title: 3183-3-2N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3121-2-MSSM2N

status: Public on Feb 23 2018

type: SRA

city: New York

first: Gabriel

middle: E

last: Hofman

state: New York

address: 1 Gustave L Levy Plaza

department: Department of Genetics and Genomics Sciences

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
RNA-seq from hiPSC-derived cell culture
NSB3121

library_source: transcriptomic

data_processing:
RNA-Seq reads were aligned to GRCh37 with STAR v2.4.0g1. Uniquely mapping reads overlapping genes were counted with featureCounts v1.4.4 using annotations from ENSEMBL v70.
Genome_build: hg19
Supplementary_files_format_and_content: raw counts are reported

molecule: total RNA

organism: Homo sapiens

source_name: HiPSC-derived cell line

growth_protocol: HFs were cultured on 0.1% (w/v) gelatin coated plates in HF medium (DMEM (ThermoFisher Scientific), 20% (v/v) FBS (Corning)). Replicating 90% confluent HFs were reprogrammed using a modified protocol; briefly, HFs were transduced with Cytotune® Sendai viruses (ThermoFisher Scientific) expressing OCT4, SOX2, KLF4 and c-MYC, as per lot specifications. Cells from a single well of a six-well plate were split 1:2, 1:3 and 1:10 onto 10-cm plates containing 1 x 106 mouse embryonic fibroblasts (mEFs; GlobalStem). Cells were switched to hiPSC media (DMEM/F12, 20% KO-Serum Replacement (v/v), 1% (v/v) GlutaMAX, 1% (v/v) nonessential amino acids (NEAA), 55 μM β‐mercaptoethanol (β‐me) (all ThermoFisher Scientific) and 20 ng ml-1 FGF2 (R & D Systems, 233-FB-10)) and fed daily. hiPSC colonies were manually picked and clonally plated onto 24-well mEF-coated plates. hiPSC lines were maintained on mEFs in hiPSC media; at early passages, hiPSCs were split using manual passaging and at higher passages, hiPSC were enzymatically passaged with Collagenase (1mg/ml in DMEM) (Sigma) until cryopreservation in cold freezing media (hiPSC media containing 10% DMSO). Individual hiPSC lines were validated using TRA-1-60 and SSEA-4 flow cytometry and NANOG, TRA-1-60, SOX2 and OCT4 immunocytochemistry. G-banded karyotyping was performed by WiCell Cytogenetic Services. The differentiation potential of the hiPSCs derived in this study was confirmed by RT-PCR for markers of the three germ layers following spontaneous differentiation of a subset of the lines into embryoid bodies. Routine (every 2 to 4 weeks) mycoplasma testing was conducted using the MycoAlert Mycoplasma detection kit (Lonza); all cells used in this study and were found to be negative.

extract_protocol: RNA Sequencing libraries were prepared using the Kapa Total RNA library prep kit with ribo-depletion and strand specific cDNA library construction (Kappa Biosystems). Paired-end sequencing reads (125bp) were generated on an Illumina HiSeq2500 platform (New York Genome Center).

treatment_protocol: NPCs were generated from unique hiPSC lines with had normal karyotypes, and then passed NPC quality control based on immunocytochemistry and FACS for SOX2 and NESTIN levels. NPCs were derived as previously described and maintained at high density, grown either growth factor reduced Matrigel (BD Biosciences) coated plates in NPC media (Dulbecco’s Modiﬁed Eagle Medium/Ham’s F12 Nutrient Mixture (ThermoFisher Scientific), 1x N2, 1x B27-RA (ThermoFisher Scientific) and 20 ng ml−1 FGF2 and split 1:3 every week with Accutase (Millipore, Billerica, MA, USA). NPCs were dissociated with Accutase and plated at 2.0 x 105 cells per cm-2 in NPC media onto growth factor reduced Matrigel-coated plates. For neuronal differentiation, media was changed to neural differentiation medium (DMEM/F12, 1xN2, 1xB27-RA, 20 ng ml-1 BDNF (Peprotech), 20 ng ml-1 GDNF (Peprotech), 1 mM dibutyryl-cyclic AMP (Sigma), 200nM ascorbic acid (Sigma) and 1 g ml-1  laminin (ThermoFisher Scientific) 1-2 days later.  NPC-derived neurons were differentiated for 6 weeks.

tag: diagnosis

value: control

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

value: KAPA Total Kit

tag: exclusion

value: yes

value: caucasian

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

value: Sanford Consortium

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot7

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: DStr_wt_3_Total

city: Montpellier

first: Emmanuel

last: Valjent

address: 141, rue de la cardonille

department: Neurobiology

country: France

institute: INSERM

description:
wild-type littermates
Stranded RNA-seq
Processed data file: Raw_Counts_RNA-Seq_Puighermanal.txt

data_processing:
Image analyses and basecalling were performed using the HiSeq Control Software and Real-Time Analysis component.
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC and Fastq Screen from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
Alignment was performed with TopHat 2.0.13 (with Bowtie 2.2.3) to the mm10 version of the Mus musculus genome. The transcript annotation was retrieved from UCSC on May 23, 2014.
Counting of reads aligned to a gene was performed with HTSeq-count 0.6.1p1.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: Raw_Counts_RNA-Seq_Puighermanal.txt: Tab-separated text file. First column is the gene identifier (Gene symbol|Entrez Gene ID), the following columns are the raw counts (non-normalized) for each sample.

organism: Mus musculus

source_name: Dorsal striatum, wild-type, total

extract_protocol:
Nac and DStr were removed and homogenized in polysome lysis buffer. Fifty microliters of the initial lysate were used for RNA extraction using Trizol protocol according to manufacturer's instructions (here referred as 'Total') and the rest of the lysate was then centrifuged in 10-50% sucrose density gradients. Ribosome profiling was then performed, samples were fractionated and RNA was isolated from heavy polysomal fractions (>4 ribosomes) using Trizol protocol (here referred as 'Heavy').
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

tag: genotype/variation

value: wild-type

tag: tissue

value: Brain

tag: brain region

value: Dorsal striatum

tag: source

value: total cytosolic RNA


title: DStr_wt_3_Heavy

source_name: Dorsal striatum, wild-type, heavy

value: RNA-bound to heavy polysomes


title: 3121-2-MSSM2F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: DStr_wt_2_Total

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 3121-2-1F

tag: diagnosis

value: control

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3113-3-21F

description:
RNA-seq from hiPSC-derived cell culture
NSB3113

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: exclusion

value: yes

tag: cnv

tag: affected gene

tag: age of onset

value: NPC lot5

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: DStr_wt_2_Heavy

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 3130-4-21F

description:
RNA-seq from hiPSC-derived cell culture
NSB3130

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 3113-3-21N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

value: Kristen Brennand

value: Sanford Consortium

value: Ian Ladran

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3084-2-2N

description:
RNA-seq from hiPSC-derived cell culture
NSB3084

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

value: black, non-hispanic

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot8

tag: npc technician

tag: npc thaw


title: DStr_wt_1_Total

tag: genotype/variation

value: wild-type

tag: tissue

value: Brain

tag: brain region

value: Dorsal striatum

tag: source

value: total cytosolic RNA


title: DStr_wt_1_Heavy

value: RNA-bound to heavy polysomes


title: Nac_KI_1_Total

description:
rpS6 knockin mice
Stranded RNA-seq
Processed data file: Raw_Counts_RNA-Seq_Puighermanal.txt

source_name: Nucleus accumbens, rpS6 knockin, total

value: rpS6 knockin

value: Nucleus accumbens


title: 3084-2-2F

tag: diagnosis

value: control

tag: Sex

value: Male

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: DStr_KI_3_Heavy

source_name: Dorsal striatum, rpS6 knockin, heavy

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 3084-1-1N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: DStr_KI_3_Total

source_name: Dorsal striatum, rpS6 knockin, total

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 2607-3-1N

description:
RNA-seq from hiPSC-derived cell culture
NSB2607

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Sanford Consortium

value: NPC lot5

value: Ian Ladran

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2607-4-2N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 2607-4-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3084-1-1F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: black, non-hispanic

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot8

tag: npc technician

tag: npc thaw


title: Nac_KI_1_Heavy

source_name: Nucleus accumbens, rpS6 knockin, heavy

tag: genotype/variation

value: rpS6 knockin

tag: tissue

value: Brain

tag: brain region

tag: source

value: RNA-bound to heavy polysomes


title: 3130-2-1N

tag: diagnosis

value: control

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

value: yes

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 3130-2-1F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 2607-1-AN

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

value: Sendai Virus

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: DStr_KI_2_Total

tag: genotype/variation

tag: tissue

tag: brain region

value: Dorsal striatum

tag: source

value: total cytosolic RNA


title: 3121-2-1N

tag: diagnosis

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

value: Sanford Consortium

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot7

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 2607-1-AF

tag: diagnosis

value: control

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: NPC lot5

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 690-2-1F

description:
RNA-seq from hiPSC-derived cell culture
NSB690

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot8

tag: npc technician

tag: npc thaw


title: DStr_KI_1_Total

tag: genotype/variation

value: rpS6 knockin

tag: tissue

value: Brain

tag: brain region

tag: source


title: 690-2-1N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: DStr_KI_2_Heavy

tag: genotype/variation

tag: tissue

tag: brain region

value: Dorsal striatum

tag: source

value: RNA-bound to heavy polysomes


title: 690-1-4N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: DStr_KI_1_Heavy

tag: genotype/variation

tag: tissue

tag: brain region

tag: source


title: 553-X-CF

description:
RNA-seq from hiPSC-derived cell culture
NSB553

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Kristen Brennand

value: NPC lot2

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 553-X-CN

tag: diagnosis

value: control

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

value: Sanford Consortium

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 690-1-4F

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: NPC lot8

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 553-3-21N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot5

tag: npc technician

tag: npc thaw


title: 553-3-21F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2607-3-1F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 553-3-1F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2962-2-1N

description:
RNA-seq from hiPSC-derived cell culture
NSB2962

tag: diagnosis

value: COS

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian-hispanic

value: Y

value: COS/ASD

tag: reprogramming method

tag: sendai batch

value: unknown (possibly lot1085255A)

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Ken Diffenderfer

tag: hipsc site

value: Salk Stem Cell Core

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 553-3-1N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

value: KAPA Total Kit

value: caucasian

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

value: Sendai Virus

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2962-2-1F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 2620-C-3N

description:
RNA-seq from hiPSC-derived cell culture
NSB2620

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

value: N

tag: family history

value: APD, SPD

value: Kristen Brennand

value: NPC lot3

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2620-C-3F

tag: diagnosis

value: COS

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 2620-B-4N

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2484-2aN

description:
RNA-seq from hiPSC-derived cell culture
NSB2484

tag: diagnosis

tag: Sex

value: Female

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

value: yes

tag: cnv

tag: affected gene

value: NRXN1 missense

tag: age of onset

value: MDD

value: PPD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot4

tag: npc technician

value: Megan Fitzgerald

tag: npc thaw


title: 2484-2aF

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

value: caucasian

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Sendai Virus

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2513-1-4N

description:
RNA-seq from hiPSC-derived cell culture
NSB2513

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: ASD

value: N

value: BD

tag: reprogramming method

tag: sendai batch

value: unknown (possibly lot1085255A)

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Ken Diffenderfer

tag: hipsc site

value: Salk Stem Cell Core

tag: karyotype result

value: 46,XY - Nonclonal finding:47,XY,+7

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot5

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 2620-B-4F

tag: diagnosis

value: COS

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

value: APD, SPD

value: Kristen Brennand

value: NPC lot3

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2513-1-4F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 2476-D1-2N

description:
RNA-seq from hiPSC-derived cell culture
NSB2476

tag: diagnosis

tag: Sex

value: Female

tag: cell type

value: NPC

tag: rna purification method

tag: rin

value: caucasian-hispanic

tag: iq

tag: developmental history

tag: clozapine response

value: Y

tag: family history

value: APD

value: Brigham Hartley

value: NPC lot8

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2476-D4-4N

tag: diagnosis

value: COS

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 2476-D4-4F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: exclusion

value: yes

tag: iq

tag: developmental history

value: clean

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2476-D1-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 2476-1-4N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: exclusion

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: unknown (possibly lot1085255A)

value: Ken Diffenderfer

value: Salk Stem Cell Core

value: NPC lot5

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2011-3-12N

description:
RNA-seq from hiPSC-derived cell culture
NSB2011

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

value: MDD

value: SPD; PPD

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot1

tag: npc technician

tag: npc thaw


title: 2011-3-2N

tag: diagnosis

value: COS

tag: Sex

value: Female

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

value: Y

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2476-1-4F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

value: yes

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian-hispanic

value: clean

value: APD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 2011-3-12F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 2011-3-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

value: MDD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 1442-4-3N

description:
RNA-seq from hiPSC-derived cell culture
NSB1442

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

value: ASD

tag: clozapine response

value: N

tag: family history

value: Sendai Virus

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 1442-3-2N

tag: diagnosis

value: COS

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot1

tag: npc technician

tag: npc thaw


title: 1442-4-3F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 1275-C-1N

description:
RNA-seq from hiPSC-derived cell culture
NSB1275

tag: diagnosis

tag: Sex

value: Female

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

value: yes

tag: cnv

tag: affected gene

tag: age of onset

value: SPD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot3

tag: npc technician

tag: npc thaw


title: 1442-2-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: library prep method

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Ian Ladran

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 1442-2-2N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

value: caucasian

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 1275-C-1F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: exclusion

tag: iq

tag: developmental history

value: MDD

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 1275-B-3F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 1275-B-3N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 676-2-3F

description:
RNA-seq from hiPSC-derived cell culture
NSB676

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: PPD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 676-2-3N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

value: N

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 676-1-2N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: exclusion

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

value: Sendai Virus

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 676-1-2F

tag: diagnosis

value: COS

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 581-3-1N

description:
RNA-seq from hiPSC-derived cell culture
NSB581

tag: diagnosis

tag: Sex

value: Male

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: SA

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

value: Kristen Brennand

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 581-2-1N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: NPC lot1

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 581-3-1F

tag: diagnosis

tag: Sex

tag: cell type

value: 6 wk FB neuron

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 581-1-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 499-X-CN

description:
RNA-seq from hiPSC-derived cell culture
NSB499

tag: diagnosis

tag: Sex

tag: cell type

value: NPC

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: clean

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

value: NPC lot2

tag: npc technician

tag: npc thaw


title: 499-X-CF

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

value: Qiagen miRNAeasy column

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: SPD

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 581-1-2N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

value: KAPA Total Kit

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

value: Ian Ladran

tag: npc thaw


title: 499-5-2N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

value: caucasian

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 499-5-2F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 581-2-1F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

value: MDD

tag: clozapine response

tag: family history

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 499-2-12N

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: N

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: 499-2-12F

tag: diagnosis

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: iq

tag: developmental history

tag: clozapine response

tag: family history

value: Sendai Virus

tag: npc rnaseq batch

tag: npc rnaseq submission date

tag: neuron rnaseq batch

tag: neuron rnaseq submission date

tag: sendai reads

tag: total reads

tag: sendai log2cpm

tag: astrocytes

tag: neuron

tag: microglia

tag: myocyte

tag: hipsc


title: 1442-3-2F

tag: diagnosis

value: COS

tag: Sex

tag: cell type

tag: rna purification method

tag: rin

tag: library prep method

tag: cnv

tag: affected gene

tag: age of onset

value: ASD

tag: reprogramming method

tag: sendai batch

tag: hipsc line

tag: hipsc date

tag: hipsc technician

tag: hipsc site

tag: karyotype result

tag: karyotype date

tag: npc line

tag: npc generation batch

tag: npc technician

tag: npc thaw


title: LN229/EGFRvIII/shTRIM24-1# (WGC090201R)

city: Shanghai

first: Haizhong

last: Feng

state: Shanghai

address: Pujian Road 160

department: Ren Ji Hospital

country: China

institute: Shanghai Jiao Tong University

description:
WGC090201R
Overexpression of EGFRvIII and treatment with a TRIM24 shRNA-#2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Fragments Per Kilobase of transcript per Million fragments mapped (FPKM) were calculated using a protocol from Trapnell et al., Nat Biotechnol, 2010. In short, A fragment corresponds to a single cDNA molecule, which can be represented by a pair of reads from each end. Exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. FPKM is conceptually analogous to the reads per kilobase per million reads sequenced (RPKM) measure, but it explicitly accommodates sequencing data with one, two, or – if needed for future sequencing platforms – higher numbers of reads from single source molecules.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

source_name: GBM cells

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

tag: cell type

value: GBM cells

tag: genotype/variation

value: Overexpression of EGFRvIII

tag: treatment

value: TRIM24 shRNA-#2


title: MYBMIM replicate 3

first: Richard

last: Koche

institute: Memorial Sloan Kettering Cancer Center

data_processing:
RNA-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using STAR (v2.4) with default parameters.
Read count tables were created using HTSeq v0.6.1.
Normalization and differential expression analysis was performed with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with read counts over all genes.

growth_protocol: MOLM13 cells were cultured in 5% CO2 in a humidified atmosphere at 37˚C in RPMI medium supplemented with 10% FBS (FBS) and antibiotics (100U/mL penicillin and 100 µg/mL streptomycin)

extract_protocol: Libraries were prepared according to Illumina's instructions accompanying the TruSeq RNA Sample Preparation Kit

treatment_protocol: Treatment protocol for cells: MOLM13 cells were resuspended to a concentration of 10 million cells/5mL of working media.  A peptide suspension was made in PBS of each  TG3 and MYBMIM peptides from the lyophilized product.  Peptide suspension was added directly to tissue culture media to a final concentration of 20μM.  Cells were incubated with peptide for 6h at  37°C and then resuspended in PBS.

value: leukemia cell line

value: MYBMIM peptide


title: LN229/EGFRvIII/shControl (WGC090195R)

description:
WGC090195R
Overexpression of EGFRvIII and treatment with a control shRNA

value: control shRNA


title: Control replicate 1


title: Control replicate 3


title: MYBMIM replicate 1


title: MYBMIM replicate 2


title: TG3 peptide control replicate 3

value: TG3 control peptide


title: Control replicate 2


title: TG3 peptide control replicate 2


title: LN229/EGFRvIII/shTRIM24-1# (WGC090200R)

description:
WGC090200R
Overexpression of EGFRvIII and treatment with a TRIM24 shRNA-#1

value: TRIM24 shRNA-#1


title: TG3 peptide control replicate 1


title: LN229/shControl (WGC090194R)

description:
WGC090194R
Treatment with a control shRNA


title: LN229/EGFRvIII/shTRIM24-1# (WGC090200)

description:
WGC090200
Overexpression of EGFRvIII and treatment with a TRIM24 shRNA-#1


title: MYB ChIP MYBMIM replicate 3

library_source: genomic

data_processing:
ChIP-seq reads were filtered for quality and 3' trimmed for adapter sequences.
Reads were aligned to human genome assembly hg19 using bwa mem (v0.7.12) with default parameters.
To create density files, the reads were extended to 200 bp, the signal was then normalized to ten million mapped reads and converted to BigWig using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files containing read densities normalized to 10 million reads

molecule: genomic DNA

growth_protocol: MV-411 cells were cultured in 5% CO2 in a humidified atmosphere at 37˚C in RPMI medium supplemented with 10% FBS (FBS) and antibiotics (100U/mL penicillin and 100 µg/mL streptomycin)

extract_protocol: ChIP-seq libraries were constructed with the NEBNext ChIP-seq library prep kit following the manufacturer’s recommended protocol (New England Biolabs, Ipswich, MA, USA).

treatment_protocol: Treatment protocol for cells: MV-411 cells were resuspended to a concentration of 10 million cells/5mL of working media.  A peptide suspension was made in PBS of each  TG3 and MYBMIM peptides from the lyophilized product.  Peptide suspension was added directly to tissue culture media to a final concentration of 20μM.  Cells were incubated with peptide for 6h at  37°C and then resuspended in PBS for Chromatin Immunoprecipitation and Sequencing.

tag: chip antibody

value: Abcam ab45150 Anti-v-Myb and c-Myb, rabbit monoclonal, Clone #EP769Y, lot # GR246427-10


title: MYB ChIP MYBMIM replicate 2


title: LN229/EGFRvIII/shControl (WGC090195)

description:
WGC090195
Overexpression of EGFRvIII and treatment with a control shRNA


title: LN229/shControl (WGC090194)

description:
WGC090194
Treatment with a control shRNA


title: MYB ChIP TG3 peptide control replicate 3


title: MYB ChIP TG3 peptide control replicate 2


title: MYB ChIP TG3 peptide control replicate 1


title: MYB ChIP control replicate 3


title: MYB ChIP control replicate 2


title: TAB-RRBS_NSC27NDM

first: Dan

last: Zhou

address: 131 Dong 'an Road, Xuhui District

institute: Fudan University

description: NGS

data_processing:
Raw sequencing reads was aligned to mouse genome hg19 and analyzed through a Streamlined Analysis and Annotation Pipeline (SAAP-RRBS)
Raw reads were mapped to mouse genome hg19. Transcripts were assembled using TopHat and quantified through Cufflinks. Fragments per kilobase of transcript per million mapped reads (FPKM) representing transcription level was generated using this package for subsequent comparison.
ChIP-seq peak calling was performed with SICER package and corrected for input (parameter setting: window size 200bp, gap size 200bp, effective genome size 0.74, FDR 0.01). Differential enrichment were identified using SICER-diff at FDR<0.01.
Genome_build: hg19

source_name: Cell line

growth_protocol: Tumor tissue from Patient-Derived Xenograft (PDX) were mechanically dissociated and selected in stem cell culture medium (ThermoFisher, StemPro NSC SFM A1050901) containing L-glutamin and Penicillin-Streptomycin in laminin (#L2020) -coated flasks to reduce culture condition-introduced heterogeneity. Neural stem cells were expanded on Matrigel (CORNING 356230) or fibronectin-coated 6-well plate in stem cell growth medium (GM) containing DEME/F12 plus Glutamax (Life Technologies 10565-018), BIT9500 Serum Substitute (1x, Stem Cell Technologies 09500), Heparin (20ug/mL Sigma H3149), Primocin (1x, InvivoGen ant-pm-1), human bFGF (20ng/Ml, Stemgent 03-0002), human EGF (20ng/mL, R&D Biosystems 236-EG).

extract_protocol:
Genomic DNA was isolated and purified from homogenized liver tissue using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturer’s protocol.
Total RNA samples are converted to Illumina sequencing libraries using Illumina’s Truseq RNA Sample Preparation Kit; The final libraries from RRBS were prepared for sequencing as per the manufacturer’s instructions in the Illumina cBot and HiSeq Paired end cluster kit version 3. ChIP-seq library is prepared with ThruPLEX DNA-seq kit.
RRBS, RNA-seq, ChIP-seq

value: fetal brain-derived neural stem/progenitor cells

tag: passages


title: MYB ChIP control replicate 1


title: TAB-RRBS_NSC27ADM

description: NGS


title: TAB-RRBS_GSC84FBS

description: NGS

value: patient-derived Xenograph glioma stem cells

value: 2 to 3


title: TAB-RRBS_GSC64FBS

description: NGS


title: LN229/EGFRvIII/shTRIM24-1# (WGC090201)

description:
WGC090201
Overexpression of EGFRvIII and treatment with a TRIM24 shRNA-#2


title: RRBS_NSC27ADM

description: NGS


title: Input control


title: TAB-RRBS_GSC6FBS

description: NGS


title: MAB-RRBS_GSC143

description: NGS


title: RRBS_GSC84FBS

description: NGS


title: RRBS_GSC64FBS

description: NGS


title: MAB-RRBS_GSC80

description: NGS


title: RRBS_GSC6FBS

description: NGS


title: MAB-RRBS_GSC64

description: NGS


title: RRBS_NSC27NDM

description: NGS


title: MAB-RRBS_GSC6

description: NGS


title: MAB-RRBS_GSC39 Sample 31

description: NGS


title: MYB ChIP MYBMIM replicate 1


title: MAB-RRBS_GSC10 Sample 28

description: NGS


title: MAB-RRBS_GSC12 Sample 29

description: NGS


title: TAB-RRBS_GSC143 Sample 26

description: NGS


title: TAB-RRBS_GSC102 Sample 25

description: NGS


title: TAB-RRBS_GSC84 Sample 24

description: NGS


title: TAB-RRBS_GSC64 Sample 22

description: NGS


title: TAB-RRBS_GSC39 Sample 21

description: NGS


title: TAB-RRBS_GSC12 Sample 19

description: NGS


title: TAB-RRBS_GSC14 Sample 20

description: NGS


title: TAB-RRBS_GSC10 Sample 18

description: NGS


title: MAB-RRBS_GSC102 Sample 35

description: NGS


title: TAB-RRBS_GSC6 Sample 17

description: NGS


title: MAB-RRBS_GSC84 Sample 34

description: NGS


title: MAB-RRBS_GSC14 Sample 30

description: NGS


title: RRBS_GSC84 Sample 14

description: NGS


title: RRBS_GSC143 Sample 16

description: NGS


title: RRBS_GSC80 Sample 13

description: NGS


title: RRBS_GSC14 Sample 10

description: NGS


title: RRBS_GSC39 Sample 11

description: NGS


title: RRBS_GSC102 Sample 15

description: NGS


title: MAB-RRBS_NSC27 Sample 6

description: NGS


title: RRBS_GSC64 Sample 12

description: NGS


title: MAB-RRBS_NSC23 Sample 5

description: NGS


title: RRBS_GSC6 Sample 7

description: NGS


title: RRBS_GSC12 Sample 9

description: NGS


title: RRBS_NSC23 Sample 1

description: NGS


title: TAB-RRBS_GSC80 Sample 23

description: NGS


title: FPKM_NSC27ADM Sample 62

description: NGS

data_processing:
Raw sequencing reads was aligned to mouse genome hg19 and analyzed through a Streamlined Analysis and Annotation Pipeline (SAAP-RRBS)
Raw reads were mapped to mouse genome hg19. Transcripts were assembled using TopHat and quantified through Cufflinks. Fragments per kilobase of transcript per million mapped reads (FPKM) representing transcription level was generated using this package for subsequent comparison.
ChIP-seq peak calling was performed with SICER package and corrected for input (parameter setting: window size 200bp, gap size 200bp, effective genome size 0.74, FDR 0.01). Differential enrichment were identified using SICER-diff at FDR<0.01.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM


title: FPKM_GSC84FBS Sample 67

description: NGS


title: FPKM_NSC30ADM Sample 64

description: NGS


title: FPKM_NSC30 Sample 49

description: NGS


title: TAB-RRBS_NSC27 Sample 4

description: NGS


title: RRBS_NSC27 Sample 2

description: NGS


title: FPKM_GSC64FBS Sample 66

description: NGS


title: FPKM_GSC6FBS Sample 65

description: NGS


title: FPKM_GSC187 Sample 61

description: NGS


title: FPKM_NSC27NDM Sample 63

description: NGS


title: FPKM_GSC184 Sample 60

description: NGS


title: FPKM_GSC143 Sample 59

description: NGS


title: FPKM_GSC84 Sample 57

description: NGS


title: FPKM_GSC102 Sample 58

description: NGS


title: RRBS_GSC10 Sample 8

description: NGS


title: FPKM_GSC80 Sample 56

description: NGS


title: FPKM_GSC64 Sample 55

description: NGS


title: TAB-RRBS_NSC23 Sample 3

description: NGS


title: FPKM_GSC14 Sample 53

description: NGS


title: FPKM_GSC10 Sample 51

description: NGS


title: FPKM_GSC12 Sample 52

description: NGS


title: FPKM_GSC6 Sample 50

description: NGS


title: FPKM_NSC23 Sample 47

description: NGS


title: H3K27ac_GSC187

description: NGS

data_processing:
Raw sequencing reads was aligned to mouse genome hg19 and analyzed through a Streamlined Analysis and Annotation Pipeline (SAAP-RRBS)
Raw reads were mapped to mouse genome hg19. Transcripts were assembled using TopHat and quantified through Cufflinks. Fragments per kilobase of transcript per million mapped reads (FPKM) representing transcription level was generated using this package fo
ChIP-seq peak calling was performed with SICER package and corrected for input (parameter setting: window size 200bp, gap size 200bp, effective genome size 0.74, FDR 0.01). Differential enrichment were identified using SICER-diff at FDR<0.01.
Genome_build: hg19

growth_protocol: Tumor tissue from Patient-Derived Xenograft (PDX) were mechanically dissociated and selected in stem cell culture medium (ThermoFisher, StemPro NSC SFM A1050901) containing L-glutamin and Penicillin-Streptomycin in laminin (#L2020) -coated flasks to reduc

extract_protocol:
Genomic DNA was isolated and purified from homogenized liver tissue using a serial phenol: chloroform extraction. Trizol reagent was used for extracting total RNA following the manufacturers protocol.
Total RNA samples are converted to Illumina sequencing libraries using Illuminas Truseq RNA Sample Preparation Kit; The final libraries from RRBS were prepared for sequencing as per the manufacturers instructions in the Illumina cBot and HiSeq Paired en


title: TG1-miR-302-367 H3K27me3

city: Paris

first: Alexandra

last: Bogeas

address: 7 quai St Bernard

institute: Inserm U1130, CNRS UMR 8246,University P. & M. Curie

data_processing:
Image analyses and base calling were performed using the HiSeq Control Software and Real-Time Analysis component (Illumina)
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2).
Alignment to the hg19 human reference genome was performed with CASAVA 1.8.2
Peak calling was performed using MACS (v1.4.2)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files with MACS results. Columns are: chromosome, peak start, peak end, MACS peak identifier, MACS score (=-10*log10(pvalue))

source_name: glioblastoma surgical resection

growth_protocol: All cells were routinely generated by re-plating d 7 floating oncospheres (typically 1 × 106 cells into a T75 flask) on uncoated plastic in defined medium containing bFGF and EGF.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-Seq libraries were constructed with the DNA Seq sample prep. kit (ref. IP-102-1001) from Illumina according to the manufacturer’s instructions.

value: glioblastoma stem-like cells, transduced with miR-302-368

tag: tumor stage

value: human glioblastoma multiformis

value: H3K27me3 (Millipore, 07-449)


title: TG1-miR-302-367 H3K4me3

value: glioblastoma stem-like cells, transduced with miR-302-367

value: H3K4me3 (Millipore, 07-473)


title: H3K27ac_GSC184

description: NGS


title: TG1 Input (A)

value: glioblastoma stem-like cells, transduced with shControl


title: H3K27ac_GSC143

description: NGS


title: H3K27ac_GSC102

description: NGS


title: TG1 H3K4me3


title: TG1 H3K27me3


title: H3K27ac_GSC80

description: NGS


title: H3K27ac_GSC84

description: NGS


title: H3K27ac_GSC64

description: NGS


title: H3K27ac_GSC39

description: NGS


title: H3K27ac_GSC14

description: NGS


title: FPKM_GSC39 Sample 54

description: NGS


title: H3K27ac_GSC12

description: NGS


title: H3K27ac_GSC6

description: NGS


title: H3K27ac_GSC10

description: NGS


title: FPKM_NSC27 Sample 48

description: NGS


title: TG1-miR-302-367 Input (B)

value: glioblastoma stem-like cells, transduced with miR-302-369


title: DLBCL5_relapse

city: Helsinki

first: Suvi-Katri

last: Leivonen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

data_processing:
Adapter and quality trimming with FastX-Toolkit (M=6, l=15,qual=-64, a=ATCTCGTATGCCGTCTTCTGCTT), filtering out samples with less than 20% of raw sequenced reads surviving trimming.
Bowtie alignment to the reference genome, allowing for 1 mismatch (-m 20 --best --strata --un @folder1@/unaligned.map)
Aligned samples filtered for a minimum 60% of reads to map to somewhere on the genome.
Bowtie alignment of genome-mapped reads to known miRNA transcripts in same genome build, using the same parameters above.
Aligned samples filtered for a minimum 50% of reads to map to known miRNA transcripts.
Annotation and quantification of mapped reads to known mature and precurosr miRNAs (miRBase version 20) using HTSeq.
Filter miRNA expression such that a miRNA is minimally expressed with a raw count of 2 in at least 25% of the samples.
Novel miRNA discovery using miRanalyzer and reads aligning to the genome but not to any known miRNA transcripts (unaligned.map files after second alignment)
Merging raw count output of novel miRNA discovery for each sample into overlapping genomic regions using the PointDistance component of Anduril (anduril.org)
Expression normalization and Differential expression analysis using R bioconductor packages EdgeR and DESeq.
Perform same preprocessing, alignment and expression quantification of control samples (GSE15229)
DLBCL1_R failed the filtering step after initial alignment to the reference genome due to low sequence content.
Genome_build: human NCBI genome build 37 version 70
Supplementary_files_format_and_content: tab-delimited text file of raw counts for mature miRNAs (miRBase version 20) across samples
Supplementary_files_format_and_content: Expression normalization and Differential expression analysis using R bioconductor packages EdgeR and DESeq.

source_name: diffuse large B-cell lymphoma

extract_protocol:
Total RNAs from fresh-frozen tissue samples were isolated with NucleoSpin TriPrep (Machery-Nagel, Düren, Germany) according to manufacturer's protocol.
TruSeq small RNA sample preparation kit (Illumina, Inc. CA, USA) was used for library construction according to manufacturer’s protocol.

tag: tissue

value: fresh frozen tumor

tag: tumor status

value: relapsed tumor


title: DLBCL4_relapse


title: DLBCL4_primary

value: primary tumor


title: DLBCL5_primary


title: DLBCL2_relapse


title: DLBCL6_relapse


title: DLBCL7_relapse


title: DLBCL7_primary


title: DLBCL3_relapse


title: H3K27ac_NSC30

description: NGS


title: GSC187_input

description: NGS


title: H3K27ac_NSC23

description: NGS


title: DLBCL3_primary


title: H3K4me1_GSC187

description: NGS


title: DLBCL1_primary


title: GSC143_input

description: NGS


title: DLBCL2_primary


title: H3K4me1_GSC143

description: NGS


title: H3K4me1_GSC184

description: NGS


title: H3K4me1_GSC102

description: NGS


title: GSC84_input

description: NGS


title: DLBCL6_primary


title: H3K4me1_GSC84

description: NGS


title: GSC80_input

description: NGS


title: GSC64_input

description: NGS


title: GSC39_input

description: NGS


title: H3K4me1_GSC64

description: NGS


title: H3K4me1_GSC14

description: NGS


title: H3K4me1_GSC12

description: NGS


title: GSC14_input

description: NGS


title: H3K4me1_GSC39

description: NGS


title: small_intestine_mock_rep3

city: Geneva

first: Mirco

last: Schmolke

address: Rue Michel Servet 1

department: Department of Microbiology and Molecular Medicine

country: Switzerland

institute: University of Geneva

description:
I5
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt

data_processing:
Illumina Casava1.8.2 software was used for basecalling.
Quality Control  (QC) was done with FastQC v.0.11.5 and biological QC was done with PicardTools v.1.141
Reads were mapped with TopHat2 v.2.0.11
The gene features were counted with HTSeq v.0.6p1
Normalization and differential expression analysis was performed with the statistical analysis R/Bioconductor package edgeR v. 3.4.2
Genome_build: UCSC mm10
Supplementary_files_format_and_content: tab-delimited text file with raw counts and normalized counts in cpm (counts per million). Excel file with lists of differentially expressed genes.

growth_protocol: C57BL/6J mice (female, 8-9 weeks of age) were purchased from Charles River Laboratories (France) and housed under SPF/BSL2 conditions.

extract_protocol:
Organs were collected 7 days post mock treatment or infection, respectively, and stored in RNAlater (Qiagen) over night, then stored at -70 °C until further use. Total RNA was extracted using TRIzol (Invitrogen), following manufacturer's instruction
The libraries were prepared with 800 ng of total RNA as starting material and processed with the Illumina Truseq mRNA stranded kit according to the manufacturer instruction. (polyA selection).

treatment_protocol: For infection, mice were injected i.p. a mix of ketamin/xylazine (100mg/kg and 5mg/kg, respectively) in 100 µl of sterile PBS. Upon reaching deep anesthesia mice were inoculated with 40 µl of PBS or virus via the intranasal route.

tag: strain

tag: gender

value: female

tag: age

value: 9 weeks old

value: mock-treatment

tag: administration

value: intranasal

tag: virus used

value: PBS

tag: day (dpi)

value: small intestine, duodenum-jejunum


title: small_intestine_iav_rep3

description:
I8
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt

value: iav-infected

value: IAV A/Viet Nam/1203/2004 (VN/1203) HALo (low pathogenic version)


title: GSC10_input

description: NGS

value: patient-derived Xenograph glioma stem cells

value: 2 to 3


title: GSC12_input

description: NGS


title: small_intestine_iav_rep4

description:
I10
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt


title: small_intestine_iav_rep2

description:
I7
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt


title: H3K4me1_GSC10

description: NGS


title: small_intestine_mock_rep1

description:
I2
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt


title: GSC184_input

description: NGS


title: GSC102_input

description: NGS


title: GSC6_input

description: NGS


title: small_intestine_iav_rep1

description:
I6
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt


title: lung_iav_rep4

description:
L10
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt

value: lung, total


title: small_intestine_mock_rep2

description:
I4
processed data file:
raw_intestine_counts.txt
normalized_counts_intestine_cpm.txt
all_genes_fold_changes_intestine_iav_vs_mock.txt


title: STM815 wt in symbiosis with bean_3

city: Zürich

first: Gabriella

last: Pessi

address: Winterthurerstrasse 190

institute: University of Zürich

data_processing:
The sequences of the reads were quality trimmed using the program fastq_quality_trimmer
Sequencing reads were mapped to the Pp STM815 genome using CLC Genomics Workbench v7.0 (CLCbio) allowing up to 2 mismatches per read
RNA-Seq count data were subsequently analyzed with the DESeq software (Anders & Huber 2010)
Genome_build: STM815 genome sequence (accession no. NC_010622.1, NC_010623.1, NC_010625.1 and NC_010627.1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM and mean values for each sample; data exported from CLC

organism: Paraburkholderia phymatum STM815

source_name: Pp STM815 bacteroid cells

extract_protocol:
Cells were flash frozen on dry ice, and RNA was harvested using hot phenol protocol (Pessi et al 2007) . For RNA extracted from nodules, first nodules were disrupted with TissueLyzer and then rRNA of plants was removed using Ribo-zero kit (Epicentre). The cDNA was produced and nugen libraries obtained.
RNA libraries were prepared using Encore Complete Prokaryotic RNA-Seq DR Muliplex System

tag: genotype

value: wt

tag: host organism

value: Phaseolus vulgaris

tag: growth phase

value: nodules harvested 21 days post infection

tag: growth medium

value: inside bean nodules


title: H3K4me1_NSC30

description: NGS

tag: cell type

value: fetal brain-derived neural stem/progenitor cells


title: NSC30_input

description: NGS


title: H3K4me1_GSC80

description: NGS


title: NSC23_input

description: NGS


title: STM815 wt in symbiosis with bean_2


title: lung_iav_rep3

description:
L8
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt

tag: treatment


title: lung_iav_rep2

description:
L7
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt


title: STM815 wt in symbiosis with bean_1


title: H3K4me1_NSC23

description: NGS

tag: chip antibody


title: lung_iav_rep1

description:
L6
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt


title: STM815 wt nitrogen starved_3

source_name: Pp STM815 planktonic cells

value: planktonic cells, OD600 equal 0.4

value: minimal medium 0.5 mM NH4


title: H3K4me1_GSC6

description: NGS

tag: passages


title: Treatment-CCN-R3

city: Beijing

first: Changlong

last: Chen

address: Haidian District, No. 12 Zhongguancun South Street

department: Institute of Crop Sciences

institute: Chinese Academy of Agricultural Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were assembled together for all the nematode samples using Trinity (Grabherr et al., 2011). Clean data from each sample were aligned against the assembled transcripts or unigenes and the mapped reads were used for further analyses.
To evaluate the expression levels (in the form of FPKM) of unigenes, the reads of each sample were aligned with the assembled unigene database by Bowtie (Langmead et al., 2009) and analyzed by RSEM (Li & Dewey, 2011)
genome build: none
An excel file includes gene counts for each Sample

organism: Heterodera avenae

source_name: whole nematode

extract_protocol:
Each sample of wheat roots and nematodes were collected and frozen in liquid nitrogen, and RNA was harvested using Trizol reagent.
NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, USA) was used with 1 ug of total RNA for the construction of transcriptome sequencing libraries following manufacturer’s recommendations.

treatment_protocol: Five to six germinated wheat seeds with roots 2-3 cm long were transferred into a Petri dish (9 cm in diameter) containing 25,000~30,000 J2s suspended in 15 ml Pluronic F-127 gel (23%, w/v) for three hours for the attraction assay, which was defined as the treatment. The experiment sets with wheat seedlings or nematodes independently alone in the gel were used as two negative controls

value: whole nematode

tag: pathotype

tag: developmental stage

value: infective second-stage juvenile


title: Treatment-wheat-R1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.33
An excel file includes gene counts for each Sample

organism: Triticum aestivum

source_name: root

tag: tissue

value: root

tag: cultivar

value: Wenmai 19

value: geminated of 2 days


title: Treatment-wheat-R3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.35
An excel file includes gene counts for each Sample


title: Treatment-wheat-R2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.34
An excel file includes gene counts for each Sample


title: Treatment-CCN-R2


title: STM815 wt nitrogen starved_2

tag: strain


title: lung_mock_rep2

description:
L4
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt

tag: gender

value: female

tag: age

value: 9 weeks old

value: mock-treatment

value: intranasal

value: PBS


title: Treatment-CCN-R1


title: STM815 wt nitrogen replete_2

value: wt

value: planktonic cells, OD600 equal 0.7

value: minimal medium 30 mM NH4


title: lung_mock_rep1

description:
L2
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt

tag: administration

tag: virus used

value: lung, total


title: Control-wheat-R3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.32
An excel file includes gene counts for each Sample


title: Control-CCN-R2


title: Phf8 knock out_H3K20me1_ChIP-seq

first: Xuemei

address: 320 Yueyang Road

department: State Key Laboratory of Molecular Biology

institute: Chinese Academy of Sciences

data_processing:
ChIP-seq reads were aligned to the ensembl release 88 genome assembly using mem version0.7.12-r1039 with the following configurations -T 25；-k 18
Aligned sam files were converted to bam files using samtools version 0.1.19-44428cd
Bam files were converted to bw files using bamCoverage version 1.5.12
Genome_build: ensembl Mus musculus release 88
Supplementary_files_format_and_content: bw files genereated by bamCoverage

source_name: hippocampus

extract_protocol:
Lysates were clarified from sonicated hippocampus tissue and H3K27me3-DNA complexes were pulled down by antibody using Millipore EZChIP kit .
Libraries were prepared for sequencing using NEB ultra DNA  Library Prep Kit for Illumina.

tag: strain background

tag: genotype/variation

value: Phf8 knock out

value: 10 weeks old

value: hippocampus

value: H3K20 me1

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat. #

tag: chip antibody lot #


title: WT_H3K20me1_ChIP-seq

value: WT


title: Control-CCN-R3

value: whole nematode

value: infective second-stage juvenile


title: Control-CCN-R1


title: STM815 wt nitrogen replete_1

tag: genotype

tag: growth phase

value: planktonic cells, OD600 equal 0.6

tag: growth medium


title: Control-wheat-R1

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.30
An excel file includes gene counts for each Sample

value: root

value: Wenmai 19

value: geminated of 2 days


title: LNCaP shRB CDT Rep 2

status: Public on Feb 22 2018

city: Philadelphia

first: Christopher

last: McNair

state: PA

address: 833 Chestnut Street Ste 1140

department: Medical Oncology

institute: Thomas Jefferson University

description: ATAC_shRB_CDT_Rep1and2_ppr.IDR0.1.filt_merged_scored.narrowPeak

data_processing:
data was processed and analyzed using the ENCODE ATAC-Seq pipeline (https://www.encodeproject.org/atac-seq/)
Genome_build: hg19
Supplementary_files_format_and_content: BED format called ATAC-Seq peaks

source_name: LNCaP Cell Line

growth_protocol: LNCaP cells (either shCON or shRB) were cultured in hormone proficient media unless otherwise indicated.

extract_protocol: ATAC-Seq was performed as previously described (Buenrostro et al 2015). Briefly, cells plated and treated as indicated by the condition.  Next, 75,000 cells were collected and lysed in ATAC lysis buffer.  Cells were then re-suspended in the transposition reaction mix, and the transposition reaction incubated at 37oC for 30 minutes. Transposed DNA was purified using AMPure purification methods as specified by the manufacturer.  Purified DNA was then amplified utilizing custom barcoded Nextera primers as (previously listed and available in  (Buenrostro et al 2015)).  Library size and quality was validated using a Bioanalyzer and libraries sequenced on a NextSeq 500

treatment_protocol: Cells were treated with CDT for 72 hours prior to harvest for CDT condition, and treated with DHT for 3 hours prior to harvest in DHT conditions

tag: treatment

value: 72 hour CDT

tag: knockdown

value: shRB


title: LNCaP shCON CDT Rep 2

description: ATAC_shCON_CDT_Rep1and2_ppr.IDR0.1.filt_merged_scored.narrowPeak

value: shCON


title: LNCaP shCON CDT Rep 1


title: LNCaP shCON DHT Rep 1

description: ATAC_shCON_DHT_Rep1and2_ppr.IDR0.1.filt_merged_scored.narrowPeak

value: 72 hour CDT, 3 hour DHT


title: LNCaP shCON DHT Rep 2


title: LNCaP shRB CDT Rep 1


title: lung_mock_rep3

description:
L5
processed data file:
raw_lung_counts.txt
normalized_counts_lung_cpm.txt
all_genes_fold_changes_lung_iav_vs_mock.txt

value: female

value: 9 weeks old

value: mock-treatment

value: intranasal

value: PBS

tag: day (dpi)

tag: tissue

value: lung, total


title: STM815 wt nitrogen replete_3

tag: strain

value: wt

value: planktonic cells, OD600 equal 0.7

value: minimal medium 30 mM NH4


title: Control-wheat-R2

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Clean reads were then mapped to the wheat reference genome sequence by Tophat2 tools （Kim et al., 2013）.
The abundance of transcripts was calculated as fragments per kilobase of transcript per million fragments mapped (FPKM) (Florea et al., 2013) using the Cuffquant and Cuffnorm components in Cufflinks software (Trapnell et al., 2010)
genome build: IWGSC1.0+popseq.31
An excel file includes gene counts for each Sample

tag: cultivar

tag: developmental stage


title: A2780cis control 12h rep3

city: Dresden

first: Konrad

last: Grützmann

address: Schubertstraße 15

department: Core Unit for Molecular Tumor Diagnostics

country: Germany

institute: National Center for Tumor Diseases partner site Dresden

data_processing:
Reads were converted from Illumina bcl to fastq format using bcl2fastq (version v2.17.1.14) allowing for 1 barcode mismatch
Reads were trimmed for quality, sequence adapters and cropped to 75nt using trimmomatic with the following parameters: TruSeq3-PE.fa:2:30:10:2:true LEADING:15 TRAILING:15 SLIDINGWINDOW:4:15 MINLEN:36 CROP:75.
Reads were aligned to the Gencode genome (GRCh38.p7 primary assembly) using STAR (2.5.2b) in a 2-pass mapping mode: first, an index was created using the genome sequence and gene annotation (here, Gencode GRCh38.p7 comprehensive gene annotation), against which all reads are aligned. Second, all detected splice junctions of all samples are merged and used as guide for the second mapping step. The following parameters were used in both steps: --readFilesCommand zcat --alignIntronMax 500000 --alignMatesGapMax 500000 --outSAMtype BAM SortedByCoordinate --outSAMprimaryFlag OneBestScore --outFilterMultimapNmax 100 --outFilterMismatchNmax 2 --alignSJstitchMismatchNmax 5 -1 5 5. For the second step, additional parameters are: --sjdbFileChrStartEnd allSJ.out.tab --limitSjdbInsertNsj 100000000, where allSJ.out.tab denotes the collected splice junctions.
Read counts of all annotated genes were extracted from the alignments using featureCounts method of the Rsubread package (1.24.1) with the following parameters: GTF.featureType = "exon", GTF.attrType="gene_id", useMetaFeatures = T, isPairedEnd=T, requireBothEndsMapped=F, allowMultiOverlap=T, countMultiMappingReads=T, fraction=T. lincRNA and rRNA genes, and genes with 0 counts for all samples were discarded
DESeq2 (2_1.14.1) was used to find differentially expressed genes using standard parameters. Only genes with multiple testing adjusted p-values (padj from DESeq2) < 0.05 were kept.
Genome_build: GRCh38.p7 primary assembly
Supplementary_files_format_and_content: read counts from data processing steps above (before DESeq application), columns represent samples, rows represent genes (Ensembl Gene ID)

source_name: A2780cis control 12h

growth_protocol: The isogenic human OC cell lines A2780 (platinum-sensitive), A2780cis (platinum-resistant) were purchased from Sigma-Aldrich (Taufkirchen, Germany) and were cultured in RPMI1640 medium, supplemented with 2 mM glutamine, 10 % fetal calf serum, 100 U/ml penicillin and 100 mg/ml streptomycin (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Every 2-3 passages, the medium of A2780cis cells was additionally supplemented with 1 µM cisplatin for one passage, in order to maintain their platinum-resistant characteristics.

extract_protocol:
After further 6 h or 12 h, cells were harvested for RNA extraction, according to the miRNeasy Mini Kit (Qiagen, Hilden, Germany), including on column DNA digestion, in order to remove residual contaminating genomic DNA.
TruSeq Stranded Total RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol, starting with 1 µg of DNAse-treated human total RNA. All barcoded libraries were pooled and sequenced on an Illumina NextSeq500 platform using a High Output Kit v2 75 cycles (75 bp, single reads) to obtain on average 10 Mio reads per library

treatment_protocol: For Whole-Transcriptome Sequencing (RNA-Seq), 2x10E6 cells (A2780) or 2.5x10E6 cells (A2780cis) were seeded in T-75 flasks. After 48 h, medium was removed and medium with 1 µM 5-FdU-ECyd or standard growth medium (as control) was added.

tag: cell line

value: ovarian cancer cell line A2780cis

tag: platinum-sensitivity

value: platinum-resistant

tag: agent

value: control

tag: time


title: A2780cis control 12h rep2


title: A2780cis 5-FdU-Ecyd 12h rep1

source_name: A2780cis 5-FdU-Ecyd 12h


title: STM815 wt nitrogen starved_1

value: planktonic cells, OD600 equal 0.4

value: minimal medium 0.5 mM NH4


title: A2780 5-FdU-Ecyd 12h rep3

source_name: A2780 5-FdU-Ecyd 12h

value: ovarian cancer cell line A2780

value: platinum-sensitive


title: A2780cis 5-FdU-Ecyd 12h rep2


title: A2780 control 12h rep2

source_name: A2780 control 12h


title: A2780 5-FdU-Ecyd 12h rep1


title: A2780cis control 12h rep1


title: A2780 5-FdU-Ecyd 12h rep2


title: A2780 control 12h rep3


title: A2780 control 12h rep1


title: A2780cis 5-FdU-Ecyd 6h rep1

source_name: A2780cis 5-FdU-Ecyd 6h


title: A2780cis 5-FdU-Ecyd 6h rep3


title: A2780cis control 6h rep2

source_name: A2780cis control 6h


title: A2780cis control 6h rep1


title: A2780cis control 6h rep3


title: A2780 5-FdU-Ecyd 6h rep3

source_name: A2780 5-FdU-Ecyd 6h


title: A2780 5-FdU-Ecyd 6h rep2


title: A2780 5-FdU-Ecyd 6h rep1


title: A2780 control 6h rep1

source_name: A2780 control 6h


title: A2780 control 6h rep3


title: aHT_2884

city: Los Angeles

first: Dhruv

last: Sareen

state: CA California

address: 8700 Beverly Blvd

department: Board of Governors Regenerative Medicine Institute

institute: Cedars-Sinai Medical Center

description: Healthy phenotype

data_processing:
Raw reads were aligned to the transcriptome using Bowtie (version 1.1.1) with default parameters, using a custom human GRCh38 transcriptome reference based on human GENCODE version 23.
Expression counts for each gene in all samples were normalized by the sequencing depth to Transcripts Per Million reads, or TPM.
Differential expression analysis was performed using the DESeq2 Bioconductor package for R on the raw expression counts to identify differences in expression between the iPSC derived hypothalamic neuron samples versus the adult post-mortem hypothalamic samples and between the obese patient iPSC-hypothalamic neurons versus the control-derived iPSC-hypothalamic neurons.
Expression counts for each gene (TPM: transcripts per million or FPKM: Fragments Per Kilobase of transcript per Million) in all samples were normalized by the sequencing depth.
Genome_build: GRCh38 transcriptome based on human GENDODE v. 23
Supplementary_files_format_and_content: CSV file containing the differential expression results, the TPM-normalized expression scores, and the raw read counts

source_name: Adult HT tissue

growth_protocol: Induced Pluripotent Stem Cells were differentiated into hypothalamic neurons for the iHT samples.  IPSCs were differentiated into motor neurons for the iMN samples.  Adult brains were dissected post-mortem to harvest natural hypothalamic neurons.

extract_protocol:
RNA was extracted from all samples using the QIAGEN RNeasy mini kit.
Libraries were constructed using the Illumina TruSeq Stranded mRNA library preparation kit.

tag: cell type

value: Hypothalamus neuron

tag: generation source

value: Post-mortem brain sections

tag: disease state

value: Control

tag: Sex

value: M

tag: age

tag: race

value: Caucasian

tag: parent line

value: Brain section


title: aHT_2266

description: Healthy phenotype

value: F


title: A2780cis 5-FdU-Ecyd 12h rep3


title: Reference

source_name: human Universal Reference RNA sample, which serves as a positive control for library prep and sequencing


title: aHT_1843

description: Healthy phenotype


title: iMN_87iCTR

description: Healthy phenotype

source_name: Motor neuron (MN) samples

value: Motor neuron

value: induced Pluripotent Stem Cells (iPSC)

value: Unknown


title: aHT_1838

description: Healthy phenotype


title: aHT_1662

description: Healthy phenotype


title: iMN_201iCTR

description: Healthy phenotype


title: iHT_02iOBS

description: Body mass index = 50; 389 pounds; diabetes; enteritis; hypertension; hyperthyroidism; family history of diabetes and hyperthyroidism; obese spouse is GM14303

source_name: Obesity iPSC HT neurons

value: Obese


title: A2780cis 5-FdU-Ecyd 6h rep2

value: ovarian cancer cell line A2780cis

value: platinum-resistant


title: iHT_90iOBS

description: Body mass index > 50; 330 pounds; irregular menses

value: Hispanic


title: iHT_688iCTR

description: Healthy phenotype

source_name: Control iPSC HT neurons


title: iHT_77iOBS

description: Body mass index > 50; 400 pounds; bad hips; mother and grandmother are obese

value: Black


title: iHT_87iCTR

description: Healthy phenotype


title: iHT_03iOBS

description: Body mass index = 50; 400 pounds; diabetes; arthritis; hypertension; family history of diabetes, obesity, and hypertension; obese spouse is GM14302


title: iHT_80iCTR

description: Healthy phenotype


title: iHT_02iCTR

description: Healthy phenotype


title: LN shCON E2F1 CDT ChIP-Seq

description: LNCaP E2F1 shCON CDT

data_processing:
alignment to hg19 genome with bowtie
peak calling with MACS2 with a 0.01 q-value cutoff
Genome_build: hg19
Supplementary_files_format_and_content: BED file

extract_protocol:
ChIP-Seq was prepared as previously described (Xu et al 2012)
ChIP-Seq libraries were constructed ThruPLEX-FD Prep Kit (Rubicon Genomics) with approximately 10 ng of ChIP DNA

treatment_protocol: Cells were treated with CDT for 72 hours prior to harvest

tag: cell cycle arrest treatment

value: 72 hour CDT

tag: knockdown

value: shCON

tag: chip antibody


title: iHT_03iCTR

description: Healthy phenotype

value: Hypothalamus neuron


title: LN shRB E2F1 CDT ChIP-Seq

description: LNCaP E2F1 shRB CDT

value: shRB


title: MCF-7 H9 TamR 24h GDNF

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description:
nascent RNA
Herein

data_processing:
Library strategy: PRO-Seq
We trimmed adapter sequences and mapped PRO-seq data using BWA.
Data was converted into bigWig format.
Genome_build: hg19
Supplementary_files_format_and_content: PRO-seq data are provided in standard bigWig and raw fastq formats.
Supplementary_files_format_and_content: dREG/dREG-HD interpretation of TREs based on PRO-seq data are provided in bigWig and BED formats
Supplementary_files_format_and_content: MCF-7 TamS/ TamR combined data
Supplementary_files_format_and_content: Combined data from MCF-7 subclones
Supplementary_files_format_and_content: mcf7.bedgraph.gz.bed.gz_imputedDnase.bw
Supplementary_files_format_and_content: mcf7_tamSR_dREG.bw
Supplementary_files_format_and_content: mcf7.bedgraph.gz.bed.gz_dREG_HD_stringent.bed
Supplementary_files_format_and_content: MCF-7 TamS/ TamR GDNF timecourse combined data
Supplementary_files_format_and_content: Combined data from MCF-7 subclones across the GDNF timecourse
Supplementary_files_format_and_content: GDNF, 0h, 1h, 24h
Supplementary_files_format_and_content: mcf7.gdnf.bedgraph.gz.bed.gz_imputedDnase.bw
Supplementary_files_format_and_content: mcf7_gdnf_dREG.bw
Supplementary_files_format_and_content: mcf7.gdnf.bedgraph.gz.bed.gz_dREG_HD_stringent.bed

source_name: MCF-7 cells subclone

growth_protocol: Tamoxifen sensitive (TamS; B7TamS and C11TamS) and resistant (TamR; G11TamR and H9TamR) MCF-7 cells (Gonzalez-Malerva et al., 2011) were a gift from Dr. Joshua LaBaer. TamS cells were grown in Dulbecco's Modified Eagle Medium supplemented with 5% fetal bovine serum and 1% Penicillin Streptomycin, and TamR cells were grown in the same media supplemented with 1 μM tamoxifen. TamS and TamR lines were grown in 150mm TC-treated culture dish in their respective normal culture media. Cells were rinsed with PBS for at least three times 24 hours after plating. Both the TamS and TamR cells were grown in Dulbecco's Modified Eagle Medium supplemented with 5% fetal bovine serum and 1% Penicillin Streptomycin for an additional three days until ~80% confluency in the absence of tamoxifen, in order to measure the difference between TamS and TamR cells pre-treatment. For estrogen (E2) and tamoxifen treated TamS and TamR cells, cells were instead grown in phenol-red free Dulbecco's Modified Eagle Medium supplemented with 5% charcoal-stripped fetal bovine serum and 1% Penicillin Streptomycin for three days. The cells were then treated with either EtOH (vehicle control), 100 nM E2, or with 1 M tamoxifen for 40 min. For GDNF treated TamS and TamR cells, the same experimental set up as the pre-treatment was performed. In addition, the cells were treated with 10 ng/mL GDNF for 0, 1, or 24 hours.

extract_protocol:
Nuclei were isolated as described in previously (Core et al., 2008). Briefly, cells were rinsed three times with ice-cold PBS and lysed using lysis buffer (10 mM Tris-HCl pH 7.4, 2 mM MgCl2, 3 mM CaCl2, 0.5% NP-40, 10% Glycerol, 1 mM DTT, 1X PIC (Roche; Cat# 11836153001), and 1 ml/10 mL SUPERase-In (ThermoFisher; Cat# AM2694) dissolved in DEPC water). Cells were homogenized by gently pipetting at least 30 times and the nuclei were harvested by centrifugation at 1000g for five minutes at 4°C. The isolated nuclei were washed twice with lysis buffer and were resuspended in 100 mL freezing buffer (50 mM Tris HCl pH 8.3, 5 mM MgCl2, 40% Glycerol, 0.1 mM EDTA pH 8.0, and 4 U/mL SUPERase-In). The isolated nuclei were used for nuclear run-on and precision nuclear run-on sequencing (PRO-seq) library preparation.
We prepared PRO-seq libraries as described in Kwak et. al. (2013) Science.

treatment_protocol: Ligand treatments were applied for the indicated time as described in our paper.

tag: clone

tag: resistance

value: TamR

tag: treatment

value: GDNF, 24h


title: MCF-7 H9 TamR 1h GDNF

description:
nascent RNA
Herein

value: GDNF, 1h


title: MCF-7 H9 TamR 0h GDNF

description:
nascent RNA
Herein

value: GDNF, 0h


title: MCF-7 C11 TamS 24h GDNF

description:
nascent RNA
Herein

value: TamS


title: MCF-7 G11 TamR 0h GDNF

description:
nascent RNA
Herein


title: MCF-7 G11 TamR 1h GDNF

description:
nascent RNA
Herein


title: MCF-7 G11 TamR 24h GDNF

description:
nascent RNA
Herein


title: MCF-7 C11 TamS 0h GDNF

description:
nascent RNA
Herein


title: MCF-7 C11 TamS 1h GDNF

description:
nascent RNA
Herein


title: iHT_74iOBS

description: BMI = 50, 319 lbs

value: F


title: iHT_25iCTR

description: Healthy phenotype

value: induced Pluripotent Stem Cells (iPSC)

value: Control

value: M


title: MCF-7 B7 TamS 0h GDNF

description:
nascent RNA
Herein


title: MCF-7 B7 TamS 24h GDNF

description:
nascent RNA
Herein


title: MCF-7 B7 TamS 1h GDNF

description:
nascent RNA
Herein


title: MCF-7 B7 TamS Tam

description:
nascent RNA
Herein

value: Tam, 40m


title: MCF-7 G11 TamR Tam

description:
nascent RNA
Herein


title: MCF-7 G11 TamR DMSO

description:
nascent RNA
Herein

value: DMSO, 40m


title: iHT_201iCTR

description: Healthy phenotype

value: Unknown


title: MCF-7 B7 TamS E2

description:
nascent RNA
Herein


title: MCF-7 G11 TamR None

description:
nascent RNA
Herein


title: A2780 control 6h rep2

tag: cell line

value: ovarian cancer cell line A2780

value: platinum-sensitive

value: control


title: MCF-7 H9 TamR None

description:
nascent RNA
Herein


title: MCF-7 C11 TamS None

description:
nascent RNA
Herein