title: U251 monolayer cells biological replicate 1- control

city: Vandoeuvre-lès-Nancy

first: Sebastien

last: Hergalant

address: Faculté de Médecine. 9 avenue de la forêt de Haye

department: Bioinformatics

country: France

institute: INSERM

data_processing:
RNA-seq libraries were quality controlled and trimmed using FastQC (www.bioinformatics.babraham.ac.uk/projects/fastqc/) and cutadapt respectively. The data was mapped using HISAT2 against reference genome GRCh38. Properly paired and uniquely mapped sequencing reads were retained for downstream analysis. Isoforms were reconstructed from alignments using Stringtie. Raw abundance data was processed following the TMM normalization method.
Genome_build: hg38
Supplementary_files_format_and_content: log2 normalized counts per million (cpm)

source_name: U251 glioblastoma cell line

extract_protocol:
Total RNA was extracted using TrizolTM reagent (Ambion, 15596018)
RNA was fragmented and converted to library using NEBNext® Small RNA Library kit (NEB E7330S).

value: adherent monolayer cells

tag: passage


title: U251 monolayer cells biological replicate 3- control

status: Public on Jul 01 2019

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell type


title: U251 tumor spheres biological replicate 1

value: tumor spheres


title: CapEP_WT_13M_sRNA

city: Boston

first: Chen

last: Chu

state: MA

address: 450 Brookline Ave, Smith 914

country: USA

institute: Dana-Farber Cancer Institute

description: 18 -40 nt

data_processing:
For transcriptome sequencing, one hundred-base pair (bp) single-ended reads were mapped to mouse genome (mm9) using the TopHat2 short read mapper version 2.1.0 and differential gene expression analysis was quantified using the ‘generalized fold change (GFOLD)’ differential expression analysis program version 1.1.4.
Small RNA sequence tags from the Solexa sequencing were subjected to data cleaning, which filtered low quality tags and contaminants. The small RNA clean reads were mapped to the mouse mm9 genome using bowtie (version 0.12.7) with settings -k 1 -v 2.Small RNA reads with 100% match to the genome were used for further analysis. Small RNA annotation was performed by alignment to GenBank (http://www.ncbi.nlm.nih.gov/genbank/), mirBase (http://mirbase.org/) , Rfam (http://rfam.sanger.ac.uk/)  and piRNABank (http://pirnabank.ibab.ac.in/) .
Genome_build: mm9
Supplementary_files_format_and_content: Processed data are in 'txt' format and contain small RNA reads information as well as the transcriptome RPKM comparison of WT and KO.

organism: Mus musculus

source_name: Epididymal Caput tissue

growth_protocol: Normal growth

extract_protocol:
Pooled biological samples instead of biological replicates were used for deep sequencing experiments. Total RNA isolation was performed using Trizol reagent (Invitrogen). Total RNA concentration was measured by Nanodrop ND-2000 (Thermo Scientific), and quality was assessed using an Agilent 2100 Bioanalyzer.
For transcriptome sequencing, cDNAs were prepared from full-length mRNA transcripts using a reverse transcriptase with terminal transferase activity. A total of 2.7 μg cDNA for each sample was sonicated to 200 - 400 bp and used for library preparation with the Illumina Nextera DNA Sample Prep Kit following the standard protocol.The libraries were sequenced by Illumina Hiseq 2000. Small RNA sequencing libraries were created following the Illumina TruSeq Small RNA Sample Preparation protocol. In brief, 5’ and 3’ RNA adapters that were specifically modified to target the ends of small RNA molecules were ligated to 1 μg of high quality total RNA. Reverse transcription was performed to generate cDNA libraries and PCR was used to amplify and add unique index sequences to each library. The amplified cDNA constructs were loaded and separated by polyacrylamide gel electrophoresis (PAGE), and the fraction corresponding to 18 - 40 nt small RNAs was excised, purified and sequenced by Illumina GAIIx orHiseq 2000.

treatment_protocol: Tissue samples were prepared from seven 13-month-old WT mice and seven 13-month-old Gpx5-/- mice that were sacrificed by cervical dislocation. Epididymides were removed and freed of connective, especially fat tissues. Epididymides were then divided into caput, corpus and cauda regions. Testes and corpus epididymides were directly collected for RNA extraction. Caput and cauda epididymides were transferred to a small glass dish containing 1 ml PBS. Repeated punctures with a 26-gauge needle and a 15-min incubation at 37℃ were performed to remove spermatozoa. After sperm cell dispersion, the tissues were collected for RNA extraction.

tag: strain

tag: genotype/variation

value: WT

tag: tissue

value: Caput

tag: age

value: 13 month old


title: U251 tumor spheres biological replicate 3


title: U251 monolayer cells biological replicate 2- control


title: control H2O at 1h, biological rep1

type: RNA

city: Kizugawa

first: Md

middle: Zobaer

last: Hasan

state: Kyoto

address: Kunimidai 6-5-4

department: Safety Design Center

country: Japan

institute: Rohto Pharmaceutical CO.,Ltd

description:
H2O_1H-1
Gene expression data from reconstructedhuman epidermis (StratiCELL) topically treated with H2O for 1 h

hyb_protocol: Hybridization, washing and staining were performed according to the Affymetrix user manual. The hybridization cocktail was prepared using the Affymetrix GeneChip® Expression Amplification Reagent Hybridization Controls (Cat# 900454; Lot# 4245935) and the Hybridization Module for GeneChip® Hybridization, Wash and Stain Kit (Cat# 900720; Lot# 4275620) and mixed with amplified cDNA samples. GeneChip® Human Gene 2.0 ST Arrays (Cat# 902112; Lot# 4360273) were treated according to the manual instruction and prepared for hybridization. Hybridization was performed over night for 18 hours in the GeneChip® Hybridization Oven 640. Washing and staining of the arrays was done in the GeneChip® Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Affymetrix).

data_processing:
The data were analyzed after RMA normalization with Affymetrix GeneChip™ Command Console Software for QC. Statistical analyses were performed with “Moderated t” method implemented in  R package Limma 3.26.8 (Smyth, 2004).
#%affymetrix-algorithm-param-apt-engine=ProbesetSummarizeEngine
#%affymetrix-algorithm-param-apt-program-name=Expression Console
#%affymetrix-algorithm-param-apt-opt-chip-type=HuGene-2_0-st
#%affymetrix-algorithm-param-apt-opt-probe-count=2598544
#%affymetrix-algorithm-param-apt-opt-analysis-name=rma-gene-full
#%affymetrix-algorithm-param-apt-opt-set-analysis-name=rma-gene-full
#%affymetrix-algorithm-param-quantification-name=med-polish
#%affymetrix-algorithm-param-quantification-version=1.0
#%affymetrix-algorithm-param-quantification-scale=log2
#%affymetrix-algorithm-param-quantification-type=signal
#%affymetrix-algorithm-param-apt-version=1.3.1.187

label: biotin

source_name: Reconstructed human epidermis topically treated with H2O for 1 h

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Reconstruction of the human epidermis by the manufacturer (Episkin RHE/S/17) for 14 days at the air-liquid interface

extract_protocol: Qiagen RNeasy kit, protocol following the manufacturer's instructions.

treatment_protocol: Tissue samples were topically treated with lactic acid at 5% and methyl paraben at 0,2%, applied on the top of the stratum corneum of RHE/S/17

value: reconstructed human epidermis

tag: treatment

value: H2O for 1 h


title: U251 tumor spheres biological replicate 2


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep3_chip430B

city: Ulm

first: Stephan

last: Schiekofer

address: Robert Koch Str. 8

department: Department of Internal Medicine I

country: Germany

institute: Ulm University

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice 4wks POST AAC 1

hyb_protocol: standard Affymetrix procedures

scan_protocol: standard Affymetrix procedures

data_processing: Affymetrix Microarray Suite version 5.0

source_name: heart tissue

label_protocol: standard Affymetrix procedures

extract_protocol: Ultraspec(TM)-II RNA Isolation System

tag: Strain

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:12 weeks, Tissue:heart tissue


title: YSL_H1437

city: Taipei

first: Sung-Liang

last: Yu

address: Jen Ai Road Section1

department: Clinical Laboratory Sciences and Medical Biotechnology

country: Taiwan

institute: National Taiwan University

description: Parental, non-treated cells

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: To focus on the functional miRNAs we only analyzed the miRbase annotated miRNAs (858 out of 1146 miRNAs). The data were treated by log2 transformation and quantile normalization using JMP software.

source_name: Lung cancer cells, was purchased from ATCC

label_protocol: cRNA were prepared with the labeling Cy3 (Illumina) for Illumina Expression BeadChip

growth_protocol: All human lung adenocarcinoma cell lines were grown in RPMI-1640 media supplemented with 10% FBS. All cell lines were incubated at 37°C in a humidified 20% O2/5% CO2 environment.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: All 16 cells were parental and non-treated.

value: Lung

tag: tumor type

value: lung adenocacinoma


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep2_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice AKT ON 2wks POST AAC 6wks 2


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep2_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice 4wks POST AAC 2


title: YSL_HOP-62

description: Parental, non-treated cells

source_name: Lung cancer cells, was purchased from NCI-60


title: YSL_EKVX

description: Parental, non-treated cells


title: YSL_H1650

description: Parental, non-treated cells


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep3_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice before AAC

value: Tet-myrAkt1/?MHC-tTA, Gender:male, Age:8 weeks, Tissue:heart tissue


title: YSL_VL107

description: Parental, non-treated cells

source_name: Lung cancer cells, was established from taiwan lung adenocarcinoma  patients


title: YSL_HOP-92

description: Parental, non-treated cells


title: YSL_H1975

description: Parental, non-treated cells


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep2_chip430B


title: YSL_A549

description: Parental, non-treated cells


title: YSL_VL080

description: Parental, non-treated cells


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep2_chip430B


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep1_chip430A

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice AKT ON 2wks POST AAC 6wks 1


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep3_chip430B

description: heart tissue from Tet-myrAkt1/?MHC-tTA mice AKT ON 2wks POST AAC 6wks 3


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep1_chip430B


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep1_chip430A


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep2_chip430B


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep1_chip430B


title: YSL_H1755

description: Parental, non-treated cells


title: YSL_PE-089

description: Parental, non-treated cells


title: YSL_H1568

description: Parental, non-treated cells


title: Tet-myrAkt1_aMHC-tTA_heart_3wkAkt/6wkpost_rep3_chip430A


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep2_chip430A


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep3_chip430B


title: Tet-myrAkt1_aMHC-tTA_heart_4wkpost_rep3_chip430A


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep1_chip430A


title: YSL_CL1-5

description: Parental, non-treated cells


title: YSL_NCI-H23

description: Parental, non-treated cells


title: YSL_NCI-H522

description: Parental, non-treated cells


title: YSL_CL1-0

description: Parental, non-treated cells


title: ILC1 from tonsil #1

city: Gaithersburg

first: Jingya

last: Wang

state: Maryland

address: 1 Medimmune Way

department: Early respiratory and immunology

institute: Astrazeneca

data_processing:
Fastq files were generated using bcl2fastq.
Sequencing reads were aligned to human reference genome hg19 using Hisat2 (v2.0.2), with default parameters.
Count tables were generated using HTseq.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.sort.readcount.txt: Tab-delimited text files include count values for each sample.

extract_protocol:
RNA was isolated using a modified protocol with AmPure XP beads.
RNA libraries were prepared for sequencing using SMART-seq Ultra low input RNA kit.

value: ILC1 from tonsil

tag: donor disease status

value: Healthy


title: ILC1 from tonsil #2


title: Kit- ILC2 from blood #3

value: Kit- ILC2 from blood


title: Kit+ CCR6+ ILC2 from blood #2

value: Kit+ CCR6+ ILC2 from blood


title: Kit- ILC2 from blood #2


title: CD56 high NK from blood #1

value: CD56 high NK from blood


title: CD56 high NK from blood #3


title: Kit+ CCR6+ ILC2 from blood #1


title: Kit+ CCR6+ ILC2 from blood #3


title: Kit- ILC2 from blood #1


title: NKp44+ ILC3 from tonsil #3

value: NKp44+ ILC3 from tonsil


title: ILC1 from tonsil #3


title: FT282+EV_RNA-seq

city: Bethesda

first: Elena

last: Pugacheva

state: MD

department: NIAID

institute: NIH

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie program (http://bowtie-bio.sourceforge.net) with default parameters
Peaks were called using Model-based Analysis for ChIP-Seq (MACS) (http://liulab.dfci.harvard.edu/MACS) using default parameters. After MACS, we applied Peak Splitter algorithm (MACS) to call sub-peaks, summit of peaks and improve peak resolution.
RNA-seq reads were aligned  to UCSC Human reference (build hg19) using TopHat2 with the default parameter setting of 20 alignments per read and up to 2 mismatches per alignment.
RNA-seq aligned reads (BAM files) were analyzed with Cufflinks 2.0.0 to estimate the transcripts relative abundance using the UCSC reference annotated transcripts (build hg19). The expression of each transcript was quantified as the number of reads mapped to a transcript divided by the transcript length in kilobases and the total number of mapped reads in millions (FPKM).
Genome_build: hg19
Narrow peak (bed) and wig files were generated by MACS

source_name: Normal human fallopian tube tissue

growth_protocol: A clonal derivative of FT282 was generated a previously described [35], and cultured in DMEM/Ham's F-12 50/50 Mix (DMEM:F12) without L- glutamine (Corning) supplemented with 10% US origin fetal bovine serum(FBS, Peak Srum) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
After overnight incubation of DiaMag magnetic beads (Diagenode, Inc.) with either CTCF or BORIS monoclonal antibodies (characterized and described by PMID:15731119; PMID: 21659515), precipitated chromatin was washed, decrosslinked, and digested with proteinase K. The resulting DNA purified using phenol/chloroform/isoamyl alcohol. DNA concentration  assessed with Quant‐it PicoGreen dsDNA kit (Invitrogen) and 5–10 ng was used to generate sequencing libraries.
TruSeq ChIP Sample Preparation Kit (Illumina, Inc., USA). RNA-seq libraries were prepared using either Ion Total RNA-seq v2 kit or TruSeq Stranded RNA LT Kit (Illumina).

treatment_protocol: For ChIP-seq 60 million of asynchronously growing cells were crosslinked with 1% formaldehyde for 10 min at room temperature, followed by quenching with 125 mM glycine for 10 min, washed twice with 1x PBS, and resuspended in ChIP lysis buffer (150 mM NaCl, 1% Triton X‐100, 0.1% SDS, 20 mM Tris–HCl pH8.0, 2 mM EDTA). Chromatin was sheared to an average length of 200–500 bp using a Bioruptor sonication.

tag: cell line

tag: expressed vector

value: FT282 stably expressing Empty Vector (EV)

tag: chip antibody


title: CTCF_Abs_FT282+BORIS_ChIP-seq

library_source: genomic

molecule: genomic DNA

value: FT282 stably expressing BORIS

value: custom mouse monoclonal CTCF (characterized in PMID:15731119)


title: BORIS_Abs_FT282+BORIS_ChIP-seq

value: custom mouse monoclonal BORIS  (characterized in PMID:21659515)


title: Input_FT282_ChIP-seq


title: CTCF_Abs_FT282+EV_ChIP-seq


title: NKp44+ ILC3 from tonsil #1


title: NKp44+ ILC3 from tonsil #2


title: ILC3 from blood #2

value: ILC3 from blood


title: ILC3 from blood #1


title: NKp44- ILC3 from tonsil #3

value: NKp44- ILC3 from tonsil


title: CD56 high NK from blood #2


title: NKp44- ILC3 from tonsil #2


title: FT282+BORIS_RNA-seq


title: Twbc72

city: Chengdu

first: xiaomeng

last: liu

address: No.55,Section 4,South Renmin Road

country: Colombia

institute: Sichuan Cancer Hospital & Institute, Sichuan Cancer Center

description:
genomic DNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz

data_processing:
(1) Illumina CASAVA version 1.8 were used to the basecalling.
(2) Sequencing adapters, low quality sequences and amplification primers were trimmed from the raw sequencing reads.
(3) Whole or any subsets of adaptor sequences were trimmed at 3'- end of the reads.
(4) The MCTA-Seq primer sequences including 6 bp at the 5'- end and 12 bp at the 3'- end of reads were trimmed.
(5) Low-quality reads, as > 10% bases being N, or Phred quality of > 50% bases being <5 or having  > 3 unmethylated CHs, were discarded.
(6) Cytosines in a read were computationally replaced with thymines and then mapped to computationally converted hg19 references using the Bismark and Bowtie programs.
(7) The reads were discarded if there was < 2 genomic CpG sites ± 3 bp surrounding the position corresponding to the 5'- end of the aligned reads.
(8) For a certain CpG site following a certain CGCGCGG, the methylation value is calculated as the number of fully methylated reads, i.e., all CpGs from the CGCGCGG site to the CpG site on the read were methylated, normalized by the total number of reads uniquely mapped to the whole human genome and expressed as methylated alleles per million mapped reads (MePM).
(9) For all of the amplicons from the 9,513 CGIs with no CGCGCGGs, the duplication rates were calculated by dividing the reads by the "HHHHH" unique molecule identifiers (UMIs) on primer A.
(10) When duplication rate of plasma sample was larger than that of paired white blood cell (WBC) samples, then plasma sample data were normalized to a duplication rate which similar to WBC by random extraction.
Genome_build: hg19
Supplementary_files_format_and_content:  All_samples_sumT_mepm.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-8.
Supplementary_files_format_and_content:  nor_samples.txt.gz file include the MePM (methylated alleles per million mapped reads) value of each CGCGCGG sites which was processed by step 1-10.

source_name: white blood cell

extract_protocol:
Genomic DNAs were extracted using the Dneasy Blood & Tissue Kit (Qiagen) according to the manufacturer's protocol.
The plasma cell-free DNAs were extracted using the QIAamp DNA Blood Midi Kit (Qiagen) according to the manufacturer's protocol.
Library were constructed following the MCTA-Seq library preparation protocol in PMID:26620315

value: white blood cell

tag: disease state

value: healthy individual


title: NKp44- ILC3 from tonsil #1


title: Twbc73


title: Twbc48


title: Twbc17


title: Twbc23


title: Twbc25


title: Twbc13


title: Twbc21


title: Twbc12


title: Twbc31


title: Twbc14


title: Twbc66


title: Twbc51


title: Twbc32


title: Twbc15


title: Twbc26


title: Twbc50


title: Twbc33


title: Twbc8


title: Twbc6


title: Twbc7


title: Twbc67


title: Twbc22


title: Twbc3


title: Twbc9


title: Twbc2


title: Twbc4


title: Pn21

description:
ccfDNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz

source_name: plasma

value: plasma


title: Twbc1


title: Pn28


title: Pn10


title: Twbc5


title: Pn17


title: Pn16


title: Pn9


title: Pn11


title: Pn20


title: Pn8


title: Pn18


title: Twbc78


title: Twbc81


title: Twbc27


title: Pn7


title: Twbc80


title: Twbc24


title: Twbc30


title: Twbc77

description:
genomic DNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz
nor_samples.txt.gz


title: Pn6


title: Twbc28


title: Tet-myrAkt1_aMHC-tTA_heart_control_rep1_chip430B


title: Twbc34


title: Twbc29


title: Twbc18


title: Pn26

description:
ccfDNA
protocol: MCTA-Seq
all_samples_sumT_mepm.txt.gz
nor_samples.txt.gz


title: Twbc70


title: Twbc19


title: Twbc76


title: Pn22


title: Pn2


title: Pn3


title: Pn4


title: Pn29


title: Pn32


title: Pn25


title: Pn27


title: Pn24


title: Pn23


title: Pn19


title: Pn14


title: Pn13


title: Liver2

source_name: liver

value: liver


title: Liver3


title: Liver1


title: Lu-Aty2 Atypical Carcinoids (ACs)

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

description:
2 x 100 paired end sequence reads
log2TPM_all_genes_Lung_Carcinoids.txt

data_processing:
Raw fastq files were probed for sequencing quality control using FastQC. Sequencing reads were mapped to human transcripts corresponding to Genepattern genome (hg19 version) GTF annotations using RSEM with default parameters. RSEM package was used to prepare the reference genome with given GTF and calculated expression from mapped BAM files. STAR aligner was used to map reads in RSEM algorithm. Transcripts mapped data were normalized to TPM (Transcript Per Million) from RSEM and log2 transformed (Supplementary file). This log2 (x+1) TPM normalized values were used for all downstream analysis.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: log2 (x+1) TPM normalized values for each sample using RSEM and STAR

source_name: Lung Carcinoids

extract_protocol:
Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: diagnosis

value: Atypical Carcinoids (ACs)

tag: tumor in specimen

value: Lung

tag: tumor location

value: Peripheral

tag: lcs subtype

value: LC2 Subtype of Lung Carcinoids

tag: phenotype

value: Well Differentiated Lung Carcinoids

value: Pulmonary neuroendocrine cells

tag: gender

value: M

tag: age (years)


title: Lu-ty16 Typical Carcinoids (TCs)

value: Typical Carcinoids (TCs)

value: Central

value: LC3 Subtype of Lung Carcinoids

tag: cell type

value: F


title: Lu-ty15 Typical Carcinoids (TCs)

value: LC1 Subtype of Lung Carcinoids


title: Lu-Aty1 Atypical Carcinoids (ACs)


title: Lu-ty13 Typical Carcinoids (TCs)


title: Lu-ty14 Typical Carcinoids (TCs)


title: Lu-ty11 Typical Carcinoids (TCs)


title: Lu-Aty12 Atypical Carcinoids (ACs)


title: Lu-ty10 Typical Carcinoids (TCs)


title: Lu-ty12 Typical Carcinoids (TCs)


title: Lu-Aty9 Atypical Carcinoids (ACs)


title: Lu-ty7 Typical Carcinoids (TCs)


title: Lu-ty5 Typical Carcinoids (TCs)


title: Lu-ty6 Typical Carcinoids (TCs)


title: Lu-Aty10 Atypical Carcinoids (ACs)


title: Lu-Aty8 Atypical Carcinoids (ACs)


title: Lu-Aty7 Atypical Carcinoids (ACs)


title: Lu-Aty13 Atypical Carcinoids (ACs)


title: Lu-Aty5 Atypical Carcinoids (ACs)


title: Lu-ty9 Typical Carcinoids (TCs)


title: Lu-ty17 Typical Carcinoids (TCs)


title: Lu-ty8 Typical Carcinoids (TCs)


title: Lu-ty3 Typical Carcinoids (TCs)


title: Lu-Aty4 Atypical Carcinoids (ACs)


title: Lu-Aty11 Atypical Carcinoids (ACs)


title: Lu-ty1 Typical Carcinoids (TCs)


title: Lu-ty2 Typical Carcinoids (TCs)


title: Lu-Aty3 Atypical Carcinoids (ACs)


title: FLAG-MSI2-1_RNASeq

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

description:
FLAG-MSI2 1 total RNA
FLAG_MSI2_RNA_Seq_genes.fpkm_table

data_processing:
CASAVA Illumina in house
TopHat alignment
Cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: bed, excel

growth_protocol: K562 cells were grown in RPMI-1640 media supplemented with 10% fetal bovin serum.

extract_protocol:
iCLIP per Huppert I et. al. Methods. 2014 Feb;65(3):274-287, PMID: 24184352  Methods. 2014 Feb;65(3):274-87.PMID:24184352  24184352
Polysome profiling: Polysome RNA extracted by Trizol extraction from control and MSI2-KD cells
RNA-Seq library prepared by Illumina Truseq v2 kit. iCLIP library prepared per custom protocol as referenced above.
RNA-Seq (SE)

tag: transgene


title: MSI2-shRNA-TotalRNA#3

description:
MSI2 knockdown 3 total RNA
Cuffdiff_Polysome.xlsx

tag: shRNA

value: MSI2-KD shRNA


title: FLAG-MSI2-2_RNASeq

description:
FLAG-MSI2 2 total RNA
FLAG_MSI2_RNA_Seq_genes.fpkm_table


title: MSI2-shRNA-PolysomeRNA#3

description:
MSI2 knockdown 3 Polysomal RNA
Cuffdiff_Polysome.xlsx


title: MSI2-shRNA-TotalRNA#2

description:
MSI2 knockdown 2 total RNA
Cuffdiff_Polysome.xlsx


title: FLAG-MSI2-2_iCLIP

description: FLAG-MSI2 2 iCLIP


title: FLAG-MSI2-3-iCLIP

description: FLAG-MSI2 3 iCLIP


title: Lu-ty4 Typical Carcinoids (TCs)


title: Lu-Aty6 Atypical Carcinoids (ACs)


title: Control-shRNA-PolysomeRNA#3

description:
Control 3 Polysomal RNA
Cuffdiff_Polysome.xlsx

value: Control shRNA


title: MSI2-shRNA-PolysomeRNA#1

description:
MSI2 knockdown 1 Polysomal RNA
Cuffdiff_Polysome.xlsx


title: Control-shRNA-PolysomeRNA#2

description:
Control 2 Polysomal RNA
Cuffdiff_Polysome.xlsx


title: MSI2-shRNA-TotalRNA#1

description:
MSI2 knockdown 1 total RNA
Cuffdiff_Polysome.xlsx


title: Control-shRNA-TotalRNA#1

description:
Control 1 total RNA
Cuffdiff_Polysome.xlsx


title: Control-shRNA-PolysomeRNA#1

description:
Control 1 Polysomal RNA
Cuffdiff_Polysome.xlsx


title: Control-shRNA-TotalRNA#2

description:
Control 2 total RNA
Cuffdiff_Polysome.xlsx


title: FLAG-MSI2-1_iCLIP

description: FLAG-MSI2 1 iCLIP


title: Control-shRNA-TotalRNA#3

description:
Control 3 total RNA
Cuffdiff_Polysome.xlsx


title: RNA-seq-CRISPRk-N4871_2

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

data_processing:
base calling:
read alignment, CRISPR screen data: Bowtie2 + castLE
read alignment, ChIP-seq and ATAC-seq data: bwa mem 0.7.5
read alignment, RNA-seq data: STAR 2.5.3.a
bedgraph track generation: custom-written python scripts
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for CRISPR screen samples, where files with log-fold change values for each guide RNA are provided

molecule: polyA RNA

extract_protocol: 2e7 K562 cells per replicate were pelleted at 500 g for 5 minutes at 4°C and then resuspended in 1x PBS buffer. Two replicates were performed for each sgRNA. RNA extraction was performed as follows: 500 uL of TRIzol was added to each sample, mixed by tube inversion, and then 5 minutes later 100 uL of chloroform was added. Samples were spun at 12,000 g for 15 minutes at 4°C. The aqueous layer was transferred to an RNase-free tube and mixed with 300 uL of 70% ethanol and vortexed. Contents were then transferred to Direct-zol miniprep columns (Zymo) and the protocol was followed according to the manufacturer’s instructions, including the on-column DNaseI treatment. RNA was eluted in 15 uL of RNase-free water and stored at -80°C and a separate 2 uL aliquot was set aside for testing RNA concentration and quality via Nanodrop. RNA-seq libraries were prepared from 700 ng of total RNA with the TruSeq RNA Library Prep kit v2 (Illumina), which uses oligo-dT beads to enrich for A-tailed mRNAs.


title: RNA-seq-CRISPRk-N4871_1


title: RNA-seq-CRISPRk-N4293_2


title: RNA-seq-CRISPRk-N4293_1


title: FLAG-MSI2-3_RNASeq

description:
FLAG-MSI2 3 total RNA
FLAG_MSI2_RNA_Seq_genes.fpkm_table


title: RNA-seq-CRISPRk-14377-GH552_1

description: RNA-seq-CRISPRk-14377-GH552_1.bedGraph.gz


title: RNA-seq-CRISPRk-14376-GH551_2

description: RNA-seq-CRISPRk-14376-GH551_2.bedGraph.gz


title: ATO Huh7

city: Shanghai

first: Xin

last: Zhang

state: -- Please select an option --

address: No.180 Fenglin Road, Zhongshan Hospital

country: China

institute: Liver Cancer Institution

description: Gene expression data from HCC cells with or without ATO therapy

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with AGCC software using Affymetrix default analysis settings and global scaling as normalization method.

source_name: Huh7 cells under low dose ATO treatment

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

value: hepatocellular carcinoma (HCC) cell line

tag: treatment

value: 3 μM ATO treatment for 7 days


title: RNA-seq-CRISPRk-13006_2


title: MSI2-shRNA-PolysomeRNA#2

description:
MSI2 knockdown 2 Polysomal RNA
Cuffdiff_Polysome.xlsx


title: U251 rep1

city: Nishinomiya city

first: Daisuke

last: Sakamoto

state: Hyogo

address: 1-1 Mukogawa-cho

department: Neurosurgery

institute: Hyogo College of Medicine

description: Gene expression data from human glioblastoma cell line

hyb_protocol: Subsequently 15 μg of cRNA was hybridized for 16 hours at 45 degrees Celsius on GeneChip Human Genome U133 Plus 2.0 Array (Thermo Fisher Scientific). The array was washed, stained with phycoerythrin-labeled streptavidin using GeneChip Fluidics Station 450 (Thermo Fisher Scientific).

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Thermo Fisher Scientific).

data_processing: Single array analysis was conducted by Microarray Suite version 5.0 (MAS5.0) with the Thermo Fisher Scientific default setting and the global scaling method to normalize the intensities. The trimmed mean target intensity of each array was arbitrarily set to 500.

source_name: GBM cell line

label_protocol: Biotinylated cRNA was synthesized from 250 ng of total RNA using GeneChip 3’ IVT PLUS Reagent Kit (Thermo Fisher Scientific) according to the manufacturer’s instructions. Biotinylated cRNA yield was determined using NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific).

growth_protocol: Tumor sphere cultures of human GSC lines X01 and X03 were prepared in DMEM-F12 (GIBCO-Invitrogen, La Jolla, CA) containing penicillin G, streptomycin sulfate, B-27 (GIBCO-Invitrogen), recombinant human epidermal growth factor (EGF) (20 ng/mL; R&D Systems, Minneapolis, MN), and recombinant human fibroblast growth factor 2 (FGF2) (20 ng/mL; R&D Systems). Cells were cultured in Heracell CO2 incubators (Thermo Fisher Scientific, Asheville, NC) at 37 degrees Celsius, >=95% relative humidity, and 5% CO2 under 20% oxygen conditions. Cells of human glioma cell lines U251 were maintained in culture in Dulbecco’s modified Eagle’s medium (DMEM; Sigma Aldrich, Milan, Italy) containing 10% fetal bovine serum (FBS) and 1% penicillin G, streptomycin sulfate. Cells were grown in 37 degrees Celsius, and 5% CO2 humidified atmospheric conditions and were enzymatically dissociated using 0.25% trypsin and 0.02% EDTA solution.

extract_protocol: Briefly, total RNAs were extracted from the GSC lines, U251, and the hGBM tissue and purified using the Qiagen RNeasy Mini Kit (QIAGEN N.V.) according to the manufacturer’s instructions.

value: GBM cell line

tag: sample type

value: cultured cell line


title: Hep3B

source_name: Hep3B cells under DMSO treatment

value: DMSO (negative control)


title: GSCs X03 rep3

description: Gene expression data from human glioma stem cell line

source_name: glioma stem cell line

value: Glioma stem cells


title: U251 rep3


title: RNA-seq-CRISPRk-14376-GH551_1

description: RNA-seq-CRISPRk-14376-GH551_1.bedGraph.gz


title: ATO Hep3B

source_name: Hep3B cells under low dose ATO treatment


title: RNA-seq-CRISPRk-14377-GH552_2

description: RNA-seq-CRISPRk-14377-GH552_2.bedGraph.gz


title: hGBM rep1

description: Gene expression data from fresh human glioblastoma tissue

source_name: tissue

value: glioblastoma multiform (GBM)

value: fresh tissue sample


title: GSCs X03 rep2


title: U251 rep2


title: RNA-seq-CRISPRk-13006_1


title: RNA-seq-CRISPRk-13004_2


title: GSCs X01 rep3


title: MEK SMI + LPS 5

city: South San Francisco

first: Mark

last: McCreary

address: 1 DNA Way, MS 93

institute: Genentech

description: Blood sample SAM636564 - Treatment: MEK SMI + LPS 5

hyb_protocol: Gene expression analysis was performed using an Affymetrix platform (HG-U133_Plus_2) following the manufacturer's protocols (Affymetrix) for hybridization.

scan_protocol: GeneChips were scanned using the GeneChip scanner.

data_processing: Raw microarray data were processed using the R programming language (http://www.r-project.org) and packages from the Bioconductor project (http://www.bioconductor.org). Monocyte microarray data were normalized using the RMA method. Probe sets were filtered; selecting a single probe set per Entrez gene, retaining the probe set that showed the highest variance. Probe sets that didn’t map to an Entrez gene were removed from the analysis. Differential expression analysis was performed using the limma package. The linear model used to identify differential gene expression included terms for LPS stimulation and the small molecule treatment cohorts, and included the cell donor as a covariate. For visualization using heat maps, microarray data were further normalized to remove the donor-specific differences, by taking the residuals of linear regression of a model that only included the donor. P-values were adjusted for multiple testing using the Benjamini-Hochberg method. Genes were considered differentially expressed if they showed a minimum 1.5-fold change with an adjusted p-value < 0.01.

source_name: Blood, MEK SMI + LPS

label_protocol: Gene expression analysis was performed using an Affymetrix platform (HG-U133_Plus_2) following the manufacturer's protocols (Affymetrix) for labeling.

growth_protocol: Untouched monocytes were purified from buffy coats using negative selection kits according to the manufacturer's instructions (Miltenyi Biotec). Monocyte purity was consistently ≥97% as assessed by FACS.

extract_protocol: RNA was isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s instructions with an on-column DNase I digestion.

treatment_protocol: Cells were resuspended in low (0.5%) serum RPMI and pretreated with vehicle (0.5% DMSO) or the specified small molecule inhibitors at least 30 min prior to stimulation.

tag: primary tissue

value: Blood

tag: treatment name

value: MEK SMI + LPS

tag: stimulation

value: LPS

tag: compound

value: MEKi

tag: replicate number


title: GSCs X01 rep2


title: GSCs X01 rep1


title: hGBM rep2


title: RNA-seq-CRISPRk-12042-GH550_2

description: RNA-seq-CRISPRk-12042-GH550_2.bedGraph.gz

tag: cell line


title: RNA-seq-CRISPRk-13004_1


title: RNA-seq-CRISPRk-12040-GH549_2

description: RNA-seq-CRISPRk-12040-GH549_2.bedGraph.gz


title: RNA-seq-CRISPRk-12042-GH550_1

description: RNA-seq-CRISPRk-12042-GH550_1.bedGraph.gz


title: Huh7

source_name: Huh7 cells under DMSO treatment


title: RNA-seq-CRISPRk-12040-GH549_1

description: RNA-seq-CRISPRk-12040-GH549_1.bedGraph.gz


title: GSCs X03 rep1


title: CRISPR-screen.tiling.Plasmid

description: processed data file: CRISPR-screen.tiling.tiling_library_with_controls.csv

extract_protocol: Oligonucleotide libraries were synthesized by Agilent and then cloned into an sgRNA expression vector (pMCB320) that had been cut with BstXI and BlpI restriction enzymes, by ligation, using the T4 Ligase. Large scale lentivirus production and infection of K562-Cas9 cells were performed as previously described (PMID: 23394947 and PMID: 23739767). Selection with puromycin was started three days after infection and continued for 3--4 days until the mCherry-positive  percentage of cells was greater than 80%, as observed by flow cytometry on a BD Accuri. Cells were maintained in log growth conditions each day by diluting cell concentrations back to a 0.5 x 10^6 cells/mL. Genomic DNA was extracted following Qiagen's Blood Maxi Kit, and the guide composition was sequenced and compared to the plasmid library using casTLE version 1.0 (available at https://bitbucket.org/dmorgens/castle.)

value: CRISPR screen


title: CRISPR-screen.tiling.dCas9_T14_Rep2


title: CRISPR-screen.tiling.CRKO_T14_Rep1


title: CRISPR-screen.tiling.dCas9_T14_Rep1


title: Tpl-2 SMI 5

description: Blood sample SAM636560 - Treatment: Tpl-2 SMI 5

source_name: Blood, Tpl-2 SMI

value: Tpl-2 SMI

value: Unstimulated


title: LPS 5

description: Blood sample SAM636562 - Treatment: LPS 5

source_name: Blood, LPS

value: Vehicle


title: CRISPR-screen.tiling.CRKO_T0


title: Tpl-2 SMI + LPS 4

description: Blood sample SAM636557 - Treatment: Tpl-2 SMI + LPS 4

source_name: Blood, Tpl-2 SMI + LPS

value: Tpl-2 SMI + LPS


title: hGBM rep3


title: Tpl-2 SMI + LPS 5

description: Blood sample SAM636563 - Treatment: Tpl-2 SMI + LPS 5


title: CRISPR-screen.tiling.CRKO_T14_Rep2


title: MEK SMI 5

description: Blood sample SAM636561 - Treatment: MEK SMI 5

source_name: Blood, MEK SMI

value: MEK SMI


title: MEK SMI + LPS 4

description: Blood sample SAM636558 - Treatment: MEK SMI + LPS 4


title: LPS 4

description: Blood sample SAM636556 - Treatment: LPS 4


title: MEK SMI 4

description: Blood sample SAM636555 - Treatment: MEK SMI 4


title: LPS 3

description: Blood sample SAM636550 - Treatment: LPS 3


title: Tpl-2 SMI 4

description: Blood sample SAM636554 - Treatment: Tpl-2 SMI 4


title: CRISPR-screen.tiling.dCas9_T0


title: Untreated 4

description: Blood sample SAM636553 - Treatment: Untreated 4

source_name: Blood, Untreated

value: Untreated


title: MEK SMI 3

description: Blood sample SAM636549 - Treatment: MEK SMI 3


title: Tpl-2 SMI 3

description: Blood sample SAM636548 - Treatment: Tpl-2 SMI 3


title: CRISPR-screen.tiling.CRISPRi_T0


title: MEK SMI + LPS 3

description: Blood sample SAM636552 - Treatment: MEK SMI + LPS 3


title: Untreated 3

description: Blood sample SAM636547 - Treatment: Untreated 3


title: Tpl-2 SMI + LPS 3

description: Blood sample SAM636551 - Treatment: Tpl-2 SMI + LPS 3


title: Untreated 5

description: Blood sample SAM636559 - Treatment: Untreated 5


title: CRISPR-screen.tiling.CRISPRi_T14_Rep1


title: CRISPR-screen.tiling.CRISPRa_T14_Rep1


title: CRISPR-screen.tiling.CRISPRa_T0

description: processed data file: CRISPR-screen.tiling.tiling_library_with_controls.csv


title: CRISPR-screen.tiling.CRISPRi_T14_Rep2


title: CRISPR-screen.CTCF.growth_screen.1794

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_K1_CTCF_rhos.csv


title: MEK SMI 2

description: Blood sample SAM636543 - Treatment: MEK SMI 2


title: LPS 2

description: Blood sample SAM636544 - Treatment: LPS 2


title: CRISPR-screen.CTCF.growth_screen.1793

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_I2_CTCF_rhos.csv


title: MEK SMI + LPS 2

description: Blood sample SAM636546 - Treatment: MEK SMI + LPS 2


title: Tpl-2 SMI + LPS 2

description: Blood sample SAM636545 - Treatment: Tpl-2 SMI + LPS 2


title: CRISPR-screen.CTCF.growth_screen.1770

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_I1_CTCF_rhos.csv


title: CRISPR-screen.tiling.CRISPRa_T14_Rep2


title: CRISPR-screen.CTCF.growth_screen.1769

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_D2_CTCF_rhos.csv


title: MEK SMI + LPS 1

description: Blood sample SAM636540 - Treatment: MEK SMI + LPS 1


title: CRISPR-screen.CTCF.growth_screen.1767

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_A2_CTCF_rhos.csv


title: CRISPR-screen.CTCF.growth_screen.1795

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_K2_CTCF_rhos.csv


title: CRISPR-screen.CTCF.growth_screen.1764


title: CRISPR-screen.CTCF.growth_screen.1763


title: CRISPR-screen.CTCF.growth_screen.1762


title: CRISPR-screen.CTCF.growth_screen.1438


title: CRISPR-screen.CTCF.growth_screen.1761


title: CRISPR-screen.CTCF.growth_screen.1437

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_D1_CTCF_rhos.csv


title: CRISPR-screen.CTCF.growth_screen.1768


title: CRISPR-screen.CTCF.growth_screen.1766

description: processed data file: CRISPR-screen.CTCF.growth_screen.T14vsPlasmid_A1_CTCF_rhos.csv


title: CRISPR-screen.CTCF.growth_screen.1765


title: MEK SMI 1

description: Blood sample SAM636537 - Treatment: MEK SMI 1


title: Tpl-2 SMI + LPS 1

description: Blood sample SAM636539 - Treatment: Tpl-2 SMI + LPS 1


title: CRISPR-screen.CTCF_Gro1.high_coverage


title: CRISPR-screen.CTCF_FineMap_T6_BR2

description: processed data file: CRISPR-screen.CTCF_FineMap.T20vsPlas_FineMapConv_BR2_CTCF_rhos.csv


title: Lamb_Input_Control

city: Saint Lucia, Brisbane

first: Tony

last: Vuocolo

state: Queensland

address: 306 Carmody Road

country: Australia

institute: CSIRO

description:
Lamb Input Sample
nucleosomal DNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then each sample individually mapped to  the unmasked OARv3.1.74  sheep genome using the NGS core tool mapping application in CLCBIO (mapping parameters: length fraction =0.7; similarity fraction =0.8; penalties, mismatch =2, insertion =3, deletion =3). H3K27ac and H3K4me3 samples that had multiple runs on the sequencer were independently merged for each sample and these merged data for each sample were mapped to the genome. Data for each independent sequence run (i.e. not merged) is provided.  A range of 75-90 % of the reads mapped uniquely and were retained for the analysis.   There were systematic genome-wide differences in absolute signals between the fetal and lamb samples for all the chromatin marks that were attributed to nucleosome extraction differences.
Genomic regions enriched for chromatin marks: Aligned reads were processed using Ngsane 0.4.0.1 [74], which first assessed data quality and library complexity. Broad enriched peaks, relative to the input control, were then determined using PeakRanger v1.16 using a sliding 500 bp window for each sample (window step =50; minimum read count =4; minimum score =5; read extension length =200; FDR q<0.1)). From the resulting bed files, union files were generated by concatenating the replicates for each chromatin mark and each tissue, as well as an overall union file over all datasets. Overlapping regions in the union files were merged and the number of reads in each union region collected (multicov) from the bam files for each sample and each chromatin mark as well as for input controls using bedtools 2.19.0 .
Gene promoter modification analysis:  Sequence tag counts within gene promoters assigned as a window 2 kb upstream and 0.5 kb downstream of the first nucleotide of exon 1,  for each of the the 24390 ENSEMBL gene models for Ovis aries OAR_v3.1.74 were counted for each sample.  The read count was corrected for library size and the corresponding region of the relevant Input Control.
Differential modification analyses using either  (i) gene promoter  or (ii) PeakRanger data was calculated using a conservative approach in conjunction with EdgeR implemented as DGE in the CLCBIO Genomics Workbench. (i) Promoter analysis: For each library, gene promoters with greater than 1.5 fold enrichment of the normalized promoter read count relative to the input control and a sequence tag signal greater than 50 in at least one sample were used.  Gene promoters attributed to the mitochondrial genome were excluded for the analysis for all 3 histone marks investigated.  In addition, genes located on the X chromosome were not included for H3K27me3.  Differentially modified gene promoters were identified using EdgeR implemented  in CLCBIO (FDR corrected P<0.1; fold change > |1.5|) . (ii) The Genome-wide analysis using Peakranger employed a similar strategy to identify regions with differential chromatin modification.  The entire genome alignment, including X chromosome and mitochondrial genome were included in this analysis. Enriched regions identified by PeakRanger for all samples were used in a data union process to define a common genomic window across all samples.  The sequence tag counts corresponding to these peak windows for each sample was counted.  No normalization was applied as this was already performed by PeakRanger. These counts were analyzed for differences between fetal and lamb perirenal adipose tissue as per the Promoter EdgeR analysis.
Peak calling comparing the H3K27me3 ChIP-Seq versus the input control was performed using MACS (Zhang et al. 2008). Only peaks found in both replicates per chromatin mark were further considered.
Genome_build: OARv3.1.74
Supplementary_files_format_and_content: Tab-delimited text files.  1) The "Promoter" files report each histone modification (H3K27me3 or H3K27ac or H3K4me3) for annotated genes that passed the filtering process.  2) The "PeakRanger" files  report  each histone modification (H3K27me3 or H3K27ac or H3K4me3) for enriched genomic regions. Files report  a genomic location, sequence tag counts  and associated EdgeR statistical information. The complete processed datasets for all samples are provided from which differential modification based on significance level may be applied.  3) The ChIPseq_peaks.xls files report output of MACS peak calling presenting peak location chr, start, end, length, summit, tags, 10 log(pvalue), fold enrichment, FDR(%).  4) The H3K27me3_fdr5_two_replicates.bed file shows H3K4me3 peaks found in both replicates and used in the analysis.

organism: Ovis aries

source_name: perirenal adipose tissue

growth_protocol: Tissues for this study were provided by Janna L Morrison and Isabella C McMillen from Sansom Institute for Health Research, The University of South Australia, Adelaide, 5001, SA, Australia.  All procedures involving animals were carried out with approval from the University of Adelaide Animal Ethics Committee.  Animals were maintained on 100% maintenance energy requirement diets and  cared for humanely as a research flock according to strict animal ethics guidelines. The  ewes for the fetal samples were housed from 110 dpc (days post conception (dpc); term, 150 d) in pens for two weeks before sampling. The pregnant ewes were maintained on a diet that provided 100% of their maintenance energy requirements. Three pregnant ewes were humanely euthanased with an intravenous overdose of sodium pentobarbitone (8.2 g Lethobarb, Virbac Pty ltd, Peakhurst, NSW, Australia) and the uterus removed and fetuses tissue collected at 132±1 dpc. Three ewes were allowed to deliver at term and the lambs were reared with ewes until weaning. At ~89±7 d after birth, lambs were humanely euthanized (as described) and tissues collected.

extract_protocol:
Perirenal adipose tissue was removed from the animals within 10 minutes of euthanasia, flash frozen in liquid nitrogen, stored on dry ice and then stored at -80 o Celcius.  ChIP DNA was isolated briefly as follows:  Frozen tissue was gently pulverised under liquid nitrogen and homogenized in a hand held glass homogenizer in nuclei extraction buffer and nuclei isolated by centrifugation. The isolated chromatin was subsequently treated with micrococcal nuclease and soluble chromatin isolated by mild sonication and centrifugation yielding a relatively homogeneous DNA fragment size of ~ 150bp.  A portion of this isolated soluble chromatin was stored away for each sample and pooled according to its respective group and used as the Input DNA for the INPUT DNA Fetal or Lamb control libraries.  The remainder of the isolated soluble chromatin  was pre-cleared with Protein A-Sepharose / salmon sperm DNA (Millipore, USA) and then subjected to immunoprecipitation using 10ug of  antibodies specific to, H3K27me3 or H3K27ac or H3K4me3.  Immune complexes were recovered by incubation with Protein A-Sepharose, buffer washes and the DNA- histone protein complexes released  using 1% SDS, 0.1 M NaHCO3, treated with proteinase K, extracted with TE-saturated phenol/chloroform (1:1) and the DNA purified using Minielute DNA columns (Qiagen). The purified DNA (20-100 ng) was quantified using Quant-IT PicoGreen and  validated for purity and size using a High Sensitivity DNA chip run on an Agilent 2100 Bioanalyzer (Agilent Technologies).
Illumina TruSeq ChIP-Seq Sample Prep Kit  was used according to Illumina recommendations with 10ng  of isolated  immuno-purified nucleosomes to generate single end read libraries for sequencing. Input nucleosomal DNA were pooled equivalently for fetal or lamb groups and used for the construction of the Input single end read sequencing libraries.
50 bp single end read libraries for the 15 samples were run on either an Illumina GA11X or HiSeq20000 sequencing platform.  Four H3K27me3 libraries (2 Fetal, 2 Lamb) and two Input DNA libraries (1 Fetal and 1 Lamb) were each run independently on a single flow cell per library on an Illumina GA11X sequencer resulting in an average read count of 34.8 m reads per sample.   Four H3K27ac (2 Fetal and 2 Lamb) and five H3K4me3 (2 Fetal and 3 Lamb) were run randomly 2 or 4/flowcell on 5 flowcells of an Illumina HiSEQ2000 sequencer.  Several sequence runs were performed for each sample run on the HiSeq2000 to increase read depth and coverage resulting in a mean read count of 234.3 m and 181.7 m reads per sample for H3K27ac and H3K4me3 libraries respectively.

treatment_protocol: No treatment was applied to the  animals.

tag: breed

value: purebred merino

tag: developmental stage

value: 80 day old lamb

tag: tissue

value: perirenal adipose tissue

tag: genotype/variation

value: wild type

tag: chip antibody


title: en>RA, biological rep1

city: SANTA FE

first: Andres

last: Dekanty

address: COLECTORA RUTA 168

country: Argentina

institute: IAL CONICET

description: Gene expression data from posterior wing disc cells of en-gal4, UAS-GFP/UAS-RA larvae

hyb_protocol: cDNA was hybridized to the microarray for 16 hours at 45ºC, washing and staining of microarrays was performed using a GeneChip Fluidics Station 450 (Affymetrix, Santa Clara, CA)

scan_protocol: Arrays scanning and CEL files generation were performed using an Affymetrix GeneChip Scanner GSC3000 (Affymetrix, Santa Clara, CA)

data_processing: gcRMA normalization method as implemented in gcrma Bioconductor R package

organism: Drosophila melanogaster

source_name: Wing disc expressing RA

label_protocol: Library preparation and amplification were performed using Ovation RNA Amp System V (Nugen;3100-60). Fragmentation and labelling were performed using Encode Biotin Module (Nugen; 4200-60)

growth_protocol: Drosophila embryos expresing a cold sensitive version of Ricin-A (RA) under the control of en-gal4 were collected for 24 h and maintain at 18°C. Early second instar larvae were switched to 29ºC until late L3.

treatment_protocol: Drosophila wing imaginal discs were dissected and posterior GFP-positive compartment was separated under a fluorescence stereoscope

value: Wing disc, posterior compartment

tag: genotype

value: yw; enGal4,UAS-GFP/UAS-RA

tag: age

value: late L3 larvae


title: Fetal_Input_Control

description:
Fetal Input Sample
nucleosomal DNA

value: 132 day old fetus


title: en>RA, biological rep2


title: en>GFP, biological rep1

description: Gene expression data from posterior wing disc cells of en-gal4, UAS-GFP larvae

source_name: Wing disc expressing GFP

value: yw; enGal4,UAS-GFP


title: en>RA, biological rep3


title: Tpl-2 SMI 1

description: Blood sample SAM636536 - Treatment: Tpl-2 SMI 1

value: Blood


title: CRISPR-screen.CTCF.growth_screen.1436

value: CRISPR screen


title: CRISPR-screen.CTCF_FineMap_T6_BR1

description: processed data file: CRISPR-screen.CTCF_FineMap.T20vsPlas_FineMapConv_BR1_CTCF_rhos.csv


title: CRISPR-screen.CTCF.growth_screen.1435


title: CRISPR-screen.CTCF_FineMap_T20_BR2


title: CRISPR-screen.CTCF_Gro2.high_coverage


title: CRISPR-screen.CTCF_FineMap_T20_BR1


title: LPS 1

description: Blood sample SAM636538 - Treatment: LPS 1

value: LPS


title: H3K27me3_L2_ChIPseq_267VEH

description:
Lamb Sample 2 H3K27me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27me3.txt
Fetal_vs_Lamb_PeakRanger_H3K27me3.txt

value: H3K27me3 (Millipore, catalog# 07-449, lot # 1959680)


title: H3K27me3_F2_ChIPseq_6D122

description:
Fetal Sample 2 H3K27me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27me3.txt
Fetal_vs_Lamb_PeakRanger_H3K27me3.txt
H3K27me3_F2_ChIPseq_peaks.xls
H3K27me3_fdr5_two_replicates.bed


title: H3K27me3_L1_ChIPseq_235VEH

description:
Lamb Sample 1 H3K27me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27me3.txt
Fetal_vs_Lamb_PeakRanger_H3K27me3.txt


title: H3K27me3_F1_ChIPseq_6D1159

description:
Fetal Sample 1 H3K27me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27me3.txt
Fetal_vs_Lamb_PeakRanger_H3K27me3.txt
H3K27me3_F1_ChIPseq_peaks.xls
H3K27me3_fdr5_two_replicates.bed


title: Wt3

city: BEIJING

first: DANQING

last: MENG

state: BEIJING

address: 1 BEICHEN WEST ROAD, CHAOYANG DISTRICT

department: Institute of Genetics and Developmental Biology

institute: Chinese Academy of Science

data_processing:
Raw sequencing reads were trimmed to remove adaptors and low-quality nucleotides using trim_galore.
Clean reads were mapped to dm3 reference genome using hisat.
Reads with multiple alignment were removed using samtools.
Cuffdiff were used to find differentially expressed genes.
Genome_build: dm3
Supplementary_files_format_and_content: Cuffdiff differentially expressed genes format

source_name: Wt, neuroblast

extract_protocol:
Total RNA was extracted from neuroblasts with TRIzol according to the manufacturer’s protocol
NEBNext Ultra II Directional RNA Library after purification with polyA binding beads

value: brain

tag: cell type

value: neuroblast

value: third instar larval stages

value: Wt


title: en>GFP, biological rep3


title: CRISPR-screen.CTCF_FineMap_Plasmid


title: Wt2


title: Wt1


title: Untreated 2

description: Blood sample SAM636541 - Treatment: Untreated 2

value: Untreated

value: Unstimulated

value: Vehicle


title: AcslMutant2

source_name: AcslMutant, neuroblast

value: Acsl mutant


title: H3K9ac_YPD_hog1Δ

type: genomic

city: Burjassot

first: Paula

last: Alepuz

state: Valencia

address: Doctor Moliner, 50

department: Biochemistry and molecular biology

country: Spain

institute: University of Valencia

description: Exponential growth in YPD - Linear dye normalization

hyb_protocol: Labeled DNA was hybridized to the Yeast Whole Genome ChIP-on-chip Microarray (Agilent p/n G4491A, AMADID: 014741) according to manufacturer instruction.

scan_protocol: Arrays were scanned in an Agilent Microarray Scanner (Agilent G2565BA) following the Agilent protocol ChIP_1010_Sep10, grid template 014741_D_F_20091202 and the metric set ChIP_QCMT_Sep10.

data_processing: Agilent Feature Extraction Software (v10.10.1.1) was used for background subtraction and linear or lowess normalization.

organism: Saccharomyces cerevisiae

source_name: IP α-H3K9ac (Upstate 06-942, lot 31636)

label_protocol: Labeling of DNA was obtained following the ‘Agilent Yeast ChIP-on-chip Analysis’ protocol Version 9.2 (Agilent Technologies, Palo Alto, California USA. p/n G4493-90010). 2000 ng of ChIP and reference samples were labeled respectively with Cyanine 5-dUTP and Cyanine 3-dUTP using the ‘CGH Labeling Kit’ from Invitrogen (p/n 18095-011) according to the manufacturer’s instructions.

growth_protocol: Cells were grown exponentially in rich medium (YPD) to OD600 0.5-0.8.

extract_protocol: Chromatin immunoprecipitation was performed as previously described [Li T, et al., 2016]. Briefly, crosslinked cell pellets were resuspended in lysis buffer (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1mM PMSF, 1mM benzamidine and protease inhibitor cocktail from Roche) and lysed by vortexing at 4ºC by 45 min with glass beads. Chromatin was sonicated to 200–1000 bp (average of 400bp). Immunoprecipitation was carried for 4h using the specified Ab and 50 µL Pan Mouse IgG Dynabeads. Beads were washed twice with lysis buffer, twice with 500 mM NaCl lysis buffer, twice with wash buffer (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5% Nonidet P-40, 0.5% sodium deoxycholate, 1 mM EDTA pH 8.0, 1 mM PMSF, 1 mM benzamidine and protease inhibitor cocktail from Roche), once with TE containing 1mM PMSF, and finally collected. Two successive elutions were performed with elution buffer (50 mM Tris-HCl pH 8.0, 10 mM EDTA, 1% SDS) by incubating 10 min at 65ºC. The eluted fraction was treated overnight at 65ºC to reverse the cross-linking. Proteins were degraded by proteinase K and DNA was purified by phenol/chloroform/isoamylic alcohol extraction. The sample as treated with RNase A and purified. Ligation Mediated PCR was used for DNA amplification. Immunoprecipitated DNA was blunted by T4 phage DNA polymerase, phenol/chloroform/isoamylic alcohol extracted and ethanol precipitated. Sample was ligated to annealed linkers oJW102 and oJW103. The sample was PCR amplified and amplified size analyzed on a 1.2% agarose gel (average size of 150 bp).

treatment_protocol: Samples were crosslinked with 1% formaldehyde for 15 min, quenched by adding glycine to a final concentration of 125 mM and washed three times with 30 mL of ice-cold PBS buffer. For osmotic stress samples, the cells were incubated with 0.4M NaCl for 10 min previous to the formaldehyde crosslink.

tag: strain/background

tag: condition

value: Non-stress

value: anti-H3K9ac (Upstate 06-942, lot 31636)


title: AcslMutant1


title: ChIP-seq-L129-CRISPRi-CTCF_8004-CTCF

extract_protocol: ChIP-seq experiments were carried out as follows. Briefly, 2x10^6 K562 cells were pelleted at 2000 g for 5 minutes at 4C and then resuspended in 1x PBS buffer; 37% formaldehyde solution (Sigma F8775) was added at a final concentration of 1%. Crosslinking was carried out at room temperature for 15 minutes, and then the reaction was quenched by adding 2.5 M Glycine solution at a final concentration of 0.25 M. Crosslinked cells were then pelleted at 2000 g for 5 minutes at 4C, washed with cold 1x PBS buffer, and stored at -80C.. CTCF ChIP was performed using a polyclonal anti-CTCF antibody (Millipore, 07-729). For each reaction, 100 uL of Protein A Dynabeads (Thermo Fisher 10001D) were washed 3 times with a 5 mg/mL BSA (Sigma A9418) solution. Beads were then resuspended in 1 mL BSA solution and 4 uL of CTCF antibody were added. Coupling of antibodies to beads was carried out overnight on a rotator at 4C. Beads were again washed 3 times with BSA solution, resuspended in 100 uL of BSA solution, mixed with 900 uL sonicated chromatin and incubated overnight on a rotator at 4C. Chromatin was sonicated using a tip sonicator (Misonix) after cells were lysed with Farnham Lysis Buffer (5 mM HEPES pH 8.0, 85 mM KCl, 0.5% IGEPAL, Roche Protease Inhibitor Cocktail), and nuclei were resuspended in RIPA buffer (1x PBS, 1% IGEPAL, 0.5% Sodium Deoxycholate, 0.1% SDS, Roche Protease Inhibitor Cocktail). The sonicated material was centrifuged at 14,000 rpm at 4C for 15 minutes to remove cellular debris, and a portion of the supernatant was saved as input. After incubation with chromatin, beads were washed 5 times with LiCl buffer (10 mM Tris-HCl pH 7.5, 500 mM LiCl, 1% NP-40/IGEPAL, 0.5% Sodium Deoxycholate) by incubating for 10 minutes at 4C on a rotator and then rinsed once with 1x TE buffer. Beads were then resuspended in 200 uL IP Elution Buffer (1% SDS, 0.1 M NaHCO_3) and incubated at 65C in a Thermomixer (Eppendorf) with interval mixing to dissociate antibodies from chromatin. Beads were separated from chromatin by centrifugation, Proteinase K was added to the supernatant and crosslinks were reversed at 65C for \sim16 hours. Input samples (100 uL) were mixed with an equal volume of IP Elution Buffer, Proteinase K was added and cross-links were reversed together with the ChIP samples. DNA was purified by phenol-chloroform-isoamyl extraction followed by MinElute column (Qiagen) clean up. DNA concentration was measured using QuBIT, and libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were sequenced on a NextSeq (Illumina) in a 2x75 bp format.

value: ChIP-seq, anti-CTCF, Millipore, 07-729


title: ChIP-seq-L128-CRISPRi-CTCF_15923-CTCF


title: H3K14ac_YPD_hog1Δ

value: anti-H3K14ac (Upstate 07-353, lot 30020)


title: H3K14ac_YPD_hog1Δ_NaCl

value: NaCl


title: ChIP-seq-L123-CRISPRk-CTCF_13004-CTCF


title: ChIP-seq-L125-CRISPRk-CTCF_14376-CTCF


title: ChIP-seq-L127-CRISPRi-CTCF_5635-CTCF


title: ChIP-seq-L130-CRISPRi-CTCF_N4293-CTCF


title: ChIP-seq-L121-CRISPRk-CTCF_8005-CTCF


title: H3K9ac_YPD_hog1Δ_NaCl


title: ChIP-seq-L126-CRISPRk-CTCF_15776-CTCF


title: ChIP-seq-L122-CRISPRk-CTCF_12040-CTCF


title: AcslMutant3


title: Untreated 1

description: Blood sample SAM636535 - Treatment: Untreated 1

value: Blood


title: 1_YB6CNT_Parabiosis RNASeq [1_S18]

city: New York

first: Paul

middle: Vincent

last: Dellorusso

state: NY

address: 701 West 168th Street, 724 Hammer Health Sciences Center

department: Genetics and Development

institute: Columbia University Irving Medical Center

data_processing:
Fastq files were ran through fastqc to check for sequencing quality. 5 of 35 samples (numbers 6, 15, 16, 27, 35) were omitted due to poor quality and / or low coverage. QC was visualized using MultiQC (Ewels et al Bioinformatics 2016)
Salmon (Patro et al Nature Methods 2017) was used to generate an index of the CHR Gencode mouse transcriptome (gencode.vM20.trasncripts.fa)
Salmon was used to quanitfy transcripts against the mouse transcriptome reference. Flags used were for automatic library type detection -l A (unstranded, single-end), --seqBias, --gcBias, and --validateMappings
Transcript quantification files (quants.sf) were convereted to gene level counts using TxImport (Soneson et al. F1000Research 2015)
Differential expresison on gene level counts was performed using DESeq2 (Love et al Genome Biology 2014). Results were generated using the lfcShrink and contrast functions, making pairwise comparsions on the indicated groups. Alpha threshold set to 0.05 and lfcThreshold to 1.
Genome_build: Read alignment was not utlized for this analysis. Gencode utilizes the GRCm38 primary assembly genome sequence as the reference for their transcriptome annotation.
Supplementary_files_format_and_content: Differential expression files include log2 fold changes generated by DESeq2 for each indicated comparison (with all samples from a given group identified by parabiont status utilized in the differential expression test). These files are listed as .csv files. A counts file is also provided with all the gene level counts for each sample that are used as the input for DESeq2, aslo as a .csv file.

source_name: Young B6 control

extract_protocol:
Hematopoietic stem cells were isolated from the bone marrow of mice through a standardized process of bone marrow extraction, creation of a single cell suspension, and flow cytometry based cell sorting. RNA was isolated using the PicoPure RNA Isolation Kit from ThermoFisher.
Purified RNA was used as input for the Nugen Ovation Trio low input RNA library preparation kit.  Samples were processed on an automated robot system at the NYU Genome Technology Center

tag: age at procedure

value: 8-12 weeks

tag: parabiont status

value: Young B6 control

tag: Sex

value: male

value: Hematopoietic stem cells


title: 28_OB6CNT_Parabiosis RNASeq [28_S43]

source_name: Old B6 control

value: 22 months old

value: Old B6 control


title: 30_OB6CNT_Parabiosis RNASeq [30_S45]


title: ChIP-seq-L124-CRISPRk-CTCF_14259-CTCF


title: ChIP-seq-L119-CRISPRa-CTCF_N4293-CTCF


title: Tpl-2 SMI 2

description: Blood sample SAM636542 - Treatment: Tpl-2 SMI 2

tag: primary tissue

tag: treatment name

value: Tpl-2 SMI

tag: stimulation


title: ChIP-seq-L120-CRISPRk-CTCF_N4293-CTCF

tag: cell line


title: 24_YB6CNT_Parabiosis RNASeq [24_S39]


title: en>GFP, biological rep2

value: Wing disc, posterior compartment

value: yw; enGal4,UAS-GFP

value: late L3 larvae


title: 29_OB6CNT_Parabiosis RNASeq [29_S44]


title: ChIP-seq-L118-CRISPRa-CTCF_15173-CTCF


title: ChIP-seq-L117-CRISPRa-CTCF_13189-CTCF


title: Osr2-Ezh2cko 3

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

data_processing:
Basecalls was performed using CASAVA (Version 1.8.2)
Data analysis was performed using Partek Flow
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 with Gencode M14 as guidance using Star 2.5.3a with default parameter settings
Gencode M14 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
Read counts per gene/transcript in all samples were offset by 1 and then normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: molar

growth_protocol: Mice were raised in animal facilities according to protocol.

extract_protocol:
molars of three-day-old Ezh2fl/fland Osr2KI-Cre;Ezh2fl/fl mice were dissected out. After removing the epithelial tissue, the mesenchymal tissue was collected for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: molar

value: post natal day 3


title: Osr2-Ezh2cko 1


title: ChIP-seq-L116-CRISPRa-CTCF_11698-CTCF


title: Osr2-Ezh2cko 4


title: Control 4


title: Osr2-Ezh2cko 2


title: Control 3


title: Control 1


title: Control 2


title: ChIP-seq-L112-CRISPRi-CTCF_N4293-Input

value: ChIP-input


title: 5_YB6CNT_Parabiosis RNASeq [5_S22]


title: ID8IPKO3

city: La Jolla

first: David

middle: D

last: Schlaepfer

state: CA

address: 3855 Health Sciences Dr.

department: Moores Cancer Center

institute: UCSD

data_processing:
Sequencing, and bioinformatic analyses were performed by Novogene, Inc.
Illumina CASAVA 1.8 software was used for basecalling.
Following adapter trimming, reads with adapter sequences, low quality, or with N>10% were removed.
Clean reads were mapped to the mm10 genome assembly using TopHat2 v2.0.9, mismatch =2.
Differential expression analysis was performed using the DESeq2 R package 2_1.6.3. The resulting P-values were adjusted using Benjamini and Hochberg's approach for controlling the False Disovery Rate (FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file; output from DESeq2. Include readcount for three replicates per group, log2FoldChange, pval, padj, and significant (TRUE, FALSE, NA) for each gene and group.

source_name: ID8-KMF Rgnef-/-

growth_protocol: ID8-KMF Rgnef-KO or Rgnef-KO + GFP-Rgnef cells were grown in 2D on tissue culture dishes seeded with 0.2% Matrigel.

extract_protocol:
Total RNA was extracted using a PureLink RNA Mini Kit (Thermo).
Library preparation was performed by Novogene, Inc., using at least 1 ug high-quality total RNA input per sample. mRNA enrichment was performed with poly-T oligo-attached magnetic beads. Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina as per manufacturer's instructions.

treatment_protocol: Subconfluent growing cells

tag: cell type source

value: ID8-KMF ovarian cancer cells

value: Derived from ID8 cells passaged in-vivo

value: Rgnef -/-


title: ChIP-seq-L110-CRISPRa-CTCF_N4293-Input


title: ATAC-seq-L234-K562-CRISPRk-15777-b

extract_protocol: ATAC-seq experiments were carried out following the Omni-ATAC-seq protocol as previously described (PMID: 28846090), using 50,000 K562 cells per biological replicate and two replicates per sgRNA.


title: ID8IPKO2


title: ATAC-seq-L233-K562-CRISPRk-15777-a


title: ATAC-seq-L231-K562-CRISPRk-15776-a


title: ATAC-seq-L230-K562-CRISPRk-N-b


title: ATAC-seq-L229-K562-CRISPRk-N-a


title: ChIP-seq-L111-CRISPRk-CTCF_N4293-Input


title: ID8IPGR2

source_name: ID8-KMF Rgnef-/- re-expressing GFP-Rgnef

value: Rgnef-/- + GFP-Rgnef (lentiviral)


title: ID8IPKO1


title: ID8IPGR3


title: ID8IPGR1


title: ATAC-seq-L227-K562-CRISPRi-15777-a


title: ATAC-seq-L226-K562-CRISPRi-15776-b


title: ChIP-seq-L115-CRISPRa-CTCF_7140-CTCF

value: ChIP-seq, anti-CTCF, Millipore, 07-729


title: ATAC-seq-L232-K562-CRISPRk-15776-b


title: ATAC-seq-L225-K562-CRISPRi-15776-a


title: 6780 DOX hMeDIP

city: Augusta

first: Jan

last: van Riggelen

state: GA

address: 1410 Laney Walker Blvd.

institute: Augusta University

description:
5hmC
EμSRα-tTA;tet-o-MYC derived T-ALL cell line

data_processing:
Library strategy: hMeDIP-Seq
MeDIP-seq and hMeDIP-seq: Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for following analysis. The fragments were 5’, 3’-adaptor trimmed and filtered ≤16 bp reads with cutadapt software. Trimmed reads (trimmed 5’, 3’-adaptor bases) are mapped to reference genome (hg19 or mm10) with Hisat2 software. The mapped reads were used for statistically significant unbiased methylation/hydroxymethylation region detection. LncRNA, mRNA and Small ncRNA associated DMRs and hDMRs enriched regions (peaks) with statistically significant were identified by diffReps (Cut-off: log2FC ≥ 1, P-value ≤ 10-4). LncRNA, mRNA and Small ncRNA associated hDMRs within promoter were annotated by the nearest gene using the UCSC RefSeq database. Promoter peaks were defined as 2,000 bp upstream and downstream from the transcription start site (TSS); Gene Body Peaks were defined as +2,000 bp downstream of the transcription start site (TSS) to the transcription termination site (TTS); and, Intergenic Peaks were defined as the other genomic regions not included in either promoters or gene body. MeDIP and hMeDIP analysis was performed by Arraystar Inc. (Rockville, MD).
RNA-seq: After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group ≥ 0.5. RNA-sequencing data analysis was performed by Arraystar Inc. (Rockville, MD).
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: wig, txt

source_name: EμSRα-tTA;tet-o-MYC

growth_protocol: Medium (RPMI1640, 10%FBS, 1%PenStrep, 1% L-glut, 50uM 2-mercaptoethanol) incubated at 37C with 5% CO2.

extract_protocol:
Nucleospin RNA and Nucleospin Tissue-gDNA (Macherey Nagel).
MeDIP and hMeDIP: Genomic DNA Sample Kit (FC-102-1002, Illumina).
RNA-seq: KAPA stranded RNA-seq library prep kit (Illumina).

treatment_protocol: 6780 DOX sample was treated with 20ng/mL doxycycline for 48hrs.

value: E<mu>SR<alpha>-tTA;tet-o-MYC derived T-ALL cell line

value: FVB/N


title: 6780 Input MeDIP/hMeDIP

description:
Input for MeDIP-Seq and hMeDIP-Seq.
EμSRα-tTA;tet-o-MYC derived T-ALL cell line

data_processing:
MeDIP-seq and hMeDIP-seq: Raw sequencing data generated from Illumina HiSeq 4000 that pass the Illumina chastity filter are used for following analysis. The fragments were 5’, 3’-adaptor trimmed and filtered ≤16 bp reads with cutadapt software. Trimmed reads (trimmed 5’, 3’-adaptor bases) are mapped to reference genome (hg19 or mm10) with Hisat2 software. The mapped reads were used for statistically significant unbiased methylation/hydroxymethylation region detection. LncRNA, mRNA and Small ncRNA associated DMRs and hDMRs enriched regions (peaks) with statistically significant were identified by diffReps (Cut-off: log2FC ≥ 1, P-value ≤ 10-4). LncRNA, mRNA and Small ncRNA associated hDMRs within promoter were annotated by the nearest gene using the UCSC RefSeq database. Promoter peaks were defined as 2,000 bp upstream and downstream from the transcription start site (TSS); Gene Body Peaks were defined as +2,000 bp downstream of the transcription start site (TSS) to the transcription termination site (TTS); and, Intergenic Peaks were defined as the other genomic regions not included in either promoters or gene body. MeDIP and hMeDIP analysis was performed by Arraystar Inc. (Rockville, MD).
RNA-seq: After quality control, the fragments were 5’, 3’-adaptor trimmed and filtered ≤20 bp reads with cutadapt software. The trimmed reads were aligned to reference genome with Hisat 2 software. The expression level (FPKM value) of known genes and transcripts were calculated using ballgown through the transcript abundances estimated with StringTie. The number of identified genes and transcripts per group was calculated based on the mean of FPKM in group ≥ 0.5. RNA-sequencing data analysis was performed by Arraystar Inc. (Rockville, MD).
Genome_build: mm10 (GRCm38), hg19 (GRCh37)
Supplementary_files_format_and_content: wig, txt


title: 6780 DOX MeDIP

description:
5mC
EμSRα-tTA;tet-o-MYC derived T-ALL cell line


title: 6780 hMeDIP


title: ATAC-seq-L228-K562-CRISPRi-15777-b


title: ATAC-seq-L223-K562-CRISPRi-N-a


title: 6780 MeDIP


title: ATAC-seq-CRISPRk-N4293-2


title: ATAC-seq-CRISPRk-N4371-2


title: ATAC-seq-CRISPRk-N4293-1


title: ATAC-seq-CRISPRk-N4371-1


title: sk9v1

city: San Francisco

first: Stephanie

middle: L

last: Parker

address: 35 Medical Center Way

institute: UCSF

data_processing:
Illumina HiSeq 4000 PE150bp reads were trimmed and clipped for quality by trim_galore 0.4.0 and paired-end settings
High-quality reads were aligned to mm10 by Bowtie2 v 2.2.5 using settings --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 1000
Reads from yeast spike-in were mapped to the yeast genome with settings --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 --no-overlap --no-dovetail
Reads were deduplicated with picard MarkDuplicates  2.18.14, then deduplicated bam files were analyzed in R/Bioconductor to generate coverage analyses and graphs
Genome_build: mm10
Supplementary_files_format_and_content: Excel file of differences in normalized K9me2 enrichment between Ctl or -VitC PGCs and soma

source_name: Vitamin C withdrawn_gonadal soma_K9me2 IP Cut&Run DNA fragments

extract_protocol:
Oct4GFP+ PGCs or Oct4GFP- soma from E13.5 were sorted by FACS into PGC buffer and cryopreserved in 10% DMSO. Upon thawing, samples were processed for Cut&Run analyses according to the protocol by Hainier et al.,  http://dx.doi.org/10.1101/286351, using 1000 cells per K9me2 or IgG IP on isolated nuclei. DNA was purified and eluted from a QIAGEN PCR purification kit, and the whole sample taken forward for library generation
Total eluted DNA fragments following Cut&Run were used for library generation using the KAPA HyperPrep kit, using recommendations for input material <1ng, including adapter concentration of 300nM and 18 cycles of PCR. Libraries were purified with AmpureXP beads, quantified and pooled for sequencing

treatment_protocol: A mouse colony dependent on diet for Vitamin C intake was either supplied with physiological Vitamin C levels or withdrawan from Vitamin C during the first two weeks of gestation.

tag: strain background

value: Gulo-/-

value: female

tag: developemental stage

value: embryonic day 13.5

tag: treatment

value: Vitamin C withdrawn

value: gonadal soma

tag: ip antibody

value: H3K9me2 (Active motif Cat# 39239)

tag: molecule subtype

value: K9me2 IP Cut&Run DNA fragments


title: sk9v2

tag: genotype/variation

tag: cell type


title: sk9v4


title: sk9c4

source_name: Vitamin C supplied_gonadal soma_K9me2 IP Cut&Run DNA fragments

value: Vitamin C supplied


title: ATAC-seq-CRISPRk-13006-2


title: sk9c3


title: ATAC-seq-CRISPRk-13004-1


title: ATAC-seq-CRISPRk-13004-2


title: ATAC-seq-CRISPRa-N4371-2


title: sk9c1


title: siggv4

source_name: Vitamin C withdrawn_gonadal soma_IgG IP Cut&Run DNA fragments

value: Rabbit IgG antibodies (Cell Signaling Cat# 2729)

value: IgG IP Cut&Run DNA fragments


title: siggv3


title: sk9c2


title: ATAC-seq-L224-K562-CRISPRi-N-b


title: ATAC-seq-CRISPRa-N4371-1


title: siggc2

source_name: Vitamin C supplied_gonadal soma_IgG IP Cut&Run DNA fragments


title: siggc3


title: siggv1


title: ATAC-seq-CRISPRa-N4293-1


title: ATAC-seq-CRISPRa-N4293-2


title: ATAC-seq-CRISPRa-15173-2


title: siggc4


title: ATAC-seq-CRISPRa-15173-1


title: pk9v5

source_name: Vitamin C withdrawn_gonadal PGCs_K9me2 IP Cut&Run DNA fragments

value: gonadal PGCs


title: ATAC-seq-CRISPRa-15171-2


title: pk9v3


title: pk9v4


title: ATAC-seq-CRISPRk-13006-1


title: ATAC-seq-CRISPRa-13189-2


title: ATAC-seq-CRISPRa-13190-2


title: ATAC-seq-CRISPRa-13190-1


title: pk9v2


title: pk9v1


title: TDL_Naive (F3) RNAseq

city: Philadelphia

first: E

middle: JOHN

last: WHERRY

state: PA

address: 421 Curie Blvd,354 BRB II/III

department: Systems Pharmacology       and Translational Therapeutics,Institute for Immunology

institute: University of Pennsylvania

data_processing:
Sequenced libraries were aligned to the hg38 reference genome using STAR
Gene expression was quantified and normalized using the PORT pipeline(https://github.com/itmat/Normalization)
limma-voom was used for differential expression analysis between groups.
Genome_build: hg38
Supplementary_files_format_and_content: LVRNAseq_CD4_gene_counts.txt

source_name: CD4 T cells

extract_protocol:
Total RNA from sorted cells was extracted using the Applied Biosystems Arcturus PicoPure RNA isolation kit
Double stranded cDNA was generated using the Clontech SMRT-seq v4 method and was fragmented using the Covaris S220 in microTubes. Indexed Illumina-compatible sequencing libraries were generated from fragmented cDNA using the NEBNext Ultra IImethodology
Libraries were quantified using Kapa Library QC kit for Illumina, pooled, and sequenced on an Illumina NextSeq 500 for 75 cycles (single end)

tag: tissue

value: Thoracic Duct Lymphnode

value: Naive


title: TDL_CXCR5Neg (F4) RNAseq


title: TDL_DIM_BR (F2) RNAseq


title: pk9c2

source_name: Vitamin C supplied_gonadal PGCs_K9me2 IP Cut&Run DNA fragments


title: pk9c3


title: pk9c4


title: ATAC-seq-CRISPRa-13189-1


title: TDL_DIM_BR (F_1) RNAseq


title: piggv5

source_name: Vitamin C withdrawn_gonadal PGCs_IgG IP Cut&Run DNA fragments


title: pk9c1


title: TDL_CXCR5Neg (E4) RNAseq


title: piggv4


title: TDL_Naive (E3) RNAseq


title: piggv3


title: pk9c5


title: TDL_DIM_BR (E_1) RNAseq


title: piggv2


title: piggv1


title: TDL_DIM_BR (E2) RNAseq


title: piggc5

source_name: Vitamin C supplied_gonadal PGCs_IgG IP Cut&Run DNA fragments


title: TDL_CXCR5Neg (D4) RNAseq


title: TDL_DIM_BR (D2) RNAseq


title: TDL_Naive (D3) RNAseq


title: piggc3


title: TDL_DIM_BR (D_1) RNAseq


title: piggc2


title: siggc1


title: PBMC_ICOSneg (H5) RNAseq

value: PBMC

value: ICOS-


title: V4F1 [FV5]

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality by trim_galore 0.4.0
High-quality reads were aligned to mm9 genome by TopHat v2.1.1
BAM files were imported into R-Studio and analyzed for differential expression by DESeq2 v1.20.1
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with counts normalized for sequencing depth and log transformed.

source_name: mouse female gonadal soma_Vit C withdrawn

extract_protocol:
Total RNA was extracted from sorted Oct4- gonadal somatic cells by Qiagen RNeasy Micro Kit
2ng total RNA was used in Clonetech SMARTer total RNA-seq kit pico input mammalian V2 kit


title: V2F2 [FV3]


title: V3F1 [FV4]


title: PBMC_Naive (H3) RNAseq


title: PBMC_ICOSneg (G5) RNAseq


title: piggc4


title: piggc1


title: PBMC_cTfh (H_1) RNAseq


title: PBMC_ICOSpos (H4) RNAseq

value: ICOS+


title: PBMC_CXCR5Neg (H2) RNAseq


title: C3F2 [FC4]

source_name: mouse female gonadal soma_Vit C supplied


title: PBMC_Naive (G3) RNAseq


title: PBMC_ICOSpos  (G4) RNAseq


title: C4F2 [FC5]


title: PBMC_CXCR5Neg (G2) RNAseq


title: V2F1 [FV2]


title: C2F2 [FC3]


title: PBMC_cTfh (G_1) RNAseq


title: C2F1 [FC2]


title: C1F1 [FC1]


title: PBMC_Naive (F_10) RNAseq


title: PBMC_CXCR5Neg (E_10) RNAseq


title: IIIb-1

city: Toronto

first: Chun

last: Peng

state: ONTARIO

address: 4200 keele street

department: Biology

country: Canada

institute: YorkU

data_processing:
LC Sciences in-house program ACGT101-miR program  was used to process the raw sequencing data allowing for 1 mismatch
Raw sequencing reads were processed using the ACGT101-miR program (LC Sciences, Houston, Texas, USA). Adaptor dimers, junk, low complexity, common RNA families and repeats were removed, and only unique sequences of 18-26 nucleotides (nt) in length were retained and compared to known zebrafish miRNAs in miRBase.
Unannotated sequences that were mapped to the zebrafish genome and had at least one predicted pre-miRNA and such pre-miRNA is able to form a hairpin structure, whose genomic coordinates should not overlap with known pre-miRNAs included in this analysis, were regarded as novel miRNAs. Sequencing counts were normalized by the library size parameter of the corresponding sample
Genome_build: GRCz11
Supplementary_files_format_and_content: tab-delimited text files include mature miRNA sequence and normalized values for each Sample

organism: Danio rerio

source_name: stage IIIb follicular cells

extract_protocol:
Follicular cells from stages IIIa and IIIb were removed and RNA was usolayed using miRNeasy kit. Construction of sequencing libraries was performed by Nanuq sequencing facility for RNA-Seq Illumina Massively Parallel Sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ovary

value: follicular cells

tag: developmental stage

value: IIIb


title: ATAC-seq-CRISPRa-15171-1

data_processing:
base calling:
read alignment, CRISPR screen data: Bowtie2 + castLE
read alignment, ChIP-seq and ATAC-seq data: bwa mem 0.7.5
read alignment, RNA-seq data: STAR 2.5.3.a
bedgraph track generation: custom-written python scripts
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph of read coverage, normalized to RPM (Read Per Million) except for CRISPR screen samples, where files with log-fold change values for each guide RNA are provided


title: IIIa-3

source_name: stage IIIa follicular cells

value: IIIa


title: PBMC_cTfh (D_10) RNAseq


title: V4F1

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality by trim_galore_v0.4.0 with parameters: --rrbs --fastqc
High-quality reads were aligned to mm9 genome by Bismark v0.14.3 using bowtie2
Methylation calls were extracted from aligned reads by bismark_methylation_extractor
CpG methylation calls were combinded into single bedgraph coverage files with bismark2bedGraph
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files of CpG genomic coordinate, methylation percentage, counts methylated, and counts unmethylated.

source_name: mouse female germ cells

extract_protocol:
gDNA was extracted from sorted Oct4+ germ cells by PureLink genomic DNA kit.
2ng gDNA was used to create RRBS (reduced representation bisulfite sequencing) libraries. Briefly, gDNA was digested with MspI then repaired with additional A addition. Methylated Illumina adapters were then ligated onto digested gDNA. Adapter ligated DNA was then bisulfite treated using EpiTect Fast Bisulfite Conversion Kit for low-concentration. Finally, libraries were amplified, size selected, and pooled before sequencing on a HiSeq4000.

value: C57BL/6 background

tag: genotype

value: Gulo-/-

value: female germ cells

tag: age

value: embryonic day 13.5

value: Vitamin C withdrawn


title: V1F1 [FV1]

tag: Sex

value: female

value: gonadal soma


title: IIIa-2


title: PBMC_ICOSneg  (B_11) RNAseq


title: V3F1


title: V3F2


title: IIIa-1


title: IIIb-3


title: PBMC_ICOSpos  (A_11) RNAseq


title: V2F2


title: 52

city: Daejeon

first: Hankuil

last: Yi

address: Daehak-ro 99 Yuseong-gu

department: Deparment of Biological Sciences

country: South Korea

institute: Chungnam National University

data_processing:
Illumina Casava1.7 software used for basecalling.
Clean reads for DEG analysis were obtained from raw reads by trimming low-quality bases with Phred score (Q < 20) and removing the reads shorter than 25 bp, using DynamicTrim and LengthSort in SolexaQA package.
Clean reads were mapped onto B. napus reference coding sequences (CDS) which were downloaded from Genoscope (http://www.genoscope.cns.fr/brassicanapus/data/,  Brassica_napus.annotation_v5.cds.fa), using Bowtie2 (v2.1.0) software allowing up to 2 bp mismatches.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Genoscope (http://www.genoscope.cns.fr/brassicanapus/data/,  Brassica_napus.annotation_v5.cds.fa)
Supplementary_files_format_and_content: A text file includes raw and normalized read values in Comma-separated value (CSV) format for each Sample.

organism: Brassica napus

source_name: developing pods

growth_protocol: Plants were grown at a greenhouse condition located in the National Institute of Agricultural Sciences (Jeonju, Republic of Korea)

extract_protocol:
Whole pods including developing seeds were harvested, and Total RNA was isolated from 1 or 2 pods depending on the pod size using PureLink™ Plant RNA Reagent.
cDNA libraries were constructed using Illumina TruSeq RNA Sample Preparation Kit v2

value: CpFatB5 transgenic

value: developing pods

value: at 25 days after fertilization


title: 42

value: CpFatB4 transgenic


title: 53

value: at 45 days after fertilization


title: 41

value: at 8 days after fertilization


title: 51


title: 43


title: LN_CXCR5Neg (C4) RNAseq

value: LymphNode


title: C2

value: Wild-type Youngsan


title: C3


title: C1


title: IIIb-2

value: ovary

value: follicular cells

value: IIIb


title: LN_nonGCTfh (C2) RNAseq


title: V1F2

value: C57BL/6 background

value: Gulo-/-


title: H3K4me3_L3_ChIPseq_281VEH

description:
Lamb Sample 3 H3K4me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K4me3.txt
Fetal_vs_Lamb_PeakRanger_H3K4me3.txt

source_name: perirenal adipose tissue

tag: breed

value: purebred merino

value: 80 day old lamb

value: perirenal adipose tissue

value: wild type

tag: chip antibody

value: H3K4me3 (Abcam, catalog# ab8580, lot # GR111321)


title: LN_GCTfh (C_1) RNAseq


title: C3F3

value: female germ cells

value: embryonic day 13.5

value: Vitamin C supplied


title: H3K4me3_L2_ChIPseq_267VEH

description:
Lamb Sample 2 H3K4me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K4me3.txt
Fetal_vs_Lamb_PeakRanger_H3K4me3.txt


title: C3F2


title: H3K4me3_L1_ChIPseq_235VEH

description:
Lamb Sample 1 H3K4me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K4me3.txt
Fetal_vs_Lamb_PeakRanger_H3K4me3.txt


title: V2F1

value: Vitamin C withdrawn


title: LN_CXCR5Neg (B4) RNAseq


title: H3K4me3_F1_ChIPseq_6D1159

description:
Fetal Sample 1 H3K4me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K4me3.txt
Fetal_vs_Lamb_PeakRanger_H3K4me3.txt

value: 132 day old fetus


title: LN_Naive (B3) RNAseq

value: LymphNode

value: Naive


title: H3K27ac_L2_ChIPseq_267VEH

description:
Lamb Sample 2 H3K27ac
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27ac.txt
Fetal_vs_Lamb_PeakRanger_H3K27ac.txt

value: H3K27ac (Abcam, catalog# ab4729, lot # GR104852)


title: H3K27ac_L1_ChIPseq_235VEH

description:
Lamb Sample 1 H3K27ac
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27ac.txt
Fetal_vs_Lamb_PeakRanger_H3K27ac.txt


title: H3K4me3_F2_Chipseq_6D122

description:
Fetal Sample 2 H3K4me3
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K4me3.txt
Fetal_vs_Lamb_PeakRanger_H3K4me3.txt


title: LN_Naive (C3) RNAseq


title: LN_nonGCTfh (B2) RNAseq


title: H3K27ac_F1_ChIPseq_6D1159

description:
Fetal Sample 1 H3K27ac
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27ac.txt
Fetal_vs_Lamb_PeakRanger_H3K27ac.txt


title: H3K27ac_F2_Chipseq_6D122

description:
Fetal Sample 2 H3K27ac
chromatin immunoprecipitated nucleosomal DNA
Fetal_vs_Lamb_Promoter_H3K27ac.txt
Fetal_vs_Lamb_PeakRanger_H3K27ac.txt


title: LN_GCTfh (B_1) RNAseq


title: C1F3


title: LN_CXCR5Neg (A4) RNAseq


title: C2F3


title: C2F2


title: L1 RNAseq 235VEH

description: Lamb Sample 1

data_processing:
Sequence reads were trimmed for adaptor sequence removal and masked for low-complexity or low-quality sequence. Sequence reads for each sample were independently mapped to each of the 24,390 ENSEMBL gene models for the OARv3.1.74  sheep genome using the mapping tool in CLC Genomocs Workbench (v7.0). Reads were mapped using the mapping protocol in the CLC Genomics Workbench (v7.0) (maximum length fraction =0.8; minimum similarity fraction =0.8; penalties were mismatch =2, insertion =3, deletion =3). On average, 68.3% of the reads mapped with 53.4% mapping uniquely. Only uniquely mapped reads were kept for the analysis.
Reads Per Kilobase of exon per Million reads  (RPKM) were calculated for each gene based on the ENSEMBL gene models using  the CLCBIO Genomics Workbench (v7.0).
Differential gene expression was analysed using  EdgeR implemented as DGE in the CLCBIO Genomics Workbench. Briefly, the data for the 24390 mapped genes was prefiltered to remove genes without reads associated with all samples, which reduced the input gene list to 17,010.  This pre-filtered data was used as the input data set for the statistical analysis of gene expression using EdgeR.
Genome_build: OARv3.1.74
Supplementary_files_format_and_content: tab-delimited text files that include RPKM values, expression values and EdgeR analysis data for each sample .

source_name: 12wk-old lamb_perirenal adipose tissue

growth_protocol: Tissues for this study were provided by Janna L Morrison and Isabella C McMillen from Sansom Institute for Health Research, The University of South Australia, Adelaide, 4001, SA, Australia.  All procedures involving animals were carried out with approval from the University of Adelaide Animal Ethics Committee.  Animals were maintained on 100% maintenance energy requirement diets and  cared for humanely as a research flock according to strict animal ethics guidelines. The  ewes for the fetal samples were housed from 110 dpc (days post conception (dpc); term, 150 d) in pens for two weeks before sampling. The pregnant ewes were maintained on a diet that provided 100% of their maintenance energy requirements. Three pregnant ewes were humanely euthanased with an intravenous overdose of sodium pentobarbitone (8.2 g Lethobarb, Virbac Pty ltd, Peakhurst, NSW, Australia) and the uterus removed and fetuses tissue collected at 132±1 dpc. Three ewes were allowed to deliver at term and the lambs were reared with ewes until weaning. At ~89±7 d after birth, lambs were humanely euthansed (as described) and tissues collected.

extract_protocol:
Perirenal adipose tissue was removed from animals within 10 minutes of euthanasia, flash frozen in liquid nitrogen, stored on dry ice and then stored at -80 degrees Celcius.  RNA was extracted using Trizol reagent (Life Technologies) and further purified using RNeasy purification (QIAGEN) and treated with DNase1 to remove any contaminating DNA. RNA quantity and integrity were assessed using the Bioanalyzer 2100 (RIN scores >9; Agilent, Santa Clara, USA).
Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 5 ug of total RNA for the construction of single end read sequencing libraries.
Single end 50bp read libraries for the 6 samples were multiplexed and run on a single flowcell of an Illumina HiSeq20000 sequencing platform.  A mean number of reads of ~33.2 million reads was obtained from each library.

value: pure bred merino

value: 89 day old lamb (80 days after birth)

value: perirenal adipose tissue (PRAT)


title: F2 RNAseq 6D122

description: Fetal Sample 2

source_name: fetus_perirenal adipose tissue

value: 132 day old fetus (132 d post conception (dpc))


title: F3 RNAseq 318

description: Fetal Sample 3


title: 4V F2

data_processing:
Illumina HiSeq 4000 reads were trimmed and clipped for quality by trim_galore_v0.4.0 with parameters: --clip_R1 3 --fastqc
High-quality reads were aligned to mm9 genome by TopHat v2.0.13
BAM files were imported into R-Studio and analyzed for differential expression by DESeq2 v1.10.1
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files with RPKM counts normalized for sequencing depth and log transformed.

extract_protocol:
Total RNA was extracted from sorted Oct4+ germ cells by Qiagen RNeasy Micro Kit
1ug total RNA was used in Clonetech SMARTR-seq RNA library prep kit

value: C57BL/6 background

value: Gulo-/-


title: LN_Naive (A3) RNAseq


title: F1 RNAseq 6D1159

description: Fetal Sample 1


title: Branca

city: São Paulo

middle: de Carvalho

last: Papa

state: São Paulo

address: Av. Prof. Dr. Orlando Marques Paiva, 87

department: Surgery

country: Brazil

institute: School of Veterinary Medicine and Animal Science, University of São Paulo

data_processing:
software CASAVA v1.8.2 was used to FASTQ file generation
The reads were mapped against the reference genome  using TopHat v2.0.9
The transcripts were assembled using Cufflinks and identified by their Ensembl name.
The relative abundance of transcripts of RNA-seq fragments was measured by Cufflinks in fragment per kilobase of exon model per million mapped reads (FPKM)
Genome_build: Canis_familiaris. CanFam 3.1.75.dna.toplevel.fa
Supplementary_files_format_and_content: spreadsheet in Excel with FPKM of each gene during diestrus

organism: Canis lupus familiaris

source_name: corporea lutea

extract_protocol:
The corpora lutea were collected via ovariosalpingohysterectomy and immediately frozen in liquid nitrogen for total RNA extraction. Total RNA was extracted using TRIzo® reagent  in accordance with the manufacturer’s instructions.
The libraries were constructed  using Truseq RNA library Preparation kit v2 (Illumina, San Diego, CA, USA) in accordance with the manufacturer’s standard procedure

tag: days post-ovulation

value: corporea lutea


title: 4V F1

tag: strain


title: Sissi


title: C3F1


title: L2 RNAseq 267VEH

description: Lamb Sample 2

value: wild type


title: Meg


title: LN_nonGCTfh (A2) RNAseq


title: Safira


title: 3V F1


title: L3 RNAseq 281VEH

description: Lamb Sample 3


title: A_LV_S138 ATACseq

data_processing:
Paired-end reads were mapped to the hg19 reference genome using Bowtie2
Only concordantly mapped pairs were kept for further analysis
Peak calling was performed using MACS v1.4 to identify areas of sequence tag enrichment
BedTools was used to find common intersection between identified peaks (1bp minimum overlap) and to create a merged peak list
ATAC-seq tag enrichment, DNA motif analysis across the merged peak list,and GO term assessment were computed using HOMER (homer.salk.edu)
Genome_build: hg19
Supplementary_files_format_and_content: bed files generated by peak calling

extract_protocol:
Mononuclear cells from mesenteric LN, TDL, and PBMC were thawed, rested overnight, and sorted in cell numbers of 5-25,000 into complete RPMI with 50% FBS. Nuclei from cell pellets (5,000-25,000 cells) were isolated using a lysis buffer and pelleted in low-bind 1.5mL tubes (Eppendorf).
Nuclei were resuspended in 25ml TD buffer with Tn transposase (Illumina). The transposition reaction was continued for 45 minutes at 37°C. The resulting DNA fragments were purified using the MinElute PCR purification Kit (Qiagen). Libraries were prepared using Nextera (Illumina) and sequenced by the Children’s Hospital of Philadelphia partnership with the Bejing Genomics Institute on two lanes of a Hiseq 4000 paired-end sequencing (100 bp read length).

value: Thoracic Duct Lymphnode

value: CXCR5+PD-1 bright


title: Lola Fran


title: LN_GCTfh (A_1) RNAseq


title: Pitica


title: Teca


title: Mel Bom


title: 1V F2

value: female germ cells

value: embryonic day 13.5


title: Preta


title: 2V F1

value: Vitamin C withdrawn


title: Mel


title: Catita


title: Xuxa


title: 1V F1


title: A_LV_S133 ATACseq

value: CXCR5+PD-1 dim


title: 4C F2

value: Vitamin C supplied


title: A_LV_S130 ATACseq


title: A_LV_S134 ATACseq


title: Lola


title: 4C F1


title: 3C F2


title: A_LV_S129 ATACseq


title: Pitucha


title: Madona


title: 2C F2


title: Pandora


title: A_LV_S125 ATACseq

value: PBMC


title: A_LV_S122 ATACseq


title: Lilica


title: A_LV_S119 ATACseq

value: Icos Hi


title: 1C F2


title: A_LV_S118 ATACseq

value: Icos low


title: Princesa


title: A_LV_S115 ATACseq


title: A_LV_S111 ATACseq

value: LymphNode


title: A_LV_S108 ATACseq


title: 1C F1