title: Cell_103 (I7)

data_processing:
After demultiplexing sequencing libraries to individual cell FASTQ files, each library was aligned to an indexed mm10 RefSeq genome using RSEM version 1.2.1242, and bowtie2 version 2.2.3 with the following options enabled: rsem-calculate- expression -p $CORES—bowtie2—paired-end -output- genome-bam.
Genome_build: mm10

extract_protocol: Sorted mammary epithelial cells were washed and resuspended at a concentration of ~500 cells/µl. For Fluidigm microfluidics scRNAseq, primary cell suspensions were mixed with Fluidigm C1 Suspension Reagents (Fluidigm 100-5315) at a ratio of 8:2 before loading mix onto C1 chip (Fluidigm 100-5760). Captured cells were visualized and counted using a Keyence BZ-X710 microscope (Keyence Corporation, Itasca, Illinois, USA). Single-cell RNA isolation and amplification were performed using the Fluidigm C1 Single Cell Auto Prep IFC following the Fluidigm Protocol: 100-7168 I1. cDNA library preparation was performed following the Fluidigm C1 Protocol: 100-7168 I1 (1771x/1772x/1773x). RNA spike-in controls were omitted. Next, reverse transcription and cDNA pre-amplification were performed using the SMARTer Ultra Low RNA Kit (Clontech) and processed in the C1 system by running script mRNA Seq: RT and Amp (1771x/1772x/1773x). After completion of RT and cDNA amplification, the samples were harvested and quantified through the PicoGreen assay (Thermo-Fisher) using the Agilent Bioanalyzer (Agilent Genomics). Equal amounts of cDNA from each sample were tagmented and prepared for library synthesis using the using Nextera XT DNA Sample preparation kit with 96 indices (Illumina), per the protocol supplied by Fluidigm. Libraries were multiplexed and sequenced as paired-end on a Next-Seq 4000 Illumina sequencing platform. cDNA amplification, library preparation, quality control, and sequencing were performed at the Genomics High Throughput Sequencing facility at the University of California, Irvine.


title: A_S8137

status: Public on Mar 08 2022

type: SRA

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

country: USA

institute: University of Pennsylvania

library_source: genomic

data_processing:
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001. Peaks present in at least 2 samples were iincluded
Normalization and differential accessibility analysis was done with DESeq2.
Batch correction was performed using combat for library preparation group and sample location.
Genome_build: hg19
Supplementary_files_format_and_content: chromatin accessbility counts file

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013 using 0.1% Tween 20 instead of IGEPAL CA-630.Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell

tag: donor type

value: Older

tag: donor id

tag: age

tag: Sex

value: Male

tag: cmv serostatus

tag: cell type

tag: cell subset

tag: library preparation group

tag: sample acquisition location

value: NIA


title: A_S8138


title: Cell_102 (I6)

city: Irvine

first: Lupe

last: Gutierrez

state: CA

address: 825 Health Sciences Rd D288

institute: University of California, Irvine

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: Mouse mammary gland

growth_protocol: All mouse lines were maintained and bred following the procedures that conform with and have been approved by the UC Irvine Institutional Animal Care and Use Committee (IACUC).

treatment_protocol: No treatment

tag: strain

tag: tissue

value: Mouse mammary gland


title: A_S8135

value: UPenn


title: Cell_101 (I5)


title: Cell_100 (I4)


title: A_S8134


title: Cell_99 (I3)


title: A_S8133


title: Cell_98 (I2)


title: Cell_97 (I1)


title: CD4_WT_Naive3_ATAC

city: columbus

first: Ruoning

last: Wang

state: OH

address: 700 Children's Drive

institute: Nationwide children's hospital

description: ATAC seq of naive WT CD4 T cell

data_processing:
Cells were suspended in  tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components
ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles, and excess primers were removed by size selection with AMPure XP beads.
reads are scanned for adaptor sequences and trimmed with cutadapt (version 2.3). Reads are then mapped to mm10 with bowtie2 (version 2.3.4.3). Properly aligned, non-mitochondrial read pairs were retained for peak calling with MACS2 (version 2.2.4).
Genome_build: mm10

source_name: ATAC seq of naive WT CD4 T cell

growth_protocol: CD4+ T cells isolated from mice as naïve or activated for 30hrs.

extract_protocol:
Cells were suspended in  tagmentation master mix prepared from Illumina Tagment DNA TDE1 Enzyme and Buffer Kit components
RNA libraries were prepared for sequencing using standard protocols at the nationwidechildrens hospital.
ATAC-seq libraries were amplified with barcoded Nextera primers for 14 cycles, and excess primers were removed by size selection with AMPure XP beads.

value: CD4 T cell

tag: genotype

value: Wild Type

tag: treatment

value: naive


title: A_S8132

value: Negative


title: A_S8130


title: Cell_96 (H12)


title: Cell_95 (H11)


title: A_S8129


title: A_S8128

value: Female


title: A_S8127


title: CKO2_S5_L008

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

data_processing:
. Raw reads were trimmed and filtered using sickle (v0.7)
remaining reads aligned to the mm10 reference genome with the subjunc aligner from the subread package (v2.0)
Resulting BAM files were used for gene counts against the ENSEMBL GRCm38 v95 annotation with the featureCounts tool also from the subread package
Differential Expression was performed with DESeq2 (v1.3). Enrichment analysis was performed with the clusterProfiler package (v3.16). All downstream analysis of differentially expressed genes were filtered by an adjusted p-value <= 0.05.

source_name: sciatic nerve

extract_protocol:
RNA was extracted from sciatic nerves using TRIzol (Invitrogen) and the RNeasy Mini Kit (Qiagen, 74106) with on-column DNase treatment. RNA purity was assessed by measuring the A260/A280 ratio using a NanoDrop, and RNA quality checked using an Agilent 2100 Bioanalyzer (Agilent Technologies).
For RNA-sequencing, approximately 150 ng of total RNA per sample was used for library construction and sequenced using the Illumina HiSeq 4000 instrument.

value: C57 Bl

value: CnpCre Actl6afl/fl

value: postnatal day 3


title: Cell_94 (H10)


title: Cell_93 (H9)


title: A_S8126


title: Cell_92 (H8)


title: A_S8120


title: Cell_90 (H6)


title: Zeb1MSKO_8WK

data_processing:
FASTQ files were aligned utilizing 10x Genomics Cell Ranger 2.1.0.
Each library was aligned to an indexed mm10 genome using Cell Ranger Count.
Cell Ranger Aggr function was used to normalize the number of mapped reads per cells across all the libraries for the control and MSKO experiments.
Genome_build: mm10

molecule: polyA RNA

extract_protocol: FACS-sorted cells were washed in PBS containing 0.04% BSA and resuspended at a concentration of approximately 1,000 cell/mL. Library generation was performed following the Chromium Single Cell 3ʹ Reagents Kits v2 (following the CG00052 Rev B. user guide) where we target 10,000 cells per sample for capture. Additional reagents included: nuclease-free water (Thermo Fisher Scientific; AM9937), low TE buffer (Thermo Fisher Scientific; 12090-015), ethanol (Millipore Sigma; E7023-500ML), SPRIselect Reagent Kit (Beckman Coulter; B23318), 10% Tween 20 (Bio-Rad; 1662404), glycerin (Ricca Chemical Company; 3290-32), QIAGEN Buffer EB (QIAGEN; 19086). Each library was sequenced on the Illumina HiSeq 4000 platform to achieve an average of approximately 50,000 reads per cell

tag: cell barcode suffix for aggr file


title: A_S8117


title: A_S8116


title: Cell_89 (H5)


title: Cell_88 (H4)


title: A_S8114


title: Cell_87 (H3)


title: Cell_86 (H2)


title: A_S8113


title: Cell_85 (H1)


title: A_S8110


title: Cell_83 (G11)


title: A_S8109


title: A_S8108


title: Cell_82 (G10)


title: A_S8106


title: A_S8105


title: Cell_80 (G8)


title: Cell_78 (G6)


title: A_S8101


title: Cell_81 (G9)


title: A_S8104


title: Cell_79 (G7)


title: A_S8102


title: A_S8125


title: A_S8095


title: A_S8096


title: Cell_76 (G4)


title: A_S8093


title: Cell_73 (G1)


title: Cell_91 (H7)


title: Cell_72 (F12)


title: A_S8091


title: Cell_71 (F11)


title: A_S8086


title: A_S8087


title: Cell_70 (F10)


title: A_S8085


title: A_S8112


title: Cell_84 (G12)


title: A_S8084


title: A_S8082


title: Cell_66 (F6)


title: Cell_68 (F8)


title: Cell_67 (F7)


title: A_S8081


title: Cell_65 (F5)


title: A_S8078


title: Cell_77 (G5)


title: A_S8076


title: Cell_63 (F3)


title: Cell_64 (F4)


title: A_S8075


title: A_S8072


title: Cell_75 (G3)


title: Cell_62 (F2)


title: Cell_61 (F1)


title: Cell_74 (G2)


title: A_S8071


title: Cell_60 (E12)


title: A_S8092


title: Cell_58 (E10)


title: A_S8070


title: A_S8069


title: A_S8067


title: A_S8068


title: Cell_56 (E8)


title: Cell_59 (E11)


title: Cell_57 (E9)


title: A_S8066


title: A_S8065


title: Cell_54 (E6)


title: Cell_69 (F9)


title: A_S8083


title: Cell_55 (E7)


title: A_S8064


title: Cell_53 (E5)


title: A_S8062


title: Cell_52 (E4)


title: A_S8061


title: Cell_51 (E3)


title: Cell_50 (E2)


title: A_S8047


title: A_S8045


title: Cell_49 (E1)


title: A_S8046


title: Cell_46 (D10)


title: Cell_47 (D11)


title: A_S8044


title: Cell_48 (D12)


title: A_S8042


title: A_S8043


title: Cell_45 (D9)


title: A_S8041


title: Cell_44 (D8)


title: Cell_43 (D7)


title: A_S8037


title: Cell_42 (D6)


title: A_S8035


title: Cell_39 (D3)


title: Cell_40 (D4)


title: A_S8033


title: A_S8032


title: Cell_41 (D5)


title: Cell_38 (D2)


title: A_S8031


title: A_S8026


title: Cell_37 (D1)


title: Cell_36 (C12)


title: A_S8063


title: A_S8025


title: Cell_35 (C11)


title: A_S8024


title: A_S8022


title: A_S8023


title: Cell_33 (C9)


title: A_S8021


title: Cell_34 (C10)


title: Cell_31 (C7)


title: Cell_29 (C5)


title: A_S8016


title: Cell_28 (C4)


title: A_S8014


title: A_S8015


title: Cell_30 (C6)


title: A_S8013


title: Cell_27 (C3)


title: Cell_26 (C2)


title: A_S8036


title: Cell_25 (C1)


title: A_S8011


title: A_S8007


title: Cell_24 (B12)


title: Cell_23 (B11)


title: A_S8006


title: Cell_22 (B10)


title: A_S8005


title: Cell_21 (B9)


title: A_S8004


title: A_S8003


title: Cell_20 (B8)


title: Cell_19 (B7)


title: A_S8002


title: A_S8001


title: Cell_18 (B6)


title: A_S7140

value: Young


title: Cell_32 (C8)


title: Cell_17 (B5)


title: Cell_16 (B4)


title: A_S7138


title: Cell_15 (B3)


title: A_S7137


title: A_S7130


title: Cell_14 (B2)


title: Cell_13 (B1)


title: Cell_12 (A12)


title: A_S7129


title: A_S7128

value: Positive


title: Cell_11 (A11)


title: A_S8012


title: A_S7127


title: A_S7126


title: A_S7125


title: Cell_9 (A9)


title: Cell_8 (A8)


title: A_S7124


title: Cell_7 (A7)


title: A_S7122


title: Cell_6 (A6)


title: A_S7121


title: Cell_5 (A5)


title: Cell_4 (A4)


title: A_S7120


title: A_S7119


title: A_S7117


title: Cell_3 (A3)


title: Cell_2 (A2)


title: small RNA-seq: RPE-1-AtRDR1(+)Dox

city: Beijing

first: Li

last: Ding

state: Beijing

address: No.5, Yiheyuan Road

country: China

institute: Peking University

description: Gel-purified 15-50nt small RNAs

data_processing:
To analyze polyA(+) RNA-seq data, adapters of raw data were trimmed with Trimmomatic software. The quality of these data was evaluated by FastQC software. HISAT2 software with default parameters was used to align sequences to the human genome (hg38, UCSC) and the mouse genome (mm10, UCSC) based on the origin of the cell lines. Output files after sequence alignment were used to obtain gene count matrix with featureCounts software using corresponding UCSC RefSeq as gene annotations. For further analyses, gene counts in each sample were normalized to the total reads of the library to calculate reads per million (RPM).
Perl and python scripts were used to analyze small RNA-seq data. Adapters of sequences were trimmed and sequences with a length of 19-25nt were retained. To build the index of miRNA, we downloaded the mature miRNA sequences from miRBase, 3nt upstream and 3nt downstream of mature miRNA were added to the references. Each sequence was aligned to the reference using Bowtie software using the following parameters: -a -v 1 -3 3.In order to compare the miRNA expression in the line, the count of miRNAs was normalized. In RDR1 expression group, two ways were used to normalize miRNA data. Fly miRNA was added as spike-in in some samples. In non-spike-in method (including A549, HeLa, HepG2, HCT116 and NIH/3T3), the numbers of miRNAs were normalized to the numbers of total reads of the corresponding library to calculate RPM. In spike-in method (including H1299, Jurkat and RPE-1), the number of miRNAs was multiplied by a factor to make the count of fly miRNAs equal in all samples in a cell line. We used the top-10 highest expressed miRNAs as reference, which did not contain identical miRNAs in fly and human/mouse. Each of these 10 miRNAs was used to calculate a factor and the mean of these 10 factors was used as the factor for this sample for normalization. After normalization between samples within cell lines, the normalized reads of the sample with higher miRNA expression level was set at one million. In cell cycle inhibition, AGO2-CLIP and AGO2 knockdown experiments, miRNA expression was normalized with non-spike-in method. Some cell lines of RDR1 expression group were used in this analysis (A549, HeLa, HepG2). In order to be consistent with the previous analysis in RDR1 expression group, the normalized reads of the sample with higher miRNA expression level of RDR1 expression group was set at one million. In the miR-34c transfection assay, miRNA expression was normalized to the expression of endogenous miRNA, which was set at one million.
Genome_build: mm10, hg38
Supplementary_files_format_and_content: miRNA exression matrix

source_name: RPE-1-AtRDR1 stable cell line

extract_protocol:
TRIzol reagent (Invitrogen) was used to isolate total RNA according to the manufacturer’s instructions.
RNA-seq libraries preparation using the TruSeq Stranded mRNA Sample Prep Kits (Illumina), VAHTS Stranded mRNA-seq Library Prep Kits (Vazyme) and VAHTS Ribo-off Globin & rRNA Depletion Kits(Vazyme). Small RNA-seq libraries preparation using the NEBNext® Small RNA Library Prep Set for Illumina kits. Single-cell RNA-seq libraries preparation using the Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics).

tag: cell type and treatment

value: RPE-1-AtRDR1 with Dox induction for 6 days

value: RPE-1-AtRDR1 stable cell line


title: A_S7114


title: A_S7112


title: small RNA-seq: Jurkat-AtRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: Jurkat-AtRDR1 stable cell line

value: Jurkat-AtRDR1 with Dox induction for 6 days

value: Jurkat-AtRDR1 stable cell line


title: A_S7113


title: A_S7132


title: small RNA-seq: RPE-1-WT

description: Gel-purified 15-50nt small RNAs

value: WT


title: small RNA-seq: HepG2-WT

description: Gel-purified 15-50nt small RNAs


title: small RNA-seq: HepG2-AtRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: HepG2-AtRDR1 stable cell line

value: HepG2-AtRDR1 with Dox induction for 5 days

value: HepG2-AtRDR1 stable cell line


title: A_S7111

value: UPenn


title: small RNA-seq: HeLa-OsRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: HeLa-OsRDR1 stable cell line

value: HeLa-OsRDR1 with Dox induction for 5 days

value: HeLa-OsRDR1 stable cell line


title: small RNA-seq: Jurkat-WT

description: Gel-purified 15-50nt small RNAs

source_name: Jurkat


title: A_S7108

value: Male

value: Negative


title: A_S7109

value: Female


title: A_S7110


title: Cell_10 (A10)

value: Mouse mammary gland


title: A_S7106


title: small RNA-seq: HeLa-WT

description: Gel-purified 15-50nt small RNAs

source_name: HeLa


title: small RNA-seq: HCT116-WT

description: Gel-purified 15-50nt small RNAs


title: small RNA-seq: HCT116-OsRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: HCT116-OsRDR1 stable cell line

value: HCT116-OsRDR1 with Dox induction for 6 days

value: HCT116-OsRDR1 stable cell line


title: A_S7104

value: Young


title: small RNA-seq: H1299-AtRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: H1299-AtRDR1 stable cell line

value: H1299-AtRDR1 with Dox induction for 6 days

value: H1299-AtRDR1 stable cell line


title: A_S7103


title: A_S7102


title: small RNA-seq: H1299-WT

description: Gel-purified 15-50nt small RNAs


title: small RNA-seq: A549-AtRDR1(+)Dox

description: Gel-purified 15-50nt small RNAs

source_name: A549-AtRDR1 stable cell line

value: A549-AtRDR1 with Dox induction for 6 days

value: A549-AtRDR1 stable cell line


title: A_S7101


title: A_S7116


title: Cell_1 (A1)


title: WT_HCT116_Nutlin_MED1_ChIP_rep2

city: Vienna

first: Vanja

last: Haberle

address: Campus-Vienna-Biocenter 1

country: Austria

institute: The Research Institute of Molecular Pathology (IMP)

data_processing:
Read alignment:  Single-end 50 bp long reads were mapped to a reference hg19 genome using Bowtie version 0.12.9 allowing 3 mis-matches. Only uniquely mapping reads were retained.
Genomic coverage:  Mapped reads were extended to 500bp and used to generate coverage at 1bp resolution with GenomicRanges v1.34.0 package in R. Coverage was normalized to tags per million and exported into bigWig format with rtracklayer v1.42.2.
Peak calling:  Unique fragments were used to call peaks with macs2 v2.1.2 for each condition/treatment against the respective input, using default macs2 settings (FDR≤0.05).
Genome_build: hg19
Supplementary_files_format_and_content: For each condition, peaks called with macs2 against the respective input are provided in .narrowPeak format.  BigWig files contain normalized coverage of extended fragments for each ChIP sample and respective inputs.

source_name: HCT116 cells

extract_protocol:
Cells were fixed with 1% FA in PBS for 15 min. Crosslinked cells were resuspended in lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitors) and rotated for 10 minutes at 4°C. The pellet was sonicated on a Misonix 3000 sonicator for 10 cycles at 30 s each on ice (18-21 W) with 60 s on ice between cycles. Input material was reserved and the remainder was incubated overnight at 4°C with magnetic beads bound with MED1 antibody (Bethyl #A300-793A). DNA was eluted off the beads by incubation with agitation at 65°C for 15 minutes in elution buffer. Cross-links were reversed for 12 hours at 65°C. Eluted DNA was treated with RNase A (37°C for 2 hours) and proteinase K (55°C for 30 min). DNA was purified using Qiagen PCR purification kit.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: MED14-AID-tagged cells were treated as follows:   1. water (mock) or 500µM auxin (IAA) treatment for 3h  2. water (mock) or 500µM auxin (IAA) treatment for 3h, followed by Nutlin 3a (Sigma# SML0580) treatment for 1h  WT HCT116 cells were treated with either DMSO (mock) or Nutlin 3a for 1h

tag: cell line

value: wild-type

tag: chip antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog


title: A_S7099

tag: donor type

tag: donor id

tag: age


title: A_S7100

tag: Sex

tag: cmv serostatus

tag: cell type


title: A_S7118

tag: cell subset

tag: library preparation group

tag: sample acquisition location


title: WT_HCT116_Nutlin_Input_rep2

tag: genotype


title: A_S7098


title: WT_HCT116_Nutlin_Input_rep1

tag: treatment


title: WT_HCT116_Nutlin_MED1_ChIP_rep1


title: A_S7096


title: WT_HCT116_DMSO_Input_rep2

value: DMSO (mock)


title: WT_HCT116_DMSO_MED1_ChIP_rep2


title: A_S7095

value: UPenn


title: A_S7093


title: A_S7092


title: WT_HCT116_DMSO_MED1_ChIP_rep1


title: WT_HCT116_DMSO_Input_rep1


title: A_S7090

value: Indeterminate


title: CD34+CD38- CB sh4_TBL1XR1 rep3

city: Toronto

first: Alexander

middle: James

last: Murison

state: Ontario

address: 101 College Street, TMDT room 11-706

country: Canada

institute: University Health Network

data_processing:
Raw Reads were aligned using STAR against known GENCODE 32 transcripts
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited read counts

source_name: human cord blood

growth_protocol: Lin-CB cells were cultured in low cytokine conditions using X-VIVO 10 medium with 1% BSA, 1X penicillin-streptomycin, 1X L-glutamine supplemented with the following cytokines: Flt3L (100 ng/ml), SCF (100 ng/ml), TPO (50 ng/ml) and IL-7 (10 ng/ml).

extract_protocol:
Sorted BFP+ cells (1x10^4) were washed with PBS, lysed in lysis buffer and stored at -80C until RNA extraction using PicoPure RNA Isolation Kit (Thermo Fisher).
SMART-Seq V4 Ultra Low Input RNA kit for sequencing (Clontech) was used to generate the cDNA samples. Subsequently, next-generation sequencing libraries were prepared with Nextera XT DNA Library Preparation Kit (Illumina). Equimolar quantities of libraries were pooled and sequenced on the Illumina HiSeq 2500 platform generating 125-bp paired-end sequencing reads to achieve depth of approximately 40-50M reads per sample.

treatment_protocol: Lin- CB cells were sorted to obtain CD34+CD38- CB cells that were subsequently transduced with Control and sh4_TBL1XR1 lentiviruses at a density of 5x10^5 cell/ml. Fresh medium was added 24 hours post-transduction. BFP+ cells were sorted on day 3 post-transduction.

value: CD34+CD38- CB cells

tag: days post-transduction

value: 3 days post-tranduction

tag: condition


title: CD34+CD38- CB sh4_TBL1XR1 rep2


title: A_S7105

value: Male

value: Negative


title: CD34+CD38- CB sh4_TBL1XR1 rep1


title: A_S7089

value: Female


title: CD34+CD38- CB shCtrl rep3

value: shControl


title: A_S7088


title: A_S7085


title: A_S7084


title: A_S7086


title: CD34+ CB miR-130a OE rep 3

description: CB3 130

data_processing:
Raw Data was aligned to hg38 using STAR
HT-Seq count was used to obtain read counts over all GENCODE 32 genes
Genome_build: hg38
Supplementary_files_format_and_content: tab delimited read counts

extract_protocol:
Sorted for mO+CD34+ cells (5x10^4) were washed with PBS, lysed in lysis buffer and stored at -80C until RNA extraction using PicoPure RNA Isolation Kit (Thermo Fisher).
SMART-Seq V4 Ultra Low Input RNA kit for sequencing (Clontech) was used to generate the cDNA samples. Subsequently, next-generation sequencing libraries were prepared with Nextera XT DNA Library Preparation Kit (Illumina). Equimolar quantities of libraries were pooled and sequenced on the Illumina HiSeq 2500 platform generating 125-bp paired-end sequencing reads to achieve depth of approximately 40-50M reads per sample.

treatment_protocol: Lin- CB cells were transduced with Control and miR-130a OE lentiviruses at a density of 5x10^5 cell/ml. Fresh medium was added 24 hours post-transduction and cells were harvested 72 hour post-transduction

value: CD34+ hematopoietic stem/progenitor cells

value: miR130a overexpression


title: CD34+CD38- CB shCtrl rep2


title: A_S7087

value: Young


title: small RNA-seq: A549-WT

description: Gel-purified 15-50nt small RNAs

tag: cell type and treatment

value: WT


title: CD34+ CB miR-130a OE rep 2

description: CB2 130


title: CD34+ CB Ctrl rep3

description: CB3 C

value: control


title: CD34+ CB miR-130a OE rep 1

description: CB1 130


title: CD34+ CB Ctrl rep2

description: CB2 C


title: A_S7080


title: CD34+ CB Ctrl rep1

description: CB1 C


title: A_S7097


title: CD34+CD38- CB shCtrl rep1


title: Flag_AE_Kasumi miR-130a KD rep 3

source_name: FLAG-AML1-ETO Kasumi-1 cells

growth_protocol: Flag-AML1-ETO Kasumi-1 cells were cultured in RPMI medium + 20% FBS, 1% Pen/Strep.

extract_protocol:
Sorted GFP+ cells (1x10^5) were washed with PBS, lysed in lysis buffer and stored at -80C until RNA extraction using PicoPure RNA Isolation Kit (Thermo Fisher).
SMART-Seq V4 Ultra Low Input RNA kit for sequencing (Clontech) was used to generate the cDNA samples. Subsequently, next-generation sequencing libraries were prepared with Nextera XT DNA Library Preparation Kit (Illumina). Equimolar quantities of libraries were pooled and sequenced on the Illumina HiSeq 2500 platform generating 125-bp paired-end sequencing reads to achieve depth of approximately 40-50M reads per sample.

treatment_protocol: Transduction of  Flag-AE Kasumi-1 cells was performed at a density of 2x10^6 cells/ml in RPMI medium with 20% FBS, 1% Pen/Strep. Cells were infected in 24-well suspension plates and centrifuged at 1,400 rpm for 60 min at 32°C and fresh medium was added on the next day.

value: t(8;21) AML cell line

value: miR-130a KD


title: A_S7076


title: A_S7075


title: Flag_AE_Kasumi miR-130a KD rep 1


title: Flag_AE_Kasumi miR-130a KD rep 2


title: A_S7091


title: Flag_AE_Kasumi Control rep 3


title: A_S7073


title: A_S7074


title: Flag_AE_Kasumi Control rep 2


title: A_S7072


title: A_S7071


title: Flag_AE_Kasumi Control rep 1


title: MLL4_psAuxin_rep4 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
MLL4_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

data_processing:
Library strategy: STARR-seq
Read alignment:  Paired-end STARR-seq reads were trimmed to 50 bp and mapped as paired-end to a reference hg19 genome and to 9 custom spike-in sequences using Bowtie version 0.12.9 allowing 3 mis-matches. Only uniquely mapping read pairs were retained.
Genomic coverage:  Genomic fragments defined by sequenced read pairs from all replicates of each COF/condition were merged and used to generate coverage at 1bp resolution with GenomicRanges v1.34.0 package in R. Coverage was normalized to tags per million and scaled by a factor obtained from relative spike-in abundance. Coverage was exported into bigWig format with rtracklayer v1.42.2.
Peak calling:  Unique fragments from merged replicates of each COF/treatment were used to call peaks with macs2 v2.1.2, against previously sequenced STARR-seq input library (Muerdter et al. Nat Methods 2018) as control. Only peaks with more than 3-fold enrichment over input on both strands and at least 3 tags per million were kept. A common referent set of 6249 STARR-seq enhancers was compiled by combining peaks across all COFs/treatments.
Quantification and differential analysis:  Sequenced fragments overlapping each enhancer were counted for each individual replicate of COF/treatment to obtain raw counts per enhancer. For each COF differential analysis between auxin (IAA) and water (mock) treatment was performed with edgeR v3.24.3 supplying custom scaling factors from relative spike-in abundance, and resulting log2 fold-change values for each enhancer were reported.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of a referent set of 6249 STARR-seq enhancers compiled across all STARR-seq samples and tag counts at those enhancers as follows: 1) Raw tag counts in each individual replicate of all COFs and treatments are provided in Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt file and 2) Log2 fold-change between auxin (IAA) and water (mock) treatment calculated from normalized counts (normalized to spike-in) after merging replicates per CoF/treatment are provided in the Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt file. BigWig files contain normalized coverage of STARR-seq fragments averaged across biological replicates for each COF/treatment.

growth_protocol: 4x10^8 cells were grown in square plates (Thermo Scientific #166508) with a seeding density ~20Mill. cells 2 days/square plate before transfection.

extract_protocol:
After 6h of treatment cells were harvested and total RNA was isolated using RNeasy Maxi kit (Qiagen #75162) containing beta-Mercaptoethanol supplemented RLT buffer. Spike-in control was added in a 1:1000 ratio to the isolated total RNA. polyA+ mRNA was isolated via Oligo-dT25 beads  (Invitrogen #61005) followed by 1h 37°C TurboDNase I treatment (Invitrogen #AM2238).
Isolated mRNA was cleaned via AMPure XP beads (Beckman Coulter #A63882) 1:1.8 ratio (RNA:beads) followed by reverse transcription utilizing SuperScript III (Invitrogen #18080093) using a gene specific primer (GSP): 50°C for 1h, 70°C for 15min, 4°C for 10min. cDNA was treated with RNaseA (Thermo Fisher #EN0531), 37°C for 1h followed by cleanup via AMPure XP beads 1:1.8 ratio. Next, junction PCR which allows enrichment of reporter transcripts was performed using KAPA 2x HiFi (KapaBiosystems #KK2601) and “junction primers” spanning over the spliced intron utilizing the thermocycler program: 98°C - 45 sec, 98°C - 15 sec, 65°C - 30 sec 16 cycles, 72°C - 70 sec, 72°C - 120 sec followed by purification with AMPure XP 1:0.8 ratio (DNA:beads). Sequencing-ready PCR was performed on the junction PCR products using Illumina primers with the thermocycler program: 98°C - 45 sec, 98°C - 15 sec, 65°C - 30 sec 5 cycles, 72°C - 45 sec, 72°C - 120 sec. Illumina adapter containing STARR-seq library fragments were cleaned using SPRIselect beads (Beckman Coulter #B23318) with a stringent ratio of 1:0.5 (DNA:beads) and subjected to paired end deep sequencing.

treatment_protocol: Genome wide STARR-seq library (Addgene #99296) was electroporated via Maxcyte STX into 85% confluent OsTir1+/-;COF-AID+/+ tagged cells.  After 30min recovery phase cells were split in 2 conditions, receiving medium containing water (mock) or auxin (IAA; 500µM final conc.; 2x10^8 cells) for 6h.

tag: cell line

value: CRISPR/Cas9 edited cells

value: auxin (IAA)


title: MLL4_psAuxin_rep3 [STARR-seq]


title: A_S7069

value: Positive

value: UPenn


title: A_S7068


title: A_S7067


title: MLL4_psAuxin_rep2 [STARR-seq]


title: A_S7083

value: Indeterminate


title: A_S7066


title: MLL4_psAuxin_rep1 [STARR-seq]


title: MLL4_msAuxin_rep4 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
MLL4_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

value: water (mock)


title: A_S7065

value: Male


title: A_S7064


title: MLL4_msAuxin_rep3 [STARR-seq]


title: A_S7082


title: A_S7081


title: MLL4_msAuxin_rep2 [STARR-seq]


title: Med14_psAuxin_rep3 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Med14_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: A_S7077

value: Negative


title: A_S7063


title: A_S7062


title: Med14_psAuxin_rep4 [STARR-seq]


title: A_S7061


title: A_S7060


title: A_S7059


title: Med14_psAuxin_rep2 [STARR-seq]


title: Med14_msAuxin_rep3 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Med14_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: A_S7058


title: Med14_msAuxin_rep1 [STARR-seq]


title: Med14_msAuxin_rep4 [STARR-seq]


title: A_S7056


title: A_S7057


title: A_S7055


title: siDHX16-1_IAV

city: Galveston

first: Adam

last: Hage

state: Texas

address: 301 University Blvd

department: Microbiology and Immunology

institute: University of Texas Medical Branch at Galveston

description: DHX16-targeting (Infected)

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.17.1 converter
A genome index was built with STAR (v2.5.1b) using the human hg38 genome .
Reads were aligned to the hg38 reference using the STAR software version 2.5.1b with the parameters recommended for the ENCODE consortium.
Read counts per gene were produced with the --quantMode GeneCounts function of STAR.
Differential gene expression was analyzed with the R (version 3.3.1) software DESeq2 (version 1.12.1)
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited table of raw read counts per gene

extract_protocol:
Total cellular RNA was extracted using  Trizol Reagent (Life Technologies, CA) according to the manufacturer’s recommendations.
Poly-A plus RNA was enriched from  ~0.1 ug of total RNA and used to generate libraries using the Illumina TruSeq kit.

value: adenocarcinomic human alveolar basal epithelial cells

tag: sirna

tag: agent

value: influenza A virus


title: siDHX16-2_IAV

description: DHX16-targeting (Infected)


title: A_S7054

tag: donor type


title: CDK9_psAuxin_rep2 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK9_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: siNTC-1_IAV

description: Non-targeting control (Infected)

value: siNTC


title: CDK9_psAuxin_rep1 [STARR-seq]


title: siNTC-2_IAV

description: Non-targeting control (Infected)


title: siDHX16-2_Mock

description: DHX16-targeting (Mock)

value: Mock


title: siDHX16-1_Mock

description: DHX16-targeting (Mock)


title: A_S7052

value: Young

tag: donor id


title: CDK9_msAuxin_rep2 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK9_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: siNTC-2_Mock

description: Non-targeting control (Mock)


title: A_S7051

tag: age


title: CDK9_msAuxin_rep1 [STARR-seq]


title: siNTC-1_Mock

description: Non-targeting control (Mock)


title: IgG_input

city: Dundee

first: Dimitrinka

last: Ditsova

state: Scotland

address: 64 Atholl Street

department: Division of Gene Regulation and Expression

country: United Kingdom

institute: University of Dundee

data_processing:
Sequencing was performed with a read length of 2 x 75bp (paired reads) using Illumina MiSeq.
Quality of the reads was assessed with fastqc.
Reads were extracted using their unique molecular identifier (UMI) usng umi_tools.
Adapters were trimmed using cutadapt.
Trimmed sequences were aligned to human genome assembly hg35 using STAR 2.5.
Sequences were indexed using samtools.
PCR duplicates were removed using umi_tools.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files showed the reads per kilobase per million (RPKM) of CLIP read densities within the 10bp windows of genomic region for each sample.

source_name: Jurkat cells

growth_protocol: Jurkat cells were grown in Roswell Park Memorial Institute (RPMI) 1640 medium with 10% FBS, 0.5 μM β-mercaptoethanol, 50 units/ml penicillin and 50µg/ml streptomycin. Jurkats wer cultured in flasks or dishes at 37oC with 5% CO2.

extract_protocol:
Cells were UV cross-linked at 254 nM with an energy setting of 400 mJ/cm2.RNA isolation and library preparation was performed as described by Van Nostrand et al, 2018. Lysates were treated with RNase I diluted 1:150. IPs were performed with 7.5µg anti-p65 Santa Cruz antibody sc-8008 or 7.5µg mouse IgG. The chromatin was sonicated in Bioruptor (Diagenode) at low power for 5 min (30 s on/off). Antibodies were tethered to 100µl protein G magnetic beads for 1h at room temperature and afterwards, the lysates were incubated with the beads overnight at 4oC. The next day 2% of lysate+bead was set aside as input. IP and input samples were resolved on an SDS-PAGE gel, then transferred to nitrocellulose membranes, and digested with Proteinase K. RNA was isolated with phaselock gel tubes and Zymo-spin columns. MyOne Silane beads were used for RNA library clean up. AmpureXP beads were used for cDNA library clean up.
Libraries were constructred as described in Van Nostrand et al, 2018. Primers used included InvRiL19, InvRand3Tr3, InvAR17, D5x_qPCR, D7x_qPCR
CLIP-seq

value: untreated


title: A_S7050

source_name: PBMC

tag: Sex


title: p65_input


title: IgG_CLIP

tag: antibody

value: mouse IgG1κ (eBioscience;14-4714-82)


title: CDK8_psAuxin_rep4 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK8_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

tag: cell type


title: MLL4_msAuxin_rep1 [STARR-seq]


title: A_S7049

tag: cmv serostatus

tag: cell subset


title: Med14_msAuxin_rep2 [STARR-seq]


title: p65_CLIP

value: anti-p65 (Santa Cruz; sc-8008)


title: Med14_psAuxin_rep1 [STARR-seq]


title: CDK8_psAuxin_rep1 [STARR-seq]


title: A_S7046

tag: library preparation group

tag: sample acquisition location


title: A_S7053


title: A_S7048


title: CDK8_msAuxin_rep4 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK8_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

tag: genotype

tag: treatment


title: CDK8_psAuxin_rep3 [STARR-seq]


title: CDK8_psAuxin_rep2 [STARR-seq]


title: CDK8_msAuxin_rep3 [STARR-seq]


title: SAMPLE 12_LPA (1 μM) + S1P (2 μM) + Albumin (1%)

type: RNA

city: Macau

first: Guokai

last: Chen

address: University of Macau Avenida da Universidade Taipa, Macau, China

institute: University of Macau

hyb_protocol: cRNA was hybridized onto HumanHT-12 v4 Expression BeadChip (Illumina) using standerd protocol.

scan_protocol: BeadChips were scanned with the iScanner (Illumina).

data_processing:
Data was normalized by quantile normalization.
www.arrayanalysis.org computed the normalized signal intensity.

label: biotin

source_name: Human embryonic stem cell H1

label_protocol: RNA was converted to cRNA using the TargetAmp™-Nano Labeling Kit for Illumina Expression BeadChip (Epibio).

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cells are passaged at 70% confluence by 1:12 with 5 μM ROCK inhibitor Y27632. Y27632 was romoved after 24 hrs. Cells were given treatments for 2 days and then collected for analysis.

extract_protocol: Toatal RNA was isolated by Qiagen Rneasy kit.

treatment_protocol: E8: E8 medium. AlbuMAX: E8 medium supplemented with 1.6% AlbuMAX. Albumin: E8 medium supplemented with 1% Albumin. CDL: E8 medium supplemented with 1% chemically defined lipid concentrate. hCDL: E8 medium supplemented with homemade chemically defined lipid mixture. LPA: E8 medium supplemented with 1 μM lysophosphatidic acid (18:1). S1P: E8 medium supplemented with 2 μM sphingosine-1-phosphate.

value: Human embryonic stem cell H1

value: LPA (1 μM) + S1P (2 μM) + Albumin (1%)


title: A_S7047


title: CDK8_msAuxin_rep2 [STARR-seq]

value: CRISPR/Cas9 edited cells


title: SAMPLE 11_S1P (2 μM) + Albumin (1%)

value: S1P (2 μM) + Albumin (1%)


title: SAMPLE 6_CDL (1%, without Tween 80)

value: CDL (1%, without Tween 80)


title: SAMPLE 4_S1P (2 μM)

value: S1P (2 μM)


title: SAMPLE 7_hCDL (0.001%)


title: MCAS_cell lysate

city: Hirosaki

first: Kayo

last: Horie

address: 66-1 Hon-cho

country: Japan

institute: Hirosaki university

description: Gene expression ovarian cancer cell

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°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 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MCAS_cell lysate

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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: Ovarian cancer cells were purchased from Japanese Collection of Research Bioresources Cell Bank. These cells were routinely cultured in RPMI medium supplemented with 10% fetal bovine serum at 37ºC in 5% CO2.

extract_protocol: Micro RNA including Total RNA was extracted by using the RNeasy micro kit(QIAGEN) modified protocol  (Qiagen, Tokyo, Japan).

treatment_protocol: Cells were cultured in without FBS culture media on 48 hours and collectd. Next, exosome isolation was used ExoEasy Maxi kit(QIAGEN)

tag: sample type

value: Human ovarian cancer cell

value: Endometrioid carcinoma (TOV112D)


title: CDK7_psAuxin_rep4 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK7_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

value: auxin (IAA)


title: A_S7045

value: Male

value: Negative

value: UPenn


title: A_S7044


title: SAMPLE 21_CHIR99201+2DG

data_processing: Data was normalized by quantile normalization.

growth_protocol: Human ESCs (H1) were maintained in E8 medium on matrigel-coated plates with daily medium change. Cells are passaged at 70% confluence by 1:12 with 5 μM ROCK inhibitor Y27632. Y27632 was romoved after 24 hrs. Cells were given treatments for 6 days and then collected for analysis.

treatment_protocol: E6 (E8 medium without FGF2 and TGFb) + supplements: E6 supplemented with BMP4, BMP4+FGF2, BMP4+GF109203X, BMP4+PD+SB+DAPT or BMP4+PD+SB+DAPT+GF109203X. Medium-containing-factors is changed every other day.

tag: gender

value: male


title: HOSE_cell_1 lysate

description: Gene expression control

source_name: HOSE_cell_1 lysate

value: Ovarian Surface Epithelial Cell

tag: cell line

value: Ovarian Surface Epithelial Cells (HOSE)


title: CDK8_msAuxin_rep1 [STARR-seq]

value: water (mock)


title: CDK7_psAuxin_rep2 [STARR-seq]


title: SAMPLE 20_CHIR99201+DAPT


title: A_S7043

value: Young


title: HOSE_exosome_2

description: Gene expression control


title: HAC-2_cell lysate

description: Gene expression ovarian cancer cell

source_name: HAC-2_cell lysate

value: Mucinous carcinoma (MCAS)


title: A_S7042


title: SAMPLE 24_TPA+LDN193189

value: Human embryonic stem cell H1


title: SAMPLE 19_CHIR99201+TPA


title: SAMPLE 22_TPA

value: TPA


title: A_S7041


title: A_S7040

value: Female


title: HRA_cell lysate

description: Gene expression ovarian cancer cell

source_name: HRA_cell lysate

value: Serous carcinoma (HRA)


title: A_S7037


title: CDK7_psAuxin_rep3 [STARR-seq]

value: CRISPR/Cas9 edited cells


title: CDK7_msAuxin_rep3 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
CDK7_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: A_S7039


title: HAC-2_exosome

description: Gene expression ovarian cancer cell

value: Human ovarian cancer cell


title: HOSE_exosome_1

description: Gene expression control


title: HOSE_cell_2 lysate

description: Gene expression control

source_name: HOSE_cell_2 lysate


title: CDK7_msAuxin_rep2 [STARR-seq]


title: SAMPLE 23_TPA+GF109203X


title: A_S7038


title: SAMPLE 18_CHIR99021+GF109203X


title: CDK7_psAuxin_rep1 [STARR-seq]


title: TOV112D_cell lysate

description: Gene expression ovarian cancer cell

source_name: TOV112D_cell lysate

value: Clear cell carcinoma (HAC2)


title: SAMPLE 17_CHIR99021


title: SAMPLE 14_PD0325901+GF109203X


title: A_S7033


title: CDK7_msAuxin_rep1 [STARR-seq]


title: S09 ST-4-cy3

first: Nivedita

last: Banerjee

address: 301 University Blvd,

institute: University of Texas Medical Branch

description: total RNA samples

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

source_name: Sulforaphane + Trichloroethylene

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: mirVana miRNA isolation kit was used for total RNA extraction following manufacturer's protocol.

treatment_protocol: TCE (10 mmol/kg in corn oil, ip, every fourth day) with/without antioxidant sulforaphane (SFN; 8 mg/kg in corn oil, ip, every other day) for 6 weeks.

tag: tissue

value: liver

value: female

value: MRL+/+


title: A_S7036

value: Negative

value: UPenn


title: CDK7_msAuxin_rep4 [STARR-seq]


title: A_S7032


title: TOV112D_exosome

description: Gene expression ovarian cancer cell


title: A_S7034


title: HRA_exosome

description: Gene expression ovarian cancer cell


title: S07 ST-1-cy3

description: total RNA samples


title: Brd4_psAuxin_1h_predegradation [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Brd4_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

value: auxin (IAA)


title: SAMPLE 15_BMP4+PD0325901+SB431542+DAPT

value: male


title: MCAS_exosome

description: Gene expression ovarian cancer cell

value: Endometrioid carcinoma (TOV112D)


title: Brd4_msAuxin_referent [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Brd4_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

value: water (mock)


title: S08 ST-3-cy3

description: total RNA samples


title: SAMPLE 16_BMP4+PD0325901+SB431542+DAPT+GF109203X


title: A_S7030

value: Young


title: Brd4_psAuxin_referent [STARR-seq]


title: S05 TCE-3-cy3

description: total RNA samples

source_name: Trichloroethylene


title: SAMPLE 11_DAPT

value: Human embryonic stem cell H1

value: DAPT


title: SAMPLE 12_DAPT+GF109203X


title: Brd4_psAuxin_rep1 [STARR-seq]


title: A_S7031

value: Female


title: A_S7035


title: S06 TCE-4-cy3

description: total RNA samples


title: S04 TCE-1-cy3

description: total RNA samples


title: A_S7029


title: A_S7027


title: Brd4_psAuxin_16h_predegradation [STARR-seq]


title: SAMPLE 9_SB431542


title: A_S7028


title: SAMPLE 10_SB431542+GF109203X


title: SAMPLE 7_BMP4+FGF2+GF109203X


title: Brd4_msAuxin_rep1 [STARR-seq]


title: SAMPLE 8_BMP4+FGF2+2DG


title: Brd4_msAuxin_rep2 [STARR-seq]


title: Parental_psAuxin_rep3 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Parental_psAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt


title: SAMPLE 6_BMP4+FGF2


title: S01 Control-1-cy3

description: total RNA samples

source_name: control


title: S02 Control-2-cy3

description: total RNA samples


title: SAMPLE 13_PD0325901


title: S03 Control-4-cy3

description: total RNA samples


title: SAMPLE 5_BMP4+2DG


title: A_S7025


title: RNA-seq_Pericardium replicate 2

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

country: Switzerland

institute: University of Bern

data_processing:
Basecalls performed using CASAVA version 1.8 (Illumina)
Adapters from the fastq files were trimmed using fastp software
Reads were aligned to GRCz11 danRer11 v102 assembly from Ensembl using STAR. The reads were summarized using featureCounts.
The counts data were imported to Deseq2 and genes who had expression across all samples (rowSums) greater than or equal to 10 were kept ensuring the realiable expression estimates. The differential expression analysis was performed using ‘ashr’ LFC Shrikange
Genome_build: Ensembl GRCz11 danRer11 v102
Supplementary_files_format_and_content: Raw and normalized gene counts for every gene in every sample

organism: Danio rerio

source_name: Pericardium

extract_protocol:
Dorsal pericardium, proepicardium and heart-tube were manually dissected, with wolfram needles, from 60 hpf epi:eGFP;myl7:mRFP zebrafish larvae. A minimum of 10  of each tissue/organ were collected for each sample in ice cold PBS. Cells were centrifuged for 7 minutes at 250 g. The excess liquid was removed, and the cells were stored at -80oC until further use
RNA was directly transformed and amplified into cDNA from the lysed tissue using the SMARTer® Ultra™ Low Input RNA for Illumina® Sequencing – HV kit. cDNA quality control was verified using the Agilent 2200 BioAnalyzer and the High Sensitivity DNA Chip from Agilent’s High Sensitivity DNA Kit

value: Pericardium

tag: strain

value: AB

value: 60 hpf


title: Parental_msAuxin_rep3 [STARR-seq]

description:
PCR amplified cDNA (STARR-seq reporter transcript)
Parental_msAuxin.bw
Raw_counts_per_COF_and_replicate_for_common_set_of_enhancers.txt
Log2FC_psAuxin_vs_msAuxin_per_COF_for_common_set_of_enhancers.txt

value: CRISPR/Cas9 edited cells


title: A_S7026

tag: donor type


title: RNA-seq_Pericardium replicate 1


title: SAMPLE 4_BMP4+GF109203X


title: A_S7024

tag: donor id


title: RNA-seq_Heart tube replicate 3

source_name: Heart tube

value: Heart tube

tag: age


title: A_S7023

tag: Sex


title: Med14_psAuxin_Nutlin_rep2

description: Med14_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

data_processing:
Library strategy: PRO-seq
UMI removal and adapter trimming: Sequenced reads consist of a 8nt long UMI (for counting unique RNA molecules), followed by PolII active site-associated RNA sequence and potentially a part of the Illumina sequencing adapter (in cases where RNA was shorter than 42nt). Prior to mapping, the UMI sequence (8nt at the 5' end of the read) was removed and noted for later counting. Illumina adapter was trimmed off with cutadapt v1.18.
Read alignment: All reads longer than 15nt after adapter trimming were mapped to a merged reference consisting of hg19 and dm3 (spike-in) genome using Bowtie version 0.12.9 allowing 2 mis-matches. Reads mapping to multiple positions were randomly assigned to one mapping position.
Genomic coverage:  5' ends of mapped reads (the last nucleotide transcribed by PolII) were counted per genomic position taking into account only unique UMIs. Coverage was generated separately for positive and negative strands. Coverage was normalized to tags per million and scaled by a factor obtained from relative spike-in abundance. Coverage was generated with GenomicRanges v1.34.0 package in R and exported into bigWig format with rtracklayer v1.42.2.
Quantification and differential analysis:  5' ends of mapped, UMI-collapsed reads overlapping promoter+pause region (from +1 to +150bp downstream of the TSS) and gene body region (from +150bp to annotated gene end) were counted for each individual sample/replicate. Gene annotation from Ensembl v83 was used, and annotated TSSs were corrected to nearest CAGE-defined TSS from FANTOM5 collection. Provided raw counts were used for downstream differential analysis between different conditions with DEseq2 v1.22.2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include genomic coordinates of a referent set of 19631 genes/transcripts with Ensembl v83 gene/transcript IDs, gene names, TSS positions corrected by CAGE and annotated transcription end sites. For each gene raw counts in each individual replicate are provided, separately for promoter+pause region (from +1 to +150bp downstream of the TSS) and gene body region (from +150bp to annotated gene end).  BigWig files contain normalized genome-wide coverage of 5' ends of PRO-seq reads, separately for positive and negative strands (the values for negative strand are shown as negative).

molecule: nuclear RNA

source_name: HCT116 cells

extract_protocol:
After treatment the cells were harvested and nuclei were isolated. Spike-in control (D. melanogaster S2 cell nuclei; 1% of total human HCT116 cells/nuclei) were added at the level of nuclei permeabilization step. Nuclear-run-on was performed for 3min at 37°C with biotin labeled CTPs (Perkin Elmer #NEL542001EA) followed by RNA extraction and base hydrolysis. Biotin-tagged nuclear-run-on RNA was enriched via M280 streptavidin beads (Invitrogen #112.06D) and precipitated via Phenol-Chloroform treatment.
3’ RNA adapters were ligated to isolated RNA and second biotin RNA enrichment followed by RNA 5’ cap modification via TAP (Biozym #187005) treatment was performed. Furthermore, 5’ hydroxyl repair via PNK (NEB #M0201S) treatment and subsequent 5’ adapter ligation was carried out. Afterwards, cDNA was generated from enriched RNA via reverse transcription (Super Script III Reverse Transcriptase, Invitrogen #18080-044). 10µl of the cDNA library was amplified via KAPA Amplification reaction (Roche #7959028001) on a qPCR machine (Biorad CFX Connect RealTime System). KAPA reaction: 10µl cDNA, 1µl forward primer 35µM (RP1-RP20), 1µl of reverse primer 35µM (RP1: 5’-AATGATACGGCGACCACCGAGATCTACAGTTCAGAGTTCTACAGTCCGA-3’), 25µl 2x KAPA SYBER master mix, 13µl water. PCR program: 98°C - 45 sec, 98°C - 15 sec, 60°C - 30 sec, 72°C - 30 sec, 72°C - 10 sec. Samples were removed from the qPCR machine after 12-15 cycles and cleaned with Ampure beads (Beckman #A63881) in a 1:1.4 (DNA:beads) ratio. DNA bound to the beads was eluted in 11µl of water and subjected to single-end deep sequencing.

treatment_protocol: 1x10^7 COF-AID tagged cells per replicate were treated as follows:   1. water (mock) treatment for 3h or 12h, for BRD4- and MED14-AID-tagged cells, respectively  2. 500µM auxin (IAA) treatment for 3h [BRD4]  3. 500µM auxin (IAA) treatment for 12h [MED14]  4. 500µM auxin (IAA) treatment for 12h and subsequent 10µM Nutlin 3a (Sigma# SML0580) treatment for 6h [MED14]

value: auxin (IAA) +Nutlin-3a


title: RNA-seq_Heart tube replicate 2


title: Med14_psAuxin_Nutlin_rep1


title: A_S7022

data_processing:
The fastqs were aligned to hg19 using bowtie2.
Unmapped, unpaired, and mitochondrial reads were removed using samtools.
ENCODE Blacklist regions were removed.
PCR duplicates were removed using Picard.
Peak calling was performed with MACS2 with a FDR q-value < 0.001. Peaks present in at least 2 samples were iincluded
Normalization and differential accessibility analysis was done with DESeq2.
Batch correction was performed using combat for library preparation group and sample location.
Genome_build: hg19
Supplementary_files_format_and_content: chromatin accessbility counts file

extract_protocol:
Transposed DNA was prepared with Tn5 (Illumina #FC-121-1031) as described in Buenrostro et al. 2013 using 0.1% Tween 20 instead of IGEPAL CA-630.Libraries were barcoded with Nextera Index Kit (Illumina # FC-121-1012)
The libraries were sequenced on an Illumina NextSeq machine using a 150 cycle high output flow cell


title: Med14_psAuxin_rep2


title: A_S7021


title: SAMPLE 2_E6+GF109203X


title: SAMPLE 3_BMP4


title: RNA-seq_Proepicardium replicate 4

source_name: Proepicardium

value: Proepicardium


title: RNA-seq_Heart tube replicate 1


title: Med14_psAuxin_rep1


title: RNA-seq_Proepicardium replicate 3


title: ATC_1

city: Memphis

first: JUN

last: YANG

state: TN

address: 262 Danny Thomas Place

department: Surgery

institute: St Jude Children's Research Hospital

data_processing:
Total stranded RNA sequencing data were processed by  the internal AutoMapper pipeline.First the raw reads were firs trimmed (Trim-Galore version 0.60),  mapped to mouse genome assembly (mm10) (STAR v2.5.3a).
The gene level expression values were quantified (htseq-count, v 0.6.1p1) based on mouse GENCODE M11 GTF.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include htseq counts values for each Sample.

source_name: T cell_WT

growth_protocol: Total CD3+ T cells isolated from mice were activated with IL-2 as well as plate-bound anti-mCD3/CD28 antibodies for 30hrs.

extract_protocol:
Total RNA was isolated according to the RNeasy Mini Kit (Qiagen) and treated with DNase I.
RNA libraries were prepared for sequencing using standard Illumina protocols at the St. Jude Hartwell Center.

treatment_protocol: no treatment

tag: strain background

value: Wild Type active

value: 8 weeks

value: T cell


title: A_S7019

value: Male

value: Negative

tag: cell type

value: UPenn


title: SAMPLE 1_E6

value: male


title: Med14_msAuxin_Nutlin_rep2

value: water (mock) +Nutlin-3a


title: SDK_2

source_name: T cell_SDHB KO

value: SDHB KO active


title: RNA-seq_Proepicardium replicate 2


title: Med14_msAuxin_Nutlin_rep1


title: A_S7018

source_name: PBMC

value: Young

tag: cmv serostatus


title: RNA-seq_Proepicardium replicate 1


title: A_S7017

tag: cell subset


title: Med14_msAuxin_rep1

value: water (mock)


title: A_S7016

tag: library preparation group


title: Med14_msAuxin_rep2


title: BRD4_psAuxin_rep2

description: Brd4_raw_counts_per_condition_for_promoter_and_genebody_regions.txt

value: auxin (IAA)


title: MCF7_DMSO_rep2

city: 上海

first: Xueting

last: Wu

state: 上海

address: Fenglin Road 300, Xuhui District

institute: CAS China

description: Gene expression data from human breast cancer cell line MCF7

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US)and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions.

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US)

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

source_name: Human breast cancer cell line MCF7

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The MCF7 cells were cultured in MEM/EBSS supplemented with 10% fetal bovine serum, 1mmol/L sodium pyruvate, 0.1mmol/L MEM non-essential amino acids, 100 unit/mL penicillin, and 100 mg/mL streptomycin in a incubator containing 5% CO2 at 37℃.

extract_protocol: Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: The MCF7 cells were treated by NB001, DMSO for 12h.

value: cancer cell line MCF7

value: DMSO

tag: treatment duration


title: MCF7_DMSO_rep1


title: BRD4_psAuxin_rep1

value: CRISPR/Cas9 edited cells

tag: genotype


title: A_S7015

tag: sample acquisition location


title: A_S7014


title: ATC_2


title: BRD4_msAuxin_rep2

tag: treatment


title: S27_S28 CD200pos fraction

city: TOULOUSE

first: Frederic

last: Deschaseaux

state: HAUTE-GARONNE

address: 4 BIS AVENUE HUBERT CURIEN, BATIMENT INCERE

department: Research

country: France

institute: EFS-Occitanie, Inserm U1031

description:
gene expression of CD271pos/CD200pos from bone marrow sample fractions of 27_28 patient
Ps_27_28_CD200pos

hyb_protocol: The Cy3- labeled cDNAs were hybridized overnight (17 hours, 65°C) to an Agilent Whole Human Genome Oligo Microarrays 8x60K using Agilent’s recommended hybridization chamber and oven. Finally, the microarrays were washed once with the Agilent Gene Expression Wash Buffer 1 for 1 min at room temperature followed by a second wash with preheated Agilent Gene Expression Wash Buffer 2 (37 °C) for 1 min.

scan_protocol: Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent’s Microarray Scanner System (Agilent Technologies).

data_processing:
The Agilent Feature Extraction Software (FES) was used to read out and process the microarray image files. The software determines feature intensities (including background subtraction), rejects outliers and calculates statistical confidences. For determination of differential gene expression FES derived output data files were further analyzed using the Rosetta Resolver gene expression data analysis system (Rosetta Biosoftware). This software offers – among other features – the possibility to compare two single intensity profiles in a ratio experiment. Pre-processing of micro-array data:  raw intensity data were extracted from Feature Extraction output files for Agilent Whole Human Genome Oligo Microarrays 8X60K v2 (Agilent Technologies, Inc) with the use of Rosetta Resolver software (Rosetta, Inpharmatics, LLC). All subsequent calculations were performed with the use of R/Bioconductor and software packages therein. Background-corrected intensity values were normalized between arrays by means of quantile normalization. Reliable signal intensities were considered at P ≤ 0.01, according to the Rosetta error model. Log2-transformed normalized intensity values were used for subsequent statistical anal
The ratios are always calculated by dividing sample signal intensity (from CD45neg/CD31neg/CD271pos/CD200pos fraction) through control (CD45neg/CD31neg/CD271pos/CD200neg fraction) signal intensity.Data preprocessing covers all necessary data transformations as well as an assessment of variability between the samples, and detection of potential outliers by a global correlation analysis. The background-corrected intensity data of all individual microarrays included in the analysis were compiled in one file. After background correction, quantile normalization was conducted between arrays. Finally, the normalized intensities were log2-transformed and served as basis for further analysis.

source_name: Bone marrow CD271pos/CD200pos sorted cells from 27_28 patient sample

label_protocol: 250 ng of each of the cDNAs were used as template for Cy3 labeling which was performed according to Miltenyi Biotec’s undisclosed protocol.

growth_protocol: Cells were obtained from fresh human bone marrow samples

extract_protocol: human cell samples were lysed using SuperAmpTM Lysis Buffer and stored appropriately by the customer according to the instructions of the SuperAmp Preparation Kit. SuperAmp RNA amplification was performed according to Miltenyi Biotec’s undisclosed procedure. Briefly, the amplification is based on a global PCR protocol using mRNA-derived cDNA. mRNA was isolated via magnetic bead technology. Amplified cDNA samples were quantified using the ND-1000 Spectrophotometer (NanoDrop Technologies). The integrity of the cDNA was checked via the Agilent 2100 Bioanalyzer platform (Agilent Technologies).

treatment_protocol: Bone marrow (BM) human mononuclear cells were sorted by using flow cytometer according to the expression of specific markers. After their staining by fluorescent monoclonal antobodies, cells were separated thanks to the negative expression of CD45 and CD31 markers and to the positive expression of CD271. The CD200pos and CD200neg populations of cells were then selected among the whole  CD45neg/CD31neg/CD271pos population of cells. Sorted cells were then treated for RNA extraction.

tag: individual

value: 27_28 patient

value: Bone Marrow

value: CD271pos/CD200pos sorted cells

tag: gender

value: Female


title: IP_Stimulated_RNase_IgG_3

data_processing:
Sequencing was performed with a read length of 2 x 100bp using Illumina NovaSeq 6000.
Quality of the reads was assessed with fastqc.
Adapters were trimmed using cutadapt (Martin, 2011).
Trimmed sequences were aligned to human genome assembly hg38 using STAR 2.7.5.
The PCR duplicates from the mapped reads were removed using Picard (Wysoker et al., 2013)
The bigWig files were generated by deepTools (Ramírez et al., 2016)
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files showed the reads per kilobase per million (RPKM) of ChIP read densities within the 10bp windows of genomic region for triplicate of samples. The 3 replicates for each condition were merged

source_name: Jurkat cells

extract_protocol:
Cells were cross-linked with 1% parafolmaldehyde for 10 minutes and glycine was added to quench the reaction. The cell lysates were prepared as described (Varshney et al., 2018). The chromatin was sonicated in Bioruptor (Diagenode) at high power for 40 min (30 s on/off). 40 micrograms of the sonicated chromatin were used for each IP. 5% of each extract used in the IPs were taken as inputs.For p65, 7.5ug of anti-p65 rabbit polyclonal (Invitrogen; 51-0500) or Rabbit IgG Isotype Control (ThermoFisher; 02-6102) antibody were added to samples and incubated overnight at 4oC, before incubation with 30ul Protein G Dynabeads (Life Technologies) for an additional 2h. Beads were eluted as desribed by Varshney et al before Proteinase K treatment and reverse crosslinking at 42oC overnight. Eluted DNA was purified by QIAquick PCR purification kit (QIAGEN).
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit and NEBNext® Multiplex Oligos (Index Primers Set 1) for Illumina.

treatment_protocol: For two of our experimental conditions Jurkat cells were stimulated with 200ng/ml PMA and 300ng/ml ionomycin for 3 hours. All cells were permeabilized with 0.05% Tween-20 in PBS for 10 minutes. Some of the stimulated cells were further treated with 2mg/ml PureLink RNase A (ThermoFisher) for 30 minutes at room temperature.

value: PMA + Ionomycin stimulation + Rnase treatment

tag: antibody


title: BRD4_msAuxin_rep1

tag: cell line


title: S27_S28 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 27_28 patient
Ps_27_28_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 27_28 patient sample

tag: tissue

value: CD271pos/CD200neg sorted cells


title: MCF7_NB001_10μM_rep2


title: Med14_psAuxin_Nutlin_MED1_ChIP

data_processing:
Read alignment:  Single-end 50 bp long reads were mapped to a reference hg19 genome using Bowtie version 0.12.9 allowing 3 mis-matches. Only uniquely mapping reads were retained.
Genomic coverage:  Mapped reads were extended to 500bp and used to generate coverage at 1bp resolution with GenomicRanges v1.34.0 package in R. Coverage was normalized to tags per million and exported into bigWig format with rtracklayer v1.42.2.
Peak calling:  Unique fragments were used to call peaks with macs2 v2.1.2 for each condition/treatment against the respective input, using default macs2 settings.
Genome_build: hg19
Supplementary_files_format_and_content: For each condition, peaks called with macs2 against the respective input are provided in .narrowPeak format.  BigWig files contain normalized coverage of extended fragments for each ChIP sample and respective inputs.

extract_protocol:
Cells were fixed with 1% FA in PBS for 15 min. Crosslinked cells were resuspended in lysis buffer (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, protease inhibitors) and rotated for 10 minutes at 4°C. The pellet was sonicated on a Misonix 3000 sonicator for 10 cycles at 30 s each on ice (18-21 W) with 60 s on ice between cycles. Input material was reserved and the remainder was incubated overnight at 4°C with magnetic beads bound with MED1 antibody (Bethyl #A300-793A). DNA was eluted off the beads by incubation with agitation at 65°C for 15 minutes in elution buffer. Cross-links were reversed for 12 hours at 65°C. Eluted DNA was treated with RNase A (37°C for 2 hours) and proteinase K (55°C for 30 min). DNA was purified using Qiagen PCR purification kit.
Purified immunoprecipitated DNA were prepared for sequencing according to a modified version of the Solexa Genomic DNA protocol. Fragmented DNA was end repaired and subjected to 18 cycles of LM-PCR using oligos provided by Illumina. Amplified fragments between 150 and 300bp (representing shear fragments between 50 and 200nt in length and ~100bp of primer sequence) were isolated by agarose gel electrophoresis and purified.

treatment_protocol: MED14-AID-tagged cells were treated as follows:   1. water (mock) or 500µM auxin (IAA) treatment for 3h  2. water (mock) or 500µM auxin (IAA) treatment for 3h, followed by Nutlin 3a (Sigma# SML0580) treatment for 1h

value: auxin (IAA) +Nutlin-3a

tag: chip antibody

tag: antibody manufacturer

value: Bethyl

tag: antibody catalog


title: IP_Stimulated_RNase_p65_3

value: anti-p65 rabbit polyclonal (Invitrogen; 51-0500)


title: A_S7011

tag: donor type

tag: donor id

tag: age

tag: Sex

value: Male

value: Negative

value: UPenn


title: input_Stimulated_Rnase_3


title: MCF7_NB001_10μM_rep1

tag: cell type


title: S25_S26 CD200pos fraction

description:
gene expression of CD271pos/CD200pos from bone marrow sample fractions of 25_26 patient
Ps_25_26_CD200pos

source_name: Bone marrow CD271pos/CD200pos sorted cells from 25_26 patient sample

value: 25_26 patient


title: SDK_1

tag: strain background

value: SDHB KO active

value: 8 weeks

value: T cell


title: Med14_psAuxin_Nutlin_Input

value: CRISPR/Cas9 edited cells

tag: genotype


title: A_S7007

value: Young

tag: cmv serostatus

tag: cell subset

tag: library preparation group

tag: sample acquisition location


title: S23_S24 CD200pos fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 13_14 patient
Ps_23_24_CD200pos

source_name: Bone marrow CD271pos/CD200pos sorted cells from 23_24 patient sample

tag: individual

value: 23_24 patient

value: Bone Marrow

tag: gender


title: Med14_psAuxin_MED1_ChIP

tag: cell line

tag: treatment

value: auxin (IAA)


title: S23_S24 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 23_24 patient
Ps_23_24_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 23_24 patient sample

tag: tissue


title: IP_Stimulated_IgG_3

value: PMA + Ionomycin stimulation

tag: antibody

value: Rabbit IgG Isotype Control (ThermoFisher; 02-6102)


title: S21_S22 CD200pos fraction

description:
gene expression of CD271pos/CD200pos from bone marrow sample fractions of 21_22 patient
Ps_21_22_CD200pos

source_name: Bone marrow CD271pos/CD200pos sorted cells from 21_22 patient sample

value: 21_22 patient

value: CD271pos/CD200pos sorted cells

value: Female


title: IP_Stimulated_p65_3

value: anti-p65 rabbit polyclonal (Invitrogen; 51-0500)


title: A_S7006

tag: donor type

value: Negative


title: Med14_psAuxin_Input

tag: chip antibody

tag: antibody manufacturer

tag: antibody catalog


title: A_S7005

tag: donor id

tag: age

tag: Sex

tag: cell type

value: UPenn


title: S21_S22 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 21_22 patient
Ps_21_22_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 21_22  patient sample

value: 21_22  patient

value: CD271pos/CD200neg sorted cells


title: Med14_msAuxin_Nutlin_MED1_ChIP

tag: genotype

value: water (mock) +Nutlin-3a

value: Bethyl


title: A_S7004

tag: cmv serostatus

tag: cell subset

tag: library preparation group


title: A_S7013

value: Male

tag: sample acquisition location


title: IP_DMSO_IgG_3

value: untreated


title: Med14_msAuxin_Nutlin_Input

tag: cell line

value: CRISPR/Cas9 edited cells


title: S17_S18 CD200pos fraction

description:
gene expression of CD271pos/CD200pos from bone marrow sample fractions of 17_18 patient
Ps_17_18_CD200pos

source_name: Bone marrow CD271pos/CD200pos sorted cells from 17_18 patient sample

tag: individual

value: 17_18 patient

value: Bone Marrow

tag: gender


title: Brd4_psAuxin_rep2 [STARR-seq]

tag: treatment

value: auxin (IAA)


title: A_S7003

tag: donor type

value: Young


title: S25_S26 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 25_26 patient
Ps_25_26_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 25_26 patient sample

value: 25_26 patient

tag: tissue


title: IP_DMSO_p65_3

tag: antibody


title: S17_S18 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 17_18 patient
Ps_17_18_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 17_18 patient sample


title: S13_S14 CD200pos fraction

description:
gene expression of CD271pos/CD200pos from bone marrow sample fractions of 13_14 patient
Ps_13_14_CD200pos

source_name: Bone marrow CD271pos/CD200pos sorted cells from 13_14 patient sample

value: 13_14 patient

value: CD271pos/CD200pos sorted cells


title: input_Stimulated_3

value: PMA + Ionomycin stimulation


title: Med14_msAuxin_MED1_ChIP

source_name: HCT116 cells

value: water (mock)

tag: chip antibody

tag: antibody manufacturer

tag: antibody catalog


title: A_S7002

tag: donor id

tag: age

tag: Sex

value: Female

value: Negative

value: UPenn


title: A_S7001

tag: cmv serostatus

tag: cell type


title: input_DMSO_3


title: A_S7020

tag: cell subset

tag: library preparation group


title: Med14_msAuxin_Input

tag: cell line

tag: genotype


title: IP_Stimulated_RNase_IgG_2

value: PMA + Ionomycin stimulation + Rnase treatment

value: Rabbit IgG Isotype Control (ThermoFisher; 02-6102)


title: 8-CONTsi

city: Jerusalem

first: Ruth

last: Sperling

address: The Edmond J. Safra Campus - Givat Ram

department: Department of Genetics

country: Israel

institute: The Hebrew University of Jerusalem

description: CONTsi rep2

data_processing:
BCL files were converted to fastq files via bcl2fastq (version 2.17) with the following options: minimum-trimmed-read-length set to 1, mask-short-adapter-reads set to 1, and barcode-mismatches set to 1.
Reads from each sequencing lane (4 lanes per sample) were aligned independently with STAR (version 2.3.1y) against hg19 assembly of the human genome. For the alignment step, hg19 was indexed (125-bp read overhang) using Gencode v19 annotation and junction information for all latent splice sites. The value of the STAR parameter “--alignSJDBoverhangMin” was set to 2.
Read quantification was done with the QoRTs package (Hartley and Mullikin, 2015) for each bam file separately, and results were aggregated for each sample from four files associated with the four sequencing lanes.
Genome_build: hg19
Supplementary_files_format_and_content: gene_read_counts.txt: tab delimited text file with 5 columns. Column 1: gene Ensembl ID; columns 2-5: count of reads mapped for samples 1-NCLsi, 2-CONTsi, 7-NCLsi, 8-CONTsi, respectively.
Supplementary_files_format_and_content: splice_junction_counts.txt: tab delimited text file with 8 columns. Columns are: 1: chromosome; 2: junction end 1; 3: junction end 2; 4: strand; 5-8: counts of split reads aligned at this junction for samples 1-NCLsi, 2-CONTsi, 7-NCLsi, 8-CONTsi, respectively. Columns 2 and 3 provide bed-style coordinates (column 2 is 0-based) of the intronic region separating the two exons.

source_name: cell culture

growth_protocol: Human HEK 293 cells were grown to 20-40% confluency in tissue culture plates.

extract_protocol:
Total RNA were extracted (RNeasy Qiagen 74104) according to the manufacturer’s instructions.
The library preparation was done with the TruSeq® Stranded mRNA Sample Preparation kit (Illumina) with 500 ng starting material from each of 4 samples: 1-NCLsi, 2-CONTsi, 7-NCLsi, and 8-CONTsi. Sequencing libraries were constructed with barcodes to allow multiplexing of 4 samples on 4 sequencing lanes.

treatment_protocol: Knockdown using siRNA was performed by transfecting HEK 293 cells grown in 6-well plates with 45 nM siRNA targeted to NCL (L-003854-00-0005, ON-TARGETplus Human NCL (4691) siRNA- SMARTpool, Dharmacon), and non-targeting siRNA as control (D-001810-01-05 ON-TARGETplus Non-targeting siRNA #1, Dharmacon), using TransIT-X2 (mc-MIR-6003, Mirus) according to the manufacturer’s instructions. After 24 hr, medium was changed and cells were transfected again, as before. Cells were harvested 48 hr after transfection .

value: HEK 293

tag: sirna

tag: sample pair


title: S13_S14 CD200neg fraction

description:
gene expression of CD271pos/CD200neg from bone marrow sample fractions of 13_14 patient
Ps_13_14_CD200neg

source_name: Bone marrow CD271pos/CD200neg sorted cells from 13_14 patient sample

tag: individual

value: CD271pos/CD200neg sorted cells

tag: gender


title: Muscle HSD rep2 [HS3M]

city: shanghai

first: Fei

last: Mao

state: State...

address: Fudan university

institute: Fudan University

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by thesoftware of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Hisat2.
HTSeq(0.9.1) statistics were used to compare the Read Count values on each gene as theoriginal expression of the gene, and then used FPKM to standardize the expression.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: Muscle

extract_protocol:
Livers, WAT,muscles were all removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq Stranded Total RNA Library Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

tag: tissue

value: Muscle

value: wild type

tag: treatment

value: 12wks high salt diet fed


title: Melanoma Cancer Cells - PES43_NIVO+sPDL1_24h_rep2

city: Napoli

first: Luigi

last: Portella

address: M. Semmola

department: Research Department

country: Italy

institute: Istituto Nazionale Tumori di Napoli - IRCCS fondazione "Pascale"

data_processing:
RNAseq FASTQ sample sequences were mapped on HG38 genome (Dec. 2013 assembly) with STAR software (v. 2.7.3a) and default options
The resulting BAM files were then processed with feature Countsfunction present into the Rsubread R/Bioconductor package (v.2.4.2) on Ensembl HG38 GTF (v. 102) to produce a count matrix of 64252 genes and 46 samples
To remove lowly expressed genes a proportion test has been performed by the aid of the filtered.data function present into the NOISeq R/Bioconductor package (v. 2.34.0) resulting in 16842 genes for the 46 samples matrix
Samples were then divided for cell line and normalized with RUVs procedure present in the RUVSeq R/Bioconductor package (v.1.24.0).
A different "k" parameter is chosen for each cell line on the best normalization afforded for each case (Cell Line HCT116 k=3, HT29 k=5, PES43 k=1).
Then, for each cell line to test differentially expressed genes, the glmQLFit combined with glmQLFTest from the edgeR R/Bioconductor package (v. 3.32.0).
Functional enrichment analysis was then performed with gProfiler2 R package (v. 0.2.0).
Genome_build: HG38 genome (Dec. 2013 assembly)

source_name: Melanoma Cancer Cells

growth_protocol: Human colon cancer cells HCT116 were cultured in high-glucose Dulbecco’s modified Eagle’s medium (DMEM) (Gibco BRL, Grand Island, NY). HT29 were cultured in RPMI (Invitrogen, San Diego, CA, USA). PES43 human melanoma cancer cells (Scala, 2006) were cultured in IMDM. Each medium was supplemented with 10% fetal bovine serum (FBS), penicillin (100 μg/mL), streptomycin (100 μg/mL) (Invitrogen, Carlsbad, CA). All the cells were maintained in an incubator with a humidified atmosphere of 5% CO2 at 37°C and were proved mycoplasma-free.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit according to manufacture protocol
Total RNA was quantified using the Qubit fluorometer (ThermoFisher) with Qubit™ RNA HS Assay Kit (ThermoFisher). Polyadenylated RNA libraries were prepared using QIAseq Stranded mRNA Select Kit (Qiagen). The mRNA Enrichment was obtained starting from 1ug of total RNA using Oligo-dT probes attached to the surface of magnetic beads. Fragmentation was then performed at the reaction temperature of 95°C to obtain an insert size of ~350 bp. Double-stranded cDNA was achieved by a reaction with Rnase H-Reverse Transcriptase in combination with random primers followed by a second-strand synthesis, end repair, and A-addition step. The dual index technology was used to sequence multiple samples thanks to the ligation of Illumina-compatible adapters. Finally, the last amplification step was performed on the purified libraries using the CleanStart PCR Mix, also able to degrade contaminating material. QIAseq Beads were used for reaction cleanups between protocol steps. The quality control and quantification of libraries were performed using the Agilent 2100 Bioanalyzer instrument and High Sensitivity DNA Kit (Agilent). Each QIAseq Stranded library was diluted to a concentration of 4 nM. Then, the libraries with different sample indexes were pooled in equimolar amounts. The pooled libraries at concentration of 1.6 pM were sequenced on Illumina NGS NextSeq 500 platform using 2x 150 bp paired-end mid-output sequencing kit (Illumina).

treatment_protocol: HT29 and HCT116 cells treated with NIVO, sPD-L1 and combination sPD-L1 + NIVO for 6-24 hours and compared to PES43 cells

value: Skin

tag: disease

value: Melanoma

value: NIVO+sPDL-2 for 24h


title: 7-NCLsi

description: NCLsi rep2

value: L-003854-00-0005, ON-TARGETplus Human NCL (4691) siRNA- SMARTpool, Dharmacon


title: IP_Stimulated_RNase_p65_2

tag: antibody

value: anti-p65 rabbit polyclonal (Invitrogen; 51-0500)


title: Muscle HSD rep1 [HS2M]

tag: age


title: Muscle WT rep3 [CON72M]

value: control


title: input_Stimulated_Rnase_2


title: 2-CONTsi

description: CONTsi rep1

value: D-001810-01-05 ON-TARGETplus Non-targeting siRNA #1, Dharmacon


title: A_S7012

city: Philadelphia

first: E

last: WHERRY

address: 421 Curie Blvd,354 BRB II/III

institute: University of Pennsylvania

source_name: PBMC

tag: donor type

value: Young

tag: donor id

tag: Sex

value: Male

tag: sample acquisition location


title: Melanoma Cancer Cells - PES43_sPDL1_24h_rep2

value: solubile-PDL-1 (sPDL-1) for 24h


title: IP_Stimulated_IgG_2

source_name: Jurkat cells

value: PMA + Ionomycin stimulation


title: 1-NCLsi

description: NCLsi rep1

tag: cell type


title: Muscle WT rep2 [CON71M]


title: IP_Stimulated_p65_2


title: Muscle WT rep1 [CON16M]


title: Melanoma Cancer Cells - PES43_sPDL1_24h_rep1


title: input_Stimulated_2


title: Melanoma Cancer Cells - PES43_NIVO_24h_rep2

value: NIVOLUMAB (NIVO) for 24h


title: WAT HSD rep3 [HS5W]

source_name: WAT

value: WAT


title: IP_DMSO_IgG_2

value: untreated

value: Rabbit IgG Isotype Control (ThermoFisher; 02-6102)


title: DamID_freedam_set7_N7476

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

description: DamID

data_processing:
DamID-seq mapping and analysis was done using the Galaxy public server (Afgan et al., 2018).
The Barcode Splitter was used to filter for reads with a GATC at the 5’ end and these reads were mapped using Bowtie2 (Langmead and Salzberg, 2012).
Files for biological replicates were merged using MergeBam.
Merged bam files were used as input for bamCoverage (RPKM, 50bp bins) to generate bigwig files for viewing on IGV and running bigwigCompare.
The output from bamCoverage was used with computeMatirx to generate files to use for plotProfile and output graphs.
neurospora crassa genome (OR74A)
bigwig

organism: Neurospora crassa

source_name: nuclei from germinated condia

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 24 hours at 32oC.

extract_protocol:
Preparation of N6-methyladenine-containing DNA for sequencing was performed using a previously reported procedure (Bernstein et al. 2012) with the following modifications: 5 μg of genomic DNA from N. crassa strains expressing a Dam fusion was digested with 1 μL of DpnI (NEB, 20 units/μL); ligation to primer 5050 was carried out overnight at 16 °C; amplification reactions of ligated DNA with primer 5051 were performed in triplicate, contained 5 μL dNTPs, and an additional PCR cycle was added to the 2nd and 3rd phase of the PCR protocol (4 and 18 cycles respectively); 3 μg of pooled, amplified DNA was sheared using a Bioruptor (Diagenode) twice on high for 10 minutes (30 seconds on/off) at 4 °C.
Biotinylated DNA was purified using 250 μL slurry of streptavidin-agarose beads (Sigma) and prepared for high-throughput sequencing using the NEBNext DNA Library Prep Master Mix Set for Illumina (NEB).

treatment_protocol: Mycelia were harvested, lyophilized, pulverized and resuspended in salt detergent. Lysates were cleared by centrifugation and TCA/ethanol treatment. Total genomic DNA was isolated by phenol-chloroform extraction and isopropanol precipitation and resuspended in TE buffer

tag: sample type

value: nuclei


title: Melanoma Cancer Cells - PES43_NIVO_24h_rep1


title: DamID_freedam_WT_N7802

description: DamID


title: Melanoma Cancer Cells - PES43_ctr_24h_rep2


title: WAT HSD rep2 [HS3W]

tag: genotype

value: wild type

value: 12wks high salt diet fed


title: Muscle HSD rep3 [HS5M]

value: Muscle


title: DamID_crf4-2_dam_set7_N8114

description: DamID


title: WAT HSD rep1 [HS2W]


title: input_DMSO_2


title: Melanoma Cancer Cells - PES43_ctr_24h_rep1

value: Skin

value: Melanoma


title: WAT WT rep3 [CON72W]


title: Melanoma Cancer Cells - PES43_NIVO+sPDL1_6h_rep2

value: NIVO+sPDL-2 for 6h


title: DamID_crf4-2_dam_WT_N8146

description: DamID


title: IP_Stimulated_RNase_IgG_1

value: PMA + Ionomycin stimulation + Rnase treatment


title: Melanoma Cancer Cells - PES43_NIVO+sPDL1_6h_rep1

value: NIVO+sPDL-1 for 6h


title: WAT WT rep2 [CON71W]

value: control


title: IP_Stimulated_RNase_p65_1

value: anti-p65 rabbit polyclonal (Invitrogen; 51-0500)


title: DamID_crf4-2_dam_WT_N8115

description: DamID


title: WAT WT rep1 [CON16W]


title: Melanoma Cancer Cells - PES43_NIVO+sPDL1_24h_rep1

value: NIVO+sPDL-1 for 24h


title: Melanoma Cancer Cells - PES43_sPDL1_6h_rep2

value: solubile-PDL-1 (sPDL-1) for 6h


title: input_Stimulated_Rnase_1


title: RNAseq_WT_N3753_rep4

description: RNA-seq

data_processing:
Sequence reads were aligned to the neurospora crassa genome (OR74A) using STAR program (version 2.7.3a)
Total aligned reads per neurospora gene were calculated using RSEM software (version 1.3.1) and normalized using DESeq2 software (version 1.24.0)
Batch effect were corrected using R package, limma (version 3.44.1).
FDR < 0.05 and log2 fold-change > 2 were used as a threshold to identify significantly up- or downreagulated genes.
neurospora crassa genome (OR74A)
tab-deliminated text files of gene ID and expected read count obtained from RSEM calculation

growth_protocol: 5 ml cultures were grown in Vogels medium and 1.5% sucrose (standard minimal medium), shaking for 16 hours at 32oC.

extract_protocol:
Samples were cleared by centrifugation, and the aqueous (top) phase was mixed with 350uL of chloroform. After centrifugation, the aqueous phase was divided into two tubes containing 650uL cold 100% EtOH.  Samples were precipitated at -20oC, pelleted by centrifugation, washed twice with 1mL 70% EtOH, and resuspended in DEPC-treated dH2O. RNA was treated with DNAseI, amplification grade (Thermo Fisher Scientific) and cleaned (Agencourt® RNAclean XP® beads, Beckman Coulter).
RNA-seq libraries were prepared using the KAPA Stranded mRNA-seq kit (KAPA Biosystems).

treatment_protocol: Mycelia were harvested and added to a tube containing ~350uL glass beads (260-300 micrometer, acid washed [Sigma Aldrich] and resuspended in sdH2O), 350uL NETS buffer (10mM Tris pH 7.5, 300mM NaCl, 1mM EDTA, 0.2% SDS) and 350uL phenol:chloroform:isoamyl alcohol (25:24:1) and lysed by a bead beater for 3 minutes at room temperature.


title: Melanoma Cancer Cells - PES43_sPDL1_6h_rep1


title: Liver HSD rep3 [HS5L]

source_name: Liver

value: Liver


title: Liver HSD rep2 [HS4L]


title: RNAseq_WT_N3752_rep3

description: RNA-seq


title: IP_Stimulated_IgG_1

value: PMA + Ionomycin stimulation


title: DamID_freedam_set7_N7477

description: DamID


title: Liver HSD rep1 [HS2L]


title: RNAseq_set7_N4730

description: RNA-seq


title: IP_Stimulated_p65_1


title: Melanoma Cancer Cells - PES43_NIVO_6h_rep1

value: NIVOLUMAB (NIVO) for 6h


title: input_Stimulated_1


title: RNAseq_set7_N4718

description: RNA-seq


title: Liver WT rep3 [CON72L]


title: Melanoma Cancer Cells - PES43_ctr_6h_rep2

value: untreated


title: IP_DMSO_p65_2


title: IP_DMSO_IgG_1

value: Rabbit IgG Isotype Control (ThermoFisher; 02-6102)


title: RNAseq_WT_N3752_rep2

description: RNA-seq

value: nuclei


title: DamID_crf4-2_dam_set7_N8113

description: DamID


title: Melanoma Cancer Cells - PES43_ctr_6h_rep1


title: Liver WT rep2 [CON16L]

value: wild type


title: RNAseq_WT_N3752_rep1

description: RNA-seq


title: Colorectal Cancer Cells - HCT116_NIVO+sPDL1_24h_rep2

source_name: Colorectal Cancer Cells

value: Colon

value: Colorectal carcinoma

value: NIVO+sPDL-2 for 24h


title: input_DMSO_1


title: CD-D-ATAC

city: Indianapolis

first: Núria

last: Morral

state: IN

address: 975 West Walnut, IB130

department: Medical and Molecular Genetics

institute: Indiana University School of Medicine

data_processing:
peak
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab delimited txt files; data show differential peak and expression between the two groups

source_name: Liver tissue

extract_protocol: ChIP-seq, RNA-seq, ATAC-seq

treatment_protocol: mouse fed a high fat diet (60% kcal fat) or a control diet (18% kcal fat) for 10 weeks

value: mouse fed a control diet (18% fat)