title: TAK1 mKO macrophage 3

city: Pittsburgh

first: Yejie

last: Shi

state: PA

address: S-510 Biomedical Science Tower, 3500 Terrace Street

department: Neurology

institute: University of Pittsburgh

data_processing:
Genome alignment to GRCm38 using HISAT2 in Chipster v3.15
Counting reads using HTSeq in Chipster v3.15
Genome_build: GRCm38
Supplementary_files_format_and_content: tsv files include read counts for each sample

source_name: brain macrophages

extract_protocol:
Single-cell suspensions were prepared from mouse brains 3 days after stroke. Mice were transcardially perfused with sterile 0.9% NaCl. The ipsilesional brain hemisphere was harvested, and cell suspensions were prepared using the Neural Tissue Dissociation Kit and gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec). Suspensions were passed through a 70 μm cell strainer, and fractionated on a 30% and 70% Percoll gradient at 500 g for 30 min. Mononuclear cells at the interface were collected. Isolated mononuclear cells were washed, resuspended at 1×10^6 per mL, and stained with fluorophore-conjugated antibodies and the appropriate isotype controls. Fluorescence-activated cell sorting was performed using the FACS Aria I sorter and FACS Diva software (BD Biosciences). Microglia and macrophages were gated as CD11c–Ly6G–CD11b+CD45low and CD11c–Ly6G–CD11b+CD45high, respectively, and sorted for bulk RNA-seq.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: TAK1 mKO

tag: full genotype

tag: cell marker

value: CD11b+ CD45high


title: 1502_IRN_144h_1

status: Public on Mar 10 2020

type: SRA

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

country: USA

institute: UT Health Science Center at San Antonio

library_source: transcriptomic

data_processing:
Illumina Casava v1.8.2 software used for base-calling
All RNA-seq FastQ reads were aligned with the reference genome (UCSC human genome build hg19) using TopHat2 default settings. To remove RNA species from host (mouse RNA), a custom-designed algorithm was performed to align reads using TopHat2 to both host genome (mm9) and graft genome (hg19). We kept reads as human-specific or human/mouse-common based on number of mis-match bases, number of gaps and alignment QC scores. The human RNA sequence reads (unique to human + common human/mouse) were then re-aligned to graft genome hg19 using TopHat2, and the BAM files obtained after alignment were processed using HTSeq-count to obtain the counts per gene
gene count measurements were obtained using HTSeq-count
Genome_build: hg19
Supplementary_files_format_and_content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

molecule: total RNA

organism: Homo sapiens

source_name: Ewing sarcoma

growth_protocol: C.B.17SC scid−/− (C.B-Igh-1b/IcrTac-Prkdcscid) female mice (Taconic Farms, Germantown NY) were used to propagate subcutaneously implanted tumors. All mice were maintained under barrier conditions and experiments were carried out using protocols and conditions approved by the institutional animal care and use committee of UTHSA.

extract_protocol:
Total RNA was extracted from snap-frozen xenografts chilled under liquid nitrogen to prevent thawing. RNA was extracted with TRIzol reagent and purified on an RNeasy mini column (Qiagen). On-column DNase digestion was performed with Qiagen RNase-free DNase kit.
RNA-seq library preparation by following the Illumina TruSeq stranded mRNA sample preparation guide

treatment_protocol: Mice were randomized into groups of 10, and treatment was started when tumors were 200-400 mm^3. Eribulin was dissolved in sterile water and administered days 1 and 8, and irinotecan was dissolved in saline and administered days 1-5, with the cycle repeated at day 21. Eribulin was dosed at 1 mg/kg and irinotecan at 2.5 mg/kg. Both drugs were administered by intraperitoneal injection.

tag: tissue

value: Ewing sarcoma

tag: tumor

value: ES4 xenograft

tag: treatment

value: irinotecan, 2.5mg/kg

tag: harvest time

value: 144 hour


title: SAMPLE 88: Control 10, BS

type: genomic

city: Odense

first: Rasmus

last: Rydbirk

address: Fioniavej 34

department: Functional Genomics and Biochemistry

country: Denmark

institute: University of Southern Danmark

hyb_protocol: BS or oxBS converted genomic DNA was hybridized to Illumina Infinium MethylationEPIC BeadChips according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Illumina iScan instrument.

data_processing:
Data were analysed using ChAMP v. 2.13.5. Probes were filtered according to standard settings before imputation and BMIQ normalization.
Matrix table is BMIQ normalized beta

label: Cy5 and Cy3

molecule: genomic DNA

source_name: Prefrontal cortex 10

label_protocol: Not provided

extract_protocol: Genomic DNA was extracted using the PCI method.

tag: sample type

value: Prefrontal cortex

tag: Sex

value: Male

tag: age

tag: pmi (hours)

tag: condition

value: CTRL

tag: brain bank

value: MRC London Neurodegenerative Diseases Brain Bank

tag: identifier

value: Brain

tag: conversion

value: BS


title: CCOC-4_H3K27ac_ChIP-seq

city: Los Angeles

first: Kate

last: Lawrenson

state: CA

address: 8700 Beverly Blvd

department: Women's Cancer Program

institute: Cedars-Sinai Medical Center

library_source: genomic

data_processing:
ChIP-seq data was processed using AQUAS v0.3.3
RNA-seq data was first aligned using STAR v2.5.1b to GRCh38.p10 (GENCODE 26)
then read counts for mapped reads were generated using featureCounts v1.5.0-p1
Genome_build: ChIP-seq: hg19, RNA-seq: hg38
Supplementary_files_format_and_content: narrowPeaks generated with AQUAS v0.3.3
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample ...

source_name: Epithelial ovarian cancer

extract_protocol:
Chromatin was incubated at 4°C overnight with 1 µg H3K27ac antibody (DiAGenode, C15410196, Denville, NJ) that had been coupled with protein A and protein G beads (Life Technologies, Carlsbad, CA)
ChIP-seq libraries were built using the ThruPLEX-FD Prep Kit (Rubicon Genomics, Ann Arbor, MI). RNA was extracted using the AllPrep kit (QIAgen, Hilden, Germany).

treatment_protocol: One flash frozen 3 mm core was biopsied from an epithelial-rich portion of the tumor. The tissue was pulverized in a pulverization bag (TT05) using the Covaris CryoPrep system (Covaris, Woburn, MA) twice at intensity 4. The tissue was then fixed using 1% formaldehyde (Thermo fisher, Waltham, MA) in Phosphate-buffered saline solution for 10 minutes at room temperature with rotation, and quenched with 125 mM glycine for 10 min at room temperature, also with rotation. One core was reserved for RNA-seq, this tissue was disrupted using an Omni Tissue Homogenizer.

value: Clear cell ovarian cancer


title: 1502_IRN_24h_2

value: 24 hour


title: TAK1 mKO macrophage 2

organism: Mus musculus

tag: strain

tag: genotype


title: 1502_IRN_24h_1


title: SAMPLE 87: Control 9, BS

source_name: Prefrontal cortex 9

value: Female

value: Bispebjerg Brain Bank


title: TAK1 mKO macrophage 1


title: 1502_IRN_144h_2


title: Slow.IP.rep2

city: Tel Aviv

first: Ran

last: Elkon

address: Ramat Aviv

department: Human Genetics

country: Israel

institute: Tel Aviv University

description:
4264_12_Slow-2_IP_GTCCGC_S26_L004
slow-elongated version of RNAPII - replicate 2

data_processing:
library strategy: RIP-seq (m6A-seq)
MeRIP data was aligned to the genome (hg19) using Tophat2.
MACS2 was used to detect m6A peaks (at FDR=1%).
Genome_build: hg19
Supplementary_files_format_and_content: m6A peaks

source_name: HEK293_expressing slow-elongated version of RNAPII

growth_protocol: DMEM, 10%FCS, 37 degrees, 5% CO2

extract_protocol:
Trizol
MeRIP library was prepared using EpiMark® N6-Methyladenosine Enrichment Kit and Illumina Truseq RNA kit according to the manufacturer's manual. Briefly, RNA was fragmented and bound to m6A antibody-coupled protein G beads for 3h. Beads were then washed with reaction buffer, low salt buffer, and high salt buffer. Enriched RNA was eluted with buffer RLT and purified with Dynabeads MyOne silane. Input RNA and enriched RNA were then reverse-transcribed, end-repaired and dA-tailed, following ligation with sequencing adaptors. The library was PCR amplified, purified and analyzed on Bioanalyzer before sequencing.

treatment_protocol: Doxycyclin (1ug/ml) for for 24 hours, then Doxycyclin in parallel with alpha-amanitin 2.5ug/ml for 42 hours

tag: cell line

tag: genotype/variation

value: alpha-amanitin mutant of RNAPII


title: Slow.IP.rep1

description:
4264_11_Slow-1_IP_AGTTCC_S25_L004
slow-elongated version of RNAPII - replicate 1


title: TAK1 mKO microglia 3

source_name: brain microglia

value: TAK1 mKO

tag: full genotype

tag: cell marker

value: CD11b+ CD45low


title: SAMPLE 86: Control 8, BS

source_name: Prefrontal cortex 8

tag: tissue


title: SAMPLE 85: Control 7, BS

source_name: Prefrontal cortex 7


title: TAK1 mKO microglia 2


title: 1502_1502_144h_2

value: Ewing sarcoma

tag: tumor

tag: treatment

value: eribulin, 1 mg/kg


title: 1502_1502_144h_1

value: ES4 xenograft

tag: harvest time


title: DG75-P1-2

type: RNA

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description: Gene expression data from diaphragm from animal with PDAC PDX, cohort 1.

hyb_protocol: The labeled, fragmented DNA was hybridized to the Affymetrix Mouse Gene 2.0 ST Array for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.

scan_protocol: After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus.

data_processing: Raw Affymetrix CEL files were normalized to produce Entrez Gene-identifier-specific expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1), using R version 2.15.1 and the Brainarray mogene20stmmentrezgcdf R package (version 17.0.0).

label: biotin

source_name: diaphragm from animal with PDAC PDX

label_protocol: Biotin labeling was performed using the WT Plus reagent kit (Affymetrix, Santa Clara, CA) according to the manufacturer's protocol.

growth_protocol: Mice were maintained in a temperature and humidity-controlled facility with a 12-h light/dark cycle and water and standard diet were provided ad libitum.

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

treatment_protocol: Adult female NSG mice were implanted with tumor resected from cachectic pancreatic ductal adenocarcinoma (PDAC) patients, and sham controls underwent surgery but had no tumor implantation. Mice were sacrificed when tumor-bearing mice exhibited severe cachexia or the tumors reached over 3cm in diameter.

tag: cohort

value: cohort 1

value: diaphragm

value: PDAC PDX


title: DG75-P2-2


title: DG75-P3-2


title: SAMPLE 84: Control 6, BS

source_name: Prefrontal cortex 6

tag: sample type

value: Prefrontal cortex

tag: Sex

value: Male

tag: age

value: CTRL


title: WT macrophage 2

value: wild type

value: CD11b+ CD45high


title: TAK1 mKO microglia 1


title: DG75-S3-2

description: Gene expression data from diaphragm from sham control animal, cohort 1.

source_name: diaphragm from sham control animal

value: sham


title: 1502_1502_24h_3

value: 24 hour


title: DG75-S2-2


title: 1502_1502_24h_2


title: SAMPLE 83: Control 5, BS

source_name: Prefrontal cortex 5

value: Female

tag: pmi (hours)

tag: condition

tag: brain bank

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain

value: BS


title: SAMPLE 82: Control 4, BS

source_name: Prefrontal cortex 4

value: Bispebjerg Brain Bank

tag: conversion


title: 1502_1502_144h_3

value: Ewing sarcoma

value: eribulin, 1 mg/kg

value: 144 hour


title: SAMPLE 81: Control 3, BS

source_name: Prefrontal cortex 3

tag: identifier


title: WT macrophage 1

tag: strain

tag: genotype


title: WT microglia 3

tag: full genotype

value: CD11b+ CD45low


title: 1502_1502_24h_1

value: ES4 xenograft


title: SAMPLE 80: Control 2, BS

source_name: Prefrontal cortex 2

value: Prefrontal cortex


title: SAMPLE 79: Control 1, BS

source_name: Prefrontal cortex 1

value: Male


title: WT microglia 1

tag: cell marker


title: WT microglia 2


title: 1502_Control_3

tag: tissue

value: control


title: M2_input_rep1

city: Braunschweig

first: Andreas

last: Kloetgen

state: NI

address: Inhoffenstr 7

department: Department for Computational Biology of Infection Research

country: Germany

institute: Helmholtz Centre for Infection Research

data_processing:
Read alignment: Reads were aligned against the reference sequence mm10 with bowtie2 (version 2.3.1) with standard parameters and only uniquely mapped reads were kept with MAPQ > 20.
Deduplication: Aligned reads were filtered for duplicated reads using picard-tools version 2.6.0.
Peak-calling: Peak calling for Atf4 was performed using MACS2 (version 2.0.1) using narrow option (sepcial parameters: --no-model).
Differential binding: To identify differentially bound peaks, we performed diffBind (version 2.2.12) analysis, using the normalization option DBA_EDGER.
Bigwig: For visualization purposes, we generated fold-enrichment bigwig files by applying MACS2 (version 2.0.1) bdgcmp over input (-m FE)
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, peak (bed)

growth_protocol: Bone marrow derived macrophages grown by adding M-CSF to culture medium for 5-7 days

extract_protocol:
Chromatin-IP was performed according to Cell Signaling ChIP kit # 9003 protocol
Libraries were prepared according to NEBNext® Ultra™ II DNA Library Prep Kit for Illumina kit instructions (NEB #E7103). Briefly, DNA was end-repaired, using NEBNext Ultrea II end prep Enzyme mix. The blunt, phosphorylated ends were treated with fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected using Ampure AMPure XP. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on Illumina HiSeq/NextSeq.

treatment_protocol: Addition of IL-4 (40 ng/ml) overnight

tag: strain background

tag: genotype/variation

value: wild type

value: m-CSF + IL-4


title: 1502_Control_1

tag: tumor

tag: treatment

tag: harvest time


title: SAMPLE 78: MSA 41, oxBS

source_name: Prefrontal cortex 78

tag: sample type

tag: Sex

value: MSA

value: oxBS


title: 1502_Control_2

source_name: Ewing sarcoma

value: 24 hour


title: TAG75-P2-2

description: Gene expression data from tibialis anterior from animal with PDAC PDX, cohort 1.

tag: cohort

value: cohort 1

value: tibialis anterior

value: PDAC PDX


title: YW67 control sample 3 [Y8]

city: Iowa City

first: David

middle: H

last: Price

state: IA

address: 500 Newton Road

department: Biochemistry and Molecular Biology

institute: University of Iowa

description: Control imaginal wing discs of 3rd instar larvae. Third technical replicate of the first biological replicate

data_processing:
Conventional base calling was performed using Sanger/Illumina 1.9 encoding.
Sequenced reads were trimmed for adaptor sequence using Trimmomatic-0.22. An average quality of 20 was maintained for all sequences. Aberrant bases (15 bp from the start and bases after 125bp)  were trimmed of each sequence based on fastqc analysis . Trimmed sequences between 36bp and 125bp were retained for further analysis. Reads from the two lanes were then combined to generate one alignment file for each of the 8 samples using bowtie. Reads were mapped to dmel r5.7 gene exons using bowtie2-2.1.0 with default parameters.
The eXpress tool was used to generate uniquely mapped read counts for each exon of a gene. The sum of unique read counts for each gene was generated using a custom python script. The DESeq2 package in R was used to compute normalized fold-change and P value for each gene, comparing Myb mutant to control.
Genome_build: dmel r5.7
Supplementary_files_format_and_content: The processed data file is a tab delimited file that contains flybase id, associated refSeq gene symbol, read counts for each gene per sample and additional data generated using DESeq2 package in R such as log2 fold change (mutant/control), p-value and adj p-value.

organism: Drosophila melanogaster

source_name: Wing discs of control 3rd instar larvae

growth_protocol: Flies were mantined at 25°C in malt-based media (Archon Scientific).

extract_protocol: Total RNA was isolated from yw67 control (3 biological replicates) and Myb mutant (5 biological replicates) 3rd instar mesothoracic wing discs and cDNA was generated from polyadenylated mRNA captured with oligo-dT beads. The cDNA was then sequenced on two lanes (all 8 samples) of anIllumina HiSeq 4000 (Iowa Institute of Human Genetics).

treatment_protocol: 3rd instar larvae were dissected in 1X PBS (pH 7.4)

value: Yellow white (yw^67)

tag: phenotype

value: Yellow body and white eyes

value: male

tag: developmental stage

value: 3rd instar larvae

value: wing discs


title: YW67 control sample 2 [Y7]

description: Control imaginal wing discs of 3rd instar larvae. Second technical replicate of the first biological replicate


title: SAMPLE 77: MSA 40, oxBS

source_name: Prefrontal cortex 77

value: Female

tag: age

tag: pmi (hours)

tag: condition

tag: brain bank

value: Bispebjerg Brain Bank

value: Brain

tag: conversion


title: SAMPLE 76: MSA 39, oxBS

source_name: Prefrontal cortex 76

value: Prefrontal cortex

value: Male


title: M2_ATF4_ChIP_rep2

description:
processed data file:
M2_ATF4.bw
M2_peaks.bed

value: wild type

value: m-CSF + IL-4

tag: chip antibody

value: ATF4 antibody (D4B8, Cell Signaling Technology Cat. #11815)


title: TAG75-P3-2

source_name: tibialis anterior from animal with PDAC PDX

tag: tissue


title: TAG75-P1-2


title: YW67 control sample 1 [Y6]

description: Control imaginal wing discs of 3rd instar larvae. First technical replicate of the first biological replicate


title: TAG75-S3-2

description: Gene expression data from tibialis anterior from sham control animal, cohort 1.

value: sham


title: D119-P4

description: Gene expression data from diaphragm from animal with PDAC PDX, cohort 4.

value: cohort 4

value: diaphragm


title: TAG75-S1-2

source_name: tibialis anterior from sham control animal

value: cohort 1

value: tibialis anterior


title: TAG75-S2-2


title: Myb mutant sample 5 [M5]

description: Myb mutant imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the third biological replicate

source_name: Wing discs of Myb mutant 3rd instar larvae

value: Myb^MH107:mutation induced by P-element mobilization by Delta2-3 transposase

value: Lethal-early pupal stage


title: M0_ATF4_ChIP_rep3

description:
processed data file:
M0_ATF4.bw
M0_peaks.bed

tag: strain background

value: m-CSF


title: SAMPLE 74: MSA 37, oxBS

source_name: Prefrontal cortex 74

value: MSA

value: oxBS


title: Myb mutant sample 4 [M4]

description: Myb mutant imaginal wing discs of 3rd instar larvae. Third technical replicate of the third biological replicate

tag: genotype/variation

value: male

value: 3rd instar larvae

value: wing discs


title: SAMPLE 75: MSA 38, oxBS

source_name: Prefrontal cortex 75

value: Prefrontal cortex

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank

tag: identifier

value: Brain


title: M0_ATF4_ChIP_rep2

value: wild type

tag: treatment

value: ATF4 antibody (D4B8, Cell Signaling Technology Cat. #11815)


title: M2_ATF4_ChIP_rep3

value: m-CSF + IL-4


title: SAMPLE 73: MSA 36, oxBS

source_name: Prefrontal cortex 73

value: Male


title: M0_input_rep1


title: Myb mutant sample 3 [M3]

description: Myb mutant imaginal wing discs of 3rd instar larvae. Second technical replicate of the third biological replicate


title: SAMPLE 71: MSA 34, oxBS

source_name: Prefrontal cortex 71


title: SAMPLE 72: MSA 35, oxBS

source_name: Prefrontal cortex 72


title: Myb mutant sample 2 [M2]

description: Myb mutant imaginal wing discs of 3rd instar larvae. First technical replicate of the third biological replicate


title: Myb mutant sample 1 [M1]

description: Myb mutant imaginal wing discs of 3rd instar larvae. Fourth technical replicate of the second biological replicate


title: mMDSC_GCN2KO_RNA_rep3

description:
processed data file:
RNAseq_FPKM_mMDSC.tsv

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19 (human) or mm10 (mouse). Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Read counting: STAR aligner version 2.5.0.c integrated read-counting was used on annotated genes from Ensembl V75 (human) or Ensembl V85 (mouse).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 (human) or Ensembl Genes V85 (mouse) was used to calculate FPKM values for filtered genes.
Genome_build: mm10 / hg19
Supplementary_files_format_and_content: tsv - FPKM

growth_protocol: Subcutaneously injected B16 F10 whole tumors were obtained from BL6 or GCN2 Lys M Cre mice and dissociated using Collagenase IV and Dnase 1. Tumor associated macrophages ("TAMs") and MDSCs were FACS sorted or whole tumors were used. For human peripheral blood macrophages, CD14+ monocytes were differentiated using m-CSF for 7 days resulting in M0 population. Resulting M0 macrophages were either treated with LPS and INFgamma overnight (M1) or IL-4 overnight (M2). Human melanoma tumor associated macrophages ("TAM") were obtained by FACS sorting.

extract_protocol:
Extraction of RNA was performed using Norgen Single Cell RNA extraction kit or Rneasy Plus  Mini extraction kit
SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech #634894) was used per manufacturer’s instructions for amplification of RNA and subsequent cDNA synthesis, All samples proceeded through NexteraXT DNA Library Preparation (Illumina FC-131-1096) using NexteraXT Index Kit V1 or V2 Set A (FC-131-1002 or FC-131-2001) followed by manufacturer’s instructions.

treatment_protocol: For knock-down experiments in human PB macrophages, M0, M1 or M2 macrophages were transfected with siRNAs using human macrophage nucleofector kit from Lonza. siRNAs were purchased from Ambion cat #AM16704 (siRNA #260008 for siGCN2; siRNA #122168 for siATF4) and TermoFisher Silencer Select Negative Control No. 1 (siRNA #4390843 for non-targeting siCTRL).

value: GCN2fl/fl Lys M

tag: disease/tumor type

value: Melanoma

tag: cell type

value: mMDSC


title: mMDSC_GCN2KO_RNA_rep1


title: SAMPLE 70: MSA 33, oxBS

source_name: Prefrontal cortex 70

tag: sample type

tag: Sex


title: SAMPLE 69: MSA 32, oxBS

source_name: Prefrontal cortex 69


title: mMDSC_WT_RNA_rep3


title: D119-P1

source_name: diaphragm from animal with PDAC PDX

tag: cohort

value: cohort 4

value: diaphragm

value: PDAC PDX


title: D119-S2

description: Gene expression data from diaphragm from sham control animal, cohort 4.

source_name: diaphragm from sham control animal

value: sham


title: D119-P2


title: D119-S3


title: D119-P3


title: DG75-S1-2

value: cohort 1


title: SAMPLE 68: MSA 31, oxBS

source_name: Prefrontal cortex 68

value: MSA

value: Bispebjerg Brain Bank

value: oxBS


title: iPSC479b

city: Darlinghurst

first: Jamie

middle: Ian

last: Vandenberg

state: NSW

address: 405 Liverpool Street

department: Molecular Cardiology and Biophysics

country: Australia

institute: Victor Chang Cardiac Research Institute

description: Total RNA

hyb_protocol: RNA samples (100ng input) were hybridized to the reporter CodeSet and the capture ProbeSet provided by NanoString following the manufacturer’s protocol. The reporter probes are molecular barcodes provided by NanoString. The samples were placed in a pre-heated 65°C thermal cycler and incubated for 20h to allow the hybridization.

scan_protocol: Scanning was conducted using the nCounter Digital Analyser according to the manufacture's instructions using the nCounter® MAX Analysis System. The images are processed, and each lane generates one RRC (Reporter Code Count) file that contains the number of reporters counted

data_processing: Data is analysed using nSolverAnalysisSoftware3.0.22

source_name: iPSC-derived cardiac myocytes

growth_protocol: HiPSC colonies were maintained on Matrigel® (Corning) coated plates in chemically defined medium (mTeSR1™, StemCell technologies), and passaged using Dispase (StemCell technologies). For differentiation, hiPSCs were dissociated by incubating at 37°C for 7 minutes with TrypLE™ Express (ThermoFisher) and seeded at 125000 cells/cm2 on a Matrigel® coated 12 well plate, in mTeSR™1 medium supplemented with StemMACS™ Y27632 (Miltenyi Biotec). Once the cells reached greater than 95% confluency, differentiation was initiated using STEMdiff™ Cardiomyocyte (CM) differentiation and Maintenance Kit (StemCell technologies). At day 15, CMs were dissociated by incubation in Collagenase Type I (ThermoFisher) for 45 minutes at 37°C to break up the matrix and then incubated in 0.25% Trypsin with EDTA for 7 minutes at room temperature followed by filtering through a 40 µm cell strainer (51). The CMs were seeded on a Matrigel coated 96-well plate (Greiner Bio-One) and maintained in CM maintenance medium for 10-15 days before they were harvested for mRNA expression analysis.

extract_protocol: Total RNA was obtained from 40,000 hiPSC-CMs lysed using QIAzol Lysis reagent (Qiagen). The RNA was purified using miRNeasy® Mini Kit (Qiagen), and all samples had RIN values >7.5, and were analysed using Agilent Bioanalyzer pico-chip

treatment_protocol: Lines were exposed to cisparide (200nM) for 5 minutes followed by nifedipine (50nM) for 5 minutes

value: cardiac myocytes


title: mMDSC_WT_RNA_rep2


title: SAMPLE 67: MSA 30, oxBS

source_name: Prefrontal cortex 67

value: Prefrontal cortex

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: mMDSC_WT_RNA_rep1

value: wild type


title: D119-S1


title: TA119-P3

description: Gene expression data from tibialis anterior from animal with PDAC PDX, cohort 4.

value: tibialis anterior


title: TA119-P2


title: gMDSC_GCN2KO_RNA_rep3

description:
processed data file:
RNAseq_FPKM_gMDSC.tsv

value: GCN2fl/fl Lys M

value: Melanoma

value: gMDSC


title: iPSC15b

description: Total RNA


title: iPSC479a

description: Total RNA


title: SAMPLE 66: MSA 29, oxBS

source_name: Prefrontal cortex 66


title: SAMPLE 65: MSA 28, oxBS

source_name: Prefrontal cortex 65


title: TA119-P1

source_name: tibialis anterior from animal with PDAC PDX

value: cohort 4


title: iPSC15a

description: Total RNA


title: TA119-P4

value: PDAC PDX


title: gMDSC_GCN2KO_RNA_rep2


title: TA119-S3

description: Gene expression data from tibialis anterior from sham control animal, cohort 4.

value: sham


title: gMDSC_GCN2KO_RNA_rep1


title: iPSC8b

description: Total RNA


title: gMDSC_WT_RNA_rep3


title: iPSC274b

description: Total RNA


title: SAMPLE 63: MSA 26, oxBS

source_name: Prefrontal cortex 63


title: SAMPLE 62: MSA 25, oxBS

source_name: Prefrontal cortex 62

value: Male


title: SAMPLE 64: MSA 27, oxBS

source_name: Prefrontal cortex 64

value: MSA


title: TA119-S1

source_name: tibialis anterior from sham control animal


title: gMDSC_WT_RNA_rep2


title: iPSC274a

description: Total RNA


title: D112-P5

description: Gene expression data from diaphragm from animal with PDAC PDX, cohort 3.

value: cohort 3

value: diaphragm


title: iPSC273b

description: Total RNA

value: cardiac myocytes


title: D112-P4


title: gMDSC_WT_RNA_rep1


title: SAMPLE 61: MSA 24, oxBS

source_name: Prefrontal cortex 61

value: Prefrontal cortex

value: Bispebjerg Brain Bank

value: oxBS


title: MDSC_GCN2KO_RNA_rep1

description:
processed data file:
RNAseq_FPKM_MDSC.tsv

value: MDSC


title: iPSC273a

description: Total RNA


title: SAMPLE 60: MSA 23, oxBS

source_name: Prefrontal cortex 60

value: Brain


title: MDSC_GCN2KO_RNA_rep3


title: iPSC142b

description: Total RNA


title: MDSC_GCN2KO_RNA_rep2


title: iPSC8a

description: Total RNA


title: D112-S3

description: Gene expression data from diaphragm from sham control animal, cohort 3.


title: mMDSC_GCN2KO_RNA_rep2

value: mMDSC


title: 273-C1d

description: Total RNA

treatment_protocol: Control cell lines


title: SAMPLE 58: MSA 21, oxBS

source_name: Prefrontal cortex 58

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank


title: MDSC_WT_RNA_rep3

value: wild type

value: Melanoma


title: SAMPLE 59: MSA 22, oxBS

source_name: Prefrontal cortex 59


title: iPSC142a

description: Total RNA


title: D112-P2

value: PDAC PDX


title: 274-C1b

description: Total RNA


title: D112-P3


title: TA119-S2

value: cohort 4

value: tibialis anterior

value: sham


title: MDSC_WT_RNA_rep2


title: SAMPLE 57: MSA 20, oxBS

source_name: Prefrontal cortex 57

value: Male

value: MSA


title: SAMPLE 56: MSA 19, oxBS

source_name: Prefrontal cortex 56


title: D112-P1

source_name: diaphragm from animal with PDAC PDX

value: cohort 3

value: diaphragm


title: TAM_GCN2KO_RNA_rep3

description:
processed data file:
RNAseq_FPKM_TAM.tsv

value: GCN2fl/fl Lys M

value: TAM


title: SAMPLE 54: MSA 17, oxBS

source_name: Prefrontal cortex 54

value: Prefrontal cortex

value: oxBS


title: D112-S2

source_name: diaphragm from sham control animal


title: SAMPLE 55: MSA 18, oxBS

source_name: Prefrontal cortex 55

value: Bispebjerg Brain Bank

value: Brain


title: MDSC_WT_RNA_rep1

value: MDSC


title: TAM_GCN2KO_RNA_rep2


title: TA112-P5

description: Gene expression data from tibialis anterior from animal with PDAC PDX, cohort 3.


title: TA112-P4


title: 273-C1c

description: Total RNA

source_name: iPSC-derived cardiac myocytes

value: cardiac myocytes


title: 274-C1a

description: Total RNA


title: 15-C1b

description: Total RNA


title: 273-C1b

description: Total RNA


title: 422-C1b

description: Total RNA


title: SAMPLE 53: MSA 16, oxBS

source_name: Prefrontal cortex 53

value: MRC London Neurodegenerative Diseases Brain Bank


title: SAMPLE 51: MSA 14, oxBS

source_name: Prefrontal cortex 51

value: Female


title: SAMPLE 52: MSA 15, oxBS

source_name: Prefrontal cortex 52


title: TAM_GCN2KO_RNA_rep1

value: Melanoma


title: SAMPLE 50: MSA 13, oxBS

source_name: Prefrontal cortex 50


title: D112-S1


title: TA112-P2

source_name: tibialis anterior from animal with PDAC PDX

value: tibialis anterior

value: PDAC PDX


title: TA112-P1


title: TA112-P3


title: SAMPLE 49: MSA 12, oxBS

source_name: Prefrontal cortex 49


title: TAM_WT_RNA_rep3

value: wild type


title: TAM_WT_RNA_rep2


title: 422-C1a

description: Total RNA


title: SAMPLE 47: MSA 10, oxBS

source_name: Prefrontal cortex 47

value: MSA


title: 273-C1a

description: Total RNA


title: iPSC8

description: Total RNA


title: SAMPLE 46: MSA 9, oxBS

source_name: Prefrontal cortex 46

value: Male


title: SAMPLE 48: MSA 11, oxBS

source_name: Prefrontal cortex 48


title: tMCAO_7d_2_ipsilateral

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Reads were aligned versus the Ensembl mouse genome version mm10 (GRCm38) using STAR 2.5.2b with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Annotation was performed versus Gencode version vM15.
Differentially expressed genes were identified using DESeq2 version 1.6.2. Functional classification and enrichment was obtained by KOBAS 3.0.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include library size normlized counts

extract_protocol:
RNA was extracted from MVMBs using Qiagen RNeasy Mini Kit (Qiagen, Düsseldorf/Germany)
250ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: Mice were subjected to either 60 minutes transient middle cerebral artery occlusion with a silicone rubber-coated monofilament (6-0 medium, Doccol, Sharon/USA) or sham surgery with immediate retraction of the filament after reaching the branching point. Post-stroke mortality was reduced by warming of the mice, s.c. saline injections and oral feeding adapted to the animals' clinical status monitored by daily temperature and body wheight control.

tag: strain

value: male

value: 10 to 12 weeks

tag: mouse group

value: transient middle cerebral artery occlusion (tMCAO)

tag: time point

value: 7 days after stroke onset

value: brain microvessels


title: tMCAO_7d_3_contralateral

tag: age


title: iPSC6

description: Total RNA


title: tMCAO_7d_3_ipsilateral


title: D111-P5

description: Gene expression data from diaphragm from animal with PDAC PDX, cohort 2.

value: cohort 2

value: diaphragm


title: D111-P4


title: TA112-S1

description: Gene expression data from tibialis anterior from sham control animal, cohort 3.

value: cohort 3

value: sham


title: tMCAO_7d_2_contralateral


title: TA112-S3

source_name: tibialis anterior from sham control animal


title: iPSC7

description: Total RNA

value: cardiac myocytes


title: TA112-S2


title: D111-P3


title: 15-C1a

description: Total RNA


title: SAMPLE 45: MSA 8, oxBS

source_name: Prefrontal cortex 45

value: Prefrontal cortex

value: Female

tag: pmi (hours)

tag: condition

tag: brain bank

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain

value: oxBS


title: tMCAO_7d_1_contralateral

tag: tissue


title: SAMPLE 43: MSA 6, oxBS

source_name: Prefrontal cortex 43

value: MSA

tag: conversion


title: tMCAO_7d_1_ipsilateral


title: SAMPLE 44: MSA 7, oxBS

source_name: Prefrontal cortex 44

value: Male

value: Bispebjerg Brain Bank


title: iPSC3

description: Total RNA


title: iPSC2

description: Total RNA


title: SAMPLE 42: MSA 5, oxBS

source_name: Prefrontal cortex 42


title: tMCAO_1d_3_ipsilateral

value: male

value: 10 to 12 weeks

value: 24 hrs after stroke onset


title: iPSC1

description: Total RNA


title: tMCAO_1d_3_contralateral

value: transient middle cerebral artery occlusion (tMCAO)

value: brain microvessels


title: SAMPLE 40: MSA 3, oxBS

source_name: Prefrontal cortex 40


title: D111-P2

source_name: diaphragm from animal with PDAC PDX

value: cohort 2

value: diaphragm

value: PDAC PDX


title: SAMPLE 41: MSA 4, oxBS

source_name: Prefrontal cortex 41


title: SAMPLE 39: MSA 2, oxBS

source_name: Prefrontal cortex 39


title: PFC_MC_#20

city: BeiJing

first: Wang

last: Yan

address: 16# LinCui Road

country: China

institute: Institute of Psychology

data_processing:
Reads were aligned against the miRBase (v21) using Bowtie allowing one mismatch. Unaligned sequences were pooled together to identify novel miRNAs using the software package miRDeep (v2.0.0.5) with default parameters. In order to investigate the expression profiles of miRNAs, the frequency of miRNA counts were normalized to TPM (tags per million) using the following formula: normalized expression = actual miRNA read count /total clean read count × 106. Differentially expressed miRNAs between the paired groups were analyzed by using DEGseq
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

source_name: PFC

extract_protocol:
Two hours after the (day 10) CPP test, the animals were killed and their mPFCs surgically excised. The tissue was stored in liquid nitrogen immediately after extraction and then transferred to the -80°C freezer. Total RNA was extracted from the frozen tissues using the TIANamp DNA/RNA Isolation Kit (TIANGEN), including additional treatment with RNase-free DNase I (Ambion) for 30 minutes at 37°C to remove contaminating DNA.
18-30nt RNA segments were separated and recovered by PAGE gel. The steps which followed were the same as for generating the mRNA sequencing library from the addition of poly-A. The miRNA DNBs were loaded into the patterned nanoarrays and single-end reads of 50 bp were read through on the BGISEQ-500 platform at Beijing Genomics Institute (BGI; Shenzhen, China).

treatment_protocol: During the methionine (Sigma, USA) experiments, mice were injected subcutaneously with 1 g/kg (6.6 mmol/kg) L-methionine twice a day for 10 consecutive days using the CPP procedure (including pre-test, training and post-test days). This was found to be the most effective dose and duration for increasing methylation level at certain DNA regions in the brain [25]. During training, mice were injected with methionine 1 h before each behavioral experiment. Animals were divided into 4 groups: (1) saline+saline (SS), (2) MET+saline (MS), (3) MET+cocaine (MC) and (4) cocaine+saline (CS).

value: prefrontal cortex

tag: treatment group

value: MET+cocaine (MC)


title: tMCAO_1d_2_ipsilateral


title: PFC_MC_#17


title: PFC_MC_#16


title: tMCAO_1d_2_contralateral


title: tMCAO_1d_1_ipsilateral


title: SAMPLE 37: Control 37, oxBS

source_name: Prefrontal cortex 37

value: Prefrontal cortex

value: CTRL

tag: identifier


title: SAMPLE 38: MSA 1, oxBS

source_name: Prefrontal cortex 38

value: Female

value: Brain


title: PFC_SS_#14

value: saline+saline (SS)


title: PFC_SS_#13


title: tMCAO_1d_1_contralateral


title: D111-P1

tag: treatment


title: D111-S1

description: Gene expression data from diaphragm from sham control animal, cohort 2.

source_name: diaphragm from sham control animal

value: sham


title: SAMPLE 36: Control 36, oxBS

source_name: Prefrontal cortex 36

value: MRC London Neurodegenerative Diseases Brain Bank

value: oxBS


title: D111-S3


title: sham_7d_3_ipsilateral

value: male

value: 10 to 12 weeks

value: sham surgery

value: 7 days after stroke onset


title: PFC_CS_#10

value: cocaine+saline (CS)


title: TA111-P2

description: Gene expression data from tibialis anterior from animal with PDAC PDX, cohort 2.

value: cohort 2

value: tibialis anterior


title: D111-S2

value: diaphragm


title: SAMPLE 35: Control 35, oxBS

source_name: Prefrontal cortex 35


title: TA111-P4

source_name: tibialis anterior from animal with PDAC PDX

value: PDAC PDX


title: sham_7d_3_contralateral

value: brain microvessels


title: SAMPLE 34: Control 34, oxBS

source_name: Prefrontal cortex 34

value: Prefrontal cortex

value: Male

value: CTRL

value: Bispebjerg Brain Bank


title: PFC_CS_#9

value: prefrontal cortex


title: TA111-P5


title: PFC_CS_#8


title: sham_7d_2_ipsilateral


title: sham_7d_2_contralateral


title: SAMPLE 33: Control 33, oxBS

source_name: Prefrontal cortex 33

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: TA111-P1


title: PFC_SS_#12

value: saline+saline (SS)


title: TA111-S3

description: Gene expression data from tibialis anterior from sham control animal, cohort 2.

value: sham


title: SAMPLE 32: Control 32, oxBS

source_name: Prefrontal cortex 32

value: oxBS


title: sham_7d_1_ipsilateral

value: male

value: 10 to 12 weeks

value: sham surgery

value: 7 days after stroke onset


title: PFC_MS_#23

value: MET+saline (MS)


title: TA111-P3

value: cohort 2

value: tibialis anterior

value: PDAC PDX


title: PFC_MS_#4


title: SAMPLE 31: Control 31, oxBS

source_name: Prefrontal cortex 31

value: Prefrontal cortex

value: Male

value: CTRL


title: sham_7d_1_contralateral

value: brain microvessels


title: PFC_MS_#3

value: prefrontal cortex


title: SAMPLE 29: Control 29, oxBS

source_name: Prefrontal cortex 29

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: sham_1d_3_contralateral

value: 24 hrs after stroke onset


title: YW control H3K27me3 Chip 2 Biological Replicate 2

description:
Sample 4
Control imaginal wing discs of 3rd instar larvae. Chip two of biological replicate two

hyb_protocol: Hybridization was performed following their standard protocol. See www.agilent.com.

scan_protocol: Scanning was performed following their standard protocol. See www.agilent.com.

data_processing:
Raw data was extracted utilizing Agilent feature extraction V9.5.1. Data was normalized by applying blank subtraction, intra array (dye-bias) median and white error model normalization.
Blank substracted, intra-array (dye-bias), median normalized log2 ratio (ChIP/Input)

source_name: Input - Sonicated genomic DNA

label_protocol: Labeling was performed following their standard protocol. See www.agilent.com.

extract_protocol: The tissue was fixed with 1.8% formaldehyde and incubated for 15 mins at room temperature on a rotating wheel. Crosslinking was stopped by adding glycine to a final concentration of 125mM in 0.1% PBS-Triton and incubated for 5 mins at room temperature. Samples were washed twice with lysis buffer (50 mM Tris-HCl, pH 8, 10 mM EDTA, 0.5% N-laurylsarcosine, and Roche Complete Protease Inhibitor Cocktail), snap-frozen in liquid nitrogen and stored at -80°C. Chromatin for each immunoprecipitation experiment was prepared from a total of 1000 wing imaginal discs and sonicated (30 pulses of 15 sec ON/ 15 sec OFF, high energy setting) in a Bioruptor (Diagenode) resulting in an average DNA fragment size of 400 bp. Samples were pre-cleared by adding 20 µl of Dynabeads® (Invitrogen) Protein A equilibrated in IP buffer (16.7 mM Tris-HCl, 167 mM NaCl, 1.2 Mm EDTA, 1.1% Triton, 0.1% SDS + 0.5% BSA)  for 2 hrs at 4°C. 1% of the sample was saved as input. Immunoprecipitation was performed at 4°C overnight. The immunocomplexes were recovered by adding 20 µl of Dynabeads® Protein A (Invitrogen) (previously equilibrated) for 3 hrs at 4°C and washed with the following buffers: 1X  for 10 mins with 1 ml of RIPA (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1 mM EDTA, 1% NP-40, 0.7% Na-Deoxycholate);  5X for 10 mins with 1 ml of RIPA + 0.5M NaCl; 1X for 10 mins with 1 ml of LiCl buffer (250 mM LiCl, 10 mM Tris-HCl, pH 8, 1mM EDTA, 5% NP-40, 0.5% Sodium-deoxycholate ); and 2X  for 10 mins with TE. DNA was released from the beads by adding elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) and incubating the samples at 65°C for 15 mins with occasional vortexing. TE was added to the eluted sample and input following by incubation in the presence of RNase A was to a final concentration of 0.2 mg/mL and incubated at 37°C for 1 hr. Proteinase K was added to a final concentration of 20 mg/mL and incubated at at 37°C overnight.  The samples were then moved to 65°C and incubated for 6hrs to reverse the crosslinks. Finally, DNA was phenol/chloroform extracted and ethanol precipitated. DNA from the ChIP experiments were differentially labeled with Cy3- and Cy5-coupled random nanomers (Agilent), hybridized onto a custom Drosophila melanogaster tiled array

tag: genotype

value: Yellow white (yw^67)

tag: phenotype

value: Yellow body and white eyes

tag: gender

tag: developmental stage

value: 3rd instar larvae

value: Imaginal wing discs

source_name: Immunoprecipitated H3K27me3


title: YW control H3K27me3 Chip 2 Biological Replicate 1

description:
Sample 3
Control imaginal wing discs of 3rd instar larvae. Chip two of biological replicate one


title: SAMPLE 28: Control 28, oxBS

source_name: Prefrontal cortex 28

tag: sample type

tag: Sex

value: oxBS


title: sham_1d_2_contralateral

tag: strain

value: male

value: 10 to 12 weeks

tag: mouse group

value: sham surgery


title: Myb mutant H3K27me3 Chip 2 Biological Replicate 2

description:
Sample 2
Myb mutant imaginal wing discs of 3rd instar larvae. Chip two of biological replicate two

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

value: Lethal-early pupal stage


title: TA111-S2

source_name: tibialis anterior from sham control animal

tag: cohort

value: cohort 2

value: tibialis anterior

value: sham


title: SAMPLE 27: Control 27, oxBS

source_name: Prefrontal cortex 27

value: Prefrontal cortex

value: Female

tag: age

tag: pmi (hours)

value: CTRL


title: TAG75-P3

description: Gene expression data from tibialis anterior from animal with PDAC PDX.

treatment_protocol: Adult female NSG mice were implanted with tumor resected from a cachectic pancreatic ductal adenocarcinoma (PDAC) patient, and sham controls underwent surgery but had no tumor implantation. Mice were sacrificed when tumor-bearing mice exhibited severe cachexia or the tumors reached over 3cm in diameter.

value: PDAC PDX


title: TA111-S1


title: sham_1d_1_ipsilateral

tag: time point

value: 24 hrs after stroke onset

value: brain microvessels


title: Myb mutant H3K27me3 Chip 2 Biological Replicate 1

description:
Sample 1
Myb mutant imaginal wing discs of 3rd instar larvae. Chip two of biological replicate one

value: Male

value: 3rd instar larvae

tag: tissue


title: TAG75-P2


title: sham_1d_1_contralateral


title: YW control H3K4me3 Chip 2 Biological Replicate 2

value: Yellow white (yw^67)

value: Yellow body and white eyes

value: Imaginal wing discs

source_name: Immunoprecipitated H3K4me3


title: TAG75-P1


title: SAMPLE 30: Control 30, oxBS

source_name: Prefrontal cortex 30

tag: condition

tag: brain bank

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain

tag: conversion

value: oxBS


title: sham_1d_3_ipsilateral

value: male

value: 10 to 12 weeks

value: sham surgery


title: SAMPLE 26: Control 26, oxBS

source_name: Prefrontal cortex 26

value: Prefrontal cortex

tag: identifier


title: TAG75-S3

description: Gene expression data from tibialis anterior from sham control animal.

value: tibialis anterior

tag: treatment

value: sham


title: 8w_3

city: Durham

first: Li

last: Wang

address: 111 T.W. Alexander Dr

institute: NIH

data_processing:
Raw reads were filtered by cutadpt v1.8.1,-m 20 --trim-n --max-n 0.7 -q 20
Contaminants were filtered by fastq_screen (v0.5.1. 4)
Clean reads were mapped to UCSC mm10 genome via STAR v2.5.2b
Then assigned to Ensembl genes (GRCh37.75) by featureCounts (subread-1.4.6-p1 command line)
Genome_build: mm10
Supplementary_files_format_and_content: csv

molecule: polyA RNA

extract_protocol:
Selected cells were removed from low temperature and reversed to get cDNA by a reaction including 5M Betaine Solution (Sigma B0300-1VL) 56 uL, 25 mM dNTP mix (Clontech 639132) 24 uL, 1M MgCl2 (Thermo Fisher Scientific AM9530G) 3.2 uL, 100 mM DTT (Sigma 43816-10ML) 8.8 uL, SMARTScribeTM 5X First-Strand Buffer (Clontech 639537) 61.9 uL, SeqAmpTM 2X PCR Buffer (Clontech 638504) 33.3 uL, 100 uM RT E5 Oligo (WaferGen 430-000240-0001) 4.0 uL, Amp Primer (WaferGen 430-000241-0001) and 100% Triton X-100 (Sigma T8787) 1.6 uL. ,
The library were prepared by using Nextera XT Library Prep Kit (illumina, 15032350) with some modification.

treatment_protocol: Tissues were cut into slices by using Vibrating-blade Microtome (Leica, VT1200S) and homogenized in low temperature and then the tissues were digested using XXIV protease (Sigma, P8038-250) and Collagenase II (Worthington LS004176) to enrich myocites; tissues were  homogenized and  digested using Cardiomyocyte Isolation Enzyme 1 (with papain) for Pierce Primary Cell Isolation Kits (Thermo 88288) to enrich non-cadiomyocites.

tag: individual

tag: disease stage


title: sham_1d_2_ipsilateral


title: TAG75-S2


title: YW control H3K4me3 Chip 2 Biological Replicate 1

tag: genotype

tag: phenotype

tag: gender

tag: developmental stage


title: Myb mutant H3K4me3 Chip 2 Biological Replicate 2

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

value: Lethal-early pupal stage


title: SAMPLE 23: Control 23, oxBS

source_name: Prefrontal cortex 23

tag: sample type

tag: Sex

value: CTRL


title: SAMPLE 24: Control 24, oxBS

source_name: Prefrontal cortex 24

value: Male

tag: age


title: DG75-P2

description: Gene expression data from diaphragm from animal with PDAC PDX.

source_name: diaphragm from animal with PDAC PDX

value: diaphragm

value: PDAC PDX


title: 8w_1


title: Myb mutant H3K4me3 Chip 2 Biological Replicate 1

value: 3rd instar larvae


title: SAMPLE 21: Control 21, oxBS

source_name: Prefrontal cortex 21

value: Female

tag: pmi (hours)


title: SAMPLE 25: Control 25, oxBS

source_name: Prefrontal cortex 25

value: Bispebjerg Brain Bank


title: DG75-P3


title: 8w_2


title: 5w_7


title: SAMPLE 20: Control 20, oxBS

source_name: Prefrontal cortex 20

value: MRC London Neurodegenerative Diseases Brain Bank

value: Brain


title: YW control RNA polymerase Chip 2 Biological Replicate 1

value: Yellow white (yw^67)

value: Yellow body and white eyes

value: Imaginal wing discs

source_name: Immunoprecipitated RNA polymerase


title: 5w_6


title: 5w_5


title: YW control RNA polymerase Chip 2 Biological Replicate 2


title: Myb mutant RNA polymerase Chip 2 Biological Replicate 2


title: TAG75-S1


title: DG75-S3

description: Gene expression data from diaphragm from sham control animal.

source_name: diaphragm from sham control animal


title: TAM_WT_RNA_rep1

tag: strain background

tag: genotype/variation

value: wild type

tag: disease/tumor type

value: Melanoma

tag: cell type

value: TAM


title: DG75-P1

tag: tissue


title: DG75-S2

value: sham


title: 5w_4


title: DG75-S1


title: Myb mutant RNA polymerase Chip 2 Biological Replicate 1

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

value: Lethal-early pupal stage


title: SAMPLE 22: Control 22, oxBS

source_name: Prefrontal cortex 22

value: Prefrontal cortex

value: Male

tag: condition

value: CTRL

tag: brain bank

tag: identifier

tag: conversion

value: oxBS


title: SAMPLE 17: Control 17, oxBS

source_name: Prefrontal cortex 17


title: A75-P3

description: Gene expression data from abdominal muscle from animal with PDAC PDX.

value: abdominal muscle

tag: treatment

value: PDAC PDX


title: 5w_3

tag: individual

tag: disease stage


title: A75-P2

source_name: abdominal muscle from animal with PDAC PDX


title: SAMPLE 16: Control 16, oxBS

source_name: Prefrontal cortex 16

value: Female

value: MRC London Neurodegenerative Diseases Brain Bank


title: Myb binding Chip 2 Biological Replicate 2

description:
Wing imaginal wing discs of 3rd instar larvae. Chip two of biological replicate two
sample2

data_processing:
Raw data was extracted utilizing Agilent feature extraction V9.5.1. Data was normalized by applying blank subtraction, intra array (dye-bias) median and white error model normalization. Bound regions were detected using Whitehead Per-Array Neighborhood Model in which two consecutive probes had to be at a maximal distance of 1000bp with an average p value of less than 0.05 between the central probe and at least 4 of its neighbors.
Blank substracted, intra-array (dye-bias), median normalized log2 ratio (ChIP/Input)

source_name: Input - Sonicated genomic DNA

tag: genotype

value: Yellow white (yw^67)

tag: phenotype

tag: gender

tag: developmental stage

value: 3rd instar larvae

source_name: Immunoprecipitated Myb protein


title: YW control H3K27me3 Chip 1 Biological Replicate 2

description:
Sample 4
Control imaginal wing discs of 3rd instar larvae. Chip one of biological replicate two

value: Yellow body and white eyes

value: Imaginal wing discs

source_name: Immunoprecipitated H3K27me3


title: Myb binding Chip 2 Biological Replicate 1

description:
Wing imaginal wing discs of 3rd instar larvae. Chip two of biological replicate one
sample1


title: 5w_2


title: 5w_1


title: SAMPLE 15: Control 15, oxBS

source_name: Prefrontal cortex 15

tag: sample type

tag: Sex

tag: age

tag: pmi (hours)

value: Brain


title: A75-P1


title: SAMPLE 14: Control 14, oxBS

source_name: Prefrontal cortex 14


title: 2w_2


title: YW control H3K27me3 Chip 1 Biological Replicate 1

description:
Sample 3
Control imaginal wing discs of 3rd instar larvae. Chip one of biological replicate one


title: Myb mutant H3K27me3 Chip 1 Biological Replicate 2

description:
Sample 2
Myb mutant imaginal wing discs of 3rd instar larvae. Chip one of biological replicate two


title: SAMPLE 13: Control 13, oxBS

source_name: Prefrontal cortex 13


title: PV_10_CKO_6

city: Cincinnati

first: Jeffrey

middle: D

last: Steimle

email: jeffrey.steimle@cchmc.org, jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu

state: OH

address: 240 Albert Sabin Way

department: Molecular Cardiovascular Biology

institute: Cincinnati Children's Medical Hospital Center

data_processing:
Reads were aligned to the mouse genome (mm10, retrieved from UCSC May 23, 2012) using TopHat2 (version 2.1.1)
Reads were filtered to remove poorly mapped reads (MAPQ<10), duplicated, and unmapped reads using BamTools (version 2.4.1)
Post-alignment, post-filtered reads were assigned to transcripts using StringTie (v1.3.3).
Differential expression testing was performed using edgeR (v3.18.1) and limma (v3.32.10) in R (v3.4.0). Low level genes were removed within each condition using median log-transformed counts per gene per million mapped reads (cpm) cutoff of 1. A generalized linear model (GLM) framework was used to test for differential expressed genes between conditional mutants and controls.
Genome_build: mm10
Supplementary_files_format_and_content: The per sample strg.gtf.gz files are gtf outputs from StringTie with columns corresponding to: seqname, source, feature, start, end, score, strand, frame, and attributes. The comma-deliminated txt file (gene_count_matrix.csv) is the per gene read count obtained using prepDE.py (http://ccb.jhu.edu/software/stringtie/dl/prepDE.py), which includes the 10 samples from this study and the 10 matching samples of the left atrial appendage previously published in Nadadur et al 2016 (Science Translational Medicine). The tab-deliminated txt file (ResultsTable_LA_PV.txt) is differential expression output from edgeR, which includes the ensembl gene ID, mouse gene symbol (geneID), and the log2FC, p-value, and FDR for each comparison. The comparisons correspond to 1. PVLA is the comparison between the wildtype samples from the previously published left atrial appendange (Nadadur et al 2016 Science Translational Medicine) and peri-pulmonary vein; 2. LACKO corresponds to the conditional mutant and control left atrial appendage; and 3. PVCKO corresponds to the conditional mutant and control peri-pulmonary vein.

source_name: peri-pulmonary vein portion of left atrium

extract_protocol:
One week after tamoxifen injection, the mice were euthanized by carbon dioxide asphyxiation followed by cervical dislocation. The heart was removed from the chest cavity and the left atria was detached. In order to isolate the peri-pulmonary vein portion of the left atrium, first the left atrial appendage was removed. Next, most of the pulmonary veins were removed leaving only 1-2 mm of venous tissue. RNA was isolated using TRIzol.
rRNA was removed from the samples using the Ribo-Zero rRNA Removal Kit (Illumina). Following rRNA removal, libraries were prepared using the TruSeq RNA Sample prep kit v2 (Illumina). Samples were pooled in equimolar ratios and sequenced on the HiSeq4000 on 2 lanes. Library preparation was performed by the University of Chicago Genomics Core Facility.

treatment_protocol: The mice were treated with tamoxifen for 3 days by intraperitoneal injection at 6 weeks of age.

value: R26creERT2/creERT2; Tbx5 flox/flox

tag: tamoxifen timing

value: 1 week post treatment

value: left atrium - peri-pulmonary vein


title: 2w_1


title: SAMPLE 12: Control 12, oxBS

source_name: Prefrontal cortex 12

tag: tissue


title: SAMPLE 18: Control 18, oxBS

source_name: Prefrontal cortex 18

tag: condition


title: A75-S2

description: Gene expression data from abdominal muscle from sham control animal.

value: sham


title: Myb mutant H3K27me3 Chip 1 Biological Replicate 1

description:
Sample 1
Myb mutant imaginal wing discs of 3rd instar larvae. Chip one of biological replicate one

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

value: Lethal-early pupal stage


title: PV_09_CKO_5


title: A75-S1

source_name: abdominal muscle from sham control animal


title: PV_08_CKO_4


title: YW control H3K4me3 Chip 1 Biological Replicate 2

value: Male

source_name: Immunoprecipitated H3K4me3


title: 0w_2


title: SAMPLE 11: Control 11, oxBS

source_name: Prefrontal cortex 11

value: Prefrontal cortex

value: CTRL

tag: brain bank

value: Bispebjerg Brain Bank

value: oxBS


title: PV_07_CKO_3


title: SAMPLE 10: Control 10, oxBS

source_name: Prefrontal cortex 10

value: MRC London Neurodegenerative Diseases Brain Bank

tag: identifier


title: PV_06_CKO_2


title: YW control H3K4me3 Chip 1 Biological Replicate 1

value: Yellow white (yw^67)


title: Myb mutant H3K4me3 Chip 1 Biological Replicate 2

value: 3rd instar larvae


title: SAMPLE 9: Control 9, oxBS

source_name: Prefrontal cortex 9

value: Female

tag: conversion


title: A75-S3

value: abdominal muscle

tag: treatment


title: Myb mutant H3K4me3 Chip 1 Biological Replicate 1

value: Imaginal wing discs


title: PV_05_CKO_1

value: R26creERT2/creERT2; Tbx5 flox/flox


title: 0w_1

tag: individual


title: PV_04_Ctrl_4

value: R26creERT2/creERT2; Tbx5+/+

value: 1 week post treatment


title: 11w_2

tag: disease stage


title: YW control RNA polymerase Chip 1 Biological Replicate 2

tag: genotype

value: Yellow body and white eyes

source_name: Immunoprecipitated RNA polymerase


title: SAMPLE 7: Control 7, oxBS

source_name: Prefrontal cortex 7

value: Brain


title: SAMPLE 6: Control 6, oxBS

source_name: Prefrontal cortex 6


title: Myb mutant RNA polymerase Chip 1 Biological Replicate 2

source_name: Input - Sonicated genomic DNA

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

tag: phenotype

value: Lethal-early pupal stage


title: 11w_1

tag: gender

value: Male


title: PV_03_Ctrl_3

value: left atrium - peri-pulmonary vein


title: Nf1-KO injured (14dpi) rep 1

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
The analyses were performed using the Eoulsan pipeline [1], including read filtering, mapping, alignment filtering, read quantification, normalisation and differential analysis
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the Mus Musculus  genome from Ensembl version mm10 using STAR (version 2.5.2b) [2]
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools[3]
To compute gene expression, Mus musculus GFF3 genome annotation version 91 from Ensembl database was used.
All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3 [4]
The sample counts were normalized using DESeq2
Statistical treatments and differential analyses were also performed using DESeq2
1.Laurent Jourdren, Maria Bernard, Marie-Agnès Dillies and Stéphane Le Crom. Bioinformatics (2012) 28 (11): 1542-1543; http://dx.doi.org/10.1093/bioinformatics/bts165
2.Alexander Dobin, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras: STAR: ultrafast universal RNA-seq aligner Bioinformatics (2013) 29 (1): 15-21 first published online October 25, 2012 doi:10.1093/bioinformatics/bts635
3.Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
4.S Anders, T P Pyl, W Huber: HTSeq — A Python framework to work with high-throughput sequencing data. Bioinformatics (2014); http://dx.doi.org/10.1093/bioinformatics/btu638
5.Anders S and Huber W (2010). “Differential expression analysis for sequence count data.” Genome Biology, 11, pp. R106. http://dx.doi.org/10.1186/gb-2010-11-10-r106
Genome_build: mm10 from Ensembl91
Supplementary_files_format_and_content: tsv file containing raw counts

source_name: Skin

extract_protocol:
Total RNA from wounded and intact skin was harvested using Rneasy Fibrous Tissue kit (Qiagen)
Smart-Seq V4 Sample Prep Kit (TAKARA) was used with 10 ng of total RNA for cDNA amplification, and Nextera XT DNA library ( Illumina) for the construction of sequencing libraries.

tag: strain

value: 3 months


title: YW control RNA polymerase Chip 1 Biological Replicate 1

tag: developmental stage


title: PV_02_Ctrl_2


title: CTRL injured (14dpi) rep3


title: SAMPLE 5: Control 5, oxBS

source_name: Prefrontal cortex 5

tag: sample type

value: Prefrontal cortex

tag: Sex

value: CTRL

value: oxBS


title: RbFox2_3d_Dox_II

city: Urbana

first: Sushant

last: Bangru

state: Illinois

address: 600 S Mathews Avenue

department: Biochemistry

institute: University of Illinois, Urbana-Champaign

data_processing:
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina)
Adaptors were trimmed from the reads using trimmomatic
Reads were mapped to the genome using STAR_2.4.2a
Insert distrubution calculated with Picard_1.119
TPM values generated from counts obtaind from HTseq and DESeq2
FPKM values were generated and compared between sets of samples using CuffDiff_2.2.1
Gene Ontology was determined using DAVID_6.8
Genome_build: GRCm38 vM10 mm10 (mus musculus)
Supplementary_files_format_and_content: consists of values outputted for all samples from cuffdiff

source_name: Mouse cardiomyocytes

extract_protocol:
RNA was isolated from the cardiomyocytes using Qiagen kit
RNA libraries were prepared for sequencing using standard Illumina protocols for “TruSeq Stranded mRNAseq Sample Prep kit”

value: C57BL x FVB

tag: cell type

value: cardiomyocytes


title: Myb mutant RNA polymerase Chip 1 Biological Replicate 1

value: 3rd instar larvae


title: Myb binding Chip 1 Biological Replicate 2

description:
Wing imaginal wing discs of 3rd instar larvae. Chip one of biological replicate two
sample2

value: Yellow white (yw^67)

value: Imaginal wing discs

source_name: Immunoprecipitated Myb protein


title: SAMPLE 3: Control 3, oxBS

source_name: Prefrontal cortex 3

tag: age

tag: pmi (hours)

value: MRC London Neurodegenerative Diseases Brain Bank


title: RbFox2_3d_Dox_I


title: PV_01_Ctrl_1

source_name: peri-pulmonary vein portion of left atrium

value: R26creERT2/creERT2; Tbx5+/+

tag: tamoxifen timing

value: 1 week post treatment

tag: tissue


title: CTRL injured (14dpi) rep1


title: Myb binding Chip 1 Biological Replicate 1

description:
Wing imaginal wing discs of 3rd instar larvae. Chip one of biological replicate one
sample1

value: Yellow body and white eyes


title: Nf1-KO uninjured rep3


title: SAMPLE 8: Control 8, oxBS

source_name: Prefrontal cortex 8

value: Female

tag: condition

tag: brain bank

value: Bispebjerg Brain Bank

value: Brain


title: CTRL injured (14dpi) rep2


title: YW_control_biol_rep2_chip2

description:
Control imaginal wing discs of 3rd instar larvae. Chip two of the second biological replicate
SAMPLE 4

hyb_protocol: Hybridization was performed following their standard protocol. See www.roche.com.

scan_protocol: Scanning was performed following their standard protocol. See www.roche.com.

data_processing:
Raw data (.pair files) were run in NimbleScan to produce .gff files
Signal intensities of individual probes corresponding to specific genomic locations.

source_name: Wing discs of control 3rd instar larvae

label_protocol: Labeling was performed following their standard protocol. See www.roche.com.

extract_protocol: RNA was extracted using TRIzol (Invitrogen) and purified with RNeasy Mini Kit (Qiagen). Double-stranded cDNA was generated using Double-Stranded cDNA Synthesis Kit with random hexamer (Invitrogen). RNA and cDNA quality were analyzed using Experion RNA and DNA analysis kits (Bio-Rad), respectively.

value: Male

value: Imaginal wing disc


title: SAMPLE 2: Control 2, oxBS

data_processing:
Data were analysed using ChAMP v. 2.13.5. Probes were filtered according to standard settings before imputation and BMIQ normalization.
Matrix table is BMIQ normalized beta

source_name: Prefrontal cortex 2

value: Prefrontal cortex

tag: conversion


title: Nf1-KO uninjured rep2

value: 3 months


title: Nf1-KO injured (14dpi) rep 3


title: MHC_3d_Dox_II

description: MHC

value: MHC


title: Nf1-KO injured (14dpi) rep 2


title: SAMPLE 1: Control 1, oxBS

source_name: Prefrontal cortex 1

value: CTRL

tag: identifier

value: oxBS


title: MHC_3d_Dox_I

description: MHC

value: C57BL x FVB

value: cardiomyocytes


title: YW_control_biol_rep1_chip2

description:
Control imaginal wing discs of 3rd instar larvae. Chip two of the first biological replicate
SAMPLE 3

value: Yellow white (yw^67)

value: 3rd instar larvae


title: Myb_mutant_biol_rep2_chip2

description:
Myb mutant imaginal wing discs of 3rd instar larvae. Chip two of the second biological replicate
SAMPLE 2

source_name: Wing discs of Myb mutant 3rd instar larvae

value: Myb^MH107:"mutation induced by P-element mobilization by Delta2-3 transposase"

value: Lethal-early pupal stage


title: CTRL uninjured rep3


title: SAMPLE 4: Control 4, oxBS

source_name: Prefrontal cortex 4


title: Myb_mutant_biol_rep1_chip2

description:
Myb mutant imaginal wing discs of 3rd instar larvae. Chip two of the first biological replicate
SAMPLE 1


title: VadR, rep3

city: Jena

first: Kathrin

last: Fröhlich

state: Thuringia

address: Winzerlaer Straße 2

department: Fakultät für Biowissenschaften, Bacterial RNA Biology

institute: Friedrich-Schiller-Universität Jena

description:
NDVadR3_GCCAAT
ΔvadR + pBAD-vadR
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx

data_processing:
Sequencing of the cDNA libraries was performed by the LAFUGA service unit (Gene Center, Munich, Blum group).
cDNA reads were imported into CLC Genomics Workbench v11.0 and analysed using mostly standard parameters.
3'adaptor- and quality trimming was performed using the trim reads command with the following settings: Sequence = TGACTGGAGTTCAGACGTGTGCTCTTCCGATCT, Strand = Minus, Action = Remove adapter, Scores = Mismatch: 2, Gapcost: 3, Cutoff: 10, Cutoff at end: 4.
The trimmed reads were checked for quality and mapped to the V. cholerae reference genome: NCBI Acc.number: NC_002505.1, NC_002506.1 using the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Reverse, Maximum number of hits for a read = 1.
Reads mapping in CDS were counted, and genes with a total count cutoff of >10 in all samples were considered for analysis. Read counts were normalized (CPM), and transformed (log2). Differential expression was tested using the built in tool corresponding to edgeR in exact mode with tagwise dispersions. Genes with a fold-change of > 1.75 and a FDR adjusted p-value < 1E-3 were considered to be differentially expressed.
Genome_build: NC_002505.1, NC_002506.1
Supplementary_files_format_and_content: VadR_Pulse_Expression_Read_Counts.xlsx: Read count table.

organism: Vibrio cholerae C6706

source_name: whole bacterial cells

growth_protocol: Vibrio cholerae C6706 ΔvadR strains carrying pBAD-ctr or pBAD-vadR plasmids were grown to exponential growth phase (OD600=0.2) in 50 ml LB media containing 50 µg / ml kanamycin. At this point, 0.2% L-arabinose was added to induce vadR expression and cells were harvested 10 minutes after induction.

extract_protocol:
RNA was isolated using Tri-reagent according to standard protocols. Prepared RNA was DNase digested and cleaned up using standard nucleic acid precipitation procedures. Depletion of ribosomal RNA was performed using Ribo-Zero kits (Epicentre) for Gram-negative bacteria. Integrity of the prepared RNA was tested using a Bioanalyzer.
Directional cDNA libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB E7760) according to the manufacturer's instructions. Quality of the prepared libraries was tested using a Bioanalyzer.

treatment_protocol: The cells were treated with 0.2% L-arabinose in exponential phase (OD600=0.2). After 10 minutes of treatment 4 OD600 units of cells were harvested in tubes containing 1/5 vol. "stop-mix" (95% ethanol, 5% phenol) and snap frozen in liquid nitrogen until further processing.

tag: genotype/variation

value: <delta>vadR + pBAD-vadR

tag: growth phase

value: exponential

tag: treatment

value: 0.2% L-arabinose


title: Untreated_170

city: Rochester

first: Saad

last: Kenderian

state: MN

address: 200 First Street SW

department: Hematology Research

institute: Mayo Clinic

description:
None
None

data_processing:
Binary base call data converted to fastq using Illumina bcl2fastq software
Check quality with FastQC, trim adapters with trimmomatic, and re-check quality with FastQC
Latest human reference genome GRCh38 was downloaded from NCBI and indexed using STAR
Paired end reads were mapped to the genome, and HTSeq was used to generate expression counts for each gene
DeSeq2 was used to calculate differential expression, and gene ontology was assessed using Enrichr
Genome_build: CRCh38
Supplementary_files_format_and_content: tab-delimted text files contain the gene expression counts for each sample; csv is DeSeq2 dataset; text files with enriched GO terms from Enrichr

source_name: brain tissue of NSG primary acute lymphoblastic leukemia (ALL) xenografts

extract_protocol:
RNA was isolated using miRNeasy Micro kit (Qiagen, Gaithersburg, MD, USA) and treated with RNase-Free DNase Set (Qiagen, Gaithersburg, MD, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NSG mice were IP injected with 30mg/kg busulfan. The following day, mice received 1,000,000-3,000,000 primary blasts derived from the peripheral blood of patients with ALL. Mice were monitored for engraftment for ~10-13 weeks via tail vein bleeding for engraftment. Some mice received high dose CAR-T cell therapy and an isotype control antibody treatment

tag: cancer

value: acute lymphoblastic leukemia


title: VadR, rep2

description:
NDVadR2_ACAGTG
ΔvadR + pBAD-vadR
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx


title: CTRL uninjured rep2

tag: strain

tag: genotype


title: VadR, rep1

description:
NDVadR1_TGACCA
ΔvadR + pBAD-vadR
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx


title: CTRL uninjured rep1


title: IgG_169

description:
CRS
IgG

value: brain tissue of NSG primary acute lymphoblastic leukemia (ALL) xenografts


title: Control, rep2

description:
NDCtr2_CGATGT
ΔvadR + pBAD-ctr
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx

value: <delta>vadR + pBAD-ctr


title: YW_control_biol_rep1_chip1

description:
Control imaginal wing discs of 3rd instar larvae. Chip one of the first biological replicate
SAMPLE 3

tag: phenotype

value: Yellow body and white eyes

tag: gender

value: Male

tag: developmental stage

value: Imaginal wing disc


title: YW_control_biol_rep2_chip1

description:
Control imaginal wing discs of 3rd instar larvae. Chip one of the second biological replicate
SAMPLE 4


title: Control, rep3

description:
NDCtr3_TTAGGC
ΔvadR + pBAD-ctr
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx


title: Myb_mutant_biol_rep2_chip1

description:
Myb mutant imaginal wing discs of 3rd instar larvae. Chip one of the second biological replicate
SAMPLE 2


title: Control, rep1

description:
NDCtr1_ATCACG
ΔvadR + pBAD-ctr
processed data file: VadR_Pulse_Expression_Read_Counts.xlsx


title: IgG_161

description:
CRS
IgG


title: IgG_162

description:
CRS
IgG


title: Nf1-KO uninjured rep1

tag: age

value: 3 months


title: Untreated_172

description:
None
None


title: Myb_mutant_biol_rep1_chip1

description:
Myb mutant imaginal wing discs of 3rd instar larvae. Chip one of the first biological replicate
SAMPLE 1


title: E8.5_KO3 [miRNA-seq]

status: Public on Mar 09 2020

city: Houston

first: Rachel

last: Keuls

state: TX

address: One Baylor Plaza, Alkek N1020

institute: Baylor College of Medicine

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
128F

data_processing:
Illumina FastQ generation v1.0.0 was used to generate .fastq files from each lane of the flow cell which were subsequently concatenated for each read 1 and read2 for each sample
FastQC v0.11.5 was used to check read quality. No trimming was necessary
STAR 2.7.0f was used for alignment
SummarizeOverlaps was used to produce a summarized experiment object
count matrix was constructed and CPM was normalized for read depth
DE-Seq was used for KO versus WT comparisons. BH method was used for the adjusted p-value
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts for each age and then further analyzed by grouping into miRNA family or cluster. Mfuzz gene cluster analysis of the WT Timecourse for which CPM values for each gene were averaged for each age.

source_name: Wnt1-Cre+ Neural Crest

growth_protocol: Embryos were allowed to develop until E7.5, E8.5, or E9.5 and were harvested and dissected in PBS

extract_protocol:
Total RNA was extracted from E7.5 mouse embryos or sorted cells using the Qiagen miRNeasy Mini Kit protocol as stated except that Trizol-LS was used instead of Qiazol and RNA was eluted off the column in 11ul.
half of the toal RNA obtained was used as input for the NEXTflex® Small RNA-Seq Kit v3 from Bioo Scientific. The protocol was followed as stated and gel extraction was used for size selection

treatment_protocol: Whole mebryos at E7.5 were put into Trizol-LS, flash frozen and stored at -80 until RNA isolation. For E8.5 and E9.5 timepoints, cells were FACS sorted directly into Trizol-LS

value: Pre and post migratory neural crest

value: KO


title: E8.5_KO4 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
169A


title: E9.5_KO1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
171D

source_name: Sox10+ Neural Crest

value: Post migratory neural crest


title: E9.5_KO2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
171E


title: E9.5_WT2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
209F

value: WT


title: E8.5_KO1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
157B


title: E8.5_WT1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
163A


title: E9.5_WT1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
209E


title: E8.5_WT3 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
214E


title: Untreated_164

description:
None
None


title: HBMECs_methaphetamine-treated_6h

city: Nanjing

last: Yang

state: Jiangsu

address: Dingjiaqiao 87

department: Pharmacology

institute: Southeast University

description: The sample exposed to meth (100uM) for 6h and then isolated with Trizol.

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://www.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 　L 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 Cy3 dye were circulated through the microfluidic chip for dye staining.

scan_protocol: 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)

source_name: human cerebral microvesscular endothelial cells (HBMECs)

label_protocol: Labeling of total RNA was performed according to the protocol from LC Sciense for a single-color experiment with modification.

growth_protocol: The HBMECs were purchased from ScienCell (Carlsbad, CA, USA), cultured in an RPMI-1640 medium (Life Technologies) and used at passages 4–14. The culture was incubated to confluence in T25 flasks in a humid atmosphere at 37℃ with 5% CO2.

extract_protocol: At 4 and 12 h post-infection, cells were washed three times with PBS, and 1 ml TRIZOL reagent (Invitrogen) was added to each well. Total RNA was isolated according to the manufacturer’s protocols.

treatment_protocol: Treatment with Meth (100 μM) for 6 h

value: human brain

tag: cell type


title: E7.5_WT2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
239H

source_name: Whole E7.5 Embryo

value: in-vivo embryonic pluripotency


title: HBMECs_vechicle_6h

description: The sample acts as control group

value: human cerebral microvesscular endothelial cells (HBMECs)


title: E7.5_WT1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
239G


title: E7.5_KO2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
239C


title: E7.5_KO1 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
239E


title: E9.5_WT2 [RNA-seq]

description:
E9.5_NormalizedCounts.csv
E9.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E9.5 _SigDown.csv
209F

data_processing:
Illumina FastQ generation v1.0.0 was used to generate .fastq files from each lane of the flow cell which were subsequently concatenated for each read 1 and read2 for each sample
FastQC v0.11.5 was used to check read quality. No trimming was necessary
STAR 2.7.0f was used for alignment
SummarizeOverlaps was used to produce a summarized experiment object
count matrix was constructed and CPM was normalized for read depth
DE-Seq was used for KO versus WT comparisons. BH method was used for the adjusted p-value
miRNA targets were identified from target scan and are inclused in the miRNA target analysis file
mfuzz was used to identify gene clusters with unique expression patterns which are included in the RNA-seq_Timecourse_And_ClusterAnalysis file
Genome_build: mm10
Supplementary_files_format_and_content: normalized counts and DE-seq results for each age. Mfuzz gene cluster analysis of the WT Timecourse for which CPM values for each gene were averaged for each age. Analysis of predicted miRNA targets of timecourse, KO versus WT comparison, and miRNA co-targeting.

extract_protocol:
Total RNA was extracted from E7.5 mouse embryos or sorted cells using the Qiagen miRNeasy Mini Kit protocol as stated except that Trizol-LS was used instead of Qiazol and RNA was eluted off the column in 11ul.
half of the toal RNA obtained was converted to cDNA using the SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and libraries were constructed with the Illumina Nextera XT Library Preparation Kit. The protocol was followed as stated except that libraries were prepped at half of the reaction volume stated in protocol.


title: E8.5_KO2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
128C


title: E9.5_WT1 [RNA-seq]

description:
E9.5_NormalizedCounts.csv
E9.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E9.5 _SigDown.csv
209E


title: E9.5_KO2 [RNA-seq]

description:
E9.5_NormalizedCounts.csv
E9.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E9.5 _SigDown.csv
171E


title: E9.5_KO1 [RNA-seq]

description:
E9.5_NormalizedCounts.csv
E9.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E9.5 _SigDown.csv
171D


title: E8.5_WT1_5s [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
163A


title: E8.5_WT2 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
169C


title: E8.5_KO4 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
169A


title: E8.5_KO4_5s [RNA-seq]

description:
E8.5_NormalizedCounts.csv
miR-302target_selection_analysis
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
163D


title: E8.5_WT3 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
214E


title: E8.5_WT2 [miRNA-seq]

description:
smRNA_mouse_clustering_analysis.xlsx
smRNA_mouse_Normalizedcount_analysis.xlsx
169C


title: E8.5_KO3 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
157B


title: E7.5_WT2 [RNA-seq]

description:
E7.5_NormalizedCounts.csv
E7.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E7.5 _SigDown.csv
239H


title: E8.5_KO1 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
128C


title: E8.5_KO2 [RNA-seq]

description:
E8.5_NormalizedCounts.csv
E8.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E8.5 _SigDown.csv
128F


title: E7.5_WT1 [RNA-seq]

description:
E7.5_NormalizedCounts.csv
E7.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E7.5 _SigDown.csv
239G


title: E7.5_KO1 [RNA-seq]

description:
E7.5_NormalizedCounts.csv
E7.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E7.5 _SigDown.csv
239E


title: E7.5_KO2 [RNA-seq]

description:
E7.5_NormalizedCounts.csv
E7.5 _SigUp.csv
RNA-seq_Timecourse_And_ClusterAnalysis.xlsx
miRNA_target_analysis.xlsx
E7.5 _SigDown.csv
237C


title: small RNA_HRCS_ATF7+/-_LPD_rep3

city: Tsukuba

first: Keisuke

last: Yoshida

state: Ibaraki

address: 3-1-1 Koyadai,

country: Japan

institute: RIKEN

description: small length of RNA

data_processing:
After trimming of adapter sequence, small RNA reads were extracted and counted using CLC Genomics Workbench (version 11.0) with default setting.
Extracted reads were annotated to 28-36 nt of 5' tRNA sequence obtained from GtRNAdb using CLC Genomics Workbench (version 11.0) with default setting..
Counts of tRNA fragments were normalized by read number annotated to tRNA flagment in each sample, using CLC Genomics Workbench (version 11.0).
tRNA fragments with lower read counts (<45 count) in any sample were omitted for downstream analysis.
Genome_build: mm10
Supplementary_files_format_and_content: Results of 12 samples were summarized in tab-delimited txt file. The table contains normalized expression values in each sequence that matches 5' terminal of tRNA.

source_name: HRCS

growth_protocol: Caudal epididymis and vas deferens were incubated in M2 medium for 1 hour at 37C to prepare total sperm fraction. After mild sonication to separate sperm head from the tail, HRCS was isolated from total sperm fraction by 82% Percoll precipitation.

extract_protocol:
Total RNA was extracted from HRCS by treatments with sperm lysis buffer and Trizol.
RNA-seq libraries were prepared by the NEBNext small RNA Library Prep Kit (New England Biolabs), and sequenced on Illumina Nextseq 500 (36-bp paired end).

treatment_protocol: Male mice were fed with control diet or low protein diet at 3-12 weeks age,

tag: diet

value: low protein diet

value: histone replacement-completed sperm (HRCS)


title: small RNA_HRCS_ATF7+/-_LPD_rep1

description: small length of RNA


title: small RNA_HRCS_ATF7+/-_LPD_rep2

description: small length of RNA


title: small RNA_HRCS_ATF7+/-_CD_rep2

description: small length of RNA

value: control diet


title: small RNA_HRCS_ATF7+/-_CD_rep3

description: small length of RNA


title: small RNA_HRCS_ATF7+/-_CD_rep1

description: small length of RNA


title: small RNA_HRCS_WT_LPD_rep3

description: small length of RNA

value: wild-type


title: small RNA_HRCS_WT_LPD_rep2

description: small length of RNA


title: small RNA_HRCS_WT_CD_rep1

description: small length of RNA


title: input_ATF7+/-_LPD

data_processing:
ChIP-seq and input reads were aligned to the mm9 genome assembly using CLC Genomics Workbench (version 11.0) with default setting, and non-specific reads were ignored.
BAM files were converted to BED files by BED tool, BAMtoBED (v2.27.0).
Length of reads in BED files was adjusted to insert size by extention of the end coordinate by BED tool, slopbed (v2.27.0).
BED files were converted to BedGraph files by BED tool, genomecov (v2.27.0) with normalization by read number mapped to the regions.
BedGraph files were converted to BW files by Wig/BedGraph-to-bigWig converter (Galaxy Version 1.1.0).
Genome_build: mm9
Supplementary_files_format_and_content: BW files show read coverage after scaling by read number mapped to 3kb around TSS.

source_name: testicular germ cells

growth_protocol: Testes were collected from each group of mice at 11-12 weeks age. TGCs were prepared from seminiferous tubules by collagenase and trypsin treatment, and cross-linked with 1% FA for 8 min at room temparature.

extract_protocol:
Cell ysates were prepared from sonicated TGCs, and ATF7-DNA complexes were isolated by ATF7 antibody.
ChIP-seq libraries were prepared by the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs), and sequenced on Illumina Nextseq (36-bp paired end).

value: testicular germ cells

tag: chip antibody


title: small RNA_HRCS_WT_LPD_rep1

description: small length of RNA


title: input_ATF7+/-_CD


title: small RNA_HRCS_WT_CD_rep2

description: small length of RNA


title: SAMPLE 19: Control 19, oxBS

city: Odense

first: Rasmus

last: Rydbirk

address: Fioniavej 34

institute: University of Southern Danmark

source_name: Prefrontal cortex 19

extract_protocol: Genomic DNA was extracted using the PCI method.

tag: sample type

value: Prefrontal cortex

tag: Sex

tag: pmi (hours)

tag: condition

value: CTRL

value: MRC London Neurodegenerative Diseases Brain Bank

tag: tissue

value: Brain

value: oxBS


title: ATF7_TGCs_ATF7+/-_LPD_rep2

value: ATF7 antibody (prepared in our lab; clone number 2F10)


title: input_WT_CD


title: input_WT_LPD


title: ATF7_TGCs_ATF7+/-_CD_rep2


title: ATF7_TGCs_WT_LPD_rep1


title: ATF7_TGCs_WT_CD_rep2


title: ATF7_TGCs_ATF7+/-_LPD_rep1


title: ATF7_TGCs_ATF7+/-_CD_rep1


title: ATF7_TGCs_WT_CD_rep1


title: PRO-cap-02-NELFC-AID-treated-rep1

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: PRO-cap

data_processing:
Library strategy: PRO-cap
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg19 and mouse mm9 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, plotProfile (Ramírez et al., 2016). ChIP-seq peaks were called using MACS 2.1.0 (Zhang et al., 2008) with a q-value cutoff of 0.05. Peaks were annotated using HOMER 4.10 (Heinz et al., 2010).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg19 and fly dm3 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Protein coding transcripts were chosen from Ensembl version 75 database by R 3.3.3, according to the previously described protocol (Liang et al., 2018) with minor modifications. Briefly, we selected RefSeq-validated transcripts with TSSs that overlapping NELF-C ChIP-seq peaks. We filtered out transcripts that are ≤ 2 kb long and ≤ 2 kb away from the nearest genes. Next, we chose transcripts that have ≥ 2 rpm total PRO-seq coverage at the region between TSS – 100 bp and TSS + 300 bp, using 3 independent PRO-seq data in untreated NELF-C-AID cells. In these selected transcripts, the nucleotide position with maximum PRO-seq coverage in the region between TSS – 100 bp and TSS + 300 bp was assigned to the 1st pause region. Transcripts that have ≤ 0.2 rpm coverage at the 1st pause region nucleotide were excluded. The resulting transcripts with assigned the 1st pause regions were used for further analyses. The nucleotide positions with maximum PRO-seq coverage in 1h auxin-treated NELF-C-AID cells at the region from +10 to +500 bp downstream of the 1st pause region was assigned to the 2nd pause region. For Heat shock experiments, transcripts with ≥ 1.5-fold increase or decrease in PRO-seq coverage at gene bodies (the 1st pause regions +500 to +100kb or to transcription termination sites) upon heat shock were assigned to HS-upregulated or HS-downregulated genes, respectively. Heatmaps and metaplots of PRO-seq signals were generated by deepTools 3.0.0/3.1.1/3.1.2 computeMatrix, plotHeatmap, and plotProfile (Ramírez et al., 2016). Log2 fold change of PRO-seq signals at nucleotide resolution were calculated by deepTools 3.0.0/3.1.1/3.1.2 bigwigCompare with pseudocount 0.25 rpm.
For PRO-cap, raw reads were processed as described for PRO-seq above, requiring a read length of 18–36 bp. Processed paired-end reads were aligned to a concatenated genome comprised of hg19 and dm3 assemblies using bowtie2 with options (--very-sensitive -X 1000 --no-mixed --no-discordant --no-unal) (Langmead and Salzberg, 2012). The 5’ ends of aligned R2 reads with MAPQ ≥ 40 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options. Read counts were normalized to total reads aligned to the spike-in genome. de novo transcription start sites were identified from PRO-cap data using HOMER 4.11 with findcsRNATSS option (Duttke et al., 2019; Heinz et al., 2010). TSS identified in untreated and auxin-treated samples were merged then defined as TSS regions. Distances between TSS in each sample were measured using HOMER 4.11 annotatePeaks. Raw PRO-cap reads were counted using HOMER 4.11 annotatePeaks. Read counts were normalized to spike-in counts using RUVseq with RUVg option (Risso et al., 2014) in R 3.3.3. Differential expression analysis was performed using DESeq2 (Love et al., 2014) and visualized in R 3.3.3. TSS with significant gain of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Up TSS, while TSS with significant loss of PRO-cap signals upon NELF loss (adjusted p-value < 0.05) was defined as Cap Down TSS. Metaplots of PRO-cap and PRO-seq at Cap Up TSS or Cap Down TSS were generated using deepTools 3.1.1. For heatmaps of ChIP-seq and MNase-seq at TSS, TSS were first merged with gap of no longer than 600 bp to obtain TSS clusters, heatmaps were then generated at Cap Up TSS clusters and Cap Down TSS clusters.
Genome_build: hg19, dm3, mm9
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

molecule: nuclear RNA

growth_protocol: DLD-1 cells were grown in DMEM (Corning) supplemented with 10% FBS (Corning), 1X GlutaMAX (Gibco), 2 µg/ml puromycin (Gibco), 100 U/ml Penicillin and 100 µg/ml Streptomycin (Gibco).

extract_protocol:
For ChIP-seq, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014) for NELF-C, NELF-E, SPT5, Pol II CTD Ser2P, Pol II CTD Ser5P, XRN2, DCP2 ChIP-seq in NELF-C-AID cells. Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Protein A/G-agarose beads (Santa Cruz) or Dynabeads Protein G (Invitrogen).  PRO-seq sample preparation was performed according to the previously published protocol (Mahat et al., 2016b) with minor modifications. 10 million DLD-1 nuclei were mixed with spike-in Drosophila S2 nuclei. Nuclear run-on assay was performed with 4 biotinylated nucleotides (PerkinElmer). 5’ cap was removed by RppH (NEB).  PRO-cap libraries were prepared as described previously (Kwak et al., 2013; Mahat et al., 2016b) with minor modifications. NELF-C-AID cells were treated with or without 500 µM auxin for 2 h, followed by nuclear extraction. ~10 million NELF-C-AID nuclei with 0.5 million spike-in drosophila S2 nuclei were subjected to nuclear run-on reaction.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA) and sequenced on the NextSeq 500 or NovaSeq 6000 (Illumina). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. DNA Libraries were size selected by PippinHT (Sage) or AMpure XP (Beckman Coulter) and sequenced on a NextSeq 500 (Illumina). For PRO-cap, PRO-seq adapter sequences were used instead of PRO-cap adapters. Libraries were then sequenced by NextSeq 500 in paired-end sequencing mode.

treatment_protocol: Cells were treated with 500 µM Auxin (3-indole-acetic acid sodium salt, abcam), 1 µM Flavopiridol (Cayman), or 250 nM NVP-2 (MedChemExpress). Heat shock treatment at 42 ˚C for 1 h was carried out as described previously (Mahat et al, 2016)

value: Colorectal adenocarcinoma

value: NELF-C-AID OsTIR1

value: Auxin

tag: cell line