth_protocol: HEK293 cells were maintained in DMEM with 10% fetal bovine serum

extract_protocol:
DNA were purified from chromatin IP products.
For ChIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

value: sc-899 X, Santa Cruz Biotechnology (discontinuited antibody)

value: DMSO


title: AML71

description: Pan Cancer Immune panel


title: ChIP-seq 293 Input NM 15 minutes

source_name: ChIP-seq 293 Input NM 15 minutes


title: iBlast-control-rep3 [RNA-seq]

value: control


title: iBlast-control-rep2 [RNA-seq]


title: ChIP-seq LEO1 NM 15 minutes R2

source_name: ChIP-seq

value: A300-175A, Bethyl Laboratories

value: 1-NM-PP1 for 15 minutes


title: AML70

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia


title: AML69

description: Pan Cancer Immune panel

value: Diagnosis


title: iBlast-control-rep1 [RNA-seq]


title: ChIP-seq 293 Input DMSO

source_name: ChIP-seq 293 Input DMSO


title: ChIP-seq LEO1 NM 15 minutes R1

value: HEK293 CDK12as


title: iLSC-RUNX1 KD-rep3 [RNA-seq]


title: AML76

description: Pan Cancer Immune panel


title: iLSC-RUNX1 KD-rep2 [RNA-seq]


title: iLSC-RUNX1 KD-rep1 [RNA-seq]


title: AC1


title: ChIP-seq LEO1 DMSO R2


title: AML68

description: Pan Cancer Immune panel


title: AML67

description: Pan Cancer Immune panel


title: ChIP-seq LEO1 DMSO R1


title: AML65

description: Pan Cancer Immune panel


title: iLSC-control-rep3 [RNA-seq]


title: AML66

description: Pan Cancer Immune panel


title: AML64

description: Pan Cancer Immune panel


title: ChIP-seq Input LEO1 NM 15 minutes R2


title: ChIP-seq Input LEO1 NM 15 minutes R1


title: iLSC-control-rep2 [RNA-seq]


title: iLSC-control-rep1 [RNA-seq]


title: ChIP-seq Input LEO1 DMSO R2


title: AML63

description: Pan Cancer Immune panel


title: AML62

description: Pan Cancer Immune panel


title: ChIP-seq Input LEO1 DMSO R1


title: AML61

description: Pan Cancer Immune panel


title: HUVEC infected with Ot UT176 3

city: Würzburg

first: Lars

last: Barquist

state: Bayern

address: Josef-Schneider-Straße 2 / Bau D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Reads trimmed using cutadapt v1.9.1 for minimum base quality of 20
Read mapping and quantification using READemption v0.4.3 and segemehl v.0.2.0
Bacterial read quantification using Salmon v0.9.1
differential expression using edgeR v3.20.9
Genome_build: GRCh38 (human), LS398548.1 (Karp), LS398547.1 (UT176)
Supplementary_files_format_and_content: XLSX, differential expression results

source_name: HUVEC

growth_protocol: The clinical isolate strains (Karp and UT176) of Orientia tsutsugamushi were propagated in a confluent monolayer of host cells (HUVEC, Human Umbilical Vein Endothelial Cells) for 5 days at MOI 100:1. Cells were cultured using Media200 (Thermo Fisher, Catalog no. M200-500) supplemented with LVES media (Thermo Fisher, Catalog no. A14608-01) at 35 ¡C and 5% CO2. The infectivity was determined by qPCR of the single copy Ot gene 47kDa at day 5-7.

extract_protocol:
Both uninfected cells and infected cells were harvested by incubating the cells on ice and quickly resuspending in RNAprotect Bacteria Reagent (Qiagen, catalog no. 76506), then storing at -80 ¡C until use.  RNA extraction was performed using the Qiagen RNeasy Plus kit (Qiagen, catalog number 74136) according to manufacturer's instructions and as described previously (Atwal, 2017).
The integrity of the DNase-treated RNA samples was assessed in a Bioanalyzer (Agilent). All samples had RIN (RNA integrity number) values ³8.0. Ribosomal transcripts were removed using the Ribo-Zero Gold (epidemiology) kit (Illumina). Following the manufacturer's instructions, 500 ng of total, DNase-treated RNA was used as an input to the ribo-depletion procedure. rRNA-depleted RNA was precipitated in ethanol for 3 h at -20¡C. cDNA libraries for Illumina sequencing were generated by Vertis Biotechnologie AG, Freising-Weihenstephan, Germany. rRNA-free RNA samples were first sheared via ultrasound sonication (four 30-s pulses at 4¡C) to generate on average 200- to 400-nt fragments. Fragments of 20 nt were removed using the Agencourt RNAClean XP kit (Beckman Coulter Genomics) and the Illumina TruSeq adapter was ligated to the 3' ends of the remaining fragments. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase (NEB) wherein the 3' adapter served as a primer. The first-strand cDNA was purified, and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10 to 20 ng/µl using a high fidelity DNA polymerase. The TruSeq barcode sequences were part of the 5' and 3' TruSeq sequencing adapters. The cDNA library was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics) and analyzed by capillary electrophoresis (Shimadzu MultiNA microchip).For sequencing, cDNA libraries were pooled in approximately equimolar amounts. The cDNA pool was size fractionated in the size range of 200 to 600 bp using a differential cleanup with the Agencourt AMPure kit (Beckman Coulter Genomics). Aliquots of the cDNA pools were analyzed by capillary electrophoresis (Shimadzu MultiNA microchip). Sequencing was performed on a NextSeq 500 platform (Illumina) at Vertis Biotechnologie AG, Freising-Weihenstephan, Germany (single-end mode; 75 cycles).

tag: infecting strain

value: Orientia tsutsugamushi str. UT176


title: HUVEC infected with Ot UT176 2


title: AML60

description: Pan Cancer Immune panel


title: HUVEC infected with Ot UT176 1


title: S5Pab mNET-seq NM 15 min R2

data_processing:
Library strategy: mNET-seq
Adapters were trimmed with Cutadapt v1.9.1
Mapping to the hg19 genome was performed with Tophat2 v2.1.0 (mNET-seq) or with Bowtie2 v2.2.5 (ChIP-seq)
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v. 1.6
Mapped reads were de-duplicated with Picard (ChIP-seq)
For mNET-seq profiles, only the most 3' nucleotide of the second read was used with the strandedness of the first read
Bigwig files were generated with the Deeptools2 bamCoverage tool
Genome_build: hg38 (except HEK293 CDK12as Pol II, Ser2P, and Ser5P ChIP-seq which are mapped on the hg19)
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: S5Pab mNET-seq NM 15 min R2

extract_protocol:
Nascent RNAs were purified from Pol II IP products of solublilized chromatin. DNA were purified from chromatin IP products.
Libraries were prepared according to the protocols of NEBNext small RNA library preparation kit (NEB) for mNET-seq. For ChIP-seq, libraries were prepared using Illumina's TruSeq ChIP library Preparation Kit according to Illumina's instructions.

treatment_protocol: Cells were treated with 1-NM-PP1 for 15 or 30 minutes.

value: NM 15 min

value: ab5131:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S5) antibody - ChIP Grade. Abcam


title: HUVEC infected with Ot Karp 2

value: Orientia tsutsugamushi str. Karp


title: S5Pab mNET-seq DMSO 15 min R1

source_name: S5Pab mNET-seq DMSO 15 min R1

value: DMSO 15 min


title: S5Pab mNET-seq NM 15 min R1

source_name: S5Pab mNET-seq NM 15 min R1


title: AML59

description: Pan Cancer Immune panel

value: Complete remission

value: Bone Marrow


title: HUVEC control 3


title: S5Pab mNET-seq DMSO 15 min R2

source_name: S5Pab mNET-seq DMSO 15 min R2


title: HUVEC infected with Ot Karp 3


title: HUVEC infected with Ot Karp 1


title: S2Pab mNET-seq NM 15 min R1

source_name: S2Pab mNET-seq NM 15 min R1

value: ab5095:Anti-RNA polymerase II CTD repeat YSPTSPS (phospho S2) antibody - ChIP Grade. Abcam


title: S2Pab mNET-seq NM 15 min R2

source_name: S2Pab mNET-seq NM 15 min R2


title: AML58

description: Pan Cancer Immune panel

value: Relapse


title: AML56

description: Pan Cancer Immune panel


title: AML57

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Diagnosis


title: AML55

description: Pan Cancer Immune panel


title: AML54

description: Pan Cancer Immune panel


title: S2Pab mNET-seq DMSO 15 min R2

source_name: S2Pab mNET-seq DMSO 15 min R2


title: AML53

description: Pan Cancer Immune panel


title: RR186_P9

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_12

data_processing:
Quality Control of sequenced samples was performed by FASTQC software
After trimming for adapters using trim_galore (Babraham Bioinformatics), mapping of the reads were obtained using the STAR program against mouse musculus genome (mm10) and the quantification of genes and transcripts were done with the RSEM program using GENECODE annotation (release M15)
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Genome_build: mm10
Supplementary_files_format_and_content: RSEM expected counts

source_name: retina

extract_protocol:
Rnasy micro kit after HA IP
Universal Plus mRNA-Seq (NuGEN). Stranded mRNA library

treatment_protocol: IP tamoxifen injection at P1&P2

value: retinal pericytes

tag: strain

value: retina

tag: age

value: Postnatal day 9


title: S2Pab mNET-seq DMSO 15 min R1

source_name: S2Pab mNET-seq DMSO 15 min R1


title: S2P mNET-seq NM 15 min R2

source_name: S2P mNET-seq NM 15 min R2

value: MABI0602:Anti-Phospho RNA Polymerase II CTD (Ser2) mAb. MBL International Corporation.


title: AML52

description: Pan Cancer Immune panel


title: RR189_P9

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_11


title: AML51

description: Pan Cancer Immune panel


title: S2P mNET-seq DMSO 15 min R2

source_name: S2P mNET-seq DMSO 15 min R2


title: RR151_P9

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_10


title: RR149_P9

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_9


title: S2P mNET-seq NM 15 min R1

source_name: S2P mNET-seq NM 15 min R1


title: AML49

description: Pan Cancer Immune panel


title: S2P mNET-seq DMSO 15 min R1

source_name: S2P mNET-seq DMSO 15 min R1


title: HUVEC control 2


title: Total mNET-seq NM 15 min R2

source_name: Total mNET-seq NM 15 min R2

value: MABI0601:Anti-RNA Polymerase II CTD mAb. MBL International Corporation.


title: RR119_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_6

value: Postnatal day 3


title: HUVEC control 1


title: AML48

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia

value: Diagnosis


title: AML47

description: Pan Cancer Immune panel


title: Total mNET-seq DMSO 15 min R2

source_name: Total mNET-seq DMSO 15 min R2


title: RR144_P9

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_7


title: AML45

description: Pan Cancer Immune panel


title: RR101_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_5


title: Total mNET-seq DMSO 15 min R1

source_name: Total mNET-seq DMSO 15 min R1


title: RR97_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_4


title: AML41

description: Pan Cancer Immune panel


title: Mp_Maize5

city: Cambridge

first: Archana

last: Singh

state: England

address: Downing Street

department: Plant Science

institute: Cambridge University

data_processing:
Raw fastq files were converted to fasta format.
Adapter sequences and reads less than 20 nt were trimmed using Trim Galore
Trimmed reads were aligned to the human genome (v.38) using HISAT2
Count matrix for genes was created using Kallisto
Differential expression analysis was done using the DESeq2 package available in R
Genome_build: Myzus persicae

organism: Myzus persicae

source_name: Aphid fed on Zea mays

growth_protocol: M.persicae were reared in a SANYO versatile chamber with 14 he day/10 hr night

extract_protocol:
Total RNA was extracted  using RNeasy Mini Kit (250) from QIAGEN
Strand-specific libraries constructed using the Illumina TruSeq RNA Library Preparation kit following manufacturer’s instructions

treatment_protocol: M. persicae on different plant species were kept separately in quarter cages. M. persicae population on B. rapa were originated from a single asexually female.

tag: line

value: Fed on Zea mays

value: No treatment

value: whole body


title: AML39

description: Pan Cancer Immune panel

tag: subject status


title: RR81_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_3


title: Total mNET-seq NM 15 min R1

source_name: Total mNET-seq NM 15 min R1

value: NM 15 min


title: AML36

description: Pan Cancer Immune panel

tag: age (years)


title: RR75_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_2


title: RR145_P9

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_8


title: Mp_Maize3


title: AML35

description: Pan Cancer Immune panel

tag: disease stage at sampling


title: RR69_P3

description:
Polysome mRNA
RNA extracted after ribosomal IP
AC-20_1

tag: tissue


title: Mp_Maize2


title: D4: γδT cells from WT Mice fed MCD diet

first: Varshini

last: Vasudevaraja

address: 550 1st Avenue

department: Pathology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were aligned to the mouse genome (build mm10/GRCm38, respectively) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Heatmaps and other statistics was performed using R3.2
Genome_build: mm10
Supplementary_files_format_and_content: csv files include raw read counts table for genomic features and Transcript FPKM counts.

source_name: γδT cells

growth_protocol: WT and TCRγδ-/- mice were housed in animal facility

extract_protocol:
Cells of interest were FACS sorted directly into lysis buffer and RNA was harvest using Qiagen RNeasy Micro Kit protocol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 7 week old WT and TCRγδ-/- mice were fed either a Ctl or MCD diet for 6 weeks

value: <gamma><delta>T cells

value: wild type C57BL/6

tag: diet

value: MCD


title: AML34

description: Pan Cancer Immune panel

value: Bone Marrow


title: Mp_Maize1


title: AML30

description: Pan Cancer Immune panel


title: D3: CD4+ T-cells from WT Mice fed MCD diet

source_name: CD4+ T-cells

value: CD4+ T-cells


title: D2-D1_GDT: γδT cells from WT Mice fed MCD diet


title: Mp_Pota5

source_name: Aphid fed on Solanum tuberosum

value: Fed on Solanum tuberosum


title: AML28

description: Pan Cancer Immune panel


title: D1: CD4+ T-cells from WT Mice fed MCD diet


title: C2: CD4+ T-cells from  γδTCR-/- Mice fed MCD diet

value: gammadeltaTCR-/-


title: Mp_Pota3


title: AML27

description: Pan Cancer Immune panel


title: Mp_Pota2


title: AML26

description: Pan Cancer Immune panel


title: Mp_Maize4


title: AML25

description: Pan Cancer Immune panel


title: Mp_Pota1


title: C1: CD4+ T-cells from  γδTCR-/- Mice fed MCD diet


title: AML23

description: Pan Cancer Immune panel


title: AML24

description: Pan Cancer Immune panel


title: Mp_Bean5

source_name: Aphid fed on Phaseolus vulgaris

value: Fed on Phaseolus vulgaris


title: B7: γδT cells from WT Mice fed Ctl diet

value: control


title: B6: γδT cells from WT Mice fed Ctl diet


title: Mp_Bean4


title: B3: CD4+ T-cells from WT Mice fed Ctl diet


title: AML21

description: Pan Cancer Immune panel

source_name: AML_bone marrow_Diagnosis


title: Mp_Bean3


title: Mp_Bean2


title: Mp_Pota4


title: AML20

description: Pan Cancer Immune panel


title: A2: CD4+ T-cells from γδTCR-/- Mice fed Ctl diet


title: A1: CD4+ T-cells from γδTCR-/- Mice fed Ctl diet


title: AML18

description: Pan Cancer Immune panel


title: Mp_Pea5

source_name: Aphid fed on Pisum sativum

value: Fed on Pisum sativum


title: Mp_Bean1


title: AML17

description: Pan Cancer Immune panel


title: AML19

description: Pan Cancer Immune panel


title: Mp_Pea4


title: Mp_Pea3


title: AML15

description: Pan Cancer Immune panel


title: AML14

description: Pan Cancer Immune panel


title: Mp_Pea1


title: AML16

description: Pan Cancer Immune panel


title: B2: CD4+ T-cells from WT Mice fed Ctl diet


title: AML12

description: Pan Cancer Immune panel


title: AML11

description: Pan Cancer Immune panel


title: AML13

description: Pan Cancer Immune panel


title: Mp_Nb4

source_name: Aphid fed on Nicotiana benthamiana

value: Fed on Nicotiana benthamiana


title: Mp_Nb3


title: AML10

description: Pan Cancer Immune panel

value: patient with acute myeloid leukaemia


title: Mp_Pea2


title: Mp_Nb1


title: Mp_Nb2


title: AML9

description: Pan Cancer Immune panel

value: Diagnosis


title: AML8

description: Pan Cancer Immune panel


title: AML7

description: Pan Cancer Immune panel


title: Mp_Nb5


title: Mp_Sun5

source_name: Aphid fed on Helianthus annuus

value: Fed on Helianthus annuus


title: Mp_Sun4

value: No treatment


title: R6/2_Striatum_rep2

city: Kyotanabe-shi

first: Haruko

last: Miyazaki

state: Kyoto

address: 1-3 Tatara Miyakodani

department: Graduate School of Brain Science

country: Japan

institute: Doshisha University

description:
10-R62-6
Gene expression of striatum in 4-week-old R6/2 mouse.

hyb_protocol: Hybridization was performed by DNA Chip Research Inc. (Yokohama, Japan) using Agilent standard protocol.

scan_protocol: The scanned images were analyzed by DNA Chip Research Inc. (Yokohama, Japan) using Agilent standard protocol.

data_processing: Microarray quality control was performed by GeneSpring13 (Agilent Technologies). The 75th percentile normalization was applied to assure comparability across samples.

source_name: R6/2, Striatum

label_protocol: cDNA labeling was performed by DNA Chip Research Inc. (Yokohama, Japan) using Agilent standard protocol.

extract_protocol: Total RNAs from striatal samples of 4-week-old male WT and R6/2 mice were isolated by Trizol® reagent (Invitrogen) and then purified using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.

tag: gender

value: Male

value: 4 weeks

value: Striatum


title: R6/2_Striatum_rep3

description:
12-R62-8
Gene expression of striatum in 4-week-old R6/2 mouse.


title: AML5

description: Pan Cancer Immune panel


title: R6/2_Striatum_rep1

description:
9-R62-5
Gene expression of striatum in 4-week-old R6/2 mouse.


title: WT_Striatum_rep3

description:
4-WT-8
Gene expression of striatum in 4-week-old control mouse.

source_name: WT, Striatum

value: WT


title: WT_Striatum_rep1

description:
1-WT-5
Gene expression of striatum in 4-week-old control mouse.


title: R6/2_Striatum_rep4

description:
14-R62-10
Gene expression of striatum in 4-week-old R6/2 mouse.


title: Mp_Sun2

value: whole body


title: R6/2;Scn4b-Venus_MSN_rep4

description:
20-191R62-4
Gene expression of MSNs in 4-week-old R6/2 mouse.

source_name: R6/2;Scn4b-Venus, MSN

extract_protocol: Approximately 4-20 ng total RNAs were extracted from Venus (+)/PI (-) MSNs of R6/2;Scn4b-Venus and its control using RNeasy Micro Kit (Qiagen) according to manufacturer’s instructions.

tag: cell type

value: Purified medium spiny neurons (MSNs)


title: WT_Striatum_rep4

description:
7-WT-11
Gene expression of striatum in 4-week-old control mouse.


title: R6/2;Scn4b-Venus_MSN_rep2

description:
10-191R62-6
Gene expression of MSNs in 4-week-old R6/2 mouse.


title: AML4

description: Pan Cancer Immune panel

value: Bone Marrow


title: WT_Striatum_rep2

description:
2-WT-6
Gene expression of striatum in 4-week-old control mouse.


title: Mp_Sun1

tag: treatment


title: Mp_Ch5

source_name: Aphid fed on Chrysanthemum indicum

value: Fed on Chrysanthemum indicum


title: 165-SS

city: Gödöllő

first: Éva

last: Várallyay

address: 4 Szent-Györgyi Albert Street

department: Agricultural Biotechnology Institute

country: Hungary

institute: National Agricultural Research and Innovation Centre

data_processing:
The quality check of the sequenced small RNA libraries and trimming was done by FastQC program embedded in CLC Genomic workbench
Abundancy of the small RNA reads were analysed by Small RNA analysis tool of CLC Genomic workbench
Genome_build: it is small RNA library and investigated for the presence of viruses. Consensus sequences of these virus genomes were prepared using CLC genomic Workbench.
Supplementary_files_format_and_content: tab limited text file containing sequenced small RNA reads together with their size and count

organism: Erigeron annuus

source_name: leaf

extract_protocol:
phenol-chloroform extraction method
modified Illumina Trueseq small RNA kit protocol: https://doi.org/10.1007/978-1-4939-7683-6_9

value: leaf


title: 164-TS


title: AML3

description: Pan Cancer Immune panel

extract_protocol: RNA extraction was carried out using Qiagen RNeasy RNA isolation kits. Quantitation of RNA was performed using Nanodrop and Qubit RNA high sensitivity assay.


title: Mp_Ch4


title: R6/2;Scn4b-Venus_MSN_rep3

description:
19-191R62-2
Gene expression of MSNs in 4-week-old R6/2 mouse.

tag: genotype/variation


title: 116_SC

organism:
Medicago sativa
Solanum tuberosum
Zea mays


title: AML6

description: Pan Cancer Immune panel


title: AML2

description: Pan Cancer Immune panel


title: 115_TC


title: AML46

description: Pan Cancer Immune panel


title: mAb monocyte 3

first: Guangan

last: Hu

state: MA

address: 500 Main Street

department: Koch Institute

institute: MIT

data_processing:
Illumina software used for basecalling.
Sequences were aligned to the human genome using bowtie2
Raw counts of each gene for each sample were calculated by Rsem program
Raw counts of each sample normaized with TMM in calcNormFactors() of edgeR, values log2-transformed
Differentially expressed genes between paired samples before and after treatment were performed using the program edgeR
Genome_build: hg19
Supplementary_files_format_and_content: txt files include count values for each sample

growth_protocol: human PBMC monocytes were treated with isotype or anti-LILRB3 antibody for 18hrs

extract_protocol:
Qiagen RNeasy Micro Kit
SMARTer Universal Low Input RNA Kit

tag: patient

value: donor 3

value: mAb


title: isotype monocyte 4

value: donor 4

value: isotype


title: mAb monocyte 4


title: Mp_Ch1


title: isotype monocyte 3


title: WT;Scn4b-Venus_MSN_rep4

description:
17-191-11
Gene expression of MSNs in 4-week-old control mouse.

source_name: WT;Scn4b-Venus, MSN


title: WT;Scn4b-Venus_MSN_rep3

description:
16-191-10
Gene expression of MSNs in 4-week-old control mouse.


title: WT;Scn4b-Venus_MSN_rep1

description:
2-191-2
Gene expression of MSNs in 4-week-old control mouse.


title: R6/2;Scn4b-Venus_MSN_rep1

description:
8-191R62-3
Gene expression of MSNs in 4-week-old R6/2 mouse.


title: WT;Scn4b-Venus_MSN_rep2

description:
14-191-8
Gene expression of MSNs in 4-week-old control mouse.


title: Mp_Carb5

source_name: Aphid fed on Brassica rapa

value: Fed on Brassica rapa


title: Adult planarians (pooled), sublibrary 2

city: Oxford

first: Nathan

middle: J

last: Kenny

address: Headington

institute: Oxford Brookes

description:
Dugesia japonica pooled with Schmidtea mediterranea as part of pipeline, and sequenced together before being bioinformatically separated
Dugesia japonica whole adult sample, sublibrary 2
Schmidtea mediterranea whole adult sample, sublibrary 2
Dugesia_japonica_reannotation.gtf.gz
Schmidtea_mediterranea_reannotation.gtf.gz

data_processing:
Base calling performed by provider (Novogene), Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor, chimeric and low-quality sequence using CutAdapt v2.8 and read quality confirmed with FastQC. Read pairs were matched using Makepairs.
Novel gene annotations were generated using HiSat 2.1.0. StringTie and StringTie-merge. Drop-seq_tools-2.3.0 was used to create reference files from these annotations.
SPLiTseq toolbox (incorporating Drop-seq_tools-2.3.0 and STAR-2.7.3a) was used to generate matrix count files for each species.
Column headers are the cell barcodes.
The barcode is split across 3 positions in read 2 (3x8bp), and the UMI (1x10bp) at a further location as follows:
Position 1-10 UMI
Position 11-18 PCR_rd2_BC
Position 49 -56 PCR_RD1_BC
Position 87-94 RT_BC
Dugesia japonica geneIDs can be found here: http://www.planarian.jp/seq/gff5.zip (host website: http://www.planarian.jp/download.html)
Schmidtea mediterranea geneIDs can be found here: http://planmine.mpi-cbg.de/planmine/model/bulkdata/smes_v2_hconf_SMESG.gff3.zip (host website: http://planmine.mpi-cbg.de/planmine/aspect.do?name=Gene%20Predictions)
Genome_build: Schmidtea mediterranea S2F2 genome (Grohme et al PMID: 29364871) Dugesia japonica v1.0 (An et al 2018 PMID: 30181897)
Supplementary_files_format_and_content: GTF files for each species, with re-annotated gene structures and co-ordinates. 3 matrix files for each species, one for each of the 3 sublibraries sequenced.

organism:
Dugesia japonica
Schmidtea mediterranea

source_name: Whole adult tissue

extract_protocol:
ACME protocol (described in this paper)
SPLiTseq (Rosenberg et al 2018, PMID: 29545511)

value: whole adult

tag: genotype

value: wild type

tag: strain (dugesia japonica)

value: laboratory clonal asexual strain

tag: strain (schmidtea mediterranea)

value: asexual strain, Berlin-1 (described in Solana, Irimia et al eLife 2016).


title: Adult planarians (pooled), sublibrary 3

description:
Dugesia japonica pooled with Schmidtea mediterranea as part of pipeline, and sequenced together before being bioinformatically separated
Dugesia japonica whole adult sample, sublibrary 3
Schmidtea mediterranea whole adult sample, sublibrary 3
Dugesia_japonica_reannotation.gtf.gz
Schmidtea_mediterranea_reannotation.gtf.gz


title: mAb monocyte 2

value: donor 2


title: Adult planarians (pooled), sublibrary 1

description:
Dugesia japonica pooled with Schmidtea mediterranea as part of pipeline, and sequenced together before being bioinformatically separated
Dugesia japonica whole adult sample, sublibrary 1
Schmidtea mediterranea whole adult sample, sublibrary 1
Dugesia_japonica_reannotation.gtf.gz
Schmidtea_mediterranea_reannotation.gtf.gz


title: Mp_Ch3

value: No treatment


title: Mp_Carb3


title: Mp_Carb2


title: mAb monocyte 1

value: donor 1


title: isotype monocyte 1


title: Mp_Ara5

source_name: Aphid fed on Arabidopsis.thaliana

value: Fed on Arabidopsis.thaliana

value: whole body


title: Mp_Ara4


title: Mp_Carb1


title: isotype monocyte 2


title: Mp_Ch2


title: Mp_Carb4


title: Mp_Ara3


title: Mp_Ara2


title: Mp_Ara1


title: Relapse 8

city: New york

first: Jihye

last: Paik

address: 1300 York Ave.

institute: Weill Cornell Medical College

description: whole exome sequencing

data_processing:
Library strategy: DNA-seq
Raw reads were mapped to mouse genome mm10 (GRCm38) using SpeedSeq version 0.1.0 with default parameters.
The variants were detected using SpeedSeq version 0.1.0 and VarScan version 2.3.9.
Genome_build: Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: vcf

source_name: iEIP relapse tumor line

growth_protocol: Tumor cells were temporarily cultured in neural stem cell media

extract_protocol:
Qiagen DNeasy kit
Processed for whole exome sequencing (WES) analysis using Agilent SureSelect XT Mouse All Exon Kit (cat# 1000001746) following manufacturer’s protocols.

tag: disease state

value: glioma

value: iEIP

value: brain

tag: treatment status

value: relapse glioma


title: ΔhbtRC+pVSV105::lacI-hbtRC_3

city: Honolulu

first: Brittany

middle: Dawn

last: Bennett

state: HI

address: 41 Ahui St.

department: Pacific Biosciences Research Center

institute: University of Hawaii

description: Ribosome-depleted RNA

data_processing:
Reads were trimmed and filtered with Trimmomatic to remove adaptor sequences and discard reads not matching the V. fischeri genome (maximum mismatch:1, LEADING:3, TRAILING:3, SLIDINGWINDOW:4,20, MINLEN:35).
Reads were mapped to the V. fischeri genome with Bowtie2 (-un-con,  --sensitive).
Reads were counted with featureCounts (-p disabled,  -t=gene,  -g=locus_tag,  -Q=10,  -s).
Differential expression was analyzed with DESeq2 (outliers filtering and independent filtering turned on).
Genome_build: NC_006840.2, NC_006841.2, NC_006842.2
Supplementary_files_format_and_content: Tab-delimited text files containing normalized read counts for each gene.

organism: Aliivibrio fischeri

source_name: Bacterial culture

growth_protocol: Bacteria were grown in liquid seawater-tryptone medium with 1.75 mM IPTG to mid-log phase

extract_protocol:
Cells were lysed with RNAprotect Bacterial Reagent (Qiagen). RNA was extracted with RNeasy Mini Kit (Qiagen). DNA was degraded with TURBO Dnase (Invitrogen).
Ribosomal reduction (RiboZero) and strand-specific library preparation (TruSeq) were performed at the University of Minnesota Genomics Center per standard Illumina protocols. Paired-end 50-bp sequence analysis was performed on an Illumina HiSeq 2500 on high-output mode.

tag: strain

value: hbtRC+


title: ΔhbtRC+pVSV105::lacI-hbtRC_2

description: Ribosome-depleted RNA


title: Microglia, WT3

city: Nanjing

first: Chunmei

last: Ma

address: 101 Longmian road,Nanjing

country: China

institute: Nanjing medical university

description: Expression data from microglia

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Clariom D human Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Microglia isolated from brains and spinal cords of WT and AIM2/- mice by FACS sorting.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: WT and AIM2-/- mice were treated with MOG and M.tuberculosis to induce EAE mice model

value: WT

value: EAE mice model


title: ΔhbtRC+pVSV105::lacI-hbtRC_1

description: Ribosome-depleted RNA


title: ΔhbtRC+pVSV105_3

description: Ribosome-depleted RNA

value: deltahbtRC


title: Microglia, WT2

description: Expression data from microglia


title: 147

description: whole exome sequencing


title: 165-SA

organism: Solidago canadensis

value: leaf


title: Microglia, KO3

description: Expression data from microglia


title: ΔhbtRC+pVSV105_2

description: Ribosome-depleted RNA


title: 163-TB

organism: Erigeron canadensis


title: Microglia, WT1

description: Expression data from microglia


title: ΔhbtRC+pVSV105_1

description: Ribosome-depleted RNA


title: Kp33

city: Pretoria

first: John

last: Osei Sekyere

state: Gauteng

address: 05 Bopheloweg Off Dr. Savage Road

department: Department of Medical Microbiology

country: South Africa

institute: University of Pretoria

data_processing:
Library strategy: DNA-seq
Automatic minimum seed read length calculation HGAP 2.0
Allow partial alignments
Trimming FASTQ output using HGAP 2.0
Determining genome size using SMRT Analysis v2.0
Supplementary_files_format_and_content: gff files were generated

organism: Klebsiella pneumoniae

source_name: Urine

growth_protocol: 37°C overnignt

extract_protocol:
Genomic DNA was extracted from cells grown overnight in Brain heart infusion broth using the bacterial/fungal ZymoResearch extraction kit.
Libraries were prepared according to the PacBio Technical note (Library Prep)

tag: host

value: Homo sapiens

tag: sequence type

tag: capsule type


title: donor5.chip_input_IL1b.F

status: Public on Jun 02 2020

city: Tucson

first: Lindsey

middle: Kathleen

last: Stolze

state: AZ

address: 1333 N Martin Ave

institute: The University of Arizona

data_processing:
demultiplexed ATAC-seq and ChIP-seq fastq data were aligned to hg19 using Bowtie2.
Aligned sam files were made into tagDirectories in HOMER. Reads mapping to mitochondiral DNA were discarded for ATAC seq.
ChIP-seq peaks were identified using the findPeaks function.
Genome_build: hg19

source_name: human aortic endothelial cell_IL-1B treated_input

growth_protocol: HAEC were isolated from heart transplant donor specimens, and grown in culture to 90% confluence on 6-well, 10 cm, or 15 cm plates before treatment and harvesting for ChIP-seq, RNA-seq, or ATAC-seq.

extract_protocol:
For ChIP-seq, Cells were fixed with formaldehyde, lysates were sonicated, and complexes precipitated with antibody. For RNA-seq, RNA was extracted using the the Quick-RNA Micro Prep kit from ZymoResearch and poly-A selected. For ATAC-seq, nuclei were extracted with nuclear isolation buffer and DNA was size-selected for 125-175 bp fragments on a TBE gel
For RNA-seq, cDNA was synthesized using the SuperScript III system from Invitrogen, followed by second strand synthesis, ds End Repair and UDG treatment to recover strand-specific libraries. Libraries were barcoded with BioO Nextflex adapters and amplified prior to sequencing. ChIP-seq libraries were synthesized similarly omiting the UDG treatment. ATAC-seq libraries were extracted from TBE gel, amplified, and sequenced.

treatment_protocol: Cells were treated with M-199 containing 1% FBS (control), or additionally containing either 40 µg/mL Ox-PAPC, or 10 ng/mL human recombinant IL-1B

tag: donor id

value: human aortic endothelial cell

tag: passage

value: IL-1B treated

tag: chip antibody

value: none; input


title: donor6.chip_input_IL1b.F


title: donor8.chip_input_IL1b.F


title: donor9.chip_input_IL1b.F


title: donor51.chip_input_IL1b.F


title: donor47.chip_input_IL1b.F


title: donor50.chip_input_IL1b.D


title: 175

description: whole exome sequencing

tag: tissue


title: donor4.chip_input_IL1b.F

tag: cell type


title: Microglia, KO1

description: Expression data from microglia


title: donor44.chip_input_IL1b.F

tag: treatment


title: 2QX

description: whole exome sequencing

source_name: iEIP primary tumor line

value: primary glioma


title: Microglia, KO2

description: Expression data from microglia


title: donor43.chip_input_IL1b.F


title: QX

description: whole exome sequencing


title: donor39.chip_input_IL1b.D


title: donor3.chip_input_IL1b.F


title: donor42.chip_input_IL1b.F


title: donor41.chip_input_IL1b.F


title: donor49.chip_input_IL1b.D


title: donor38.chip_input_IL1b.F


title: donor37.chip_input_IL1b.F


title: donor36.chip_input_IL1b.F


title: donor35.chip_input_IL1b.F


title: donor33.chip_input_IL1b.F


title: donor45.chip_input_IL1b.D


title: donor43.chip_input_IL1b.D


title: donor31.chip_input_IL1b.F


title: donor32.chip_input_IL1b.D


title: donor28.chip_input_IL1b.F


title: donor25.chip_input_IL1b.F


title: donor26.chip_input_IL1b.F


title: donor27.chip_input_IL1b.D


title: donor27.chip_input_IL1b.F


title: donor2.chip_input_IL1b.F


title: donor24.chip_input_IL1b.F


title: donor42.chip_input_IL1b.D


title: donor40.chip_input_IL1b.D


title: donor22.chip_input_IL1b.F


title: donor22.chip_input_IL1b.D


title: donor21.chip_input_IL1b.F


title: donor1.chip_input_IL1b.F


title: donor19.chip_input_IL1b.F


title: donor18.chip_input_NT.F

source_name: human aortic endothelial cell_Untreated_input

value: Untreated


title: donor23.chip_input_IL1b.F


title: donor16.chip_input_IL1b.F


title: donor14.chip_input_IL1b.F


title: donor33.chip_input_IL1b.D


title: donor17.chip_input_IL1b.F


title: donor30.chip_input_NT.F


title: donor15.chip_input_IL1b.D


title: donor13.chip_input_IL1b.F


title: donor12.chip_input_IL1b.F


title: donor12.rna_notx.rep1

description: processed data file: RNA_expression_table_RPKM.txt.gz

data_processing:
demultiplexed ATAC-seq and ChIP-seq fastq data were aligned to hg19 using Bowtie2.
RNA-seq data was aligned to hg19 using STAR
Aligned sam files were made into tagDirectories in HOMER. Reads mapping to mitochondiral DNA were discarded for ATAC seq.
ATAC and ChIP-seq peaks were identified using the findPeaks function.
Normalized expression matrix for RNA-seq was made using HOMER command analyzeRepeats.pl with options -rpkm -count exons -strand plus -condenseGenes
Genome_build: hg19
Supplementary_files_format_and_content: peak files are in the original HOMER output format (http://homer.salk.edu/homer/), and gene expression from RNA-seq experiments is normalized using RPKM within the analyzeRepeats program in HOMER.

source_name: human aortic endothelial cell_untreated_RNA-seq

value: donor 12

value: untreated


title: donor10.chip_input_IL1b.F


title: donor12.rna_notx.rep2

value: donor 13


title: donor11.chip_input_IL1b.F


title: donor51.p65_il1b.rep1

source_name: human aortic endothelial cell_IL-1B treated_p65

value: Santa Cruz Antibodies sc-372x, Lot #E0916


title: donor53.p65_il1b.rep1


title: donor49.p65_il1b.rep1


title: donor47.p65_il1b.rep1


title: donor44.p65_il1b.rep1


title: donor41.p65_il1b.rep1


title: donor18.chip_input_IL1b.D


title: donor45.p65_il1b.rep1


title: donor36.p65_il1b.rep1


title: donor39.p65_il1b.rep1


title: donor40.p65_il1b.rep1


title: donor15.chip_input_IL1b.F


title: donor38.p65_il1b.rep1


title: donor35.p65_il1b.rep1


title: donor33.p65_il1b.rep1


title: donor28.p65_il1b.rep1


title: donor27.p65_il1b.rep2

description:
processed data file:
donor27.p65_il1b.peaks.txt.gz


title: donor31.p65_il1b.rep1


title: donor27.p65_il1b.rep1


title: donor25.p65_il1b.rep1


title: donor26.p65_il1b.rep1


title: donor22.p65_il1b.rep1


title: donor52.p65_il1b.rep1


title: donor21.p65_il1b.rep1


title: donor16.p65_il1b.rep1


title: donor17.p65_il1b.rep1


title: donor14.p65_il1b.rep1


title: donor11.p65_il1b.rep1


title: donor13.p65_il1b.rep1


title: donor10.p65_il1b.rep1


title: donor8.p65_il1b.rep1


title: donor9.p65_il1b.rep1


title: donor7.p65_il1b.rep1


title: donor6.p65_il1b.rep1


title: donor3.p65_il1b.rep1


title: donor47.erg_notx.rep1

source_name: human aortic endothelial cell_untreated_ERG

value: abcam #ab110639


title: donor2.p65_il1b.rep1


title: donor53.erg_notx.rep1


title: donor46.erg_notx.rep1


title: donor51.erg_notx.rep1


title: donor49.erg_notx.rep1


title: donor5.p65_il1b.rep1


title: donor28.erg_notx.rep2


title: donor38.erg_notx.rep1


title: donor33.erg_notx.rep1


title: donor39.erg_notx.rep1


title: donor44.erg_notx.rep1


title: donor24.p65_il1b.rep1


title: donor40.erg_notx.rep1


title: donor28.erg_notx.rep1


title: donor24.erg_notx.rep1


title: donor17.erg_notx.rep1


title: donor21.erg_notx.rep1


title: donor19.erg_notx.rep1


title: donor14.erg_notx.rep1


title: donor16.erg_notx.rep1


title: donor13.erg_notx.rep2

description:
processed data file:
donor13.erg_notx.peaks.txt.gz


title: donor26.erg_notx.rep1


title: donor4.p65_il1b.rep1


title: donor13.erg_notx.rep3


title: donor5.erg_notx.rep1


title: donor4.erg_notx.rep1


title: Mp_Sun3

source_name: Aphid fed on Helianthus annuus

tag: line

value: Fed on Helianthus annuus

value: No treatment

value: whole body


title: donor1.erg_notx.rep1


title: donor53.h3k27ac_il1b.rep1

source_name: human aortic endothelial cell_IL-1B treated_h327ac

value: Active Motif #39135


title: donor44.h3k27ac_il1b.rep1


title: donor51.h3k27ac_il1b.rep1


title: donor49.h3k27ac_il1b.rep1


title: donor52.h3k27ac_il1b.rep1


title: donor13.erg_notx.rep1


title: donor47.h3k27ac_il1b.rep1


title: donor41.h3k27ac_il1b.rep1


title: donor43.h3k27ac_il1b.rep1


title: donor40.h3k27ac_il1b.rep1


title: donor39.h3k27ac_il1b.rep1


title: donor36.h3k27ac_il1b.rep1


title: donor38.h3k27ac_il1b.rep1


title: donor37.h3k27ac_il1b.rep1


title: donor35.h3k27ac_il1b.rep1


title: donor45.h3k27ac_il1b.rep1


title: donor33.h3k27ac_il1b.rep1


title: donor32.h3k27ac_il1b.rep1


title: donor31.h3k27ac_il1b.rep1


title: donor30.h3k27ac_il1b.rep1


title: donor25.h3k27ac_il1b.rep2

description:
processed data file:
donor25.h3k27ac_il1b.peaks.txt.gz


title: donor26.h3k27ac_il1b.rep1


title: donor25.h3k27ac_il1b.rep1


title: donor29.h3k27ac_il1b.rep1


title: donor23.h3k27ac_il1b.rep1


title: donor24.h3k27ac_il1b.rep1


title: donor21.h3k27ac_il1b.rep1


title: donor22.h3k27ac_il1b.rep1


title: donor19.h3k27ac_il1b.rep1


title: donor17.h3k27ac_il1b.rep1


title: donor16.h3k27ac_il1b.rep1


title: donor15.h3k27ac_il1b.rep1


title: donor14.h3k27ac_il1b.rep1


title: donor13.h3k27ac_il1b.rep1


title: donor10.h3k27ac_il1b.rep1


title: donor9.h3k27ac_il1b.rep1


title: donor5.h3k27ac_il1b.rep1


title: donor4.h3k27ac_il1b.rep1


title: donor7.h3k27ac_il1b.rep1


title: donor2.h3k27ac_il1b.rep2

description:
processed data file:
donor2.h3k27ac_il1b.peaks.txt.gz


title: donor1.h3k27ac_il1b.rep1


title: donor2.h3k27ac_il1b.rep1


title: donor53.h3k27ac_notx.rep1

source_name: human aortic endothelial cell_untreated_h327ac


title: donor12.h3k27ac_il1b.rep1


title: donor49.h3k27ac_notx.rep1


title: donor52.h3k27ac_notx.rep1


title: donor47.h3k27ac_notx.rep1


title: donor44.h3k27ac_notx.rep1


title: donor43.h3k27ac_notx.rep1


title: donor41.h3k27ac_notx.rep1


title: donor18.h3k27ac_il1b.rep1


title: donor41.h3k27ac_notx.rep2

description:
processed data file:
donor41.h3k27ac_notx.peaks.txt.gz


title: donor43.h3k27ac_notx.rep2

description:
processed data file:
donor43.h3k27ac_notx.peaks.txt.gz


title: donor46.h3k27ac_notx.rep1


title: donor40.h3k27ac_notx.rep1


title: donor39.h3k27ac_notx.rep1


title: donor36.h3k27ac_notx.rep1


title: donor3.h3k27ac_il1b.rep1


title: donor38.h3k27ac_notx.rep1


title: donor31.h3k27ac_notx.rep2


title: donor33.h3k27ac_notx.rep1


title: donor32.h3k27ac_notx.rep1

description:
processed data file:
donor31.h3k27ac_notx.peaks.txt.gz


title: donor31.h3k27ac_notx.rep1


title: donor30.h3k27ac_notx.rep1


title: donor37.h3k27ac_notx.rep1


title: donor24.h3k27ac_notx.rep2

description:
processed data file:
donor24.h3k27ac_notx.peaks.txt.gz


title: donor51.h3k27ac_notx.rep1


title: donor28.h3k27ac_notx.rep1


title: donor24.h3k27ac_notx.rep1


title: donor25.h3k27ac_notx.rep1


title: donor29.h3k27ac_notx.rep1


title: donor25.h3k27ac_notx.rep2

description:
processed data file:
donor25.h3k27ac_notx.peaks.txt.gz


title: donor26.h3k27ac_notx.rep1


title: donor27.h3k27ac_notx.rep1


title: donor23.h3k27ac_notx.rep1


title: donor22.h3k27ac_notx.rep2

description:
processed data file:
donor22.h3k27ac_notx.peaks.txt.gz


title: donor19.h3k27ac_notx.rep1


title: donor18.h3k27ac_notx.rep1


title: donor14.h3k27ac_notx.rep1


title: donor16.h3k27ac_notx.rep1


title: donor13.h3k27ac_notx.rep1


title: donor17.h3k27ac_notx.rep1


title: donor21.h3k27ac_notx.rep1


title: donor11.h3k27ac_notx.rep1


title: donor10.h3k27ac_notx.rep1


title: donor9.h3k27ac_notx.rep1


title: donor7.h3k27ac_notx.rep1


title: donor5.h3k27ac_notx.rep1


title: donor4.h3k27ac_notx.rep1


title: donor2.h3k27ac_notx.rep1


title: donor3.h3k27ac_notx.rep1


title: donor1.h3k27ac_notx.rep1


title: donor53.atac_il1b.rep1

source_name: human aortic endothelial cell_untreated_ATAC-seq


title: donor22.h3k27ac_notx.rep1


title: donor46.atac_il1b.rep1


title: donor47.atac_il1b.rep1


title: donor50.atac_il1b.rep1


title: donor48.atac_il1b.rep1


title: donor45.atac_il1b.rep1


title: donor36.atac_il1b.rep1


title: donor39.atac_il1b.rep1


title: donor49.atac_il1b.rep1


title: donor42.atac_il1b.rep1


title: donor35.atac_il1b.rep1


title: donor41.atac_il1b.rep1


title: donor32.atac_il1b.rep1


title: donor28.atac_il1b.rep1


title: donor31.atac_il1b.rep1


title: donor29.atac_il1b.rep1


title: donor30.atac_il1b.rep1


title: donor33.atac_il1b.rep1


title: donor25.atac_il1b.rep1


title: donor24.atac_il1b.rep1


title: donor23.atac_il1b.rep1


title: donor22.atac_il1b.rep1


title: donor51.atac_il1b.rep1


title: donor18.atac_il1b.rep1


title: donor21.atac_il1b.rep1


title: donor44.atac_il1b.rep1


title: donor17.atac_il1b.rep1


title: donor16.atac_il1b.rep1


title: donor15.atac_il1b.rep1


title: donor5.atac_il1b.rep1


title: donor11.atac_il1b.rep1


title: donor4.atac_il1b.rep1


title: donor8.atac_il1b.rep1


title: donor7.atac_il1b.rep1


title: donor14.atac_il1b.rep1


title: donor3.atac_il1b.rep1


title: donor51.atac_notx.rep1


title: donor49.atac_notx.rep1


title: donor48.atac_notx.rep1


title: donor1.atac_il1b.rep1


title: donor50.atac_notx.rep1


title: donor53.atac_notx.rep1


title: donor44.atac_notx.rep1


title: donor10.atac_il1b.rep1


title: donor2.atac_il1b.rep1


title: donor42.atac_notx.rep1


title: donor19.atac_il1b.rep1


title: donor20.atac_il1b.rep1


title: donor40.atac_notx.rep1


title: donor39.atac_notx.rep1


title: donor38.atac_notx.rep1


title: donor41.atac_notx.rep1


title: donor34.atac_notx.rep1


title: donor33.atac_notx.rep1


title: donor43.atac_notx.rep1


title: donor35.atac_notx.rep1


title: donor13.atac_il1b.rep1


title: donor6.atac_il1b.rep1


title: donor32.atac_notx.rep1


title: donor31.atac_notx.rep1


title: donor23.atac_notx.rep1


title: donor20.atac_notx.rep1


title: donor24.atac_notx.rep1


title: donor26.atac_notx.rep1


title: donor27.atac_notx.rep1


title: donor30.atac_notx.rep1


title: donor18.atac_notx.rep1


title: donor17.atac_notx.rep1


title: donor16.atac_notx.rep1


title: donor25.atac_notx.rep1


title: donor19.atac_notx.rep1


title: donor14.atac_notx.rep1


title: donor13.atac_notx.rep1


title: donor15.atac_notx.rep1


title: donor11.atac_notx.rep1


title: donor12.atac_notx.rep1


title: donor10.atac_notx.rep1


title: donor7.atac_notx.rep1


title: donor6.atac_notx.rep1


title: donor4.atac_notx.rep1


title: donor5.atac_notx.rep1


title: donor8.atac_notx.rep1


title: donor1.atac_notx.rep1


title: donor3.atac_notx.rep1


title: donor2.atac_notx.rep1


title: donor53.rna_il1b.rep2

description:
processed data file:
RNA_expression_table_RPKM.txt.gz

source_name: human aortic endothelial cell_IL-1B treated_RNA-seq


title: donor53.rna_il1b.rep1


title: donor28.atac_notx.rep1


title: donor21.atac_notx.rep1


title: donor52.rna_il1b.rep2


title: donor51.rna_il1b.rep2


title: donor47.rna_il1b.rep2


title: donor50.rna_il1b.rep2


title: donor49.rna_il1b.rep1


title: donor47.rna_il1b.rep1


title: donor51.rna_il1b.rep1


title: donor50.rna_il1b.rep1


title: donor46.rna_il1b.rep2


title: donor49.rna_il1b.rep2


title: donor44.rna_il1b.rep1


title: donor45.rna_il1b.rep2


title: donor43.rna_il1b.rep2


title: donor46.rna_il1b.rep1


title: donor45.rna_il1b.rep1


title: donor42.rna_il1b.rep2


title: donor42.rna_il1b.rep1


title: donor43.rna_il1b.rep1


title: donor44.rna_il1b.rep2


title: donor41.rna_il1b.rep2


title: donor38.rna_il1b.rep1


title: donor39.rna_il1b.rep1


title: donor38.rna_il1b.rep2


title: donor40.rna_il1b.rep1


title: donor39.rna_il1b.rep2


title: donor37.rna_il1b.rep2


title: donor40.rna_il1b.rep2


title: donor52.rna_il1b.rep1


title: donor37.rna_il1b.rep1


title: donor48.rna_il1b.rep1


title: donor36.rna_il1b.rep2


title: donor35.rna_il1b.rep1


title: donor34.rna_il1b.rep2


title: donor33.rna_il1b.rep2


title: donor41.rna_il1b.rep1


title: donor31.rna_il1b.rep1


title: donor32.rna_il1b.rep1


title: donor29.rna_il1b.rep2


title: donor33.rna_il1b.rep1


title: donor28.rna_il1b.rep2


title: donor28.rna_il1b.rep1


title: donor27.rna_il1b.rep2


title: donor31.rna_il1b.rep2


title: donor26.rna_il1b.rep2


title: donor26.rna_il1b.rep1


title: donor24.rna_il1b.rep3


title: donor24.rna_il1b.rep2


title: donor27.rna_il1b.rep1


title: donor24.rna_il1b.rep1


title: donor36.rna_il1b.rep1


title: donor23.rna_il1b.rep2


title: donor23.rna_il1b.rep1


title: donor34.rna_il1b.rep1


title: donor22.rna_il1b.rep2


title: donor32.rna_il1b.rep2


title: donor35.rna_il1b.rep2


title: donor22.rna_il1b.rep1


title: donor21.rna_il1b.rep2


title: donor30.rna_il1b.rep2


title: donor30.rna_il1b.rep1


title: donor29.rna_il1b.rep1


title: donor21.rna_il1b.rep1


title: donor20.rna_il1b.rep1


title: donor19.rna_il1b.rep2


title: donor19.rna_il1b.rep1


title: donor18.rna_il1b.rep2


title: donor17.rna_il1b.rep2


title: donor18.rna_il1b.rep1


title: donor17.rna_il1b.rep1


title: donor25.rna_il1b.rep1


title: donor13.rna_il1b.rep2


title: donor12.rna_il1b.rep2


title: donor12.rna_il1b.rep1


title: donor14.rna_il1b.rep1


title: donor15.rna_il1b.rep1


title: donor16.rna_il1b.rep2


title: donor15.rna_il1b.rep2


title: donor14.rna_il1b.rep2


title: donor13.rna_il1b.rep1


title: donor11.rna_il1b.rep2


title: donor11.rna_il1b.rep1


title: donor16.rna_il1b.rep1


title: donor10.rna_il1b.rep2


title: donor20.rna_il1b.rep2


title: donor9.rna_il1b.rep2


title: donor10.rna_il1b.rep1


title: donor7.rna_il1b.rep2


title: donor9.rna_il1b.rep1


title: donor16.rna_il1b.rep3


title: donor8.rna_il1b.rep2


title: donor7.rna_il1b.rep1


title: donor8.rna_il1b.rep1


title: donor6.rna_il1b.rep1


title: donor6.rna_il1b.rep2


title: donor4.rna_il1b.rep1


title: donor16.rna_il1b.rep4


title: donor5.rna_il1b.rep2


title: donor5.rna_il1b.rep1


title: donor3.rna_il1b.rep2


title: donor3.rna_il1b.rep1


title: donor1.rna_il1b.rep2


title: donor2.rna_il1b.rep2


title: donor2.rna_il1b.rep1


title: donor1.rna_il1b.rep1


title: donor53.rna_notx.rep1


title: donor53.rna_notx.rep2


title: donor52.rna_notx.rep2


title: donor4.rna_il1b.rep2


title: donor49.rna_notx.rep1


title: donor50.rna_notx.rep1


title: donor47.rna_notx.rep2


title: donor51.rna_notx.rep1


title: donor50.rna_notx.rep2


title: donor51.rna_notx.rep2


title: donor52.rna_notx.rep1


title: donor44.rna_notx.rep2


title: donor46.rna_notx.rep1


title: donor44.rna_notx.rep1


title: donor49.rna_notx.rep2


title: donor43.rna_notx.rep2


title: donor47.rna_notx.rep1


title: donor45.rna_notx.rep1


title: donor42.rna_notx.rep1


title: donor43.rna_notx.rep1


title: donor40.rna_notx.rep2


title: donor40.rna_notx.rep1


title: donor38.rna_notx.rep1


title: donor38.rna_notx.rep2


title: donor42.rna_notx.rep2


title: donor37.rna_notx.rep2


title: donor37.rna_notx.rep1


title: donor36.rna_notx.rep2


title: donor39.rna_notx.rep1


title: donor36.rna_notx.rep1


title: donor48.rna_notx.rep2


title: donor48.rna_notx.rep1


title: donor34.rna_notx.rep1


title: donor35.rna_notx.rep1


title: donor34.rna_notx.rep2


title: donor33.rna_notx.rep1


title: donor32.rna_notx.rep2


title: donor35.rna_notx.rep2


title: donor32.rna_notx.rep1


title: donor41.rna_notx.rep1


title: donor29.rna_notx.rep2


title: donor31.rna_notx.rep1


title: donor28.rna_notx.rep2


title: donor31.rna_notx.rep2


title: donor30.rna_notx.rep2


title: donor30.rna_notx.rep1


title: donor33.rna_notx.rep2


title: donor29.rna_notx.rep1


title: donor27.rna_notx.rep1


title: donor27.rna_notx.rep2


title: donor26.rna_notx.rep2


title: donor28.rna_notx.rep1


title: donor26.rna_notx.rep1


title: donor25.rna_notx.rep2


title: donor24.rna_notx.rep2


title: donor24.rna_notx.rep1


title: donor23.rna_notx.rep1


title: donor25.rna_notx.rep1


title: donor24.rna_notx.rep3


title: donor23.rna_notx.rep2


title: donor22.rna_notx.rep2


title: donor22.rna_notx.rep1


title: donor21.rna_notx.rep2


title: donor18.rna_notx.rep2


title: donor20.rna_notx.rep1


title: donor20.rna_notx.rep2


title: donor19.rna_notx.rep2


title: donor17.rna_notx.rep2


title: donor17.rna_notx.rep1


title: donor16.rna_notx.rep2


title: donor16.rna_notx.rep4


title: donor16.rna_notx.rep3


title: donor15.rna_notx.rep1


title: donor16.rna_notx.rep1


title: donor14.rna_notx.rep2


title: donor15.rna_notx.rep2


title: donor14.rna_notx.rep1


title: donor19.rna_notx.rep1


title: donor18.rna_notx.rep1


title: donor13.rna_notx.rep2


title: donor8.rna_notx.rep2


title: donor9.rna_notx.rep2


title: donor9.rna_notx.rep1


title: donor10.rna_notx.rep1


title: donor11.rna_notx.rep2


title: donor10.rna_notx.rep2


title: donor8.rna_notx.rep1


title: donor21.rna_notx.rep1


title: donor6.rna_notx.rep2


title: donor7.rna_notx.rep1


title: donor5.rna_notx.rep1


title: donor6.rna_notx.rep1


title: donor5.rna_notx.rep2


title: donor4.rna_notx.rep2


title: donor4.rna_notx.rep1


title: donor3.rna_notx.rep2


title: donor3.rna_notx.rep1


title: donor2.rna_notx.rep2


title: donor2.rna_notx.rep1


title: donor13.rna_notx.rep1


title: siDF3_ActD_2h_2

first: Samie

last: Jaffrey

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: RNAseq

data_processing:
For Riboseq,  adapters and low-quality based reads were trimmed using flexbar v2.5: flexbar -n 20 -a AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1
The Ribo-seq reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite.
The processed reads were aligned first to the ribosomal DNA, then to the following siRNA sequences: siDF1 CATCAGGCTGGAGAATAACGACAACAA, TTTTTAGCAAACATAAGAAACCATGAGTC, CAATCAGACTGATCTAATGTGAAATGTA; siDF2 TTGCAGTTTAAGTATTGGAATTTCACAA; siDF3 AAATAGCAATACAGTAGATTTGAATACC. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner using the following parameters -outFilterMultimapNmax 8  --alignEndsType EndToEnd
Mapped reads were then analyzed for different criteria (length, mappability to coding sequence region, P site offset) to select only high quality reads that represent ribosome protected fragments.
For RNAseq, low-quality based reads and short reads were trimmed using flexbar v2.5: flexbar -n 20 -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1. Reads were then mapped to the ribosomal DNA and the siRNA sequences as described for the Riboseq samples. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are in txt files: Ribo_RNA_TE_siDF1_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1 silencing, Ribo_RNA_TE_siDF2_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF2 silencing,  Ribo_RNA_TE_siDF3_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF3 silencing, Ribo_RNA_TE_siDF123_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1, DF2 and DF3 silencing, RNA_siDF12_HeLa.txt file contains the RNAseq changes upon DF1 and DF2 silencing, RNA_siDF13_HeLa.txt file contains the RNAseq changes upon DF1 and DF3 silencing , RNA_siDF23_HeLa.txt file contains the RNAseq changes upon DF2 and DF3 silencing

source_name: HeLa

extract_protocol:
Total RNA was harvested using either Trizol (RNAseq), or using the cell lysis Ribosome profiling conditions (Riboseq input/Ribosome protected fragments)
Libraries were constructed using either NEBNext Ultra II Directional RNA library prep kit (Ribosome protected fragments inputs/RNAseq), or using the miCLIP cloning protocol (Ribosome protected fragments)

tag: sirna

value: DF3 siRNA

tag: rna processing

value: rRNA depleted RNA

value: Actinomycin D for 2 hours

tag: spike-in

value: ERCC-1 spike in


title: donor1.rna_notx.rep1

value: human aortic endothelial cell


title: donor1.rna_notx.rep2


title: donor11.rna_notx.rep1


title: siDF3_ActD_2h_1

description: RNAseq


title: siDF2_ActD_2h_2

description: RNAseq

value: DF2 siRNA


title: siDF2_ActD_2h_1

description: RNAseq


title: siDF1_ActD_2h_2

description: RNAseq

value: DF1 siRNA


title: siNC1_ActD_2h_2

description: RNAseq

value: control siRNA


title: siDF1_ActD_2h_1

description: RNAseq


title: siDF13_1

description:
RNAseq
RNA_siDF13_HeLa.txt

value: DF1 and DF3 siRNAs


title: siDF13_2

description: RNAseq


title: siDF23_1

description:
RNAseq
RNA_siDF23_HeLa.txt

value: DF2 and DF3 siRNAs


title: siNC1_ActD_2h_1

description: RNAseq


title: riboseq_siDF1_1

description:
Ribosome protected fragments
Ribo_RNA_TE_siDF1_HeLa.txt

data_processing:
Library strategy: Ribo-seq
For Riboseq,  adapters and low-quality based reads were trimmed using flexbar v2.5: flexbar -n 20 -a AGATCGGAAGAGCGGTTCAG -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1
The Ribo-seq reads were then demultiplexed using pyBarcodeFilter.py and de-deduplicted using pyFastqDuplicateRemover.py from the pyCRAC software suite.
The processed reads were aligned first to the ribosomal DNA, then to the following siRNA sequences: siDF1 CATCAGGCTGGAGAATAACGACAACAA, TTTTTAGCAAACATAAGAAACCATGAGTC, CAATCAGACTGATCTAATGTGAAATGTA; siDF2 TTGCAGTTTAAGTATTGGAATTTCACAA; siDF3 AAATAGCAATACAGTAGATTTGAATACC. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner using the following parameters -outFilterMultimapNmax 8  --alignEndsType EndToEnd
Mapped reads were then analyzed for different criteria (length, mappability to coding sequence region, P site offset) to select only high quality reads that represent ribosome protected fragments.
For RNAseq, low-quality based reads and short reads were trimmed using flexbar v2.5: flexbar -n 20 -f i1.8 --pre-trim-phred 30 -t output -r Read1.fastq -s  --max-uncalled 1. Reads were then mapped to the ribosomal DNA and the siRNA sequences as described for the Riboseq samples. Reads unmapped to the ribosomal DNA and the siRNA target sequence were mapped to the transcriptome using STAR aligner.
Genome_build: hg38
Supplementary_files_format_and_content: Processed data are in txt files: Ribo_RNA_TE_siDF1_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1 silencing, Ribo_RNA_TE_siDF2_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF2 silencing,  Ribo_RNA_TE_siDF3_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF3 silencing, Ribo_RNA_TE_siDF123_HeLa.txt file contains the Ribosome profiling, RNAseq and Translation efficiency changes upon DF1, DF2 and DF3 silencing, RNA_siDF12_HeLa.txt file contains the RNAseq changes upon DF1 and DF2 silencing, RNA_siDF13_HeLa.txt file contains the RNAseq changes upon DF1 and DF3 silencing , RNA_siDF23_HeLa.txt file contains the RNAseq changes upon DF2 and DF3 silencing

molecule: cytoplasmic RNA

value: RNase digested and rRNA depleted RNA


title: riboseq_input_siDF123_3

description: Ribosome protected fragments input

value: DF1,DF2 and DF3 siRNAs


title: riboseq_siDF1_2

description: Ribosome protected fragments


title: siDF23_2

description: RNAseq


title: riboseq_input_siDF3_3

description: Ribosome protected fragments input


title: siDF3_4

description: RNAseq


title: siDF1_4

description: RNAseq


title: siNC1_4

description: RNAseq


title: Glc-lpin1-3

city: Daejeon

first: Seung-Jae

middle: V

last: Lee

address: 291 Daehak-ro

department: Biological Sciences

country: South Korea

institute: KAIST

data_processing:
Sequencing pairs were aligned to the C. elegans genome WBcel235 (ce11) and Ensembl transcriptome (release 97) by using STAR (v.2.7.0e). Aligned pairs on genes or transcripts were quantified by using RSEM (v.1.3.1). Detailed parameters of alignment and quantification were calculated by following guidelines of ENCODE long RNA-Seq processing pipeline.
Differentially expressed genes (fold change > 2 and adjusted p value < 0.05) were identified by using DESeq2 (v.1.22.2). Wald test p values are adjusted for multiple testing using the procedure of BH.
Genome_build: WBcel235 (ce11)
Supplementary_files_format_and_content: txt files with read counts were generated by using RSEM (v.1.3.1)

organism: Caenorhabditis elegans

source_name: Glc-lpin1_whole body

growth_protocol: All strains were maintained at 20°C on NGM seeded on E. coli OP50 as previously described in 'Maintenance of C. elegans (Stiernagle T, WormBook, 2006)'.

extract_protocol:
RNA extraction was performed as previously described (Son et al., Nature Comm, 2017). Total RNA in the animals was extracted using RNAiso plus (Takara, Seta, Kyoto, Japan).
Libraries were constructed with TruSeq stranded RNA Library Prep Kit v2 (Illumina, CA, USA) by Macrogen Inc. (Seoul, South Korea) following the manufacture’s instruction.

treatment_protocol: Worms that were grown on dsRNA-expressing bacteria-seeded NGM plates from eggs were transferred to 10 μM FUdR-containing plates to inhibit progeny hatching with or without additional 2% glucose at young (day 1) adult stage. To induce RNAi, 10 mM IPTG was treated on the bacteria seeded NGM plates.

tag: strain background

tag: genotype/variation

value: lpn-1 RNAi

tag: development stage

value: adult

tag: media

value: high glucose


title: Glc-lpin1-2

value: whole body


title: Glc-ctrl-3

source_name: Glc-ctrl_whole body

value: control RNAi


title: Glc-ctrl-2


title: Con-ctrl-2

source_name: Con-ctrl_whole body

value: control


title: Con-ctrl-3


title: Con-ctrl-1


title: Con-lpin1-1

source_name: Con-lpin1_whole body


title: Con-lpin1-2


title: Con-lpin1-3


title: Glc-ctrl-1


title: siDF2_4

description: RNAseq

value: rRNA depleted RNA


title: Glc-lpin1-1


title: NPC_NAT1 KO1_d6

city: Kyoto

first: Kazutoshi

last: Takahashi

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Application

institute: Kyoto University

hyb_protocol: Manufature's protocol

scan_protocol: Slides were scanned on the G2565CA Microarray Scanner System (Agilent).

data_processing: GeneSpring GX. Signals were normalized to percentile.

source_name: Human neural progenitor cells, NAT1 knockout (DOX-) on day 6

label_protocol: Manufature's protocol

growth_protocol: Primed human iPSCs were maintained in StemFiT media (Ajinomoto) supplemented with 100 ng/ml bFGF on Laminin 511 E8 fragment-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.  Naïve-like human iPSCs were maintained in StemFiT supplemented with 1 μM PD0325901 (Stemgent), 3 μM CHIR99021 (Stemgent), 10 ng/ml human LIF (Millipore) and 1 μM OMPT (Avanti Polar Lipids) on mitomycin C-treated MEF feeder in a humidified incubator with 5% O2 and 5% CO2.  Neural progenitor cells were maintained in STEMdiff Neural Progenitor medium (Stem Cell Technologies) on Matrigel-coated plates at 37 ºC in a humidified incubator with 20% O2 and 5% CO2.  Wildtype cells were cultured in the presence of  1 μg/ml doxycycline (DOX). Knockout cells were cultured in the absence of DOX for 6 or 12 days.

extract_protocol: RNA was prepared using the miReasy Purification kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies).

treatment_protocol: NAT1 conditional knockout human iPSCs and NPCs were cultured with or without DOX.

tag: cell line

value: NPCs, N18 iPSC-derived

tag: genotype

value: NAT1 knockout (DOX-)

tag: time

value: day 6


title: NPC_NAT1 KO3_d12

source_name: Human neural progenitor cells, NAT1 knockout (DOX-) on day 12

value: day 12


title: iPSC_NAT1 WT2_2iL

source_name: Human induced pluripotent stem cells, NAT1 wildtype (DOX+) in 2iL condition

value: iPSCs

value: NAT1 wildtype (DOX+)

tag: condition

value: 2iL condition (naïve-like)


title: NPC_NAT1 KO3_d6


title: iPSC_NAT1 KO2_2iL

source_name: Human induced pluripotent stem cells, NAT1 knockout (DOX-) in 2iL condition


title: iPSC_NAT1 WT3_2iL


title: NPC_NAT1 KO2_d12


title: NPC_NAT1 WT3_d6

source_name: Human neural progenitor cells, NAT1 wildtype (DOX+) on day 6


title: NPC_NAT1 WT1_d12

source_name: Human neural progenitor cells, NAT1 wildtype (DOX+) on day 12


title: NPC_NAT1 KO1_d12


title: NPC_NAT1 WT3_d12


title: iPSC_NAT1 WT3_F/A

source_name: Human induced pluripotent stem cells, NAT1 wildtype (DOX+) in F/A condition

value: F/A condition (primed)


title: NPC_NAT1 KO2_d6


title: iPSC_NAT1 WT1_2iL


title: iPSC_NAT1 KO3_2iL


title: iPSC_NAT1 KO3_F/A

source_name: Human induced pluripotent stem cells, NAT1 knockout (DOX-) in F/A condition


title: iPSC_NAT1 KO1_2iL


title: Hippocampus_db/m_rep3

city: Nanning

first: Chunlin

last: Zou

address: No. 22 Shuangyong Road

institute: Guangxi Medical University

description: gene expression in 18 weeks db/m mice hippocampus

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: hippocampus, db/m mice

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and Rnase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany)

treatment_protocol: After behavioral tests, microarray analysis was performed on the hippocampal tissues of 3 db/db and 3 db/m mice at the age of  18 weeks.

value: hippocampus

tag: gender

value: male

tag: age

value: 18 weeks

tag: mice

value: db/m


title: iPSC_NAT1 WT1_F/A

tag: cell type


title: NPC_NAT1 WT2_d12


title: NPC_NAT1 WT2_d6


title: iPSC_NAT1 KO2_F/A


title: iPSC_NAT1 WT2_F/A


title: Hippocampus_db/m_rep2

tag: tissue


title: Hippocampus_db/db_rep1

description: gene expression in 18 weeks db/db mice hippocampus

source_name: hippocampus, db/db mice

value: db/db


title: Hippocampus_db/db_rep3


title: Hippocampus_db/m_rep1


title: IR_248

city: Ann Arbor

first: Megan

middle: Hastings

last: Hagenauer

state: MI

address: 205 Zina Pitcher Pl.

department: MBNI

institute: University of Michigan

data_processing:
Alignment & Generation of Count Summaries: the RNA-Seq reads were aligned to the rat genome (Rnor_6.0) using the SubRead aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) using default parameters with the exception of indel detection (maximum length of indel that can be detected=0). The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl v.81). This count summary dataset was then filtered to exclude rows of data from genes that did not meet a minimum threshold of 4 samples with greater than or equal to 10 counts. Rows that lacked official gene symbol annotation were also excluded.
Normalization: Our current analysis used the log2 fragments per million gene-level summary output for each sample provided by the voom() function (R package limma; Ritchie et al. 2015, Nucleic Acids Res. 43: e47).
Quality Control: Quality control was performed in R (R Studio v.3.3.2, R v.3.2.2) and included 1) visualization of the overall log (base2) transformed transcript expression across all subjects via boxplot, 2) examination of the overall reads (mean and standard deviation) per subject, 3) visualization of a subject/subject correlation matrix to identify particularly atypical samples (R<.95). No outlier samples were identified.  The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Log(2) fragments per million (FPM) gene level summary output for each sample (rat ID), annotated using Ensembl (v.81).

organism: Rattus norvegicus

source_name: Whole Hippocampus

extract_protocol:
The rats were sacrificed in adulthood (bHR/bLR=P160-P167, bIR=P126-134) by rapid decapitation and the whole hippocampus was extracted on ice, rapidly frozen, and stored at -80 degrees C.  Nucleotides were extracted using Qiagen AllPrep DNA RNA miRNA Universal Kit 50. Extracted RNA was evaluated for total concentration and quality using a Nanodrop spectrophotometer (concentration range 285-432 ng/ul, 260/280 ratio range 1.61-1.80).
At the sequencing core, the RNA was re-assessed for quality using the TapeStation automated sample processing system (Agilent, Santa Clara, CA) and only samples with RNA integrity numbers (RINs) of  >8 were included in the analysis. The cDNA library was constructed using 0.1-3ug of total RNA and the Illumina TruSeq Stranded mRNA Library Preparation kit (Catalog #s RS-122-2101, RS-122-2102) (Illumina, San Diego, CA).   The final cDNA libraries were checked for quality once again by TapeStation (Agilent) as well as qPCR through the use of Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835, Kapa Biosystems,Wilmington MA). The samples were clustered on a cBot automated cluster generation system (Illumina) for clonal amplification. The samples were then hybridized to the slide (“flow cell”) of a HiSeq 2000 (Illumina) with 6.66 samples per lane and underwent a 100 cycle paired end run in High Output mode using version 3 reagents.

tag: bred line

value: bred Intermediate Responder (bIR)

value: adult

tag: Sex

tag: generation of selective breeding

value: F37 bHRxbLR F1 Cross

tag: total locomotor activity score in a novel environment

tag: fecal boli produced (elevated plus maze)

tag: distance traveled (elevated plus maze)

tag: time immobile (elevated plus maze)

tag: percent time in the open arm (elevated plus maze)


title: Hippocampus_db/db_rep2


title: HR_34

value: bred High Responder (bHR)


title: HR_26


title: IR_261


title: HR_22


title: LR_8

value: bred Low Responder (bLR)


title: LR_32


title: LR_48


title: IR_213


title: LR_20


title: IR_158


title: IR_149


title: HR_38


title: iPSC_NAT1 KO1_F/A

tag: cell line

value: NAT1 knockout (DOX-)


title: LR_16


title: HR_10


title: IR_293


title: HR_2


title: P14L01HC

data_processing:
Alignment & Generation of Count Summaries: Reads were mapped to the rat reference genome (RGSC v3.4) using Tophat2 and Bowtie2 with default parameters and a standard sequence read output. Only reads that aligned with the genome once were maintained for later differential expression analysis. Transcript assembly was collected using Cufflinks and Cuffmerge (Trapnell et al. 2012; Nat Protoc. 7: 562–578).
Differential expression: bHR vs. bLR differential expression was assessed for each age group (P14 and adult) using CuffDiff (Trapnell et al. 2012; Nat Protoc. 7: 562–578).
Genome_build: RGSC v3.4
Supplementary_files_format_and_content: CuffDiff_gene_exp.diff, q1 = bLR, q2 = bHR, A positive log fold change means up in bHR.

extract_protocol:
Rats were sacrificed through rapid decapitation, followed by immediate brain extraction. The whole hippocampus was rapidly dissected on ice, fast-frozen at –40°C, and stored at –80°C before processing. TRIzol reagent (Invitrogen, Calsbad, CA) was used to extract total RNA, followed by purification using RNeasy RNA purification columns (Qiagen, Valencia, CA). The quality and concentration of the RNA was determined using an Agilent bioanalyzer (Palo Alto, CA) and wavelength absorbance (260/280 nm ratio) by Nanodrop.
Purified RNA was shipped to the Genomic Services Laboratory at HudsonAlpha (https://gsl.hudsonalpha.org/index) for short-read (50 bp length) single-end sequencing. RNA Qubit was used to assess concentration (range: 720-1120 ng/uL). The dilutions were denatured through heat application at 70˚C for two minutes and then checked for quality with a RNA Nano bioanalysis chip. Indexed non-stranded cDNA libraries were then prepared using standard Illumina procedures and a TruSeq library preparation kit (Illumina) after which they were pooled for sequencing with four samples per pool. The pooled libraries were clustered on a HiSeq flowcell (Illumina) and sequenced using a first generation HiSeq 2000 sequencer.


title: P14H02HC


title: P14L03HC


title: AdH03HC

value: Adult


title: AdH02HC


title: AdL02HC


title: P14H01HC


title: AdL01HC


title: LR_CONT_5

data_processing:
Alignment & Generation of Count Summaries: the RNA-Seq reads were aligned to the rat genome (Rnor_6.0) using the SubRead aligner (Liao et al. 2014, Bioinformatics. 30: 923–930) using default parameters with the exception of indel detection (maximum length of indel that can be detected=0).  The featureCounts program (Liao et al. 2014, Bioinformatics. 30: 923–930) then generated the gene-level RNA-Seq count summaries for each sample based on ENSEMBL annotation (Ensembl v.85).
Normalization: Our current analysis used the log2 fragments per million gene-level summary output for each sample provided by the voom() function (R package limma; Ritchie et al. 2015, Nucleic Acids Res. 43: e47).
Quality control was performed in R (R Studio v.3.3.2, R v.3.2.2) and included 1) visualization of the overall log (base2) transformed transcript expression across all subjects via boxplot, 2) examination of the overall reads (mean and standard deviation) per subject, 3) visualization of a subject/subject correlation matrix to identify particularly atypical samples (R<.95). No outlier samples were identified.  The full analysis code is available at: https://github.com/isabellie4/PhenotypeProject and https://github.com/hagenaue/bHRbLR_MetaAnalysisProject.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Log(2) fragments per million (FPM) gene level summary output for each sample (rat ID), annotated using Ensembl (v.85).

extract_protocol:
One hour after undergoing testing on the elevated plus maze, the animals were sacrificed by rapid decapitation and the brains were flash frozen in isopentane cooled on dry ice. The whole hippocampus was dissected from each brain on a dry ice and wet ice mixture and immediately put in TRIzol™. RNA was extracted using the Zymo RNA isolation Kit.
The cDNA library was constructed using 0.1-3ug of total RNA and the Illumina TruSeq Stranded mRNA Library Preparation kit (Catalog #s RS-122-2101, RS-122-2102) (Illumina, San Diego, CA).   The final cDNA libraries were checked for quality once again by TapeStation (Agilent) as well as qPCR through the use of Kapa’s library quantification kit for Illumina Sequencing platforms (catalog # KK4835, Kapa Biosystems,Wilmington MA). The samples were clustered on a cBot automated cluster generation system (Illumina) for clonal amplification. The samples were then hybridized to the slide (“flow cell”) of a HiSeq 2000 (Illumina) and underwent non-stranded short read (50-bp length) single-end sequencing in High Output mode using version 3 reagents.

treatment_protocol: The original study compared repeated injections of either antidepressant medication (fluoxetine or desipramine) or vehicle (VEH=1:1 saline and water) solution in bHR and bLR rats (14 days of intraperitoneal injections - P78-P92, 1 per day) under either standard laboratory housing conditions or chronic variable stress. This upload only includes the data from the control subjects: generation F43 adult male bHR VEH rats and bLR VEH rats housed in standard conditions (n=5 rats/group).

value: adult (P92)

tag: treatment

value: 14 days of vehicle injections

tag: social interaction score


title: HR_CONT_5


title: HR_CONT_2


title: LR_CONT_2


title: LR_CONT_1


title: HR_CONT_1


title: HR_CONT_4


title: LR_CONT_4


title: LR_CONT_3


title: HR_CONT_3


title: LR_44


title: minimal change disease 10

city: Bari

first: Fabio

last: Sallustio

state: Bari

address: Piazza G. Cesare N°11

country: Italy

institute: University of Bari

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using log2 normalisation with Illumina Genomestudio

source_name: minimal change disease _renal biopsy

label_protocol: Biotinylated cDNA was prepared with the Illumina WG-DASL asay

extract_protocol: RNA was extracted with QIAGEN miRNeasy FFPE kit in accordance with the prescribed protocol provided with the kit.

tag: subject status

value: minimal change disease

tag: classification

value: renal biopsy


title: minimal change disease 5


title: primary tumor of RJPDAC04

city: Shanghai

first: Ping

last: Lin

address: No.320 Yueyang Road, Xuhui District

institute: Shanghai Institute of Nutrition and Health

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC04PT

data_processing:
TrimGalore (v0.5.0) were used to trim bad-quality bases or reads of raw sequencing data.
The resulting clean reads were then mapped to human genome reference (hg19) by using STAR (v2.5.2b) algorithm.
Htseq-count (v0.6.0) were used to count the total number of uniquely mapped reads mapped to each gene.
Genome_build: hg19
Supplementary_files_format_and_content: expression count table (txt file)

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
Total RNA was prepared with QIAzol Lysis Reagent and RNeasy MinElute Cleanup Kit (Qiagen, Germany). The RNA quality and integrity were analyzed by Qubit 2.0(Life Technologies, USA) and Bioanalyzer 2100 (Agilent, Germany).
For library preparation, 3 ug total RNA were captured by NEBNext Oligo d(T) 25 beads (NEB, USA), sheared to fragements of ~250bp, and reverse transcripted by NEBNext RNA first and second Strand Synthesis Module (NEB, USA). The products were end-repaired, A-tailed and ligated to Illumina sequencing adapters and amplified by PCR. The sequencing library were qualified by Qubit 2.0 (Life technologies, USA) and Bioanalyzer 2100 (Agilent, Germany), then sequenced on Illumina Hiseq X-Ten with 2×150 bp paired-end sequencing, which were controlled by Hiseq Control Software (HCS).

treatment_protocol: All assessed samples were treatment-naive tissues (No chemo- or targeted- therapy history before sample collection)

value: Primary tumor

value: untreatment

tag: tumor stage

value: stage IV


title: liver metastasis of RJPDAC09

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC09HM

value: Hepatic metastasis


title: primary tumor of RJPDAC09

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC09PT


title: liver metastasis of RJPDAC08

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC08HM


title: primary tumor of RJPDAC08

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC08PT


title: tumor adjacent control tissue of RJPDAC08

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC08N

value: Normal tissue


title: minimal change disease 9


title: minimal change disease 4


title: minimal change disease 7


title: minimal change disease 3


title: minimal change disease 12


title: Membranous glomerulonephritis 11

source_name: Membranous glomerulonephritis _renal biopsy

value: Membranous glomerulonephritis


title: minimal change disease 2


title: primary tumor of RJPDAC07

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC07PT


title: minimal change disease 11


title: minimal change disease 1


title: minimal change disease 8


title: Membranous glomerulonephritis 10


title: Membranous glomerulonephritis 6


title: Membranous glomerulonephritis 8


title: NPC_NAT1 WT1_d6

value: NPCs, N18 iPSC-derived

tag: genotype

value: NAT1 wildtype (DOX+)

tag: time

value: day 6


title: Membranous glomerulonephritis 9

tag: tissue


title: liver metastasis of RJPDAC07

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC07HM


title: liver metastasis of RJPDAC04

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC04HM


title: minimal change disease 6


title: liver metastasis of RJPDAC01

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC01HM


title: primary tumor of RJPDAC01

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC01PT


title: primary tumor of RJPDAC18

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC18PT


title: Membranous glomerulonephritis 5


title: Membranous glomerulonephritis 7


title: Membranous glomerulonephritis 4


title: liver metastasis of RJPDAC02

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC02HM


title: tumor adjacent control tissue of RJPDAC15

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC15N


title: primary tumor of RJPDAC03

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC03PT


title: liver metastasis of RJPDAC03

description:
Sample were collected from synchronous surgery of liver oligometastasis and paired primary tumor
RJPDAC03HM