title: phi80-3

city: Oviedo

first: Lucia

last: Fernandez

address: C/ Francisco Pintado Fe 26

institute: Instituto de Productos Lacteos de Asturias (IPLA-CSIC)

data_processing:
Quality of the sequences was verified with FastQC 0.11.2
EDGE-pro 1.3.1 workflow was employed for read processing. The pipeline as described by T.Magoc, et al., Evolutionary Bioinformatics, 2013, employs Bowtie2 (v2.2.3) to map reads to the reference genome (NCTC 8325), filters multimapped reads based on scoring alignments and determines read coverage for each genomic position and gene.
EDGE-pro output files were formated using the edgeToDeseq script provided in the EDGE-pro package and used as input for DESeq2 (v1.12.4) to calculate RPKMs per gene and quantify differential expression between conditions.
Reads for phi11 and phi80 replicates were reprocessed using the EDGE-pro 1.3.1 and DESeq2, using phi11 and phi80alpha reference genomes.
Genome_build: S. aureus subsp. aureus NCTC 8325 (Assembly GCA_000013425.1, Mar 2010), phage phi11  (Assembly GCA_000841245.1, February 2002) and phage phi80alpha (Assembly     GCA_000871605.1, May 2006)
Supplementary_files_format_and_content: 450_vs_Phi11.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in 450 and phi11 replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
phi11.phage_11.RPKM.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phi11 genes in each phi11 replicate.
450_vs_Phi80.txt: Tab-delimited text File. The file includes RPKM values for NCTC 8325 genes in 450 and phi80 replicates as well as differential expression estimations, expressed as a log2 fold change between conditions.
phi80.phage_80_alpha.RPKM.txt: Tab-delimited text file. The file includes read counts and RPKM values for phage phi80alpha genes in each phi80 replicate.

organism: Staphylococcus aureus

source_name: Biofilm cells

growth_protocol: Biofilms were formed for 5 hours at 37ºC, then adhered cells were harvested

extract_protocol:
Bacterial cells were harvested, treated with RNA protect (Qiagen) and kept at -80ºC until RNA purification. RNA was obtained by mechanical disruption in the presence of acid phenol and subsequent purification was carried out with illustra RNA spin minikit (GE Healthcare)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell state

value: cells adhered to biofilm


title: 450-3

status: Public on Aug 20 2018

type: SRA

country: Spain

library_source: transcriptomic

molecule: total RNA

tag: strain


title: phi80-2


title: 29P

type: RNA

city: New Haven

first: Lajos

last: Pusztai

state: CT

address: 300 George St., Suite 120

country: USA

institute: Yale University

hyb_protocol: RNA was hybridized to capture probes by nCounter analysis system

scan_protocol: nCounter analysis system

data_processing: The expression values were normalized using housekeeping genes using the nSolver 2.6 package following the manufacturer’s recommendations

label: nanostring

organism: Homo sapiens

source_name: primary breast cancer

label_protocol: NanoString manufactuerer's protocol

extract_protocol: RNA was extracted from 3, 10 micron FFPE sections of each cancer using the High Pure RNA Paraffin Kit from Roche Applied Science.

tag: localization

value: breast


title: WT-3D

city: Nanjing

first: HONGWEI

last: LIANG

state: Jiangsu Province

address: Qixia District, Xianlin Road No.163

country: China

institute: Nanjing University

data_processing:
Quality control: The raw reads were filtered by removing reads containing adapter, ploy-N and low quality reads  for subsequent analysis.  The steps of sequencing data filtering:  1) removing reads containing adapter;  2) removing reads containing ploy-N (i.e., unrecognized bases), reads with a ratio greater than 5%;  3) removing low-quality reads (the number of base which is Q≤10 is more than 50% of the entire  read);  All the downstream analyses were based on clean data with high quality.
Mapping to the reference genome: The reference genome and gene model annotation files were downloaded directly from the  genome website. The reference genome index was built using Bowtie2 (v2.2.9)[1], and paired-end  clean reads were aligned to the reference genome using TopHat (v2.1.1)[2]
Transcriptome assembly: The mapped reads of each sample were assembled using Cufflinks (v2.2.1)[3] with a  reference-based approach. This method employed spliced reads to determine exon connectivity.  Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression levels  of a minimal set of isoforms, which provides a maximum likelihood explanation of the expression  data in a given locus.
Quantification of gene expression levels: Cuffdiff (v1.3.0) was used to calculate FPKMs for coding genes in each sample. Gene FPKMs  were computed by summing the FPKMs of the transcripts in each gene group. FPKM stands for  “fragments per kilobase of exon per million fragments mapped”, and it is calculated based on the  length of the fragments and the reads count mapped to each fragment.
Differential expression analysis: Cuffdiff (v2.2.1)[3] provides statistical routines for determining differential expression in digital  transcript or gene expression datasets using a model based on a negative binomial distribution.  Genes with corrected p values less than 0.05 and the absolute value of log2 (fold change) < 1 were  assigned as significantly differentially expressed.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Mus musculus

source_name: colon epithelial cells

extract_protocol:
colon epithelial cells were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.the VAHTS mRNA-seq v2 Library  Prep Kit for Illumina® (Vazyme, NR601)  was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: Wild Type

tag: tissue

value: colon epithelium

tag: treatment

value: treated with  2.5% DSS for 3 days


title: 450-2


title: phi11-2


title: phi11-3


title: 116P


title: Patients with stable graft function [S11]

city: Berlin

first: Pawel

last: Durek

address: Charitéplatz 1

country: Germany

institute: Deutsches Rheuma-Forschungszentrum

description:
SGF
S11
Small RNA-Seq

data_processing:
MicroRNAs were identified and quantified using miRDeep2.0.0.8.
Differential expression was analyzed using DESeq2 1.18.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include number of miRNA raw read counts.

source_name: Blood

growth_protocol: Kidney transplanted patients with stable graft function, antibody-mediated rejection or T cell-mediated rejection episodes.

extract_protocol:
Total RNA (tRNA) was isolated from blood cells contained in PAXgene Blood RNA Tubes with the PAXgene blood miRNA Kit (PreAnalytix, Qiagen, Hilden, Germany) according to the manufacturer's instruction. Total RNA concentration and quality of each sample were determined with the NanoDrop ND-Lite (peqlab, Erlangen, Germany) and Qubit fluorometer (ThermoFisher Scientific, Darmstadt, Germany). Dependent on quantity and quality of RNA, six samples from patients with ABMR, six samples from patients with SGF and 4 samples from patients with TCMR were chosen for high-throughput sequencing.
The "TruSeq® small RNA library Prep" kit (Illumina, San Diego, CA, USA) was used to prepare cDNA libraries for small RNA sequencing from a maximum of 1µg of total RNA isolated from the whole blood of patients with Tx according to manufacturer’s instruction. RNA quality was assessed on a Bioanalyzer using the RNA 6000 Pico Kit (Agilent Technologies, Waldbronn, Germany) and only RNA with a RIN >8 was considered for further processing. After quality control (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany) the resulting cDNA libraries were purified by gel-electrophoresis for the small RNA containing cDNA fraction at ~150 bp. The final small RNA cDNA libraries were quality checked (High sensitivity DNA Kit, Agilent Technologies, Waldbronn, Germany) and quantified (Qubit dsDNA HS Assay Kit, Invitrogen, Darmstadt, Germany). The final libraries were single-end (50 bp) sequenced on a HiSeq2500 Illumina Next Generation Sequencing Device (Illumina, San Diego, CA, USA).

value: Blood

tag: cell type

value: Whole blood cells

value: Kidney transplant

tag: transplant result

value: stable graft function


title: Patients with stable graft function [S10]

description:
SGF
S10
Small RNA-Seq


title: Patients with stable graft function [S9]

description:
SGF
S9
Small RNA-Seq


title: 117P


title: 94P1


title: 88P


title: Patients with stable graft function [S8]

description:
SGF
S8
Small RNA-Seq


title: 5M

source_name: metastatic breast cancer

value: soft tissue


title: 11P


title: 37M

value: ovary


title: Patients with T cell mediated rejection [S13]

description:
TCMR
S13
Small RNA-Seq

value: T cell-mediated rejection


title: 37P


title: Patients with antibody mediated rejection [S6]

description:
ABMR
S6
Small RNA-Seq

value: antibody-mediated rejection


title: 6P1


title: Patients with antibody mediated rejection [S5]

description:
ABMR
S5
Small RNA-Seq


title: Pin1-Crispr-1

city: Boston

first: Chenxi

last: Qiu

state: MA

address: NRB 858, 77 Avenue Louis Pasteur

institute: Harvard Medical School

description: miRNAs

scan_protocol: NanoString nCounter

data_processing: Expression profiling of global microRNAs in these samples was determined by Dana-Farber Cancer Institute Molecular Biology Core Facilities using NanoString nCounter microRNA Expression Assays, followed by data analysis using the NanoString nCounter software. Dot plots were created using GraphPad PRISM7.0a (GraphPad Software, Inc., USA).

source_name: Breast Cancer Cell line

extract_protocol: After 3 days’ treatments with DMSO, ATO and/or ATRA, cell pellets were collected, along with Pin1 CRISPR KO cells, followed by isolating total RNA using miRNeasy Mini kit (QIAGEN, Germany) according to the manufacture instruction, as described.

value: Breast Cancer Cell line


title: Pin1-Crispr-2

description: miRNAs


title: Patients with antibody mediated rejection [S3]

description:
ABMR
S3
Small RNA-Seq


title: Vec-control-2

description: miRNAs


title: Patients with antibody mediated rejection [S2]

description:
ABMR
S2
Small RNA-Seq


title: 6P2


title: Patients with antibody mediated rejection [S1]

description:
ABMR
S1
Small RNA-Seq


title: 6M


title: 110P


title: Vec-control-1

description: miRNAs


title: 20P


title: Patients with antibody mediated rejection [S4]

description:
ABMR
S4
Small RNA-Seq


title: ATO-2

description: miRNAs


title: ATO+ATRA-2

description: miRNAs


title: Patients with stable graft function [S7]

description:
SGF
S7
Small RNA-Seq


title: 36P


title: ATRA-2

description: miRNAs


title: 20M

value: brain


title: ATO+ATRA-1

description: miRNAs


title: 87P


title: 93M2


title: Control-1

description: miRNAs


title: Control-2

description: miRNAs


title: ATRA-1

description: miRNAs


title: 28M

value: fallopian tube


title: 2_A44_6hr_ctrl_November

status: Public on Aug 19 2018

city: Seattle

first: Alexander

middle: Isaac

last: Salter

state: WA

address: 1100 Fairview Avenue North, D3-100

department: Clinical Research Division

institute: Fred Hutchinson Cancer Research Center

data_processing:
The RNA sequencing (RNA-seq) data were aligned to the human genome (UCSC Human Genome Assembly GRCh38 reference) using STAR.
Gene quantification was performed using RSEM.
Genes with less than 10 non-zero read counts (taking into account technical replicates) were discarded, leaving 18,498 expressed genes. All libraries passed the quality control criteria (libraries with more than 200,000 reads, 12,000 detected genes and an exon range > 60%).
Samples sequenced on two lanes were pooled together.
Genome_build: GRCh38
Supplementary_files_format_and_content: csv file include count values for each sample

source_name: Peripheral Blood CD8+ T Cells

growth_protocol: CD8+ T cells were isolated from the peripheral blood of healthy donors and transduced with a CD28/CD3z or 4-1BB/CD3z CAR. CAR-expressing T cells were purified by FACS and expanded in vitro.

extract_protocol:
T cells were washed in 1x phosphate buffered saline and anti-CAR or control magnetic beads were removed during washing. RNA was extracted using a Macherey-Nagel NucleoSpin RNA Kit (Cat # 740955.50) as per manufacturer's instructions.
Total RNA integrity was checked using an Agilent 4200 TapeStation (Agilent Technologies) and quantified using a Trinean DropSense96 spectrophotometer (Caliper Life Sciences). RNA-seq libraries were prepared from 500ng total RNA using the TruSeq RNA Sample Prep Kit v2 (Illumina Cat # RS-122-2001) and a Sciclone NGSx Workstation (PerkinElmer). Library size distributions were validated using an Agilent 4200 TapeStation. Additional library quality control, blending of pooled indexed libraries, and cluster optimization were performed using a Qubit 2.0 Fluorometer (ThermoFisher).
RNA-seq libraries were pooled and clustered (6-8-plex) onto a flow cell lane. For sequencing in July, 12 samples were split across 2 flow cell lanes (average of 6 samples per lane). Sequencing was performed using an Illumina HiSeq 2500 in rapid mode employing a paired-end, 50 base read length (PE50) sequencing strategy.

treatment_protocol: CAR T cells were stimulated by incubation with anti-CAR beads, or left unstimulated by incubation with control beads.

tag: sampleID

tag: lane

value: November

tag: donor

tag: car

tag: antigen

tag: time

tag: condition

value: Ctrl

tag: hutchbasesamplename


title: 4_A43_6hr_ctrl_August

value: August


title: 5_A42_24hr_stim_August

value: Stim


title: 3_A43_6hr_stim_August


title: 3_A45_6hr_stim_November


title: 7_A43_24hr_stim_August


title: 8_A43_24hr_ctrl_August


title: ATO-1

description: miRNAs


title: 1_A42_6hr_stim_August


title: 2_A42_6hr_ctrl_August


title: 6_A44_24hr_ctrl_July

value: July


title: 7_A45_24hr_stim_July


title: 12_A43_24hr_ctrl_July


title: 8_A45_24hr_ctrl_July


title: 10_A42_24hr_ctrl_July


title: 11_A43_24hr_stim_July


title: 1_A44_6hr_stim_July


title: 4_A45_6hr_ctrl_July


title: 3_A45_6hr_stim_July


title: 2_A44_6hr_ctrl_July


title: 4_A45_6hr_ctrl_November


title: 1_A44_6hr_stim_November


title: 6_A42_24hr_ctrl_August


title: 5_A44_24hr_stim_July


title: 9_A42_24hr_stim_July


title: Treatment PI116, 96 h

city: Cornella de Llobregat

first: Tamara

last: Maes

state: Barcelona

address: Carrer Sant Ferran 74

department: R&D

institute: Oryzon Genomics S.A.

description:
SI-107
P116 TvsV, 96 h

hyb_protocol: Cy3 and Cy5 labeled cRNA for the control probes (Zea mays Zmmyb42 and Expansin) were added to the Cy3- and Cy5-labelled sample cRNA mixes and hybridized to microarrays according to the manufacturer’s instruction.

scan_protocol: Raw data were obtained using Agilent's DNA Microarray Scanner G2505B Images were quantified using Agilent Feature Extraction software (v10.1)

data_processing: The raw fluorescence intensity data were processed using proprietary Oryzon Genomics SA Polyphemus software, which involves the following steps: 1. Spatial data compensation of the signals in the 2 channels based on the spike probes distributed over the array and generating signal at several discrete levels. 2. Noise filtering based on negative controls.  3. Data normalization by modified nonlinear Q-splines normalization method (Workman et al., 2002) and Log2(sample/control) value calculation without background correction. Differential expression assessment using robust statistics on the average of 3 technical replicates per gene oligo after removal of eventual outlier points (caused by dust or array imperfections). Criteria for outlier elimination are established automatically based on the intra-array technical variability of the signal distribution of the controls probes. The p-values are calculated after outlier elimination based on the absolute value of the regularized t-statistics (Baldi et al., 2001), which uses a Bayesian framework to derive the algorithm. Control probes have SPOTID ORY_C* and each is present in 2103 copies; gene oligos have SPOTID ORY_P* and each is present in triplicate, respectively, in the crossref file. The Agilent design file and AgilentOryzonRrossRef file are provided

source_name: P116-ORY-1001 treated-96h

label_protocol: Total RNA (0.5 μg) amplification and labeling with Cy3 or Cy5 was carried out using a modified Eberwein mRNA amplification procedure employing the MessageAmp™ aRNA amplification kit from Ambion (Applied Biosystems).

growth_protocol: cells were grown in RPMI-1640 +10%FBS

extract_protocol: Total RNA was extracted using the Qiagen RNeasy extraction kit. Evaluation of RNA quality was performed with the Agilent 2100 bioanalyzer and NanoDrop™ ND-1000 (Thermo Scientific).

treatment_protocol: cells were treated for 96 h with 5 nM ORY-1001, 0.001% DMSO in growth medium

tag: cell line

tag: disease

value: Acute T-cell leukemia

value: T-lymphocyte

tag: subtype

value: Lymphoid

source_name: P116-vehicle treated-96h

treatment_protocol: cells were treated for 96 h with 0.001% DMSO in growth medium


title: Treatment JVM-2, 96 h

description:
SI-107
JVM-2 TvsV, 96 h

source_name: JVM-2-ORY-1001 treated-96h

value: Mantle cel lymphoma

value: Lymphoblast

source_name: JVM-2-vehicle treated-96h


title: Control KOPN, 96 h

description:
SI-093
KOPN VvsV, 96 h

source_name: KOPN-vehicle treated-96h

growth_protocol: cells were grown in RPMI-1640+10% FBS

value: Acute lymphoblastic leukemia

value: B cell precursor leukemia


title: Control JVM-2, 96 h

description:
SI-107
JVM-2 VvsV, 96 h


title: Control PI116, 96 h

description:
SI-107
P116 VvsV, 96 h


title: Control JURKAT, 96 h

description:
SI-093
JURKAT VvsV, 96 h

source_name: JURKAT-vehicle treated-96h


title: Treatment KOPN, 96 h

description:
SI-093
KOPN TvsV, 96 h

source_name: KOPN-ORY-1001 treated-96h


title: Treatment BDCM, 96 h

description:
SI-107
BDCM TvsV, 96 h

source_name: BDCM-ORY-1001 treated-96h

value: Acute myelogenous leukemia

value: B lymphoblast

tag: aml fab

source_name: BDCM-vehicle treated-96h


title: Control MOLT4, 96 h

description:
SI-093
MOLT4 VvsV, 96 h

source_name: MOLT4-vehicle treated-96h

value: T-lymphoblast


title: Control ARH-77, 96 h

description:
SI-107
ARH-77 VvsV, 96 h

source_name: ARH-77-vehicle treated-96h

value: Plasma cell leukemia


title: Treatment JURKAT, 96 h

description:
SI-093
JURKAT TvsV, 96 h

source_name: JURKAT-ORY-1001 treated-96h


title: Treatment ARH-77, 96 h

description:
SI-107
ARH-77 TvsV, 96 h

source_name: ARH-77-ORY-1001 treated-96h


title: Treatment CCRF/CEM, 96 h

description:
SI-093
CCRF/CEM TvsV, 96 h

source_name: CCRF/CEM-ORY-1001 treated-96h

value: T-Lymphoblast

source_name: CCRF/CEM-vehicle treated-96h


title: Control BDCM, 96 h

description:
SI-107
BDCM VvsV, 96 h


title: Control SUP-T1, 96 h

description:
SI-093
SUP-T1 VvsV, 96 h

source_name: SUP-T1-vehicle treated-96h

value: T-cell lymphoblastic lymphoma


title: Treatment SUP-T1, 96 h

description:
SI-093
SUP-T1 TvsV, 96 h

source_name: SUP-T1-ORY-1001 treated-96h


title: Treatment RS4-11, 96 h

description:
SI-107
RS4-11 TvsV, 96 h

source_name: RS4-11-ORY-1001 treated-96h

source_name: RS4-11-vehicle treated-96h


title: Control CCRF/CEM, 96 h

description:
SI-093
CCRF/CEM VvsV, 96 h


title: Human islets_palmitate_12hours_rep5

city: Uppsala

first: Ernest

last: Sargsyan

address: Husargatan 3

country: Sweden

institute: Uppsala University

hyb_protocol: not provided

scan_protocol: not provided

data_processing:
program-name = Expression Console
program-version = 1.3.1.187

label: biotin

source_name: pancreatic islets_12hours

label_protocol: not provided

extract_protocol: total RNA extraction

tag: gender

value: female

tag: age

value: 48 years old

value: pancreatic islets


title: Treatment MOLT4, 96 h

description:
SI-093
MOLT4 TvsV, 96 h

source_name: MOLT4-ORY-1001 treated-96h


title: Treatment CCRF-HSB-2, 96 h

description:
SI-107
CCRF-HSB-2 TvsV, 96 h

source_name: CCRF-HSB-2-ORY-1001 treated-96h

growth_protocol: cells were grown in IMDM+10% FBS

source_name: CCRF-HSB-2-vehicle treated-96h


title: Control CCRF-HSB-2, 96 h

description:
SI-107
CCRF-HSB-2 VvsV, 96 h


title: Human islets_palmitate_4hours_rep5

source_name: pancreatic islets_4hours

tag: tissue


title: Human islets_palmitate_7days_rep4

source_name: pancreatic islets_7days

value: male

value: 66 years old


title: Human islets_palmitate_2days_rep5

source_name: pancreatic islets_2days


title: Human islets_palmitate_7days_rep5


title: Human islets_control_rep5

source_name: pancreatic islets_control


title: Human islets_palmitate_1day_rep5

source_name: pancreatic islets_1day


title: Treatment KE-37, 96 h

description:
SI-107
KE-37 TvsV, 96 h

source_name: KE-37-ORY-1001 treated-96h

tag: cell type

value: T-cell leukemia

source_name: KE-37-vehicle treated-96h


title: Treatment MEG-01, 96 h

description:
SI-107
MEG-01 TvsV, 96 h

source_name: MEG-01-ORY-1001 treated-96h

growth_protocol: cells were grown in RPMI-1640 +10% FBS

value: Chronic myelogenous leukemia

value: Megakaryoblast

value: Myeloid

source_name: MEG-01-vehicle treated-96h


title: Human islets_palmitate_1day_rep4


title: Human islets_palmitate_4hours_rep4


title: Control RS4-11, 96 h

description:
SI-107
RS4-11 VvsV, 96 h

value: Acute lymphoblastic leukemia

value: Lymphoid


title: Treatment KU812E, 96 h

description:
SI-107
KU812E TvsV, 96 h

source_name: KU812E-ORY-1001 treated-96h

growth_protocol: cells were grown in RPMI-1640 +20% FBS

value: Basophil

source_name: KU812E-vehicle treated-96h


title: Control KE-37, 96 h

description:
SI-107
KE-37 VvsV, 96 h


title: Control 8E5, 96 h

description:
SI-107
8E5 VvsV, 96 h

source_name: 8E5-vehicle treated-96h

value: Lymphoblast


title: Treatment K562, 96 h

description:
SI-093
K562 TvsV, 96 h

source_name: K562-ORY-1001 treated-96h

source_name: K562-vehicle treated-96h


title: Human islets_palmitate_12hours_rep4

source_name: pancreatic islets_12hours


title: Control MEG-01, 96 h

description:
SI-107
MEG-01 VvsV, 96 h


title: Control KU812E, 96 h

description:
SI-107
KU812E VvsV, 96 h


title: Treatment 8E5, 96 h

description:
SI-107
8E5 TvsV, 96 h

source_name: 8E5-ORY-1001 treated-96h


title: Control Monomac-01, 96 h

description:
SI-107
Monomac-01 VvsV, 96 h

source_name: Monomac-01-vehicle treated-96h

value: Acute monocytic leukemia

value: Monocyte


title: Treatment Monomac-01, 96 h

description:
SI-107
Monomac-01 TvsV, 96 h

source_name: Monomac-01-ORY-1001 treated-96h


title: Human islets_palmitate_2days_rep4


title: Control THP-1, 96 h

description:
SI-077
THP-1 VvsV, 96 h

source_name: THP-1-vehicle treated-96h

treatment_protocol: cells were treated for 96 h with 0.015% DMSO in growth medium


title: Human islets_control_rep4


title: Human islets_palmitate_1day_rep3

value: 39 years old


title: Human islets_palmitate_12hours_rep3


title: Human islets_control_rep3


title: Control K562, 96 h

description:
SI-093
K562 VvsV, 96 h


title: Human islets_palmitate_7days_rep2

source_name: pancreatic islets_7days

value: 34 years old


title: Human islets_palmitate_1day_rep2

value: female


title: Human islets_palmitate_2days_rep3

source_name: pancreatic islets_2days


title: Human islets_palmitate_4hours_rep3

source_name: pancreatic islets_4hours


title: Human islets_palmitate_12hours_rep2


title: RSC_2_Input

city: Farmington

first: Justin

last: Cotney

address: 400 Farmington Avenue

department: Genetics and Genome Sciences

institute: UConn Health

library_source: genomic

data_processing:
Align to genome using bowtie 1.1.1
Generate ChIP-seq signals by extending each aligned read to 300bp, normalize fragment counts per 1 million aligned reads (Reilly et al., 2015)
Identify enriched regions using sliding window method (Mikkelsen, Xu et al. 2010)
Divide enriched regions into functional categories based on overlap with genomic features (Bedtools 2.19.0 with Ensembl v67)
Genome_build: mm9
Supplementary_files_format_and_content: bowtie alignment files
Supplementary_files_format_and_content: sorted bed files for enriched regions
Supplementary_files_format_and_content: sorted bed files for enriched regions overlapping enhancer annotations
Supplementary_files_format_and_content: bigwigs for ChIP-seq signals

molecule: genomic DNA

source_name: Adult (P56) cortical tissue

growth_protocol: All animal work complies with the Norwegian Animal Welfare Act and the European Convention for the Protection of Vertebrate Animals used for Experimental and Other Scientific Purposes.

extract_protocol:
Cotney and Noonan, CSHL Protocols 2015.
Rubicon Genomics Thruplex 48S

treatment_protocol: Horizontal or coronal 500 µm sections of brain were cut on a Leica VT 1000 S microtome and kept at 4 °C until dissection. Bilateral dissection was performed applying architectonic criteria (Jones and Witter 2007, Witter 2011, Boccara, Kjonigsen et al. 2015, O'Reilly, Flatberg et al. 2015, Sugar and Witter 2016)  to unstained tissue. The tissue samples were snap-frozen in liquid nitrogen, kept at -80oC and shipped on dry ice.

tag: strain

value: retrosplenial cortex (RSC)

tag: h3k27ac antibody

tag: h3k4me2 antibody


title: RSC_2_H3K4me2


title: Human islets_palmitate_2days_rep2

value: pancreatic islets


title: RSC_1_H3K4me2


title: RSC_2_H3K27ac


title: Control THP-1, 24 h

description:
SI-077
THP-1 VvsV, 24 h

source_name: THP-1-vehicle treated-24h

treatment_protocol: cells were treated for 24 h with 0.015% DMSO in growth medium


title: RSC_1_H3K27ac


title: Treatment THP-1, 24 h

description:
SI-077
THP-1 TvsV, 24 h

source_name: THP-1-ORY-1001 treated-24h

treatment_protocol: cells were treated for 24 h with 5 nM ORY-1001, 0.015% DMSO in growth medium


title: MEC_2_Input

value: medial entorhinal cortex (MEC)


title: Treatment MV(4;11), 96 h

description:
SI-084
MV(4;11) TvsV, 96 h

treatment_protocol: cells were treated for 96 h with 5 nM ORY-1001, 0.015% DMSO in growth medium

value: Lymphoblast, macrophage

source_name: MV(4;11)-vehicle treated-96h


title: Control MV(4;11), 24 h

description:
SI-084
MV(4;11) VvsV, 24 h

source_name: MV(4;11)-vehicle treated-24h


title: Human islets_control_rep2

source_name: pancreatic islets_control


title: Human islets_palmitate_1day_rep1

source_name: pancreatic islets_1day

value: male

value: 59 years old


title: Human islets_palmitate_4hours_rep2


title: Human islets_palmitate_7days_rep1


title: Control MV(4;11), 96 h

description:
SI-084
MV(4;11) VvsV, 96 h


title: Control OCI-AML3, 96 h

description:
SI-093
OCI-AML3 VvsV, 96 h

source_name: OCI-AML3-vehicle treated-96h

value: Acute myeloid leukemia


title: Human islets_palmitate_4hours_rep1


title: RSC_1_Input


title: Human islets_palmitate_12hours_rep1


title: Treatment OCI-AML3, 96 h

description:
SI-093
OCI-AML3 TvsV, 96 h

source_name: OCI-AML3-ORY-1001 treated-96h

value: Myeloid


title: Human islets_palmitate_2days_rep1


title: Treatment MV(4;11), 24 h

description:
SI-084
MV(4;11) TvsV, 24 h


title: Treatment NB4, 24 h

description:
SI-077
NB4 TvsV, 24 h

source_name: NB4-ORY-1001 treated-24h

value: Acute promyelocytic leukemia

value: Promyeloblast

source_name: NB4-vehicle treated-24h


title: Human islets_control_rep1


title: Treatment NB4, 96 h

description:
SI-077
NB4 TvsV, 96 h

source_name: NB4-ORY-1001 treated-96h

source_name: NB4-vehicle treated-96h


title: Treatment THP-1, 96 h

description:
SI-077
THP-1 TvsV, 96 h

source_name: THP-1-ORY-1001 treated-96h

source_name: THP-1-vehicle treated-96h


title: MEC_2_H3K27ac


title: MEC_1_Input


title: MEC_1_H3K4me2


title: LDL1pro::LDL1:GFP_input

city: Taipei

first: Fu-Yu

last: Hung

address: Institute of Plant Biology, National Taiwan University

country: Taiwan

institute: NTU, IPB

data_processing:
The raw sequence data were processed using the Illumina sequence data analysis pipeline GAPipeline 1.3.2. Bowtie was then employed to map the reads to the Arabidopsis genome (TAIR10).
To determine the correlation between biological repeats, Pearson correlation was computed using R statistical software on normalized signal intensity for ChIP binding peaks. The alignments were first converted to Wiggle (WIG) files using MACS. The data were then imported into the Integrated Genome Viewer (IGV) for visualization. The program SICER was used to identify ChIP-enriched domains (peaks).
The binding correlation analysis was completed by Expasy ChIP-Seq tools (http://ccg.vital-it.ch/chipseq/chip_cor.php).
Genome_build: TAIR 10
Supplementary_files_format_and_content: Bed files

organism: Arabidopsis thaliana

source_name: 14 days old plants

growth_protocol: The transgenic Arabidopsis seedlings were grown under Long-day conditions at 22°C and harvested after 14 days.

extract_protocol:
10 ng of DNA from at least 5 ChIPs was pooled to ensure that there are enough starting DNA for library construction. Two biological replicates were prepared and sequenced for each ChIP-seq experiment. The ChIP DNA was first tested by qRT-PCR and then used to prepare ChIP-seq libraries.
End repair, adaptor ligation, and amplification were carried out using the Illumina Genomic DNA Sample Prep kit according to the manufacturer's protocol.

tag: ecotype

value: 14 days old


title: MEC_1_H3K27ac


title: LDL1pro::LDL1:GFP_2

tag: antibody

value: anti-GFP antibody (ab290; ABCAM)


title: Human islets_palmitate_7days_rep3

source_name: pancreatic islets_7days


title: LEC_2_Input

source_name: Adult (P56) cortical tissue

value: lateral entorhinal cortex (LEC)


title: Control NB4, 96 h

description:
SI-077
NB4 VvsV, 96 h


title: LEC_2_H3K4me2


title: CelSeq2_Mixture 383 samples

city: Melbourne

first: Shian

last: Su

state: Victoria

address: 1G Royal Parade

department: Molecular Medicine

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: gene counting matrix, rows repsent genes and each column is a well

molecule: polyA RNA

source_name: lung adenocarcinoma

growth_protocol: The human lung adenocarcinoma cell lines H2228, H1975 and HCC827 were retrieved from ATCC (https://www.atcc.org/) and cultured in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% fetal calf serum (FCS) and 1% Penicillin-Streptomycin.  The cells were grown independently at 37C  with 5% carbon dioxide until near 100% confluency.

extract_protocol:
For the three cell lines, cells were dissociated into single cell suspensions in FACS buffer and sorted for 9-cell-mixture and single cell experiment (see below for sorting strategy).   The remaining cells were centrifuged and frozen at -80C for later RNA extraction. The RNA was then extracted using a Qiagen RNA miniprep kit. The amount of RNA was quantified using both Invitrogen Qubit fluorometric quantitation and an Agilent 4200 bioanalyzer to get an accurate estimation. The extracted RNA was then diluted to 60 ng\ul and then mixed in different proportions, according to the study design. The different mixtures were further diluted to create an RNA series that ranged from 3.75pg to 30pg that was dispensed into CEL-seq2 and SORT-seq primer plates using a Nanodrop II dispenser. Prepared RNA mixture plates were sealed and immediately frozen upside down at -80C.
For CEL-seq2, Single cells were flow sorted into chilled 384-well PCR plates containing 1.2ul of primer/ERCC mix using a BD FACSAria III flow cytometer. Sorted plates were sealed and immediately frozen upside down at -80C. Then these plates, together with the mRNA mixture plates, were taken from -80C and processed using an adapted Cel-Seq2 protocol with the following variations. The second strand synthesis was performed using NEBNext Second Strand Synthesis module in a final reaction volume of 8 ul and NucleoMag NGS Clean-up and Size select magnetic beads were used for all DNA purification and size selection steps. For the 9-cell-mixture plates, clean up of the PCR product was performed with 2X0.7-0.9 bead/DNA ratio. For the single cell and mRNA mixture plates, two different clean up ratios for the PCR product were used (0.8 followed by 0.9). The choice of clean-up ratio was optimized from the QC results of the 9-cell-mixture data and the SORT-seq protocols.

value: lung adenocarcinoma cells


title: LEC_1_Input


title: LEC_2_H3K27ac


title: LEC_1_H3K4me2


title: LEC_1_H3K27ac


title: Control NB4, 24 h

description:
SI-077
NB4 VvsV, 24 h


title: ACC_2_Input

value: anterior cingulate cortex (ACC)


title: ACC_1_Input


title: ACC_2_H3K27ac


title: ACC_2_H3K4me2


title: ACC_1_H3K4me2


title: LDL1pro::LDL1:GFP_1


title: Control HL60, 96 h

description:
SI-093
HL60 VvsV, 96 h

source_name: HL60-vehicle treated-96h


title: ACC_1_H3K27ac


title: Treatment HL60, 96 h

description:
SI-093
HL60 TvsV, 96 h

source_name: HL60-ORY-1001 treated-96h


title: Treatment KG1, 96 h

description:
SI-107
KG1 TvsV, 96 h

source_name: KG1-ORY-1001 treated-96h

growth_protocol: cells were grown in IMDM plus 20% FBS

value: Acute Myelogenous Leukemia

value: Myeloblast, macrophage

source_name: KG1-vehicle treated-96h


title: Control KG1, 96 h

description:
SI-107
KG1 VvsV, 96 h


title: TAPG CNA cohort patient 107

status: Public on Aug 18 2018

type: genomic

city: New York

first: Haley

last: Hieronymus

state: New York

address: 1275 York Ave.

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: Per manufacturer's instructions.

scan_protocol: Per manufacturer's instructions.

data_processing: GC-normalized

source_name: Primary prostate cancer from TAPG CNA cohort patient 107

label_protocol: Random primed (Bioprime, Invitrogen) and labeled according to manufacturer's instructions.

extract_protocol: FFPE DNA was extracted using Agilent recommended protocol followed by clean-up by Qiagen column.

value: primary prostate cancer

tag: disease status

value: prostate cancer

source_name: Promega male reference DNA from pooled normal tissue

extract_protocol: Promega

value: pooled tissues

value: normal

tag: sample type

value: reference


title: Control KG1a, 96 h

description:
SI-107
KG1a VvsV, 96 h

source_name: KG1a-vehicle treated-96h

value: Promyeloblast, macrophage


title: Treatment KG1a, 96 h

description:
SI-107
KG1a TvsV, 96 h

source_name: KG1a-ORY-1001 treated-96h


title: TAPG CNA cohort patient 97

source_name: Primary prostate cancer from TAPG CNA cohort patient 97


title: TAPG CNA cohort patient 93

source_name: Primary prostate cancer from TAPG CNA cohort patient 93


title: TAPG CNA cohort patient 88

source_name: Primary prostate cancer from TAPG CNA cohort patient 88


title: TAPG CNA cohort patient 99

source_name: Primary prostate cancer from TAPG CNA cohort patient 99


title: TAPG CNA cohort patient 95

source_name: Primary prostate cancer from TAPG CNA cohort patient 95


title: TAPG CNA cohort patient 102

source_name: Primary prostate cancer from TAPG CNA cohort patient 102


title: TAPG CNA cohort patient 106

source_name: Primary prostate cancer from TAPG CNA cohort patient 106


title: TAPG CNA cohort patient 86

source_name: Primary prostate cancer from TAPG CNA cohort patient 86


title: TAPG CNA cohort patient 98

source_name: Primary prostate cancer from TAPG CNA cohort patient 98


title: TAPG CNA cohort patient 90

source_name: Primary prostate cancer from TAPG CNA cohort patient 90


title: TAPG CNA cohort patient 105

source_name: Primary prostate cancer from TAPG CNA cohort patient 105


title: TAPG CNA cohort patient 96

source_name: Primary prostate cancer from TAPG CNA cohort patient 96


title: TAPG CNA cohort patient 92

source_name: Primary prostate cancer from TAPG CNA cohort patient 92


title: TAPG CNA cohort patient 89

source_name: Primary prostate cancer from TAPG CNA cohort patient 89


title: TAPG CNA cohort patient 101

source_name: Primary prostate cancer from TAPG CNA cohort patient 101

source_name: Promega male reference DNA from pooled normal tissue


title: TAPG CNA cohort patient 87

source_name: Primary prostate cancer from TAPG CNA cohort patient 87


title: TAPG CNA cohort patient 94

source_name: Primary prostate cancer from TAPG CNA cohort patient 94


title: TAPG CNA cohort patient 100

source_name: Primary prostate cancer from TAPG CNA cohort patient 100


title: TAPG CNA cohort patient 103

source_name: Primary prostate cancer from TAPG CNA cohort patient 103


title: Healthy volunteer TST/QTF conversion after 540 days [8381688026_L]

city: Cleveland

first: Rafick-Pierre

last: Sekaly

state: OH

address: 2103 Cornell Rd. 5129 WRB

department: Pathology

institute: Case Western Reserve University

description:
8381688026_L
Healthy volunteer TST/QTF conversion after 540 days

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Normalization was performed directly from the IDAT files using the R programming language with the lumi and immuminaio packages.

source_name: Whole Blood PAXgene

label_protocol: A Biotin-16-UTP label was incorporated into amplified RNA during the in vitro transcription process (Perkin Elmer Life and Analytical Sciences, Woodbridge, Ontario, Canada). Amplification gave yields ranging from 1 μg to 25 μg.

extract_protocol: Gene expression microarrays were undertaken using whole blood samples collected in PAXgene tubes. The Illumina RNA Amplification Kit (Ambion, Austin, TX, USA) was used to amplify a median of 124 ng (range 63–174 ng) of the extracted RNA.

value: blood

tag: draw day

tag: patientid

tag: latent tb status at blood draw

value: TRUE

tag: time of conversion (days)

tag: relative time from conversion (days)


title: TAPG CNA cohort patient 85

source_name: Primary prostate cancer from TAPG CNA cohort patient 85


title: TAPG CNA cohort patient 104

source_name: Primary prostate cancer from TAPG CNA cohort patient 104


title: Healthy volunteer TST/QTF conversion after 360 days [8381688026_K]

description:
8381688026_K
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 61

source_name: Primary prostate cancer from TAPG CNA cohort patient 61


title: TAPG CNA cohort patient 59

source_name: Primary prostate cancer from TAPG CNA cohort patient 59


title: TAPG CNA cohort patient 58

source_name: Primary prostate cancer from TAPG CNA cohort patient 58


title: TAPG CNA cohort patient 91

source_name: Primary prostate cancer from TAPG CNA cohort patient 91


title: Healthy volunteer TST/QTF conversion after 540 days [8381688026_I]

description:
8381688026_I
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381688026_J]

description:
8381688026_J
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 62

source_name: Primary prostate cancer from TAPG CNA cohort patient 62


title: TAPG CNA cohort patient 57

source_name: Primary prostate cancer from TAPG CNA cohort patient 57


title: TAPG CNA cohort patient 60

source_name: Primary prostate cancer from TAPG CNA cohort patient 60


title: TAPG CNA cohort patient 56

source_name: Primary prostate cancer from TAPG CNA cohort patient 56


title: TAPG CNA cohort patient 55

source_name: Primary prostate cancer from TAPG CNA cohort patient 55


title: TAPG CNA cohort patient 53

source_name: Primary prostate cancer from TAPG CNA cohort patient 53

source_name: Promega male reference DNA from pooled normal tissue


title: TAPG CNA cohort patient 54

source_name: Primary prostate cancer from TAPG CNA cohort patient 54


title: Healthy volunteer TST/QTF conversion after 360 days [8381688026_G]

description:
8381688026_G
Healthy volunteer TST/QTF conversion after 360 days

value: FALSE


title: Healthy volunteer TST/QTF conversion after 360 days [8381688026_A]

description:
8381688026_A
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381688026_D]

description:
8381688026_D
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381688026_H]

description:
8381688026_H
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381653006_L]

description:
8381653006_L
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 52

source_name: Primary prostate cancer from TAPG CNA cohort patient 52


title: Healthy volunteer TST/QTF conversion after 180 days [8381653006_K]

description:
8381653006_K
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 47

source_name: Primary prostate cancer from TAPG CNA cohort patient 47


title: TAPG CNA cohort patient 48

source_name: Primary prostate cancer from TAPG CNA cohort patient 48


title: TAPG CNA cohort patient 49

source_name: Primary prostate cancer from TAPG CNA cohort patient 49


title: TAPG CNA cohort patient 50

source_name: Primary prostate cancer from TAPG CNA cohort patient 50


title: TAPG CNA cohort patient 46

source_name: Primary prostate cancer from TAPG CNA cohort patient 46


title: TAPG CNA cohort patient 51

source_name: Primary prostate cancer from TAPG CNA cohort patient 51


title: Healthy volunteer TST/QTF conversion after 720 days [8381653006_G]

description:
8381653006_G
Healthy volunteer TST/QTF conversion after 720 days

source_name: Whole Blood PAXgene


title: Healthy volunteer TST/QTF conversion after 360 days [8381653006_I]

description:
8381653006_I
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381653006_H]

description:
8381653006_H
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 45

source_name: Primary prostate cancer from TAPG CNA cohort patient 45


title: TAPG CNA cohort patient 43

source_name: Primary prostate cancer from TAPG CNA cohort patient 43


title: TAPG CNA cohort patient 41

source_name: Primary prostate cancer from TAPG CNA cohort patient 41


title: Healthy volunteer TST/QTF conversion after 360 days [8381653006_J]

description:
8381653006_J
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 42

source_name: Primary prostate cancer from TAPG CNA cohort patient 42


title: TAPG CNA cohort patient 44

source_name: Primary prostate cancer from TAPG CNA cohort patient 44


title: TAPG CNA cohort patient 40

source_name: Primary prostate cancer from TAPG CNA cohort patient 40


title: Healthy volunteer TST/QTF conversion after 720 days [8381653006_D]

description:
8381653006_D
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381653006_C]

description:
8381653006_C
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381688026_E]

description:
8381688026_E
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 360 days [8292044004_L]

description:
8292044004_L
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381653006_F]

description:
8381653006_F
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381653006_E]

description:
8381653006_E
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 180 days [8292044004_K]

description:
8292044004_K
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381653006_B]

description:
8381653006_B
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381688026_B]

description:
8381688026_B
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 180 days [8292044004_I]

description:
8292044004_I
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 33

source_name: Primary prostate cancer from TAPG CNA cohort patient 33


title: TAPG CNA cohort patient 37

source_name: Primary prostate cancer from TAPG CNA cohort patient 37

source_name: Promega male reference DNA from pooled normal tissue


title: TAPG CNA cohort patient 38

source_name: Primary prostate cancer from TAPG CNA cohort patient 38


title: TAPG CNA cohort patient 39

source_name: Primary prostate cancer from TAPG CNA cohort patient 39


title: TAPG CNA cohort patient 34

source_name: Primary prostate cancer from TAPG CNA cohort patient 34


title: TAPG CNA cohort patient 36

source_name: Primary prostate cancer from TAPG CNA cohort patient 36


title: Healthy volunteer TST/QTF conversion after 180 days [8292044004_J]

description:
8292044004_J
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 35

source_name: Primary prostate cancer from TAPG CNA cohort patient 35


title: TAPG CNA cohort patient 32

source_name: Primary prostate cancer from TAPG CNA cohort patient 32


title: Healthy volunteer TST/QTF conversion after 540 days [8292044004_H]

description:
8292044004_H
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 540 days [8292044004_G]

description:
8292044004_G
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 720 days [8292044004_F]

description:
8292044004_F
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 360 days [8292044004_E]

description:
8292044004_E
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 540 days [8292044004_B]

description:
8292044004_B
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 180 days [8292044004_D]

description:
8292044004_D
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 720 days [8292044004_C]

description:
8292044004_C
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 29

source_name: Primary prostate cancer from TAPG CNA cohort patient 29


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_L]

description:
8381645096_L
Healthy volunteer TST/QTF conversion after 360 days

source_name: Whole Blood PAXgene


title: TAPG CNA cohort patient 28

source_name: Primary prostate cancer from TAPG CNA cohort patient 28


title: Healthy volunteer TST/QTF conversion after 360 days [8381688026_F]

description:
8381688026_F
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_K]

description:
8381645096_K
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 30

source_name: Primary prostate cancer from TAPG CNA cohort patient 30


title: TAPG CNA cohort patient 23

source_name: Primary prostate cancer from TAPG CNA cohort patient 23


title: TAPG CNA cohort patient 26

source_name: Primary prostate cancer from TAPG CNA cohort patient 26


title: TAPG CNA cohort patient 27

source_name: Primary prostate cancer from TAPG CNA cohort patient 27


title: Healthy volunteer TST/QTF conversion after 180 days [8292044004_A]

description:
8292044004_A
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381688026_C]

description:
8381688026_C
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 31

source_name: Primary prostate cancer from TAPG CNA cohort patient 31


title: TAPG CNA cohort patient 25

source_name: Primary prostate cancer from TAPG CNA cohort patient 25


title: TAPG CNA cohort patient 22

source_name: Primary prostate cancer from TAPG CNA cohort patient 22


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_H]

description:
8381645096_H
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 24

source_name: Primary prostate cancer from TAPG CNA cohort patient 24

source_name: Promega male reference DNA from pooled normal tissue


title: Healthy volunteer TST/QTF conversion after 180 days [8381645096_I]

description:
8381645096_I
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645096_J]

description:
8381645096_J
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 84

source_name: Primary prostate cancer from TAPG CNA cohort patient 84


title: TAPG CNA cohort patient 83

source_name: Primary prostate cancer from TAPG CNA cohort patient 83


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_F]

description:
8381645096_F
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 21

source_name: Primary prostate cancer from TAPG CNA cohort patient 21


title: Healthy volunteer TST/QTF conversion after 720 days [8381645096_E]

description:
8381645096_E
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645096_G]

description:
8381645096_G
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 20

source_name: Primary prostate cancer from TAPG CNA cohort patient 20


title: TAPG CNA cohort patient 82

source_name: Primary prostate cancer from TAPG CNA cohort patient 82


title: Healthy volunteer TST/QTF conversion after 180 days [8381645096_C]

description:
8381645096_C
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 81

source_name: Primary prostate cancer from TAPG CNA cohort patient 81


title: TAPG CNA cohort patient 19

source_name: Primary prostate cancer from TAPG CNA cohort patient 19


title: TAPG CNA cohort patient 80

source_name: Primary prostate cancer from TAPG CNA cohort patient 80


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_D]

description:
8381645096_D
Healthy volunteer TST/QTF conversion after 360 days

source_name: Whole Blood PAXgene


title: Healthy volunteer TST/QTF conversion after 180 days [8381645095_L]

description:
8381645095_L
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645096_B]

description:
8381645096_B
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381645096_A]

description:
8381645096_A
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 18

source_name: Primary prostate cancer from TAPG CNA cohort patient 18


title: TAPG CNA cohort patient 78

source_name: Primary prostate cancer from TAPG CNA cohort patient 78


title: TAPG CNA cohort patient 79

source_name: Primary prostate cancer from TAPG CNA cohort patient 79


title: TAPG CNA cohort patient 17

source_name: Primary prostate cancer from TAPG CNA cohort patient 17


title: TAPG CNA cohort patient 16

source_name: Primary prostate cancer from TAPG CNA cohort patient 16


title: Healthy volunteer TST/QTF conversion after 180 days [8381645095_G]

description:
8381645095_G
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 77

source_name: Primary prostate cancer from TAPG CNA cohort patient 77


title: Healthy volunteer TST/QTF conversion after 360 days [8381645095_J]

description:
8381645095_J
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645095_I]

description:
8381645095_I
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645095_K]

description:
8381645095_K
Healthy volunteer TST/QTF conversion after 540 days


title: TAPG CNA cohort patient 15

source_name: Primary prostate cancer from TAPG CNA cohort patient 15


title: Healthy volunteer TST/QTF conversion after 540 days [8381645095_E]

description:
8381645095_E
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645095_H]

description:
8381645095_H
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 14

source_name: Primary prostate cancer from TAPG CNA cohort patient 14

source_name: Promega male reference DNA from pooled normal tissue


title: TAPG CNA cohort patient 76

source_name: Primary prostate cancer from TAPG CNA cohort patient 76


title: TAPG CNA cohort patient 75

source_name: Primary prostate cancer from TAPG CNA cohort patient 75


title: Healthy volunteer TST/QTF conversion after 360 days [8381645095_D]

description:
8381645095_D
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645095_C]

description:
8381645095_C
Healthy volunteer TST/QTF conversion after 540 days


title: TAPG CNA cohort patient 74

source_name: Primary prostate cancer from TAPG CNA cohort patient 74


title: Healthy volunteer TST/QTF conversion after 180 days [8381645095_A]

description:
8381645095_A
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645095_B]

description:
8381645095_B
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645095_F]

description:
8381645095_F
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 12

source_name: Primary prostate cancer from TAPG CNA cohort patient 12


title: TAPG CNA cohort patient 13

source_name: Primary prostate cancer from TAPG CNA cohort patient 13


title: Healthy volunteer TST/QTF conversion after 540 days [8381645088_L]

description:
8381645088_L
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381645088_K]

description:
8381645088_K
Healthy volunteer TST/QTF conversion after 180 days


title: TAPG CNA cohort patient 73

source_name: Primary prostate cancer from TAPG CNA cohort patient 73


title: Healthy volunteer TST/QTF conversion after 540 days [8381645088_G]

description:
8381645088_G
Healthy volunteer TST/QTF conversion after 540 days


title: TAPG CNA cohort patient 72

source_name: Primary prostate cancer from TAPG CNA cohort patient 72


title: Healthy volunteer TST/QTF conversion after 360 days [8381645088_J]

description:
8381645088_J
Healthy volunteer TST/QTF conversion after 360 days

source_name: Whole Blood PAXgene


title: TAPG CNA cohort patient 70

source_name: Primary prostate cancer from TAPG CNA cohort patient 70


title: TAPG CNA cohort patient 71

source_name: Primary prostate cancer from TAPG CNA cohort patient 71


title: TAPG CNA cohort patient 11

source_name: Primary prostate cancer from TAPG CNA cohort patient 11


title: TAPG CNA cohort patient 10

source_name: Primary prostate cancer from TAPG CNA cohort patient 10


title: TAPG CNA cohort patient 8

source_name: Primary prostate cancer from TAPG CNA cohort patient 8


title: TAPG CNA cohort patient 69

source_name: Primary prostate cancer from TAPG CNA cohort patient 69


title: Healthy volunteer TST/QTF conversion after 720 days [8381645088_C]

description:
8381645088_C
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645088_E]

description:
8381645088_E
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645088_D]

description:
8381645088_D
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645088_F]

description:
8381645088_F
Healthy volunteer TST/QTF conversion after 720 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645088_I]

description:
8381645088_I
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 180 days [8381645088_H]

description:
8381645088_H
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 720 days [8381645078_K]

description:
8381645078_K
Healthy volunteer TST/QTF conversion after 720 days


title: TAPG CNA cohort patient 7

source_name: Primary prostate cancer from TAPG CNA cohort patient 7


title: TAPG CNA cohort patient 9

source_name: Primary prostate cancer from TAPG CNA cohort patient 9


title: TAPG CNA cohort patient 68

source_name: Primary prostate cancer from TAPG CNA cohort patient 68

source_name: Promega male reference DNA from pooled normal tissue


title: TAPG CNA cohort patient 5

source_name: Primary prostate cancer from TAPG CNA cohort patient 5


title: Healthy volunteer TST/QTF conversion after 360 days [8381645088_A]

description:
8381645088_A
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 540 days [8381645088_B]

description:
8381645088_B
Healthy volunteer TST/QTF conversion after 540 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_I]

description:
8381645078_I
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 6

source_name: Primary prostate cancer from TAPG CNA cohort patient 6


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_J]

description:
8381645078_J
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_L]

description:
8381645078_L
Healthy volunteer TST/QTF conversion after 360 days


title: TAPG CNA cohort patient 4

source_name: Primary prostate cancer from TAPG CNA cohort patient 4


title: TAPG CNA cohort patient 67

source_name: Primary prostate cancer from TAPG CNA cohort patient 67


title: TAPG CNA cohort patient 66

source_name: Primary prostate cancer from TAPG CNA cohort patient 66


title: Healthy volunteer TST/QTF conversion after 180 days [8381645078_G]

description:
8381645078_G
Healthy volunteer TST/QTF conversion after 180 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_H]

description:
8381645078_H
Healthy volunteer TST/QTF conversion after 360 days


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_D]

description:
8381645078_D
Healthy volunteer TST/QTF conversion after 360 days


title: SKMel-239_SIRT6.1-1_ATACseq

first: Emily

last: Bernstein

state: NY

address: 1470 Madison Avenue, 6th floor Rm 302

department: Oncological Sciences

institute: Mount Sinai School of Medicine

description: BRAF metastatic melanoma

data_processing:
Native ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10
XL ChIP-seq: Reads were trimmed from Illumina adapters using in-house script. Reads were aligned using Bowtie (version 0.12.7) with parameters –l 65 –n 2 –S –best –k 1 –m 20. BAM files were generated using SAMtools. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters -f BAM -g 2.7e9 -s 100 -q0.0005 --keep-dup 1.
ATAC-seq: Reads were trimmed from Illumina adapters using in-house script. Reads (75bp Paired-end) were aligned using Bowtie2 (version  2.1.0) with parameters -q -X 2000. BAM files were generated using SAMtools. Reads that align to mtDNA, with quality value Q<30, as well as duplicated reads, were discarded using in-house scripts and Samtools.. bigwig files were generated from BAM files using deepTools bamCoverage (version 2.4.1) with parameters –normalizeUsingRPKM –binsize 10. Significant peaks were called using MACS2 callpeak (version 2.1.1.2) with parameters –nomodel –nolambda –keepdup all –slocal 10000
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: fastq - raw illumina reads. bigwig - aligned reads pileup. csv - gene expression using Voom normalized raw counts

source_name: Cell culture

extract_protocol:
All ATAC-seq libraries were prepared essentially as previously described with modifications43. Briefly, 50k cells were resuspended in 1mL of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). After centrifugation, cell pellets were resuspended in 50 µL of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. This cell lysis reaction was incubated on ice for 3 min. Nuclei were isolated using 1 mL of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) and centrifugation. Nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer43, 2.5 μl transposase44 (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking. Reactions were cleaned up with Qiagen miniElute PCR Purification columns. ATAC-seq libraries were PCR amplified with 5 to 7 cycles, size selected (100-800bp), and purified using XPure magnetic beads45. Libraries were sequenced on NextSeq500 (75bp paired-end reads). Reads were aligned to the GRCh37/hg19 using Bowtie2 (version 2.1.0) with parameters –S –X 200046. Reads aligned to mtDNA, with quality value Q < 30, as well as duplicated reads, were removed using in-house scripts and Samtools. Significant peaks were identified using MACS2 with parameters –nomodel –nolambda –keepdup all –slocal 10000. Coverage tracks were generated using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10.
All ATAC-seq libraries were prepared essentially as previously described with modifications43. Briefly, 50k cells were resuspended in 1mL of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). After centrifugation, cell pellets were resuspended in 50 µL of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin. This cell lysis reaction was incubated on ice for 3 min. Nuclei were isolated using 1 mL of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) and centrifugation. Nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer43, 2.5 μl transposase44 (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water). Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking. Reactions were cleaned up with Qiagen miniElute PCR Purification columns. ATAC-seq libraries were PCR amplified with 5 to 7 cycles, size selected (100-800bp), and purified using XPure magnetic beads45. Libraries were sequenced on NextSeq500 (75bp paired-end reads). Reads were aligned to the GRCh37/hg19 using Bowtie2 (version 2.1.0) with parameters –S –X 200046. Reads aligned to mtDNA, with quality value Q < 30, as well as duplicated reads, were removed using in-house scripts and Samtools. Significant peaks were identified using MACS2 with parameters –nomodel –nolambda –keepdup all –slocal 10000. Coverage tracks were generated using deepTools bamCoverage with parameters –normalizeUsingRPKM –binsize 10.

treatment_protocol: untreated

tag: growth protocol

value: grown in RPMI supplemented with 10% FBS, penicillin and streptomycin.

tag: experiment

value: ATAC-seq


title: TAPG CNA cohort patient 3

source_name: Primary prostate cancer from TAPG CNA cohort patient 3


title: Healthy volunteer TST/QTF conversion after 180 days [8381645078_C]

description:
8381645078_C
Healthy volunteer TST/QTF conversion after 180 days

source_name: Whole Blood PAXgene


title: TAPG CNA cohort patient 65

source_name: Primary prostate cancer from TAPG CNA cohort patient 65


title: myb-1 RNAi intact animals 2

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

description:
3 RNAi feeds, RNA extracted 6 days after last feed
myb-1(RNAi) counts 2

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Differentially expressed genes were identified by DESeq2 analysis
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt
Supplementary_files_format_and_content: Excel, raw CPM and DeSeq2 output

organism: Schmidtea mediterranea

source_name: Wildtype animals (30 animals)

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to starting RNAi treatment.

extract_protocol:
All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
RNA-seq.  Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: control(RNAi) and Smed-myb-1(RNAi) animals were fed 3 times over 1 week. RNA was collected 6 days after the last feed. Samples were sequenced to a depth of >40 million reads.  Each condition was biologically triplicated.

value: Asexual CIW12

value: All  Tissues

tag: treatment

value: myb-1 RNAi


title: myb-1 RNAi intact animals 1

description:
3 RNAi feeds, RNA extracted 6 days after last feed
myb-1(RNAi) counts 1

value: Asexual CIW10

tag: tissue


title: TAPG CNA cohort patient 1

source_name: Primary prostate cancer from TAPG CNA cohort patient 1


title: myb-1 RNAi intact animals 3

description:
3 RNAi feeds, RNA extracted 6 days after last feed
myb-1(RNAi) counts 3

value: Asexual CIW14


title: TAPG CNA cohort patient 63

source_name: Primary prostate cancer from TAPG CNA cohort patient 63


title: CelSeq2_SC_383_Samples

description: single cell from a mixed pool of H2228, H1975 and HCC827 cell lines

source_name: lung adenocarcinoma

treatment_protocol: For the three cell lines, cells were dissociated into single cell suspensions in FACS buffer and sorted for 9-cell-mixture and single cell experiment (see below for sorting strategy).   The remaining cells were centrifuged and frozen at -80C for later RNA extraction. The RNA was then extracted using a Qiagen RNA miniprep kit. The amount of RNA was quantified using both Invitrogen Qubit fluorometric quantitation and an Agilent 4200 bioanalyzer to get an accurate estimation. The extracted RNA was then diluted to 60 ng\ul and then mixed in different proportions, according to the study design. The different mixtures were further diluted to create an RNA series that ranged from 3.75pg to 30pg that was dispensed into CEL-seq2 and SORT-seq primer plates using a Nanodrop II dispenser. Prepared RNA mixture plates were sealed and immediately frozen upside down at -80C.

tag: umi position

value: Bases 1 to 6 on R1

tag: barcode position

value: Bases 7 to 14 on R1

tag: cell type


title: NN86_SC_Dropseq_Mixture

description: Mixture of single cells from H2228, H1975 and HCC827 human lung adenocarcinoma cell lines

data_processing:
gene counting matrix generated using scPipe 1.3.0
reads were aligned using Rsubread 1.29.6
Genome_build: ENSEMBL Homo_sapiens.GRCh38.88
Supplementary_files_format_and_content: dropseq_gene_count.csv: gene counting matrix, rows repsent genes and each column is a well
Supplementary_files_format_and_content: index_anno.csv: top 4000 most abundant barcode sequences detected, with the number of times they are detected

value: mixture of cell lines H2228, H1975 and HCC827

value: Bases 1 to 12 on R1

value: Bases 13 to 20 on R1


title: unc22 RNAi intact animals 3

description:
3 RNAi feeds, RNA extracted 6 days after last feed
control(RNAi) counts 3

tag: strain

value: Asexual CIW8

value: control RNAi


title: Healthy volunteer TST/QTF conversion after 540 days [8381645078_F]

description:
8381645078_F
Healthy volunteer TST/QTF conversion after 540 days

value: blood


title: TAPG CNA cohort patient 2

source_name: Primary prostate cancer from TAPG CNA cohort patient 2

value: primary prostate cancer

value: prostate cancer

value: pooled tissues

value: normal

value: reference


title: SKMel-239_SIRT6.1-1_H3K27ac

description: BRAF metastatic melanoma

extract_protocol:
Native ChIP was done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: grown in RPMI supplemented with 10% FBS, penicillin and streptomycin.

tag: antibodies

value: H3K27ac (Abcam, ab4729)


title: unc22 RNAi intact animals 1

description:
3 RNAi feeds, RNA extracted 6 days after last feed
control(RNAi) counts 1

value: Asexual CIW4

value: All  Tissues


title: SKMel-239_SIRT6.1-1_SIRT6

description: BRAF metastatic melanoma

extract_protocol:
For SIRT6, 50x10^6 cells, were crosslinked with 0.4% PFA for 10 min at RT. ChIP was performed essentially as previously described (Roe, J.S., et al., BET Bromodomain Inhibition Suppresses the Function of Hematopoietic Transcription Factors in Acute Myeloid Leukemia. Mol Cell, 2015. 58(6): p. 1028-39).
Libraries for ChIP-seq were done as previously described (Hasson D., et al., The octamer is the major form of CENP-A nucleosomes at human centromeres. Nat Struct Mol Biol. 2013 Jun;20(6):687-95).

value: SIRT6 (Abcam, ab62739)


title: unc22 RNAi intact animals 2

description:
3 RNAi feeds, RNA extracted 6 days after last feed
control(RNAi) counts 2

value: Asexual CIW6


title: SKMel-239_SIRT6.1-1_H3K56ac

description: BRAF metastatic melanoma

value: H3K56ac (Abcam, ab76307)


title: SKMel-239_SIRT6.1-1_H3K9ac

description: BRAF metastatic melanoma

value: H3K9ac (Abcam, ab10812)


title: Healthy volunteer TST/QTF conversion after 360 days [8381645078_E]

description:
8381645078_E
Healthy volunteer TST/QTF conversion after 360 days

value: TRUE


title: A177-5

city: Cambridge

first: Yrjö

last: Helariutta

address: 47 Bateman Street,

department: Sainsbury Laboratory

country: United Kingdom

institute: University of Cambridge

data_processing:
Quality filtering was performed using cutadapt 1.16 with the following non-default options: '--trim-n --quality-cutoff 20 --minimum-length 30 --max-n 0'.
Transcript abundance was estimated using salmon 0.9.1 in 'quant' mode with options '--seqBias --posBias'.
Salmon transcript counts were used for differential expression analysis using DESeq2. Analysis scripts available at: https://github.com/JIC-Enrico-Coen/antirrhinum-ros-analysis
Genome_build: Antirrhinum majus v1 http://bioinfo.sibs.ac.cn/am/
http://bioinfo.sibs.ac.cn/Am/download_v2.php, snapdragon.IGDBv1_mapped_to_JICv1.gff2, snapdragon.chr.IGDBv1.transcript.beta.fa
Supplementary_files_format_and_content: tab-delimited salmon transcript count files

organism: Antirrhinum majus

source_name: corolla from flower bud 5-10mm long

growth_protocol: Plants were grown together on outside benches at the John Innes Centre

extract_protocol:
The corolla of a 5-10mm flower bud was collected from each plant and immediately placed on dry-ice, after which it was stored at -80°C until RNA extraction. For RNA extraction, the tissue was disrupted using a TissueLyser (Qiagen) before extraction with the RNeasy Plant Mini Kit (Qiagen), following the manufacturer' protocol and including on-column DNase digestion. Samples were stored at -80°C until use.
Illumina Truseq 50bp single-end libraries

value: corolla (plant ontology term PO:0009059)

tag: flower development stage

value: stage 12-13 (see Vincent & Coen https://doi.org/10.1139/b04-042)

tag: coen lab plant id

tag: ros genotype

value: recombinant allele with upstream from A. m. striatum and downstream from A. m. pseudomajus

tag: el genotype

value: recessive allele from A. m. pseudomajus

tag: corolla phenotype

value: pale


title: TAPG CNA cohort patient 64

source_name: Primary prostate cancer from TAPG CNA cohort patient 64

value: primary prostate cancer

tag: disease status

value: prostate cancer

value: pooled tissues

tag: sample type


title: A177-20


title: A177-9


title: A182-17

value: recessive allele from A. m. striatum

value: dominant allele from A. m. striatum

value: white


title: A174-4

value: dominant allele from A. m. pseudomajus

value: eluta


title: A182-28


title: SKMel-239_SIRT6.1-1_H3K4me3

description: BRAF metastatic melanoma

value: grown in RPMI supplemented with 10% FBS, penicillin and streptomycin.

value: H3K4me3 (Abcam, ab1012)


title: SKMel-239_SIRT6.1-1_H3K4me1

description: BRAF metastatic melanoma

value: H3K4me1 (Abcam, ab8895)


title: A174-12


title: SKMel-239_L-C-B_ATACseq

description: BRAF metastatic melanoma

value: ATAC-seq


title: A174-28

value: corolla (plant ontology term PO:0009059)


title: A181-10

value: stage 12-13 (see Vincent & Coen https://doi.org/10.1139/b04-042)

value: magenta


title: Rat_Brain_Beef_Nitrate_7

city: Baltimore

first: Robert

last: Yolken

state: MD

address: 600 N Wolfe st

institute: Johns Hopkins

description: Sample 27

hyb_protocol: 17hrs at 45° C with rotation (60rpm) as described by Affymetrix in their GeneChip Expression Analysis Technical Manual.

scan_protocol: Using Affymetrix’ GeneChip Scanner 3000 7G and default parameters described by the manufacturer in their GeneChip Expression Analysis Technical Manual.

data_processing:
Affymetrix CEL files were extracted with the Partek GS 6.6 platform and their data RMA and quantile-normalized to create log2 transcript signal values, which were used in subsequent ANOVA analyses.    Transcript annotation was subsequently updated.
probe group file: Clariom_S_Rat.r1.pgf
meta-probeset file: Clariom_S_Rat.na36.rn6.transcript.csv

organism: Rattus norvegicus

label_protocol: The Affymetrix GeneChip 3' IVT Pico Kit was used according to the manufacturer's protocol in the JHMI DeepSequencing & Microarray Core facility.

growth_protocol: adult male Sprague-Dawley rats were randomly divided into 2 weight-matched groups following 1 week of habituation and provided ad libitum access to one of the diets listed below

extract_protocol: Rats were killed via rapid decapitation on day 35 of dietary exposure in the middle of the light cycle, with order of sacrifice alternated between experimental groups. Brains were removed and divided along the midsagittal plane. The left hemisphere of the brain was immediately frozen on powdered dry ice and then stored at -80oC. The right hemisphere was further fresh dissected to remove the right whole hippocampus, which was immediately frozen in liquid nitrogen and stored at -80oC for microarray analysis.  RNA extraction utilized the QIAGEN RNeasy Kit following manufacturer's protocol.

treatment_protocol: Animals were treated with one of two diets: 1) a modified isocaloric AIN-93M 35% kcal protein beef diet (“ChowAIN+Beef” group, n=10), 2) a modified isocaloric AIN-93M beef and nitrate diet with sodium nitrate added.

value: Sprague-Dawley

tag: age

value: adult

tag: Sex

value: male

tag: diet

value: brain; hippocampus


title: A182-8


title: Rat_Brain_Beef_Nitrate_10

description: Sample 39

value: AIN-93M beef and nitrate diet with sodium nitrate added


title: A182-27

value: recessive allele from A. majus stock line rosea-dorsea


title: SKMel-239_SIRT6.2-7_ATACseq

description: BRAF metastatic melanoma

tag: growth protocol

tag: experiment


title: Rat_Brain_Beef_Nitrate_8

description: Sample 31

tag: tissue


title: A181-28

value: recessive allele from A. m. pseudomajus


title: Rat_Brain_Beef_Nitrate_9

description: Sample 35


title: A181-32

value: white


title: Rat_Brain_Beef_Nitrate_4

description: Sample 15


title: A181-23

value: dominant allele from A. m. pseudomajus


title: Rat_Brain_Beef_Nitrate_2

description: Sample 7


title: Rat_Brain_Beef_Nitrate_6

description: Sample 23


title: Rat_Brain_Beef_Nitrate_3

description: Sample 11


title: Rat_Brain_Beef_9

description: Sample 34

value: ChowAIN+Beef


title: NS5_Rep2

city: San Francisco

first: A.

middle: Jeremy

last: Willsey

state: CA

address: 675 Nelson Rising Lane

department: Psychiatry

institute: UCSF

data_processing:
library strategy: AmpliSeq
Ion Torrent Suite Sever v5.8.0 (Thermo Fisher) software used for basecalling.
coverageAnalysis plugin v5.8.0.8 with default settings was used to align reads to the hg19_AmpliSeq_Transcriptome_v1.1 reference and generate quality information (tmap mapall -q 50000 -f hg19_AmpliSeq_Transcriptome_v1.1.fasta -r Sample_1.fastq stage1 map4)
ampliSeqRNA plugin v5.8.0.3 with default settings was used for read quantification
Genome_build: hg19_AmpliSeq_Transcriptome_v1.1
Supplementary_files_format_and_content: csv files including read quantification and additional sample information for each sample

extract_protocol:
At 12 hours post-stimulation, total cellular RNA was purified by RNeasy column (Qiagen)
cDNA was synthesized using SuperScript IV VILO Master Mix with ezDNase Enzyme (Thermo Fisher). Libraries were generated with the Ion Ampliseq Transcriptome Human Gene Expression, Chef-Ready Kit (Life Technologies) recommended protocol, using 10ng of starting cDNA across all samples

treatment_protocol: A549 cells were transfected with GFP- or NS5-expressing plasmid using Polyjet (Signagen) according to manufacturer instructions, and 30 hours later stimulated with polyIC (Tocris) as previously described (Marazzi et al., 2012)

tag: cell line

tag: tissue source

value: Lung

value: Human Lung Adenocarcinoma

tag: genotype


title: NS5_polyIC_Rep2

tag: cell type

value: NS5 + polyIC


title: Rat_Brain_Beef_Nitrate_1

description: Sample 3

tag: strain


title: NS5_Rep1


title: NS5_polyIC_Rep1


title: Rat_Brain_Beef_10

description: Sample 38


title: GFP_polyIC_Rep2

value: GFP + polyIC


title: Rat_Brain_Beef_8

description: Sample 30


title: Rat_Brain_Beef_Nitrate_5

description: Sample 33


title: A172-19

value: corolla (plant ontology term PO:0009059)

tag: flower development stage

tag: coen lab plant id

value: dominant allele from A. majus stock line JI7

value: dominant allele from A. m. striatum

value: eluta


title: A172-16

value: stage 12-13 (see Vincent & Coen https://doi.org/10.1139/b04-042)

tag: ros genotype

tag: el genotype


title: Rat_Brain_Beef_7

description: Sample 26

value: Sprague-Dawley

value: adult

value: male


title: GFP_polyIC_Rep1


title: Rat_Brain_Beef_6

description: Sample 22

value: brain; hippocampus


title: A172-6

tag: corolla phenotype


title: GFP_Rep2

value: GFP


title: A183-26

value: recessive allele from A. majus stock line JI7

value: magenta


title: GFP_Rep1


title: Rat_Brain_Beef_2

description: Sample 6

value: ChowAIN+Beef


title: Rat_Brain_Beef_4

description: Sample 14


title: K562 NoAb ChIP-seq 1-step (alt ChIP-seq)

status: Public on Aug 17 2018

city: University Park

first: Matthew

middle: John

last: Rossi

state: Pennsylvania

address: 453 N Frear Bldg

department: Biochemistry & Molecular Biology

institute: Penn State University

description:
PSU10807
NoAb_K562_ChIP-seq1step_peaks.gff

data_processing:
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to sacCer3 or GRch37(hg19) genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: gff, peak pair calls filtered for significance over background

growth_protocol: Yeast cells were grown to an O.D600 of 0.8 - 1.0 at 25°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
Libraries were prepared for sequencing using standard Illumina protocols with modifications; Reference paper:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 1.0%.

tag: chip antibody

tag: cell description

value: Haematopoietic and lymphoid


title: Pol II ChIP-nexus (ChIP-exo 2.0)

description:
PSU09184
PolII_ChIP-exo2.0_peaks.gff

data_processing:
Library strategy: ChIP-exo
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to sacCer3 or GRch37(hg19) genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: sacCer3
Genome_build: GRch37/hg19
Supplementary_files_format_and_content: gff, peak pair calls filtered for significance over background

value: RNA polymerase II (Santa Cruz sc899, Lot#A2014)


title: Rat_Brain_Beef_5

description: Sample 21

tag: age

tag: Sex


title: K562 NoAb ChIP-exo 5.0

description:
PSU11262
NoAb_K562_ChIP-exo5.0_peaks.gff


title: Rat_Brain_Beef_3

description: Sample 10

tag: diet


title: K562 NoAb ChIP-exo 3.0

description:
PSU09872
NoAb_K562_ChIP-exo3.0_peaks.gff


title: K562 NoAb ChIP-seq

description:
PSU10786
NoAb_K562_ChIP-seq_peaks.gff


title: A183-9


title: CTCF ChIP-seq 1-step (alt ChIP-seq)

description:
PSU10803
CTCF_ChIP-seq1step_peaks.gff


title: CTCF ChIP-exo 5.0 Replicate 1

description:
PSU11239
CTCF_ChIP-exo5.0_peaks.gff


title: K562 NoAb ChIP-exo 1.1 Replicate 3

description:
PSU09552
NoAb_K562_ChIP-exo1.1_peaks.gff


title: K562 NoAb ChIP-exo 1.1 Replicate 2

description:
PSU09548
NoAb_K562_ChIP-exo1.1_peaks.gff


title: K562 NoAb ChIP-exo 1.1 Replicate 1

description:
PSU09541
NoAb_K562_ChIP-exo1.1_peaks.gff


title: CTCF ChIP-exo 1.1 Replicate 1

description:
PSU09542
CTCF_ChIP-exo1.1_peaks.gff


title: CTCF ChIP-exo 5.0 Replicate 2

description:
PSU11030
CTCF_ChIP-exo5.0_peaks.gff


title: CTCF ChIP-seq

description:
PSU10782
CTCF_ChIP-seq_peaks.gff


title: Rat_Brain_Beef_1

description: Sample 2


title: CTCF ChIP-exo 1.1 Replicate 3

description:
PSU09553
CTCF_ChIP-exo1.1_peaks.gff


title: microRNA profile of exosomes derived from acidic microenvironment culture (S1)

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

description: HCC cell line culture under acidic condition

hyb_protocol: The labeled RNAs were hybridized to the array with a 1×hybridization solution (5× Denhart’s solution, 0.5% SDS, 5× SSC) in a Hybridization Chamber (Corning Inc, Corning, NY, USA) at 46°C for 12 to 16 hours.

scan_protocol: Scanned in a InnoScan 710 Microarray Scanner (Innopsys,Carbonne, France).The microarray scanning images were digitized with GenPix Pro 6.0 program.

data_processing: The raw signal data were extracted, computed the average and subtracted background.Then we normalized (Quantile normalization)

source_name: SMMC-7721 culture supernantant

label_protocol: 2.5 μg of total RNA of tissue was employed with 100 nmol/L of pCp-DY647 (Dharmacon, Lafayette, CO, USA) and 15 Units of T4 RNA ligase (Life Technologies, Carlsbad, CA, USA) in a total reaction volume of 20 µL at 16°C overnight

extract_protocol: Total RNA was extracted using an acid phenol/chloroform extraction method followed by ethanol precipitation.

value: HCC cell line

tag: treatment

value: acidic condition


title: A183-16

tag: tissue

value: corolla (plant ontology term PO:0009059)


title: DKO GW-3

city: CHARLOTTESVILLE

first: Ira

middle: Glenn

last: Schulman

state: Virginia

address: 1340 Jefferson Park Ave, Jordan Hall, room 5218

department: Pharmacology

institute: University of Virginia

data_processing:
Base-calling was carried out by the HudsonAlpha Genomics Services laboratory
Illumina adaptors were trimmed.
Read abundances per transcript were quantified using Kallisto
Abundance estimates were converted to counts of reads mapping to Ensembl genes using the tximport package in the R statistical computing environment.
The DESeq2 Bioconductor package to normalize count data, estimate dispersion, and fit a negative binomial model for each gene.
Genome_build: GRCm38
Supplementary_files_format_and_content: Comma-separated values files including normalized count values for each individual replicate, log2 fold change for treatment relative to vehicle and adjusted p values.

source_name: bone marrow derived macrophage, DKO, GW

growth_protocol: Bone marrow cells from C57BL/6J and LXRalpha + LXRbeta double knockout mice were cultured in DMEM/20% FBS/30% L929 conditioned media to promote macrophage differentiation. After 4 days the media was removed, cells were washed twice with DPBS and fresh was added.

extract_protocol:
Total RNA was isolated using Qiagen Rneasy mini kits
RNA-Seq libraries from individual mice were produced using 500 ng of RNA and the SMARTer Stranded Total RNA Sample Prep Kit-Hi Mammalian (Clontech).

treatment_protocol: On day 5 cells were treated with vehicle, 100 ng/ml kdo2-lipidA (KLA) or 1 micromolar GW3965 for 17 hours.

value: DKO (LXR negative)

value: 8-12 weeks

value: BMDM

value: GW3965 1 micromolar


title: DKO GW-2


title: DKO GW-1


title: DKO AcLDL-3

source_name: bone marrow derived macrophage, DKO, AcLDL

value: Acetylated LDL 50 ug/ml


title: microRNA profile of exosomes derived from non-acidic microenvironment culture (S2)

description: HCC cell line culture under non-acidic condition

tag: cell line

value: non-acidic condition


title: CTCF ChIP-exo 1.1 Replicate 2

description:
PSU09549
CTCF_ChIP-exo1.1_peaks.gff


title: DKO AcLDL-1


title: A174-15

value: stage 12-13 (see Vincent & Coen https://doi.org/10.1139/b04-042)

value: recessive allele from A. majus stock line rosea-dorsea

value: white


title: DKO AcLDL-2


title: DKO KLA-2

source_name: bone marrow derived macrophage, DKO, KLA

value: Kado2-Lipid A 100 ng/ml


title: DKO KLA-1


title: DKO KLA-3


title: DKO Veh-2

source_name: bone marrow derived macrophage, DKO, Veh

value: Vehicle treated


title: DKO Veh-3


title: DKO Veh-1


title: LXR GW-3

source_name: bone marrow derived macrophage, LXR, GW

value: LXR positive


title: LXR GW-1


title: LXR AcLDL-1

source_name: bone marrow derived macrophage, LXR, AcLDL


title: LXR AcLDL-2


title: LXR AcLDL-3


title: LXR GW-2


title: LXR KLA-3

source_name: bone marrow derived macrophage, LXR, KLA


title: Healthy volunteer TST/QTF conversion after 180 days [8381645078_B]

description:
8381645078_B
Healthy volunteer TST/QTF conversion after 180 days

source_name: Whole Blood PAXgene

value: blood

tag: draw day

tag: patientid

tag: latent tb status at blood draw

value: TRUE

tag: time of conversion (days)

tag: relative time from conversion (days)


title: LXR KLA-1

tag: strain

tag: genotype

tag: cell type


title: LXR KLA-2


title: LXR Veh-3

source_name: bone marrow derived macrophage, LXR, Veh


title: LXR Veh-1


title: LXR Veh-2


title: Control input [wt-3-input]

city: St. Louis

first: Michael

middle: A

last: Rieger

state: MO

address: 660 S. Euclid, Box 8232

department: Genetics

institute: Washington University in St. Louis

description: crosslinked, RNase digested, total RNA, PAGE size-selected

data_processing:
Trimmomatic, extract UMIs as first 10 nucleotides of read 2.
Trimmomatic, trim for quality: ILLUMINACLIP:adapters.fa:2:55:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15  MINLEN:30 CROP:30
STAR: align to ribosomal RNA and use unaligned reads in next step
STAR: align non-rRNA reads to mm10 genome
FGBio: AnnotateBamWithUmis -i bamfile -f UMI_fastq -o output_annotated.bam
PicardTools: MarkDuplicates, BARCODE_TAG=RX REMOVE_DUPLICATES=true
Samtools merge: Combine BAM alignments across lanes 1-8 (1-4 on each sequencer run)
Subread: featureCounts -p -s 2, count BAMs using GTFs for 5utr, 3utr, introns, CDS
Samtools merge: Combine BAMs across  yfp-(1-4)-ip samples
Bedtools makeChromosomeWindows -g chromosomeSizeFile -w 100 -s 50 (100 nt windows, 50 nt overlap)
Subread: featureCounts: compute counts per window, reformat to BED file, -p -s 2 -t bin -f -O -M -g binName, allows reads to map to more than one window to accommodate adjacent windows. Make separate BEDs for + and - strand for peak calling.
Piranha: Piranha -o PEAKFILE -s  -p 1.0 -c -u 0 -d ZeroTruncatedNegativeBinomial -v BEDFILE
Assemble peaks with p<0.1 (not particularly conservative at this stage as differential enrichment is performed on per-sample count files) into a GTF
Adjust coords to 100 bp around peak maxima as Piranha peaks have very wide widths in our experience
Subread: featureCounts -p -s 2, count BAMs using Piranha peaks GTF
Genome_build: mm10
Supplementary_files_format_and_content: YFPMerge_Peaks.bed is the output of Piranha and contains and extra column including the Piranha p-value for whether read counts in a specific row's bin are significantly enriched with respect to the background; count files are output of subread featureCounts and contain chromosome position information and strand, length of feature, and final column is count for each feature

source_name: brain

growth_protocol:
CELF6-HA/YFP mice were crossed to C57BL6/J wild-type animals
On post-natal day 6, toe clippings were removed for genotyping to identify YFP+ animals and WT littermates

extract_protocol:
On post-natal day 9, mice were rapidly decapitated and brains were removed, with cortices/cerebella discarded. Remaining tissue was pooled per litter among YFP and WT samples and snap frozen according to method above in “summary”
After immunoprecipitation, samples were separated by SDS-PAGE and transferred to PVDF. A region 80-150 kDa (MW Celf6 HA-YFP ~78kDa) was cut and RNA was liberated with Proteinase K digestion, and extracted with acid phenol/chloroform, and purified and treated with DNase on a Zymo-5 RNA Clean and Concentrator column.
Follows Van Nostrand et. al. eCLIP method (Nat. Methods 2016) with some oligonucleotide sequence modifications for adapter ligation and library PCR with index (“read 3”) primers for sample demultiplexing

value: brain (cortices/cerebella removed)

value: post-natal day 9

tag: genotype/variation

value: wildtype


title: Control input [wt-1-input]


title: Control input [wt-2-input]


title: Control CLIP [wt-1-ip]

description: crosslinked, RNase digested, immunoprecipitated, PAGE size-selected


title: Control CLIP [wt-3-ip]


title: Control CLIP [wt-2-ip]


title: input [yfp-3-input]

value: YFP+


title: input [yfp-4-input]


title: CELF6 CLIP [yfp-4-ip]


title: input [yfp-1-input]


title: CELF6 CLIP [yfp-3-ip]


title: CELF6 CLIP [yfp-1-ip]


title: input [yfp-2-input]


title: CELF6 CLIP [yfp-2-ip]


title: CTCF ChIP-exo 5.0 mouse liver

data_processing:
For paired end reads from NextSeq, basecalls were performed using Bcl2fastq version 2.16.
Reads were aligned to mm10 genome assembly using bwa mem version 0.7.9a for paired reads.
GeneTrack peak caller; https://github.com/ialbert/chipexo/tree/master/genetrack (-s 5 -e 10)
Genome_build: mm10
Supplementary_files_format_and_content: gff, peak pair calls

source_name: liver

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with IgG antibody.
ChIP-exo 5.0 libraries were prepared for sequencing using standard Illumina protocols, Reference paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3813302/ with modifications throughout the protocol that reduced the number of steps and incubation times compared to ChIP-exo 1.1.
ChIP-exo

treatment_protocol: Cells were crosslinked with formaldehyde to a final concentration of 0.3%.

tag: chip antibody


title: CTCF ChIP-exo 5.0 mouse brain


title: CTCF ChIP-exo 5.0 mouse liver 270 thousand cells


title: CTCF ChIP-exo 5.0 mouse kidney

source_name: kidney


title: CTCF ChIP-exo 5.0 mouse liver 2.7 million cells


title: CTCF ChIP-exo 5.0 mouse liver 27 thousand cells


title: Hippocampal-RNA-seq_KO_repl.1

city: Chicago

first: Chuan

last: He

state: ILLINOIS

address: 929 E 57th St., GCIS E319

department: Department of Chemistry

institute: The University of Chicago

description:
C4
Quantification of transcripts abundance of hippocampus of Ythdf1-KO mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx

data_processing:
Sequencing data were mapped to mouse genome version mm10 downloaded from UCSC using Tophat v2.0.14.
For RNA-seq analysis, RPKM were calculated by Cuffnorm. For CLIP-seq experiments, after removing the adapter by Cutadapt, the reads were aligned to the mouse genome (mm10) by Bowtie2.
Peaking calling in Ythdf1-CLIP-seq. All mapped reads were treated as background and mutations were treated as signals for peak calling. PARalyzer was use for peak calling in CLIP-seq sample with a few modifications: (1) mutations in both "CLIP" and “Input” are removed in "CLIP"; (2) sites with 100% mutations rate were also removed. The remaining mutations were used for peak calling. At least two mutation sites are need in each peak (MINIMUM_CONVERSION_LOCATIONS_FOR_CLUSTER =2).
Peak calling in m6A-CLIP-seq. We followed the same peak calling method as reported in Nature volume 542, pages 475–478 (23 February 2017)
For m6A-RIP-seq: Low-quality bases and adaptor sequences from original reads were removed using Trimmomatic. The remaining reads were then mapped to the mouse genome (mm10) using STAR aligner. Mapped reads between samples were normalized using DESeq2. The “Input” and “RIP” libraries were normalized respectively.
Genome_build: mm10
Supplementary_files_format_and_content: CLIP-seq: peak list including gene name, genome coordinates, strand, and number of muations under the peak; RNA-seq: rpkm; m6A-RIP-seq: readcounts and rpkm.

source_name: Hippocampus

growth_protocol: All animals were maintained under a 12/12 h light/dark cycle with lights on at 7:00 AM, and temperature and humidity were kept at 22 ± 1 °C, 55% ± 5%, with ad libitum access to food and water.

extract_protocol:
Total RNA from WT littermate control and Ythdf1-KO mouse hippocampus was extracted using Trizol (Invitrogen) and isopropanol precipitation.  mRNA extraction was performed by poly(A)+ RNA selection once using Dynabeads  mRNA DIRECT  Purification Kit (Invitrogen)
Truseq stranded mRNA sample prep kit (illumina)

value: Hippocampus

value: 8-16 weeks (adult)

tag: ip antibody


title: Hippocampal-RNA-seq_WT_repl.1

description:
C1
Quantification of transcripts abundance of hippocampus of WT control mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx

tag: age


title: m6A-CLIP-seq_repl.3

description:
B3
polyA RNA fragments, anti-m6A-antibody enriched
B_m6A_CLIP_seq_peak_list.xlsx

extract_protocol:
After 2hr-incubation of polyA RNA and anti-m6A antibody, the mixture was UV crosslinked and then subjected to partial RNase T1 digestion. Then protein A/G beads were added to the mixture and rotated for another 2 hrs. After the incubation, the beads were washed, and then partially digested by RNase T1 again. After extensive wash, the RNA fragments were end-repaired on beads by T4 PNK, and eluted by protease K digestion and final clean-up. Eluted RNA was subject library preparation.
NEBNext multiplex small RNA library preparation kit (NEB)

value: Rabbit anti-m6A (202 003, SYSY)


title: Hippocampal-RNA-seq_KO_repl.2

description:
C5
Quantification of transcripts abundance of hippocampus of Ythdf1-KO mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx


title: Hippocampal-RNA-seq_WT_repl.3

description:
C3
Quantification of transcripts abundance of hippocampus of WT control mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx


title: Ythdf1-CLIP-seq_CLIP_repl.3

description:
A6
RNA crosslinked and co-immunoprecipipated with anti-Ythdf1 antibody
A_Ythdf1_CLIP_seq_peak_list.xlsx

extract_protocol:
Adult mouse hippocampi were dissected, homogenized, and UV crosslinked. After lysis and partial digestion with RNase T1, anti-Ythdf1-antibody conjugated with Protein A/G beads were added to the mixture, and incubated for 3 hr. After the incubation, the beads were washed and subjected to a second partial RNase T1 digestion. After additional extensive wash, the RNA fragments co-IP'ed were end-repaired on beads by T4 PNK. Then the RNA-Ythdf1 complex were size-selected using SDS-PAGE gel. The RNA fragments were extracted by Protease K digestion of the gel slices. After a final clean-up step by ethanl precipitation, the RNA was subject to library preparation.
NEBNext multiplex small RNA library preparation kit (NEB)

value: Rabbit anti-Ythdf1 antibody (17479-1-AP, Proteintech)


title: Hippocampal-RNA-seq_KO_repl.3

description:
C6
Quantification of transcripts abundance of hippocampus of Ythdf1-KO mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx


title: CTCF ChIP-exo 5.0 mouse lung

source_name: lung


title: Hippocampal-RNA-seq_WT_repl.2

description:
C2
Quantification of transcripts abundance of hippocampus of WT control mice
C_Hippocampal_RNA_seq_WT_KO_processed.xlsx


title: m6A-CLIP-seq_repl.1

description:
B1
polyA RNA fragments, anti-m6A-antibody enriched
B_m6A_CLIP_seq_peak_list.xlsx


title: Ythdf1-CLIP-seq_input_repl.3

description:
A3
RNA crosslinked with proteins with the same size of Ythdf1
A_Ythdf1_CLIP_seq_peak_list.xlsx

extract_protocol:
Adult mouse hippocampi were dissected, homogenized, and UV crosslinked. After lysis, the input samples were aliquoted and subject to the same two rounds of partial RNase T1 digestion, gel size-selection, and RNA extraction in parallel with the IP samples. The RNA were then end-repaired using T4 PNK and subject to library preparation.
NEBNext multiplex small RNA library preparation kit (NEB)


title: Ythdf1-CLIP-seq_CLIP_repl.1

description:
A4
RNA crosslinked and co-immunoprecipipated with anti-Ythdf1 antibody
A_Ythdf1_CLIP_seq_peak_list.xlsx


title: m6A-CLIP-seq_repl.2

description:
B2
polyA RNA fragments, anti-m6A-antibody enriched
B_m6A_CLIP_seq_peak_list.xlsx


title: Ythdf1-CLIP-seq_CLIP_repl.2

description:
A5
RNA crosslinked and co-immunoprecipipated with anti-Ythdf1 antibody
A_Ythdf1_CLIP_seq_peak_list.xlsx


title: Ythdf1-CLIP-seq_input_repl.1

description:
A1
RNA crosslinked with proteins with the same size of Ythdf1
A_Ythdf1_CLIP_seq_peak_list.xlsx