title: 21719

city: London

first: Istvan

last: Nagy

address: 369 Fulham Road

country: United Kingdom

institute: Imperial College London

description: Sample 7

data_processing:
Base calling was done following the HiSeq2500 instrument manufacturer's base calling software.
Reads were aligned against the Rattus norveigicus reference genome (Ensembl Rnor 5.0 release) using TopHat version 2.0.9
After alignment reads were associated with known genes based on annotations derived from Ensembl and number of reads aligned with each gene was counted using Htseq tool version 0.5.4p3.
Data were normalized using TMM normalisation method of the edgeR R/Bioconductor package (R version 3.0.1, Biocunductor version 2.12)
For statistical testing data were log transformed using voom approach in the limma package.
Genome_build: Ensembl Rnor5.0 release
Supplementary_files_format_and_content: tab delimited text file including count values for each sample

organism: Rattus norvegicus

source_name: Hind paw - dorsal aspect skin

growth_protocol: Sprague-Dawley rats (125-200g) were housed in climate-controlled rooms on a 12 h light/dark cycle and with food and water ad libitum.

extract_protocol:
Skin from both the burn and control sampling sites were excised and stored in RNAlater for further processing. The tissue underwent rotor-stator homogenisation prior to RNA extraction, which was conducted with RNeasy Fibrous Tissue Mini and Midi kits (Qiagen, UK) according to the manufacturer’s protocols.
poly(A) enrichment (NEB, Ipswich, MA)

treatment_protocol: Rats were anaesthetized with 1.5 g/kg urethane by intraperitoneal (i.p.) injection. Body temperature was monitored and maintained at 37oC with a heat blanket, rectal thermometer and homeothermic control unit (50-7061-F; Harvard Apparatus).  A deep partial-thickness burn model was induced by submerging one hind paw into 60oC saline to the ankle for 2 minutes. The contralateral paw was simultaneously submerged in room temperature saline as a control for fluid immersion. Upon completion of the experiments, animals were terminally anaesthetised with i.p. sodium pentobarbital (40 mg) and the microdialysis sites were excised to verify probe depth and collect skin samples for RNA extraction.

tag: treatment

value: Control

value: Sprague-Dawley


title: 21721

status: Public on Aug 31 2018

type: SRA

description: Sample 8

library_source: transcriptomic

molecule: total RNA

tag: strain


title: High salinity 25C

city: Seville

first: Carmen

last: Vargas

state: Seville

address: C/profesor García Gonzalez n2

country: Spain

institute: University of Seville

description: High salinity

data_processing:
Basecalls performed using SOLiD™ Instrument Control Software
Sequenced reads were trimmed for adaptor sequence. BioScope (version 1.3, Applied Biosystems, CA) was used to map the color sequences of each bead to the annotated NC_007963 reference genome obtained from the National Center for Biotechnology Information (NCBI).
Low quality mapped reads were evaluated and eliminated by using Picard Tools.
Assembling, identification, and quantification was performed by Bayesian inference by using the cufflinks v2.02 software
To assess the genes differentially expressed in the different stress conditions, the HTSeq software (http://www-huber.embl.de/users/anders/HTSeq) was used to determine the number of reads per gene.
The EDAseq software from the Bioconductor package was used to perform the different normalization procedures. For the differential expression analysis, a negative binomial distribution was assumed using DESeq.
Genome_build: NC_007963.1
Supplementary_files_format_and_content: Excel file includes a matrix table with raw counts of sequencing reads and normalized abundance measurements

molecule: polyA RNA

organism: Chromohalobacter israelensis DSM 3043

source_name: bacterial cells

growth_protocol: Cells were grown in M63 minimal medium with 20 mM glucose as the sole carbon source. Cultures were incubated in an orbital shaker at 200 rpm. Three different growth conditions were used: low salinity (0.6 M NaCl, 37 ºC), high salinity (2.5 M NaCl, 37 ºC) and high salinity plus high temperature (2.5 M, 45 ºC). Three replicate cultures were grown for each condition.

extract_protocol:
Cell total RNA was extracted using the High Pure RNA isolation kit (Roche). Depletion of 23S and 16S rRNA was performed using the MICROBExpress™ Bacterial mRNA Enrichment Kit (Ambion) followed by Ribo-Zero rRNA.Removal kit for Gram-negative bacteria (Epicentre)
RNA libraries were prepared for sequencing using standard SOLiD protocols

tag: growth medium

value: Glucose 20 mM M63 minimal medium suplemented with 2.5 M of NaCl

tag: growth temperature

value: 37 ºC


title: 21716

description: Sample 5


title: 21709

description: Sample 1

value: Burn


title: 21710

description: Sample 2


title: npr1-1 4ºC

city: MADRID

first: EMA

middle: YOLANDA

last: OLATE

state: MADRID

address: RAMIRO DE MAEZTU 9

department: MOLECULAR BIOLOGY

institute: CIB-CSIC

data_processing:
RNAseq reads were aligned to the TAIR10 Col-0 reference genome using TopHat2 (Kim et al, 2013) with default parameters
Uniquely mapped reads were counted per representative gene model (excluding introns) according to the TAIR10 annotation using custom R scripts
Differential expression between WT and mutant in each condition was calculated using DEseq2 (Love et al. 2014) following its manual
Genome_build: TAIR10
Supplementary_files_format_and_content: Text files include cpm counts for each sample

organism: Arabidopsis thaliana

source_name: leaves from two-week-old plants

growth_protocol: Plants were grown under long-day photoperiods (photon flux of 90µmol m-2 s-1) in pots containing a mixture of organic substrate and vermiculite (3:1, v/v)

extract_protocol:
Stressed plants were collected, inmediately frozen on liquid nitrogen ang homogenized to a fine powder. Total RNA was extracted using TRIzol® Reagent (Life Technologies) and cleaned with RNeasy Plant Mini Kit (Quiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cold treatment, plants were exposed to 4ºC for 24h under long-day photoperiods (photon flux of 40µmol m-2 s-1).

tag: developmental stage

value: two-week-old

tag: tissue

value: leaves

tag: genotype


title: 21711

description: Sample 3


title: Col-0 4ºC

value: wildtype (Col-0)


title: CM_day30_C1_024

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

country: Japan

institute: CyberomiX Inc

description: Gene expression of differentiated cells 30 days after the initial differentiation

data_processing:
Basecalls performed using BCL2FASTQ Conversion Software 1.8.4 in the CASAVA 1.8.2 pipeline.
Data were filtered using Illumina's Quality Filtering and 101th bases in reads were not used.
RNA-seq reads were aligned to the hg19 genome assembly using TopHat version 2.0.8b with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calcurated using RPKMforGenes, downloaded on 19th, October 2012.
Genome_build: hg19
Supplementary_files_format_and_content: Text file which contain RPKM were calculated using RPKMforGenes, downloaded on 19th, October 2012.

organism: Homo sapiens

source_name: differentiated CMs day30

growth_protocol: Undifferentiated iPSCs were dissociated, and then suspended in StemPro34 medium supplemented with Y-27632 and BMP4 and allowed to form EBs by being placed into 96-well dish. On day 1, media, which included activin A, BMP4 and bFGF, were added into the wells. On day 3, EBs were collected and dissociated, and then suspended in differentiation media supplemented with VEGF and  IWP-3. Approximately 10000-20000 cells were put in each well to again form aggregates for 4 days. On day 7, the media were changed to StemPro 34 media supplemented with VEGF and bFGF. For the maintenance of iPSC-CMs, the culture media were refed every 2-3 days.

extract_protocol:
RNA extraction and cDNA synthesis of single cells were performed using SMARTer Ultra Low Input RNA for Illumina Sequencing (TaKaRa) with the C1 Single-Cell Auto-prep with IFC for 10-17 µm (Fluigidm) according to the manufacturer’s instruction.
Sequencing libraries were constructed using Nextera XT DNA Sample Prep kit (Illumina) and Nextera XT Index Kit (Illumina) according to Fluigidm’s instruction, which is modified from Illumina’s original protocol.

treatment_protocol: After cardiac differentiation, we collected GFP positive cardiomyocytes by FACS sorting on day21 and 30.

tag: cell type

value: Differentiated cells from human induced pluripotent stem cells


title: CM_day30_C1_023


title: CM_day30_C1_021


title: CM_day30_C1_018


title: CM_day30_C1_019


title: 21717

description: Sample 6


title: CM_day30_C1_020


title: CM_day30_C1_016


title: CM_day30_C1_022


title: CM_day30_C1_015


title: CM_day30_C1_014


title: MN_day7_r2

city: New York City

first: Josefina

middle: Inés

last: del Mármol

state: NY

address: 1230 York Avenue

country: USA

institute: The Rockefeller University

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab17

data_processing:
For analysis of RNA-seq data, reads were uploaded to the Galaxy environment (usegalaxy.org) and were curated and trimmed according to the quality of the sequences using default options.
Curated sequences were ran through Tophat for Illumina using a built- in reference genome mm10 (GRCm38/mm10) for mapping the reads to the mouse genome
Sequences were then ran through the Cufflinks package which assembles transcripts and estimates their abundances to obtain, for each sample, a list of transcripts with their associated transcript counts. Transcript counts are obtained as FPKMs (fragments per kilobase of transcript per million mapped reads), a normalized quantification in which each transcript’s FPKM is relatively proportional to the abundance of that particular transcript in the sample
Genome_build: mm10
Supplementary_files_format_and_content: Processed data is presented in a single excel file with 1 tab per sample. Each tab contains the gene id (e.g. NM_001289465), locus (chr1:4490927-4497354), FPKM value and low and high conf intervals for FPKM for that sample.

organism: Mus musculus

source_name: ES to Moter Neuron differntiation, day 7

growth_protocol: Hb9-GFP-mESCs were kept in serum-free 2i +LIF medium. Embryonic bodies were formed in serum-free medium (DMEM/F12, Neurobasal, L-Glutamine, beta-ME and KSR) in untreated culture dishes for two days, and motor neuron differentiation was initiated by adding 1 µM retinoic acid and 1 µM Smoothened agonist.

extract_protocol:
Total RNA was extracted at days 0 (mouse embryonic stem cells), 2, 3, 4, 5, and 7 (motor neurons) of each differentiation using a Trizol/RNeasy hybrid protocol. Briefly, cells are homogeneized using a recommended volume of Trizol (Invitrogen), chloroform is added in the recommended volume and the mix is shaken vigorously. After centrifugation to allow phase separation, the aqueous phase is kept and mixed with 70% ethanol 1:1. The protocol follows using an RNeasy column (QIAGEN) and following the manufacture’s instructions. For days 5 and 7 a step was added previous RNA extraction: cells were sorted using a BDFACSAria Cell Sorter (BD) to isolate only the GFP-positive fraction, therefore enriching the sample in motor neurons. GFP-positive cells were sorted into Trizol LS (Invitrogen) and extraction of RNA proceeded as before
The RNA samples were first treated with DNase, then one library per sample was prepared using Illumina’s TruSeq RNA Sample Prep Kit, where polyA-fragments were selected, followed by cDNA synthesis and ligation of amplification and sequencing adapters. Libraries were then individually barcoded and then pooled with 6 libraries per lane on an Illumina HiSeq 2500 instrument (Illumina).

tag: cell line

value: Hb9-GFP mouse ES cells

tag: time point


title: CM_day30_C1_017


title: MN_day5_r2

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab15

source_name: ES to Moter Neuron differntiation, day 5


title: MN_day5_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab14


title: MN_day7_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab16


title: AKAP12KO-Rep2

status: Public on Sep 01 2018

city: Seoul

first: Hye Shin

last: Lee

department: College of pharmacy

country: South Korea

institute: Seoul National 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 mm10 whole genome using STAR v2.5.2b
Raw counts were calculated using featureCounts from Subread package v1.5.1
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include raw counts for each sample

source_name: AKAP12KO, liver

extract_protocol:
liver was removed, snap frozen in liquid nitrogen, RNA was isolated using Trizol Reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult

value: AKAP12 null

value: liver


title: Tud/+ female lacking germline 3 days post-mating rep 1

city: Tallahassee

first: Michelle

last: Arbeitman

state: FL

address: 1115 West Call Street

department: Department of Biomedical Sciences

institute: Florida State University

data_processing:
Sequences from Illumina adapters were trimmed using Trimmomatic ( version 0.32, minlen set to 50, 2 seed mismatches )
Unique reads were aligned to Drosophila Melanogaster genome, release 71 (Ensembl) using Tophat ( version 2.0.8, --read-mismatches and --read-edit-dist set to 6 )
Expression was quantified for genes, to raw counts using easyRNASeq ( from Bioconductor version 3.0.2, geneModels summarization )
edgeR, Fisher's exact test for differential expression ( from Bioconductor version 3.0.2, tagwise dispersion, Benjamini-Hochberg FDR correction )
Cufflinks quantification to Fragments Per Kilobase Per Million Mapped Reads (FPKM) (Cufflinks version 2.1.1, -- no-effective-length-correction )
Genome_build: Ensembl release 71

organism: Drosophila melanogaster

source_name: Head

extract_protocol:
Flies were flash frozen and heads were separated from the bodies. Total RNA was extracted from the heads using Trizol, mRNA was isolated using MicroPoly(A) Purist columns (Ambion).
After adding the spike-in control RNAs, samples were fragmented to ∼250 bp by chemical fragmentation. First-strand cDNA was synthesized using SuperScript II reverse transcriptase (Invitrogen) and a combination of random hexamer and oligo (dT) primers; second-strand cDNA was synthesized using DNA polymerase I in combination with ribonuclease H. Double-stranded cDNA templates were blunt ended using End-It Repair kit (Epicentre), and A-overhangs were added at both ends with Klenow fragment (3′→5′ exo-minus). Illumina GAII sequencing adaptors were then ligated to both ends of the cDNA templates using Fast-Link DNA ligation kit (Epicentre). We then enriched for cDNA templates by performing multiplex incorporating PCR reactions (18 cycles) and isolated 250- to 550-bp fragments by gel purification

tag: Sex

value: Female

tag: age

value: 8 days post-eclosion

tag: mated

value: Mated

tag: days post-mating

tag: female genotype

value: tud/+ no germline

tag: male genotype

value: Wildtype


title: High salinity 25B

description: High salinity


title: MN_day4_r3

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab12

source_name: ES to Moter Neuron differntiation, day 4


title: CM_day30_C1_010


title: CM_day30_C1_013


title: CM_day30_C1_011


title: CM_day30_C1_009


title: MN_day4_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab10


title: CM_day30_C1_012


title: MN_day3_r3

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab9

source_name: ES to Moter Neuron differntiation, day 3


title: MN_day4_r2

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab11


title: CM_day30_C1_007


title: MN_day3_r2

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab8


title: 21712

description: Sample 4

value: Sprague-Dawley


title: CM_day30_C1_008


title: CM_day30_C1_005


title: CM_day30_C1_006


title: MN_day4_r4

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab13


title: CM_day30_C1_003


title: MN_day3_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab7


title: MN_day2_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab4

source_name: ES to Moter Neuron differntiation, day 2


title: MN_day0_r3

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab3

source_name: ES to Moter Neuron differntiation, day 0


title: CM_day30_C1_002


title: CM_day21_C1_023

description: Gene expression of differentiated cells 21 days after the initial differentiation

source_name: differentiated CMs day21


title: CM_day30_C1_001


title: MN_day0_r1

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab1


title: CM_day21_C1_021


title: miR34a/p53_1

city: Munich

first: Matjaz

last: Rokavec

address: Thalkirchner Str. 36

department: Institute of Pathology

country: Germany

institute: Ludwig-Maximilians-University Munich

description:
total RNA from 6x AOM induced miR-34a/p53 IEC deficient tumors
NG-9023_5811_dko_lib104650_4323_3_1

data_processing:
CLC Genomics Workbench 7.5 software was used
Sequenced reads were mapped to mm10 genome using CLC Workbench default parameters
Reads were normalized using RUVs
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized reads values for each Sample

source_name: intestinal mouse tumor tissue

growth_protocol: Mouse facility. Treated with Azoxymethane for 6 weeks. Experiment ended 16 weeks after 1st injection.

extract_protocol:
Total RNA from tumors was isolated using the RNAeasy Kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Azoxymethane was injected intraperitoneally (i.p.) once a week for 6 weeks at 10mg/kg.

tag: background strain

value: FvB

value: colon tumor


title: miR34a/p53_2

description:
total RNA from 6x AOM induced miR-34a/p53 IEC deficient tumors
NG-9023_5822_dko_lib104651_4323_2_1


title: miR34a/p53_3

description:
total RNA from 6x AOM induced miR-34a/p53 IEC deficient tumors
NG-9023_5825_dko_lib104652_4323_2_1


title: p53_3

description:
total RNA from 6x AOM induced p53 IEC deficient tumors
NG-9023_6069_viTp53_lib104649_4323_3_1


title: MN_day2_r2

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab5


title: p53_2

description:
total RNA from 6x AOM induced p53 IEC deficient tumors
NG-9023_5838_viTp53_lib104648_4323_3_1


title: p53_1

description:
total RNA from 6x AOM induced p53 IEC deficient tumors
NG-9023_5837_viTp53_lib106353_4354_1_1


title: CM_day21_C1_017


title: CM_day21_C1_016


title: miR34a_1

description:
total RNA from 6x AOM induced miR-34a IEC deficient tumors
NG-9023_5848_viMir34a_lib106351_4354_1_1


title: CM_day21_C1_014


title: CM_day21_C1_019


title: miR34a_3

description:
total RNA from 6x AOM induced miR-34a IEC deficient tumors
NG-9023_5853_viMir34a_lib104646_4323_3_1


title: miR34a_2

description:
total RNA from 6x AOM induced miR-34a IEC deficient tumors
NG-9023_5850_viMir34a_lib104644_4323_3_1


title: MN_day0_r2

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab2


title: MN_day2_r3

description: gene_expression_mouse_ES_to_MN_differentiation_-_RNA_seq_data.xlsx_tab6


title: CM_day21_C1_022


title: wt_3

description:
total RNA from 6x AOM induced wt tumors
NG-9023_5839_wt_lib104642_4323_3_1


title: CM_day21_C1_012


title: CM_day21_C1_011


title: wt_2

description:
total RNA from 6x AOM induced wt tumors
NG-9023_5834_wt_lib104641_4323_2_1


title: CM_day21_C1_020


title: CM_day21_C1_013


title: CM_day21_C1_018


title: CM_day21_C1_010


title: CM_day21_C1_008


title: CM_day21_C1_015


title: Epi5

city: New York

first: Chae Ho

last: Lim

state: New York

address: 550 First Ave.

department: Dermatology

institute: New York University School of Medicine

data_processing:
Illumna standard procedure for base-calling
Using Bowtie aligner for reads alignment
using Samtools for duplicate reads removal
reads counts with htseq-count protocol
reads normalization with trimmed mean of M-values methods and general linear modeling for p value of genes
Genome_build: Mus_musculus.NCBIM37.67
Supplementary_files_format_and_content: E14_5d-vs-WT_Derm.xlsx: Comparison of gene expression profile between E14.5d and WT skin dermis
Supplementary_files_format_and_content: E14_5d-vs-WT_Epi.xlsx: Comparison of gene expression profile between E14.5d and WT skin epidermis
Supplementary_files_format_and_content: Shh-vs-E14_5d_Derm.xlsx: Comparison of gene expression profile between Shh overexpressing and E14.5d skin dermis
Supplementary_files_format_and_content: Shh-vs-E14_5d_Epi.xlsx: Comparison of gene expression profile between Shh overexpressing and E14.5d skin epidermis
Supplementary_files_format_and_content: Shh-vs-WT_Derm.xlsx: Comparison of gene expression profile between Shh overexpressing and WT skin dermis
Supplementary_files_format_and_content: Shh-vs-WT_Epi.xlsx: Comparison of gene expression profile between Shh overexpressing and WT skin dermis
Supplementary_files_format_and_content: Shh-vs-E14_5-Derm-downregulated_genes.xlsx: Upregulated genes in both Shh overexpressing and E14.5d skin dermis compared to WT skin dermis
Supplementary_files_format_and_content: Shh-vs-E14_5-Derm-upregulated_genes.xlsx: Downregulated genes in both Shh overexpressing and E14.5d skin dermis compared to WT skin dermis

source_name: Skin epidermis

extract_protocol:
Skin wound tissues (2 days after scab detachment) of control and K14-CreERT2; LSL-Shh mice and embryonic skin (E14.5d) were incubated in 20 mM EDTA solution at 37 oC for 2 hrs. After separation of epidermis from dermis, total RNA were isolated from epidermis and dermis using RNeasy Plus Micro-Kit (Qiagen) as described by manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mixed

value: Skin epidermis

value: wild type


title: wt_1

description:
total RNA from 6x AOM induced wt tumors
NG-9023_6068_wt_lib104643_4323_1_1


title: CM_day21_C1_005

description: Gene expression of differentiated cells 21 days after the initial differentiation


title: CM_day21_C1_006


title: CM_day21_C1_007


title: CM_day21_C1_009


title: Epi7


title: Tg-9101-Epi

value: 4-5 week old

value: K14-CreER; LSL-Shh


title: Epi3


title: Con-9229-Epi


title: CM_day21_C1_004

value: Differentiated cells from human induced pluripotent stem cells


title: Tg-9231-Epi


title: Con-9098-Epi


title: CM_day21_C1_003


title: iPSC_day0_C1_048

description: Gene expression of iPSC

source_name: Human induced pluripotent stem cells

value: Human induced pluripotent stem cells


title: iPSC_day0_C1_047

description: Gene expression of iPSC


title: CM_day21_C1_001


title: Derm4

source_name: Skin dermis

value: Skin dermis


title: iPSC_day0_C1_046

description: Gene expression of iPSC


title: Con-9097-Epi


title: Derm3


title: Tg-9233-Epi


title: Tg-9233-Derm


title: Epi4


title: iPSC_day0_C1_044

description: Gene expression of iPSC


title: iPSC_day0_C1_043

description: Gene expression of iPSC


title: CM_day30_C1_004

description: Gene expression of differentiated cells 30 days after the initial differentiation


title: Derm5


title: Tg-9101-Derm


title: CM_day21_C1_002


title: iPSC_day0_C1_042

description: Gene expression of iPSC


title: iPSC_day0_C1_041

description: Gene expression of iPSC


title: Con-9098-Derm


title: iPSC_day0_C1_039

description: Gene expression of iPSC


title: Con-9097-Derm


title: iPSC_day0_C1_038

description: Gene expression of iPSC


title: iPSC_day0_C1_040

description: Gene expression of iPSC


title: iPSC_day0_C1_036

description: Gene expression of iPSC


title: iPSC_day0_C1_045

description: Gene expression of iPSC


title: Derm7


title: iPSC_day0_C1_031

description: Gene expression of iPSC


title: iPSC_day0_C1_030

description: Gene expression of iPSC


title: iPSC_day0_C1_032

description: Gene expression of iPSC


title: iPSC_day0_C1_034

description: Gene expression of iPSC


title: iPSC_day0_C1_029

description: Gene expression of iPSC


title: iPSC_day0_C1_033

description: Gene expression of iPSC


title: iPSC_day0_C1_028

description: Gene expression of iPSC


title: iPSC_day0_C1_027

description: Gene expression of iPSC


title: iPSC_day0_C1_024

description: Gene expression of iPSC


title: Tg-9231-Derm


title: iPSC_day0_C1_025

description: Gene expression of iPSC


title: iPSC_day0_C1_022

description: Gene expression of iPSC


title: iPSC_day0_C1_023

description: Gene expression of iPSC


title: iPSC_day0_C1_026

description: Gene expression of iPSC


title: iPSC_day0_C1_037

description: Gene expression of iPSC


title: iPSC_day0_C1_020

description: Gene expression of iPSC


title: iPSC_day0_C1_017

description: Gene expression of iPSC


title: iPSC_day0_C1_035

description: Gene expression of iPSC


title: iPSC_day0_C1_019

description: Gene expression of iPSC


title: iPSC_day0_C1_013

description: Gene expression of iPSC


title: iPSC_day0_C1_015

description: Gene expression of iPSC


title: iPSC_day0_C1_012

description: Gene expression of iPSC


title: iPSC_day0_C1_014

description: Gene expression of iPSC


title: iPSC_day0_C1_011

description: Gene expression of iPSC


title: iPSC_day0_C1_009

description: Gene expression of iPSC


title: iPSC_day0_C1_021

description: Gene expression of iPSC


title: iPSC_day0_C1_008

description: Gene expression of iPSC


title: iPSC_day0_C1_010

description: Gene expression of iPSC


title: iPSC_day0_C1_007

description: Gene expression of iPSC


title: iPSC_day0_C1_004

description: Gene expression of iPSC


title: iPSC_day0_C1_003

description: Gene expression of iPSC


title: iPSC_day0_C1_002

description: Gene expression of iPSC


title: iPSC_day0_C1_006

description: Gene expression of iPSC


title: iPSC_day0_C1_001

description: Gene expression of iPSC


title: Brain_rep2_24 hours_ sugar_ starvation

city: Oxford

first: Naveen

last: Prasad

state: Oxfordshire

address: Mansfield Road

department: Dept of Physiology, Anatomy & Genetics

institute: Centre for Neural Circuits & Behaviour

data_processing:
Reads were trimmed using Trimmomatic.  Tophat2 was used to align the reads to Drosophila genome. Subsequently cufflinks was used to assemble the reads and cuffmerge was used to assemble the transcripts. We used Cuffdiff to identify diffrentially expresed genes under various conditons.
Genome_build: dm3
Supplementary_files_format_and_content: excel sheet containing gene names, fly base gene id, locus, FPKM of the transcript under different conditons, log 2(fold change), p and q values
Supplementary_files_format_and_content: differentially expressed genes under sugar starvation regime
Supplementary_files_format_and_content: differentially expressed genes under complete starvation regime

source_name: brain

growth_protocol: Flies were reared on regular yellow food, wandering third instar larvae were picked up from the fly bottles, washed in cold Phosphate buffered saline (PBS), pH 7.4 and transferred to holidic food. The flies were maintained for 5 days post eclosion in holidic medium.

extract_protocol:
Total RNA was isolated from dissected fly brains using TRIzol (Invitrogen) and QIAGEN RNAeasy mini kit according to manufacturer's guidelines. RNA quality was checked using bioanalyzer (Agilent) and high quality samples were used for library preparation and sequencing.
mRNA was isolated from total RNA and second strand cDNA synthesis was carried out. The  cDNA was end repaird, A- tailed and adapter ligated. Thw prepared libraries were multiplexed and paired end seuqning (100bp) was carried out over one Rapid Flow Cell (Illumina)

treatment_protocol: 5 day old adult flies were transferred to holidic medium lacking sugar  (for sugar starvation regime) or to agar solution (for complete starvation regime) for 24 hours.

value: canton- s (cs)

value: brain

value: male

tag: regime

value: 24 hours_ sugar_ starvation


title: iPSC_day0_C1_016

description: Gene expression of iPSC


title: Brain_rep4_24 hours_ complete_ starvation

tag: strain

value: 24 hours_ complete_ starvation


title: Brain_rep4_24 hours_ sugar_ starvation


title: Brain_rep1_24 hours_ complete_ starvation


title: Brain_rep1_24 hours_ sugar_ starvation


title: Brain_rep3_24 hours_ complete_ starvation


title: Brain_rep2_24 hours_ complete_ starvation


title: iPSC_day0_C1_018

description: Gene expression of iPSC


title: Brain_rep3_24 hours_ sugar_ starvation


title: Brain_rep2_normal_feeding


title: Brain_rep4_normal_feeding


title: Brain_rep3_normal_feeding


title: Brain_rep1_normal_feeding


title: 2X4_En_RNA

city: Nanjing

first: Limei

last: Wang

address: 1 Weigang Road

department: State Key Laboratory of Crop Genetics and Germplasm Enhancement

country: China

institute: Nanjing Agricultural University

description:
mRNA
processed_data_file: 02428_genes.fpkm_tracking
replicates q7,q8,q9

data_processing:
Illumina CASAVA_v1.8.2 software used for basecalling.
Raw small RNA sequence reads were parsed to remove 3’ adapters and retain 18-30-nt reads using cutadapt, then mapped onto the Oryza sativa genome (MSU version 7.0) using bowtie. To reduce ambiguity, only the perfectly matched reads were used for further analysis. The sequences from ribosomal RNAs, transfer RNAs, snoRNAs, and snRNAs were excluded from the analysis using perl script.
Low-quality reads in the raw RNA-seq data were examined using NGSQCToolkit_v2.3 and eliminated, and the high-quality reads were mapped onto the Oryza sativa genome (MSU version 7.0) and assembled using Tophat, and then the Cufflink, Cuffmerge and Cuffdiff were used for producing the genes.fpkm_tracking file.
Genome_build: Oryza sativa genome (MSU version 7.0)
Supplementary_files_format_and_content: txt files were produced by perl script and fpkm_tracking files were produced by Cuffdiff. The samples q1,q2,q3 in the file 02428_genes.fpkm_tracking refer to a genotype not included in this study: 2X_En_RNA.  All other sample identifiers (q*) can be found in description field of each sample.  The headers for the small RNA text files are: "Chr", "Strand", "Start", "End", "Hits", "Ref sequence", "Length", "Sequence", "Reads", "RPTM", respectively.

organism: Oryza sativa Japonica Group

source_name: endosperm

extract_protocol:
Each biological replication from 5 or more endosperms and 1-2 seedlings were used for RNA extract. Total RNA was isolated using miRVana kit (Ambion 1561) and Plant RNA Isolation Aid (Ambion 9690) to be used for RNA libraries and small RNA libraries.
RNA libraries and small RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6 day after pollination

value: endosperm


title: 4X_En_RNA

description:
mRNA
processed_data_file: 02428_genes.fpkm_tracking
replicates q4,q5,q6


title: 4X_En_smallRNA

description: small RNA


title: 4X2_En_RNA

description:
mRNA
processed_data_file: 02428_genes.fpkm_tracking
replicates q10,q11,q12


title: 2X4_En_smallRNA

description: small RNA


title: 4X2_En_smallRNA

description: small RNA


title: 4X_L_smallRNA

description: small RNA

source_name: leaves

value: trefoil stage

value: leaves


title: S13290 right midbrain

city: Nijmegen

first: Clyde

last: Francks

address: Wundtlaan 1

department: Language & Genetics

country: Netherlands

institute: Max Planck Institute for Psycholinguistics

data_processing:
base-calling with BGI internal software
filtering raw reads: Raw reads were filtered to exclude reads with more than 5% unknown bases, reads which contained more than 20% bases with quality score below 15, and reads with adapters.
alignment: Clean reads were aligned to the Human reference GRCh38 from UCSC using Hisat2 (v2.0.4, (Kim, et al., 2015)).
read counts: Using the same reference with RefSeq gene annotations, reads were counted per gene using RSEM (v1.3.0 (Li and Dewey, 2011)).  Both packages use bowtie2.
Genome_build: GRCh38
Supplementary_files_format_and_content: gene count files containing estimated read counts per gene and FPKM with Entrez ID and Symbol as identifiers (txt file)
Supplementary_files_format_and_content: supplementary file: matrix with per gene per sample expression as log2(cpm). Genes have been filtered to have at least five reads in at least three libraries.

source_name: midbrain

extract_protocol:
RNA was extracted at HDBR Newcastle. Tissue samples were divided into sub-samples each weighing thirty milligrams (mg). The sub-samples were homogenised using a Precellys 24 bead mill homogeniser (Bertin Corp. Rockville, MD, USA) using ceramic 1.4mm beads for soft tissue homogenising (CK14) with 600ul of RTL plus Buffer with 10µl/ml of β-Mercaptoethanol and 5µl/ml of reagent DX (Qiagen, Venlo, the Netherlands). RNA and DNA was extracted from the tissue with a QIAcube using an AllPrep DNA/RNA Mini Kit (Qiagen) following the manufacturer’s recommended protocol. RNA was then pooled from all 30 mg sub-samples belonging to a given embryo's left or right midbrain, or left or right forebrain.  RNA quality was assessed using an Agilent 2100 Bioanalyzer (Applied Biosystems, Santa Clara, CA, USA), and then RNA was shipped on dry ice to Beijing Genomics Institute (BGI) Shenzhen/HongKong, China.
Oligo(T)'s were used to enrich for mRNA out of the pool of total RNA. After fragmentation, cDNA was generated with random hexamer primers, and the cDNA fragments were connected with adapters, all with the usual quality control steps. Barcoded cDNA fragments were sequenced in two lanes of an Illumina HiSeq 4000 sequencer.  We used paired-end sequencing with a read length of 100 bases.

value: midbrain

tag: Stage

value: Carnegie stage 16

tag: side

value: right


title: S13192 left midbrain

value: left


title: S13290 left midbrain


title: S13192 right midbrain


title: S13290 right forebrain

source_name: forebrain

value: forebrain


title: S13128 left midbrain

value: Carnegie stage 15


title: S13128 right forebrain


title: S13128 left forebrain


title: S13052 right midbrain


title: Con-9229-Derm

value: Mixed

value: 4-5 week old

value: wild type


title: S13097 left forebrain


title: S13052 left forebrain


title: S13128 right midbrain


title: S13290 left forebrain


title: S13048 right midbrain

value: female


title: Cnot3_02

city: Akita

first: Keiji

last: Kuba

address: 1-1-1 Hondo

department: Biochemistry and metabolic science

institute: Akita University

data_processing:
Illumina Casava 1.8 software used for basecalling.
Removal of adapter sequences for each sample was manually confirmed from FastQC output. Sequenced reads were mapped to UCSC mm10 whole genome using bowtie2 v2.2.5 with the default parameters, and Tophat 2.1.0 to detect splicing junctions.
Raw read counts were extracted using R bioconductor package Rsubread with UCSC mm10 gtf. Raw read counts were then normalized by R bioconductor package edgeR (TMM normalization).
Genome_build: mm10
Supplementary_files_format_and_content: a single tab-delimited text file includes normalized counts for all samples

source_name: whole heart

extract_protocol:
RNA was extracted from mouse hearts (Input) and ani-Cnot3 IgG- or control IgG-immunoprecipitated samples using TRIZOL reagent (Invitrogen).
RNA libraries were prepared for sequencing in the laboratory of Yutaka Suzuki, The University of Tokyo (Tokyo, Japan).

tag: antibody

value: 4 weeks

value: heart


title: Cnot3_01

tag: tissue


title: S13052 left midbrain

value: male


title: IgG_01

value: control IgG-RIP


title: H19KO rep3_muscle

status: Public on Aug 30 2018

city: Farmington

last: Zhang

state: CT

address: 400 Farmington Ave

department: Genetics and Genome Sciences

institute: UConn Health

data_processing:
RTA 2.4.11 software was used for basecalling
Alignment was performed by using STAR 2.5.0a, and gene read counts were assessed using Cufflinks 2.2.1 (RNA-Seq Alignment 1.0.0 embedded in illumina BaseSpace platform).
Relative differential expression of genes between WT and H19 KO samples was determined by using DESeq2 1.0.0 (DESeq2 App embedded in illumina BaseSpace platform).
Genes that have significant differentiatial expression between WT and H19 KO triplicates (q Value < 0.05) were presented in the processed data file.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes mean counts for each gene

source_name: Soleus muscle

growth_protocol: Mice were housed at 22ºC–24ºC with a 12 h light/12 h dark cycle with regular chow and water provided ad libitum.

extract_protocol:
Total RNA was extracted from harvested mice soleus muslces by using PureLink RNA Mini Kit.
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing   adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

value: 21 weeks old

tag: genotype

value: Soleus muscle


title: IgG_02


title: S13097 right forebrain


title: WT rep3_muscle


title: S13052 right forebrain


title: WT HFD ad lib ZT24 rep 2

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

data_processing:
Reads of length 76 were trimmed to 51 nt
Reads were aligned to the mouse GRCm38 genome with STAR
Read counts per gene were calculated using FeatureCounts
DESeq2 was used to generate FPKM values
Genome_build: GRCm38
Supplementary_files_format_and_content: comma-separated values containing FPKM quantification for all samples

source_name: Liver

extract_protocol:
Liver were dissected out, flash frozen in liquid nitrogen, and RNA was prepared using Qiagen RNeasy Mini Kit.
Libraries were prepped using Illumina’s TruSeq Stranded mRNA HT kit according to manufacturer’s instructions, starting with 1ug of RNA

value: Liver

value: 24 weeks

value: WT

tag: feeding group

value: FA

tag: time


title: Input_02

value: Input


title: WT rep1_muscle


title: H19KO rep2_muscle


title: WT HFD ad lib ZT20 rep 2


title: WT HFD ad lib ZT24 rep 1


title: WT HFD ad lib ZT20 rep 1


title: WT rep2_muscle


title: WT HFD ad lib ZT16 rep 2


title: WT HFD ad lib ZT16 rep 1


title: H19KO rep1_muscle


title: WT HFD ad lib ZT12 rep 2


title: Input_01


title: iPSC_day0_C1_005

description: Gene expression of iPSC

tag: cell type

value: Human induced pluripotent stem cells


title: WT HFD ad lib ZT12 rep 1


title: S13048 right forebrain

value: forebrain

tag: Sex

value: Carnegie stage 16

value: right


title: WT HFD ad lib ZT8 rep 2

tag: age


title: WT HFD ad lib ZT4 rep 1


title: WT HFD ad lib ZT8 rep 1


title: WT HFD ad lib ZT4 rep 2


title: caNrf2 1

city: Zurich

first: Paul

last: Hiebert

address: Otto-Stern-Weg 7

country: Switzerland

institute: ETH Zurich

data_processing:
Base calling was performed with CASAVA v.1.8
Expression values were computed using RSEM 1.2.21 using the genome build GRCm38 and associated Ensemble annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: The processd data files have tabular format and contain TPM and FPKM values, as well as the expected counts ("transcriptCount" column) and the corresponding posterior estimates produced by RSEM.

source_name: skin of newborn transgenic mice with Cre-recombinase expressed in fibroblasts

extract_protocol:
Total RNA was isolated using Trizol reagent (Life technologies) according to the manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Primary dermal fibroblasts

tag: passages


title: caNrf2 3


title: S13048 left midbrain

value: midbrain

value: female

value: left


title: caNrf2 2


title: ctrl 1


title: ctrl 2


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT24 rep1

value: Rev-erb[alpha]/[beta]-liverdoubleKO


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT18 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT15 rep1

value: FT


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT24 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT9 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT12 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT21 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT9 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT6 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT3 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD TRF ZT18 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT21 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT12 rep1


title: Cry1Cry2 double KO HFD TRF ZT24 rep1

value: Cry1Cry2 double KO


title: Cry1Cry2 double KO HFD TRF ZT18 rep1


title: Cry1Cry2 double KO HFD TRF ZT21 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT3 rep1


title: Cry1Cry2 double KO HFD TRF ZT12 rep1


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT6 rep1


title: Cry1Cry2 double KO HFD TRF ZT9 rep1


title: ctrl 3


title: Cry1Cry2 double KO HFD TRF ZT3 rep1


title: Tuner_3A

city: Muscat

first: Adviti

last: Naik

address: Al Khoud

department: Biology

country: Oman

institute: Sultan Qaboos University

data_processing:
Hiseq Control Software v3.3.52 Real-time Analysis v2.7.3, bcl2fastq2 v2.16 were used for base calling
Sequenced reads were filtered by removing adaptor sequence, reads with >10% unknown bases and low-quality reads.
Clean reads were mapped to reference gene using the BowTie2 software v2.2.5 (64.bit) with the following parameter for SE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200  and HISAT2 v2.0.1-beta (64-bit) was used to map to GRCh human reference genome with the following paramters: -p 8 --phred64 --sensitive -I 1 -X 1000
RSEM tool was used for transcript quantification that computes Maximum likelihood abundance estimates using the Expectation Maximization algorithm as described by Li et al (2011, BMC Bioinformatics). FPKM method was used to calculate expression level
NOISeq was utilized to identify differentially expressed genes as a log2 fold-change between the average of the two replicates in wild-type group vs the NRP-1 overexpressing cells group.
Genome_build: GRCh38 hg19
Supplementary_files_format_and_content: Tab-separated excel files with FPKM values for each sample and DEGs between samples

source_name: BT-474 breast cancer cell line

growth_protocol: Cells were grown in RPMI-1640 media supplemented with 10% FBS. Cells harbouring the NRP-1 overexpression vector were selected using Geneticin antibiotic. Cells were maintained at 37°C in 5% CO2.

extract_protocol:
RNA was extracted using the Trizol reagent and a QC was conducted using the Agilent Bioanalyzer. Total RNA was treated with Dnase I and mRNA was enriched using the oligo (dT) magnetic beads. mRNA was fragmented into short fragments and cDNA was synthesized using random hexamer primer. The double strand cDNA was purified with magentic beads. End reparation and 3'-end single nucleotide adenine addition was performed. Finally, sequencing adaptors were ligated to the fragments. The fragments were enriched by PCR amplification.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

tag: cell line tissue source

value: Human breast cancer (luminal B-like)

tag: genotype/variation

value: NRP-1 overexpression


title: Cry1Cry2 double KO HFD TRF ZT6 rep1

value: Liver

value: 24 weeks


title: Tuner_2A


title: Cry1Cry2 double KO HFD ad lib ZT24 rep1

value: FA


title: BT474_2A

value: wild-type


title: Rev-erb[alpha]/[beta]-liverdoubleKO HFD ad lib ZT15 rep1


title: Cry1Cry2 double KO HFD ad lib ZT21 rep1


title: Cry1Cry2 double KO HFD ad lib ZT15 rep1


title: Cry1Cry2 double KO HFD ad lib ZT12 rep1


title: Bmal1-liverKO HFD TRF ZT8 rep1


title: BT474_1A


title: Cry1Cry2 double KO HFD ad lib ZT3 rep1


title: Bmal1-liverKO HFD TRF ZT24 rep1


title: Bmal1-liverKO HFD TRF ZT20 rep1


title: Cry1Cry2 double KO HFD TRF ZT15 rep1


title: Bmal1-liverKO HFD TRF ZT16 rep1


title: Cry1Cry2 double KO HFD ad lib ZT6 rep1


title: Cry1Cry2 double KO HFD ad lib ZT18 rep1


title: Bmal1-liverKO HFD ad lib ZT24 rep1


title: Bmal1-liverKO HFD TRF ZT4 rep1


title: Bmal1-liverKO HFD ad lib ZT12 rep1


title: Bmal1-liverKO HFD TRF ZT12 rep1


title: Bmal1-liverKO HFD ad lib ZT20 rep1


title: Bmal1-liverKO HFD ad lib ZT16 rep1


title: WT HFD TRF ZT24 rep2

value: WT


title: Bmal1-liverKO HFD ad lib ZT8 rep1


title: WT HFD TRF ZT24 rep1


title: Bmal1-liverKO HFD ad lib ZT4 rep1


title: WT HFD TRF ZT20 rep1


title: WT HFD TRF ZT16 rep1


title: WT HFD TRF ZT16 rep2


title: WT HFD TRF ZT12 rep2


title: WT HFD TRF ZT8 rep2


title: WT HFD TRF ZT4 rep2


title: WT HFD TRF ZT4 rep1


title: T47D_siCTR_rep2_ATAC-seq

city: Miami

first: Ho Lam

last: Chan

address: 1501 NW 10th Ave. BRB 742A

department: Human Genetics

institute: University of Miami

library_source: genomic

data_processing:
FASTQ data  were processed with Trimmomatic v0.32 to remove adapters and low-quality reads.
ChIP-seq reads were aligned to the  hg19 human genome using BWA v0.7.13-r1126 with the following parameters: aln -q 5 -l 32 -k  2. RNA-seq reads were aligned to the hg19 human genome using STAR aligner (version 2.5.3a) with default parameters  and RSEM (version 1.2.31) to obtain expected gene counts against the human RefSeq (release  76). ATAC-seq reads were aligned to the hg19 human genome using Bowtie2 v2.2.6.
Duplicate reads were removed using Picard tools (version 1.126 -  http://broadinstitute.github.io/picard).
RNA-seq differential expression was determined using DESeq2 and R (version 3.2.3) with q-value <0.05.
ChIP-seq peaks were called using MACS2.1 with default  parameters and –shiftsize 160 –nomodel –p 0.01 for all data except RING1B in human iPSCs. For all  H3k27me3 and H2AK119ub1 data, we added the option –broad. Whole-cell extract input  from the corresponding cell line were used as control. ATAC-seq peaks were called using the MACS2.1  with the parameters: -g hs -p 0.01 --nomodel --shift -75 --extsize 150 and a cutoff of q-value <0.05.
Homer annotatePeaks v4.8.3 was used for peak  annotation.
Bedtools v2.26.0 intersect was used to determine peak overlaps.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain the indexed tag chromosome coordinates and score produced from MACS2 peak calling.

molecule: genomic DNA

growth_protocol: T47D were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of RPMI-1640 that was supplemented with 10% FBS,10μg/ml insulin (Sigma-Aldrich cat# 91077C), 1x penicillin/streptomycin, and 1x glutamax.

extract_protocol:
ATAC-seq experiments were performed as previously described (Buenrostro et al., 2013) with the following modifications: 25,000 cells for each cell line were used to perform the transposon reaction. Samples were purified with a MinElute Reaction Cleanup kit (Qiagen cat# 28206) and DNA eluted in 13μl of EB Buffer.
To calculate the number of cycles for library amplification, 2μl of transposed DNA were amplified by qPCR for a total of 25 cycles. The 10μl qPCR reaction was set up as follows: 2μl of transposed DNA, 0.3μl 25μM Ad1_noMX, 0.3μl 25μM Ad2.X (custom oligos synthesized by Integrated DNA Technologies), 5μl NEBNext High-Fidelity 2X PCR Master Mix (New England BioLabs, #M0541S), 0.1μl 100X SYBR Green I (10,000X stock from Invitrogen, #S7563) and 2.3μl nuclease-free water with the following program on a Bio-Rad CFX96 Optics Module Thermal Cycler machine: 1) 72°C for 5 minutes, 2) 98°C for 30 seconds, 3) 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 30 seconds, 25 cycles, 4) 72°C for 1 minute, and 5) hold at 10°C. The Ct value of each sample reflects the number of PCR cycles for optimal amplification in the linear range of the reaction. A 50ul PCR reaction was then set up as follows: 10μl transposed DNA, 1.5μl 25μM Ad1_noMX, 1.5 μl 25μM Ad2.X (unique for each sample), 12μl of nuclease free water, and 25μl NEBNext High-Fidelity 2X PCR Master Mix with the same program as for the qPCR, but substituting the cycle number with the Ct-value obtained from the qPCR reaction. The PCR was performed on a Bio-Rad C1000 Touch Thermal Cycler. After PCR, the 50μl reactions were cleaned up and size selected by adding 25 μl of AMPure XP beads (Beckman Coulter #A63881) to remove fragments higher than 800bp. The supernatant was transferred to a new tube and 65μl of AMPure XP beads were added to remove fragments smaller than 100bp, then washed twice with freshly prepared 80% ethanol and eluted in 25μl of water. To determine the average fragment size of each library, samples were run through a High-sensitivity DNA screentape (Agilent Technologies cat# 5067-5584) following the manufacturer’s instructions on an Agilent Technologies 2200 TapeStation machine. To determine the concentration of each library, Qubit dsDNA high sensitivity reagents (Thermo Fisher Scientific cat# Q32851) were used following the manufacturer’s instructions on a Qubit 3 fluorometer.

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

tag: cell source

value: ATCC #HTB-133

tag: modifications

value: siCTR transiently transfected cells


title: T47D_siCTR_rep1_ATAC-seq


title: T47D_siRING1B_rep2_ATAC-seq

value: siRING1B transiently transfected cells


title: T47D_siRING1B_rep1_ATAC-seq


title: T47D_H3K4me1_ChIP-seq

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 1% formaldehyde (Sigma-Aldrich cat# 252549) added directly to culture media for 15min shaking gently at RT. During crosslinking, 1.25M glycine solution (10X) was prepared, then added to plates at a final concentration of 0.125M for 5min shaking gently at RT. The supernatant was aspirated, cells washed 1x with PBS, and harvested on ice using cell scrapers into 15ml sonication tubes (Diagenode cat# C01020031). Cells were pelleted at 2000rpm for 3min at 4°C, washed 1x with 10ml cold PBS, and pelleted once more. Cell pellet was resuspended in 1.3ml cold ChIP Buffer (2 volumes of SDS ChIP Buffer [100mM NaCl, 50mM Tris-HCl pH 8.1, 5mM EDTA pH 8.0, 0.5% SDS] with 1 volume TXT ChIP Buffer [100mM Tris-HCl pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 5% Triton X-100]). Cells were then sonicated on a Bioruptor Pico at 4°C for 20min of 30’’ ON-OFF cycles. After sonication, samples were centrifuged at maximum speed for 15min at 4°C and supernatant transferred to a new 1.5ml microtube. To check sonication efficiency, 20µl of sonicated samples was transferred to a new microtube with 80µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 30µl H2O. 6µl of orange DNA dye was added and 12µl and 24µl of each sample were run in a 1% agarose gel at 100V for 15min and imaged on a Bio-rad ChemiDoc XRS+. Protein concentration in sonicated samples was measured by Bradford assay, and 200µg of total protein was transferred to a 1.5ml LoBind tube (Eppendorf cat# 0030108051) and brought up to 500µl final volume with ChIP buffer. 5µl was removed as input material (1%) and placed in a separate microtube at 4°C. 2µg antibody was used for each histone ChIP (see Key Resources table for list of antibodies). The samples were rotated end-to-end overnight at 4°C. Protein A sepharose beads (GE Healthcare cat# 17528001) were washed 3x with ChIP buffer and 30µl bead slurry was added to each sample. Samples were incubated with beads for 2hr at 4°C rotating end-to-end. Following incubation, samples were centrifuged at 2000rpm for 3min at 4°C, washed 2x with ChIP Low Salt Buffer (50mM HEPES pH7.5, 140mM NaCl, 1% Triton X-100, 1x protease inhibitors), and 1x with ChIP High Salt Buffer (50mM HEPES pH7.5, 500mM NaCl, 1% Triton X-100, 1x protease inhibitors). Beads were dried after the last wash with a 28G needle fitted to a 1ml syringe. Elution Buffer (1% SDS, 0.1M sodium carbonate) was prepared fresh before use and 110µl was added to each sample and 95µl to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 2000rpm at RT and 100µl of supernatant was transferred to a new tube, being careful not to aspirate beads. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 60µl H2O and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Parental cells

tag: chip antibody

value: Diagenode # C15410194


title: T47D_shRING1B_rep2_RNA-seq

extract_protocol:
RNA was isolated from fresh or frozen cell pellets using TRIzol reagent (Thermo Fisher Scientific cat# 15596018) according to manufacturer's instructions.
Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit (New England Biolabs cat# E6310) starting with 1µg total RNA and following the manufacturer’s instructions. Ribo-depleted RNA was then further processed with the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs cat# E7420) for library preparation following the manufacturer’s instructions.

value: pLKO_shRING1B stable cells


title: T47D_shCTR_rep1_RNA-seq

value: pLKO_shCTR stable cells


title: T47D_shCTR_rep2_RNA-seq


title: WT HFD TRF ZT20 rep2

tag: strain

value: FT


title: T47D_H3K36me3_ChIP-seq

value: Abcam # ab9050


title: T47D_H3K4me3_ChIP-seq

value: Diagenode # C15410003


title: T47D_PCGF2_ChIP-seq

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and processed using the High Sensitivity ChIP-IT Kit (Active Motif cat #53040).
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.

value: Santa Cruz # sc-10744 X


title: T47D_H3K27ac_ChIP-seq

value: Abcam # ab4729


title: T47D_ERa_ChIP-seq

value: Diagenode # C15100066


title: T47D_Input_ChIP-seq


title: T47D_H2AK119ub1_ChIP-seq

value: Cell Signaling # 8240


title: T47D_H3K27me3_ChIP-seq

value: Active Motif # 39155


title: T47D_RING1B_ChIP-seq

value: Active Motif # 39663


title: MDAMB231_siRING1B_rep1_ATAC-seq

growth_protocol: MDA-MB-231 were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of DMEM that was supplemented with 10% FBS, 1x penicillin/streptomycin, and 1x glutamax.

value: Mammary gland adenocarcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-26


title: MDAMB231_siCTR_rep2_ATAC-seq

value: siCTR transiently transfected cells


title: MDAMB231_siRING1B_rep2_ATAC-seq

value: siRING1B transiently transfected cells


title: MDAMB231_siCTR_rep1_ATAC-seq


title: MDAMB231_shRING1B_rep2_RNA-seq


title: MDAMB231_shCTR_rep2_RNA-seq


title: T47D_shRING1B_rep1_RNA-seq

value: Mammary gland ductal carcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-133


title: MDAMB231_shRING1B_rep1_RNA-seq

value: pLKO_shRING1B stable cells


title: Cry1Cry2 double KO HFD ad lib ZT9 rep1

value: Liver

value: 24 weeks

value: Cry1Cry2 double KO

value: FA


title: WT HFD TRF ZT8 rep1

value: WT

value: FT


title: MDAMB231_BRD4_ChIP-seq

value: Parental cells

value: Bethyl Laboratories # A301-985A100


title: MDAMB231_PCGF2_ChIP-seq

value: Santa Cruz # sc-10744 X


title: MDAMB231_H3K4me1_ChIP-seq

value: Diagenode # C15410194


title: MCF10A_H3K27ac_ChIP-seq

growth_protocol: MCF10A were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations. Complete culture media comprised of DMEM/Ham’s F-12 (1:1) that was supplemented with 5% horse serum, 10ng/ml EGF (Thermo Fisher Scientific cat# PHG0311), 50ng/ml cholera toxin (Sigma-Aldrich cat# C8052), 10μg/ml insulin (Sigma-Aldrich cat# 91077C), 500ng/ml hydrocortisone (Sigma-Aldrich cat# H0888), 1x penicillin/streptomycin, and 1x glutamax.

value: Mammary gland fibrocystic disease  epithelial cells

value: ATCC #CRL-10317

value: Abcam # ab4729


title: MCF10A_H3K36me3_ChIP-seq

value: Abcam # ab9050


title: MDAMB231_H3K27me3_ChIP-seq

value: Mammary gland adenocarcarcinoma epithelial cells derived from metastatic site

value: ATCC #HTB-26

value: Active Motif # 39155


title: MDAMB231_Input_ChIP-seq


title: MDAMB231_H2AK119ub1_ChIP-seq

value: Cell Signaling # 8240


title: iPSC_rep2_RNA-seq

source_name: iPSC

growth_protocol: Human iPSCs were maintained in complete feeder-free mTESR1 culture medium (STEMCELL Technologies cat# 85850) on matrigel-coated plates (Corning ca# 354277) at 37°C with 5% CO2. The culture medium was changed daily and colonies were enzymatically passaged with StemPro Accutaste cell dissociation reagent (Thermo Fisher Scientific cat# A1110501) at a 1:4-1:6 split ratio every 4-7 days. DMEM/F-12 media (STEMCELL Technologies cat# 36254) was used to detach colonies. ROCK inhibitor Y-27632 (STEMCELL Technologies cat# 72302) was used in every split and when cells were thawed from liquid nitrogen. If identified, spontaneously differentiated cells were mechanically removed prior to passaging.

value: iPSC

value: Heart-derived sendai virus reprogrammed induced pluripotent stem cell

value: ATCC #ACS-1021


title: MCF10A_Input_ChIP-seq


title: MCF10A_H3K27me3_ChIP-seq


title: MDAMB231_H3K27ac_ChIP-seq


title: MDAMB231_H3K36me3_ChIP-seq


title: MDAMB231_H3K4me3_ChIP-seq

value: Diagenode # C15410003


title: MCF10A_rep2_RNA-seq


title: iPSC_H3K27ac_ChIP-seq

extract_protocol:
Cells were grown to 80% confluence on 150cm plates and fixed with 1% formaldehyde (Sigma-Aldrich cat# 252549) added directly to culture media for 15min shaking gently at RT. During crosslinking, 1.25M glycine solution (10X) was prepared, then added to plates at a final concentration of 0.125M for 5min shaking gently at RT. The supernatant was aspirated, cells washed 1x with PBS, and harvested on ice using cell scrapers into 15ml sonication tubes (Diagenode cat# C01020031). Cells were pelleted at 2000rpm for 3min at 4°C, washed 1x with 10ml cold PBS, and pelleted once more. Cell pellet was resuspended in 1.3ml cold ChIP Buffer (2 volumes of SDS ChIP Buffer [100mM NaCl, 50mM Tris-HCl pH 8.1, 5mM EDTA pH 8.0, 0.5% SDS] with 1 volume TXT ChIP Buffer [100mM Tris-HCl pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 5% Triton X-100]). Cells were then sonicated on a Bioruptor Pico at 4°C for 10min of 30’’ ON-OFF cycles. After sonication, samples were centrifuged at maximum speed for 15min at 4°C and supernatant transferred to a new 1.5ml microtube. To check sonication efficiency, 20µl of sonicated samples was transferred to a new microtube with 80µl PBS and incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm to decrosslink. DNA was purified with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 30µl H2O. 6µl of orange DNA dye was added and 12µl and 24µl of each sample were run in a 1% agarose gel at 100V for 15min and imaged on a Bio-rad ChemiDoc XRS+. Protein concentration in sonicated samples was measured by Bradford assay, and 200µg of total protein was transferred to a 1.5ml LoBind tube (Eppendorf cat# 0030108051) and brought up to 500µl final volume with ChIP buffer. 5µl was removed as input material (1%) and placed in a separate microtube at 4°C. 2µg antibody was used for each histone ChIP (see Key Resources table for list of antibodies). The samples were rotated end-to-end overnight at 4°C. Protein A sepharose beads (GE Healthcare cat# 17528001) were washed 3x with ChIP buffer and 30µl bead slurry was added to each sample. Samples were incubated with beads for 2hr at 4°C rotating end-to-end. Following incubation, samples were centrifuged at 2000rpm for 3min at 4°C, washed 2x with ChIP Low Salt Buffer (50mM HEPES pH7.5, 140mM NaCl, 1% Triton X-100, 1x protease inhibitors), and 1x with ChIP High Salt Buffer (50mM HEPES pH7.5, 500mM NaCl, 1% Triton X-100, 1x protease inhibitors). Beads were dried after the last wash with a 28G needle fitted to a 1ml syringe. Elution Buffer (1% SDS, 0.1M sodium carbonate) was prepared fresh before use and 110µl was added to each sample and 95µl to each input sample that was previously set aside. To elute immunocomplexes from beads, samples were incubated at 65°C for 3hr on an Eppendorf Thermomixer shaking at 1000rpm. Tubes were centrifuged for 3min at 2000rpm at RT and 100µl of supernatant was transferred to a new tube, being careful not to aspirate beads. DNA purification was performed with the QIAquick PCR Purification Kit (Qiagen cat# 28106) and eluted in 60µl H2O and quantified by Qubit.
Immunoprecipitated DNA was used to generate libraries using the NEBNext Ultra DNA Library Prep Kit for Illumina (New England Biolabs cat# 7370) following the manufacturer’s instructions.


title: iPSC_H3K4me3_ChIP-seq


title: iPSC_H2AK119ub1_ChIP-seq


title: siH19 rep3

data_processing:
RTA 2.4.11 software was used for basecalling
Alignment was performed by using STAR 2.5.0a, and gene read counts were assessed using Cufflinks 2.2.1 (RNA-Seq Alignment 1.0.0 embedded in illumina BaseSpace platform).
Relative differential expression of genes between siCon and siH19 samples was determined by using DESeq2 1.0.0 (DESeq2 App embedded in illumina BaseSpace platform).
Genes that have significant differentiatial expression between siCon and siH19 triplicates (q Value < 0.05) were presented in the processed data file.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes mean counts for each gene

source_name: HepG2 (ATCC)

growth_protocol: HepG2 cells (American Type Culture Collection, Manassas, VA, USA; ATCC HB-8065) were authenticated and were free from mycoplasma contamination. The cells were maintained in ATCC-formulated EMEM (30-2003) supplemented with 10% fetal bovine serum, heat inactivated, and 1% penicillin/streptomycin.

extract_protocol:
Total RNA was harvested using PureLink RNA Mini Kit (Cat. no. 12183018A).
RNA-seq libraries were prepared using illumina TruSeq Stranded Total RNA LT kit with Ribo-Zero Human/Mouse/Rat, setA (Cat# rs-122-2201) according to the sample preparation protocol. Briefly, 1 ug total RNA was subjected to Ribo-Zero depletion to remove rRNAs. The remaining RNA was purified, fragmented, and primed with random hexamers for cDNA synthesis. After first and second cDNA synthesis, cDNA fragments were adenylated and then ligated to indexing   adapters. The cDNA fragments were enriched by PCR, purified, and then sequenced on an illumina NextSeq500 using paired-end chemistry and 76-bp cycles.

treatment_protocol: In a 6-well plate scale,  cells were transfected with either control siRNA or H19 siRNA. 48h later, cells were harvested for RNA extraction.

tag: sirna


title: iPSC_RING1B_ChIP-seq

value: Homemade (ref. Morey et al., Cell Stem Cell, 2015)


title: MCF10A_rep1_RNA-seq

value: Parental cells


title: siCon rep3

value: siControl


title: MCF10A_H2AK119ub1_ChIP-seq


title: siH19 rep2


title: iPSC_rep1_RNA-seq


title: siH19 rep1


title: iPSC_H3K27me3_ChIP-seq


title: MDAMB231_RING1B_ChIP-seq

value: Active Motif # 39663


title: MCF10A_H3K4me3_ChIP-seq


title: MCF10A_RING1B_ChIP-seq


title: siCon rep2


title: H&H 35_Mesenchyme_II

city: Arlington

first: Ang

last: Li

state: TX

address: 655 W Mitchell St, SEIR 244

department: Kinesiology

institute: University of Texas at Arlington

data_processing:
Prealignment QA/QC, adaptor sequence trimming, alignment of reads (TOPHAT 2, UCSC galGal4), and postalignment QA/AC were done in Partek Flow
Reads Per Kilobase of exon per Megabase of library size (RPKM) were caculated in Partek Genomic Suite
Genome_build: galGal4
Supplementary_files_format_and_content: Excel files include RPKM value for each sample

organism: Gallus gallus

source_name: dorsal skin mesenchyme

extract_protocol:
Dorsal skin epithelium and mesenchyme were separated in 2xCMF, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit Version2 was used with 4 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: dorsal skin mesenchyme

tag: batch

value: II


title: H&H 35_Mesenchyme_I

tag: tissue

value: I


title: H&H 31_Epithelium_II

source_name: dorsal skin epithelium

value: dorsal skin epithelium


title: H&H 31_Epithelium_I


title: H&H 31_Mesenchyme_I


title: MDAMB231_shCTR_rep1_RNA-seq

value: pLKO_shCTR stable cells


title: Menin-KO-dGln

city: Toon

first: Junpei

last: Suzuki

address: Shitukawa

department: Graduate School of Medicine

institute: Ehime University

data_processing:
MiSeq Control Software (illumina) was used for basecalling
Sequenced reads  mapped to mm9 whole genome using TopHat v2.0.11
Fragments Per Kilobase of exon per Million mapped sequence reads (FPKM) were calculated using Cufflinks v2.1.1
Genome_build: mm9

source_name: splenic naïve CD8 T cell

growth_protocol: WT or Menin KO naïve CD8 T (CD44lowCD62Lhigh) cells were prepared using a Naïve CD8+ T cell Isolation kit (cat#130-096-543; Miltenyi Biotec).  Naïve CD8 T cells (1.5 × 106) were stimulated with immobilized anti-TCR-β mAb (3 μg/ml, H57-597; BioLegend) and anti-CD28 mAb (1 μg/ml, 37.5; BioLegend) for 36 hours in the presence of IL-2 (10 ng/ml, Pepro Tech).  The cells were cultured in RPMI 1640 with L-glutamine (cat#189-02025) supplemented with 10 % fetal bovine serum, 2 mM L-glutamine (16948-04; nacalai tesque), 1 mM sodium pyruvate (cat#06977-34; nacalai tesque), 1% MEM nonessential amino acids (cat#06344-56; nacalai tesque), 10 mM HEPES (cat#15630-080; Gibco), 55 μM 2-Mercaptoethanol (cat#21985-023; gibco) and 1% penicillin-streptomycin (cat#26253-84; nacalai tesque).  For glutamine deprived conditions, the cells were cultured in RPMI 1640 without L-glutamine (cat#183-02165; Wako) supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, 1 % MEM nonessential amino acids, 10 mM HEPES, 55 μM 2-mercaptoethanol and 1% penicillin-streptomycin.

extract_protocol:
Total RNA was isolated with PureLink RNA Mini Kit (lifetechnologies) according to the manufacture's protocol
Libraries were preared according to illumina's instructions  TruSeq RNA sample preparation kit v2 (illumia) according to

value: spleen

tag: culture conditions

value: glutamine deprived conditions

value: Menin KO


title: Menin-KO-Ctrl

value: normal conditions


title: iPSC_input_ChIP-seq

value: iPSC


title: WT-Ctrl

value: wild type


title: Control Liver

data_processing:
BaseCalling performed using BCL2Fastq version 1.8.4
Using Bismark v0.14.3 to align reads against mouse mm10 reference genome
Methylation calling performed by Zymo Research proprietary pipeline
Genome_build: mouse mm10
Supplementary_files_format_and_content: bed file

growth_protocol: CD-1 mice were obtained from Charles River Laboratories (Wilmington, MA, USAS). Mice were housed at 22°C–24°C with a 12 hr light/12 hr dark cycle with standard chow (Purina Chow; Purina Mills, Richmond, IN, USA) and water provided ad libitum.

extract_protocol:
Genomic DNA was extracted from frozen liver samples by using Quick-gDNA MicroPrep kit from Zymo Research company according to the protocol.
Libraries were prepared from 200-500 ng of genomic DNA digested with 60 units of TaqαI and 30 units of MspI (NEB) sequentially and then extracted with Zymo Research (ZR) DNA Clean & Concentrator™-5 kit (Cat#: D4003). Fragments were ligated to pre-annealed adapters containing 5’-methyl-cytosine instead of cytosine according to Illumina’s specified guidelines (www.illumina.com). Adaptor-ligated fragments of 150–250 bp and 250–350 bp in size were recovered from a 2.5% NuSieve 1:1 agarose gel (Zymoclean™ Gel DNA Recovery Kit, ZR Cat#: D4001). The fragments were then bisulfite-treated using the EZ DNA Methylation-Lightning™ Kit (ZR, Cat#: D5020). Preparative-scale PCR was performed and the resulting products were purified (DNA Clean & Concentrator™ - ZR, Cat#D4005) for sequencing on an Illumina HiSeq.

treatment_protocol: For fasting experiments, 12-week-old mice were fasted for 12 hr and then sacrificed by ether anesthesia followed by cervical dislocation. Liver samples were collected and snap frozen in liquid nitrogen and stored at -80°C for further analysis.

value: Liver


title: Fasting Liver


title: WT-dGln


title: siCon rep1


title: H&H 35_Epithelium_II


title: H&H 35_Epithelium_I


title: S13048 left forebrain

value: forebrain

value: female

tag: Stage

value: Carnegie stage 16

tag: side

value: left


title: shCT_0h_2

city: Barcelona

first: Enrique

last: Blanco

address: Dr. Aiguader 88

department: Gene Regulation, Stem Cells and Cancer

institute: Center for Genomic Regulation (CRG)

description:
RNAseq experiment
FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt

data_processing:
ChIPseq analysis: Alignment: Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the option -m 1. RNAseq analysis: Alignment: Sequence reads were mapped against the mm9 mouse genome assembly using TopHat (PubMed ID 22383036) with the option ‐g 1. Cufflinks (PubMed ID 22383036) was run to quantify the expression in FPKMs of each annotated transcript in RefSeq. ATACseq analysis:  Sequence reads were mapped to the Mouse genome (mm9, July 2007) using BOWTIE (PubMed ID 19261174) with the options -m 1, --chunkmbs 2000 and -X 2000.
Peak-calling: Peak detection was performed with MACS (PubMed ID: 18798982). ChIPseq and ATACseq profiles were produced by MACS in BedGraph format. Peaks were reported in BED format.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BedGraph, genome-wide ChIP profile)
Supplementary_files_format_and_content: ChIP_LB1_0h_11732_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_8h_11733_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ChIP_LB1_24h_11734_R2.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_0h_11864.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_8h_11865.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: ATAC_24h_11866.bdg.gz (BED, signal enriched regions)
Supplementary_files_format_and_content: FPKM_0h-8h-24h.txt (FPKM values)
Supplementary_files_format_and_content: FPKMs_0CT1_0CT2_0shLB1_0shLB2-8CT1_8CT2_8shLB1_8shLB2-24CT1_24CT2_24shLB1_24shLB2.txt (FPKM values)

source_name: mouse mammary epithelial cells

growth_protocol: NMuMG cells were maintained in Dubelcco’s modified Eagle’s medium (Invitrogen) with 10% fetal bovine serum (Invitrogen) supplemented with 10μg/ml of insulin (Sigma) at 37ºC in 5% CO2.

extract_protocol:
ChIP experiments were performed as previously described (Herranz et al., 2008, PubmedID: 18519590). RNA extraction was performed with GenEluteTM Mammalian Total RNA Miniprep Kit (Sigma-Aldrich). ATAC experiments were performed as previously described (Buenrostro et al., 2013, PubmedID: 24097267).
Libraries were prepared according to Illumina instructions.

treatment_protocol: TGFβ was added at a final concentration of 1-5 ng/ml to induce EMT in NMuMG cells.

value: NMuMG


title: shCT_0h_1


title: shCT_24h_1


title: shCT_8h_2


title: shLB_8h_1


title: shLB_24h_1


title: shCT_8h_1


title: RNA_8h_1

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: RNA_24h_2

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: shLB_0h_1


title: shCT_24h_2


title: RNA_24h_1

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: RNA_0h_1

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: shLB_24h_2


title: TAP CLIP-seq 1

city: Madrid

first: Begona

last: Aguado

state: Madrid

address: Nicolas Cabrera 1

department: Genomics and NGS Service

institute: CBMSO

description: RNA isolation from tandem affinity purified RNP complexes bound to TAP peptide (IgG sepharose resin, calmodulin agarose resin)

data_processing:
For the TAP sample, the peaks of both replicate 1 and 2 were combined and used as a single TAP control.
CLIP analysis software: pyicoclip. Default parameters.
Peaks in each replicate of RBS1 and RBS2 that appear in the TAP reads were removed.
The overlapping peaks of the RBS1 or RBS2 replicates were considered as the final set of peaks using fjoin.py.
Addition of 20 flanking nts.
Peaks annotation.
Peaks assumed to be in intergenic regions were removed.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular files containing peaks. Column1=chromosome; column2=start; column3=end; column4=number of reads in hit after filtering; column5=strand; column6=hit sequence; column7=ENSEMBL gene id; column8=gene short name; column9=ENSEMBL transcript id;  column10=feature; column11=feature type

source_name: HEK293 transfected cells

growth_protocol: HEK293 cells, grown in Dulbecco’s Modified Eagle Medium (DMEM), were transfected with the plasmids pcDNA3-CTAP, pcDNA3-RBS1-CTAP and pcDNA3-RBS2-CTAP using lipofectamine (Thermo Scientific) according to the manufacturer instructions. 24 h post-transfection, monolayers were washed with ice-cold PBS prior to UV irradiation (150 mJ/cm2 at 254 nm).

extract_protocol:
The RNA-protein complexes associated to RBS1, RBS2 or the TAP polypeptide were isolated as in the tandem affinity purification procedure  (IgG sepharose resin, calmodulin agarose resin) until the second purification step. After washing the calmodulin resin with the associated complexes, beads were incubated with 500 µl of Proteinase K Buffer (10 mM Tris-HCl pH 8, 100 mM NaCl, 0.5% SDS, 2 mM EGTA, 1 mM EDTA, proteinase K 0.2 mg/ml) at 65°C, during 2 h with gentle rocking. The elution products are recovered by gravity flow. RNAs were then extracted with phenol-chloroform, ethanol precipitated and resuspended in 20 µl of H20. Each RNA preparation was monitored using the Agilent 2100 Bioanalyzer (Agilent technologies).
RNA (about 100 ng) obtained from two independent biological replicates of each sample (RBS1, RBS2 and TAP) were used to generate cDNA libraries using the TruSeq Stranded mRNA Sample Prep Kit v2 (Illumina) according to the manufacturer's protocol, but omitting the polyA+ selection step. All purifications steps were done using AMPure XP beads (Beckman Coulter). cDNA libraries were subjected to Illumina adapter ligation with TruSeq Universal Adapter 5’AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT3’ and TruSeq Adapter, Index 5’GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCTCGTATGCCGTCTTCTGCTTG3’ and were sequenced in an Illumina HiSeq2000 sequencer. Reads length were 50 bp in a single-read run cycle.
CLIP-Seq

tag: cell type

value: human embryonic kidney cells


title: shLB_0h_2


title: RNA_8h_2

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: RNA_0h_2

description:
RNAseq experiment
FPKM_0h-8h-24h.txt


title: ATAC_8h

description: ATAC experiment


title: RBS2 CLIP-seq 1

description: RNA isolation from tandem affinity purified RNP complexes bound to Gemin5 RBS2-TAP fusion protein (IgG sepharose resin, calmodulin agarose resin)


title: ATAC_24h

description: ATAC experiment


title: RBS1 CLIP-seq 2

description: RNA isolation from tandem affinity purified RNP complexes bound to Gemin5 RBS1-TAP fusion protein (IgG sepharose resin, calmodulin agarose resin)


title: ATAC_0h

description: ATAC experiment

value: Not applicable (NA)


title: ChIP_LB1_24h

description: chromatin IP against LaminB1


title: RBS1 CLIP-seq 1


title: ChIP_LB1_8h

description: chromatin IP against LaminB1


title: RBS2 CLIP-seq 2


title: ChIP_LB1_0h

description: chromatin IP against LaminB1


title: 4dpi_Zebrafish_Retina_RNAseq

city: Mohali

first: Rajesh

last: Ramachandran

state: Punjab

address: Knowledge city, Sector 81, SAS Nagar, Manauli

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education and Research, Mohali

data_processing:
Base calling: bowtie2 (version 2.2.2)
Read alignment software: Tophat program (Version 2.1.0)
cufflinks program (version 2.2.1)
Genome_build: GRCz10
Supplementary_files_format_and_content: Tab-delimited text files contain comparison of gene expression levels between different time points or treatment.

organism: Danio rerio

source_name: retina_4 days post injury

growth_protocol: Zebrafish were maintained at 26-28 degree C before or after retinal injury with 14-10 hours light-dark cycles.

extract_protocol:
Retinae were disected out and taken into 250uL of TRIzol reagent, and homogenised followed by aquous phase seperation by adding chloroform. RNA was precipitated from aquous phase by isopropanol mediated chilling. Finally it was solubilised in appropriate volume of water.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Valproic acid treatment, post retinal injury, fish were dipped in 100uM VPA for 4days.

tag: genotype

tag: age

value: 10 months

value: Retina


title: Uninjured_Zebrafish_Retina_RNAseq


title: 4dpi_VPA_Zebrafish_Retina_RNAseq

source_name: retina_4 days post injury_and VPA treatment


title: PBK inhibition in C4-2 cell DMSO control rep 5

city: Cambridge

first: Chandra

last: Chilamakuri

address: Robinson Way

institute: Cancer Research UK Cambridge Institute

description: RNA seq from C4-2 cells treated with DMSO control

data_processing:
Single-end 40 bp reads generated on Illumina HiSeq were aligned to the human genome version GRCh37.64 using TopHat v2.0.4 (Trapnell et al., 2009). Read counts were obtained using HTSeq-count v0.5.3p9 (Anders et al., 2014), normalised and tested for differential gene expression using the Bioconductor package DESeq v1.10.1 (Anders and Huber, 2010).
Multiple testing corrections were applied using the Benjamini-Hochberg method (Benjamini and Hochberg, 1995). Genes were selected as differentially expressed such that FDR < 0.05.
Genome_build: GRCh37.64
Supplementary_files_format_and_content: HTSeq-count gene counts

source_name: prostate cancer epithelium

growth_protocol: Cells were grown in RPMI media with 10% FBS at 37C

extract_protocol:
Total RNA (miRNeasy kit, Qiagen) from the flow sorted cells was used to prepare libraries using the TruSeq RNA sample preparation kit (Illumina).
as per instructions from the TruSeq RNA sample preparation kit

treatment_protocol: 1 micro molar of PBKi was used to treat C4-2 cells grown in 10%RPMI media.

tag: sample group

tag: cell line

value: prostate cancer epithelium


title: PBK inhibition in C4-2 cell rep 2

description: RNA seq from C4-2 cells treated with PBKi

value: PBKi

tag: antibodies

value: anti-PBK (Abnova)cat no. H00055872


title: PBK inhibition in C4-2 cell DMSO control rep 6


title: PBK inhibition in C4-2 cell rep 5


title: PBK inhibition in C4-2 cell DMSO control rep 3


title: PBK inhibition in C4-2 cell rep 3


title: PBK inhibition in C4-2 cell DMSO control rep 4


title: 12hpi_Zebrafish_Retina_RNAseq

source_name: retina_12h post injury


title: PBK knockdown in C4-2 cell rep 4

description: RNA seq from C4-2 cells knocking down PBK

treatment_protocol: 50nM of siRNA pool was used using Lipofectamine RNAi MAX reagents transfected using Reverse transfection protocol.

value: SiPBK

value: anti-PBK (Abnova) cat no. H00055872


title: PBK knockdown in C4-2 cell rep 5


title: PBK knockdown in C4-2 cell rep 6


title: PBK knockdown in C4-2 cell rep 3


title: PBK inhibition in C4-2 cell rep 6


title: PBK inhibition in C4-2 cell rep 4


title: PBK inhibition in C4-2 cell rep 1


title: s2 cell H3K4me2 ChIP-seq rep2

status: Public on Aug 29 2018

city: Berlin-Buch

first: Scott

middle: Allen

last: Lacadie

address: Robert-Rössle-Str. 10

department: Berlin Institute for Medical Systems Biology

institute: Max Delbrück Center for Molecular Medicine

data_processing:
ATAC-seq reads were trimmed for adapters using flexbar v2.5 (-f i1.8 -u 10 -ae RIGHT -at 1.0) and mapped with bowtie2 v2.0.2 in default paired-end mode and restricting pair distances to 1500 (-X 1500 -- no-discordant) to version dm6 of the fly genome or ce16 of the worm genome followed by removal of multimappers. PCR duplicates were removed using Picard Tools MarkDuplicates v1.90 and reads were converted to .bed format using bedtools bamToBed v2.23. Mapped pairs were split into single reads and converted to a 38-bp fragment reflecting the theoretical minimal spacing required for a transposition event by Tn5 transposome using bedtools slop on the read 5’ends (-l 15 -r 22). Replicates were concatenated after confirming high concordance. All reads that intersected ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists ) were removed. Signal bigwig files for ATAC-Seq were generated using JAMM signal generator pipeline (Ibrahim et al., 2015).
The sequencing library for S2 H3K4me2 ChIP-Seq data set was prepared with Unique Molecular Identifiers, therefore the first 9 bases of each read were removed using flexbarv2.4 (Dodt et al., 2012) and reads were aligned to dm6 genome build using bowtie2 in paired-end mode keeping only concordantly aligned mates. All ChIP-seq datasets were collapsed using samtools rmdup (Li et al., 2009). All reads that intersected ENCODE blacklisted regions (https://sites.google.com/site/anshulkundaje/projects/blacklists ) were removed and all replicate BED files were concatenated together for peak calling and signal generation. Signal bigwig files were generated using JAMM signal generator pipeline (Ibrahim et al., 2015).
PEAT data was processed as follows. Fastq files from each mate were first matched and trimmed for the 5’end adapter using cutadapt (Martin, 2011) (parameters -a GTTGGACTCGAGCGTACATCGTTAGAAGCT -O 30 -m 20 --untrimmed-output). The sequences that were not matched for 5’end were then matched and trimmed for the 3’end adapter using cutadapt (Martin, 2011)(parameters -a GTCGGATAGGCCGTCTTCAGCCGCCTCAAG -O 30 -m 20 --untrimmed-output). The two resulting fastq files matching each end were combined, reverse complemented, and then unpaired mates discarded and paired mates matched based on read IDs using custom scripts. The resulting paired fastq files were then mapped using STAR (Dobin et al., 2013) (parameters --outFilterMultimapNmax 1 --outFilterMismatchNmax 1 --chimSegmentMin 30 --chimJunctionOverhangMin 30 --outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignIntronMin 20 --alignIntronMax 1000000 --alignEndsType EndToEnd --alignMatesGapMax 1000000 --alignSJoverhangMin 12 --alignSJDBoverhangMin 3) to the dm6 genome assembly. Signal bigWig files were generated using bamCoverage from deepTools for each strand separately and normalizing for RPKM.
Genome_build: dm6 or ce6
Supplementary_files_format_and_content: bigWig

source_name: S2 cells

growth_protocol: Drosophila S2 cells were obtained from Life Tech (#R69007) and grown at 25°C in Schneider’s Cell medium (Life Tech, #21720024) with 10% FBS (Sigma, #F7524) and 10% L-Glutamine (Sigma, #G7513) without antibiotics. Cells were grown in T75 flasks at 25°C to a confluency of ~70%.

extract_protocol:
For H3K4me2 ChIP-seq, formaldehyde was added to media to a final concentration of 1% and incubated for 10 minutes on a shaker at room temperature. The reaction was quenched by adding glycine to a final concentration of 125 mM followed by 5 minutes of incubation on a shaker at room temperature. The cells were collected by centrifugation at 500 x g for 5 min at 4 °C and washed twice with ice-cold PBS. The cell pellet was resuspended in 10 ml ice-cold cell lysis buffer (5 mM HEPES (pH8), 85 mM KCl, 0.5% NP-40) with protease inhibitors (cOmplete™ ULTRA Tablets, Mini, EDTA-free, EASYpack Protease Inhibitor Cocktail, Roche # 05892791001) and incubated for 10 minutes at 4°C. Nuclei were released by 10 strokes with a Wheaton Dounce Homogenizer (tight pestle). The crude nuclear extract was collected by centrifugation at 500 x g for 5 min at 4°C, resuspended in 1 ml ice–cold nuclear lysis buffer (50 mM HEPES (pH 8), 10 mM EDTA, 0.5% N-Lauroylsarcosine with protease inhibitors) and incubated for 20 minutes at 4°C. After addition of 1 ml nuclear lysis buffer samples were sonicated using a Diagenode Bioruptor for 18 cycles (30” ON / 30” OFF) on “high”. After sonication samples were centrifuged at 14000 x g for 10 minutes at 4°C and the supernatant was aliquoted to DNA-low binding tubes. The chromatin was flash frozen in liquid nitrogen and stored at -80°C.
Protein A Sepharose (PAS) beads (Sigma #P9424) were washed twice with RIPA140 (140 mM NaCl, 10 mM Tris-HCl (pH 8), 1mM EDTA, 1% Triton X100, 0.1% SDS, 0.1% Na-Deoxycholate) with proteinase inhibitors and 1mg/ml BSA (Sigma #A7906) and incubated overnight. Chromatin was thawed on ice. 50µg of Chromatin was used per ChIP experiment. RIPA140 with proteinase inhibitor was added to a total volume of 1 ml and incubated with 2 µg of H3K4me2 antibody (Abcam, ab32356, Lot#: GR209821-1; or Epicypher 13-0013, Lot#: 14247001) for 16 hours at 4°C on a rotating mixer (40 rpm). 1% of the chromatin was used as input controls. Blocked beads were added to the chromatin-antibody complex solution and incubated for 3 hours at 4°C on a rotating mixer at 40 rpm. Complexes were washed once with 1ml RIPA140, 4 times with 1 ml RIPA500 (500 mM NaCl, 10 mM Tris-HCl (pH 8), 1mM EDTA, 1% Triton X100, 0.1% SDS, 0.1% Na-Deoxycholate) for 10 minutes each. Complexes were subsequently washed once in 1 ml LiCl-Buffer (250 mM LiCl, 10 mM Tris-HCl (pH 8), 1mM EDTA, 0.5% NP-40, 0.5% Na-Deoxycholate) and TE (10mM Tris-HCl (ph 8), 1mM EDTA) for 2 minutes each. Between each wash, beads were spun down at 500 x g for 2 minutes and the supernatant was discarded. Beads were resuspended in 100 µl TE and RNase A was added to a final concentration of 50 µg/ml followed by incubation at 37°C for 30 minutes. The samples were adjusted to a final concentration of 0.5% SDS and Proteinase K was added to a final concentration of 500µg/ml. Proteins were digested at 37°C for 90 minutes followed by reverse cross-linking overnight at 65°C. DNA was purified using phenol-chloroform extraction followed by ethanol precipitation. Libraries were prepared using the NEXTflex qRNA-Seq Kit v2 from Bioo Scientific (Catalog #5130-11) and sequenced on an Illumina NextSeq 500 sequencer.


title: s2 cell PEAT

growth_protocol: Drosophila S2 cells were grown to a density of 3 million per ml in Schneider's Medium (Invitrogen) supplemented with 10% FCS and 1x Antibiotics.

extract_protocol: PEAT library was constructed as described (Ni et al., 2010).


title: PBK knockdown in C4-2 cell rep 1


title: PBK knockdown in C4-2 cell rep 2


title: s2 cell H3K4me2 ChIP-seq input


title: s2 cell H3K4me2 ChIP-seq rep1


title: PBK inhibition in C4-2 cell DMSO control rep 1


title: s2 cell ATAC-seq rep2

growth_protocol: Drosophila S2 cells were grown at 25°C in ExpressFive SFM medium (Life Tech, #10486025) with 10% heat-inactivated FBS (Life Tech, #16000044) and 12% L-Glutamine (Life Tech, #25030024) and 1% Penicillin-Streptomycin (Life Tech, #15070063). Cells were grown in dishes to a confluency of ~80-95%.

extract_protocol:
For ATAC-seq, 200,000 cells were subjected to tagmentation as described (Buenrostro et al., 2013) with a total of 13 or 15 PCR cycles.
Library preparation was done following a protocol published in Buenrostro et al. 2013. Cell pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase) (Illumina Nextera DNA Library preparation kit, #FC-121-1030). The transposition reaction was carried out for 60 min at 37ºC. The samples were purified using Zymo DNA Clean & Concentrator kit; following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 12 to 14 cycles and sequenced using paired-end-sequencing length of 75 nucleotides using NextSeq 500/550 High Output v2 kit (Illumina) on a NextSeq500 machine (Illumina) following manufacturer's protocol.


title: s2 cell ATAC-seq rep1


title: Ah NOD Rep3

city: Kolkata

first: Maitrayee

last: DasGupta

state: WestBengal

address: 35 Ballygunge Circular Road

department: Biochemistry

institute: University of Calcutta

data_processing:
Image analysis are performed with the Illumina HiSeq Control Software (HCS). Image analysis identify clusters position, intensity and associated background noise.
The base calling is done by the RTA sofware provided by Illumina
Samples quality control are done by FastQC software.
Contaminants screening done by software FastQ Screen and PhiX genome  and Illumina adapters (TruSeq and Nextera) are also tested for this screening
Reads have been aligned to the Arachis duranensis and Arachis ipaensis references using TopHat2. It aligns RNA-Seq reads using the ultra high-throughput short read aligner Bowtie2, and then analyzes the mapping results to identify splice junctions between exons.
Genome_build: Arachis duranensis & Arachis ipaensis
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample

organism: Arachis hypogaea

source_name: ROOT

growth_protocol: Arachis hypogaea seeds were surface sterilized and alloowed to germinate in soil

extract_protocol:
Infected roots were harvested at different mentioned time point, flash frozen in Liq Nitrogen, total RNA was isolated using Trizol reagent(Ambion). Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The different time point Infection was done to Arachis hypogaea  by SEMIA 6144

tag: symbiont

value: Bradyrhizobium sp. (SEMIA 6144)

value: ROOT

value: 28 days after infection


title: Ah 12DPI Rep2

value: 12 days after infection


title: Ah 12DPI Rep1


title: Ah 8DPI Rep2

value: 8 days after infection


title: Ah 8DPI Rep1


title: Ah 8DPI Rep3


title: Ah 1DPI Rep3

value: 1 day after infection


title: Ah 4DPI Rep2

value: 4 days after infection


title: Ah 4DPI Rep1


title: AhUN Rep3

value: 10 days after germination


title: Ah 12DPI Rep3


title: Ah 1DPI Rep1


title: whole L3 worm ATAC-seq rep2

organism: Caenorhabditis elegans

source_name: whole worms

growth_protocol: C. elegans strains were maintained on OP50 bacteria and NGM agar plates at 15ºC. Worms were transferred to fresh food once a week.

extract_protocol:
Synchronized L4 animals were washed 5 times in M9 buffer and collected on ice.  Nuclei were isolated using a glass Dounce homogenizer with 50 strokes tight-fitting insert in buffer A (15 mM Tris–HCl pH7.5, 2 mM MgCl2, 340 mM sucrose, 0.2 mM spermine, 0.5 mM spermidine, 0.5 mM phenylmethanesulfonate [PMSF], 1mM DTT, 0.1% Trition X-100 and 0.25% NP-40 substitute). The debris were removed by spinning at 100×g for 5 min and nuclei were counted by Methylene blue staining. 100.000 nuclei per sample were pelleted by spinning at 1000×g for 10 min and proceeded immediately to transposition step of the ATACseq protocol
Library preparation was done following a protocol published in Buenrostro et al. 2013. Cell pellet was resuspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase) (Illumina Nextera DNA Library preparation kit, #FC-121-1030). The transposition reaction was carried out for 60 min at 37ºC. The samples were purified using Zymo DNA Clean & Concentrator kit; following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 12 to 14 cycles and sequenced using paired-end-sequencing length of 75 nucleotides using NextSeq 500/550 High Output v2 kit (Illumina) on a NextSeq500 machine (Illumina) following manufacturer's protocol.

value: stage L3


title: AhUN Rep1


title: NCX-Graft rep 3

city: New Haven

first: Stephen

last: Strittmatter

address: 295 Congress avenue

department: Neurology

institute: Yale University

description:
maria_teresa.gene.RPKM.2ndRun.txt
maria_teresa.gene.count.2ndRun.txt

data_processing:
The sequenced reads were clipped one nucleotide in both ends, leaving 74 nucleotide long reads for sequence alignment to human reference genome (GRCh38/hg38) by using the STAR software. Beyond default parameters in the alignment procedure, human gene annotation retrieved from the GENCODE project (version 21, http://www.gencodegenes.org/releases/21.html) was additionally provided to improve exon-exon junction mapping. To quantify accurately the origin of the genomic locus of short sequenced reads, only the uniquely mapped reads were used for downstream analyses. FeatureCounts was used  to quantify expression profiles of each type of annotation entry retrieved from GENCODE v21. Additional quality control measures were introduced to assess potential issues including reads classification, mitochondrial contamination, and gene coverage uniformity.  R package DESeq2 was used to identify DEX genes. We generated two types of gene expression value, read counts and RPKM (reads per kilobase of exon model per million mapped reads). The reads count per gene served as the input for DESeq2. When performing the comparisons, DESeq2 first gets the mean expression level as a joint estimate for both groups, and then calculates the difference as well as the P value for the statistical significance of this change. The adjusted P value was calculated based on multiple testing with the Benjamini-Hochberg procedure, estimating the false discovery rate (FDR). To detect statistically significant DEX genes, FDR was set to be minor than 0.01.
R package DESeq2 was used to identify DEX genes. We generated two types of gene expression value, read counts and RPKM (reads per kilobase of exon model per million mapped reads). The reads count per gene served as the input for DESeq2. When performing the comparisons, DESeq2 first gets the mean expression level as a joint estimate for both groups, and then calculates the difference as well as the P value for the statistical significance of this change. The adjusted P value was calculated based on multiple testing with the Benjamini-Hochberg procedure, estimating the false discovery rate (FDR). To detect statistically significant DEX genes, FDR was set to be minor than 0.01.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values and read count values for each sample

source_name: Human neocortex

growth_protocol: NES cells were kept in proliferation in T25 flasks coated  with poly-L-ornithine (0.01%), laminin (5 μg/ml) and fibronectin (1 μg/ml). Cells were expanded in NES medium  and split 1:2 approximately every 7 days with 0.25% trypsin. For cryopreservation, cells were trypsinized and ~  2 X 106 cells were pelleted (200 x g for 3 minutes) and resuspended in cryopreservation medium containing  10% DMSO and 90% NES medium. For resuscitation, cells were rapidly thawed at 37 ºC, resuspended in prewarmed  culture media, centrifuged for 3 minutes at 200 x g, resuspended in NES medium, and replated on  coated plates. Neuronal differentiation of NES cells was performed in two steps. For the pre-differentiation step  NES cells were seeded at a density of 0.5 x 105 cells/cm2 in a T25 coated flask in NES medium without EGF  and FGF2. After 7 days, cells were dissociated and replated at a density of 0.8-1 x 105 cells/cm2 in BrainPhys  Medium (Stem Cell Technologies, Cambridge, MA, #05790) supplemented with B27 (2%), N2 (1%) and BDNF  (20 ng/ml). Half volume of the medium was changed every 2-3 days and neurons were differentiated up to 3  months.

extract_protocol:
In vitro samples were collected using RNA later and frozen at -80 C. Spinal cords containing the grafts were dissected and the portion containing the cells was isolated and kept in RNA later at -80 C.Total RNA was extracted using the RNeasy plus minikit (Quiagen, #74134) according to manufacturer’s instruction.  mRNA libraries were prepared according to the TruSeq RNA Illumina kit protocol and sequenced using a  HighSeq 2500 sequencing system (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 6 weeks post conception

tag: status

value: differentiated in vivo for two months upon transplantation in the lesioned spinal cord.


title: AhUN Rep2


title: NCX-Neuron rep 2

value: differentiated in vitro for two months.


title: NCX-Neuron rep 3


title: Ah NOD Rep2


title: NCX-Neuron rep 1


title: NCX-Graft rep 1


title: NCX-NES cells rep 3

value: undifferentiated, in proliferation.


title: NCX-Graft rep 2


title: Ah 4DPI Rep3


title: NCX-NES cells rep 1


title: SC-Neuron rep 3

source_name: Human spinal cord


title: NCX-NES cells rep 2


title: SC-Neuron rep 2


title: SC-Graft rep 2


title: SC-Graft rep 3


title: SC-Neuron rep 1


title: whole L3 worm ATAC-seq rep1