title: WT10M_rep4

city: Singapore

first: Joonki

last: Kim

address: 2 Medical drive, Blk MD9

department: Physiology, School Of Medicine

country: Singapore

institute: National University of Singapore

description: Wild Type

data_processing:
Raw image data file from high-throughput sequencing (Illumina) was transformed to Sequenced Reads (Raw data or Raw reads) by CASAVA base recognition (Base calling).
Low quality reads was trimmed using command-line.
Alignment to reference genome was performed using TopHat2 (Kim et al., 2013).
Quantitative analysis of mRNA and lncRNA screening were performed by Cuffdiff software to get the FPKM of mRNA and lncRNA of every sample.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (Anders et al., 2010).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Excel files containing quantified 'FPKM' values of all 20 samples (for mRNA, lncRNA, transcripts, and TUCP).

source_name: Cerebral cortex

extract_protocol:
Total RNA was extracted from the frozen brain tissue samples using a micro-tube tissue homogenizer and EZ-10 DNAaway RNA extraction mini-prep kit following manufacturer's instruction. Samples with only RIN above 7 were seleted for the rest of the procedures.
Purified RNA was used for library preparation for sequencing using standard Illumina protocols.

tag: tissue

value: Cerebral cortex

value: 10 months


title: WT10M_rep2

status: Public on Jun 23 2019

type: SRA

description: Wild Type

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: age


title: WT10M_rep3

description: Wild Type


title: eH41

city: Zurich

first: Csaba

last: Földy

state: Zurich

address: Winterthurerstrasse 190

department: Brain Research Institute

country: Switzerland

institute: University of Zurich

description:
ENS_counts.tsv
gene_counts.tsv

data_processing:
Illumina RTA v1.12 was used for base calling, and Illumina bc12fastq v2.20 for demultiplexing and fastq file generation
Sequenced reads were pre-processed using Trimmomatic and Flexbar. Reads were aligned to GRCm38 genome using STAR aligner with parameters trimLeft=10, minTailQuality=15, minAverageQuality=20, and minReadLength=30.
Aligned reads were converted to gene counts using featureCounts. Outputs for different cells were merged into a single file (ENS_counts.tsv) using custom Python code
Ensembl names were converted to gene names using Ensembl's Mus_musculus.GRC38.86.gtf file (gene_counts.tsv)
Reads were normalized using scran, and normalized values are stored in normalized_gene_counts.tsv
Genome_build: GRCm38
Supplementary_files_format_and_content: tab delimited text files. ENS_counts.tsv contains raw counts, with genes labeled by their Ensembl ENS numbers. gene_counts.tsv contains raw counts, with genes labeled by their gene names. normalized_gene_counts.tsv contains normalized (scran) counts of cells that passed quality control

source_name: Neural embryonic cell

extract_protocol:
cytosol aspiration via patch-clamp pipettes
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Neural embryonic cell

tag: driver line

value: Htr3a Cre line

tag: cell type

value: Undefined

tag: quality control

value: Failed


title: eH38

description:
ENS_counts.tsv
gene_counts.tsv
normalized_gene_counts.tsv

value: CGE-derived

value: Passed


title: WT10M_rep5

description: Wild Type


title: WT03M_rep5

description: Wild Type

value: 3 months


title: eH37


title: WT03M_rep4

description: Wild Type


title: eH36

value: MGE-derived 2


title: WT03M_rep2

description: Wild Type


title: WT03M_rep3

description: Wild Type


title: eH35

value: MGE-derived 1


title: eH34

value: Glutamatergic 1


title: WT03M_rep1

description: Wild Type


title: eH33


title: eH32


title: TG10M_rep4


title: TG10M_rep5


title: eH30

value: Glutamatergic 2


title: TG10M_rep2


title: TG10M_rep3


title: eH31


title: eH29


title: eH28


title: eH39


title: TG10M_rep1


title: WT10M_rep1

description: Wild Type


title: eH40

value: VZ-derived


title: eH27


title: eH26


title: Common dendritic cell progenitor (CDP)

city: St. Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Department of Pathology

country: USA

institute: Washington University School of Medicine

data_processing:
Single-cell gene measured with the Chromium system using Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10X Genomics). Cell density and viability of sorted cells were determined by Vi-CELL XR cell counter (Beckman Coulter), and all processed samples had cell viability at >90%. The cell density was used to impute volume of single cell suspension needed in the reverse transcription (RT) master mix, to achieve ~6,000 cells per sample.  After Gel Bead-in-Emulsion reverse transcription (GEM-RT) reaction and clean-up, a total of 12 cycles of PCR amplification was performed to obtain cDNAs.  Libraries for RNA-seq were prepared following the manufacturer’s user guide (10x Genomics), profiled using Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified with Kapa Library Quantification Kit (Kapa Biosystems).  Each single-cell RNA-seq library was sequenced in one lane of HiSeq4000 (Illumina).  Sequencing data were pooled from two runs of 4,796 and 4,758 individual cells.  Run 1 had 2,354 median genes and 85,247 means reads per cell. Run 2 had 2,247 median genes and 85,265 mean reads per cell. Sequencing was filtered and processed using the Seurat R toolkit
Genome_build: mm10

source_name: Bone marrow

extract_protocol:
100,000 CDPs (Live,Lineage-CD117intCD135+CD115+MHC-II-CD11c-) cells were sorted and single-cell gene measured with the Chromium system
Chromium Single Cell 3' Library and Gel Bead Kit v2 (10X Genomics)
Library profiled using Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified with Kapa Library Quantification Kit (Kapa Biosystems). Sequenced in one lane of HiSeq4000 (Illumina)

value: Bone marrow

tag: manipulation

value: cell sorting


title: TG03M_rep3


title: TG03M_rep4


title: TG03M_rep2


title: eH25


title: TG03M_rep5


title: TG03M_rep1


title: eH23


title: eH22

value: Cajal Retzius


title: eH21


title: eH20


title: eH19


title: eH16


title: eH17


title: eH15


title: eH14


title: eH24


title: eH13


title: eH11


title: eH12


title: SKNAS JMJD6 shRNA-2, vehicle control, repeat B

type: RNA

city: Sydney

first: matthew

middle: kwok kei

last: wong

state: New South Wales

address: Lowy cancer centre, University of New South Wales

department: histone modification group

country: Australia

institute: Children's Cancer Institute

hyb_protocol: 2.3 ug of fragmented, labeled cDNA was prepared for hybridisation. Samples were hybridised to arrays for 17 hours at 45°C rotating at 60 rpm in the Affymetrix Hybridisation Oven. Arrays were washed on the Affymetrix Fluidics 4500 Station as per manufacturer’s protocol using program FS450_0007.

scan_protocol: Arrays were scanned in the GCS 3000 7G scanner.

data_processing:
The microarray data were analyzed in R (http://www.r-project.org/) with bioconductor packages (http://www.bioconductor.org/), using Robust-Multi-Array Average for normalization.
Limma was used for differential expression analysis (DOXJ2 - NTJ2)-(DOXscr - NTscr) with gene expression normalized to log2-RMA values. Pre-ranked Gene set enrichment analysis (GSEA) was performed by ranking genes with fold change of > 1.5, p-value<0.05 and adjusted p < 0.20 using the t-test statistical value as outputted by Limma. The pre-ranked list was ran against the molecular signature database C3: Motif gene sets.

label: Biotin

organism: Homo sapiens

source_name: Doxycycline inducible JMJD6 shRNA-2 neuroblastoma SK-N-AS cells, treated with vehicle control

label_protocol: We used the Affymerix GeneChip WT Plus Reagent Kit: Manual Target Preparation for GeneChip Whole Transcript Expression Arrays (Affymetrix_WT_Plus_User_Guide). 100 ng of total RNA was used for input.

growth_protocol: Stable Doxycycline inducible JMJD6 shRNA-1,  JMJD6 shRNA-2 and Control shRNA CHP-134 neuroblastoma cells were cultured in Roswell Park Memorial Institute medium (RPM1) supplemented with 10% fetal calf serum and 1% L-glutamine.. Stable Doxycycline inducible JMJD6 shRNA-2, and Control shRNA SK-N-AS neuroblastoma cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum.

extract_protocol: Total RNA was extracted using Rneasy kit (Qiagen, Hamburg, Germany) according to the manufacturer's instructions.

treatment_protocol: Stable Doxycycline inducible JMJD6 shRNA, and Control shRNA CHP-134 and SKN-N-AS neuroblastoma cells were treated with 2ug/ml Doxycycline media or vehicle control media for 40 hours.

value: Human brain tissue; derived from metastatic site:bone marrow

tag: cell line

value: SK-N-AS neuroblastoma cells

tag: shRNA

value: JMJD6 shRNA-2

tag: treatment

value: vehicle control


title: SKNAS SCR Control shRNA, vehicle control, repeat B

source_name: Doxycycline inducible SCR shRNA neuroblastoma SK-N-AS cells, treated with vehicle control

value: SCR shRNA


title: SKNAS JMJD6 shRNA-2, vehicle control, repeat C


title: SKNAS JMJD6 shRNA-2, doxycycline, repeat C

source_name: Doxycycline inducible JMJD6 shRNA-2 neuroblastoma SK-N-AS cells, treated with doxycycline

value: doxycycline


title: SKNAS JMJD6 shRNA-2, vehicle control


title: SKNAS SCR Control shRNA, doxycycline, repeat C

source_name: Doxycycline inducible SCR shRNA neuroblastoma SK-N-AS cells, treated with doxycycline


title: SKNAS SCR Control shRNA, vehicle control, repeat C


title: eH10

value: Neural embryonic cell

value: Htr3a Cre line


title: SKNAS SCR Control shRNA, doxycycline, repeat B


title: eH9

value: Passed


title: Batf3 KO pre-cDC1 cDC2-2

description: cDC2 derived from Batf3 KO pre-cDC1

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: cDC2 derived from Batf3 KO pre-cDC1

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: Bone marrow was harvested from the femur, tibia, and pelvis of mice. Bones were collected and fragmented by mortar and pestle in MACS buffer, and debris was removed by passing cells through a 70-um stainer. RBCs were lysed with ACK lysis buffer. Pre-cDC1s were identified as either Lin–CD117intCD135+Zbtb46-GFP+ or as Lin–CD117intCD135+CD226+. Pre-cDC2s were identified as Lin—CD117loCD135+CD115+. Lineage markers included CD3, CD19, CD105, CD127, NK1.1, Ter119, and Ly6G.DC progenitors were cultured at 37⁰C in 200 µL total volume of cIMDM supplemented with 100 ng/mL Flt3L (Peprotech) for five days before sorting cDC2s derived from in vitro culture of Batf3–/– or IRF8 +32 kb KO pre-cDC1s, cDC1s derived from in vitro culture of WT pre-cDC1s, or cDC2s derived from in vitro culture of WT pre-cDC2s

value: bone marrow; Flt3L in vitro culture


title: 32 KO pre-cDC1 cDC2-2

description: cDC2 derived from 32 KO pre-cDC1

source_name: cDC2 derived from 32 KO pre-cDC1


title: WT pre-cDC2-cDC2-2

description: cDC2 derived from WT pre-cDC2

source_name: cDC2 derived from WT pre-cDC2


title: 32 KO pre-cDC1 cDC2

description: cDC2 derived from 32 KO pre-cDC1


title: WT pre-cDC1-cDC1-2

description: cDC1 derived from WT pre-cDC1

source_name: cDC1 derived from WT pre-cDC1


title: WT CD172a+_2

description: Splenic CD172a+

source_name: Splenic CD172a+

treatment_protocol: Splenic WT CD24+CD17a+ cDC2, WT CD24+ cDC1, and WT CD24-CD172a+ cDC2 were sorted for RNA extraction and hybridization on Affymetrix microarrays.

value: Spleen


title: SKNAS JMJD6 shRNA-2, doxycycline, repeat B


title: WT pre-cDC1-cDC1

description: cDC1 derived from WT pre-cDC1


title: SKNAS SCR Control shRNA, doxycycline


title: SKNAS JMJD6 shRNA-2, doxycycline


title: SKNAS SCR Control shRNA, vehicle control


title: CHP134 JMJD6 shRNA-1, doxycycline, repeat F

source_name: Doxycycline inducible JMJD6 shRNA-1  neuroblastoma CHP-134  cells, treated with doxycycline

value: Human neuroblastoma tumor mass of left adrenal gland

value: CHP134 MYCN-amplified neuroblastoma cells

value: JMJD6 shRNA-1


title: WT pre-cDC2-cDC2

description: cDC2 derived from WT pre-cDC2


title: WT CD24+CD172a+_1

description: Splenic CD24+CD172a+

source_name: Splenic CD24+CD172a+


title: WT CD172a+_1

description: Splenic CD172a+


title: WT CD24+CD172a+_2

description: Splenic CD24+CD172a+


title: eH7

value: MGE-derived 1


title: CHP134 SCR Control shRNA, doxycycline, repeat F

source_name: Doxycycline inducible SCR shRNA neuroblastoma CHP-134  cells, treated with doxycycline


title: WT CD24+_1

description: Splenic CD24+

source_name: Splenic CD24+


title: eH8


title: WT CD24+_2

description: Splenic CD24+


title: eH5


title: eH4

value: Undefined


title: Id2 KO Zbtb46-GFP+ rep 1

description: Zbtb46-GFP+cKit intermediate cells from Id2 KO Zbtb46-GFP chimeric mice

treatment_protocol: BM was harvested from the pelvis, tibia and femurs, collected by spinning at 3000g, re-suspended in PBS supplemented with 0.5% BSA and 2mM EDTA, then was passed through a 70-µm filter. Red blood cells were lysed with ammonium chloride-potassium bicarbonate lysis buffer. A FACSAria Fusion was used for sorting cells into IMDM plus 10% FBS with 5% Flt3L conditioned media.

value: Zbtb46-GFP+cKit intermediate cells

value: bone marrow

tag: genotype

value: Id2 KO Zbtb46-GFP chimeric mice


title: eH2

value: Glutamatergic 2


title: Id2 KO Zbtb46-GFP+ rep 2

source_name: Zbtb46-GFP+cKit intermediate cells from Id2 KO Zbtb46-GFP chimeric mice


title: Id2 KO CDP rep 1

description: CDPs from Id2 KO Zbtb46-GFP chimeric mice

value: CDPs


title: CHP134 SCR Control shRNA, vehicle control, repeat F

source_name: Doxycycline inducible SCR shRNA neuroblastoma CHP-134  cells, treated with vehicle control

value: SCR shRNA

value: vehicle control


title: CHP134 JMJD6 shRNA-1, doxycycline, repeat E

value: doxycycline


title: Id2 KO Zbtb46-GFP+ rep 3


title: eH3

source_name: Neural embryonic cell

value: Neural embryonic cell

value: Htr3a Cre line


title: eH6

value: Cajal Retzius

value: Passed


title: Batf3 KO pre-cDC1 cDC2

description: cDC2 derived from Batf3 KO pre-cDC1

value: bone marrow; Flt3L in vitro culture


title: Batf3 KO Zbtb46-GFP+ rep 3

description: Zbtb46-GFP+cKit intermediate cells from Batf3 KO Zbtb46-GFP mice

value: Batf3 KO Zbtb46-GFP mice


title: CHP134 JMJD6 shRNA-1, vehicle control, repeat F

source_name: Doxycycline inducible JMJD6 shRNA-1 neuroblastoma CHP-134  cells, treated with vehicle control

value: Human neuroblastoma tumor mass of left adrenal gland

value: CHP134 MYCN-amplified neuroblastoma cells

value: JMJD6 shRNA-1


title: Id2 KO CDP rep 2

source_name: CDPs from Id2 KO Zbtb46-GFP chimeric mice


title: Batf3 KO Zbtb46-GFP+ rep 2

source_name: Zbtb46-GFP+cKit intermediate cells from Batf3 KO Zbtb46-GFP mice

value: Zbtb46-GFP+cKit intermediate cells


title: Batf3 KO CDP rep 2

description: CDPs from Batf3 KO Zbtb46-GFP reporter mice

value: bone marrow


title: Batf3 KO Zbtb46-GFP+ rep 1


title: CHP134 SCR Control shRNA, vehicle control, repeat E


title: WT Zbtb46-GFP+ rep 1

description: Zbtb46-GFP+cKit intermediate cells from Zbtb46-GFP chimeric mice

value: Zbtb46-GFP chimeric mice


title: CHP134 JMJD6 shRNA-1, vehicle control, repeat E


title: eH1

value: Undefined


title: L46

value: Lhx6 Cre line

value: MGE-derived 2


title: WT Zbtb46-GFP+ rep 3

source_name: Zbtb46-GFP+cKit intermediate cells from Zbtb46-GFP chimeric mice


title: WT CDP rep 1

description: CDPs from Zbtb46-GFP chimeric mice

source_name: CDPs from Zbtb46-GFP chimeric mice

value: CDPs


title: WT Zbtb46-GFP+ rep 2


title: Batf3 KO CDP rep 1

source_name: CDPs from Batf3 KO Zbtb46-GFP reporter mice


title: L45

description:
ENS_counts.tsv
gene_counts.tsv

value: Failed


title: CHP134 SCR Control shRNA, doxycycline, repeat E

value: SCR shRNA

value: doxycycline


title: WT CDP rep 2

description: CDPs from Zbtb46-GFP chimeric mice


title: Id2 KO cDC2 rep 2

description: Splenic cDC2 from Id2 KO Zbtb46-GFP chimeric mice

hyb_protocol: Following fragmentation with NuGen Encore Biotin Module,2.5 ug of cDNA were hybridized into the GeneChip Hybridization Oven 640 for 18 hr at 45C on Gene 1.0 ST Array. GeneChip were washed and stained in the Affymetrix Fluidics Station 450.

label_protocol: Biotinylated cDNA were prepared according to the standard NuGen Ovation PicoSL WTA System V2 system from 500pg-50 ng total RNA.

treatment_protocol: cDC2 were harvested from spleen and red blood cells were lysed with ammonium chloride-potassium bicarbonate lysis buffer. A FACSAria Fusion was used for sorting cells into FACS buffer.

value: Splenic cDC2

value: spleen

value: Id2 KO Zbtb46-GFP chimeric mice


title: CHP134 JMJD6 shRNA-1, doxycycline, repeat B


title: L21

value: Neural embryonic cell

value: Passed


title: L20


title: CHP134 SCR Control shRNA, doxycycline, repeat B duplicate

value: Human neuroblastoma tumor mass of left adrenal gland

value: CHP134 MYCN-amplified neuroblastoma cells


title: WT cDC2 rep 1

description: Splenic cDC2 from Zbtb46-GFP chimeric mice


title: Id2 KO cDC2 rep 1

source_name: Splenic cDC2 from Id2 KO Zbtb46-GFP chimeric mice


title: WT cDC2 rep 2

source_name: Splenic cDC2 from Zbtb46-GFP chimeric mice


title: ZI DKO - rep1

description: cDC1s from Zeb2 Id2 DKO mouse spleen

source_name: cDC1s from Zeb2 Id2 DKO mouse spleen

treatment_protocol: Spleens were minced and digested with stirring for 30 min at 37ºC in 5ml of IMDM plus 10% FBS with 30U/ml DNaseI (Sigma-Aldrich) and 250ug/ml collagenase B (Roche). For removal of debris, cells were passed through a 70-µm filter before red blood cells were lysed with ammonium chloride–potassium bicarbonate lysis buffer.

value: Zeb2 Id2 DKO


title: CHP134 JMJD6 shRNA-1, vehicle control, repeat B

value: JMJD6 shRNA-1

value: vehicle control


title: CHP134 SCR Control shRNA, doxycycline, repeat A duplicate


title: ZN DKO - rep2

description: cDC1s from Nfil3 Zeb2 DKO mouse spleen

source_name: cDC1s from Nfil3 Zeb2 DKO mouse spleen

value: Nfil3 Zeb2 DKO


title: ZI DKO - rep2

description: cDC1s from Zeb2 Id2 DKO mouse spleen


title: CHP134 SCR Control shRNA, vehicle control, repeat B duplicate


title: L22

value: Lhx6 Cre line

value: Undefined


title: CHP134 JMJD6 shRNA-1, doxycycline, repeat A

source_name: Doxycycline inducible JMJD6 shRNA-1  neuroblastoma CHP-134  cells, treated with doxycycline


title: ZKO - rep2

description: cDC1s from Zeb2 KO mouse spleen

source_name: cDC1s from Zeb2 KO mouse spleen

value: Zeb2 KO


title: ZKO - rep3

description: cDC1s from Zeb2 KO mouse spleen


title: ZN DKO - rep1

description: cDC1s from Nfil3 Zeb2 DKO mouse spleen


title: WT - rep3

description: cDC1s from WT mouse spleen

source_name: cDC1s from WT mouse spleen

value: WT


title: CHP134 SCR Control shRNA, vehicle control, repeat A duplicate

value: SCR shRNA


title: CHP134 JMJD6 shRNA-1, vehicle control, repeat A


title: L17

value: VZ-derived


title: L18

description:
ENS_counts.tsv
gene_counts.tsv

value: Failed


title: ZKO - rep1

description: cDC1s from Zeb2 KO mouse spleen

value: spleen


title: L19

description:
ENS_counts.tsv
gene_counts.tsv


title: L16

value: MGE-derived 1


title: WT - rep2

description: cDC1s from WT mouse spleen


title: L15

value: Neural embryonic cell


title: WT - rep1

description: cDC1s from WT mouse spleen


title: L14

description:
ENS_counts.tsv
gene_counts.tsv


title: Id2-GFP+ pre-CD8 rep 1

description: Id2-GFP+ pre-CD8s from Id2-IRES-GFP reporter mouse

value: Id2-GFP+ pre-CD8s

value: bone marrow

value: heterozygous Zbtb46-GFP reporter mice


title: L12

value: GABAergic

value: Passed


title: L9


title: Id2-GFP- pre-CD8 rep 2

description: Id2-GFP- pre-CD8s from Id2-IRES-GFP reporter mouse

value: Id2-GFP- pre-CD8s


title: CHP134 JMJD6 shRNA-2 doxycycline, repeat D

source_name: Doxycycline inducible JMJD6 shRNA-2 neuroblastoma CHP-134  cells, treated with doxycycline

value: Human neuroblastoma tumor mass of left adrenal gland

value: CHP134 MYCN-amplified neuroblastoma cells

value: JMJD6 shRNA-2

value: doxycycline


title: Id2-GFP- pre-CD8 rep 1

source_name: Id2-GFP- pre-CD8s from Id2-IRES-GFP reporter mouse


title: Id2-GFP+ pre-CD8 rep 2

source_name: Id2-GFP+ pre-CD8s from Id2-IRES-GFP reporter mouse


title: CHP134 JMJD6 shRNA-2, vehicle control, repeat D

source_name: Doxycycline inducible JMJD6 shRNA-2 neuroblastoma CHP-134  cells, treated with vehicle control

value: vehicle control


title: Id2-GFP+CDP rep 1

description: Id2-GFP+ CDPs from Id2-IRES-GFP reporter mouse

value: Id2-GFP+ CDPs


title: L13

source_name: Neural embryonic cell

value: Lhx6 Cre line


title: Id2-GFP-CDP rep 1

description: Id2-GFP- CDPs from Id2-IRES-GFP reporter mouse

value: Id2-GFP- CDPs

value: heterozygous Id2-IRES-GFP reporter mice


title: Zeb2low CDPs - rep2

description: Zeb2low CDPs from Zeb2-GFP reporter BM

source_name: Zeb2low CDPs from Zeb2-GFP reporter BM

value: Zeb2low CDPs

value: heterozygous Zeb2-GFP fusion reporter


title: Zeb2low CDPs - rep3

description: Zeb2low CDPs from Zeb2-GFP reporter BM


title: Id2-GFP-CDP rep 2

source_name: Id2-GFP- CDPs from Id2-IRES-GFP reporter mouse


title: Id2-GFP+CDP rep 2

source_name: Id2-GFP+ CDPs from Id2-IRES-GFP reporter mouse


title: CHP134 JMJD6 shRNA-2, vehicle control, repeat C


title: Zeb2low CDPs - rep1

description: Zeb2low CDPs from Zeb2-GFP reporter BM


title: CHP134 JMJD6 shRNA-2 doxycycline, repeat C


title: Zeb2hi CDPs - rep2

description: Zeb2hi CDPs from Zeb2-GFP reporter BM

source_name: Zeb2hi CDPs from Zeb2-GFP reporter BM

value: Zeb2hi CDPs


title: Zeb2hi CDPs - rep3

description: Zeb2hi CDPs from Zeb2-GFP reporter BM

value: bone marrow


title: CHP134 SCR Control shRNA, doxycycline, repeat D

source_name: Doxycycline inducible SCR shRNA neuroblastoma CHP-134  cells, treated with doxycycline

value: SCR shRNA


title: L7

value: Neural embryonic cell

value: MGE-derived 1


title: CHP134 SCR Control shRNA, vehicle control, repeat C

source_name: Doxycycline inducible SCR shRNA neuroblastoma CHP-134  cells, treated with vehicle control


title: Zeb2hi CDPs - rep1

description: Zeb2hi CDPs from Zeb2-GFP reporter BM


title: CHP134 SCR Control shRNA, doxycycline, repeat C


title: CHP134 SCR Control shRNA, vehicle control, repeat D


title: Pre-CD8 DCs (Zeb2) - rep2

description: Pre-CD8 DCs from Zeb2-GFP reporter BM

source_name: Pre-CD8 DCs from Zeb2-GFP reporter BM

value: Pre-CD8 DCs


title: L6

value: MGE-derived 2

value: Passed


title: L8

description:
ENS_counts.tsv
gene_counts.tsv

value: Failed


title: L5


title: Pre-CD8 DCs (Zeb2) - rep1

description: Pre-CD8 DCs from Zeb2-GFP reporter BM


title: Pre-CD8 DCs - rep2

description: Pre-CD8 DCs from Zbtb46-GFP reporter BM

source_name: Pre-CD8 DCs from Zbtb46-GFP reporter BM

value: heterozygous Zbtb46-GFP reporter mice


title: L4


title: L3


title: CHP134 JMJD6 shRNA-2 doxycycline, repeat B

value: Human neuroblastoma tumor mass of left adrenal gland

value: CHP134 MYCN-amplified neuroblastoma cells

value: JMJD6 shRNA-2

value: doxycycline


title: Pre-CD8 DCs - rep3

description: Pre-CD8 DCs from Zbtb46-GFP reporter BM


title: L2

value: Lhx6 Cre line


title: L1


title: Pre-CD8 DCs - rep1

description: Pre-CD8 DCs from Zbtb46-GFP reporter BM


title: 1mA 2nd miCLIP HEK 293T Diagenode replicate 1

city: New York

first: Anya

last: Grozhik

state: New York

address: 1300 York Ave, Room LC-523

institute: Weill Cornell Medicine

data_processing:
Reads resulting from 1mA miCLIP or RNA-Seq library sequencing were trimmed of the 3’ linker sequence (5’ AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGAC 3’) and barcoded reverse transcription primer sequences (5’ NNXXXXNNNAGATCGGAAGAGCGTCGTGT 3’, where N = random nucleotide, and XXXX = fixed barcode sequence; barcode sequences correspond to iCLIP barcodes in Konig et al., Nature Structural and Molecular Biology, 2010) using Flexbar (version 2.5). To demultiplex reads belonging to individual biological replicates, the pyBarcodeFilter.py script of the pyCRAC suite (version 1.2.2) was used to demultiplex the samples based on the fixed portion of the reverse transcription barcode. The random portion of the reverse transcription barcode was then moved into the sequence header using a custom awk script. PCR duplicates were collapsed using pyFastqDuplicateRemover.py of the pyCRAC suite. Finally, reads were aligned to hg19 for HEK 293T cells or mm10 for mouse brain using Bowtie (version 1.1.2; command: bowtie -f -s 0 -v 2 -m 10 --best --maxbts 800 --strata -S /genomeindex input.fasta output.sam). To view aligned reads in a genome browser, .sam files produced by Bowtie were converted to .bedgraph files of reads and 5’ ends of reads (“terminations”) using bedtools (version 2.25.0). 1mA miCLIP clusters of unique reads were generated using the CIMS software package for analysis of HITS-CLIP data (Moore, Zhang, et al., Nature Protocols, 2014); HEK 293T clusters have a minimum score of 20, and mouse brain clusters have a minimum score of 5.
Genome_build: Human: hg19; Mouse: mm10.
Supplementary_files_format_and_content:
HEK293T.1mA.2nd.miCLIP.abcam.rep*.bed: Genomic coordinates of HEK293T cell 1mA 2nd miCLIP (abcam antibody) unique reads
HEK293T.1mA.2nd.miCLIP.diagenode.rep*.bed: Genomic coordinates of HEK293T cell 1mA 2nd miCLIP (diagenode antibody) unique reads
HEK293T.1mA.2nd.miCLIP.MBL.rep*.bed: Genomic coordinates of HEK293T cell 1mA 2nd  miCLIP (MBL antibody) unique reads
HEK293T.1mA.2nd.miCLIP.abcam.rep*.bedgraph: Coverage file of HEK293T cell 1mA 2nd miCLIP (abcam antibody)
HEK293T.1mA.2nd.miCLIP.diagenode.rep*.bedgraph: Coverage file of HEK293T cell 1mA 2nd miCLIP (diagenode antibody)
HEK293T.1mA.2nd.miCLIP.MBL.rep*.bedgraph: Coverage file of HEK293T cell 1mA 2nd miCLIP (MBL antibody)

molecule: polyA RNA

source_name: 1mA 2nd miCLIP HEK 293T Diagenode

growth_protocol: HEK 293T cells were grown at 37°C in DMEM media that was supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
Total RNA from HEK 293T cells (N = 2 biological replicates) or whole mouse brain (N = 3 biological replicates per experimental group) was extracted using TRIzol (ThermoFisher) and treated with RQ1 RNase-free DNase I (Promega) according to the manufacturers’ instructions. Poly(A) RNA was then isolated using one round of selection with oligo(dT) magnetic beads (New England Biolabs). This resulted in approximately 10 μg of poly(A) RNA for each replicate used in this study.
1mA miCLIP was performed exactly as previously described(Linder et al., Nature Methods, 2015), with the following modifications: mRNA was subjected to fragmentation using RNA Fragmentation Reagents (ThermoFisher). Fragmentation was allowed to proceed for exactly 12 minutes at 75°C. Fragmented RNA was then incubated with anti-1mA antibody and the antibody-RNA complexes were processed for crosslinking, immunoprecipitation, RNA linker ligation, purification, and reverse transcription exactly as previously described(Linder et al., Nature Methods, 2015). For mouse brain samples, immunoprecipitated antibody-RNA complexes were mock-treated or treated with AlkB prior to RNA linker ligation. Reverse transcription incorporated use of barcoded primers to allow downstream pooling of libraries. Following reverse transcription of RNA-peptide complexes, first-strand cDNA was circularized using CircLigase II ssDNA Ligase (EpiBio) to preserve the 3’ end of the cDNA, and thus, sites of 1mA-induced terminations of reverse transcription. To generate priming sites for library amplification, the cDNA was cut in the middle of its priming sequence (green bar in Fig. 2a) using a small single-stranded oligo complementary to the priming sequence and FastDigest BamHI restriction digest (ThermoFisher), as previously described(Linder et al., Nature Methods, 2015). This generated priming sites for the Illumina P5 and P3 primers on either side of the cDNA. For library amplification, Accuprime Supermix I (ThermoFisher) and Illumina P5 and P3 primers were used. PCR amplification cycle number was selected as previously described(Grozhik et al., Methods in Molecular Biology, 2017). Amplified libraries were then pooled and cleaned up using a 1.8X ratio of AMPure XP magnetic beads (Beckman Coulter). Libraries were subjected to next-generation sequencing at the Epigenomics Core of Weill Cornell Medicine. Libraries were sequenced on an Illumina HiSeq 2500/ MiSeq instrument in single-end or paired-end mode to generate 50-base single or paired-end reads.

treatment_protocol: No treatments applied prior to RNA extraction.

value: HEK 293T

tag: passage

tag: antibody

value: Anti-1mA Diagenode C15200235


title: 1mA 2nd miCLIP HEK 293T Abcam replicate 2

source_name: 1mA 2nd miCLIP HEK 293T Abcam

value: Anti-1mA Abcam ab208196


title: 1mA 2nd miCLIP HEK 293T Diagenode replicate 2


title: CHP134 SCR Control shRNA, doxycycline, repeat B


title: Zbtb46+ CDPs - rep3

description: Zbtb46+ CDPs from Zbtb46-GFP reporter BM

value: Zbtb46+ CDPs

value: bone marrow


title: 1mA 2nd miCLIP HEK 293T Abcam replicate 1


title: Zbtb46+ CDPs - rep2

source_name: Zbtb46+ CDPs from Zbtb46-GFP reporter BM


title: Zbtb46- CDPs - rep3

description: Zbtb46- CDPs from Zbtb46-GFP reporter BM

value: Zbtb46- CDPs


title: Zbtb46- CDPs - rep1

source_name: Zbtb46- CDPs from Zbtb46-GFP reporter BM


title: Zbtb46+ CDPs - rep1


title: Day3 C9-ALS2 iMN APC REPLICATE 2 (D3_APC_r2)

status: Public on Jun 22 2019

city: Los Angeles

first: Justin

last: Ichida

state: CA

address: 1425 San Pablo Street, BCC 305

department: Department of Stem Cell Biology and Regenerative Medicine

institute: University of Southern California

description: induced motor neurons converted from secondary fibroblasts

data_processing:
Reads were aligned to the hg38 transcriptome using aligner HISAT2 (v.2.1.0).
A gene count table was obtained using FeatureCounts (v.1.6.1) with strand specificity enabled.
Differential expression analysis was performed using DESeq2 (v.1.18.1).
Pathway enirchment analysis was performed by providing Enirchr web tool (accessed Jan, 2019) with a list of all genes identified by DESeq2 as having a greater than 95% chance of being deferentially expressed.
Computations were performed on the High Performing-Computing Cluster supported by the University of Southern California.
Supplementary_files_format_and_content: Reference files of the human genome build hg38 (Assembly provider ID: GRCh38), corresponding transcript annotation files (ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38_snp.tar.gz), as well as FeatureCounts (v.1.6.1) build-in Gene ID annotations, which were later translated into EntrezID.

source_name: C9-ALS2 Hb9::RFP+ iMNs, APC treatment, 3 days after withdrawal of neurotrophic factors, biological replicate 2, FACS-sorted (RFP+)

growth_protocol: Secondary fibroblasts were cultured in DMEM + 10% FBS, induced motor neurons were cultured in N3 medium

extract_protocol:
mRNA was extracted using NEBNext Poly(A) mRNA Magnetic Isolation Module according to the manufacturer's instructions
3'-Digital Gene Expression RNAseq Library Kit (3’-DGE)
3' RNA-seq libraries were generated using the3'-Digital Gene Expression RNAseq Library Kit at Amaryllis Nucleics, according to the manufacturers’ directions. Libraries were sequenced at the Amarillis Nucleics on a Illumina NextSeq 500 sequencer. A total of 10–25 million 80 bp, single end reads were obtained for each sample.

treatment_protocol: Secondary fibroblasts were converted into motor neurons by retroviral transduction with vectors encoding Ascl1, Myt1l, Brn2, Lhx3, Isl1, Ngn2, and Hb9. Motor neurons were treated with InAPC or APC.

value: C9-ALS2 Hb9::RFP+ iMNs, FACS-sorted (RFP+)

value: APC treatment

tag: timing

tag: replicates

value: biological replicate 2


title: Zbtb46- CDPs - rep2


title: CHP134 SCR Control shRNA, vehicle control, repeat B

value: SCR shRNA

value: vehicle control


title: CHP134 SCR Control shRNA, doxycycline, repeat A


title: CHP134 JMJD6 shRNA-2, vehicle control, repeat B


title: Day3 C9-ALS2 iMN InAPC REPLICATE 2 (D3_InAPC_r2)

source_name: C9-ALS2 Hb9::RFP+ iMNs, InAPC treatment, 3 days after withdrawal of neurotrophic factors, biological replicate 2, FACS-sorted (RFP+)

value: InAPC treatment


title: CHP134 SCR Control shRNA, vehicle control, repeat A

value: Human neuroblastoma tumor mass of left adrenal gland


title: CHP134 JMJD6 shRNA-2, vehicle control, repeat A

value: CHP134 MYCN-amplified neuroblastoma cells


title: 1mA 2nd miCLIP HEK 293T MBL replicate 2

source_name: 1mA 2nd miCLIP HEK 293T MBL

value: Anti-1mA MBL D345-3


title: 1mA 2nd miCLIP HEK 293T MBL replicate 1


title: Day3 C9-ALS2 iMN InAPC REPLICATE 1 (D3_InAPC_r1)

source_name: C9-ALS2 Hb9::RFP+ iMNs, InAPC treatment, 3 days after withdrawal of neurotrophic factors, biological replicate 1, FACS-sorted (RFP+)

value: biological replicate 1


title: CHP134 JMJD6 shRNA-2 doxycycline, repeat A

source_name: Doxycycline inducible JMJD6 shRNA-2 neuroblastoma CHP-134  cells, treated with doxycycline

value: JMJD6 shRNA-2

value: doxycycline


title: 5637_ctrl-2_S8

city: Livermore

first: Kelly

last: Martin

address: 7000 East Ave

institute: LLNL

data_processing:
Sequenced reads were mapped to the human genome hg38 using STAR (version 2.6.0c)
After read mapping, ‘featureCounts’ from Rsubread package (version 1.30.5) was used to generate gene-wise read counts.
Data was normalized using TMM normalization in edgeR
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include TMM normalized CPM values for each Sample .

growth_protocol: 5637 cells were grown in DMEM/F-12 cell culture media supplemented with 5% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
Qiagen RLT buffer supplemented with beta-mercaptoethanol was used to isolate RNA directly 48 hours post transfection, for subsequent RNA isolation using Qiagen RNeasy spin column kit
Libraries for sequencing were prepared using Illumina TruSeq RNA Preparation Low Sample kit version 2.0
Libraries were run on an Illumina NextSeq500 using High Output 75 cycles kit (2 x 36 cycles, single-end reads, single index)

treatment_protocol: At 50% confluency, cells were transfected using Lipofectamine 3000 to overexpress MAT1A, control cells were transfected with an empty vector control

value: 5637 bladder cancer cell line

value: control


title: 5637_ctrl-3_S9


title: 5637_ctrl-1_S7


title: HSC_TGFB_3

first: Giuseppe

middle: Alessandro

last: D'Agostino

state: Singapore

address: 11 Mandalay Road

institute: Lee Kong Chian School of Medicine - NTU

data_processing:
Sequenced libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option
Adapter sequences were then trimmed using trimmomatic6 v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35. For reference, the adapter sequences are:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA (read 1) and AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT (read 2)
Trimmed reads were aligned to human genome hg38 or mouse genome mm10 using STAR v. 2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v. 1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
Genome_build: Homo sapiens hg38 Ensembl release 86 and Mus musculus mm10 Ensembl release 86
Supplementary_files_format_and_content: Gene-level counts calculated by FeatureCounts (.txt)

source_name: hepatic stellate cells

extract_protocol:
Total RNA was extracted from either the snap-frozen liver tissues or HSCs lysate using Trizol (Invitrogen) followed by RNeasy column (Qiagen) purification.
Truseq Stranded mRNA (Poly A selection) kit

treatment_protocol: HSCs (5300, ScienCell) were cultured in stellate cells complete media (5301, ScienCell) on poly-L-lysine-coated plates (2 µg/cm2, 0403, ScienCell) and maintained at 37°C and 5% CO2 .The growth medium was renewed every 2–3 days and cells were passaged at 80-90% confluence using standard trypsinization techniques. All the experiments were carried out at low cell passage (P1-P2). Cells were serum-starved for 16 h prior to stimulations. Stimulated cells were compared to unstimulated cells that have been grown for the same duration under the same conditions (serum-free media), but without the stimuli.

value: hepatic stellate cells

tag: diet

value: TGFB1 + IgG

tag: time of treatment

value: 24 hours

tag: rin


title: HSC_TGFB_2

tag: tissue

tag: strain


title: 5637_Mat1a-1_S10

value: MAT1A overexpression


title: 5637_Mat1a-3_S12


title: HSC_BSL_2


title: Liver_sample_24: HFMCD_X203_6weeks_rep3

source_name: liver tissue

treatment_protocol: Five week old male C57BL/6N mice were fed with Methionine and Choline deficient diet supplemented with 60 kcal% fat (A06071301B16, Research Diets); control mice were fed with normal chow (NC, Specialty Feeds). Durations of diet and antibody therapies are outlined in the main text.

value: liver

value: HFMCD

value: 6 weeks


title: HSC_TGFB_1


title: HSC_BSL_3


title: Liver_sample_17: HFMCD_IgG_6weeks_rep2

value: IgG


title: Liver_sample_21: HFMCD_X209_6weeks_rep3


title: Liver_sample_20: HFMCD_X209_6weeks_rep2


title: Liver_sample_19: HFMCD_X209_6weeks_rep1


title: Liver_sample_23: HFMCD_X203_6weeks_rep2


title: Liver_sample_14: NCD_6weeks_rep2

value: NCD


title: Liver_sample_18: HFMCD_IgG_6weeks_rep3


title: Liver_sample_10: HFMCD_X203_3weeks_rep1

value: 3 weeks


title: 5637_Mat1a-2_S11


title: Day3 C9-ALS2 iMN APC REPLICATE 1 (D3_APC_r1)

source_name: C9-ALS2 Hb9::RFP+ iMNs, APC treatment, 3 days after withdrawal of neurotrophic factors, biological replicate 1, FACS-sorted (RFP+)

value: C9-ALS2 Hb9::RFP+ iMNs, FACS-sorted (RFP+)

value: APC treatment


title: Liver_sample_11: HFMCD_X203_3weeks_rep2


title: Liver_sample_9: HFMCD_X209_3weeks_rep3


title: Liver_sample_15: NCD_6weeks_rep3


title: Liver_sample_12: HFMCD_X203_3weeks_rep3


title: Liver_sample_8: HFMCD_X209_3weeks_rep2


title: Liver_sample_22: HFMCD_X203_6weeks_rep1


title: HSC_BSL


title: Liver_sample_6: HFMCD_IgG_3weeks_rep3


title: Liver_sample_7: HFMCD_X209_3weeks_rep1


title: Liver_sample_1: NCD_3weeks_rep1


title: Liver_sample_2: NCD_3weeks_rep2


title: Liver_sample_16: HFMCD_IgG_6weeks_rep1


title: CSB+H3K9me3 ChIP input for rK9

city: Baltimore

first: Jong-Hyuk

last: Lee

state: Maryland

address: 251 Bayview BLVD

institute: National Institute of Health

description: H3K9me3 input

library_source: genomic

data_processing:
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data.
Sequencing reads were mapped against the human genome (GRCh37/hg19) using Bowtie for Illumina with default parameters
The SAM format outputs were sorted by genomic coordinates and uniquely mapped reliable reads were used in subsequent steps. SAM files were preprocessed using SAMtools
We used the MACS tool to select regions that were enriched for H3K9me3 and PAR. We applied the default settings and found significant regions (P-value ≤ 10-5), using non-IP chromatin as a control to eliminate unspecific signals.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with called peaks, bw files with coverage

molecule: genomic DNA

source_name: Patient cells

growth_protocol: SV40-transformed CS1AN cells stably transfected with either CSB or empty vectors were cultured in DMEM supplemented with 10% FBS, 1% pen-strep, and 400 µg/ml geneticin and grown in 20% O2/5% CO2 at 37°C.

extract_protocol:
CSB cells were cross-linked in a solution of 1% formaldehyde in PBS for 10 min at room temperature. The cross-linking reaction was stopped by adding glycine to a final concentration of 0.125 M. The cells were harvested and washed three times with cold PBS, and cytosolic fractions were eliminated with buffer A (5 mM PIPES (pH 8.0), 85 mM KCl, 0.5% NP-40, protease inhibitor cocktail (GenDEPOT, Katy, TX, USA)). Nuclear pellets were resuspended in buffer B (100 mM Tris-Cl (pH 8.1), 1% sodium dodecyl sulfate (SDS), 10 mM EDTA, protease inhibitor cocktail), and the chromatin was sheared with S-450 sonicator (Branson, Danbury, CT, USA). Sonication condition was optimized by analyzing purified DNA samples with BIOANALYZER (Agilent, DNA1000 Kit)The prepared chromatin fraction (500 μg total sheared DNA per sample) was diluted 1/10 in IP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-Cl (pH 8.1), 167 mM NaCl and a protease inhibitor cocktail) and incubated with antibodies, overnight at 4 °C. Samples were incubated for 2–4 h at 4 °C with protein A or G beads. Then the beads were washed with TSE150 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl (pH 8.1), 150 mM NaCl), TSE500 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-Cl (pH 8.1), 500 mM NaCl), Buffer III (0.25 M LiCl, 1% NP-40, 1% sodium deoxycholate, 1 mM EDTA, 10 mM Tris-Cl (pH 8.1)) and two times with TE (pH 8.0) for 10 min in each solution. Bead-bound chromatin was eluted with elution buffer (1% SDS, 0.1 M NaHCO3 (pH 8.0)) for 1-2 hours at 65.5 °C. The supernatant containing the chromatin, without the beads, was isolated and incubated overnight at 65 °C with 200 mM NaCl to reverse cross-linking. Five hundred microliters of the sample were incubated at 50 °C after adding 10 μl of 0.5 M EDTA, 20 μl of 1 M Tris (pH 6.5) and 4 μl of Proteinase K (20 mg ml−1) and then purified with phenol/chloroform/isoamyl alcohol. Nucleic acids were precipitated by centrifugation for 30 min at 4 °C after mixing the sample with 1 μl of glycogen solution (20 mg ml−1), 20 μl 5 M NaCl and 500 μl isopropanol. Purified nucleic acid pellets were washed with 70% ethanol, dried and dissolved in nuclease-free water.
Library construction according to the manufacturer's protocol

treatment_protocol: 2.5 mM H2O2 for 30minutes, 10 or 50 ng/ml of doxycycline for 72 hours

value: Fibroblast

tag: cell line description

value: CS1AN cells that stably expressing wild type CSB that used for rK9 peak calling


title: Liver_sample_13: NCD_6weeks_rep1


title: CSB+H3K9me3 ChIP for rK9

description: H3K9me3 ChIP

tag: chip antibody

value: anti-H3K9me3, Millipore 07-442


title: SETDB1_CSB-DOX ADPr-ChAP input

description: ADPr-ChAP input

data_processing:
Library strategy: ADPr-ChAP
The sequencing data were uploaded to the Galaxy web platform, and we used the public server at usegalaxy.org to analyze the data.
Sequencing reads were mapped against the human genome (GRCh37/hg19) using Bowtie for Illumina with default parameters
The SAM format outputs were sorted by genomic coordinates and uniquely mapped reliable reads were used in subsequent steps. SAM files were preprocessed using SAMtools
We used the MACS tool to select regions that were enriched for H3K9me3 and PAR. We applied the default settings and found significant regions (P-value ≤ 10-5), using non-IP chromatin as a control to eliminate unspecific signals.
Genome_build: hg19
Supplementary_files_format_and_content: bed files with called peaks, bw files with coverage

value: CS1AN cells that stably expressing dox-inducible SETDB1


title: SETDB1_CSB-DOX ADPr-ChAP

description: ADPr-ChAP


title: SETDB1_CSB-DOX H3K9me3 input

description: H3K9me3 input


title: SETDB1_CSB-DOX H3K9me3 ChIP

description: H3K9me3 ChIP


title: SETDB1_CSB-DMSO ADPr-ChAP

description: ADPr-ChAP


title: SETDB1_CSB-DMSO H3K9me3 input

description: H3K9me3 input


title: Liver_sample_5: HFMCD_IgG_3weeks_rep2


title: CSB+H2O2 H3K9me3 input

description: H3K9me3 input

value: CS1AN cells that stably expressing wild type CSB


title: CSB-H2O2 ADPr-ChAP ipnut

description: ADPr-ChAP input

value: CS1AN cells from CSB patients


title: CSB+H2O2 ADPr-ChAP

description: ADPr-ChAP


title: SETDB1_CSB-DMSO H3K9me3 ChIP

description: H3K9me3 ChIP


title: CSB+H2O2 H3K9me3 ChIP

description: H3K9me3 ChIP


title: CSB-H2O2 H3K9me3 input

description: H3K9me3 input


title: CSB-H2O2 ADPr-ChAP

description: ADPr-ChAP


title: Liver_sample_3: NCD_3weeks_rep3


title: CSB-H2O2 H3K9me3 ChIP

description: H3K9me3 ChIP


title: CSB-DMSO H3K9me3 input

description: H3K9me3 input


title: CSB-DMSO H3K9me3 ChIP

description: H3K9me3 ChIP


title: CSB+DMSO H3K9me3 ChIP

description: H3K9me3 ChIP


title: CSB+DMSO H3K9me3 input

description: H3K9me3 input


title: WT2-rep1

city: Orangeburg

first: Sandipkumar

last: Darji

state: NY

address: 140 Old Orangeburg Rd, Bldg 39

department: Center for Dementia Research

institute: Nathan Kline Institute for Psychiatric Research

description:
2N-4
TMM_normalized_ReadCounts.txt

data_processing:
Samples DS 1-6 and 2N 1-6: For base-calling CASAVA version 1.8 was used to generate FASTQ files. Samples DS-7,8 and 2N-7, 8, 9: Retrieved from SRA: SRP039348.
Samples DS 1-6 and 2N 1-6: STAR aligner (version 2.3.1z9) was used to align sequencing files with reference genome. Samples DS-7,8 and 2N-7, 8, 9: Raw read counts obtained from public repository ARCHS4 (Lachmann A, Torre D, Keenan AB, Jagodnik KM, Lee HJ, Wang L, Silverstein MC, Ma’ayan A. Massive mining of publicly available RNA-seq data from human and mouse. Nature Communications 9. Article number: 1366 (2018)). Kallisto was used as aligner according to the publication.
Samples DS 1-6 and 2N 1-6: HTSeq (version 0.6.1p2) was used for quantifying aligned reads.
Genome_build: Samples DS 1-6 and 2N 1-6: hg19 (GRCh37). Samples DS-7,8 and 2N-7, 8, 9: hg38 (According to ARCHS4)
Supplementary_files_format_and_content: TMM_normalized_ReadCounts.txt is a tab delimited text file containing TMM normalized counts for features i.e. counts are normalized between libraries.

source_name: Skin Fibroblast

growth_protocol: Cells were were cultured in DMEM medium (Life Technologies #11995-065) containing 10% fetal bovine serum (Life Technologies #10270), 100 mg/L sodium pyruvate, 100 units/mL Penicillin-Streptomycin (Life Technologies #15140-122) at 37°C in a 5% CO2 atmosphere. Cell passage number ranged from p7 to p12, and cells at 85–90% confluency were used.

extract_protocol:
RNA was extracted  using RNeasy Micro Kit (Qiagen) according to the manufacturer’s specifications
500 ng of total RNA were prepared using TruSeq RNA Sample prep kit V2 (Ilumina Inc., San Diego, CA, USA) following manufacturers’ instructions for the samples DS-1-6 and 2N-1-6.  Quality of libraries was assessed using Agilent 2200 TapeStation system. The sequencing files for samples DS-7, DS-8, 2N-7, 2N-8 and 2N-9 were retrieved from SRA: SRP039348.

tag: condition

value: Disomic

tag: age

value: 2 years

tag: gender

value: Male

tag: batch

value: A


title: WT2-rep2

description:
2N-5
TMM_normalized_ReadCounts.txt


title: SETDB1_CSB-DMSO ADPr-ChAP input

description: ADPr-ChAP input


title: WT1-rep2

description:
2N-2
TMM_normalized_ReadCounts.txt

value: 5 months


title: DS2-rep2

description:
DS-5
TMM_normalized_ReadCounts.txt

value: Trisomic


title: CSB+H2O2 ADPr-ChAP ipnut

description: ADPr-ChAP input


title: WT1-rep1

description:
2N-1
TMM_normalized_ReadCounts.txt


title: DS1-rep3

description:
DS-3
TMM_normalized_ReadCounts.txt


title: DS2-rep3

description:
DS-6
TMM_normalized_ReadCounts.txt


title: DS1-rep1

description:
DS-1
TMM_normalized_ReadCounts.txt


title: sgNrf2 tumor-A

first: Viraj

last: Sanghvi

address: 1275 York Ave

department: CABG

institute: MSKCC

description:
MYC-NRF2 tumor_A
Nrf2_counts_scaled_DESeq

data_processing:
The FASTQ files were mapped to the mouse genome using rnaStar aligner (Dobin, 2012)
Mapping was done using 2 pass method (Engström, 2013) and the output SAM files was further processed using PICARD
The expression matrix was computed from mapped reads using HTSeq
The normalization and differential expression analysis was computed from raw matrix using R/Bioconductor package DESeq
Genome_build: UCSC MM10
Supplementary_files_format_and_content: scaled counts

source_name: murine HCC

extract_protocol:
Total RNA was extracted using Qiagen RNA extraction kit
Illumina TrueSeq RNA kit V2

tag: cell type

value: hepatocytes

tag: disease state

value: MYC-driven murine HCC

tag: genotype/variation


title: WT2-rep3

description:
2N-6
TMM_normalized_ReadCounts.txt


title: MYC/sgKeap1 tumor-2

description:
MYC-sgKeap1 tumor_2
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgKeap1 tumor-3

description:
MYC-sgKeap1 tumor_3
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgKeap1 tumor-1

description:
MYC-sgKeap1 tumor_1
Keap1_Cul3_counts_scaled_DESeq


title: control tumor B

description:
MYC control_B
repeat of MYC/sgGFP control tumor-4
Nrf2_counts_scaled_DESeq

value: control


title: MYC/sgCul3 tumor-2

description:
MYC-sgCul3 tumor_2
Keap1_Cul3_counts_scaled_DESeq


title: control tumor A

description:
MYC control_A
repeat of MYC/sgGFP control tumor-2
Nrf2_counts_scaled_DESeq


title: MYC/sgGFP control tumor-1

description:
MYC control_1
Keap1_Cul3_counts_scaled_DESeq

value: sgGFP


title: WT1-rep3

description:
2N-3
TMM_normalized_ReadCounts.txt


title: MYC/sgGFP control tumor-3

description:
MYC control_3
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgCul3 tumor-1

description:
MYC-sgCul3 tumor_1
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgCul3 tumor-3

description:
MYC-sgCul3 tumor_3
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgGFP control tumor-4

description:
MYC control_4
Keap1_Cul3_counts_scaled_DESeq


title: MYC/sgGFP control tumor-2

description:
MYC control_2
Keap1_Cul3_counts_scaled_DESeq


title: 7681.NORM

city: Memphis

first: Timothy

last: Shaw

state: TN

address: 262 Danny Thomas Pl

institute: St Jude Children's Research Hospital

description:
Normal brain cortex of athymic nude mice
SJMMNORM016461_G1-7681
SJMMNORM016461.G1.7681.NORM

data_processing:
Basecalls performed using CASAVA
fastq files werer mapped by StrongARM, an internal mapping pipeline that performs STAR and bwa mapping.
reads were counted using an internal perl script and converted to FPKM using mm9
Genome_build: mm9
Supplementary_files_format_and_content: matrix txt file with log2FPKM for each gene symbol for each sample

source_name: normal brain cortex

extract_protocol:
RNAs were extracted by Trizol (Invitrogen) from about 20 mg aliquots of the same tumor samples for proteomics analyses.
For RNAseq, libraries were generated from ~1 µg total RNA using the Illumina Stranded Total RNA kit with the Human/Mouse/Rat Ribo-Zero Gold ribosomal reduction kit. Libraries were sequenced on an Illumina HiSeq 2500 using paired-end 100 bp sequencing chemistry.

tag: host strain

value: athymic nude mice

tag: tissue type

value: normal brain cortex


title: I_E9.25_embryo_No.1

city: Beijing

first: Haiqing

last: Xiong

state: Beijing

address: 5 Yiheyuan Road,  Haidian District

country: China

institute: Peking University

description: polyA RNA

data_processing:
Basecalls performed using CASAVA version 1.8
We used cell-specific barcode sequences attached in read 2 to separate raw reads, and then we trimmed reads by removing the template switch oligo (TSO) and polyA tail sequence.
The clean reads were aligned to the mouse genome (mm10 from UCSC) with TopHat (version 2.0.12). We used HTseq to count the unique mapped reads that were grouped by cell-specific barcode
We calculated the numbers of UMIs of each gene divided by all UMIs and then multiplied  by 1,000,000, which were used to quantify the gene expression level as TPM (transcript per million)
Genome_build: mm10
Supplementary_files_format_and_content: txt files which include the TPM values of RefSeq genes.

source_name: heart

growth_protocol: Mice were housed under a 12-12-hour light-dark cycle and allowed standard laboratory take care.

extract_protocol:
Single-cell RNA-seq libraries were prepared as described previsouly but with some modifications of  Smart-seq2 protocol(Li et.al, Cell Stem Cell, 2017). In short, cardiac cells sorted by  FACS or just trypsin digestion are picked into sc-RNA lysis buffer by mouth pipette. Then reverse transcription was performed using oligo(dT) primer which carrying a 8-nt specific barcode and a 8-nt random sequence as unique molecular identifiers (UMIs).
The second stand was synthesized using TSO oligo. After 17 cycle of PCR reaction, all synthesized cDNA was pooled together. Additional 5 cycles of PCR reaction was performed using a biotinylated primer introducing a library specific index. Then cDNA was sheared by Covaris S2 and gain average 400bp fragments and 3’ terminal fragments of the cDNA were captured by Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher). Last, RNA-seq library was constructed by NEBNext Ultra DNA Library Prep Kit for Illumina(E7370) following the manufacture’s guide. All the Single-cell RNA-seq  library are subjected to 150 bp paired-end sequencing on an Illumina High seq X ten platform.

tag: embryonic stage


title: 7679.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016460_G1-7679
SJMMNORM016460.G1.7679.NORM


title: DS2-rep1

description:
DS-4
TMM_normalized_ReadCounts.txt


title: I_E8.75_embryo_No.1_2

description: polyA RNA


title: I_E8.75_embryo_No.1_1

description: polyA RNA


title: 7678.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016459_G1-7678
SJMMNORM016459.G1.7678.NORM


title: 7677.NORM

description:
Normal brain cortex of athymic nude mice
SJMMNORM016458_G1-7677
SJMMNORM016458.G1.7677.NORM


title: DS1-rep2

description:
DS-2
TMM_normalized_ReadCounts.txt


title: I_E8.25_embryo_No.2_2

description: polyA RNA


title: 1159.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016453_D1-IC_1159
SJMMHGG016453.D1.IC.1159.TPM3_NTRK1

source_name: high grade glioma with TPM3-NTRK1 Fusion

tag: injection cell

value: high grade glioma


title: sgNrf2 tumor-B

description:
MYC-NRF2 tumor_B
Nrf2_counts_scaled_DESeq


title: I_E8.25_embryo_No.2_1

description: polyA RNA


title: 7371.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016451_D1-IC_7371
SJMMHGG016451.D1.IC.7371.TPM3_NTRK1


title: 7372.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016452_D1-IC_7372
SJMMHGG016452.D1.IC.7372.TPM3_NTRK1


title: I_E7.75_embryo_No.3_2

description: polyA RNA


title: 7370.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016450_D1-IC_7370
SJMMHGG016450.D1.IC.7370.TPM3_NTRK1


title: 7675.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015502_D1-IC_7675
SJMMHGG015502.D1.IC.7675.TPM3_NTRK1


title: 7672.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015503_D1-IC_7672
SJMMHGG015503.D1.IC.7672.TPM3_NTRK1


title: N_E9.25_embryo_No.2_2

description: polyA RNA


title: N_E8.75_embryo_No.1_2

description: polyA RNA


title: 7671.TPM3_NTRK1

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human TPM3-NTRK1 fusion along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015501_D1-IC_7671
SJMMHGG015501.D1.IC.7671.TPM3_NTRK1


title: N_E9.25_embryo_No.2_1

description: polyA RNA


title: N_E8.25_embryo_No.3_2

description: polyA RNA


title: N_E8.75_embryo_No.1_1

description: polyA RNA


title: 4418.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016456_D1-IC_4418
SJMMHGG016456.D1.IC.4418.PDGFRA

source_name: high grade glioma with PDGFRA D842V mutation

value: PDGFRA D842V


title: 4419.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016457_D1-IC_4419
SJMMHGG016457.D1.IC.4419.PDGFRA


title: N_E8.25_embryo_No.3_1

description: polyA RNA


title: N_E7.75_embryo_No.2_2

description: polyA RNA


title: 4416.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016455_D1-IC_4416
SJMMHGG016455.D1.IC.4416.PDGFRA


title: 4412.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG016454_D1-IC_4412
SJMMHGG016454.D1.IC.4412.PDGFRA


title: 7664.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015500_D1-IC_7664
SJMMHGG015500.D1.IC.7664.PDGFRA


title: N_E7.75_embryo_No.2_1

description: polyA RNA


title: 7661.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015498_D1-IC_7661
SJMMHGG015498.D1.IC.7661.PDGFRA


title: I_E7.75_embryo_No.3_1

description: polyA RNA


title: PSM__Female__WT__rep3

city: Cambridge

first: Jordan

last: Lewandowski

state: MA

address: 7 Divinity Ave

institute: Harvard University

description: E11.5 female pre-somitic mesoderm, wildtype

data_processing:
Reads were mapped to the mm10 reference genome using TopHat v2.1.1 with Bowtie v2.2.8 and the following options: --no-coverage-search; --transcriptome-index with an index built from Gencode vM9.
Gene expression levels were estimated using Cuffdiff v2.2.1 with default options, using a reference transcriptome based on Gencode vM9.
Genome_build: mm10
Supplementary_files_format_and_content: gene_expression.txt contains per-replicate gene expression levels (FPKM). gene_exp.diff contains raw Cuffdiff output, including: gene-level expression estimates (average FPKM across replicates), log2 fold change between relevant conditions, and associated FDR values.

source_name: PSM [female]

extract_protocol:
Tissues were harvested and immediately homogenized in TRIzol. Total RNA was isolated according to the manufacturer's protocol (RNeasy Mini, Qiagen).
Libraries were constructed using the TruSeq RNA Sample Preparation Kit (Illumina). For each tissue, 500ng of total RNA was used as input, with the exception of lung (200ng) and pre-somitic mesoderm (80ng). Libraries were individually barcoded, amplified for only 10 PCR cycles to minimize artifacts, pooled into groups of six with a mix of wildtype and knockout samples, and then sequenced on an Illumina HiSeq 2500.

value: Pre-somitic mesoderm

tag: Sex

value: Female

value: wildtype


title: PSM__Female__KO__rep1

description: E11.5 female pre-somitic mesoderm, Firre knockout

value: Firre knockout


title: PSM__Female__KO__rep3


title: PSM__Female__WT__rep2


title: Sample_R18059821-wt-2-wt-2

city: Wuhan

first: Mengcheng

last: Luo

state: Hubei

address: 185 Donghu Road

institute: Wuhan University

data_processing:
Illumina NovaSeq 6000
Raw data were filtered using Seqtk software and cleaned using FASTX-Toolkit software to get clean reads.
Hisat2
Genome_build: GRCm38
Supplementary_files_format_and_content: Text file includes FPKM and count values for each sample.

source_name: Testis

extract_protocol:
Testes samples were collected from 18-day-old control and Sympk cKOStra8-Cre mice.Total RNA was isolated using RNeasy mini kit (Qiagen, Germany).
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. The cDNA fragments were prepared with cleaved mRNA fragments using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA polymerase and RNase H. These cDNA fragments then go through an end repair process, the addition of a single‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

value: C57BL/6-ICR mixed background

value: Testis

value: Postnatal day 18

tag: genotype

value: wild type


title: Sample_R18059823-cko-2-cko-2

tag: tissue

value: Male

value: Sympk cKO


title: Sample_R18059822-cko-1-cko-1

tag: strain


title: Sample_R18059820-wt-1-wt-1


title: PSM__Male__KO__rep2

description: E11.5 male pre-somitic mesoderm, Firre knockout

source_name: PSM [male]


title: PSM__Female__WT__rep1


title: flbioNkx2-5_E8.75_SHF_input

description: Input DNA

data_processing:
Basecalls performed using CASAVA version 1.8.2.
ChIP-seq reads were filtered by cutadapt (v1.11) with parameters to get high quality reads.
High-quality reads were aligned to mm10 mouse genome using bowtie2 (v2.3.1) with default parameters.
The PCR duplicates were removed by samtools (v1.3.1) rmdup command. The uniquely mapped reads with map quality greater than 30 were kept.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigwig files that represented ChIP signals were generated using deeptools.

extract_protocol:
Cells were lysed at 37°C before chromatin was fragmented, adaptor-ligated and released. For one bio-ChIP experiment, 10 μl streptavidin beads (Invitrogen, cat#60210) were used for incubation for 2 h at 4°C. Beads were briefly washed with 2% SDS/PBS once, and then washed with high salt buffer (1% Triton X-100, 2 mM EDTA, 50 mM HEPES pH 7.9, 500 mM NaCl, 0.1% sodium deoxycholate) for three times. Beads were re-suspended in 100 μl elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS). After reverse crosslinking and proteinase K digestion, DNA was purified through phenol-chloroform extraction.
NEBNext Ultra II Master Mix was used for PCR enrichment, followed by size selection of 200-800 bp. The resulting libraries were subjected to 2 X 150 bp paired-end sequencing on NovaSeq 6000 systems.

tag: developmental stage

value: Heart

tag: heart field

value: Second


title: 7662.PDGFRA

description:
A pooled population of p53-deficient primary mouse astrocytes was transduced with retrovirus expressing  human PDGFRA D842V mutation along with an IRES-GFP.  2 × 10^6 cells per mouse were intracranially implanted into athymic nude mice
SJMMHGG015499_D1-IC_7662
SJMMHGG015499.D1.IC.7662.PDGFRA


title: flbioNkx2-5_E8.75_SHF_rep3

tag: chip antibody

value: Streptavidin beads (Invitrogen, cat#60210)


title: PSM__Male__WT__rep3

description: E11.5 male pre-somitic mesoderm, wildtype

tag: age


title: PSM__Male__WT__rep2


title: PSM__Male__KO__rep1


title: PSM__Male__WT__rep1


title: PSM__Female__KO__rep2


title: flbioNkx2-5_E8.75_SHF_rep4


title: PSV-P+satRNA_rep2_vs_ref

city: Poznan

first: Agnieszka

last: Zmienko

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry PAS

hyb_protocol: All of the hybridization, washing and drying steps were performed in 2x105K Chambers in an HS 4800 Pro (Tecan) automatic hybridization station according to the manufacturer’s guidelines regarding Agilent microarrays treatment. A Gene Expression Hybridization Kit (Agilent) and Gene Expression Wash Buffer Kit solutions (Agilent) were used for the hybridization and washing steps, respectively.

scan_protocol: The intensity data were collected with 4200AL GenePix scanner and GenePix Pro 6.1 software at 5 µm resolution, at green and red channel.

data_processing: The scans were processed with GenePix Pro 6.1 software using morphological opening background method. Intensity data were analyzed with R/Bioconductor limma package. Background was subtracted. Loess within-array normalization and Aquantile between-array normalization was applied.

organism: Nicotiana benthamiana

source_name: pooled RNA extracted from a mix of tissues and treatments

label_protocol: Labeled cRNA samples were prepared from 200 ng RNA each, using Quick Amp Labeling Kit (Agilent). The labeling efficiency was monitored with Nanodrop 2000 spectrophotometer.

growth_protocol: N. benthamiana plants were grown in separate cabins under 14h light/ 10h dark at 21°C day/16°C night.

extract_protocol: Samples from 3 biological replicates per treatment were obtained. Total RNA was extracted from upper parts of plants using spin-columns (RNeasy Plant Mini Kit, QIAGEN) and DNase-digested with TURBO DNA-free kit (Ambion) according to the manufacturers’ standard protocols. RNA quality was determined using Nanodrop 2000 and 2100 Bioanalyzer (Agilent). All of the samples used for the study were pure (A260/A280 ≥ 1.9; A260/A230 ≥ 2) and showed no visible signs of degradation.

treatment_protocol: Plants were inoculated with Peanut stunt virus strain P (PSV-P) or PSV-P and satellite RNA-P (PSV-P+satRNA) infectious copies in 0.5 M phosphate, pH 7.5, after carborund dusting.

tag: reference

tag: treatment

value: peanut stunt virus strain P and satellite RNA-P


title: PSV-P+satRNA_rep3_vs_ref

value: pooled RNA extracted from a mix of tissues and treatments


title: flbioNkx2-5_E8.75_SHF_rep2


title: Midbrain__Female__KO__rep3

description: E11.5 female midbrain, Firre knockout

source_name: Midbrain [female]

value: Midbrain


title: PSV-P_rep1_vs_ref

value: peanut stunt virus strain P


title: PSV-P_rep3_vs_ref


title: PSV-P+satRNA_rep1_vs_ref


title: Midbrain__Female__KO__rep2

description: E11.5 female midbrain, Firre knockout


title: flbioNkx2-5_E8.75_SHF_rep1


title: PSV-P_rep2_vs_ref


title: PSM__Male__KO__rep3

value: Pre-somitic mesoderm


title: Midbrain__Female__WT__rep1

description: E11.5 female midbrain, wildtype

value: Female


title: flbioNkx2-5_E8.75_FHF_rep1

value: First


title: flbioNkx2-5_E8.75_FHF_rep3


title: Midbrain__Female__WT__rep3

description: E11.5 female midbrain, wildtype

value: wildtype


title: SG n=3

city: Bloomington

first: Brian

middle: R

last: Calvi

state: IN

department: Biology

institute: Indiana University Bloomington

description:
GSF1939-SG-n-3_S6_R1_001.fastq
Poly-A tail enriched RNA

data_processing:
Read quality analyzed with FastQC (0.11.5).
Reads mapped to Dmel R6.23 whole genome using STAR (2.6.1a) with special parameters: --outSAMtype BAM SortedByCoordinate
Aligned reads assigned to features from the Dmel R6.23 GTF annotation file using the R (3.3.1) bioconductor (3.3) Rsubread (1.24.2) featureCounts function using the special parameters: isGTFAnnotationFile=T, strandSpecific=2.
Differential expression of the raw feature counts from Rsubread performed using the R (3.3.1) bioconductor (3.3) DESeq2 (1.14.1) DESeq function with default parameters.
Genome_build: Dmel R6.23
Supplementary_files_format_and_content: Excel raw feature counts, fold-change

organism: Drosophila melanogaster

source_name: Salivary glands

growth_protocol: Flies were kept at 25ºC. After introducing males and females for 2 days, females were allowed to lay eggs for 6 hours and flipped to a new vial. Four days after egg lay, feeding 3rd instar larvae were taken from the food and BD and SG were dissected out.

extract_protocol:
RNA was harvested using TRIzol (ThermoFisher, cat# 15596026).
Libraries were generated according TruSeq Stranded mRNA Library Prep kit (Illumina, cat#20020594) standard protocols.

value: Salivary glands

tag: cell cycle

value: endoreplication


title: flbioNkx2-5_E8.75_FHF_input

description: Input DNA


title: Midbrain__Female__KO__rep1

description: E11.5 female midbrain, Firre knockout

value: Firre knockout


title: Midbrain__Female__WT__rep2

description: E11.5 female midbrain, wildtype


title: SG n=2

description:
GSF1939-SG-n-2_S4_R1_001.fastq
Poly-A tail enriched RNA


title: BD n=3

description:
GSF1939-BD-n-3_S5_R1_001.fastq
Poly-A tail enriched RNA

source_name: Brains and imaginal discs

value: Brains and imaginal discs

value: mitotic


title: Midbrain__Male__KO__rep3

description: E11.5 male midbrain, Firre knockout

source_name: Midbrain [male]

value: Male


title: flbioNkx2-5_E8.75_FHF_rep2

value: Heart


title: BD n=2

description:
GSF1939-BD-n-2_S3_R1_001.fastq
Poly-A tail enriched RNA


title: SG n=1

description:
GSF1939-SG-n-1_S2_R1_001.fastq
Poly-A tail enriched RNA


title: Midbrain__Male__KO__rep1

description: E11.5 male midbrain, Firre knockout


title: Midbrain__Male__KO__rep2

description: E11.5 male midbrain, Firre knockout


title: Midbrain__Male__WT__rep3

description: E11.5 male midbrain, wildtype


title: flbioNkx2-5_E8.75_FHF_rep4


title: Midbrain__Male__WT__rep2

description: E11.5 male midbrain, wildtype


title: Midbrain__Male__WT__rep1

description: E11.5 male midbrain, wildtype


title: Lung__Female__KO__rep3

description: E11.5 female lung, Firre knockout

source_name: Lung [female]

value: Lung


title: Lung__Female__KO__rep2

description: E11.5 female lung, Firre knockout


title: Myb dsRNA n=3

description:
GSF1414-myb-4_S19_R1_001.fastq.gz
Poly-A tail enriched RNA

source_name: embryo derived cell line

growth_protocol: S2-DGRC cells were grown in M3+BPYE media supplemented with 12% FBS at 25ºC

extract_protocol:
At t+96h total RNA was harvested using TRIzol (ThermoFisher, cat# 15596026).
Libraries were generated according TruSeq Stranded mRNA Library Prep kit (Illumina, cat#20020594) standard protocols.

treatment_protocol: 3.75mg of the indicated dsRNA was added to 5e5 cells. Cells were incubated at 25ºC for 96h.

tag: cell line

value: S2-DGRC cells

tag: RNAi

value: Myb

value: induced endoreplication


title: BD n=1

description:
GSF1939-BD-n-1_S1_R1_001.fastq
Poly-A tail enriched RNA


title: Myb dsRNA n=2

description:
GSF1414-myb-2_S18_R1_001.fastq.gz
Poly-A tail enriched RNA


title: Lung__Female__KO__rep1

description: E11.5 female lung, Firre knockout

tag: genotype/variation


title: CycA dsRNA n=3

description:
GSF1414-cycA-4_S13_R1_001.fastq.gz
Poly-A tail enriched RNA

value: CycA


title: Lung__Female__WT__rep3

description: E11.5 female lung, wildtype


title: Lung__Female__WT__rep1

description: E11.5 female lung, wildtype


title: Myb dsRNA n=1

description:
GSF1414-myb-1_S17_R1_001.fastq.gz
Poly-A tail enriched RNA


title: GFP n=3

description:
GSF1414-GFP-3_S16_R1_001.fastq.gz
Poly-A tail enriched RNA

value: GFP

value: Mitotic


title: Lung__Female__WT__rep2

description: E11.5 female lung, wildtype

value: Female


title: CycA dsRNA n=1

description:
GSF1414-cycA-1_S11_R1_001.fastq.gz
Poly-A tail enriched RNA


title: Lung__Male__KO__rep3

description: E11.5 male lung, Firre knockout

source_name: Lung [male]


title: GFP n=2

description:
GSF1414-GFP-2_S15_R1_001.fastq.gz
Poly-A tail enriched RNA


title: Lung__Male__KO__rep2

description: E11.5 male lung, Firre knockout


title: Lung__Male__KO__rep1

description: E11.5 male lung, Firre knockout


title: GFP n=1

description:
GSF1414-GFP-1_S14_R1_001.fastq.gz
Poly-A tail enriched RNA


title: Liver__Female__KO__rep3

description: E11.5 female liver, Firre knockout

source_name: Liver [female]

value: Liver


title: Liver_sample_4: HFMCD_IgG_3weeks_rep1

source_name: liver tissue

value: liver

tag: diet

value: HFMCD

value: IgG

tag: time of treatment

value: 3 weeks

tag: rin


title: Lung__Male__WT__rep3

description: E11.5 male lung, wildtype

tag: Sex

value: wildtype


title: Lung__Male__WT__rep2

description: E11.5 male lung, wildtype


title: Liver__Female__KO__rep2

description: E11.5 female liver, Firre knockout

value: Firre knockout


title: Liver__Female__KO__rep1

description: E11.5 female liver, Firre knockout


title: Liver__Female__WT__rep3

description: E11.5 female liver, wildtype


title: CycA dsRNA n=2

description:
GSF1414-cycA-2_S12_R1_001.fastq.gz
Poly-A tail enriched RNA


title: Liver__Female__WT__rep2

description: E11.5 female liver, wildtype


title: Liver__Female__WT__rep1

description: E11.5 female liver, wildtype


title: Lung__Male__WT__rep1

description: E11.5 male lung, wildtype

value: Male


title: Liver__Male__KO__rep3

description: E11.5 male liver, Firre knockout

source_name: Liver [male]


title: Liver__Male__KO__rep1

description: E11.5 male liver, Firre knockout


title: Liver__Male__KO__rep2

description: E11.5 male liver, Firre knockout


title: Liver__Male__WT__rep3

description: E11.5 male liver, wildtype


title: CAF4_0.773 kPa

city: Seoul

first: Baek Gil

last: Kim

address: 50-1 Yonsei-Ro

country: South Korea

institute: Yonsei University

hyb_protocol: After checking labeling efficiency, fragmentation of cRNA was performed by adding 10X blocking agent and 25X fragmentation buffer and incubating at 60oC for 30 min. The fragmented cRNA was resuspended with 2X hybridization buffer and directly pipetted onto assembled Agilent’s Human Oligo Microarray (60K). The arrays hybridized at 65oC for 17 hours using Agilent Hybridization oven (Agilent Technology, USA). The hybridized microarrays were washed as the manufacturer’s washing protocol (Agilent Technology, USA).

scan_protocol: The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).

data_processing: All data normalization and further analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

label_protocol: Amplified and labeled cRNA was purified on cRNA Cleanup Module (Agilent Technology) according to the manufacturer’s protocol. Labeled cRNA target was quantified using ND-1000 spectrophotometer (NanoDrop Technologies, Inc., Wilmington, DE).

growth_protocol: Breast cancer cells were cultured with DMEM cell culture medium containing 10% (v/v) fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37 °C in a humidified incubator containing 5% CO2. Primary cancer-associated fibroblasts were cultured with DMEM/F12 cell culture medium containing 10% (v/v) fetal bovine serum (FBS), 100 IU/ml penicillin, and 100 μg/ml streptomycin at 37 °C in a humidified incubator containing 5% CO2.

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

treatment_protocol: Cells were encapsulated into 0.5% alginate disk. Compressive stress were given to the cell containing alginate disks for 24h by loading weights.

tag: cell type

value: breast cancer-associated fibroblasts

tag: stress


title: Liver__Male__WT__rep1

description: E11.5 male liver, wildtype

tag: strain

tag: tissue


title: CAF4_3.866 kPa


title: CAF4_0 kPa

source_name: CAF4_0 kPa

value: 0 kPa


title: CAF4_1.546 kPa


title: CAF3_3.866 kPa


title: CAF4_0.386 kPa


title: Hindlimb__Female__KO__rep2

description: E11.5 female hindlimb, Firre knockout

source_name: Hindlimb [female]

value: Hindlimb


title: CAF3_7.732 kPa


title: CAF4_7.732 kPa


title: CAF3_1.546 kPa


title: Hindlimb__Female__KO__rep1

description: E11.5 female hindlimb, Firre knockout


title: Hindlimb__Female__WT__rep3

description: E11.5 female hindlimb, wildtype


title: Hindlimb__Female__WT__rep2

description: E11.5 female hindlimb, wildtype


title: Hindlimb__Female__KO__rep3

description: E11.5 female hindlimb, Firre knockout


title: Hindlimb__Female__WT__rep1

description: E11.5 female hindlimb, wildtype


title: CAF3_0.386 kPa


title: Hindlimb__Male__KO__rep3

description: E11.5 male hindlimb, Firre knockout

source_name: Hindlimb [male]


title: Hindlimb__Male__KO__rep1

description: E11.5 male hindlimb, Firre knockout


title: Hindlimb__Male__KO__rep2

description: E11.5 male hindlimb, Firre knockout


title: CAF2_0 kPa

source_name: CAF2_0 kPa


title: CAF2_3.866 kPa


title: CAF2_7.732 kPa


title: Hindlimb__Male__WT__rep3

description: E11.5 male hindlimb, wildtype


title: Liver__Male__WT__rep2

description: E11.5 male liver, wildtype


title: CAF2_1.546 kPa


title: Hindlimb__Male__WT__rep1

description: E11.5 male hindlimb, wildtype


title: Hindlimb__Male__WT__rep2

description: E11.5 male hindlimb, wildtype


title: CAF3_0.773 kPa


title: Heart__Female__KO__rep3

description: E11.5 female heart, Firre knockout

source_name: Heart [female]

value: Heart


title: Heart__Female__KO__rep2

description: E11.5 female heart, Firre knockout


title: CAF2_0.773 kPa


title: CAF3_0 kPa

source_name: CAF3_0 kPa


title: CAF2_0.386 kPa


title: CAF1_3.866 kPa


title: CAF1_1.546 kPa


title: MDA-MB-231_7.732 kPa

value: breast cancer cells


title: MDA-MB-231_1.546 kPa


title: CAF1_0.773 kPa


title: Heart__Male__KO__rep2

description: E11.5 male heart, Firre knockout

source_name: Heart [male]


title: Heart__Female__WT__rep2

description: E11.5 female heart, wildtype


title: MDA-MB-231_0 kPa

source_name: MDA-MB-231_0 kPa


title: MDA-MB-231_3.866 kPa


title: SK-BR-3_7.732 kPa


title: CAF1_7.732 kPa


title: Heart__Male__KO__rep1

description: E11.5 male heart, Firre knockout


title: Heart__Female__WT__rep1

description: E11.5 female heart, wildtype


title: CAF1_0.386 kPa


title: Heart__Male__WT__rep3

description: E11.5 male heart, wildtype


title: Heart__Female__WT__rep3

description: E11.5 female heart, wildtype


title: Heart__Female__KO__rep1

description: E11.5 female heart, Firre knockout


title: SK-BR-3_1.546 kPa


title: Heart__Male__WT__rep1

description: E11.5 male heart, wildtype


title: CAF1_0 kPa

source_name: CAF1_0 kPa


title: Forelimb__Female__KO__rep3

description: E11.5 female forelimb, Firre knockout

source_name: Forelimb [female]

value: Forelimb


title: Forelimb__Female__KO__rep2

description: E11.5 female forelimb, Firre knockout


title: MCF7_7.732 kPa


title: MCF7_3.866 kPa


title: SK-BR-3_3.866 kPa


title: SK-BR-3_0.386 kPa


title: SK-BR-3_0 kPa

source_name: SK-BR-3_0 kPa


title: SK-BR-3_0.773 kPa


title: MCF7_0.773 kPa


title: MCF7_0.386 kPa


title: Forelimb__Female__WT__rep3

description: E11.5 female forelimb, wildtype


title: MCF7_1.546 kPa


title: MDA-MB-231_0.386 kPa


title: MCF7_0 kPa

source_name: MCF7_0 kPa


title: Forelimb__Female__WT__rep1

description: E11.5 female forelimb, wildtype


title: Forelimb__Male__KO__rep3

description: E11.5 male forelimb, Firre knockout

source_name: Forelimb [male]


title: Forelimb__Male__KO__rep1

description: E11.5 male forelimb, Firre knockout


title: MDA-MB-231_0.773 kPa


title: Forelimb__Female__KO__rep1

description: E11.5 female forelimb, Firre knockout


title: Forelimb__Male__WT__rep3

description: E11.5 male forelimb, wildtype


title: RNA_HdAGO1

city: Edinburgh

first: Edward

middle: William Joseph

last: Wallace

address: Waddington Building, Max Born Crescent

department: Institute for Cell Biology, School of Biological Sciences

country: United Kingdom

institute: University of Edinburgh

description: polyA RNA

data_processing:
Cut out sequencing library adapters (CTGTAGGCACC) with cutadapt.
Remove rRNA reads by hisat2 alignment to the rRNA index file
Align remaining reads to a hisat2 index file
Trim 5' mismatches from reads and remove reads with more than 2 mismatches via a call to trim5pmismatch.py
Make bedgraph files using bedtools genomecov
Genome_build: CNA3 (H99) or Cryne_JEC21_1 (JEC21)
Supplementary_files_format_and_content: Bedgraphs on plus and minus strand; text files with gene-by-gene summaries.
Supplementary_files_format_and_content: H99_RiboViz_ATG_table_tidy.txt: RNA/RPF counts on ORFs and ATGs for all samples from C.neoformans H99
Supplementary_files_format_and_content: JEC21_RiboViz_ATG_table_tidy.txt: RNA/RPF counts on ORFs and ATGs for all samples from C.neoformans JEC21
Supplementary_files_format_and_content: ribosum_H99.txt: Gene expression summary in TPM for C.neoformans H99
Supplementary_files_format_and_content: ribosum_JEC21.txt: Gene expression summary in TPM for C.deneoformans JEC21

organism: Cryptococcus neoformans

source_name: exponential-phase yeast cells

growth_protocol: Cells were streaked out on yPAD plates for 2-3 days, one colony inoculated in 5mL liquid YPAD media and grown overnight, diluted to OD 0.002 in 800mL YPAD, then grown for 12-16hrs until mid-exponential phase (OD 0.6- 0.7), all at 30C with shaking of liquid media.

extract_protocol: Extract and library construction as described in Ingolia 2012: https://doi.org/10.1038/nprot.2012.086

treatment_protocol: Cycloheximide added to 100ug/mL for 2mins. For RNA-seq, 50mL culture removed, spun 3000rpm for 3mins at RT and flash-frozen. For ribosome-protected fragments, remaining 750mLculture spun 5000rpm for 3mins, resuspended in 3mL lysis buffer, flash-frozen in liquid nitrogen.

tag: strain/genotype

value: H99 delta AGO1 strain PC45

tag: submission date


title: BT-474_3.866 kPa


title: IBL-302 rep2

city: Lund

first: Kristoffer

last: von Stedingk

address: Scheelevägen 2

country: Sweden

institute: Lund University

data_processing:
Transcriptome libraries were generated using automated library preparation using the Ion AmpliSeq Transcriptome Human Gene Expression Panel.
Transcriptome libraries were seqenced on the Ion S5 XL system.
Raw data was processed on the Ion S5 XL System and transferred to the Torrent Suite software
primary data generation was performed using the AmpliSeqRNA plug-in with gene level (hg19) transcript quantification (counts).
Total counts were normalized according to total counts per sample
Genome_build: hg19 AmpliSeq Transcriptome ERCC v1
Supplementary_files_format_and_content: gene based count matrix normalized according to total count per sample

source_name: Neuroblastoma Patient Derived Orthotopic Xenograft cells

growth_protocol: PDX-derived cells were continuously kept in a mix of Dulbecco’s Modified Eagle’s Medium (DMEM) and GlutaMAXTM F-12 (3:1 ratio) supplemented with 1% penicillin/streptomycin (P/S), 2% B27 w/o vitamin A, 40 ng/ul basic Fibroblast Growth Factor (FGF) and 20 ng/ul Epidermal Growth Factor (EGF), with no addition of FBS. For adherent growth purposes, PDX-derived cells were grown in Laminin-coated wells (10µg/ml Laminin-521, Biolamina).

extract_protocol:
RNeasy Mini Kit (Qiagen)
Ion AmpliSeq Transcriptome Human Gene Experssion Panel

treatment_protocol: cells were seeded on Laminin pre-coated plates (10µg/ml Laminin-521, Biolamina) and allowed to attach for 24 hours. Cells were treated with 50nM IBL-302 or vehicle control for 48 hours before harvest.


title: RPF_HdAGO1

description: other - ribosome-protected RNA


title: IBL-302 rep1

description:
ip_310_006
*This sample was removed as an outlier in analysis of normalized data

value: Neuroblastoma Patient Derived Orthotopic Xenograft cells


title: BT-474_1.546 kPa


title: IBL-302 rep5


title: IBL-302 rep4


title: BT-474_0.386 kPa


title: BT-474_0.773 kPa


title: Forelimb__Male__WT__rep2

description: E11.5 male forelimb, wildtype

tag: age


title: Control rep5

value: control


title: Forelimb__Female__WT__rep2

description: E11.5 female forelimb, wildtype

value: Female


title: BT-474_7.732 kPa


title: Control rep2


title: RNA_H99r2

description: polyA RNA

value: H99 wild-type strain PC3


title: RPF_H99r2

description: other - ribosome-protected RNA


title: Control rep3


title: Control rep1


title: Forelimb__Male__WT__rep1

description: E11.5 male forelimb, wildtype


title: RNA_HdGWO1

description: polyA RNA

value: H99 delta GWO1 strain PC47


title: Forebrain__Female__KO__rep2

description: E11.5 female forebrain, Firre knockout

source_name: Forebrain [female]

value: Forebrain


title: RPF_HdGWO1

description: other - ribosome-protected RNA


title: Forebrain__Female__KO__rep3

description: E11.5 female forebrain, Firre knockout


title: BT-474_0 kPa


title: Forebrain__Female__WT__rep3

description: E11.5 female forebrain, wildtype


title: RPF_H99r1

description: other - ribosome-protected RNA


title: RNA_H99r1

description: polyA RNA


title: Forebrain__Female__WT__rep2

description: E11.5 female forebrain, wildtype


title: Rumen_epithelium_Late_Stage (29 months of age) 8

city: Morioka

first: Keiichiro

last: Kizaki

state: Iwate

department: Vet. Med.

country: Japan

institute: Iwate University

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.8 during the Late stage

hyb_protocol: Labeled cRNA probes (600 ng each) were hybridized to the microarray in hybridization buffer (Gene Expression Hybridization Kit, Agilent Technologies) at 65°C for 17 h. After incubation, the arrays were washed with the wash buffer pack (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Sure Scan) using one color scan setting.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5 (Agilent) using default parameters (protocol GE1_1100_Jul11) to obtain background subtracted and spatially detrended Processed Signal intensities.

organism: Bos taurus

label_protocol: Fluorescence-labeled (Cy3) cRNA probes were prepared from 200 ng of total RNA using a Low RNA Input Linear Amplification Kit (Agilent Technologies).

extract_protocol: Total RNA was extracted from the peripheral neutrophil and liver tissue using Trizol reagent (Invitrogen) according to the manufacturer's instructions.

value: Rumen epithelium

tag: experiment type

value: In vivo


title: Rumen_epithelium_Late_Stage (29 months of age) 9

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.9 during the Late stage


title: Rumen_epithelium_Late_Stage (29 months of age) 7

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.7 during the Late stage


title: Forebrain__Male__KO__rep3

description: E11.5 male forebrain, Firre knockout

source_name: Forebrain [male]

value: Firre knockout


title: Forebrain__Female__KO__rep1

description: E11.5 female forebrain, Firre knockout


title: Rumen_epithelium_Late_Stage (29 months of age) 3

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.3 during the Late stage


title: Adjuvant paste 15 days, biological rep3

city: Porto Alegre

first: Arthur

last: Fett-Neto

state: Rio Grande do Sul

address: Av. Paulo Gama, 110 - Bairro Farroupilha

department: Center for Biotechnology

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description: Gene expression data from vascular cambium of slash pine plants with stimulant paste - 15 days

data_processing:
llumina HiSeq High-Output
Raw reads were filtered before data analysis. Identification of low-quality sequences, empty sequences and sequences with only one copy was done using FastQC software.
Based on these data, the Trimmomatic software version 0.32 (Bolger et al., 2014) was used to eliminate sequences of reads with a Phred quality score below 30, as well as the adapters.
Transcript abundance estimation in RPKM values and subsequent differential expression analysis were performed using the Cufflinks program version 2.1.1.
Genome_build: The filtered reads were then anchored to the reference genome of Pinus taeda (https://treegenesdb.org/Drupal) with HISAT2 2.0.4.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pinus elliottii

source_name: Pine trees with the bark stripped and with stimulant paste (Ethrel) - 15 days

growth_protocol: In this study we used 16-year-old trees of slash pine with circumference at breast height between 65 and 90 cm. Trials were carried out at Irani Celulose forest installations at Balneário Pinhal, RS, Brazil (30◦14′S and 50◦14′W). Resin tapping and stimulant paste application followed standard commercial practices. Trees had previously been tapped for resin fortnightly during one year with conventional stimulant paste.

extract_protocol:
Total RNA of the sixteen libraries was extracted from vascular cambium of slash pine plants using Concert plant RNA reagent157 (Life Technologies). Nanodrop spectrophotometer (Thermo Scientific) was used to quantify RNA concentration. Samples were precipitated with 3 M sodium acetate, 5 mg.ml-1 glycogen and ethanol. Pellets were kept in 70 % ethanol for shipping.
Library preparation and RNA sequencing were performed with Fasteris S.A. standard protocols (single-end 1x 125 bp Illumina HiSeq High- Output) after depletion of rRNA with RiboZero kit.

treatment_protocol: Four randomly chosen trees of the internal zone of the stand were used. On the bark wound, stimulant paste (3 % of 2-chloroethylphosphonic acid (v/v) (Ethrel), a synthetic precursor of ethylene, and 20 % of sulfuric acid (v/v) was streaked right after injury. Inert components of stimulant paste included rice husk powder to promote adhesion to the wound line. In the present experiments, paste treated trees (hereafter referred to as Et) received a streak of the stimulant paste described above right after the bark stripping. Control trees (from now on referred to as C) had the bark stripped and did not receive any paste. Gene expression analyses were done with samples harvested after 5 and 15 days, obtained slightly above the wound zone, since the wound line produces poor quality RNA.

value: Vascular cambium

tag: treatment

value: Adjuvant paste 15 days - Et15d


title: Control rep4


title: Rumen_epithelium_Late_Stage (29 months of age) 4

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.4 during the Late stage


title: Rumen_epithelium_Middle_Stage (21 months of age) 9

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.9 during the Middle stage


title: Forebrain__Male__KO__rep2

description: E11.5 male forebrain, Firre knockout

value: Male


title: Forebrain__Female__WT__rep1

description: E11.5 female forebrain, wildtype

value: wildtype


title: Rumen_epithelium_Middle_Stage (21 months of age) 8

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.8 during the Middle stage


title: Forebrain__Male__KO__rep1

description: E11.5 male forebrain, Firre knockout


title: 1h TNFα 2h ICRF193 shRNA p65

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

data_processing:
trimmomatic SE /path/to/fastq/files.fastq -threads 8 HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
STAR --runThreadN 8 --genomeDir /path/to/starindex --readFilesIn /path/to/fastq/files.fastq --outFileNamePrefix out.fastq --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts
featureCounts -t exon -T 8 -g gene_id -a /path/to/gtf/file.gtf -o /path/to/output path/to/bam/input/file.bam
bamCoverage -b /path/to/bam/files.bam -o /path/to/output.bigwig -of bigwig --binSize 10 -p 8 --normalizeUsingRPKM --smoothLength 100
Genome_build: hg19
Supplementary_files_format_and_content: bigwig files were generated using deeptools bamCoverage

growth_protocol: Human KB and diploid HCT116 cells were maintained in DMEM GlutaMAX(TM) (Thermo Fisher Scientific, Waltham, MA, USA) supplemented with 10% fetal calf serum and 100 U/ml penicillin/streptomycin at 37 ºC in a humidiﬁed atmosphere containing 5% CO2

extract_protocol:
Total RNA was isolated using the RNeasy kit (Qiagen, Hilden, Germany) according to the procedure described by the manufacturer.
RNA-Seq libraries were prepared from total RNA using the TruSeq Stranded total RNA LT kit (Illumina) and the further analysis was performed as published (Riedlinger FASEB; PMID: 30526044)

treatment_protocol: Cells were pre-incubated with 5 µM CPT or ICRF193 for 2h, 20 ng/ml TNFa were added additionally for 1h

value: 1h TNFα 2h ICRF193 shRNA p65


title: Rumen_epithelium_Middle_Stage (21 months of age) 7

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.7 during the Middle stage


title: Rumen_epithelium_Late_Stage (29 months of age) 5

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.5 during the Late stage


title: Rumen_epithelium_Middle_Stage (21 months of age) 6

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.6 during the Middle stage


title: Rumen_epithelium_Late_Stage (29 months of age) 2

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.2 during the Late stage


title: Adjuvant paste 15 days, biological rep1


title: Forebrain__Male__WT__rep3

description: E11.5 male forebrain, wildtype


title: 1h TNFα 2h CPT shRNA p65

value: 1h TNFα 2h CPT shRNA p65


title: Adjuvant paste 15 days, biological rep4


title: Rumen_epithelium_Middle_Stage (21 months of age) 4

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.4 during the Middle stage


title: Rumen_epithelium_Late_Stage (29 months of age) 1

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.1 during the Late stage


title: 1h TNFα shRNA p65

value: 1h TNFα shRNA p65


title: Control 15 days, biological rep3

description: Gene expression data from vascular cambium of slash pine plants without stimulant paste - 15 days

source_name: Pine trees with the bark stripped and without stimulant paste - 15 days

value: Control 15 days - C15d


title: Forelimb__Male__KO__rep2

description: E11.5 male forelimb, Firre knockout

value: Forelimb


title: Rumen_epithelium_Late_Stage (29 months of age) 6

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.6 during the Late stage


title: Forebrain__Male__WT__rep2

description: E11.5 male forebrain, wildtype


title: Rumen_epithelium_Middle_Stage (21 months of age) 3

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.3 during the Middle stage


title: Control 15 days, biological rep2


title: Rumen_epithelium_Middle_Stage (21 months of age) 2

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.2 during the Middle stage


title: Forebrain__Male__WT__rep1

description: E11.5 male forebrain, wildtype


title: Control 15 days, biological rep1


title: Rumen_epithelium_Middle_Stage (21 months of age) 1

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.1 during the Middle stage


title: Rumen_epithelium_Middle_Stage (21 months of age) 5

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.5 during the Middle stage


title: 0h TNFα 2h ICRF193 shRNA p65

value: 0h TNFα 2h ICRF193 shRNA p65


title: 0h TNFα 2h CPT shRNA p65

value: 0h TNFα 2h CPT shRNA p65


title: 0h TNFα shRNA p65

value: 0h TNFα shRNA p65


title: Adjuvant paste 5 days, biological rep3

description: Gene expression data from vascular cambium of slash pine plants with stimulant paste - 5 days

source_name: Pine trees with the bark stripped and with stimulant paste (Ethrel) - 5 days

value: Adjuvant paste 5 days - Et5d


title: Rumen_epithelium_Early_Stage (14 months of age) 7

description: Gene expression in the rumen epithelium from Japanese Black beef cattle No.7 during the Early stage


title: 1h TNFα 2h ICRF193

value: 1h TNFα 2h ICRF193


title: Ctrl siRNA2

city: 南京

first: xiaoyun

last: zhu

address: 江苏省南京市中国药科大学

institute: China Pharmaceutical University

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 Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al. In short, 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.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Ctrl siRNA2

extract_protocol:
LX2 cells were transfected with siControl or siLIX1L, and subsequently cultured for 48h. The total RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human hepatic stellate cell

tag: sirna

value: sicontrol


title: LIX1L siRNA1

address: 江苏省南京市中国药科大学

source_name: LIX1L siRNA1

tag: cell line


title: 1h TNFα

value: 1h TNFα


title: 1h TNFα 2h CPT

value: 1h TNFα 2h CPT


title: Ctrl siRNA1

address: 江苏省南京市中国药科大学

source_name: Ctrl siRNA1