title: SM3116 Methionine Restriction

city: Baton Rouge

first: Thomas

middle: W

last: Gettys

state: LA

address: 6400 Perkins Road

department: Nutrient Sensing and Adipocyte Signaling

institute: Pennington Biomedical Research Center

data_processing:
conversion of SOLiD 5500 XSQ files to csfasta/qual files was performed using perl and bash shell scripts that were developed in-house. These scripts make use of Life Technologies XSQ conversion tools, version 1.5.
alignment of sequence tags back to a mouse reference genome was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
filtering non-unique tags, and establishing counts per RefSeq gene was performed using a modified version of the Applied Biosystems SOLiD™ SAGE™ Analysis Software v1.10 that was developed in-house.
The raw data set was filtered to remove genes where the sum of counts was less than 20  across each tissue group.  The dataset was normalized and differential expression calculated using DESeq(Bioconductor.org) version 1.8.3.  JMP Genomics version 6.0 was used for principal components analysis, heatmaps, and Venn diagrams.
Genome_build: mm10/GRCm38.p1
Supplementary_files_format_and_content: processed data file in text format contains DESeq normalized counts per gene for 14,102 mouse RefSeq genes

source_name: dissected gastrocnemius muscle

extract_protocol:
Total RNA was prepared using Trizol, RNA concentration was determined on a Qbit fluorometer, and 7-12ng RNA per sample was used for sequencing library construction.
Libraries were prepared using the Applied Biosystems SOLiDSAGE kit, according to AB's instructions for the SOLiD 4 System (except a 1:100 of Adaptor B dilution was used).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046); 1 billion fragments sequenced with 407 million fragments uniquely mapped to mouse ref-seq genes

treatment_protocol: Five week-old male C57BL/6J mice were fed Control (n=6) or Methionine-restricted diets (n=6) ad libitum for 11 weeks prior to harvest of the tissues.  The mice were housed at 23 C and fasted for 5 h before harvesting the tissues.

tag: tissue

value: Skeletal Muscle

tag: strain

tag: diet

value: Methionine Restriction


title: SM3115 Control

status: Public on May 02 2017

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: Control


title: H2_D1

city: Chicago

first: Lauren

middle: Elizabeth

last: Blake

state: Illinois

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

data_processing:
50 bp single-end RNA-seq reads from each species were trimmed and mapped to the appropriate genome (hg19 or panTro3) using Tophat2 (version 2.0.11) (Kim et al. 2013). We kept only reads that mapped uniquely.
The number of reads falling into orthologous meta-exons across 30,030 Ensembl genes from hg19, panTro3 and rheMac3 (Blekhman et al. 2010) was determined using featureCounts within SubRead (version 1.4.4) (Liao et al. 2014).
Genome_build: hg19 & panTro3
Supplementary_files_format_and_content: RNA-seq counts for orthologous genes for all individuals

organism: Homo sapiens

source_name: iPSC-derived primitive streak cells

growth_protocol: Feeder free cultures were initially maintained on Growth Factor Reduced Matrigel using Essential 8 Medium (E8) as previously described. After 10 passages in E8, all cell lines were transitioned to iDEAL feeder free medium that was prepared in house (Marinho et al. 2015). Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

extract_protocol:
RNA was extracted using the ZR-Duet DNA/RNA MiniPrep kit (Zymo) with the addition of an on column DNAse I treatment step prior to RNA elution.
Samples were pooled together in 4 pools for RNA-seq library generation using the Illumina TruSeq RNA Library Prep kit v2.  50 bp sing-end RNA-seq libraries were sequenced on the HiSeq4000 following the manufacturer's protocols.

treatment_protocol: To produce definitive endoderm and intermediate cell types, we followed a recently published three-day protocol that systematically identified and targeted pathways involved in cell fate decisions, at critical junctures in endoderm development (Loh et al. 2014) with minimal modification. At 12 hours prior to initiating differentiation, iPSC lines at 70-90% confluence were seeded at a density of 50,000 cells/cm2. Basal medial for differentiations consisted of 50/50 IMDM/F12 basal media supplemented with 0.5 mg/mL human albumin, 0.7 g/mL Insulin, 15 g/mL holo-Transferrin and 1% v/v chemically defined lipid concentrate. For differentiation, basal media was supplemented with the following: day 1 (Primitive streak induction) media included 100 ng/mL Activin A, 50 nM PI-103 (PI3K inhibitor), 2 nM CHIR99021 (Wnt agonist), days 2-3 media included 100 ng/mL Activin A and 250 nM LDN-193189 (BMP inhibitor). Two separate batches of differentiation were performed, resulting in replicates for a subset of samples. Cell culture was conducted at 37°C, 5% CO2, and atmospheric O2.

tag: cell line

tag: Sex

value: Male

tag: population

value: Caucasian


title: aP60_2_01

city: Beijing

first: Cheng-ran

last: Xu

address: NO.5 YIHEYUAN ROAD HAIDIAN DISTRICT, BEIJING, P.R.CHINA

department: School of Basic Medical Sciences

country: China

institute: Peking University

description:
Sample 883
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

data_processing:
[Bulk Cell RNA-seq (Sample 001-014)] Reads were aligned to Mus musculus reference genome GRCm38/mm10 with TopHat (v2.1.0) using parameter “-G”.
[Bulk Cell RNA-seq (Sample 001-014)] Reads aligned to genes were calculated using HTSeq (v 0.6.0) with parameters “-f bam -r pos -s reverse -a 30”.
[Bulk Cell RNA-seq (Sample 001-014)] Reads of biological replications were pooled together.
[Bulk Cell RNA-seq (Sample 001-014)] Gene expression levels were quantified as TPM (Transcripts Per Kilobase Million).
[Bulk Cell RNA-seq (Sample 001-014)] TPM was normalized by size factors, which were calculated using DESeq (v1.20.0).
[Single Cell RNA-seq (Sample 015-950)] Reads were aligned to Mus musculus reference genome GRCm38/mm10 with TopHat (v2.1.0) using parameter “-G”.
[Single Cell RNA-seq (Sample 015-950)] Reads aligned to genes were calculated using HTSeq (v 0.6.0) with parameters “-f bam -r pos -s no -a 30”.
[Single Cell RNA-seq (Sample 015-950)] Gene expression levels were quantified as TPM (Transcripts Per Kilobase Million).
Genome_build: mm10
Supplementary_files_format_and_content: values tab-delimited text files include read count and TPM values for each sample

source_name: Pancreas

extract_protocol:
[Bulk Cell RNA-seq (Sample 001-014)] Total RNA from approximately 3-5 × 10^4 sorted β-cells was extracted by the RNeasy Micro Kit (Qiagen, 74004) followed by mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490).
[Bulk Cell RNA-seq (Sample 001-014)] Strand-specific libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB #E7420) following manufacturer’s instructions.
[Single Cell RNA-seq (Sample 015-950)] cDNA synthesis and amplification were performed following the Smart-seq2 protocol.
[Single Cell RNA-seq (Sample 015-950)] The libraries were prepared with 2 ng cDNA using the TruePrep DNA Library Prep Kit (Vazyme, TD502).

tag: cell type

value: P60, Gcg-Cre, Rosa-RFP+

tag: collection method

value: manually-picked

tag: batch

value: α-cell P60-2


title: H1B_D1

value: Female


title: SM3112 Control


title: aP18_3_12

description:
Sample 882
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P18, Gcg-Cre, Rosa-RFP+

value: α-cell P18-3


title: CD34_R2

city: Montreal

first: Magalie

last: Celton

state: Quebec

address: 2950, Chemin de Polytechnique

country: Canada

institute: IRIC

library_source: genomic

data_processing:
the fastq files obtained from MiSeq and HiSeq were concatenated
Pair-end sequences were mapped to human reference genome (GRCH37/hg19) using  Bismark v0.10.1 and Bowtie 2 v2.2.5 as alignment
Bismark-methyaltion-extractor used for methylation calls extraction
PCR duplicate were removed using a Perl script provided by Krueger and Andrews,2011
Levels of methylation were calculated usting R packeage MethylKit v0.9.2 (Akalin et al., 2012)
Data were filtered with a number reads minimal of 8
Genome_build: GRCH37/hg19
Supplementary_files_format_and_content: tab-delimited text files include FreqC  values corresponding to the percentage of methylation for all sequenced cytosines for each sample:
Supplementary_files_format_and_content: chrBase  Identifiant: chromosome  chr  chromosome  base  position in the chromosome   strand  Forward (F) or Reverse (R) strand of DNA   coverage  numbers of reads  freqC  number of methylated cytosines/  Total of cytosines (methylated + unmethylated)  freqT  number of unmethylated cytosines/  Total of cytosines (methylated + unmethylated)

molecule: genomic DNA

source_name: cord blood cells

growth_protocol: Human CD34+ cord blood cells were positively selected (CD34  cells). Cells were transduced with a retrovirus containing GFP and the human MLL-AF9 fusion gene and were maintained for  in vitro culture for 80-90 days (CD34-MLL-AF9 cells).  Transduced cells were expanded in myeloid promoting culture with 15% FSC +IL3 +SCF for 4 weeks. After ~30 days of expansion cells (10 x106/mouse) from each donor sample were injected into multiple NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) immunodeficient mice. Mice were analyzed after ~20-24 weeks and the bone marrow was harvested (Model AML MLL_AF9 samples).

extract_protocol:
Genomic DNA was isolated from the cell pellets using the PureLink Genomic DNA Mini Kit.
Methyl-seq libraries were prepared for sequencing using Agilent SureSelextXT Human Methyl-seq Target enrichment system protocols

value: CD34+ cells enriched cord blood cells from one single healthy donors


title: aP18_3_10

description:
Sample 880
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: SM3109 Methionine Restriction


title: H5B_D0

source_name: induced pluripotent stem cells


title: SM3107 Control


title: H6_D0


title: aP18_3_11

description:
Sample 881
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H1A_D1


title: H6_D1


title: SM3104 Methionine Restriction


title: SM3106 Control


title: aP18_3_08

description:
Sample 878
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP60_2_04

description:
Sample 886
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H5A_D0


title: aP18_3_09

description:
Sample 879
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: SM3114 Control


title: SM3103 Control


title: aP18_3_07

description:
Sample 877
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP18_3_06

description:
Sample 876
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H2_D0


title: SM3101 Methionine Restriction


title: H1B_D0


title: aP18_3_05

description:
Sample 875
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: H3_D0


title: Liver3116 Methionine Restriction

source_name: dissected Liver

value: Liver


title: SM3102 Methionine Restriction


title: H1A_D0


title: Liver3115 Control


title: aP18_3_03

description:
Sample 873
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Liver3114 Control


title: sIEC3 mRNA

city: Durham

first: John

last: Rawls

state: North Carolina

address: Duke University 213 Research Drive, Box 3580 DUMC CARL Building 327

institute: Duke University

data_processing:
Paired End Adapter trimmed reads from Duke Sequencing and Genomic Technologies Shared Resource were mapped to the gasacu1 genome using Tophat2 (v2.0.9) with default conditions using Galaxy(0.6)
Cufflinks(v2.1.1) was used to generate FPKM values using default peramaters and BROADS1/gasAcu1 Ensembl annotations(Ensemblegenes 76) using Galaxy(0.0.6)
Peaks were identified using MACS2 2.1.0 with default values except, qvalue = 1.00e-01, broad region calling = off, subpeak summits = on
Genome_build: gasAcu1
Supplementary_files_format_and_content: Bigwig represents single base pair genomewide sequencing coverage; Bed files are tabular files containing peak coordinates; Tabular Files Contain Gene Expression Information

organism: Gasterosteus aculeatus

source_name: Intestinal Epithelial Cells_RNA-seq

growth_protocol: Stickleback were wild caught from Friant Lake, CA

extract_protocol:
To isolate stickleback IECs, intestines were dissected, splayed, and washed extensively with ice-cold 1x PBS with care taken to remove as much intestine associated fascia, adipocytes, and blood vessels as possible. Three washed intestines were transferred into dissociation reagent 1 (DR1; 30 mM EDTA, 1.5 mM DTT, 0.5x Complete protease inhibitors (Roche), in 1x PBS) for 15 minutes on ice. Segments were transferred to Dissociation Reagent 2 (DR2; 30 mM EDTA, 0.5x Complete protease inhibitors (Roche), in PBS) and moderately shaken by hand for 5 minutes until most epithelial cells were isolated in the suspension. Intestinal lamina propria was removed and 8 ml of cold 1x PBS was added to the cells on ice. Cells were pelleted at 500 x G at 4°C, washed once with 13 ml of cold 1X PBS, and re-suspended in 0.5 ml cold 1x PBS. A 0.4 ml fraction was used for FAIRE, and 0.1 ml fraction was reserved for RNA extraction. Isolated IECs were placed in TRIzol Reagent for RNA extraction.freshly isolated intestinal epithelial cells were directly fixed for 5-10 minutes in 10 ml of 1-3% w/v Formaldehyde solution (in 1x PBS) at room temperature and gentle rocking. Glycine (2.5M) was added to a final concentration of 125 mM to quench the formaldehyde. Cells were pelleted at 600 x G and washed three times in cold 1x PBS without dissociating the pellet. Fixed and washed cell pellets were flash frozen and stored at -80°C. Cells were lysed in 2 ml Lysis Buffer A (10 mMTris-HCl (pH8.0), 2% (vol/vol) Triton X-100, 1% SDS, 100 mM NaCl and 1 mM EDTA) and sonicated using a Branson Sonifier 450D equipped with a microtip for 6-13 cycles (1 second burst, 0.5 second pause, for 30 seconds/cycle at 70% intensity) allowing samples to cool on ice for 1 minute between cycles.
RNA-seq: Total RNA was submitted and library construction was performed by Duke Sequencing and Genomic Technologies Shared Resources.
FAIRE-seq: FAIRE-seq libraries were prepared using the TruSeq kit with 100ng of FAIRE DNA according to manufacturer's protocols and sequenced by UNC High Through-put Sequencing Core.

value: FRIL3 IECs Friant Lake, CA Freshwater Wild NA F p.125 158.8 5558 9.9

value: Stickleback Adult Intestinal Epithelial Cells


title: stickleback1 FAIRE-seq

source_name: Intestinal Epithelial Cells_FAIRE-seq


title: Liver3112 Control


title: Liver3113 Methionine Restriction


title: aP18_3_02

description:
Sample 872
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP15_2_21

description:
Sample 870
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P15, Gcg-Cre, Rosa-RFP+

value: α-cell P15-2


title: sIEC1 mRNA

value: FRIL1 IECs Friant Lake, CA Freshwater Wild NA M p.125 392.5 13737.5 NA


title: sIEC2 mRNA

value: FRIL2 IECs Friant Lake, CA Freshwater Wild NA F p.125 1172 41020 NA


title: H4_D0


title: Liver3109 Methionine Restriction

value: Methionine Restriction


title: Liver3107 Control

value: Control


title: PV_in_1

city: Oxford

first: Irina

last: Mohorianu

address: Headington

department: Medical Sciences Division

country: United Kingdom

institute: University of Oxford

data_processing:
Adapter removal step was conducted using the UEA sRNA workbench [Stocks et al, 2012]. The 3' adapter sequence was identified using the first 6 nt. Adapter guessing strategy was also used to double check the adapter removal procedure.
Quality checks including size class distribution, nucleotide composition analysis, complexity analysis and Jaccard similarity were done before genome matching.
Reads were mapped full length, no mis-matches or gaps allowed to the host Aspergillus fumigatus genome and also viral genomes using PatMan [Prueffer et al, 2008]
Differentially expressed virus-derived small RNAs were determined and mapped to the fungal genome to identify the potential targets.
The miRNAs were identified using the miRCat and miRprof tool within the UEA workbench.
The sRNA loci were identfied using CoLIde [Mohorianu et al, 2013]
Genome_build: A_fumigatus_Af293 genome version_s03_m04_r22
Supplementary_files_format_and_content: csv file containing the sRNA expression levels.

organism: Aspergillus fumigatus

source_name: Partitivirus-infected isolate biological replicate-1

growth_protocol: All A. fumigatus strains of interest were inoculated onto 25 ml of solid Aspergillus Complete Media (ACM) from 50% glycerol stocks which were kept at -20 °C.Plates were incubated at 37°C for 5 days and spores were harvested with 15 ml of sterile distilled water. Spore suspensions were used to inoculate 500 ml of ACM broth. Inoculated bottles were incubated at 37°C with shaking at 130 rpm. After 5 days, mycelia were harvested.

extract_protocol:
Total RNAs were extracted using Trizol and small RNAs were isolated using PEG8000 precipitation.
Libraries were constructed using Scriptminer adapters and kit components.

value: Fungal mycelia


title: aP15_2_20

description:
Sample 869
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP15_2_19

description:
Sample 868
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Liver3104 Methionine Restriction


title: Liver3106 Control


title: PV_in_2

source_name: Partitivirus-infected isolate biological replicate-2


title: aP18_3_04

description:
Sample 874
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP15_2_17

description:
Sample 866
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Liver3103 Control


title: PV_fr_1

source_name: Partitivirus-free isolate biological replicate-1


title: PV_fr_2

source_name: Partitivirus-free isolate biological replicate-2


title: aP15_2_16

description:
Sample 865
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: NK_in_2

source_name: NK virus-infected isolate biological replicate-2


title: Liver3102 Methionine Restriction


title: aP15_2_18

description:
Sample 867
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: NK_in_1

source_name: NK virus-infected isolate biological replicate-1


title: aP15_2_15

description:
Sample 864
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: Liver3101 Methionine Restriction


title: aP15_2_14

description:
Sample 863
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: IWAT3116 Methionine Restriction

source_name: dissected IWAT

value: Inguinal White Adipose Tissue


title: NK_fr_2

source_name: NK virus-free isolate biological replicate-2


title: ZF_E_biological_rep2

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
Basecalls were performed using bcl2fastq v1.8.2
The low-quality bases at the 3' read ends and the adaptors were trimmed by cutadapt-1.3
Reads of 20 bp or longer were mapped to mouse genome (mm9) with BWA 0.6.2
Peaks were called using the MACS2 plus IDR framework developed from ENCODE project (Landt et al., 2012)
Peaks falling within blacklisted regions were excluded from further analysis
Genome_build: mm9
Supplementary_files_format_and_content: RegionPeak files contain the genomic locations of peaks identified using MACS2 and the IDR framework.

source_name: Mouse embryonic fibrobrasts

growth_protocol: Reprogramming cells were cultured in KSR medium [DMEM with high glucose, 15% Knockout Serum Replacement (Life Technologies), 100 mM 2-mercaptoethanol, 1 x MEM nonessential amino acids, 0.5 x penicillin-streptomycin, 1 x L-glutamine, LIF] from the next day of infection.

extract_protocol:
5 x 10^5 MEFs were seeded onto a gelatin-coated 10 cm dish and infected with retrovial vectors the next day. 24 hours after infection, medium was replaced into KSR medium, and 48 hours after infection, cells were fixed with 1% formaldehyde in DMEM at room temperature for 5 min and quenched with glycine. Fixed cells were washed with PBS twice and treated with 0.5% NP40, 10 mM NaCl and 10 mM Tris-HCl for 10 min. Cells were scraped and collected into a tube and centrifuged at 3,000 rpm for 20 min. The cell pellet was lysed in 1% SDS, 10 mM EDTA, 1x cOmplete protease inhibitor (Roche) and 50 mM Tris-HCl, and then diluted one fourth with IP dilution buffer (50 mM Tris-HCl, 167 mM NaCl, 1.1% Triton X-100, 0.11% deoxycholate, 1x cOmplete). Cell lysates were sonicated with handy sonicator XL-2000 (Misonix) at level 7 for 10 sec 6 times and stored at -80 °C until the immunoprecipitation procedure. Before immunoprecipitation, a complex of 24 uL Dynabeads ProteinG (LifeTechnologies) and 2.4 ug anti-FLAG M2 antibody (Sigma) per 10 cm dish was formed in RIPA buffer [50 mM Tris-HCl, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% TritonX-100, 0.1% deoxycholate, 1x Protease inhibitor (Nacalai Tesque, 25954-21)] by rotating at 4 °C, O/N. Antibody-bead complex was washed with RIPA buffer twice, then combined with sonicated cell lysates and rotated at 4 °C, O/N.  The resultant complexes were successively washed with RIPA, high-salt RIPA (RIPA with 500 mM NaCl), LiCl wash buffer (10 mM Tris-HCl, 250 mM LiCl, 1 mM EDTA, 0.5% NP40, 0.5% deoxycholate), TE buffer, and eluted twice with 100 mM NaHCO3, 1% SDS and 10 mM DTT. Eluates were supplemented with 200 mM final NaCl, de-crosslinked by shaking at 65 °C, O/N and treated with 50 ug/mL RNase A at 37 °C for 1 hr and 2 mg/mL Pronase at 42 °C for 2 hr. DNA was purified with PCR Purification Kit (Qiagen).
Purified ChIP DNA (5 ng per sample) was used for end repair, 3’ end adenylation and adaptor ligation reaction with TruSeq ChIP Sample Preparation Kit (illumina) following the manufacturer’s manual. Resultant adaptor-ligated DNA was amplified by PCR, and subsequently selected for 300-450 bp fragments by gel electrophoresis followed by excision and extraction with Gel Extraction Kit (Qiagen). The resultant library DNA was quantified with Library Quantification Kit (KAPA Biosystems), and 100 mL of total 10 nM of mixture of indexed DNA libraries were used for single-end 100-bp sequencing by HiSeq 2000 (illumina).

treatment_protocol: MEFs were seeded on plastic coated with gelatin and infected with indicated retroviral transcription factors with 4 mg/mL polybrane the next day.

tag: condition

value: retroviral OSK, Esrrb and Zic3-FLAG

tag: time point

value: 2 days after infection

tag: chip antibody

value: anti-FLAG M2 (Sigma F7425)


title: ZF_biological_rep2

description: ZF.regionPeak.txt

value: retroviral OSK and Zic3-FLAG


title: aP15_2_13

description:
Sample 862
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked


title: NK_fr_1

source_name: NK virus-free isolate biological replicate-1


title: IWAT3115 Control


title: aP15_2_12

description:
Sample 861
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: EF_biological_rep2

description: EF.regionPeak.txt

value: retroviral OSK and Esrrb-FLAG


title: CV_in_2

source_name: Chrysovirus-infected isolate biological replicate-2


title: IWAT3114 Control


title: IWAT3113 Methionine Restriction


title: CV_in_1

source_name: Chrysovirus-infected isolate biological replicate-1


title: aP15_2_10

description:
Sample 859
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: Pancreas


title: IWAT3112 Control


title: input_biological_rep2

value: mixture of EF, EF_Z, ZF and ZF_E


title: ZF_biological_rep1

description: ZF.regionPeak.txt


title: ZF_E_biological_rep1


title: CV_fr_2

source_name: Chrysovirus-free isolate biological replicate-2


title: aP18_3_01

description:
Sample 871
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P18, Gcg-Cre, Rosa-RFP+

value: α-cell P18-3


title: IWAT3109 Methionine Restriction


title: aP15_2_08

description:
Sample 857
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P15, Gcg-Cre, Rosa-RFP+


title: aP15_2_09

description:
Sample 858
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: α-cell P15-2


title: CV_fr_1

source_name: Chrysovirus-free isolate biological replicate-1


title: A78_in_2

source_name: A78 virus-infected isolate biological replicate-2


title: IWAT3107 Control


title: EF_Z_biological_rep1

value: retroviral OSK, Zic3 and Esrrb-FLAG


title: IWAT3106 Control


title: EF_Z_biological_rep2


title: aP15_2_06

description:
Sample 855
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: A78_in_1

source_name: A78 virus-infected isolate biological replicate-1


title: aP15_2_05

description:
Sample 854
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: EF_biological_rep1

description: EF.regionPeak.txt


title: IWAT3104 Methionine Restriction


title: aP15_2_11

description:
Sample 860
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: A78_fr_2

source_name: A78 virus-free isolate biological replicate-2


title: P60_beta_#2

description:
Sample 014
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P60 Ins1-RFP+

value: Pancreas

tag: developmental stage

value: beta cells


title: IWAT3103 Control

value: Control


title: A78_fr_1

source_name: A78 virus-free isolate biological replicate-1

value: Fungal mycelia


title: input_biological_rep1


title: aP15_2_04

description:
Sample 853
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: P60_beta_#1

description:
Sample 013
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: aP15_2_03

description:
Sample 852
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: IWAT3102 Methionine Restriction

value: Inguinal White Adipose Tissue

value: Methionine Restriction


title: C4B_D3

organism: Pan troglodytes

source_name: iPSC-derived definitive endoderm cells

value: Male

value: Chimpanzee


title: P18_beta_#2

description:
Sample 012
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P18 Ins1-RFP+


title: aP15_2_02

description:
Sample 851
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: IWAT3101 Methionine Restriction


title: C4A_D3


title: C3B_D3

value: Female


title: BAT3116 Methionine Restriction

source_name: dissected IBAT

value: Brown Adipose Tissue


title: aP15_2_01

description:
Sample 850
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: manually-picked


title: aP15_2_07

description:
Sample 856
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: P18_beta_#1

description:
Sample 011
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: BAT3115 Control


title: aP9_4_15

description:
Sample 849
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P9, Gcg-Cre, Rosa-RFP+

value: α-cell P9-4


title: C2B_D3


title: C3A_D3


title: BAT3114 Control


title: aP9_4_14

description:
Sample 848
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: C2A_D3


title: aP9_4_13

description:
Sample 847
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BAT3112 Control


title: C1B_D3


title: P9_beta_#1

description:
Sample 007
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P9 Ins1-RFP+


title: P15_beta_#1

description:
Sample 009
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P15 Ins1-RFP+


title: BAT3113 Methionine Restriction


title: C1A_D3


title: P3_beta_#2

description:
Sample 006
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P3 Ins1-RFP+


title: BAT3109 Methionine Restriction


title: aP9_4_11

description:
Sample 845
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: P3_beta_#1

description:
Sample 005
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: BAT3107 Control


title: C4B_D2

source_name: iPSC-derived endoderm progenitor cells


title: P0_beta_#2

description:
Sample 004
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: P0 Ins1-RFP+


title: BAT3106 Control


title: P15_beta_#2

description:
Sample 010
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: aP9_4_09

description:
Sample 843
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: C4A_D2


title: aP9_4_10

description:
Sample 844
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: P0_beta_#1

description:
Sample 003
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: C3B_D2


title: aP9_4_08

description:
Sample 842
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: C3A_D2


title: BAT3103 Control


title: P9_beta_#2

description:
Sample 008
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: aP9_4_12

description:
Sample 846
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP9_4_07

description:
Sample 841
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: E17.5_beta_#1

description:
Sample 001
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz

source_name: E17.5 Ins1-RFP+


title: C2B_D2


title: BAT3102 Methionine Restriction


title: aP9_4_06

description:
Sample 840
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

source_name: Pancreas


title: aP9_4_05

description:
Sample 839
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: aP9_4_04

description:
Sample 838
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: BAT3101 Methionine Restriction


title: C1B_D2


title: C4B_D1

source_name: iPSC-derived primitive streak cells


title: aP9_4_02

description:
Sample 836
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: C3B_D1


title: C3A_D1


title: aP0_3_14

description:
Sample 834
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P0, Gcg-Cre, Rosa-RFP+

value: α-cell P0-3


title: C2A_D1


title: BAT3104 Methionine Restriction


title: C1A_D1


title: E17.5_beta_#2

description:
Sample 002
Bulk_Cell_RNA-seq_Gene_Read_Count.txt.gz
Bulk_Cell_RNA-seq_Pooled_Normalized_Gene_TPM.txt.gz


title: C1B_D1


title: C4B_D0

source_name: induced pluripotent stem cells


title: C4A_D0


title: C3B_D0


title: C3A_D0


title: C2B_D0


title: clasp-1eBL 3

status: Public on May 01 2017

city: Winnipeg

first: Mark

last: Belmonte

state: Manitoba

address: 50 Sifton Rd

department: Biological Sciences

institute: University of Manitoba

description: *note - technical bioreps merged (a and b)

data_processing:
Trimming of fastq files performed using Trimmomatic
Sample quality assessed using FastQC. Technical replicates (2 per biorep) merged prior to alignment; samples not passing QC were discarded.
Reads aligned to Arabidopsis (TAIR 10) genome using TopHat2/Bowtie2
Normalization and differential expression calling performed using the Cufflinks (Cuffnorm and Cuffdiff) suite.
Further quality control and global comparisons using the Cummer(R)bund suite.
Genome_build: TAIR10
Supplementary_files_format_and_content: Matrix of FPKMs (accumulation cutoff FPKM<5) as tab-delimited .txt file

organism: Arabidopsis

source_name: seedling root tip

growth_protocol: Arabidopsis thaliana seeds were geminated on half-strength MS (Sigma-Aldrich) plates (1% sucrose, 0.8% agar, pH 5.8) and grown vertically for 6 days under continuous light at 22 °C

extract_protocol:
TRIZOL reagent (Invitrogen, Life Technologies) and then treated with DNaseI (Amplification Grade, InvitrogenTM) to remove any residual DNA contamination.
Library preparation and quality control were carried out as in described in Chan et al. (2014) using the NuGen Ultralow DR Multiplex System.

treatment_protocol: Growth media with EtOH or 10nM eBL (Sigma-Aldrich)

tag: genotype

value: 2mm root tip; 6D seedling

tag: treatment

value: 10 nM epibrassinolide


title: clasp-1eBL 2


title: C2A_D0


title: C2A_D2


title: C1A_D0


title: C1B_D0


title: clasp-1eBL 1


title: C1A_D2


title: clasp-1 EtOH 3

value: ethanol control


title: clasp-1 EtOH 2


title: C4A_D1


title: clasp-1 EtOH 1


title: aP9_4_01

description:
Sample 835
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz


title: WT eBL 3

value: Wild type Columbia


title: C2B_D1


title: WT EtOH 2


title: WT EtOH 3


title: WT eBL 2


title: WT EtOH 1


title: WT eBL 1


title: rhesus mRNA-seq

city: Wilmington

first: Qi

last: Zheng

state: DE

address: 1701 Rockland Road

institute: Nemours Children's Health

description:
mRNA (polyA+ RNA)
RNA is polyA+ selected
rhesus_ensGene_mRNA_structScore.txt
rhesus_ensGene_expr.txt

data_processing:
Quality control of the reads. The quality scores for the raw read were carefully checked for their average values, minimum, maximum and standard deviations to make sure all library qualities were in good and comparable status. The correct labeling of 3'-adapters and multiplex indices were also checked to confirm the libraries.
Trimming of 3'-adapters. Reads were trimmed to remove 3'-adapters using Cutadapt (v1.0) program with ≤10% mismatches and ≥10 nt aligned bases. Reads ≤15 nt after trimming were discarded before all subsequent analysis. Untrimmed reads were kept separately from trimmed reads and processed independently in following steps.
Reducing to NR-tags. Both trimmed and untrimmed reads were reduced to NR-tags to save processing time and space requirements. However, the clone abundance of each NR-tag was retained and used in all subsequent abundance calculations in this study, therefore, we will call reads and NR-tags interchangeably hereafter.
Mapping to primate genomes. NR-tags (reads) were mapped to UCSC hg19, refMac2 and rheMac2 genomes using Bowtie (v.0.12.9) program for human, rhesus and cynomolgus, respectively. Note that cynomolgus only has a draft genome release and no corresponding gene model annotations, so we used the reference genome as well as genome annotation of rhesus for all cynomolgus analysis in this study. The mapping parameters for Bowtie program were carefully tuned to insure all alignments with ≤6% mismatches in the first 34 nt seeds and ≤8% mismatches in the whole reads will be reported, and up-to 100 random mapping hits were allowed. Note that for GMUCT reads up-to 10 random hits were allowed. Also note that for all libraries from cynomolgus, the mismatch criteria were 2% looser (8% for seed and 10% for entire read) for the mapping, because they were mapping to a slightly divergent genome instead their own. All mapping results were post-filtered to guarantee the mapping criteria listed above using in-house programs.
For reads with multiple hits on the genomes (multiply mapped), a max-diverge filter was also implemented, to select only those hits with a mismatch percentage no more than 4% to the best hit of each read. This filter is similar to UCSC BLAT and Bowtie “--best” mode. All mapping information, such as insert length, clone abundance, and number of locations on the genome were summarized and loaded into local MySQL databases for further queries.
Mapping across transcript splicing boundaries. To map across splicing boundaries, we first compiled our own GFF annotation files of transcript exons, including coding mRNAs (RefSeq-mRNA for human, Ensembl-mRNA for rhesus and cynomolgus), all non-coding RNAs (Rfam annotated structural RNAs for human and Ensembl-ncRNAs for rhesus and cynomolgus), and also lincRNAs for human. The unmapped reads from previous steps were collected and remapped to the genomes provided these GFF annotations using TopHap (v2.0.8) program. The parameters were tuned to meet the exact same criteria as for the Bowtie mapped reads. At last, the Tophat hits (spliced reads) were also selected for the max-diverge filter and summaries and stored into local MySQL database.
Genome_build: UCSC hg19 for human, UCSC rheMac2 for rhesus and cynomolgus libraries
Supplementary_files_format_and_content: The "*_expr.txt" files are tab-delimited text files containing the expression values of all primate mRNA transcripts in raw clone number (weighted), RPM and RPKM values.
Supplementary_files_format_and_content: The "*_structScore.txt" files are tab-delimited text files containing the calculated "structure score" of every nucleotide of all primate mRNA transcripts with sufficient dsRNA-seq and ssRNA-seq coverages, as well as other pertinent information such as their gene length, mRNA length, and (weighted) clone number of the dsRNA-seq and ssRNA-seq reads.
Supplementary_files_format_and_content: The "*_struct_hotspot_anno.txt" files are tab-delimited text files containing numerous information for all predicted "structure hotspots", defined as long regions with significantly high structure scores in three primates. They also contain many other pertinent information, such as the class, summit, average and max structure score of the hotspots, RPKM values from mRNA-seq, smRNA-seq and public GMUCT libraries for the entire mRNAs or just the structure hotspot regions. Information regarding whether they are bound by the DGCR8/Drosha microprocessor and whether are conserved between human and rhesus is also included.

organism: Macaca mulatta

source_name: brain tissue

growth_protocol: For invivo HEK293T dsRNA-seq and ssRNA-seq libraries, HEK293T cells were seeded in 15-cm standard Corning tissue-culture treated culture dishes (Sigma, St Louis, MO), grown to 90% confluence (approximately 18 million cells) in DMEM media (Life Technologies, San Diego, CA) supplemented with L-glutamine, 4.5 g/L D-glucose, 10% fetal bovine serum (FBS (Atlanta Biologics, Atlanta, GA)) and Pen/Strep (Fisher Scientific, Waltham, MA).

extract_protocol:
For all the in vitro dsRNA-seq and ssRNA-seq libraries, RNAs were treated with ssRNase (RNaseOne) and dsRNase (RNase V1), respectively; For mRNA-seq libraries poly A+ RNAs were isolated from total RNA using Dynabeads mRNA direct kit (Ambion, Austin, TX); For smRNA-seq libraries RNAs were prepared as previously described in F. Li et al., The Plant cell 24, 4346. Briefly, total RNA was run on a 15% TBE-Urea Gel and gel slices containing 15-35 nt RNAs were isolated and eluted from acrylimalyde by mixing with 0.3 M NaCl for 4 hours at RT.
The dsRNA-seq, ssRNA-seq, mRNA-seq and smRNA-seq libraries were constructed as previously described in F. Li et al., The Plant cell 24, 4346. The 3’ and 5’ adapters, Reverse Transcriptase Primer, 5’ PCR primer, and 3’ PCR Primers matching the TruSeq small RNA sequencing kit (Illumina, San Diego, CA) were synthesized and HPLC purified by IDT (Coralville, IA).

treatment_protocol: For all the in vivo dsRNA-seq and ssRNA-seq libraries, a 37% formaldehyde solution (Sigma, St. Louis, MO) was added drop-wise with mixing directly to cell culture dishes containing 90% confluent cells to a final concentration of 1% and incubated at room temperature for 10 minutes to cross-link the RNAs with proteins. The cross-linking reaction was quenched with 1 M glycine (Sigma, St Louis, MO) at a final concentration of 125 mM for 5 minutes with mixing. Then, cells were washed twice with ice-cold PBS and collected.

tag: library strategy

value: mRNA-seq

tag: enzyme treatment

tag: ngs platform

value: Illumina Hi-Seq2000 50 nt strand-specific

value: brain


title: cynomolgus dsRNA-seq

description:
dsRNA (double-stranded RNA)
RNA is treated with ssRNase (RNaseOne) in vitro
cynomolgus_ensGene_mRNA_structScore.txt
cynomolgus_ensGene_mRNA_struct_hotspot_anno.txt

organism: Macaca fascicularis

value: dsRNA-seq

value: ssRNase in vitro

tag: tissue


title: cynomolgus mRNA-seq

description:
mRNA (polyA+ RNA)
RNA is polyA+ selected
cynomolgus_ensGene_mRNA_structScore.txt
cynomolgus_ensGene_expr.txt


title: rhesus ssRNA-seq

description:
ssRNA (single-stranded RNA)
RNA is treated with dsRNase (RNase V1) in vitro
rhesus_ensGene_mRNA_structScore.txt
rhesus_ensGene_mRNA_struct_hotspot_anno.txt

value: ssRNA-seq

value: dsRNase in vitro


title: Gly RNA-seq

city: Louisville

first: Cynthia

last: Corbitt

state: Kentucky

address: 139 Life Sciences Building, University of Louisville

department: Department of Biology

institute: University of Louisville

data_processing:
Illumina Casava software used for basecalling (version unknown).
Quality control (QC) of the raw sequence data was performed using FastQC v0.10.1
Base trimming was performed using Trimmomatic v0.27 with the parameters SLIDINGWINDOW:3:20 MINLEN:20
Following trimming, sequence quality was reassessed using the QA/QC methodology of FastQC v0.10.1
Tophat2 v 2.0.4 was used to align the trimmed sequences to the mm10, Genome Reference Consortium Mouse Build 38 (GCA_000001635.2) available from the UCSC Genome Bioinformatics download site. The annotation file (mm10.gtf) was obtained from UCSC table browser using the Ensemble Genes track.
Successfully aligned sequences were assembled using cufflinks v2.1.1
Differentially expressed mRNAs were detected using Cuffdiff v2.2.1.  Comparisons were performed between groups A vs B, A vs C, A vs D, B vs C, B vs D, C vs D, AC vs BD, CD vs AB.
Enriched GeneOntology Biological Process (GO:BP) and KEGG metabolic pathways were determined using categoryCompare (Front Genet. 2014; 5:98)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file  include FPKM values for each Sample as determined by cuffnorm

source_name: Brain

extract_protocol:
Brain hemispheres harvested from mice were stored in RNALater (Ambion) overnight at 4C and subsequently stored at -20C. Total RNA was isolated from brain hemispheres of 3 mice per treatment group using Trizol/chloroform extraction, followed by spin column purifications (Qiagen RNeasy midi kit) that included DNase (Qiagen) digestions. RNA samples from biological replicates (n=2 or 3) within each treatment were pooled to obtain one sample per treatment group
Standard Illumina protocols were used to prepare RNA libraries for sequencing

treatment_protocol: Adult female CFW mice were implanted with either 17-β Estradiol (E2) or placebo pellets, allowed to acclimate for a week followed by 11 days of i.p. injections with either 50μl Glyceollin or vehicle.

tag: strain

value: CFW

tag: treatments

value: Placebo pellet + Gly injection

value: female

tag: no.of pooled samples


title: E2 RNA-seq

value: E2 pellet + vehicle injection

tag: Sex


title: E2 + Gly RNA-seq

value: E2 pellet + Gly injection


title: Control RNA-seq

value: Placebo pellet + vehicle injection


title: STING-KO_TCR/DMXAA-activated

city: Boston

first: Alexander

last: Poltorak

state: Massachusetts

address: 150 Harrison avenue

institute: Tufts University

data_processing:
The resulted data were demultiplexed using Illumina CASAVA 1.8 and fastq files for each initial sample were generated
Tophat2 alignment of raw paired reads to UCSC mm10 genome
Cuffdiff using the outputs from two previous steps with mm10 annotation
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for each sample.

source_name: T cells

growth_protocol:
T cell purification and expansion: Naïve total CD3+, CD4+, and CD8+ T cells were isolated from mouse spleens and pLN using STEMCELL Technologies (Vancouver, BC) EasySep Mouse T cell isolation kits according to manufacturer’s instructions. Expanded T cells were prepared using Mouse T activator CD3/CD28 DynaBeads (ThermoFisher Scientific) in complete RPMI with 10% FBS and 50 U/ml recombinant IL-2. Cells were rested overnight in complete media without IL-2 before experiments.
Seven to fifteen week old mice were used for each experiment. Wild type C57BL/6 mice were purchased from The Jackson Laboratory (Bar Harbor Maine). STING-/- mice obtained from Dr. Glen Barber (University of Miami).

extract_protocol:
RNA was prepared according to manufacture's instructions
Library was prepared using Truseq pair-end Illumina kit. Briefly, 10-100 ng of total RNA was reconstituted in water, mixed with Ribosomal removal Buffer containing RNAClean XP beads, and depleted from rRNA. First strand was synthesized using RT, followed by a second strand synthesis, 3' ends were adenylated and ligated to the adaptors, followed by ligateion of the 5' adaptors; the library was purified and measured on DNA-concentration

treatment_protocol: Naïve or expanded T cells were stimulated with 10 μg/ml DMXAA (Invivogen) unless otherwise indicated; for experiments involving TCR activation, tissue culture plates were coated overnight with anti-CD3 and anti-CD28 antibodies (BD Bioscience; Biolegend) at 5 μg/ml.

value: STING-KO

value: TCR/DMXAA-activated

tag: cell type

value: T cells


title: C57BL6_TCR/DMXAA-activated

value: wildtype


title: STING-KO_Unstimulated

value: Unstimulated


title: STING-KO_TCR-activated

value: TCR-activated


title: C57BL6_Unstimulated


title: mfd_3

city: Research Triangle Park

first: Rachel

last: Krasich

state: NC

address: 111 TW Alexander Dr

institute: NIEHS

description:
ANOVA_analysis_of_mfd-_cell_lines.xlsx
mfd-_bin25_counts.xlsx

data_processing:
Sequencing reads (approximately 13 to 25 million per sample) were imported into Geneious Pro (Biomatters) and assembled to the reference chromosome MG1655 (GenBank Accession Number 000913.2). The assembly process was set to medium/low sensitivity on Geneious, with the following parameters: 10% gaps allowed per read; word length of 18; index word length of 13; words repeated more than 12 times ignored; 20% maximum mismatches per read; and maximum ambiguity of 4
Read coverage maps and RPKM data was subsequently generated by Geneious.
BAM files of the resulting assembly data were exported to JMP Genomics (SAS).  TMM normalization and ANOVA analysis of the read samples were conducted in JMP Genomics

organism: Escherichia coli

growth_protocol: Cells were grown to approximately mid-log phase (OD560 = approximately 0.5) in LB.

extract_protocol:
Cell pellets were lysed and RNA collected using Qiagen’s RNeasy Plus Mini Kit with Qiagen Bacteria Protect RNA kit.  RNA samples were then treated with DNase (New England Biolabs) for 30 min at 37 °C.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MG1655 pCA24N and MG1655 pCA24N-Mfd cells were grown to an OD560 of approximately 0.25 and treated with 100 μM IPTG for 1 hour.

value: mfd-


title: MFD++_2

value: Mfd++


title: MG1655_vector_2

value: Wildtype with vector


title: MG1655_vector_1


title: MFD++_1


title: mfd_1


title: mfd_2


title: cynomolgus ssRNA-seq

description:
ssRNA (single-stranded RNA)
RNA is treated with dsRNase (RNase V1) in vitro
cynomolgus_ensGene_mRNA_structScore.txt
cynomolgus_ensGene_mRNA_struct_hotspot_anno.txt

value: ssRNA-seq

value: Illumina Hi-Seq2000 50 nt strand-specific

value: brain


title: MG1655_3

value: Wildtype


title: WT-AntiHEL-1

city: Cambridge

first: Suzanne

last: Szak

state: MA

address: 14 Cambridge Ctr

department: Drug Discovery

institute: BiogenIdec, Inc.

data_processing:
The reads were aligned with STAR (version  2.4.0c), and genes annotated in Gencode v18 were quantified with  featureCounts (v1.4.3-p1). Normalization and differential expression was   done with the Bioconductor package DESeq2.
Supplementary_files_format_and_content: DESEQ2 normalized counts for genes.

source_name: Skin

growth_protocol: Atopic Dermatitis-like disease was induced by epicutaneous treatment with HDM extract (10 μg/mouse and treatment) and SEB (500 ng/mouse and treatment) given in 2 cycles on days 1 and 4, and 14 and 17, on the shaved and tape-stripped back skin over a 23 day period according to established protocols.  In some experiments, animals were treated i.p. with 200 μg anti-TWEAK or IgG (total volume 200 ul) twice weekly throughout the experiment. Psoriasis-like disease was induced by daily application of 2.5% Imiquimod cream or vehicle control on the shaved back for 8 days.  Animals were treated subcutaneously in the rostral portion of the back with 75 or 200 μg of recombinant murine TWEAK as a N-terminal tagged Fc/IgG-fusion protein or control vehicle (irrelevant IgG) in 200 μl PBS, twice weekly over a 14-day period.

extract_protocol:
Total RNA was harvested using Trizol (Thermo Fisher Scientific) DNAse treated (Qiagen) and cleaned with the RNeasy mini extraction kit (Qiagen) according to manufacturer's recommendations.
500 ng RNA was used as starting input to Illumina TruSeq mRNA stranded library construction according to the manufacturers recommendation. High quality libraries were then pooled and sequenced on an Illumina HiSeq 2500

value: WT

value: AntiHEL


title: MG1655_2


title: WT-AntiHEL-2


title: WT-AntiHEL-4


title: WT-mFc-mTWEAK-1

value: mFc-mTWEAK


title: rhesus dsRNA-seq

description:
dsRNA (double-stranded RNA)
RNA is treated with ssRNase (RNaseOne) in vitro
rhesus_ensGene_mRNA_structScore.txt
rhesus_ensGene_mRNA_struct_hotspot_anno.txt

value: dsRNA-seq

value: ssRNase in vitro


title: WT-mFc-mTWEAK-3


title: WT-mFc-mTWEAK-4


title: KO-no-injection-4

value: TWEAK KO

value: no-injection


title: KO-no-injection-3


title: KO-no-injection-2


title: C57BL6_TCR-activated

value: wildtype

value: T cells


title: KO-AntiHEL-2


title: KO-AntiHEL-3


title: KO-AntiHEL-1


title: KO-mFc-mTWEAK-4


title: WT-no-injection-3


title: KO-mFc-mTWEAK-2


title: KO-mFc-mTWEAK-3


title: WT-no-injection-1


title: WT-no-injection-4


title: MG1655_1


title: Sample_9_Pancreatic islets_isotype_control

city: Tarrytown

first: Yurong

last: Xin

state: NY

address: 777 Old Saw Mill River Road

institute: Regeneron Pharmaceuticals, Inc.

description:
isotype control
Glucagon Receptor Inhibition-Induced Pancreatic alpha-Cell Hyperplasia in Mice

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Reads were decoded based on their barcodes. Read quality was evaluated using FastQC.
Reads were mapped to the reference genome (mouse: GRCm38) using CLC bio Genomics Workbench Version 7.0 (CLC Bio) allowing one mismatch.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

molecule: polyA RNA

source_name: Pancreatic islets

extract_protocol:
Islets were isolated by a density gradient method using Histopaque-1077 (Sigma) and total RNA including miRNA was purified from all samples using the miRNeasy Mini Kit (Qiagen, catalog# 217004) according to the manufacturer’s specifications.
Illumina NGS library was constructed with Nextera XT DNA Sample Prep kit (Illumina), according to the manufacturer’s recommendations (Protocol #100-7168 E1).

value: Pancreatic islets

value: isotype control antibody


title: Sample_8_Pancreatic islets_isotype_control


title: KO-mFc-mTWEAK-1


title: WT-mFc-mTWEAK-2


title: Sample_7_Pancreatic islets_isotype_control


title: WT-no-injection-2


title: Sample_10_Pancreatic islets_isotype_control


title: Sample_6_Pancreatic islets_isotype_control


title: KO-no-injection-1


title: Sample_4_Pancreatic islets_R1193

description:
R1193
Glucagon Receptor Inhibition-Induced Pancreatic alpha-Cell Hyperplasia in Mice

value: REGN1193 (GCGR blocking antibody)


title: Sample_3_Pancreatic islets_R1193


title: T7_AA5

city: La Jolla

first: Maike

last: Sander

state: CA

address: 2880 Torrey Pines Scenic Dr.

institute: UC San Diego

description: bulk cell RNA

data_processing:
Reads were aligned to the mm9 by STAR with parameters: --outSAMstrandField intronMotif --outFilterMultimapNmax 1 --runThreadN 5.Only the reads aligned uniquely to one genomic location were retained for subsequent analysis.
makeTagDirectory and makeUCSCfile in homer was used to generate bigWig file
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file

source_name: sorted P7 beta cell_bulk_cells

extract_protocol:
Single sorted beta cells were captured on a medium-sized (10–17 mm cell diameter) microfluidic RNA-seq chip (Fluidigm) using the FluidigmC1 system. Cells were loaded onto the chip at a concentration of 250 cells/ml, stained for viability (LIVE/DEAD cell viability assay; Molecular Probes, Life Technologies) and imaged by Zeiss Axio Oberver Z1 microscope to assess the number and viability of cells per capture site. Only single, live cells were included in the analysis. Cell lysis, cDNA synthesis, and PCR reactions were performed on the same chip using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Clonetech). For each C1 experiment, two bulk RNA controls (approximately 250 cells/sample) were processed in parallel in PCR tubes, using the same reagent mixes as used on chip as described in Fluidigm protocol 100-5950.
Libraries were prepared using the Illumina Nextera XT DNA sample preparation kit

treatment_protocol: Pancreata at P1, P7, and P14 were dissected wholly without perfusion and digested with 1mg/ml Collagenase Type IV (Sigma). P21 and P28 pancreata were perfused through the common bile duct with 125ug/ml Liberase TL (Roche). Islets were purified by density gradient centrifugation using Histopaque (Sigma), dissociated with Accumax (Life Technogies), and sorted by FACS on a FACSAria II (BD Biosciences). Dead or damaged beta cells were first excluded by gating on cells negative for the viablilty marker SYTOX Blue (1mM; Life Technologies) and forward scatter (FSC) and side scatter (SSC) plots were used to exclude doublets or cell aggregates. Using these gates, cells expressing mCherry were sorted.

value: sorted mCherry+ pancreatic beta cells

tag: age

value: postnatal day 7


title: T28_AB11

description: bulk cell RNA

source_name: sorted P28 beta cell_bulk_cells

value: postnatal day 28


title: T7_HH7

description: bulk cell RNA


title: Sample_1_Pancreatic islets_R1193


title: T7_HA8

description: bulk cell RNA


title: T28_AA11

description: bulk cell RNA


title: Sample_2_Pancreatic islets_R1193


title: T21_AB9

description: bulk cell RNA

source_name: sorted P21 beta cell_bulk_cells

value: postnatal day 21


title: T14_HD1

description: bulk cell RNA

source_name: sorted P14 beta cell_bulk_cells

value: postnatal day 14


title: T14_HC1

description: bulk cell RNA


title: S7_HH6

description: single-cell RNA

source_name: sorted P7 beta cell_single_cell


title: T1_AB1

description: bulk cell RNA

source_name: sorted P1 beta cell_bulk_cells

value: postnatal day 1


title: T1_AA1

description: bulk cell RNA


title: T7_AB5

description: bulk cell RNA


title: T14_AA7

description: bulk cell RNA


title: Sample_5_Pancreatic islets_R1193


title: S7_HH5

description: single-cell RNA


title: S7_HG7

description: single-cell RNA


title: S7_HF4

description: single-cell RNA


title: S7_HG6

description: single-cell RNA


title: S7_HF5

description: single-cell RNA


title: S7_HF7

description: single-cell RNA


title: S7_HF6

description: single-cell RNA


title: S7_HH4

description: single-cell RNA


title: S7_HE7

description: single-cell RNA


title: S7_HE6

description: single-cell RNA


title: T21_AA9

description: bulk cell RNA


title: S7_HE4

description: single-cell RNA


title: S7_HE5

description: single-cell RNA


title: S7_HD5

description: single-cell RNA


title: S7_HD7

description: single-cell RNA


title: S7_HD4

description: single-cell RNA


title: S7_HD6

description: single-cell RNA


title: T14_AB7

description: bulk cell RNA


title: S7_HC6

description: single-cell RNA


title: S7_HC4

description: single-cell RNA


title: S7_HB5

description: single-cell RNA


title: S7_HB6

description: single-cell RNA


title: S7_HB7

description: single-cell RNA


title: aP9_4_03

description:
Sample 837
Single_Cell_RNA-seq_Gene_Read_Count.txt.gz
Single_Cell_RNA-seq_Gene_TPM.txt.gz

value: P9, Gcg-Cre, Rosa-RFP+

tag: collection method

value: manually-picked

tag: batch

value: α-cell P9-4


title: S7_HA6

description: single-cell RNA


title: S7_HG4

description: single-cell RNA


title: S7_HG5

description: single-cell RNA


title: S7_HA7

description: single-cell RNA


title: S7_HB4

description: single-cell RNA


title: S7_HA5

description: single-cell RNA


title: S7_FH5

description: single-cell RNA


title: S7_FF6

description: single-cell RNA


title: S7_FH6

description: single-cell RNA


title: S7_FG6

description: single-cell RNA


title: S7_FG5

description: single-cell RNA


title: S7_FE6

description: single-cell RNA


title: S7_FE5

description: single-cell RNA


title: S7_FD6

description: single-cell RNA


title: S7_FD5

description: single-cell RNA


title: S7_HC7

description: single-cell RNA


title: S7_FB5

description: single-cell RNA


title: S7_FC6

description: single-cell RNA


title: S7_FC5

description: single-cell RNA


title: S7_FA6

description: single-cell RNA


title: S7_DH6

description: single-cell RNA


title: S7_DH5

description: single-cell RNA


title: S7_DG5

description: single-cell RNA


title: S7_DF6

description: single-cell RNA


title: S7_DD6

description: single-cell RNA


title: S7_DG6

description: single-cell RNA


title: S7_DE6

description: single-cell RNA


title: S7_DB6

description: single-cell RNA


title: S7_DA6

description: single-cell RNA


title: S7_BH6

description: single-cell RNA


title: S7_DF5

description: single-cell RNA


title: S7_DE5

description: single-cell RNA


title: S7_BH5

description: single-cell RNA


title: S7_BG6

description: single-cell RNA


title: S7_BG5

description: single-cell RNA


title: S7_DC5

description: single-cell RNA


title: S7_DD5

description: single-cell RNA


title: S7_DC6

description: single-cell RNA


title: S7_FB6

description: single-cell RNA


title: S7_HC5

description: single-cell RNA


title: S7_BF6

description: single-cell RNA


title: S7_BE6

description: single-cell RNA


title: S7_BD5

description: single-cell RNA


title: S7_BE5

description: single-cell RNA


title: S7_BD6

description: single-cell RNA


title: S7_BC6

description: single-cell RNA


title: S7_FA5

description: single-cell RNA


title: S7_BC5

description: single-cell RNA


title: S7_DB5

description: single-cell RNA


title: S7_BB6

description: single-cell RNA


title: S7_BF5

description: single-cell RNA


title: S7_BB5

description: single-cell RNA


title: S7_BA6

description: single-cell RNA


title: S7_BA5

description: single-cell RNA


title: S7_DA5

description: single-cell RNA


title: S7_AH6

description: single-cell RNA


title: S7_AH5

description: single-cell RNA


title: S7_AF5

description: single-cell RNA


title: S7_AA6

description: single-cell RNA


title: S7_AC5

description: single-cell RNA


title: S7_AD6

description: single-cell RNA


title: S7_AC6

description: single-cell RNA


title: S7_AG6

description: single-cell RNA


title: S28_HE10

description: single-cell RNA

source_name: sorted P28 beta cell_single_cell


title: S28_HC10

description: single-cell RNA


title: S28_HF10

description: single-cell RNA


title: S7_AB6

description: single-cell RNA


title: S28_FH12

description: single-cell RNA


title: S28_FH11

description: single-cell RNA


title: S28_HD10

description: single-cell RNA


title: S28_FE12

description: single-cell RNA


title: S28_FG11

description: single-cell RNA


title: S28_FE11

description: single-cell RNA


title: S28_HB10

description: single-cell RNA


title: S28_FG12

description: single-cell RNA


title: S28_FF11

description: single-cell RNA


title: S28_FD12

description: single-cell RNA


title: S28_FC12

description: single-cell RNA


title: S28_FB12

description: single-cell RNA


title: S28_FB11

description: single-cell RNA


title: S28_DH12

description: single-cell RNA


title: S28_FC11

description: single-cell RNA


title: S28_FA11

description: single-cell RNA


title: S28_FA12

description: single-cell RNA


title: S7_AD5

description: single-cell RNA


title: S28_DH11

description: single-cell RNA


title: S28_DG12

description: single-cell RNA


title: S28_DE12

description: single-cell RNA


title: S28_DE11

description: single-cell RNA


title: S28_DF11

description: single-cell RNA


title: S28_DC12

description: single-cell RNA


title: S28_DF12

description: single-cell RNA


title: S28_DD11

description: single-cell RNA


title: S28_DD12

description: single-cell RNA


title: S28_FD11

description: single-cell RNA


title: S28_DC11

description: single-cell RNA


title: S28_DA12

description: single-cell RNA


title: S28_DA11

description: single-cell RNA


title: S28_BG12

description: single-cell RNA


title: S28_BG11

description: single-cell RNA


title: S28_DB11

description: single-cell RNA


title: S28_BH12

description: single-cell RNA


title: S28_DG11

description: single-cell RNA


title: S28_BF12

description: single-cell RNA


title: S28_BF11

description: single-cell RNA


title: S28_DB12

description: single-cell RNA


title: S28_BE12

description: single-cell RNA


title: S28_BE11

description: single-cell RNA


title: S28_BH11

description: single-cell RNA


title: S28_BB11

description: single-cell RNA


title: S28_BC12

description: single-cell RNA


title: S28_BB12

description: single-cell RNA


title: S28_BA11

description: single-cell RNA


title: S28_BA12

description: single-cell RNA


title: S28_AH11

description: single-cell RNA


title: S28_AF12

description: single-cell RNA


title: S28_AG11

description: single-cell RNA


title: S28_AF11

description: single-cell RNA


title: S28_AD11

description: single-cell RNA


title: S28_AC12

description: single-cell RNA


title: S28_AD12

description: single-cell RNA


title: S28_AC11

description: single-cell RNA


title: S21_HH9

description: single-cell RNA

source_name: sorted P21 beta cell_single_cell


title: S21_FH9

description: single-cell RNA


title: S21_FG9

description: single-cell RNA


title: S21_HE9

description: single-cell RNA


title: S21_HD9

description: single-cell RNA


title: S21_HF9

description: single-cell RNA


title: S21_HG9

description: single-cell RNA


title: S21_HA10

description: single-cell RNA


title: S21_FF10

description: single-cell RNA


title: S28_BD12

description: single-cell RNA


title: S21_FE9

description: single-cell RNA


title: S28_AH12

description: single-cell RNA


title: S21_FE10

description: single-cell RNA


title: S21_FG10

description: single-cell RNA


title: S21_FD9

description: single-cell RNA


title: S21_FF9

description: single-cell RNA


title: S21_FC10

description: single-cell RNA


title: S21_FC9

description: single-cell RNA


title: S21_FD10

description: single-cell RNA


title: S21_FB9

description: single-cell RNA


title: S28_AE11

description: single-cell RNA


title: S21_FA9

description: single-cell RNA


title: S21_DH9

description: single-cell RNA


title: S21_FA10

description: single-cell RNA


title: S21_DD10

description: single-cell RNA


title: S21_DH10

description: single-cell RNA


title: S21_DG10

description: single-cell RNA


title: S21_DC9

description: single-cell RNA


title: S21_DE10

description: single-cell RNA


title: S21_DE9

description: single-cell RNA


title: S21_DF9

description: single-cell RNA


title: S21_DB9

description: single-cell RNA


title: S21_FH10

description: single-cell RNA


title: S21_DG9

description: single-cell RNA


title: S21_DD9

description: single-cell RNA


title: S21_DC10

description: single-cell RNA


title: S21_BH10

description: single-cell RNA


title: S21_DB10

description: single-cell RNA


title: S21_DF10

description: single-cell RNA


title: S21_FB10

description: single-cell RNA


title: S21_BG10

description: single-cell RNA


title: S21_DA9

description: single-cell RNA


title: S21_BE9

description: single-cell RNA


title: S21_BG9

description: single-cell RNA


title: S21_BE10

description: single-cell RNA


title: S21_BH9

description: single-cell RNA


title: S21_BF10

description: single-cell RNA


title: S21_BD9

description: single-cell RNA


title: S21_BD10

description: single-cell RNA


title: S21_BC9

description: single-cell RNA


title: S21_BC10

description: single-cell RNA


title: S21_BB9

description: single-cell RNA


title: S21_BB10

description: single-cell RNA


title: S21_DA10

description: single-cell RNA


title: S21_AH9

description: single-cell RNA


title: S21_BA9

description: single-cell RNA


title: S21_AG10

description: single-cell RNA


title: S21_AF10

description: single-cell RNA


title: S21_BA10

description: single-cell RNA


title: S21_AE9

description: single-cell RNA


title: S21_AD10

description: single-cell RNA


title: S21_AE10

description: single-cell RNA


title: S21_BF9

description: single-cell RNA


title: S21_AD9

description: single-cell RNA


title: S21_AF9

description: single-cell RNA


title: S21_AB10

description: single-cell RNA


title: S21_AA10

description: single-cell RNA


title: S14_HH10

description: single-cell RNA

source_name: sorted P14 beta cell_single_cell


title: S14_HG8

description: single-cell RNA


title: S14_HG12

description: single-cell RNA


title: S14_HH12

description: single-cell RNA


title: S14_HH11

description: single-cell RNA


title: S21_AC10

description: single-cell RNA


title: S14_HG11

description: single-cell RNA


title: S14_HG10

description: single-cell RNA


title: S21_AG9

description: single-cell RNA


title: S14_HF12

description: single-cell RNA


title: S21_AH10

description: single-cell RNA


title: S14_HE8

description: single-cell RNA


title: S14_HE12

description: single-cell RNA


title: S14_HE11

description: single-cell RNA


title: S14_HD8

description: single-cell RNA


title: S14_HD11

description: single-cell RNA


title: S21_AC9

description: single-cell RNA


title: S14_HC9

description: single-cell RNA


title: S14_HH8

description: single-cell RNA


title: S14_HB9

description: single-cell RNA


title: S14_HC12

description: single-cell RNA


title: S14_HB8

description: single-cell RNA


title: S14_HB12

description: single-cell RNA


title: S14_HA9

description: single-cell RNA


title: S14_HA11

description: single-cell RNA


title: S14_HA12

description: single-cell RNA


title: S14_FH8

description: single-cell RNA


title: S14_FH7

description: single-cell RNA


title: S14_FG8

description: single-cell RNA


title: S14_FG7

description: single-cell RNA


title: S14_FF8

description: single-cell RNA


title: S14_HF8

description: single-cell RNA


title: S14_FE7

description: single-cell RNA


title: S14_FE8

description: single-cell RNA


title: S14_HD12

description: single-cell RNA


title: S14_FD8

description: single-cell RNA


title: S14_FD7

description: single-cell RNA


title: S14_FC8

description: single-cell RNA


title: S14_HC8

description: single-cell RNA


title: S14_FA7

description: single-cell RNA


title: S14_DH8

description: single-cell RNA


title: S14_DH7

description: single-cell RNA


title: S14_FB7

description: single-cell RNA


title: S14_DF8

description: single-cell RNA


title: S14_DG7

description: single-cell RNA


title: S14_DG8

description: single-cell RNA


title: S14_DE7

description: single-cell RNA


title: S14_DE8

description: single-cell RNA


title: S14_FF7

description: single-cell RNA


title: S14_DD7

description: single-cell RNA


title: S14_DD8

description: single-cell RNA


title: S14_DC7

description: single-cell RNA


title: S14_DB7

description: single-cell RNA


title: S14_DA8

description: single-cell RNA


title: S14_BH8

description: single-cell RNA


title: S14_DB8

description: single-cell RNA


title: S14_DA7

description: single-cell RNA


title: S14_FC7

description: single-cell RNA


title: S14_FB8

description: single-cell RNA


title: S14_BH7

description: single-cell RNA


title: S14_BG8

description: single-cell RNA


title: S14_BG7

description: single-cell RNA


title: S14_FA8

description: single-cell RNA


title: S14_BF7

description: single-cell RNA


title: S14_BE8

description: single-cell RNA


title: S14_DF7

description: single-cell RNA


title: S14_BD8

description: single-cell RNA


title: S14_DC8

description: single-cell RNA


title: S14_BE7

description: single-cell RNA


title: S14_BB8

description: single-cell RNA


title: S14_BC7

description: single-cell RNA


title: S14_BD7

description: single-cell RNA


title: S14_BC8

description: single-cell RNA


title: rhesus smRNA-seq

description:
smRNA (small RNA)
small RNA in 15-35 nt range
rhesus_ensGene_mRNA_structScore.txt

value: smRNA-seq

value: Illumina GA2x with 58 nt strand-specific

value: brain


title: S14_BA8

description: single-cell RNA


title: S14_BA7

description: single-cell RNA


title: S14_AH8

description: single-cell RNA


title: S14_AH7

description: single-cell RNA


title: P30 rep3

city: Madrid

first: Ignacio

last: Benedicto

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: Centro Nacional de Investigaciones Cardiovasculares (CNIC)

data_processing:
Illumina Casava 1.8.2 software used for basecalling.
Upon quality control using FastQC, raw reads were aligned to the mouse genome (mm9) using TopHat with default parameters. CuffLinks with GC and upper quartile normalization was then used to calculate normalized expression levels (FPKM; Fragments Per Kilobase of transcripts per Million reads) according to Trapnell et al., Nat Protoc 7, 562-578 (2012).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include gene ID and FPKM values for each sample.

source_name: Choroid endothelial cells

extract_protocol:
RPE/choroid was mechanically dissected from the sclera and digested. ECs were isolated by flow cytometry and RNA was extracted immediately with TRI Reagent (Molecular Research Center, Inc.) and purified with RNeasy Mini Kit (Qiagen). cDNA libraries were prepared with the TruSeq RNA Sample Preparation Kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Post natal day 30

value: RPE/choroid


title: S14_BB7

description: single-cell RNA


title: P5 rep3

value: Post natal day 5


title: P30 rep2


title: P30 rep1


title: S14_AG8

description: single-cell RNA


title: S14_AF7

description: single-cell RNA


title: S14_AG7

description: single-cell RNA


title: S14_AF8

description: single-cell RNA


title: S14_BF8

description: single-cell RNA


title: S14_AE8

description: single-cell RNA


title: P5 rep2


title: S14_AE7

description: single-cell RNA


title: S14_AD8

description: single-cell RNA


title: S14_AD7

description: single-cell RNA


title: P5 rep1


title: S14_AC8

description: single-cell RNA


title: MOFp

city: Brasília

first: Taina

last: Raiol

state: DF

address: Av. L3 Norte, Campus Universitário Darcy Ribeiro

department: Fiocruz Brasília (GEREB)

country: Brazil

institute: Oswaldo Cruz Foundation - Fiocruz

description: MOFp experiment

data_processing:
Quality check was performed by FastQC v0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), adaptor removal using Cutadapt v1.7.1 (Martin, 2011), and read trimming using PRINSEQ (Schmieder and Edwards, 2011)
Alignments to the Mouse reference genome GRCh38.75 were performed by Tophat v2.0.11 (Trapnell et al., 2009)
HTSeq-count v0.5.0 (Anders and Huber, 2014) was used to count and compare aligned reads to annotated mouse genes
The relative gene expression was calculated using EdgeR v3.4.2 (Robinson et al., 2009) in R v3.0.3
Genome_build: Mus musculus GRCm38.75
Supplementary_files_format_and_content: Tab-delimited text files include normalized gene expression for each sample
MOFp_analysis.txt corresponds to the MOFp/MO comparison and MOCm_analysis.txt to MOCm/MO.

source_name: Macrophages

growth_protocol: Peritoneal macrophages were harvest from Balb/c peritoneal cavity with the aid of a 10 ml syringe in using cold RPMI medium (Sigma-Aldrich). The cell suspension acquired was centrifuged at 300g and re-suspended in RPMI medium supplemented with 2% Fetal Bovine Serum (Gibco – Thermo Fisher Scientific) and 80 μg/ml of gentamicin.

extract_protocol:
Total RNA was extracted with the RNeasy kit (Qiagen) according to the manufacturer's instructions. Extracted RNA was quantified in a fluorometer (Qubit) and submitted to Bioanalyzer 2100 (Agilent) to determine its integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Phagocytes were plated and infected with F. pedrosoi conidia or muriform cells at MOI 1:1 and co-cultured for 6 hours, at which time extracellular and weakly adherent fungi were removed by washing with pre-warmed RPMI.

value: Peritoneal Macrophage

value: Balb/c

tag: stimuli

value: Fonsecaea pedrosoi conidia

tag: incubation period

value: 6 hours


title: S14_AA8

description: single-cell RNA

value: sorted mCherry+ pancreatic beta cells


title: S14_AC7

description: single-cell RNA


title: S14_AB8

description: single-cell RNA


title: MOCm

description: MOCm experiment

value: Fonsecaea pedrosoi muriform cell


title: S1_HH3

description: single-cell RNA

source_name: sorted P1 beta cell_single_cell


title: MO

description: Control


title: S1_HH1

description: single-cell RNA


title: S1_HH2

description: single-cell RNA


title: S1_HG3

description: single-cell RNA


title: Lmnb1_Cont2_H3K9me3

city: Baltimore

first: Haiqing

last: Zhao

state: MD

address: 3400 N Charles St

department: Biology

institute: Johns Hopkins University

description: Sorted fluorescent cells

data_processing:
ChIP-seq reads were mapped to the mouse genome (mm9) using Bowtie.
ChIp-seq peaks were called using MACS for H3K4me3 or SICER for H3K9me3.
Bedgraph files were generated using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: bed files containing peak locations and bedgraph files containing RPKM values along the genome.

source_name: Olfactory Epithelium

growth_protocol: Mice were housed in 12-hour light/dark cycle with access to food and water ad libitum. All procedures were performed in accordance with the Johns Hopkins University IACUC guidelines.

extract_protocol:
Approximately 500,000 Tomato-positive mutant or heterozygous olfactory epithelial cells were sorted from a single mouse. Each sample was crosslinked, sonicated and subjected to ChIP with either anti-H3K9me3 or anti-H3K4me3. Libraries were prepared from precipitated DNA and sequenced, producing approximately 50 million 50 bp reads per sample.
Libraries were prepared using Illumina Prep Kit

treatment_protocol: Mice were injected IP with 50 mg/kg methimazole and allowed to recover for 4 weeks

tag: strain/background

value: Mixed

value: Regenerated Olfactory Epithelium

value: 50 mg/kg Methimazole Group 4

tag: antibody

value: H3K9me3 (1 ug/ml, Abcam ab8898)


title: Lmnb1_Mut1_H3K9me3

description: Sorted fluorescent cells

tag: treatment

value: 50 mg/kg Methimazole Group 3

tag: genotype


title: Lmnb1_Mut2_H3K9me3

description: Sorted fluorescent cells


title: S1_HF3

description: single-cell RNA

value: postnatal day 1


title: S1_HF2

description: single-cell RNA


title: S1_HG1

description: single-cell RNA


title: S1_HE2

description: single-cell RNA


title: S1_HE3

description: single-cell RNA


title: S1_HD2

description: single-cell RNA


title: S1_HD3

description: single-cell RNA


title: Lmnb1_Mut1_H3K4me3

description: Sorted fluorescent cells

value: H3K4me3 (0.5 ug/ml, Cell Signaling 9751S)


title: Lmnb1_Cont1_H3K4me3

description: Sorted fluorescent cells


title: S1_HC3

description: single-cell RNA


title: Lmnb1_Cont1_H3K9me3

description: Sorted fluorescent cells


title: Lmnb1Mut_G2

description: Sorted fluorescent cells

data_processing:
rRNA reads were removed using Bowtie2 (Langmead and Salzberg, 2012) version 2.0.6
Quality filtered using FASTQ quality filter parameters –q 28 –p 95
reads were aligned genome using Tophat version 2.0.7 standard settings (--no-covereage-search).
reads were converted to counts using HtSeq (Anders et al., 2015) using --mode=intersection-nonempty.
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files contain raw count values for each gene

extract_protocol:
Olfactory mucosal cells of one mouse were dissociated, fluorescent cells were isolated by FACS, RNA was extracted using TRIzol reagent, treated with DNaseI (Qiagen 79254), and purified using RNeasy (Qiagen 74104)
Libraries were prepared using Illumina RNA Prep Kit 2 following Ribo-Zero Gold depletion of rRNA (Illumina MRZG126).

value: 50 mg/kg Methimazole Group 2


title: S1_HC2

description: single-cell RNA


title: S14_HB11

description: single-cell RNA

value: postnatal day 14


title: S1_HB2

description: single-cell RNA


title: S1_HB1

description: single-cell RNA


title: S1_HB3

description: single-cell RNA


title: S1_HA4

description: single-cell RNA


title: S1_HG2

description: single-cell RNA


title: Lmnb1Cont_G2

description: Sorted fluorescent cells


title: S1_HA2

description: single-cell RNA


title: Lmnb1Cont_G1

description: Sorted fluorescent cells

value: 50 mg/kg Methimazole Group 1


title: S1_HA3

description: single-cell RNA


title: S1_HA1

description: single-cell RNA


title: S1_HF1

description: single-cell RNA


title: S1_FH2

description: single-cell RNA


title: S1_FG2

description: single-cell RNA


title: S1_FG1

description: single-cell RNA


title: S1_FH1

description: single-cell RNA


title: S1_HE1

description: single-cell RNA


title: S1_FE1

description: single-cell RNA


title: S1_FD2

description: single-cell RNA


title: S1_FF2

description: single-cell RNA


title: S1_FD1

description: single-cell RNA


title: S1_FC2

description: single-cell RNA


title: S1_FB2

description: single-cell RNA


title: S1_FC1

description: single-cell RNA


title: Lmnb1Mut_G1

description: Sorted fluorescent cells


title: S1_FA2

description: single-cell RNA


title: S1_FA1

description: single-cell RNA


title: S1_DH2

description: single-cell RNA


title: S1_DH1

description: single-cell RNA


title: S1_FB1

description: single-cell RNA


title: S1_DF1

description: single-cell RNA


title: S1_DG2

description: single-cell RNA


title: S1_DE2

description: single-cell RNA


title: S1_DG1

description: single-cell RNA


title: S1_DE1

description: single-cell RNA


title: S1_DD1

description: single-cell RNA


title: S1_DD2

description: single-cell RNA


title: S1_FE2

description: single-cell RNA


title: S1_DC2

description: single-cell RNA


title: S1_DB1

description: single-cell RNA


title: S1_DB2

description: single-cell RNA


title: S1_BH2

description: single-cell RNA


title: S1_DA2

description: single-cell RNA


title: S1_DA1

description: single-cell RNA


title: S1_BG2

description: single-cell RNA


title: S1_BH1

description: single-cell RNA


title: S1_BF2

description: single-cell RNA


title: S1_BG1

description: single-cell RNA


title: S1_BF1

description: single-cell RNA


title: S1_BD2

description: single-cell RNA


title: S1_BD1

description: single-cell RNA


title: S1_BE1

description: single-cell RNA


title: S1_DF2

description: single-cell RNA


title: S1_BC2

description: single-cell RNA


title: S1_BB2

description: single-cell RNA


title: S1_BC1

description: single-cell RNA


title: S1_BA2

description: single-cell RNA


title: S1_BA1

description: single-cell RNA


title: S1_DC1

description: single-cell RNA


title: S1_AH2

description: single-cell RNA


title: S1_AH1

description: single-cell RNA


title: S1_BB1

description: single-cell RNA


title: S1_AF1

description: single-cell RNA


title: S1_AF2

description: single-cell RNA


title: S1_AE2

description: single-cell RNA


title: S1_AD1

description: single-cell RNA


title: S1_AD2

description: single-cell RNA


title: S1_AG1

description: single-cell RNA


title: S1_AE1

description: single-cell RNA


title: S1_AG2

description: single-cell RNA


title: S1_AB2

description: single-cell RNA


title: S1_AC2

description: single-cell RNA


title: S1_BE2

description: single-cell RNA


title: S1_AC1

description: single-cell RNA


title: 1323-0427

city: Bar Harbor

first: Yuka

last: Takemon

state: ME

address: 600 Main St.

institute: The Jackson Laboratory

data_processing:
Illumina HiSeq 2500 was used for base calling and base call quality.
Residual illumina adapters were trimmed from trailing ends using Cutadapt v.1.2.1.
Reads less than 36bps were filtered out also using Cutadapt v.1.2.1.
Sequences were mapped to UCSC mm10 reference genome and transcriptome gtf and index files using with type fr-firststrand using Tophat v.2.0.13, Samtools v.1.2, and Bowtie2 v.2.2.3.
A transcriptome was assembled for biological replicate with using Cufflinks v.2.2.1 toolkit for, with additional parameters --compatible-hits-norm, --GTF reference, --multi-read-correct, and --frag-bias-correct.
Using Cuffquant from the Cufflinks v.2.2.1 toolkit, FPKM counts were quantified and additional parameters were applied (--frag-bias-correct, --multi-reads-correct).
Differential expression analysis was done using Cuffdiff in the Cufflinks v.2.2.1 toolkit with abundance.cxb files from the Cuffquant analysis output.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include gene differential expression analysis and FPKM count from the Cuffdiff output.

source_name: Right Kidney

extract_protocol:
Right kidneys were harvested and flash frozen in liquid nitrogen. Frozen kidneys were homogenized and RNA was extracted using Qiagen miRNeasy Mini Kit.
Libraries were prepared using Illumina TruSeq Stranded Total RNA Ribo-Zero Library Prep Kit

tag: age (months)

value: Wild-type

value: Male


title: 1323-0420


title: S1_AA2

description: single-cell RNA


title: 1323-0282

value: Homozygous Far2 Knock-out


title: human smRNA-seq

description:
smRNA (small RNA)
small RNA in 15-35 nt range
human_refGene_mRNA_structScore.txt

source_name: brain tissue

tag: library strategy

value: smRNA-seq

tag: enzyme treatment

tag: ngs platform

value: Illumina GA2x with 58 nt strand-specific

value: brain


title: 1323-0271

tag: strain


title: 1323-0274


title: PreDC_91 [RMS731]

city: Singapore

first: jinmiao

last: chen

address: 8A Biomedical Grove, #04-06 Immunos

country: Singapore

institute: Singapore Immunology Network

data_processing:
Raw reads were aligned to the human reference genome GRCh38 from GENCODE  using RSEM program version 1.2.19 with default parameters. Gene expression values in transcripts per million were calculated using the RSEM program and the human GENCODE annotation version 22. Quality control and outlier cell detection was performed using the SINGuLAR (Fluidigm) analysis toolset.
Genome_build: Human reference genome GRCh38
Supplementary_files_format_and_content: tab delimited text file,  transcript per million reads (TPM)

growth_protocol: human peripheral blood mononuclear cells

extract_protocol:
magnetic bead enrichment, FACS sorting, IFC capture, on-chip lysis & rt-pcr
Multiplex sequencing libraries were generated using the Nextera XT DNA Library Preparation Kit and the Nextera XT Index Kit (Illumina). Libraries were pooled and subjected to an indexed PE sequencing run of 2x51 cycles on an Illumina HiSeq 2000 (Illumina) at an average depth of 2.5-million row reads/cell.

treatment_protocol: no treatment

tag: tissue

value: Human peripheral blood

tag: cell subtype

value: dendritic cell precursors

tag: cell status

value: Steady state

tag: cell marker


title: PreDC_93 [RMS733]

tag: cell type

value: human peripheral blood mononuclear cells


title: PreDC_89 [RMS729]


title: PreDC_92 [RMS732]


title: PreDC_90 [RMS730]


title: input_control

city: New York

first: Martin

middle: J.

last: Walsh

address: One Gustave L. Levy Pl.

department: Structural and Chemical Biology

institute: Mount Sinai School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.4
read sequences were done QC filtering by FASTX ( -q 20 -p 90 )
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
peaks were called using MACS version 1.4.0 with default setting: PVALUE (1e-5), MFOLD (10,30).
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using input substraction method described previousely (Kharchenko, 2008) (PMID:      19029915)

source_name: Hepa1-6 hepatoma cells

growth_protocol:
Volumes are for a typical 75 cm2 flask. Removed and discarded culture medium. Then briefly rinsed the cell layer with 0.25% (w/v) Trypsin - 0.53 mM EDTA solution to remove all traces of serum which contains trypsin inhibitor. Added 2.0 to 3.0 mL of Trypsin-EDTA solution to flask and observe cells under an inverted microscope until cell layer is dispersed (usually within 5 to 15 minutes).
 Added 8.0 mL of complete growth medium and aspirate cells by gently pipetting. Added appropriate aliquots of the cell suspension to new culture vessels. Incubateed cultures at 37°C @ 5% CO2. A subcultivation ratio of 1:5 was maintained and medium was renewed three times weekly.

extract_protocol:
Lysates were clarified from sonicated nuclei of 3 x 10exp7 cells and ppargc1a -enriched DNA complexes were isolated with antibody following fixation step with 0.5% formaldehyde.
Typical ChIP-Seq library preparation was conducted using the NEB library generation kit (#E6040L). The NEBNext® DNA Library Prep Master Mix Set for Illumina® contains enzymes and buffers in convenient master mix formulations that are ideally suited for sample preparation for next-generation sequencing, and for preparation of expression libraries. Multiplexing of the samples was performed as instructed using the kit.

value: This is a derivative of the BW7756 mouse hepatoma that arose in a C57/L mouse

tag: antibody used


title: ppargc1a_total pool_ChIP-Seq

tag: genotype/variation

value: derivative of the BW7756 mouse hepatoma

value: Rabbit anti- PPARGC1A; Bethyl Laboratory, cat no. IHC-00029


title: ppargc1a_K779me pool_ChIP-Seq

value: Rabbit Anti-[K779me]PPARGC1A;  was generated by the article's co-authors


title: PreDC_84 [RMS724]


title: PreDC_88 [RMS728]


title: PreDC_86 [RMS726]


title: PreDC_85 [RMS725]


title: PreDC_83 [RMS723]


title: PreDC_81 [RMS721]


title: 1323-0416

tag: Sex


title: PreDC_80 [RMS720]


title: PreDC_82 [RMS722]


title: PreDC_78 [RMS718]


title: PreDC_76 [RMS716]


title: PreDC_77 [RMS717]


title: PreDC_71 [RMS711]


title: PreDC_75 [RMS715]


title: PreDC_74 [RMS714]


title: PreDC_73 [RMS713]


title: PreDC_70 [RMS710]


title: PreDC_69 [RMS709]


title: PreDC_68 [RMS708]


title: PreDC_87 [RMS727]


title: PreDC_67 [RMS707]


title: PreDC_66 [RMS706]


title: PreDC_63 [RMS703]


title: PreDC_62 [RMS702]


title: PreDC_65 [RMS705]


title: PreDC_64 [RMS704]


title: PreDC_61 [RMS701]


title: PreDC_60 [RMS700]


title: PreDC_79 [RMS719]


title: PreDC_59 [RMS699]


title: PreDC_58 [RMS698]


title: PreDC_56 [RMS696]


title: PreDC_57 [RMS697]


title: PreDC_51 [RMS691]


title: PreDC_54 [RMS694]


title: PreDC_55 [RMS695]


title: PreDC_52 [RMS692]


title: PreDC_53 [RMS693]


title: PreDC_47 [RMS687]


title: PreDC_72 [RMS712]


title: PreDC_46 [RMS686]


title: PreDC_49 [RMS689]


title: PreDC_50 [RMS690]


title: PreDC_45 [RMS685]


title: PreDC_41 [RMS681]


title: PreDC_43 [RMS683]


title: PreDC_42 [RMS682]


title: PreDC_37 [RMS677]


title: PreDC_35 [RMS675]


title: PreDC_34 [RMS674]


title: PreDC_32 [RMS672]


title: PreDC_38 [RMS678]


title: PreDC_33 [RMS673]


title: PreDC_40 [RMS680]


title: PreDC_31 [RMS671]


title: PreDC_30 [RMS670]


title: PreDC_29 [RMS669]


title: PreDC_36 [RMS676]


title: PreDC_48 [RMS688]


title: PreDC_25 [RMS665]


title: PreDC_26 [RMS666]


title: PreDC_23 [RMS663]


title: PreDC_24 [RMS664]


title: PreDC_44 [RMS684]


title: PreDC_22 [RMS662]


title: PreDC_21 [RMS661]


title: PreDC_18 [RMS658]


title: PreDC_28 [RMS668]


title: PreDC_17 [RMS657]


title: PreDC_20 [RMS660]


title: PreDC_15 [RMS655]


title: PreDC_16 [RMS656]


title: PreDC_13 [RMS653]


title: PreDC_14 [RMS654]


title: PreDC_39 [RMS679]


title: PreDC_11 [RMS651]


title: PreDC_12 [RMS652]


title: PreDC_9 [RMS649]


title: PreDC_6 [RMS646]


title: PreDC_8 [RMS648]


title: PreDC_7 [RMS647]


title: PreDC_5 [RMS645]


title: PreDC_10 [RMS650]


title: PreDC_27 [RMS667]


title: PreDC_4 [RMS644]


title: PreDC_3 [RMS643]


title: PreDC_2 [RMS642]


title: PreDC_19 [RMS659]


title: PreDC_1 [RMS641]


title: MM.1S_shKDM6B, replicate3

first: Hiroto

last: Ohguchi

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sequenced reads were aligned to the reference human genome (GRCh37.75/hg19) using RNA-specific STAR aligner
Reads were further assigned to respective GRCh37.75/hg19 refseq of transcripts using the featureCounts tool
Differential gene expression analysis to compare shKDM6B treated samples with control shluc treated samples was performed using DESeq
Genome_build: GRCh37.75/hg19
Supplementary_files_format_and_content: tab-delimited text files include raw read counts and normalized counts for each sample

source_name: multiple myeloma cell line

growth_protocol: MM.1S cells were maintained in RPMI-1640 medium supplemented with 10% (v/v) fetal bovine serum and 2 μM L-glutamine in 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using RNeasy Mini Kit (Qiagen). RNA was then treated with TURBO DNA-free reagents (Thermo Fisher Scientific).
Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer's instructions. The barcodes for each sample are TAGCTT(MM.1S_shLuc1), GGCTAC(MM.1S_shLuc2), CTTGTA(MM.1S_shLuc3), AGTCAA(MM.1S_shKDM6B1), AGTTCC(MM.1S_shKDM6B2), ATGTCA(MM.1S_shKDM6B3).

treatment_protocol: MM.1S cells were transduced with shRNA by lentivirus. The infected cells were selected with puromycin.

tag: cell line

value: multiple myeloma cell line

tag: transduced with

value: shRNA against KDM6B


title: MM.1S_shKDM6B, replicate1


title: ADM_iN_1

city: Stanford

first: Samuele

last: Marro

state: California

address: 256 Campus Drive

institute: Stanford University

data_processing:
Sequencing reads (100bp) were generated on Hi-Seq 2000 Illumina platforms.
Given that the samples contained a mixed population of human and mouse cells, paired-end reads were aligned to both, the human reference sequence NCBI Build hg19 and the mouse reference sequence NCBI Build 37/mm9 with the TopHat (v1.1.3
Properly paired reads were extracted using the samtools function. Only properly paired reads to the human reference were considered for subsequent analysis.
Expression levels of RefSeq annotated genes were calculated in unit of reads per kilobase of exon model per million mapped fragments (RPKM). Genes with low RPKM (average log2 RPKM across all samples less than 1) were removed.
Differential expression analysis was performed using Students’ t-Test function “t.test” in R, and genes with p-value<0.05 and at least 2-fold expression change were defined as significant.
Genome_build: hg19 and mm9
Supplementary_files_format_and_content: bigWig file containing the processed data - can be displayed in the Genome Browser as a graph

source_name: cultured cells

growth_protocol: iN cells were co-cultured with glia in Neurobasal medium supplemented with B27/Glutamax (Invitrogen) containing BDNF and 1% fetal bovine serum for 4 weeks

extract_protocol:
Total RNA was purified with Trizol following supplier’s recommended method from induced neurons co-cultured with mouse glia.
Poly-A-selected using the MicroPoly(A)Purist Kit (Ambion). Samples were processed according to the manufacturer’s protocol. Subsequently, libraries were prepared following the dUTP protocol

value: iN cells co-cultured with glia


title: MM.1S_shKDM6B, replicate2


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-9]

city: Salt Lake City

first: Mumtahena

last: Rahman

state: UT

address: 20 South 2030 East, Rm 420

department: Biomedical Informatics

institute: University of Utah

data_processing:
Quality checking with FASTQC
Alignment and quantification with R package Rsubread
FPKM normalization with edgeR and limma
TPM normalization from the FPKM values
log2 values of the TPM normalized gene counts
Genome_build: UCSC hg19
Supplementary_files_format_and_content: TPM-log2 normalized gene count processed file is a tab-delimited .txt file

growth_protocol: Human mammary epithelial cells, grown in Stemgent WIT-P culture medium at 3% CO2 and 37°C

extract_protocol:
Cells were scraped into RNA-Later and stored on ice until processing.  Then RNA was isolated from pelleted cells using a Qiagen Rneasy mini kit (with Rnase-free DNase set) and QIAshredders.
Illumina TruSeq stranded mRNA kit

treatment_protocol: Genes were introduced for over-expression by way of adenovirus.  Cells were infected with MOI 500 Adenovius for 30 hours.

value: Human mammary epithelial (HMEC) cells

value: overexpressing human KRAS wild type


title: MCF-7_input DNA

city: China

first: Xinhua

last: Liu

state: State...

address: 300070, Qixiangtai rd, Tianjin

institute: Tianjin Medical University

data_processing:
Alignment through Bowtie version2
Peak-calling through MACS version2
Genome_build: GRGH37/hg19
Supplementary_files_format_and_content: sam file contained the aligned reads; bed file contained the binding peaks; bigwig file contained binding signal

source_name: Breast cancer cell line

growth_protocol: MCF-7 cells were maintained in Dulbecco’s modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Cells were maintained in a humidified incubator equilibrated with 5% CO2 at 37°C.

extract_protocol:
Lysates were clarified from sonicated nuclei and ZNF516-DNA complexes were isolated with antibody.
The chromatin DNA precipitated by polyclonal antibodies against ZNF516 or none for input control. The DNA was purified with the Qiagen PCR purification kit.

value: Breast cancer cell line

tag: passages

tag: chip antibody


title: MM.1S_shLuc, replicate3

value: shRNA against luciferase


title: MCF-7_ZNF516_ChIPSeq

tag: chip antibody vendor

value: Bethyl

tag: chip antibody cat. #

tag: chip antibody lot #


title: MM.1S_shLuc, replicate1


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-6]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-7]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-8]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-4]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-2]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-3]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-1]


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-9]

value: overexpressing human KRAS Q61H mutant form


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-6]


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-7]


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-5]


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-4]


title: ADM_iN_2


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-3]


title: MM.1S_shLuc, replicate2


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-2]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-9]

value: overexpressing human KRAS G12V mutant form


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-1]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-8]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-7]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-6]


title: human KRAS wild type overexpressed in HMEC cells [KRAS_WT-5]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-3]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-4]


title: GFP control, overexpressed in HMEC cells [GFP30-9]

value: overexpressing GFP control


title: GFP control, overexpressed in HMEC cells [GFP30-7]


title: GFP control, overexpressed in HMEC cells [GFP30-6]


title: GFP control, overexpressed in HMEC cells [GFP30-8]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-5]


title: GFP control, overexpressed in HMEC cells [GFP30-5]


title: human KRAS Q61H mutant form overexpressed in HMEC cells [KRAS_Q61H-8]


title: GFP control, overexpressed in HMEC cells [GFP30-3]


title: GFP control, overexpressed in HMEC cells [GFP30-2]


title: GFP control, overexpressed in HMEC cells [GFP30-4]


title: human KRAS G12V mutant form overexpressed in HMEC cells [KRAS_G12V-1]


title: GFP control, overexpressed in HMEC cells [GFP30-1]