title: TKO CT

first: Andrew

middle: Zhuo

last: Xiao

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
The output sequencing reads were filtered and pre-analyzed with Illumina standard workflow. After filtration, the qualified tags (in fastq format) were aligned to the mouse genome (mm9) with bowtie2 (2.0.6).
Aligned reads were used for peak calling using the RSEG algorithm (0.4.9) in mode 3 to identify differential binding regions relative to the control samples using deadzone for 50bp reads, iteration 20, bin size 1000.
Genome_build: mm9
Supplementary_files_format_and_content: Output of rseg ChIPseq peak calling files in bed format. Sample I refers to the first file of the pair as shown in the file name.

source_name: ES cells

growth_protocol: Mouse ES cells were cultured on gelatin coating plates with indicated culture conditon. Serum ES cells were grown in DMEM (high glucose with L-glutamine, Invitrogen) supplemented with 15% fetal bovine serum (Hyclone), 1% non-essential amino acids (Invitrogen), 1mM sodium pyruvate (Invitrogen),1000 units of mLIF (EMD Millipore), 0.1 mM β-mercaptoethanol (Sigma) and PenStrep (Invitrogen). Mouse ES cells in 2i were cultured in commercially available 2i medium kit (Milipore, SF016-200). SRCi medium contains a 1:1 mixture of DMEM/F12 supplemented with N2 (Invitrogen) and Neurobasal media with glutamine (Invitrogen) supplemented with B27 (Invitrogen), 1X PenStrep (Invitrogen), 1000 units of LIF (Milipore), 1.5 μM CGP77675 (Tocris) and 3 μM CHIR99021 (Tocris). PKCi medium contains a 1:1 mixture of DMEM/F12 supplemented with N2 (Invitrogen) and Neurobasal media with glutamine (Invitrogen) supplemented with B27 (Invitrogen), PenStrep (Invitrogen), 1000 unites of mLIF (Milipore) and 5 μM Gö6976 (Tocris).

extract_protocol:
N-ChIP assay was performed as previously described. Briefly, approximately 10 million ESCs were used for each ChIP and massive parallel sequencing (ChIP-Seq) experiment. Chromatin pellets were briefly digested with MNase (New England BioLabs) and the mononucleosomes were monitored by electrophoresis 0.5ug anti-H2A.X antibody (active motif 39689) was used per ChIP experiment.
Following standard protocal of Illumina TruSeq ChIPseq library preparation kit

tag: genotype/variation

value: WT

tag: culture condition

value: Serum

tag: antibody


title: TDG KD

status: Public on Jan 01 2021

type: SRA

city: New Haven

state: CT

country: USA

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: strain

value: Tdg KD

value: anti-H2A.X antibody (active motif 39689)


title: Blood QC221

type: genomic

city: Tianjin

first: huanxin

last: chen

address: No.61, third avenue, tianjin economic and technolo

country: China

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

label: biotin

organism: Homo sapiens

source_name: healthy control_blood

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction

tag: group

value: healthy control

tag: tissue

value: blood


title: NormalDonor1_untreated_PBMC_033

city: Boston

first: Birgit

last: Knoechel

state: MA

address: 450 Brookline Ave

department: pediatric oncology

institute: Dana Farber Cancer Institute

library_source: transcriptomic

data_processing:
Adapter trimming was performed using trimmomatic version 0.36
Sequence quality was assessed using fastqc version 0.11.5
Alignment agains human genome was performed using START version 2.5.2b using following parameters -  --twopassMode Basic          --alignIntronMax 100000 --alignMatesGapMax 100000   --alignSJDBoverhangMin 10   --alignSJstitchMismatchNmax 5   -1   5   5 --outSAMstrandField intronMotif --outSAMattributes NH HI NM MD AS XS
Raw counts were obtained from aligned bam files using htseq version 0.9.1
Genome_build: hg19
Supplementary_files_format_and_content: htseq count file with raw raw counts for all the human genes for individual cells

molecule: total RNA

source_name: Blood

extract_protocol:
PBMCs were isolated using Ficoll-Paque, stained with anti-CD45 FITC, anti-CD3 PerCP-Cy5.5, anti-CD14 APC-Cy7, anti-CD19 PE and DAPI. Live single cells were sorted into 96 well plates containing TCL buffer.
Full-length single cell RNA-seq libraries were prepared using the SMART-seq2 protocol. cDNA was fragmented using Nextera XT (Illumina) and amplified with indexed Nextera PCR primers.

tag: who classification

value: Normal

tag: cell type

value: Peripherial blood mononuclear cells


title: Blood QC224

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_034


title: TDG CT


title: NormalDonor1_untreated_PBMC_028


title: control_33Q_Luc_R1

city: Irvine

first: Ryan

middle: Gar-Lok

last: Lim

state: California

address: 845 Health Sciences Rd.

department: MIND

institute: UC Irvine

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
7_CS83iCTR33n1_D37_LucLNP_R1

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence or low-quality sequence, and then mapped to mm10 or GRCh37 whole genome using Tophat2
gene counts were quantified using featureCounts and raw counts were used for normalization and differential stats using deseq2
Genome_build: mm10 or GRCh37
Supplementary_files_format_and_content: csv or tab-delimited text file includes raw count data for each Sample

source_name: medium spiny neuron-like

growth_protocol: iPSC were grown and matrigel and in mTESR and then differentiated into medium spiny neuron-like cells using a combination of growth factors, growth medium, and chemical inhibitors. Mouse tissues were collected at 8 and 13.5 Mos on GFP-positive microdissected striatal tissue

extract_protocol:
For iPSC-derived neurons, RNA was extracted from day 37 cell pellets using Qiagen RNeasy kit and QIAshredders, 1 µg of RNA with Rin values >8 for each sample were utilized for library preparation and RNAseq using illumina Truseq stranded polyA+ mRNA kit. For zQ175 mice, GFP+ micro-dissected flash frozen brain regions were homogenized in TRIzol reagent (Invitrogen) and RNA was extracted according to manufacturer’s protocol. RNA was then purified using RNEasy Mini kit (QIAGEN). Residual DNA was removed by DNase treatment incorporated into the RNEasy protocol as per manufacturer’s
RNA libraries were prepared for sequencing using standard Illumina Truseq protocols for stranded mRNAseq

treatment_protocol: Mice were treated with AAV2/1 expressing either a miRNA against Pias1 (miPias1.3), a control scrambled miRNA (miSafe) or a vehicle control (Saline) through bilateral stereotaxic striatal injections. The human iPSCs were differentiated into neural progenitors and then treated with siRNA against PIAS1 (or luciferase) via lipid nanoparticles at the iPSC stage.

value: iPSC-derived MSN-like

tag: condition

value: control

tag: polyq length

tag: treatement

value: Luc

tag: replicate


title: Blood QC219

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC218

description: Hybridized to Affymetrix SNP 6.0


title: control_33Q_Pias_R1

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
8_CS83iCTR33n1_D37_PIAS1LNP_R1

value: Pias


title: Blood QC215

description: Hybridized to Affymetrix SNP 6.0


title: 2i ESC


title: Blood QC214

description: Hybridized to Affymetrix SNP 6.0


title: PKCi

value: PKCi


title: Blood QC217

description: Hybridized to Affymetrix SNP 6.0


title: control_18Q_Luc_R1

description:
CTL sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
1_CS25iCTR18n6_D37_LucLNP_R1


title: NormalDonor1_untreated_PBMC_026


title: control_18Q_Pias_R1

description:
CTL sample  mRNAseq Pias
merged_all_piaskd_cardiff.txt
2_CS25iCTR18n6_D37_PIAS1LNP_R1


title: Blood QC216

description: Hybridized to Affymetrix SNP 6.0


title: HD_66Q_Luc_R1

description:
HD sample  mRNAseq Luciferase
merged_all_piaskd_cardiff.txt
13_CS02iHD66n4_D37_LucLNP_R1

value: HD


title: TKO KO

value: TKO


title: DNMT1 KO

value: DNMT1 KO


title: NormalDonor1_untreated_PBMC_025


title: NormalDonor1_untreated_PBMC_024


title: WIN_IL1B_rep2

city: La Jolla

first: Hai-Ri

last: Li

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: University of California, San Diego

data_processing:
Basecalls performed using bcl2fastq version 2.20
fastq files were aligned to Homo sapiens genome build hg19 using STAR
Raw counts quantified with HTseq.
Expression data was normalized  via Relative Log Expression (RLE) using DESeq2 R library
Differentially expressed genes (³2-fold and £1% false discovery rate) were identified by DESeq package
Genome_build: Homo sapiens genome build hg19
Supplementary_files_format_and_content: Raw counts

source_name: human primary astrocytes cultures

growth_protocol: Isolated primary human astrocytes were plated at a density of 1 x 107/T75 flask and cultured as adherent monolayers placed in a 5% CO2 37 °C incubator

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
libraries were prepared using the Illumina TruSeq RNA Sample Preparation Kit v2., according to the manufacturer’s instructions.

treatment_protocol: Astrocytes were either treated with vehicle (DMSO) or WIN (10uM) for 24 hours and then were stimulated with IL1B (20ng/ml) for 6 hrs.

value: primary astrocytes culture

tag: treatment

value: WIN 24hr + IL1B 6hr


title: SRCi

value: WT

value: SRCi


title: Blood QC213

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq PU.1cKO_CKP25_rep2

city: Cambridge

first: Li-Huei

last: Tsai

state: Massachusetts

department: Picower Institute for Learning and Memory

institute: MIT

description:
PU1KO-CKp25-6wk_1
160706Tsa_D16-165173_NA_sequence
processed data file: FPKM_table_CKP25.txt

data_processing:
RNA-seq data analysis: The generated fastq files were aligned to the UCSC mouse reference genome assembly mm9 using TopHat. The TopHat program used high-throughput short read aligner Bowtie to align the reads to the reference genome. The aligned reads were processed by Cufflinks 2.0.0. Relative abundance of transcript was measured by Fragments Per Kilobase of exon per Million mapped fragments (FPKM). The GTF annotation files for UCSC mm9 was used for gene annotation.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM table format for RNA-Seq data

source_name: RNA-Seq KO_CKP25

extract_protocol:
RNA-Seq: Hippocampi were isolated from the brains of mice at 3 and 4.5 months. Total RNA was extracted from FACS-purified  CD11b+CD45 microglia using QIAGEN RNA Easy Mini Kit.
RNA-Seq: cDNA was prepared using SMART-Seq v4 Ultra Low Input RNA Kit and sequencing libraries were constructed using Nextera XT DNA library preparation kit.

treatment_protocol: Adult (3-months-old) triple-transgenic Cx3cr1CreER+/-; CK-p25 mice with and without the PU.1 fl/fl, and their respective Cx3cr1CreER+/-; CK control littermates were used. IP injections of tamoxifen (50 mg/kg) were administered for 5 consecutive days at the time of p25 induction, and brain tissue was collected  6 weeks later.

tag: age

value: 4.5 months

tag: tissue/cell type

value: hippocampus, sorted microglia


title: RNA-Seq PU.1cKO_CKP25_rep3

description:
PU1KO-CKp25-6wk_2
160706Tsa_D16-165174_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: NormalDonor1_untreated_PBMC_023


title: Blood QC211

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: WIN_IL1B_rep1


title: NormalDonor1_untreated_PBMC_029

value: Normal

value: Peripherial blood mononuclear cells


title: NormalDonor1_untreated_PBMC_021


title: IL1B_rep2

value: IL1B 6hr


title: WIN_rep2

value: WIN 24hr


title: NormalDonor1_untreated_PBMC_027


title: Blood QC212

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq WT_CKP25_rep2

description:
PU1WT-CKp25-6wk_1
160706Tsa_D16-165178_NA_sequence
processed data file: FPKM_table_CKP25.txt

source_name: RNA-Seq WT_CKP25


title: NormalDonor1_untreated_PBMC_019


title: WIN_rep1


title: RNA-Seq WT_CKP25_rep3

description:
PU1WT-CKp25-6wk_2
180620Tsa_D18-162013_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: Blood QC208

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC210

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_020


title: IL1B_rep1


title: NormalDonor1_untreated_PBMC_022


title: Vehicle_rep1

value: vehicle treated


title: Blood QC209

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_017


title: RNA-Seq PU.1cKO_CKP25_rep1

description:
PU1KO-CKp25-6wk_0
160706Tsa_D16-165171_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: RNA-Seq WT_CKP25_rep1

description:
PU1WT-CKp25-6wk_0
160706Tsa_D16-165169_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: NormalDonor1_untreated_PBMC_018


title: Blood QC207

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq PU.1cKO_CX3CR1_rep3

description:
MIC_CX3CR1_2
180202Tsa_D18-883_NA_sequence
processed data file: FPKM_table_CX3CR1.txt

source_name: RNA-Seq MIC_PU.1

treatment_protocol: Adult (3-months-old) double-transgenic PU/1 fl/fl; Cx3cr1CreER+/- and their Cx3cr1CreER+/- controls were used.  IP injections of tamoxifen (50 mg/kg) were administered for 5 consecutive days, and brain tissue was collected 1 week later.

value: 3 months


title: Blood QC206

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq WT_CK_rep3

description:
PU1WT-CK-6wk_2
160706Tsa_D16-165177_NA_sequence
processed data file: FPKM_table_CKP25.txt

source_name: RNA-Seq WT_CK

value: CK


title: RNA-Seq WT_CK_rep2

description:
PU1WT-CK-6wk_1
160706Tsa_D16-165176_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: Vehicle_rep2


title: NormalDonor1_untreated_PBMC_015


title: RNA-Seq WT_CK_rep1

description:
PU1WT-CK-6wk_0
160706Tsa_D16-165170_NA_sequence
processed data file: FPKM_table_CKP25.txt


title: NormalDonor1_untreated_PBMC_016


title: N

city: Shanghai

first: Minyi

last: Ou

address: 393 Middle Huaxia Road, Pudong, Shanghai, 201210

institute: ShanghaiTech University

data_processing:
Raw reads were mapped to the hg19 reference using Hisat2 software
Fusion transcripts were identified by  SOAPfuse software
Differentially expressed genes among each cell type were identified using the R package Ballgown
Genome_build: hg19
Supplementary_files_format_and_content: Gene counts in CSV format

source_name: GW14.5 prefrontal cortex

extract_protocol:
RNA extraction was perform with miRNeasy FFPE Kit (Qiagen) following the manual.
Finished by Novogene company

treatment_protocol: Fetal cortex tissue was digested to obtain single-cell suspension. Then, cells were fixed, permeabilized, stained with primary antibodies: anti-CRYAB (Abcam, ab13496), anti-TBR2 (R&D systems, AF6166) , anti-HOPX (Sigma, HPA030180), and anti-SATB2 (Abcam, ab69995), followed by incubation of secondary antibodies conjugated with Alexa-488 or Alexa-555. Neural cells were classified as  vRGs(CRYAB+TBR2-), oRGs(HOPX+CRYAB- cells), IPs(TBR2+ cells) and neurons(SATB2+TBR2- cells).

value: neurons

value: prefrontal cortex

tag: Stage

tag: cell markers


title: oRG

value: outer RGs

value: HOPX+CRYAB-


title: Blood QC203

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC205

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC204

description: Hybridized to Affymetrix SNP 6.0


title: vRG

value: ventricular RGs


title: NormalDonor1_untreated_PBMC_014


title: Blood QC201

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq PU.1cKO_CX3CR1_rep1

description:
MIC_CX3CR1_0
180202Tsa_D18-881_NA_sequence
processed data file: FPKM_table_CX3CR1.txt

tag: genotype/variation


title: RNA-Seq WT_CX3CR1_rep3

description:
MIC_PU1_2
180202Tsa_D18-880_NA_sequence
processed data file: FPKM_table_CX3CR1.txt

source_name: RNA-Seq MIC_CX3CR1


title: Blood QC202

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq PU.1cKO_CX3CR1_rep2

description:
MIC_CX3CR1_1
180202Tsa_D18-882_NA_sequence
processed data file: FPKM_table_CX3CR1.txt


title: Blood QC200

description: Hybridized to Affymetrix SNP 6.0


title: PCa cells_C4-2_DTHIB_Rep2

city: Durham

first: Bushu

last: Dong

state: NC

address: 308 Research Dr.

department: Biochemistry

institute: Duke University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed by Trimmomatic (version 0.36.5) for adaptor sequence and mapped to human genome assembly GRCh38 using HISAT2 (version 2.1.0).
Transcript assembly was generated by StringTie (version 1.3.4) and StringTie merge (version 1.3.4).
Transcripts were counted by featureCounts (version 1.6.3) and normalized by DESeq2 (version 2.11.40.2).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited tabular files include differential expression analysis (DESeq2.result.tabular) and  raw counts (DESeq2.Normalized_counts_file.tabular) for each condition

source_name: PCa cell line C4-2

extract_protocol:
Total RNA was extracted by standard QIAGEN protocol for RNA extraction and 1 µg of total RNA was used for the construction of sequencing libraries.
Libraries were prepared for sequencing using standard Illumina protocols and the polyA+ mRNA was enriched.

treatment_protocol: C4-2 cells were treated with 1µM DTHIB (aka. E12) or DMSO solvent for 48 hours under standard culturing condition

value: CRPC

tag: cell line

value: 1µM DTHIB


title: NormalDonor1_untreated_PBMC_010


title: NormalDonor1_untreated_PBMC_012


title: RNA-Seq WT_CX3CR1_rep2

description:
MIC_PU1_1
180202Tsa_D18-879_NA_sequence
processed data file: FPKM_table_CX3CR1.txt

value: hippocampus, sorted microglia


title: NormalDonor1_untreated_PBMC_013


title: PCa cells_C4-2_DTHIB_Rep1


title: PCa cells_C4-2_DTHIB_Rep3


title: IP

value: intermediate progenitors


title: NormalDonor1_untreated_PBMC_011


title: Blood QC199

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: ChIP-Seq CK_WCE

data_processing:
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were removed by samtools. Bed alignment files were generated using bedtools. Peak calling was also performed using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq signal intensity across the genome

source_name: ChIP-Seq CK_WCE

extract_protocol:
ChIP-Seq: Hippocampi from 4.5 month old CK-p25 and age matched CK controls mice were isolated at 6 weeks after induction of p25 gene expression, and used for PU.1 ChIP-Seq.
ChIP-Seq: Libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Gjoneska et al., 2015)

treatment_protocol: Adult (3-months-old) female double-transgenic CK-p25 mice and their respective control littermates were used for the experiments. Brain tissue was collected at 6 weeks following p25 induction.

value: 4.5 months

value: hippocampus

tag: chip antibody

value: none (WCE)


title: RNA-Seq WT_CX3CR1_rep1

description:
MIC_PU1_0
180202Tsa_D18-878_NA_sequence
processed data file: FPKM_table_CX3CR1.txt


title: PCa cells_C4-2_DMSO_Rep4

value: DMSO


title: PCa cells_C4-2_DTHIB_Rep4


title: NormalDonor1_untreated_PBMC_009

value: Normal

value: Peripherial blood mononuclear cells


title: Blood QC198

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_008


title: ChIP-Seq CK_PU.1

source_name: ChIP-Seq CK_PU.1

extract_protocol:
ChIP-Seq: Hippocampi from 4.5 month old CK-p25 and age matched CK controls mice were isolated at 6 weeks after induction of p25 gene expression, and used for PU.1 ChIP-Seq.
ChIP-Seq: Libraries were prepared from ~1-5 ng ChIP (or input) DNA as described previously (Gjoneska et al., 2015).

value: CK

value: PU.1 Santa Cruz Biotechnology sc-352x


title: NormalDonor1_untreated_PBMC_007


title: PCa cells_C4-2_DMSO_Rep1


title: PCa cells_C4-2_DMSO_Rep3


title: Blood QC195

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_006


title: ChIP-Seq CKP25_WCE

source_name: ChIP-Seq CKP25_WCE


title: Blood QC197

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC196

description: Hybridized to Affymetrix SNP 6.0


title: PCa cells_C4-2_DMSO_Rep2


title: Blood QC193

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq CKP25_PU.1

data_processing:
ChIP-Seq data analysis: Sequencing reads were mapped to mouse genome assembly (mm9) using BWA aligner (samse option). Duplicate reads were removed by samtools. Bed alignment files were generated using bedtools. Peak calling was also performed using MACS2.
Genome_build: mm9
Supplementary_files_format_and_content: bedgraph format for ChIP-Seq signal intensity across the genome.

source_name: ChIP-Seq CKP25_PU.1


title: Blood QC194

description: Hybridized to Affymetrix SNP 6.0


title: NormalDonor1_untreated_PBMC_005


title: YS_MXF6838_slide050

city: New York

first: Nicholas

middle: D

last: Socci

state: NY

address: 1275 York Ave

department: Computational & Systems Biology Program

institute: Memorial Sloan Kettering Cancer Center

hyb_protocol: array-based comparative genomic hybridization (CGH)

scan_protocol: per Agilent protocols

data_processing:
Custom GC-Normalization full methods are here: http://cbio.mskcc.org/CGCC/
Copy number segmentation using Circular Binary Segmentation CBS in (https://bioconductor.org/packages/release/bioc/html/DNAcopy.html)
genome build: HG18 (N.B. not b37)
[singerS_CAN-19-1269R_IGV.seg]  Segmentation file (.seg) primary output of CBS

source_name: Tumor

label_protocol: per Agilent protocols

growth_protocol: Tumor tissue was obtained from human patients

extract_protocol:
Cryomolds were generated from human patient tumor tissue. Cryomolds containing > 75% cellularity were macrodissected to remove normal, fibrotic, inflammatory, and necrotic tissue. Genomic DNA was then prepared using a Dneasy Blood and Tissue kit (QIAGEN)
DNA libraries were prepared as per Agilent protocols

tag: histology

value: Myxofibrosarcoma

tag: tumor site

value: Thigh

tag: tumor length

source_name: Promega ref DNA

tag: sample type

value: Promega ref


title: M980513_DMSO_3

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

description: Cells were treated with DMSO (ctrl) for 24 hours and subsequently RNA was extracted

data_processing:
bcl2Fastq v2.19 software used for demultiplexing + basecalling.
reads trimmed with trimmomatic, options: ILLUMINACLIP:adapters.fa:1:20:7:5:true AVGQUAL:10 MINLEN:20
reads mapped with STAR  v2.5.4b, options: --sjdbOverhang 150 --twopassMode None --runThreadN 8 --outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --outMultimapperOrder Random --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif --outSAMattributes All --outStd BAM_Unsorted --outSAMtype BAM Unsorted
count: FeatureCounts (Bioconductor), options: allowMultiOverlap = true; countPrimaryAlignmentsOnly= true; minFeatureOverlap=10; minMapQuality= 10 ; keepMultiHits=true
differential expression analysis: EdgeR, options: normMethod = TMM; backgroundExpression =10; testMethod = glm; deTest =QL
Genome_build: Homo Sapiens, Ensemle, GRCh38.p10
Supplementary_files_format_and_content: tad-delimited, raw counts

growth_protocol: Cells were cultured in RPMI-1640 medium (L0998-500, Dominique Dutscher) enriched with 10% FCS (S181B-500, Dominique Dutscher), L-Glutamine and Na-Pyruvat,  (11360-039, Gibco) (1% each), and maintained in a humidified incubator at 37°C, 5% CO2

extract_protocol:
Total RNA of harvested cells was extracted by RNeasy Kit (QIAGEN) according to manufacturer's instruction
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: When cells reached a confluence of 70%, they were treated either with DMSO (as ctrl) or with CHIR99021 (GSK3a/b inhibitor) at 6 μM for 24 hours.

tag: cell type

value: human patient derived melanoma cell line

tag: tki sensitivity

value: Sensitive to TKI

value: DMSO (ctrl)


title: M980513_DMSO_2


title: YS_MXF9679_slide051


title: YS_MXF674_slide049

value: Chest Wall


title: NormalDonor1_untreated_PBMC_002

tag: who classification


title: Blood QC192

description: Hybridized to Affymetrix SNP 6.0

source_name: healthy control_blood

tag: group

value: healthy control

tag: tissue


title: M980513_DMSO_1

tag: treatment


title: NormalDonor1_untreated_PBMC_003

source_name: Blood


title: Blood QC191

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: M980513_CHIR_3

description: Cells were treated with GSK3a/b for 24 hours and subsequently RNA was extracted

value: GSK3a/b inhbitor


title: NormalDonor1_untreated_PBMC_001


title: M980513_CHIR_2


title: Blood QC190

description: Hybridized to Affymetrix SNP 6.0


title: YS_MXF3132_slide828

value: Abdominal Wall


title: NormalDonor1_untreated_PBMC_004


title: PD_pMFH910_slide615

value: Undifferentiated pleomorphic sarcoma


title: YS_MXF664_slide829


title: M980513_CHIR_1


title: YS_MXF2553_slide827

value: Upper arm


title: huTcell_live

city: Los Angeles

first: Pavlo

middle: A

last: Nesterenko

address: 675 Charles E Young

department: MIMG

institute: UCLA

data_processing:
Library strategy: CLInt-Seq
fastqs were processed using 10X Cell Ranger 2.2.0 Single Cell Immune Profiling (cellranger vdj)
Genome_build: hg38
Supplementary_files_format_and_content: vloupe files, contains information about clonotypes and consensus alignments.

source_name: PBMCs/Jurkat E6.1 clone

growth_protocol: Jurtkat E6.1 is grown in complete RPMI media. T cells are expanded in AimV media supllemented with 5% human serum and Glutamax with IL-7 and IL-15.

extract_protocol: 10X Genomics huTCR VDJ library construction

treatment_protocol: PFA based intracellular staining:PBMCs are washed 2 times with PBS (Fisher Scientific cat. no.  MT-46013CM) and once with TCRPMI. Then cells are resuspended in TCRPMI at 500,000 cells/100 µL of media and aliquoted into 96 well plate (Corning cat. no. 353077) for 12-hour rest prior to intracellular staining stimulation. Then, 100 µL of TCRPMI with 20 µg/ml of peptide and 2 µg/ml of CD28/49d antibodies (BD cat. no. 347690) are added to each well. AIM V complete media is used for TCR overexpression experiment. Cells are incubated for one hour at 37C 5% CO2 and 20 µL of 10X brefeldin A (Biologened cat no. 420601) is added to each well. Cells are further incubated for 8 hours. For TCR sequencing cells are stained immediately under RNAse free conditions with the FRISCR protocol adapted from (Thomsen et al). Briefly each well is washed twice with 200 µL of wash buffer, which contains nuclease free water (Thermo Fisher, cat. no. 4387936), 10X molecular biology grade PBS, 1% nuclease free BSA (Gemini cat. no. 700-106P)), and 1:400 RNAsin Plus (Promega cat. no. N2615). For TCR overexpression and subsequent sequencing experiment we used RNAsin plus at 1:40000 dilution. The cells are stained with following surface antibodies: CD3-APCCy7 (Thermo Fisher, cat. no. 47-0036-42), CD8a-PE (Thermo Fisher, cat. no. 12-0088-42), CD4-PECy7 (Biolegend, cat. no. 300512). After staining for 15 minutes at 4C cells are washed with wash buffer and fixed with 100 µL of 4% PFA (EMS cat. no. 15710) for 10 minutes at 4C. Then cells are washed twice and resuspended in 1% BSA buffer with .1% Triton X-100 (Sigma-Aldrich cat. no. T8787) for 10 minutes. Cells are then washed and subsequently stained with intracellular antibodies in wash buffer for IFNγ-APC (Biolegend cat. no. 506510), TNFα-FITC (Biolegend cat. no. 502906), FoxP3-A488 (Biolegend cat. no. 320012), msIgG1-A488 (Thermo Fisher, cat. no. MG120). Cells are then washed and resuspended in wash buffer for FACS analysis. Intracellular staining where we did not plan to do TCR sequencing was done in the absence of RNAsin plus inhibitor. CLInt-Seq staining: All buffers except crosslinker step contain 1:400 RNAsin and molecular biology grade PBS to inhibit RNA degradation. Staining is performed in a 96 well U bottom plate. Cells were first washed twice in 200µL of 1% BSA buffer with 1:400 RNAsin (wash buffer) and incubated for 15 minutes on ice with antibodies against surface antigens. DSP (ThermoFisher cat. no. 22585) is stored at -20C in a desiccant filled container. Immediately prior to experiment DSP is left at room temperature for at least 30 minutes and then prepared to a concentration of 50 mg/ml in molecular biology grade DMSO (Sigma cat. no. D8418-50ML). Then 1mg/ml solution is prepared in molecular biology grade PBS, by vortexing 20ul of DSP in a 15ml conical tube and adding 1mL of PBS with P1000. DSP is filtered using a 40μm Flowmi strainer (Sigma cat. no. BAH136800040-50EA). Then .25mg/ml solution is prepared. Cells are washed once with wash buffer and twice with PBS and resuspended in 200 µL of .25mg/ml DSP (Thermo Fisher). Cells are incubated at room temperature for 30 minutes and quenched with 20mM Tris (Thermo Fisher cat. no. AM9850G). Cells are then washed and incubated for 10 minutes with 100µL of .05% Triton X-100 (Thermo Fisher) in wash buffer. Subsequently, cells are washed and resuspended in wash buffer for 20 minutes with antibodies against intracellular antigens. Then, cells are washed again and resuspended in wash buffer for FACS sorting.

value: T cells + Jurkat E6.1


title: M111031_DMSO_3

value: Resistant to TKI


title: Blood QC188

description: Hybridized to Affymetrix SNP 6.0


title: huTcell_PFA


title: M111031_DMSO_2


title: PD_pMFH905_slide591

value: Foot


title: huTcell_EBV_tetramer

source_name: PBMCs

growth_protocol: TCRPMI was used in those experiments and contained 1640 RPMI (Thermo Fisher, cat. no. 31800089) supplemented with 10% Fetal Bovine Serum (Omega Scientific, cat. no.  FB-11), 1X Glutamax (Thermo Fisher, cat. no. 35050061), 1X sodium pyruvate (Thermo Fisher, cat. no. 11360070), 10mM HEPES (Thermo Fisher cat. no. 15630130), 1X non-essential amino acids (Thermo Fisher, cat. no.11140050) and 50 μM β-mercaptoethanol (Sigma-Aldrich, cat. no. M3148). Briefly cells were thawed into warm media and rested overnight at 5x106 million/ml in 24 well plate (Corning cat. no. 353047) in TCRPMI media. Subsequently, cells were washed once and cultured for 9 days in TCRPMI supplemented with 1ug/ml of antigenic peptide: CMV pp65 (NLVPMVATV), EBV BMLF1 (GLCTLVAML) (Elim Biopharmaceuticals Inc) and 25 U/ml IL-2 (Peprotech, cat. no. 200-02). Half of media is replaced every 2-3 days. For Regulatory T cell (Treg cell) analysis normal human PBMCs were used.

value: CD3+, CD8+ T cells


title: PD_pMFH899_slide731

value: Knee


title: Blood QC187

description: Hybridized to Affymetrix SNP 6.0


title: huTcell_EBV_ICS


title: Blood QC186

description: Hybridized to Affymetrix SNP 6.0


title: PD_PMFH898_slide743

value: Thigh


title: Blood QC185

description: Hybridized to Affymetrix SNP 6.0


title: M111031_CHIR_2


title: M111031_CHIR_3


title: PD_PMFH878_slide682

value: Promega ref


title: Pancreatic cancer associated fibroblasts CW5 - H3K27ac - Input

city: Allen

first: Wei

last: Lin

state: TX

address: 1525 Evanvale Dr.

institute: Translational Genomics Research Institute

data_processing:
ChIP-seq reads were aligned to a reference genome (version hg19) using Bowtie2 with default parameters
H3K27Ac peak finding was performed using MACS (v1.4.2) and Homer with default settings.
Peak finding for each sample was performed separately with their matched input genomic DNA as a background control.
ROSE (Young lab) was then used to call and rank Super-enhancers and their associated genes
For RNAseq raw paired-end reads were trimmed using fastx-trimmer tools prior to mapping
TopHat (version 2.0.14) was used to map reads to a reference genome with parameters ‘–library-type fr-firststrand’ (for a strand-specific library) ‘—mate-std-dev #stdev’ and ‘-r #insert-distance’. The #stdev and #insert-distance were estimated from sub-sampling of samples individually
After mapping, bam files were further analyzed using Arraystudio (Omicsoft) software with default parameters.
Genome_build: hg19
Supplementary_files_format_and_content: beg files for ChIPseq data were generated using MACS (v1.4.2)
Supplementary_files_format_and_content: tab-delimited text file that include FPKM values or htseqcounts for  RNAseq samples

source_name: Isolated from a pancreatic tumor

growth_protocol: 60 mm dishes in DMEM medium + 20% FBS to 60-80% confluency

extract_protocol:
ChIP DNA was purified by the QIAquick PCR purification kit (QIAgen)
Sequencing libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells were treated with triptolide (20nM) for 18 hours.

tag: antibody

value: H3K27ac from Active Motif (Cat. #39133)

value: Input


title: Blood QC184

description: Hybridized to Affymetrix SNP 6.0


title: huTcell_DSP


title: Blood QC189

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC183

description: Hybridized to Affymetrix SNP 6.0


title: PD_PMFH877_slide681

value: Shoulder


title: M111031_CHIR_1

value: human patient derived melanoma cell line


title: PD_PMFH876_slide680

value: Myxofibrosarcoma


title: Pancreatic cancer associated fibroblasts CW5 - H3K27ac - untreated

value: Triptolide treated


title: Pancreatic cancer associated fibroblasts CW5 - H3K27ac - Vehicle (DMSO) treated

treatment_protocol: Cells were treated with vehicle (DMSO) for 18 hours.

value: DMSO treated


title: M000921_DMSO_3

value: Sensitive to TKI

value: DMSO (ctrl)


title: PD_PMFH870_slide793

value: Undifferentiated pleomorphic sarcoma


title: huTcell_EBV_CD137


title: M111031_DMSO_1


title: Blood QC181

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: Blood QC182

description: Hybridized to Affymetrix SNP 6.0


title: M000921_DMSO_2


title: PD_pMFH867_slide552

value: Upper arm


title: Pancreatic cancer cells MIA PaCa-2 - H3K27ac Input

source_name: Pancreatic cancer cell line

growth_protocol: 60 mm dishes in RPMI-1640 medium + 10% FBS to 60-80% confluency


title: M000921_DMSO_1


title: Blood QC179

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH860_slide816

value: Lower leg


title: Pancreatic cancer cells MIA PaCa-2 - H3K27ac - Vehicle (DMSO) treated


title: M000921_CHIR_3

value: GSK3a/b inhbitor


title: PD_pMFH862_slide818

value: Thigh


title: Blood QC178

description: Hybridized to Affymetrix SNP 6.0


title: M000921_CHIR_2


title: M000921_CHIR_1


title: Sample 8: Target (-Peptide)

first: Richard

middle: Brad

last: Jones

state: New York

department: Division of Infectious Diseases

institute: Weill Cornell Medicine

data_processing:
The raw sequencing reads in BCL format were processed through bcl2fastq 2.19 (Illumina) for FASTQ conversion and demultiplexing.
RNA reads were aligned and mapped to the GRCh37 human reference genome by STAR (Version2.5.2) (https://github.com/alexdobin/STAR), and transcriptome reconstruction was performed by Cufflinks (Version 2.1.1) (http://cole-trapnell-lab.github.io/cufflinks/). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Gene expression profiles were constructed for differential expression, cluster, and principle component analyses with the DESeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html). For differential expression analysis, pairwise comparisons between two or more groups using parametric tests where read-counts follow a negative binomial distribution with a gene-specific dispersion parameter. Corrected p-values were calculated based on the Benjamini-Hochberg (B-H) method to adjusted for multiple testing.
Differential expression genes (DEGs) list between ‘real’ survivors and ‘real’ bystanders were determined with a cut-off of FDR (adjusted p-value) <0.05, and then analyzed with ingenuity pathway analysis (IPA, QIAGEN). Significantly enriched pathways were selected with a threshold of B-H multiple testing correction p-value <0.05, and displayed as -log(B-H p-value) >1.3.
Supplementary_files_format_and_content: normalized gene expression profile

source_name: CD4+ T cells

growth_protocol: 5x10^6 naïve CD4+ T cells from HIV- or HIV+ were isolated by magnetic negative selection (StemCell Technologies), then cultured at 106 cells/mL in 96-well plates using R-10 media (RPMI-1640 media supplemented with 10% FBS, 2mM L-glutamine, 100 units/ml Penicillin and 100µg/ml Streptomycin) supplemented with 12.5uL/mL of dynabeads human T-activator CD3/CD28 (Invitrogen), 2µg/mL anti-human IL-12 (PeproTech), 1µg/mL anti-human IL-4 (PeproTech), and 10ng/mL of TGF-β1. After 3 days, dynabeads were removed by magnetic selection and cells were washed, followed by culture in R-10 media supplemented with 30 IU/mL of IL-2 (R-10-30). Media was changed on days 4 and 5 with fresh R-10-30 media.

extract_protocol:
Total RNA was immediately extracted using the RNeasy Micro Kit (Qiagen) follwing the manufacture protocol, and RNA quality and concentration was determined by Agilent Bioanalyzer 2100.
TruSeq RNA Sample Preparation (Non-Stranded and Poly-A selection) (our genomic core staff did this part)

treatment_protocol: TCM CD4+ T-cells were divided into either a “real” or “mock” condition, and then sub-divided into two populations each, receiving either CFSE or cell-track far-red (CTFR) labeling (ThermoFisher Scientific). After staining, CFSE cells in the “real” condition were pulsed with 1g/mL of RR11 peptide for 30 minutes. Following extensive washing, peptide-pulsed cells were mixed with equal numbers of unpulsed CTFR+ cells and co-cultured with CTL clones at an effector:target ratio = 1:1 overnight in R10-50 media. Cells from the “mock” condition did not receive peptide, but were otherwise treated identically to the “real” condition. Following the overnight culture, cells were stained with antibodies against human- CD3, CD4, CD8, and DAPI, and then sorted by FACS Influx (BD Biosciences) directly into vessels containing lysis buffer (Qiagen)

value: Naive-derived memory CD4+ T cells

tag: donor information

value: ART-suppressed HIV+ participant


title: Blood QC175

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC174

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC176

description: Hybridized to Affymetrix SNP 6.0


title: Sample 7: Target (-Peptide)


title: Blood QC180

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH833_slide699

value: Calf

value: Promega ref


title: PD_pMFH857_slide826


title: PD_pMFH853_slide767


title: Pancreatic cancer cells MIA PaCa-2 - H3K27ac Triptolide treated

value: H3K27ac from Active Motif (Cat. #39133)


title: PD_pMFH854_slide770

value: Myxofibrosarcoma


title: Blood QC177

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC173

description: Hybridized to Affymetrix SNP 6.0


title: Sample 6: Bystander (-Peptide)


title: Sample 3: Target (+Peptide)


title: PD_pMFH865_slide830


title: Sample 5: Bystander (-Peptide)


title: Blood QC172

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH850_slide769


title: Sample 4: Target (+Peptide)


title: Blood QC171

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH859_slide815


title: PD_pMFH819_slide369

value: Shoulder


title: Blood QC169

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH818_slide368


title: Blood QC168

description: Hybridized to Affymetrix SNP 6.0


title: PD_pMFH817_slide253


title: Blood QC164

description: Hybridized to Affymetrix SNP 6.0


title: PD_PMFH816_slide745


title: Blood QC163

description: Hybridized to Affymetrix SNP 6.0


title: 9.12_miPias1.3_Het_R3

description:
HET sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
9.12_miPias1.3_Het

source_name: Striatal Tissue

value: Bulk Tissue

tag: condition

value: HET

tag: treatement

value: miPIAS

tag: replicate

tag: gender

value: Female


title: Sample 2: Bystander (+Peptide)


title: S100A9.TAM.R2.Input

city: Hangzhou

first: Ruisheng

last: Song

state: Zhejiang

address: 866 Yuhangtang Road

institute: Zhejiang University

description: Biological replicate 2

data_processing:
Sequencing FASTQ reads were aligned to the hg19 human reference genome with Bowtie2 (Langmead and Salzberg, 2012) with the following restrictions “--very-sensitive --score-min L,-0.6,-0.15” for mapping sensitivity and accuracy. Only uniquely mapped reads, and in the case of paired-end sequenced data, only uniquely mapped sequence pairs that were aligned concordantly, were used for subsequent analyses.
In S100A8 or S100A9 ChIP-seq data, confident peaks were defined as fulfilling all the following restrictions: 1) MACS2 peakcalling q-value ≤ 1e-7 against sample-corresponding chromatin input background, 2) peaks called by MACS2 were identified in at least 2 biological replicates, 3) at least 5 raw reads were aligned at the peak region.
Confident Pol II ChIP-seq peaks were defined as MACS2 paired-end peak-calling p-value ≤ 1e-8 against genomic background of 1 megabase genomic region around.
By "wigToBigWig" (UCSC), BigWig files were converted from wiggle files, which were obtained by "igvtools count" with BAM files and were further noramlized with unique alignment depth
Genome_build: HG19
Supplementary_files_format_and_content: narrowPeak files with MACS2 called peak data for S100A8 and S100A9 ChIP; BigWig files with binding signal (reads per million) for Pol II ChIP

source_name: MCF10A cells expressing ER-Src

growth_protocol: Cell culture was performed at 37°C under 5% CO2. MCF10A cells expressing ER-Src were grown in DMEM/F12 with 5% charcoal-stripped fetal bovine serum (Sigma-Aldrich) and supplements as previously described (Iliopoulos et al., 2009).

extract_protocol:
Chromatin preparations were clarified from sonicated nuclei. Anti-Flag was used in ChIP for S100A8-Flag or S100A9-Flag; anti-Pol II (8WG16) was used in ChIP for Pol II.
Sequencing libraries were constructed following standard protocol (Green et al., 2012).

treatment_protocol: Cells were treated with 1 μM 4-hydroxy-tamoxifen (Sigma-Aldrich) for 24 hours to induce transformation; treatment with ethanol as vehicle control was used for non-transformation.

tag: cell line

tag: flag-tagged protein expression

tag: chip antibody

value: TAM

tag: experiment

value: Input


title: Blood QC161

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: 27.9_miPias1.3_Het_R1

description:
HET sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
27.9_miPias1.3_Het


title: S100A9.TAM.R3.Input

description: Biological replicate 3


title: S100A9.TAM.R1.Input

description: Biological replicate 1


title: PD_pMFH814_slide448

tag: histology

value: Undifferentiated pleomorphic sarcoma

tag: tumor site

tag: tumor length

tag: sample type


title: PD_pMFH763_slide447

value: Thigh


title: 27.6_miPias1.3_WT_R3

description:
WT sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
27.6_miPias1.3_WT

tag: cell type

value: WT


title: PD_pMFH6_slide549


title: Blood QC160

description: Hybridized to Affymetrix SNP 6.0

tag: group

tag: tissue


title: 29.6_miPias1.3_WT_R1

description:
WT sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
29.6_miPias1.3_WT


title: 29.15_miPias1.3_WT_R2

description:
WT sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
29.15_miPias1.3_WT


title: PD_pMFH41_slide551

value: Scapula


title: S100A9.EtOH.R3.Input

description: Biological replicate 3

tag: treatment

value: EtOH


title: Blood QC159

description: Hybridized to Affymetrix SNP 6.0


title: S100A9.EtOH.R2.Input

description: Biological replicate 2


title: S100A9.EtOH.R1.Input

description: Biological replicate 1


title: PD_pMFH35_slide550

value: Promega ref


title: Blood QC158

description: Hybridized to Affymetrix SNP 6.0


title: Sample 1: Bystander (+Peptide)

value: Naive-derived memory CD4+ T cells

tag: donor information

value: ART-suppressed HIV+ participant


title: 22.13_miSafe_Het_R2

description:
HET sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
22.13_miSafe_Het

tag: condition

value: miSAFE


title: 30.12_miSafe_Het_R3

description:
HET sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
30.12_miSafe_Het

value: Bulk Tissue

tag: treatement


title: S100A8.TAM.R3.Input

description: Biological replicate 3


title: S100A8.TAM.R2.Input

description: Biological replicate 2


title: PD_pMFH30_slide251


title: 27.5_miPias1.3_Het_R2

description:
HET sample Total RNAseq miPIAS
pias_q175_females_20200602_counts_merged.csv
27.5_miPias1.3_Het

value: HET

tag: replicate


title: Blood QC157

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC162

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC156

description: Hybridized to Affymetrix SNP 6.0


title: 18.12_miSafe_Het_R1

description:
HET sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
18.12_miSafe_Het

tag: gender


title: S100A8.TAM.R1.Input

description: Biological replicate 1

tag: cell line


title: 30.13_miSafe_WT_R3

description:
WT sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
30.13_miSafe_WT


title: PD_MXF916_B_slide031

value: Myxofibrosarcoma


title: Blood QC155

description: Hybridized to Affymetrix SNP 6.0


title: 29.16_miSafe_WT_R2

description:
WT sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
29.16_miSafe_WT

value: Female


title: S100A8.EtOH.R1.Input

description: Biological replicate 1

tag: flag-tagged protein expression


title: S100A8.EtOH.R2.Input

description: Biological replicate 2

tag: chip antibody


title: Blood QC154

description: Hybridized to Affymetrix SNP 6.0


title: PD_MXF875_slide679


title: PD_MXF879_slide684


title: Blood QC153

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC152

description: Hybridized to Affymetrix SNP 6.0


title: 24.2_miSafe_WT_R1

description:
WT sample Total RNAseq miSAFE
pias_q175_females_20200602_counts_merged.csv
24.2_miSafe_WT


title: 52.13 miPIAS1.3 Het_R2

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
52.13 miPIAS1.3 Het

value: miPIAS

value: Male


title: Blood QC151

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: 52.14 miPIAS1.3 Het_R3

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
52.14 miPIAS1.3 Het


title: S100A9.TAM.R2.ChIP

description: Biological replicate 2

value: anti-Flag epitope (Cat. No. 2368, Cell Signaling Technology)

value: TAM

tag: experiment

value: ChIP


title: PD_MXF871_slide730

tag: histology

value: Thigh


title: PD_PMFH1042_DNA_slide624

tag: tumor site

value: Shoulder


title: S100A9.TAM.R1.ChIP

description: Biological replicate 1


title: Blood QC150

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: PD_MXF866_slide781

tag: tumor length

value: Promega ref


title: S100A9.EtOH.R3.ChIP

description: Biological replicate 3

value: EtOH


title: 1.6 miPIAS1.3 Het_R1

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
1.6 miPIAS1.3 Het


title: 52.16 miPIAS1.3 WT_R3

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
52.16 miPIAS1.3 WT

value: WT


title: S100A9.TAM.R3.ChIP

description: Biological replicate 3


title: PD_MXF874_slide796

tag: sample type


title: Blood QC149

description: Hybridized to Affymetrix SNP 6.0


title: 1.1 miPIAS1.3 WT_R2

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
1.1 miPIAS1.3 WT

tag: cell type


title: S100A9.EtOH.R2.ChIP

description: Biological replicate 2


title: PD_MXF863_slide819

value: Calf


title: Blood QC146

description: Hybridized to Affymetrix SNP 6.0

tag: group


title: 1.4 miPIAS1.3 WT_R1

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c2.csv
1.4 miPIAS1.3 WT

value: Bulk Tissue


title: PD_MXF861_slide817


title: S100A9.EtOH.R1.ChIP

description: Biological replicate 1


title: 7.11 miSAFE Het_R2

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
7.11 miSAFE Het

value: HET

value: miSAFE


title: 7.10 miSAFE Het_R3

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
7.10 miSAFE Het


title: S100A8.TAM.R2.ChIP

description: Biological replicate 2


title: PD_MXF856_slide701

value: Myxofibrosarcoma


title: PD_MXF855_slide700


title: S100A8.TAM.R3.ChIP

description: Biological replicate 3


title: Blood QC144

description: Hybridized to Affymetrix SNP 6.0

tag: tissue


title: S100A8.TAM.R1.ChIP

description: Biological replicate 1

tag: treatment


title: PD_MXF852_slide727

value: Lower leg


title: 6.6 miSAFE Het_R1

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
6.6 miSAFE Het

value: Male


title: S100A8.EtOH.R2.ChIP

description: Biological replicate 2


title: 15.13 miSAFE WT_R3

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
15.13 miSAFE WT


title: Blood QC142

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: PD_MXF864_slide829


title: Blood QC143

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC141

description: Hybridized to Affymetrix SNP 6.0


title: PD_MXF848_slide702

value: Axilla


title: PD_MXF851_slide766


title: Blood QC147

description: Hybridized to Affymetrix SNP 6.0


title: S100A8.EtOH.R1.ChIP

description: Biological replicate 1

value: anti-Flag epitope (Cat. No. 2368, Cell Signaling Technology)


title: Blood QC145

description: Hybridized to Affymetrix SNP 6.0


title: MKL2 SOX2

city: Bethesda

first: Javed

last: Khan

state: MD

address: 37 Convent Dr.

department: Genetics Branch

institute: NCI, NIH

description: DNA (ChIP-enriched)

data_processing:
ChIP enriched DNA reads were mapped to reference genome using BWA version 0.7.10
The ChIP-seq peaks were called by MACS2 version 2.1.0.  Duplicates were allowed
Enrichment of known and de novo motifs were found using HOMER version 4.8.2
Genome_build: Hg19
Supplementary_files_format_and_content: peak files are tab delimited text files (BED coordinates) for each sample.

growth_protocol: Cells were maintained in DMEM with 10% FBS and Penn/Strep at 37 °C incubation until harvesting for ChIP.

extract_protocol:
harvesting protocol:  ChIP samples harvested after 1% formaldehyde fixation for 12 minutes, sonicated, processed and ChIP-enriched via standard protocols (Active Motif ChIP-IT HS kit).  ChIP enriched DNA was treated with Proteinase K at 55 ˚C for 30 minutes followed by reversal of crosslinks by heating to 80 ˚C for 2 hours, and DNA purification by column (MiniElute PCR purification kit, Qiagen).
DNA was extracted from ChIP-seq samples prepared following the Active Motif ChIP-IT High Sensitivity kit protocol.
Standard Illumina barcodes were introduced during library preparation with the Illumina TruSeq ChIP Sample Prep Kit 48 Samples - Set A Cat# IP-202-1012

tag: virus status

value: positive

value: Merkel Cell carcinoma (MCC)

tag: antibody/treatment

value: anti-human/mouse/Rat SOX2 (pAb, goat, R&D systems cat@#AF2018)

tag: enrichment target

tag: target function

value: Transcription Factor


title: 4.12 miSAFE WT_R1

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
4.12 miSAFE WT

tag: condition

tag: treatement

tag: replicate

tag: gender


title: PD_MXF847_slide768

value: Thigh

value: Promega ref


title: 5.1 miSAFE WT_R2

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c2.csv
5.1 miSAFE WT

value: WT


title: Blood QC140

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: PD_MXF837_slide704

value: Undifferentiated pleomorphic sarcoma


title: MKL2 POU4F3

description: DNA (ChIP-enriched)

tag: cell line

value: anti-POU4F3 (mAb, mouse, abcam cat#ab58128)


title: Het 15.5 miPIAS1_R3

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
Het 15.5 miPIAS1

value: Bulk Tissue

value: HET

value: miPIAS


title: Blood QC139

description: Hybridized to Affymetrix SNP 6.0


title: MKL2 LXH3

description: DNA (ChIP-enriched)

value: anti-LHX3/LIM (pAb, rabbit, abcam cat#ab14555)


title: PD_MXF832_slide456

tag: histology

value: Myxofibrosarcoma

value: Lower leg


title: Het 28.12 miPIAS1_R1

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
Het 28.12 miPIAS1

value: Male


title: Het 5.9 miPIAS1_R2

description:
HET sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
Het 5.9 miPIAS1


title: PD_MXF836_slide459

tag: tumor site

value: Upper arm


title: MKL2 ISL1

description: DNA (ChIP-enriched)

value: positive

value: Merkel Cell carcinoma (MCC)

value: anti-Islet 1 (mAb, rabbit, abcam cat#ab109517)


title: Blood QC138

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: MKL2 INSM1

description: DNA (ChIP-enriched)

value: anti-INSM1 (A-8) X (mAb., mouse, SantaCruz, cat#sc-271408 X)

value: Transcription Factor


title: MKL2 ATOH1

description: DNA (ChIP-enriched)

value: anti-MATH1 (pAb, rabbit, ThermoFisher, cat#PA5-29392)


title: Blood QC136

description: Hybridized to Affymetrix SNP 6.0

value: blood


title: PD_MXF815_slide449

value: Thigh

tag: tumor length

value: Promega ref


title: PD_MXF730_slide779

value: Knee

tag: sample type


title: Blood QC135

description: Hybridized to Affymetrix SNP 6.0


title: WT 9.15 miPIAS1_R3

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
WT 9.15 miPIAS1

tag: cell type

value: Bulk Tissue

value: WT

value: miPIAS


title: WT 18.9 miPIAS1_R2

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
WT 18.9 miPIAS1


title: PD_MXF660_slide252

value: Myxofibrosarcoma


title: PD_MXF659_slide455

value: Lower leg


title: MKL1 SOX2

description: DNA (ChIP-enriched)

value: anti-human/mouse/Rat SOX2 (pAb, goat, R&D systems cat@#AF2018)


title: Blood QC133

description: Hybridized to Affymetrix SNP 6.0

tag: group


title: WT 30.11 miPIAS1_R1

description:
WT sample Total RNAseq miPIAS
merged_all_piasq175_c1.txt
WT 30.11 miPIAS1

value: Male


title: MKL1 POU4F3

description: DNA (ChIP-enriched)

value: positive

value: Merkel Cell carcinoma (MCC)

value: anti-POU4F3 (mAb, mouse, abcam cat#ab58128)


title: Het 27.7 miSAFE_R3

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
Het 27.7 miSAFE

value: HET

value: miSAFE


title: MKL1 LXH3

description: DNA (ChIP-enriched)

value: anti-LHX3/LIM (pAb, rabbit, abcam cat#ab14555)

value: Transcription Factor


title: Het 26.3 miSAFE_R2

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
Het 26.3 miSAFE


title: Blood QC137

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

tag: tissue

value: blood


title: MKL1 ISL1

description: DNA (ChIP-enriched)

value: anti-Islet 1 (mAb, rabbit, abcam cat#ab109517)


title: Blood QC131

description: Hybridized to Affymetrix SNP 6.0


title: Het 2.6 miSAFE_R1

description:
HET sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
Het 2.6 miSAFE

value: Bulk Tissue


title: MKL1 INSM1

description: DNA (ChIP-enriched)

value: anti-INSM1 (A-8) X (mAb., mouse, SantaCruz, cat#sc-271408 X)


title: Blood QC130

description: Hybridized to Affymetrix SNP 6.0


title: PD_MXF623_slide354

value: Forearm

value: Promega ref


title: PD_MXF633_slide353

value: Myxofibrosarcoma

value: Thigh


title: PD_MXF632_slide351

value: Upper arm


title: Blood QC134

description: Hybridized to Affymetrix SNP 6.0


title: PD_MXF2516_slide350


title: PD_MXF1041_DNA_slide623

value: Buttock


title: WT 2.3 miSAFE_R2

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
WT 2.3 miSAFE

value: WT

value: Male


title: WT 2.5 miSAFE_R3

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
WT 2.5 miSAFE


title: Blood QC128

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC132

description: Hybridized to Affymetrix SNP 6.0


title: Waga DNase rep2

description: DNA (ChIP-enriched)

source_name: Waga

value: Waga

value: positive

value: Merkel Cell carcinoma (MCC)

value: DNase

value: Open Chromatin


title: Blood QC127

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: PD_MFX912_slide617


title: MC38_5FUrep2

first: Jun

last: Lu

address: 10 Amistad St.

department: Yale Stem Cell Center

institute: Yale University

description: Replicate 2

data_processing:
Map to genome GRCm38 using STAR software (ver 2.4.1a), with transcritpome annotation (Ensembl release 81)
FPKM levels quantified with Picard (ver 2.9.0) program
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text file; contains gene level FPKM values

source_name: MC38 cells

growth_protocol: MC38 cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM, Life Sciences #11995065) with 10% fetal bovine serum (FBS, Life Sciences #16000044) and 1% penicillin/streptomycin/glutamine (PSG, Life Sciences #10378016).

extract_protocol:
Total RNA was extracted by TriZol
Standard polyA-based library preparation was performed (preparation by BGI)

treatment_protocol: Cells were treated with PBS or 5-FU (1mM) for 24 hours

tag: treatment

value: colon cancer


title: MC38_5FUrep1

description: Replicate 1


title: WT 29.3 miSAFE_R1

description:
WT sample Total RNAseq miSAFE
merged_all_piasq175_c1.txt
WT 29.3 miSAFE

value: Bulk Tissue

value: miSAFE


title: Waga DNase rep1

description: DNA (ChIP-enriched)

tag: virus status


title: MS1 DNase rep1

description: DNA (ChIP-enriched)

tag: antibody/treatment


title: Blood QC126

description: Hybridized to Affymetrix SNP 6.0

data_processing: The overall hybridization quality was estimated by the call rate obtained from Genotyping Console Software 4.2 (birdseed algorithm with default parameter settings). Partek Genomics Suite (version 6.5, Partek Inc., St. Louis, MO) was used for copy number analysis. Regions of CNV were detected using a Hidden Markov Model (HMM) algorithm in the Partek workflow for unpaired samples.

extract_protocol: Genomic DNA was extracted from peripheral blood for each patient and control subject, using QIAamp® DNA blood mini kit according to the manufacturer’s instruction


title: PD_MFX909_slide614

value: Promega ref


title: PD_MFX911_slide616

value: Myxofibrosarcoma


title: Blood QC125

description: Hybridized to Affymetrix SNP 6.0


title: MC38rep2

description: Replicate 2

value: PBS


title: MKL1 ATOH1

description: DNA (ChIP-enriched)

value: anti-MATH1 (pAb, rabbit, ThermoFisher, cat#PA5-29392)

tag: enrichment target

value: Transcription Factor


title: Blood QC129

description: Hybridized to Affymetrix SNP 6.0


title: PD_MFX908_slide613

value: Calf


title: Blood QC124

description: Hybridized to Affymetrix SNP 6.0


title: MC38rep1

description: Replicate 1


title: MKL2 DNase rep1

description: DNA (ChIP-enriched)

tag: target function


title: Blood QC123

description: Hybridized to Affymetrix SNP 6.0


title: MKL1 DNase rep2

description: DNA (ChIP-enriched)


title: PD_MFX904_slide590

value: Undifferentiated pleomorphic sarcoma

value: Lower leg


title: MKL1 DNase rep1

description: DNA (ChIP-enriched)

value: positive


title: MS1 DNase rep2

description: DNA (ChIP-enriched)

value: Merkel Cell carcinoma (MCC)


title: PD_MFX663_slide548

value: Thigh


title: RNA-Seq (Forrest) PTU WT rep2

city: Philadelphia

first: Mitchell

last: Lazar

state: PA

address: 3400 Civic Center Blvd

department: Perelman School of Medicine

institute: University of Pennsylvania

data_processing:
RNA-Seq alignment: STAR v.2.7.3a with parameters --outSAMstrandField intronMotif –outFilterMultimapNmax 1
Gene expression quantification: featureCounts v.2.0.0 from Subread package
Differential gene expression: edgeR v.3.28.1
ChIP-Seq alignment: bowtie2 v.2.4.1 with parameters “-N 1 -t”. Duplicate reads dropped and uniquely mapped reads are selected using samtools 1.3.1
ChIP-Seq coverage calculation: Homer v4.11.1. Tag directories are created with makeTagDirectory, bigWig files are created with makeUCSCfile
ChIP-Seq peak calling: Homer  v4.11.1 findPeaks, using corresponding input experiment as background
TR ChIP-Seq was additionally filtered against the WT experiment (no HA tag)
Genome_build: mm9
Supplementary_files_format_and_content: peak: Homer format peak files with additional annotations
Supplementary_files_format_and_content: bigWig: coverage tracks for ChIP-Seq data
Supplementary_files_format_and_content: tsv: edgeR results for two-conditions differential gene expression
Supplementary_files_format_and_content: tsv: featureCounts output for RNA-Seq data

molecule: polyA RNA

source_name: Mouse liver

growth_protocol: For PTU treatment, mice were provided with drinking water containing 1% perchlorate and 0.05% propylthiouracil for 3 wk. In the last five days all animals were intraperitoneally injected with vehicle (0.9% saline in 100 μl volume) for hypothyroid group or 40 μg/100 g T4 with 4μg/100g T3 for hyperthyroid group. For MMI treatment, mice were provided with 0.05% methimazole and 1% potassium perchlorate in the drinking water for 4 weeks inducing hypothyroidism, adapted from established methods (Amma et al., 2001). To induce hyperthyroidism, half of the groups were given T3 at 5 μg/ml in the same drinking water (MMI+T3).

extract_protocol:
Total RNA was extracted from snap-frozen liver tissues using TRIzol (Invitrogen) followed by RNeasy Mini Kit (Qiagen).
For RNA-seq, all samples were sequenced separately for three biological replicate. RNA integrity was examined using Agilent RNA 6000 Nano kit. RNA samples with RNA integrity number >7 (1 μg) were used for RNA cleanup, library preparation and sequencing by Novogene, Durham, NC. For MMI-treated mice, total RNA was prepared from frozen liver, using TRIzol Reagent (Invitrogen #15596-026), then mRNA enriched from 5 μg aliquots of total RNA using Dynabeads mRNA purification Kit (Ambion # 61006) and quantified using Qubit RNA Broad-range assay Kit (Thermo Fischer Scientific). Double-stranded cDNA was prepared using SuperScript Double- Stranded cDNA Synthesis Kit (Invitrogen) and cDNA libraries for sequencing were generated using ThruPLEX DNA-seq kit (Takara #R400428). Multiplex sequencing was performed, yielding single-end 50 base length reads, at the NIDDK Genomic Core using an Illumina HiSeq 2500 instrument. All RNA-seq experiments were performed with three biological replicates per condition.

tag: genotype

value: WT

tag: strain

value: Liver

value: MMI


title: Blood QC121

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: Blood QC122

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq (Forrest) PTU WT rep3


title: UISO DNase rep2

description: DNA (ChIP-enriched)

source_name: UISO

value: UISO

value: negative

value: DNase

value: Open Chromatin


title: PD_MFX906_slide592

value: Myxofibrosarcoma

value: Axilla

value: Promega ref


title: PD_MFH2938_slide634

value: Undifferentiated pleomorphic sarcoma

value: Upper arm


title: Blood QC120

description: Hybridized to Affymetrix SNP 6.0


title: MCC26 DNase rep2

description: DNA (ChIP-enriched)


title: PD_MFH662_slide728


title: RNA-Seq (Forrest) PTU+TH WT rep3


title: RNA-Seq (Forrest) PTU+TH WT rep2


title: RNA-Seq (Forrest) PTU WT rep1


title: MKL2 DNase rep2

description: DNA (ChIP-enriched)

value: positive


title: Blood QC103

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq (Forrest) PTU+TH WT rep1


title: RNA-Seq (Forrest) PTU Thrb_KO rep3


title: Blood QC102

description: Hybridized to Affymetrix SNP 6.0


title: MCC26 DNase rep1

description: DNA (ChIP-enriched)

value: Merkel Cell carcinoma (MCC)


title: Blood QC101

description: Hybridized to Affymetrix SNP 6.0


title: MCC13 DNase rep1

description: DNA (ChIP-enriched)


title: UISO DNase rep1

description: DNA (ChIP-enriched)


title: Blood QC100

description: Hybridized to Affymetrix SNP 6.0


title: Gene expression profiling of CD44-CD133+ and CD44+CD133+ Caco2 population

type: RNA

city: SEOUL

first: JUNG

middle: HOON

last: KIM

state: MAPOGU

address: SOGANG R 1206

department: LIF SCIENCE

country: South Korea

institute: SOGANG UNIV

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 9.3.2.1) was used for background subtraction and LOWESS normalization.

label_protocol: 0.2ug of total RNA was labeled using Low Input Quick Amp Labeling Kit, Two-Color (Agilent Technology) as following manufacturer's instructions.

growth_protocol: Caco-2 was cultured in MEM with 10%FBS

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

treatment_protocol: Caco-2 populations were sorted with PE conjugated anti CD133 and FITC conjugated anti CD44

tag: population


title: CYLD KO Treg cells rep2

first: Jeeho

last: Lee

address: 9420 Athena Circle

institute: La Jolla Institute for Immunology

description: gene expression data from Cyld-/- Treg cells

hyb_protocol: cRNA was hybridized for 16 hr at 45°C on GeneChip Mouse Gene 1.0 ST arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000.

data_processing: Data were analyzed by GenePattern software suite.

source_name: YFP+ Treg cells from Cyld fl/fl Foxp3-yfp-cre mice

label_protocol: Biotinylated cRNA were prepared according to standard Affymetrix protocol

growth_protocol: All mice were maintained in SPF facility. 6~8 wk-old mice were used.

extract_protocol: Total RNA extraction was performed by RNeasy Micro Kit from Qiagen according to the manufacturer's instructions.

treatment_protocol: YFP+ Treg cells from spleen were sorted by BD FACS ARIA.

value: spleen and lymph nodes

value: C57Bl6, Cyld fl/fl Foxp3-yfp-cre

tag: age

value: 6~8 weeks


title: RNA-Seq (Forrest) PTU Thrb_KO rep1

value: Liver

value: MMI


title: CYLD KO Treg cells rep1


title: Blood QC99

first: huanxin

last: chen

institute: Teda International Cardiovascular Hospital

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: RNA-Seq (Forrest) PTU+TH Thrb_KO rep2


title: Blood QC97

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq (Forrest) PTU+TH Thrb_KO rep3


title: MCC13 H3K27ac

description: DNA (ChIP-enriched)

tag: cell line

value: negative

value: anti-H3K27ac (pAb, rabbit, Active Motif, cat.#39133)

value: Active enhancers


title: MCC26 H3K27ac

description: DNA (ChIP-enriched)


title: ChIP-Seq:H3K27Ac PTU TR_3xHA input rep4

extract_protocol:
HA-TRβ and H3K27ac ChIP-seq were performed as previously described (Armour et al., 2017). Magnetic beads (Pierce) were used to perform the immunoprecipitation with H3K27ac antibody (Active Motif, Cat #: 39133) or HA aagnetic beads (Pierce) . For ChIP-seq of HA-TRβ, 3 biological replicates were used for sequencing, and WT mice were used as negative control.
The ChIP-seq library has been performed as previously described (Armour et al., 2017)

value: PTU


title: ChIP-Seq:H3K27Ac PTU TR_3xHA input rep3


title: THC4_96hpf

city: Woods Hole

first: Neelakanteswar

last: Aluru

address: 45 Water Street

department: Biology

institute: Woods Hole Oceanographic Institution

data_processing:
Pre-processed data was mapped to the zebrafish genome using STAR aligner
Htseq-count was used to get the read counts mapped.
EdgeR was used for statistical analysis
Genome_build: Danio_rerio.GRCz11.dna.toplevel.fa;Danio_rerio.GRCz11.92.gtf

organism: Danio rerio

source_name: Larvae

growth_protocol: Zebrafish embryos were exposed to either DMSO, CBD or THC throughout development and sampled either at 10 or 96 hours post-fertilization for gene expression profiling.

extract_protocol:
RNA extraction was done using an RNeasy mini-kit (Qiagen #74104) in conjunction with gDNA removal via RNase-Free DNase set (Qiagen #79254) following manufacturer’s recommended protocol
Library construction was done using TruSeq Illumina library preparation kit. paired-end 100 bp sequencing was done on a Illumina HiSeq 2000 Illumina platform.
paired-end 100 bp sequencing was done on a Illumina HiSeq 2000 Illumina platform.

value: THC

tag: time

value: Larvae


title: MKL2 H3K27ac

description: DNA (ChIP-enriched)


title: MS1 H3K27ac

description: DNA (ChIP-enriched)


title: Blood QC98

address: No.61, third avenue, tianjin economic and technolo

description: Hybridized to Affymetrix SNP 6.0


title: Waga H3K27ac

description: DNA (ChIP-enriched)

value: Waga


title: Blood QC95

description: Hybridized to Affymetrix SNP 6.0


title: THC2_96hpf


title: THC3_96hpf


title: RNA-Seq (Forrest) PTU+TH Thrb_KO rep1


title: Blood QC94

description: Hybridized to Affymetrix SNP 6.0


title: THC1_96hpf


title: RNA-Seq (Forrest) PTU Thrb_KO rep2


title: Blood QC96

description: Hybridized to Affymetrix SNP 6.0


title: MKL1 H3K27ac

description: DNA (ChIP-enriched)


title: WT Treg cells rep2

description: gene expression data from WT control Treg cells

source_name: YFP+ Treg cells from Cyld+/+ Foxp3-yfp-cre mice

value: C57Bl6, Cyld+/+ Foxp3-yfp-cre


title: UISO H3K27ac

description: DNA (ChIP-enriched)

value: UISO


title: THC4_10hpf

source_name: Embryos

value: Embryos


title: Blood QC93

description: Hybridized to Affymetrix SNP 6.0

source_name: healthy control_blood


title: WT Treg cells rep1

value: spleen and lymph nodes


title: ChIP-Seq:H3K27Ac PTU TR_3xHA input rep2


title: THC3_10hpf


title: UISO input

description: DNA (input control)

value: Merkel Cell carcinoma (MCC)

value: none (input)

value: input

value: control


title: ChIP-Seq:H3K27Ac PTU TR_3xHA input rep1

value: Liver


title: Blood QC92

description: Hybridized to Affymetrix SNP 6.0

value: healthy control

value: blood


title: THC2_10hpf


title: MCC26 input

description: DNA (input control)

value: negative


title: Blood QC91

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA input rep4

value: PTU+TH


title: Blood QC90

description: Hybridized to Affymetrix SNP 6.0


title: Waga input

description: DNA (input control)

value: positive


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA input rep3


title: MCC13 input

description: DNA (input control)


title: Blood QC88

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC89

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA input rep2


title: MS1 input

description: DNA (input control)


title: MKL2 input

description: DNA (input control)


title: Blood QC87

description: Hybridized to Affymetrix SNP 6.0


title: CBD3_96hpf

value: CBD


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA input rep1


title: CBD2_96hpf

value: Larvae


title: CBD4_96hpf


title: MKL1 input

description: DNA (input control)


title: Blood QC86

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:H3K27Ac PTU TR_3xHA rep2

value: PTU

tag: chip antibody

value: Histone H3K27ac antibody; Active Motif, Cat #:39133


title: ChIP-Seq:H3K27Ac PTU TR_3xHA rep1


title: CBD1_96hpf


title: BT549_ITGAV-gRNA4-UT-2

first: Archis

last: Bagati

state: MASSACHUSETTS

address: 450 brookline ave.

institute: Dana-Farber Cancer Institute

description:
ITGAV-gRNA-2 versus Control
20181220_BT549_ITGAV-gRNA4-UT-2_20181205_IDXB12_RV6429_S15

data_processing:
Statistics for differentially expressed genes were calculated using DESeq2 (version 3.5) (47) and Cufflinks (48).  Differential gene expression was analyzed using the DESeq2 (1.8.1) package in R using default settings (47). Principal component analyses were generated using the prcomp function in R and plotted with ggplot2. Human and mouse gene homologues were matched using the Mouse Genome Informatics annotation. Heatmaps were generated using the heatmap.2 function in R
Genome_build: hg19; mm9
Supplementary_files_format_and_content: Differential gene expression

growth_protocol: The base medium for this cell line is ATCC-formulated RPMI-1640 Medium, ATCC 30-2001. To make the complete growth medium, add the following components to the base medium: fetal bovine serum (ATCC 30-2020) to a final concentration of 10%.

extract_protocol:
Total RNA was extracted from control, SOX4 or ITGAV edited human BT549 and murine 4T1 cells cultured in complete RPMI media in biological triplicates.  RNA extraction was performed using the RNeasy Plus Mini Kit (Qiagen # 74134) following the manufacturer’s protocol. Total RNA was quality-checked using an Agilent BioAnalyzer 2000 instrument.  RNA with an integrity number of greater than 9.5 was used for subsequent analyses.
Libraries were prepared with TruSeq RNA Sample Prep Kit v2 (Illumina). Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for single-end 75bp sequencing using an Illumina NextSeq 500 instrument.

value: human TNBC cells

tag: genotype/variation

value: ITGAV-edited


title: CBD4_10hpf

value: Embryos


title: Blood QC85

description: Hybridized to Affymetrix SNP 6.0


title: THC1_10hpf

value: THC


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA rep2


title: ChIP-Seq:H3K27Ac PTU+TH TR_3xHA rep1


title: Blood QC84

description: Hybridized to Affymetrix SNP 6.0


title: CBD3_10hpf


title: BT549_ITGAV-gRNA4-UT-1

description:
ITGAV-gRNA-2 versus Control
20181220_BT549_ITGAV-gRNA4-UT-1_20181205_IDXA12_RV6429_S14


title: CBD2_10hpf


title: RNA-Seq PTU+TH TR_3xHA rep3


title: Blood QC83

description: Hybridized to Affymetrix SNP 6.0


title: BT549_ITGAV-gRNA1-UT-2

description:
ITGAV-gRNA-1 versus Control
20181220_BT549_ITGAV-gRNA1-UT-2_20181205_IDXH11_RV6429_S13


title: BT549_ITGAV-gRNA1-UT-1

description:
ITGAV-gRNA-1 versus Control
20181220_BT549_ITGAV-gRNA1-UT-1_20181205_IDXG11_RV6429_S12


title: Blood QC82

description: Hybridized to Affymetrix SNP 6.0


title: CBD1_10hpf


title: RNA-Seq PTU+TH TR_3xHA rep2


title: Blood QC81

description: Hybridized to Affymetrix SNP 6.0


title: DMSO3_96hpf

value: DMSO


title: RNA-Seq PTU+TH TR_3xHA rep1


title: RNA-Seq PTU TR_3xHA rep3


title: BT549_SOX4-gRNA2-UT-1

description:
SOX4-gRNA-2 versus Control
20181220_BT549_SOX4-gRNA2-UT-1_20181205_IDXE11_RV6429_S10


title: Blood QC80

description: Hybridized to Affymetrix SNP 6.0


title: BT549_SOX4-gRNA2-UT-2

description:
SOX4-gRNA-2 versus Control
20181220_BT549_SOX4-gRNA2-UT-2_20181205_IDXF11_RV6429_S11


title: BT549_SOX4-gRNA1-UT-2

description:
SOX4-gRNA-1 versus Control
20181220_BT549_SOX4-gRNA1-UT-2_20181205_IDXD11_RV6429_S9


title: Blood QC79

description: Hybridized to Affymetrix SNP 6.0


title: DMSO2_96hpf


title: BT549_SOX4-gRNA1-UT-1

description:
SOX4-gRNA-1 versus Control
20181220_BT549_SOX4-gRNA1-UT-1_20181205_IDXC11_RV6429_S8


title: RNA-Seq PTU TR_3xHA rep2


title: Blood QC78

description: Hybridized to Affymetrix SNP 6.0


title: RNA-Seq PTU TR_3xHA rep1


title: DMSO4_10hpf


title: Blood QC77

description: Hybridized to Affymetrix SNP 6.0


title: BT549_LacZ-UT-1

description:
Control
20181220_BT549_LacZ-UT-1_20181205_IDXA11_RV6429_S6


title: BT549_LacZ-UT-2

description:
Control
20181220_BT549_LacZ-UT-2_20181205_IDXB11_RV6429_S7


title: ChIP-Seq:TR PTU+TH TR_3xHA rep3

description: both_OldInput_Union.fully_annotated.peaks

value: Pierce™ Anti-HA Magnetic Beads #88836


title: Blood QC76

description: Hybridized to Affymetrix SNP 6.0


title: DMSO3_10hpf


title: DMSO4_96hpf


title: DMSO2_10hpf


title: ChIP-Seq:TR PTU+TH TR_3xHA rep1


title: BT549-UT-3_SOX4

data_processing:
Raw reads were aligned to hg19 using bwa. The resulting sam files were converted to bam with samtools. MACS2 was used to call peaks on the bam files. The bedGraph files containing signal per million reads produced from MACS2 were converted to bigwig files with ucsctool kit. ChIP-seq signals were extracted with bwtool from bigwig files and visualized in R. A peak catalog consisting of all possible peak intervals in ChIP-seq was produced. ChIP-seq signals were extracted with bwtool from bigwig files and then visualized in R. IGV viewer was used to visualize enriched peak relative to hg19 reference genome
Genome_build: hg19
Supplementary_files_format_and_content: bw, bed

growth_protocol: The base medium for this cell line is RPMI-1640 Medium (ATCC 30-2001). To make the complete growth medium, add the following components to the base medium: 0.023 U/ml insulin; fetal bovine serum (FBS; ATCC 30-2020) to a final concentration of 10%.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed using Accel-NGS 2S DNA library kit from Swift Biosciences. Fragments of the desired size were enriched using AMPure XP beads (Beckman Coulter). 36-bp paired-end reads were sequenced on a Nextseq instrument (Illumina).

tag: passages

value: SOX4 antibody (ab86809 Abcam)


title: ChIP-Seq:TR PTU TR_3xHA rep3

value: Liver


title: Blood QC74

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: BT549-UT-2_SOX4

tag: cell type


title: Blood QC73

description: Hybridized to Affymetrix SNP 6.0

tag: group

value: blood


title: ChIP-Seq:TR PTU TR_3xHA rep2

tag: tissue


title: BT549-UT-1_SOX4


title: DMSO1_96hpf

tag: treatment


title: ChIP-Seq:TR PTU TR_3xHA rep1


title: Blood QC72

description: Hybridized to Affymetrix SNP 6.0


title: RF-Mock-D5-2

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

data_processing:
Read library quality was assessed using FastQC and MultiQC packages.
Illumina adapters were removed and leading and trailing low quality bases (below quality 30) were trimmed using trimmomatic
Reads less than 36 bases long after trimming were dropped.
Whippet: Annotation (GTF) only index was built using GENCODE v27 annotations by Whippet.  Trimmed reads were then aligned directly to the contiguous splice graphs built from the hg38 human reference genome, and Percent Spliced In (PSI) of each AS event was quantified. After pooling the three PSI results for each biological sample, the comparison between siSDE2-1 and control, as well as siSDE2-2 and control were implemented. For both of these comparisons, three filters were applied.  The absolute difference between PSI in knockdown and in control should be greater than 0.1. The probability of this event happening as identified by Whippet algorithm should be greater than 0.9, and 7 the PSI in the knockdown condition should be greater than 0.1. The filtered results from the two comparisons were then intersected to find the significant events.
IRFinder: The IRFinder reference was built from the GENCODE v27 annotations and hg38 human reference genome, prior to aligning trimmed reads to it in FASTQ mode. The resulted unsorted BAM files from the three replicates were then concatenated and pooled together for each biological sample, producing quantification of the intron retention (RI) events for siSDE2-1, siSDE-2 and control, respectively. Next, the comparisons between siSDE2-1 and control, as well as siSDE2-2 and control were analyzed using the provided script for small amounts of replicates. For both of the results, two filters were applied. Events marked as known exons or minor isoforms were removed, and events with FDR less than 0.05 were selected. The filtered results from the two comparisons were then intersected to find the significant events.
rMATS: Mapping the trimmed reads to the reference genome was completed via STAR using the same annotation and reference genome files as noted above. The produced BAM files were then used as input for pooling and contrasting through the rMATS algorithm between knockdown and control, generating quantitative results of the five AS categories. Only FDR values less than 0.05 were considered for further analysis.
Consensus dAS events: The three sets (Whippet, IRFinder, rMATS) of overlapped results were subsequently combined to create an aggregated view with all of the AS events, after removing duplicated ones that were identified by more than one tool. The PSI in knockdown was calculated as the average of that in siSDE2-1 and siSDE2-2, and delta PSI was computed as the difference between PSI knockdown and PSI control.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated value files containing significant consensus dAS events

source_name: HeLa cells

growth_protocol: HeLa cells were cultured in Dulbeccos Modified Eagle Medium (DMEM) (10% FBS, 1% Penicillin/Streptomycin). All cells were maintained at 37°C in a humidified incubator at 5% CO2. Cell culture media and supplements were obtained from Gibco Invitrogen and all plasticware came from Corning (Corning, NY).

extract_protocol:
Cells were collected by trypsinization (Thermo Fisher #25300054) and pelleted by centrifugation. Pellet was washed in phosphate-buffered saline and RNA was extracted using a Qiagen Rneasy Mini Kit (Qiagen #74106) following the manufacturer's instructions.
Samples were submitted to the BU Microarray and Sequencing Core for library preparation and polyadenylated RNA selection using Kapa RNA HyperPrep kit with Riboerase, and sequenced yielding 2x75 bp paired-end read datasets. Read library quality was assessed using FastQC (Andrews, 2015) and MultiQC (Ewels, Magnusson, Lundin, & Käller, 2016) packages. Illumina adapters were removed and leading and trailing low quality bases (below quality 30) were trimmed using Trimmomatic (Bolger, Lohse, & Usadel, 2014). Reads which were less than 36 bases long after these steps were dropped.

treatment_protocol: Cells were transfected with either 100nM (Non-targeting control, siSDE2-2) or 20nM (siSDE2-1) siRNA using Lipofectamine RNAiMax diluted in Opti-MEM according to the manufacturer's instructions. The next day, the siRNA solution was removed from cells and replaced with fresh media. Cells were collected after 3 days.

value: HeLa

value: Mock

tag: day

tag: sirna

tag: replicate


title: ChIP-Seq:TR TR_3xHA input


title: Blood QC70

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:TR PTU+TH TR_3xHA rep2

value: PTU+TH


title: RF-Mock-D5-1


title: ChIP-Seq:TR WT inp16

value: WT


title: Blood QC75

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC69

description: Hybridized to Affymetrix SNP 6.0


title: DMSO1_10hpf


title: ChIP-Seq:TR WT inp15


title: ChIP-Seq:TR WT inp14


title: Blood QC68

description: Hybridized to Affymetrix SNP 6.0


title: Aorta of WKY rep3

city: Chongqing

first: Junyi

last: Yu

address: 10th Changjiangzhilu Road, Yuzhong District

department: Department of Cardiology

institute: Daping Hospital, The Third Military Medical University, Chongqing, P.R. China.

description: Gene expression data from thoracic aorta tissue of 24 weeks-old WKY rat.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45℃ on Affymetrix GeneChip® Rat Gene 2.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: After hybridization and washing, processed slides were scanned with the Affymetrix GeneChip Scanner 3000 7G.

data_processing: The Affymetrix Expression Console (version 1.2.1) implementation of RMA was used for quantile normalization and background correction. All gene level files were imported into Affymetrix Expression Console (version 1.2.1) and normalized by the RMA algorithm.

organism: Rattus norvegicus

source_name: thoracic aorta

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

growth_protocol: WKY and SHRs were obtained from Vital River Laboratories Animal Technology Company (Beijing), and fed in the Animal Center of Daping Hospital (Chongqing, China) under normal condition.

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

treatment_protocol: Before sacrifice, tail blood pressure was measured using Softron BP2010A Blood Pressure Meter without other treatment.

value: WKY


title: ChIP-Seq:TR WT inp13


title: RF-Mock-D5-3


title: Blood QC67

city: Tianjin

description: Hybridized to Affymetrix SNP 6.0


title: RF-Mock-D3-2

city: Boston


title: Aorta of SHR rep3

description: Gene expression data from thoracic aorta tissue of 24 weeks-old SHR.

value: SHR


title: RF-siSDE2_2-D5-3

value: SDE2 KD


title: ChIP-Seq:TR WT inp12


title: Aorta of WKY rep1


title: Aorta of WKY rep2


title: Blood QC71

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:TR WT inp11


title: Blood QC65

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_2-D5-1


title: Aorta of SHR rep2


title: RF-Mock-D3-3


title: RF-siSDE2_2-D5-2


title: Aorta of SHR rep1


title: ChIP-Seq:TR WT inp10


title: Blood QC64

description: Hybridized to Affymetrix SNP 6.0


title: RF-Mock-D3-1


title: Blood QC63

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_2-D3-3


title: Blood QC66

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_2-D3-2


title: ChIP-Seq:TR WT inp9


title: Blood QC62

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:TR WT rep8


title: U87 siLINC00152 set4

city: Leipzig

first: Stefanie

last: Binder

address: Perlickstr. 1

department: Diagnostics

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: gene expression 40h after siRNA-knockdown

hyb_protocol: 600ng of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Human Gene Expression Microarray SurePrint G3 8x60k v2 (G4851B) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides (Scan Area 61x21.6mm, Scan resolution 3, Dye channel is set to Green).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1_1105_Oct12 and Grid: 039494_D_F_20140228) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: U87, siRNA to LINC00152 exon1, replicate 4

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 1µg total RNA using the One-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: A172 and U87 glioblastoma cells were grown in DMEM/Glutamax medium supplemented with 10% FCS and 1% penicillin/streptomycin at 37°C and 5% CO2 in an H2O-saturated atmosphere.

extract_protocol: After 40h, cells were harvested, washed with PBS and total RNA isolation was performed using TRIzol (LIFE Technologies, Carlsbad, USA), following the standard protocol. Total RNA was DNase-digested using the TURBO-DNA-free Kit (LIFE Technologies) as recommended by the manufacturer. Determination of the RNA quality and concentration occurred by Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and Qubit (LIFE Technologies).

treatment_protocol: 5x10^6 A172 or U87 cells, respectively, were washed in PBS and the cell pellet was resuspended in 100µl transfection buffer together with 20pmol/ml siRNA: either a negative control siRNA with medium GC content and no RNA target sequence or an siRNA targeting LINC00152 RNA in exon 1. Transfection occurred by electroporation (one pulse at 1300V for 30ms) using the NEON transfection system by ThermoFisher. Afterwards, cells were transferred to 10ml DMEM/Glutamax medium (supplemented with 10% FCS and 1% Pen/Strep), followed by a 40h cultivation at 37°C and 5% CO2 in an H2O-saturated atmosphere.

value: siLINC00152 (exon1)

value: LINC00152 knockdown


title: Blood QC61

description: Hybridized to Affymetrix SNP 6.0


title: U87 siLINC00152 set1

source_name: U87, siRNA to LINC00152 exon1, replicate 1


title: RF-siSDE2_1-D5-3


title: U87 siLINC00152 set3

source_name: U87, siRNA to LINC00152 exon1, replicate 3


title: U87 siLINC00152 set2

source_name: U87, siRNA to LINC00152 exon1, replicate 2


title: ChIP-Seq:TR WT rep7


title: ChIP-Seq:TR WT rep6


title: Blood QC60

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC59

description: Hybridized to Affymetrix SNP 6.0


title: ChIP-Seq:TR WT rep5


title: RF-siSDE2_1-D5-2


title: Blood QC58

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_1-D5-1


title: U87 control set2

source_name: U87, negative control siRNA, replicate 2

value: scramble control

value: control


title: RF-siSDE2_1-D3-3


title: U87 control set1

source_name: U87, negative control siRNA, replicate 1


title: ChIP-Seq:TR WT rep4


title: Blood QC57

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_2-D3-1


title: RF-siSDE2_1-D3-2


title: Blood QC56

description: Hybridized to Affymetrix SNP 6.0


title: RF-siSDE2_1-D3-1


title: U87 control set3

source_name: U87, negative control siRNA, replicate 3


title: Blood QC54

description: Hybridized to Affymetrix SNP 6.0


title: RNAseq_Flox_rep4

city: San Francisco

first: Eric

middle: Joseph

last: Wigton

address: 500 Parnassus Ave.

department: Immunology

institute: UCSF

description: ready for alignment to genome

data_processing:
Raw Fastqs were binned based on barcode using python bst  and perl fastx_barcode_splitter.pl
barcodes and adapters were trimmed using parallel -j3 'cutadapt -e 0.2 -a GTGTCTTTACACAGCTACGGCGTCG -m 19 --cut 11
The fastq files were then aligned to the mm9 genome and combined into single BAM using bowtie2 and samtools
BAM files were intersected to exclude miRNA reads using miRBASE bam filed and samtools BAM files converted to SAM files using samtools for downstream use on dCLIP
For RNAseq fastq files were aligned using STAR and compared using DESeq2 to give All_genes text files
Genome_build: mm9
Supplementary_files_format_and_content: read count and DESeq analysis for RNA-seq data. dCLIP analysis produces dCLIP_output.txt and dCLIP_summary.bed files containing the results (WT file 1 input KO file 2 input) IGV tool TDF files for peak viewing of individual library samples.

source_name: activated splenic B cells

growth_protocol: Cells were grown in 96 well plates sitmulated with aCD40 (500ng/ml) IL4 (25ng/ml) and IL21 (10ng/ml) for 4 days

extract_protocol:
RNA was extracted by Trizol for RNAseq or by Ago2 immunoprecipitation for Ago2-HITS-CLIP
RNAseq library multiplexed for HISEQ4000.  Ago2-HITS-CLIP custom library design for HISEQ2500 (see Gagnon JD, et al 2019 and Loeb, et al 2012)

value: spleen

value: B cell

tag: rna fraction

value: total RNA


title: Blood QC53

description: Hybridized to Affymetrix SNP 6.0


title: U87 control set4

source_name: U87, negative control siRNA, replicate 4

tag: genotype


title: MDA231 PARP1 KO shSUZ12 rep2

city: DaeJeon

first: Mi Young

last: Kim

address: Biological science

institute: KAIST

data_processing:
Base calling was performed by Illumina Genome Studio(V2010.1).
Reference genome sequence data from Homo sapiens were obtained from the National Center for Biotechnology Information (NCBI) Genome database (assembly ID: GRCh38).
STAR was applied to tissue samples for mapping and to quantify reads to the reference genome (ver. 2.5). To estimate gene expression levels, counts per million (CPM) mapped reads values were calculated for each sample. The CPM data were normalised using quantile normalization in the R language environment (version 3.2.5).
Genome_build: GRCh38
Supplementary_files_format_and_content: excel

source_name: Breast cancer cells

growth_protocol: MDA-MB-231 cells were cultured in DMEM (Welgene, Republic of Korea) supplemented with 10% fetal bovine serum (FBS; Welgene, Republic of Korea) for 2 days.

extract_protocol:
Total RNAs were isolated using RNeasy mini kits (Qiagen, Valencia, CA).
The Libraries were prepared using the TruSeq stranded mRNA sample preparation kit (Illumina).

tag: passage

value: PARP1 and SUZ12 depletion


title: Blood QC52

description: Hybridized to Affymetrix SNP 6.0

value: healthy control


title: A172 siLINC00152 set3

source_name: A172, siRNA to LINC00152 exon1, replicate 3


title: MDA231 PARP1 KO shSUZ12 rep1


title: mutant

city: Seattle

first: Christine

last: Queitsch

state: WA

address: 3720 15th Ave NE, Foege Hall

department: Genome Sciences

institute: University of Washington

description: single cell RNA-seq data from 20 hour experiment

data_processing:
Illumina Nextseq 500 base caller is used
cellranger mkfastq was run on the nextseq output to generate fastq files
cellranger counts was run on output fastq files from each sample, to identify barcodes with sufficient reads for analysis, and to align reads to the Arabdiopsis genome using the Araport annotation.
cellranger aggr was then used to combine samples into one matrix and barcode set
Genome_build: TAIR10/ARAPORT
Supplementary_files_format_and_content: matrix.mtx is the UMI count matrix for the number of UMIs, each barcode (cell) had associated with each gene; barcodes.tsv contains barcode info, as well as experiment of origin and cell type label; genes.tsv

organism: Arabidopsis thaliana

source_name: root tissue

growth_protocol: For all plant experiments, Arabidopsis seeds were sown on 0.5× LS 0.8% agar plates, stratified at 4°C for 2 days, and grown in continuous light conditions at 22°C for respective experimental design.

extract_protocol:
Protoplast isolation was done according to Bargmann and Birnbaum (2010), with slight modifications.
10X genomics protocol

treatment_protocol: Seeds were placed on 0.5 LS+0.8% bacto-agar plate following a specific pattern to avoid seedling collision during the lateral root bend essay.  The plate was stratified during 120 hours, grown vertically for 96 hours at 22°C, rotated 90°C while keeping vertically and grown for an additional 20 hours.

value: root tissue

tag: experiment

value: 20 hour

tag: strain

value: iaa14 mutant


title: RNAseq_Flox_rep3

description: ready for alignment to genome


title: A172 siLINC00152 set2

source_name: A172, siRNA to LINC00152 exon1, replicate 2

tag: cell line


title: MDA231 PARP1 KO shEZH2 rep2

value: PARP1 and EZH2 depletion


title: 20 hour rep 2

description:
single cell RNA-seq data from 20 hour experiment
matrix.mtx
barcodes.tsv
genes.tsv


title: A172 control set3

source_name: A172, negative control siRNA, replicate 3


title: Blood QC51

description: Hybridized to Affymetrix SNP 6.0

source_name: healthy control_blood

value: blood


title: A172 siLINC00152 set1

source_name: A172, siRNA to LINC00152 exon1, replicate 1


title: A172 control set1

source_name: A172, negative control siRNA, replicate 1


title: MDA231 PARP1 KO shEZH2 rep1


title: RNAseq_Flox_rep1

description: ready for alignment to genome


title: MDA231 WT shCntr rep2

value: nontargeting shRNA


title: 08 hour rep 2

value: 08 hour


title: 00 hour rep 2

description:
single cell RNA-seq data from 08 hour experiment
matrix.mtx
barcodes.tsv
genes.tsv

value: 00 hour


title: ChIP-Seq:TR WT rep1

source_name: Mouse liver

value: WT

value: Liver

value: Pierce™ Anti-HA Magnetic Beads #88836


title: Blood QC50

description: Hybridized to Affymetrix SNP 6.0


title: Blood QC49

description: Hybridized to Affymetrix SNP 6.0


title: MDA231 WT shCntr rep1


title: RNAseq_KO_rep4

description: ready for alignment to genome


title: RNAseq_KO_rep3

description: ready for alignment to genome


title: Blood QC48

description: Hybridized to Affymetrix SNP 6.0


title: A172 control set2

source_name: A172, negative control siRNA, replicate 2

value: scramble control

value: control


title: 20 hour rep 1


title: Blood QC47

description: Hybridized to Affymetrix SNP 6.0


title: RNAseq_Flox_rep2

description: ready for alignment to genome

value: spleen

value: B cell