title: Jhd2_ChIPSeq

city: Taipei

first: Wan-Sheng

last: Lo

state: Taiwan

address: 128 Academia Road, Section 2, Nankang

department: IPMB

country: Taiwan

institute: Academia Sinica

description:
Sample 1
processed data file: SLY1576ChIP_f3_F256-W200-G200-FDR0.01-islandfiltered-normalized.wig

data_processing:
Basecalls performed using CASAVA version 1.8.
Sequenced reads were trimmed in CLC Genomics Workbench version 6.02 to a quality limit of 0.05, an ambiguous nucleotide limit of 2 and a minimum length of 35 bp for subsequent analysis. Reads were then aligned to the sacCer3 genome assembly using BWA version 0.7.4 with the following parameter settings: bwa-mem-M.
Mapped reads filtered using SAMtools version 0.1.19 with the following command: samtools view -f3 -F256.
Significant peaks were determined, relative to input DNA, using SICER version 1.1. SICER parameters were set at a window size of 200, a gap of 200, a false-discovery rate of 0.01, and sample specific DNA fragment size of 250 bp.
Genome_build: sacCer3
Supplementary_files_format_and_content: wig files were generated using SICER version1.1 ; Scores represent the read count that normalized by library size per million.

source_name: Log-phase cells

growth_protocol: Jhd2-Flag tagging strain grown up to A600~1 in SCM-Leu medium at 30°C

extract_protocol:
Cells were lysed using glass beads, and chromatin was sheared to 150-300 bp. Chromatin was isolated and used for ChIP with the anti-Flag (M2, Sigma) antibody and Magna ChIP G beads (Millipore).
Libraries were prepared according to Illumina's instructions.

treatment_protocol: Cells was fixed with 10 mM dimethyl adipimidate (DMA) for 45 min and then with 1% formaldehyde for 2 hr, followed by a 10 min incubation with 125 mM glycine prior to cell harvesting

value: Monoclonal ANTI-Flag M2 antibody (Sigma, catalog# F3165, lot# 103K6043)


title: Input DNA

status: Public on Feb 20 2017

type: SRA

description:
Sample 2
processed data file: SLY1576ChIP_f3_F256-W200-G200-FDR0.01-islandfiltered-normalized.wig

library_source: genomic

molecule: genomic DNA

organism: Saccharomyces cerevisiae

tag: strain

tag: chip antibody


title: WT - repeat 2

status: Public on Feb 19 2017

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
Reads were aligned to the tomato genome sequence SL2.50 (downloaded from the sol genomics network http://solgenomics.net/organism/Solanum_lycopersicum/genome) using Tophat (v2.0.10).
Counting reads on ITAG2.4 genes (downloaded from sol genomics network) was done with HTSeq-count (version 0.6.1p1)
Differential analysis was carried out using DESeq2 (1.6.3)
Genome_build: SL2.50
Supplementary_files_format_and_content: Excel file including the normalized counts, ratios and p-values (and adjusted p-values).

molecule: total RNA

organism: Solanum lycopersicum

source_name: WT tomato apex

growth_protocol: Seedlings were grown in a greenhouse for 14-18 days.

extract_protocol:
RNeasy kit, QIAGEN, Cat. #74004
Truseq RNA Sample prep-Illumina

treatment_protocol: Seedlings were fixed in acetone and shoot apical meristems were dissected

tag: genotype/variation

value: WT

tag: tissue

value: The sample contains the shoot apical meristem (SAM) and the two youngest leaf primordia.


title: N37-FL

city: La Jolla

first: Kun

last: Zhang

state: CA

address: 9500 Gilman Dr Mailcode: 0412

department: Bioengineering

country: USA

institute: University of California, San Diego

data_processing:
base-calling
quality trimming of fastq reads
alignment with BWA/bisReadMapper
trim overlapping pair-ends
generate methylation haplotype counts from BAM
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values: column 1 - genomic locus, column 2 - methylation haplotype call, column 3 - number of reads supporting methylation haplotype, column 4 - list of CpG positions included in methylation haplotype

organism: Homo sapiens

source_name: frontal lobe

extract_protocol: Approximately 200 ng of genomic DNA of primary tissues (N37) obtained from the Li Lab was sheared into an average size of 400 bp in a Covaris micro TUBE with Covaris E210 ultrasonicator. Fragmented genomic DNA was constructed into Illumina paired-end sequencing libraries using KAPA Library Preparation kit (KAPA Biosystems) following manufacturer’s instruction with modifications. After end-repair and dA-tailing, ligation with methylated adapters was performed at 20 ˚C for 15 min in the presence of 10-fold molar excess of Illumina methylated adapters (Illumina). The ligation mixture was purified with an equal volume of Agencourt AMPure XP beads (Beckman Coulter) and eluted with 23 µL of 10mM Tris-HCl, pH8.5. Next, 20 µL of adaptor ligated DNA was bisulfite converted using EZ DNA Methylation-Lightning kit (Zymoresearch) following manufacturer’s protocol and eluted with 30 µL of 10mM Tris-HCl, pH8.5. Bisulfite converted DNAs were amplified using iQ SYBR Green Supermix (Bio-Rad) with 200 nM each of PCR primer PE1.0 and multiplexing PCR primer for 10 cycles in 100 µL total volume. PCR products were purified with 0.8X volume of Agencourt AMPure XP beads (Beckman Coulter) and eluted with 50 µL of 10mM Tris-HCl, pH8.5, pooled in equimolar ratios, and size selected using 6% TBE gels for 400-600 bp. The concentration of sequencing libraries was quantified by qPCR using KAPA Library Quantification kit (KAPA Biosystems). Libraries were sequenced on both GAIIx for SE 36 cycles and HiSeq Run for PE 100 cycles.

tag: disease state

value: normal

value: frontal lobe


title: N37-Heart

source_name: heart

value: heart


title: N37-CRBL

source_name: cerebellum

value: cerebellum


title: N37-SI

source_name: small intestine

value: small intestine


title: N37-Lung

source_name: lung

value: lung


title: N37-Stomach

source_name: stomach

value: stomach


title: N37-SM

source_name: skeletal muscle

value: skeletal muscle


title: N37-Liver

source_name: liver

value: liver


title: N37-Pancreas

source_name: pancreas

value: pancreas


title: PC-T-7

data_processing:
base-calling
quality trimming of fastq reads
alignment with BWA/bisReadMapper
trim overlapping pair-ends
geneerate methylation haplotype counts from BAM
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values: column 1 - genomic locus, column 2 - methylation haplotype call, column 3 - number of reads supporting methylation haplotype, column 4 - list of CpG positions included in methylation haplotype

source_name: Invasive ductal adenocarcinoma of the pancreas

extract_protocol:
Genomic DNAs were extracted from 20-50 mg of primary normal and tumor tissues from lung, colon and pancreatic cancer patients using DNeasy Blood and Tissue kit (QIAGEN) following the manufacturer’s instruction and eluted in 400 µL of AE buffer (QIAGEN). The concentration and quality of genomic DNA were assessed by Qubit dsDNA HS Assay kit (Life Technologies) and NanoDrop (Thermo Scientific), respectively.
To generate RRBS sequencing libraries, 100 ng of gDNA were digested with 20 U of MspI (Thermoscientific) in 1X Tango buffer (Thermoscientific) and 1 ng of unmethylated lambda DNA (Promega) in order to assess for bisulfite conversion rate in 30µL total volume for 3 h at 37 ˚C and heat inactivated at 65 ˚C for 20 min. Next, 5U of Klenow fragment, exo- (Thermoscientifc) and a mixture of dATP, dGTP, and dCTP (New England Biolabs) were added to MspI-digested DNAs for a final concentration of 1 mM, 0.1 mM, and 0.1 mM for dATP, dGTP, and dCTP, respectively in 32 µL for end-repair and dA-tailing. The mixture was mixed and incubated at 30 ˚C for 20 min, 37 ˚C for 20 min, and heat inactivated at 75 ˚C for 10 min. dA-tailed DNA was purified with 2X volume of Agencourt AMPure XP beads (Beckman Coulter) and resuspend dA-tailed DNA with 20 µL nuclease-free water without discarding the magnetic beads. dA-tailed DNAs were then ligated to methylated adaptors in 30 µL total volume containing 30 U of T4 DNA ligase, HC (Thermoscientific), 1X Ligation buffer (Thermoscientific), and 500 nM individual TruSeq multiplexing methylated adaptors (Illumina). The ligation mixture was mixed well and incubated at 16 ˚C for 20 h, heat inactivated at 65 ˚C for 20 min, purified by adding 60 µL of PEG 8000/5M NaCl buffer (Teknova) to adaptor ligated DNA and bead mixture, and eluted in 20 µL of nuclease-free water. Next, the adaptor ligated DNA were bisulfite converted using the MethylCode(™) Bisulfite Conversion kit (Life Technologies) following manufacturer’s protocol and eluted in 35 µL of Elution buffer (Life Technologies). Bisulfite treated DNAs were amplified using 5 U of PfuTurboCX (Agilent Technologies) and 300 nM each of TruS_F and TruS_R primers for 14 cycles in 100 µL total volume. PCR products were purified with an equal volume of Agencourt AMPure XP beads (Beckman Coulter) and eluted with 50 µL of 10mM Tris-HCl, pH8.5, pooled in equimolar ratios, and size selected using 6% TBE gels for 150-400 bp. The concentration of sequencing libraries was quantified by qPCR using KAPA Library Quantification kit (KAPA Biosystems). Libraries were sequenced on HiSeq RapidRun for PE 100 cycles.

value: pancreatic cancer

tag: cancer type


title: PC-T-6

source_name: Invasive pancreatic duct adenocarcinoma

value: Invasive pancreatic duct adenocarcinoma


title: PC-T-2

source_name: Adenocarcinoma of the pancreas, ductal type, moderately to poorly differentiated


title: PC-T-1

source_name: Adenocarcinoma of the pancreas, moderately to poorly differentiated


title: TIBA-pin - repeat 1

source_name: tomato TIBA-induced pin

value: pin-like shoot induced by 1mM TIBA spraying

value: The sample contains the shoot apical meristem (SAM).


title: WT - repeat 1


title: LC-T-2

source_name: Poorly differentiated squamous cell carcinoma

value: lung cancer


title: CRC-T-4

source_name: Metastatic adenocarcinoma

value: colorectal cancer

value: Metastatic adenocarcinoma


title: LC-T-1

source_name: Invasive moderatively differentiated adenocarcinoma


title: CRC-T-2

source_name: Metastatic malignant hemagiopericytoma/malignant solitary fibrous tumor


title: LC-T-5

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma


title: LC-T-3

source_name: Metastatic melanoma

value: Metastatic melanoma


title: CRC-T-5

source_name: Metastatic mucinous adenocarcinoma

value: Metastatic mucinous adenocarcinoma


title: MARSseqB_TTGAAT

city: Martinsried

first: Christoph

last: Ziegenhain

state: Bavaria

address: Großhaderner Str. 2

department: Department Biology II

country: Germany

institute: Ludwig-Maximilians University Munich

description: Library preparations were performed with MARS-seq, as described in Jaitin et al., 2014

data_processing:
base-calls were performed with Illumina bcl2fastq
all cDNA reads were aligned with Star v2.4.0
SCRB-seq, MARS-seq, CEL-seq2 and Drop-seq protocol reads were tagged with its mate-pair UMI and cell barcode; unique reads were obtained; more information see README file
Smart-seq and Smart-seq2 reads were assigned to genes using Rsubread
only cells were considered with at least 1,000,000 reads; doublets discarded and failed libraries filtered by low nearest-neighbor correlation coefficients
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with unique gene-wise counts of cells considered for final analysis: ziegenhain_complete_data.txt

organism: Mus musculus

source_name: mouse embryonic cell line

growth_protocol: J1 mESC were cultured in ground pluripotency states by 2i/LIF culture as described previously.

extract_protocol: single-cell lysate

tag: library preparation

value: MARS-seq

tag: cell line


title: CRC-T-3

source_name: Recurrent invasive moderately to poorly differentiated adenocarcinoma


title: CRC-T-1

source_name: Poorly differentiated adenocarcinoma

value: Poorly differentiated adenocarcinoma


title: N37-Colon

source_name: colon

value: normal

value: colon


title: LC-T-4

source_name: Squamous cell carcinoma, clear cell variants, moderately differentiated


title: MARSseqB_TTGAGC


title: PC-T-4

value: Adenocarcinoma of the pancreas, ductal type, moderately to poorly differentiated


title: lfs - repeat 1

source_name: lfs tomato shoot apical meristem (SAM)

value: lfs mutant


title: MARSseqB_TTACGC


title: MARSseqB_TAATGA


title: MARSseqB_TCCAGC


title: MARSseqB_TCTCGG


title: MARSseqB_TGTCGG


title: MARSseqB_GTCTGA


title: MARSseqB_GTCGCC


title: MARSseqB_GCACAC


title: MARSseqB_TAAGCA


title: MARSseqB_GTCATC


title: MARSseqB_GCACAT


title: MARSseqB_TACTTA


title: MARSseqB_CTGTAA


title: MARSseqB_GAACCT


title: MARSseqB_GACCAG


title: NC-P-80

description: Sample 174

source_name: colorectal cancer_plasma

extract_protocol:
Plasma from patients were processed to extract circulating DNA. The DNA extracted from plasma were then concentrated using ethanol precipitation and eluted in 15 uL nuclease-free water.
1-1.5 ng of DNA were digested with 10 U of MspI (Thermoscientific), 1X Tango buffer (Thermoscientific), and 10 pg of unmethylated lambda DNA (New England Biolabs) as control for ~13 h at 37 ˚C, then heat inactivated at 65 ˚C for 20 min. Next, 5 U of Klenow fragment, exo- (Thermoscientifc) and a mixture of dATP, dGTP, and dCTP (New England Biolabs) were added for a final concentration of 1 mM, 0.1 mM, and 0.1 mM for dATP, dGTP, and dCTP respectively. The mixture was gently vortexed, and incubated at 30 ˚C for 20 min, 37 ˚C for 20 min, and finally 75 ˚C for 10 min. To perform adaptor ligation, the dA-tailed DNA were added to a 5 uL mixture of 1X Tango buffer, 30 U of T4 DNA Ligase, HC (Thermoscientific), 2.5 mM ATP, and 500 nM individual TruSeq multiplexing methylated adaptors. The combined mixture was gently vortexed, incubated at 16 ˚C for ~20 h, then heat inactivated at 65 ˚C for 20 min. The ligation mixture was purified using Agencourt AMPure XP beads (Beckman Coulter), and eluted in 20 uL of nuclease-free water. The ligated products were then bisulfite converted using the MethylCode(™) Bisulfite Conversion kit (Life Technologies). Two rounds of amplification were performed after bisulfite conversion. The first round was using PfuTurboCX (Agilent Technologies) for 12 cycles in 50 uL total volume, then the second round was performed using Phusion HotStart Flex (New England Biolabs) master mix for 9 cycles in 50 uL total volume. Final PCR products were purified, pooled in equimolar ratios, and size selected using polyacrylamide gels for 150-400 bp. Libraries were sequenced on both MiSeq and HiSeq RapidRun for PE 100 cycles.


title: NC-P-79

description: Sample 173


title: MARSseqB_GACAGT


title: MARSseqB_CGTTAC


title: MARSseqB_CTACCA


title: NC-P-76

description: Sample 170


title: NC-P-77

description: Sample 171


title: NC-P-78

description: Sample 172


title: NC-P-75

description: Sample 169


title: MARSseqB_CCAGTT


title: MARSseqB_CCTATG


title: MARSseqB_TCCTTG


title: NC-P-74

description: Sample 168


title: MARSseqB_CAGGAG


title: MARSseqB_CATGCT


title: NC-P-72

description: Sample 166


title: NC-P-73

description: Sample 167


title: NC-P-71

description: Sample 165


title: MARSseqB_CAGCAA


title: MARSseqB_GAAGAA


title: MARSseqB_CACATC


title: NC-P-70

description: Sample 164


title: MARSseqB_CCTTCG


title: NC-P-68

description: Sample 162


title: NC-P-69

description: Sample 163


title: NC-P-67

description: Sample 161


title: MARSseqB_ATAGCG


title: NC-P-66

description: Sample 160


title: MARSseqB_AGGTTA


title: MARSseqB_AATGTT


title: MARSseqB_AGGATC


title: MARSseqB_AAGGAT


title: MARSseqA_TCGGAA


title: MARSseqA_TCTCGG


title: NC-P-64

description: Sample 158


title: NC-P-61

description: Sample 155


title: NC-P-62

description: Sample 156


title: MARSseqA_TTGAAT


title: NC-P-60

description: Sample 154


title: MARSseqA_TCCTTG


title: NC-P-59

description: Sample 153


title: MARSseqA_TCGCCT


title: MARSseqA_TAATGA


title: MARSseqB_ATTCTA


title: MARSseqA_TACTTA


title: MARSseqA_TAAGCA


title: NC-P-56

description: Sample 150


title: NC-P-57

description: Sample 151


title: MARSseqB_CCTACC


title: MARSseqA_GGTCCA


title: NC-P-55

description: Sample 149


title: NC-P-53

description: Sample 147


title: MARSseqA_GAAGAA


title: NC-P-54

description: Sample 148


title: MARSseqA_CTGTAA


title: MARSseqA_CGTTAC


title: NC-P-51

description: Sample 145


title: MARSseqA_CCTATG


title: MARSseqA_GCACAC


title: NC-P-49

description: Sample 143


title: MARSseqA_CATGCT


title: NC-P-63

description: Sample 157


title: MARSseqA_CCTTCG


title: NC-P-52

description: Sample 146


title: NC-P-50

description: Sample 144


title: NC-P-48

description: Sample 142


title: NC-P-58

description: Sample 152


title: NC-P-46

description: Sample 140


title: NC-P-45

description: Sample 139


title: MARSseqA_CAGCGG


title: NC-P-44

description: Sample 138


title: MARSseqA_CAGGAG


title: MARSseqA_CACATC


title: MARSseqA_ATTGTC


title: NC-P-43

description: Sample 137


title: MARSseqA_ATTCTA


title: MARSseqA_GACCAG


title: NC-P-40

description: Sample 135


title: NC-P-41

description: Sample 136


title: MARSseqA_ATTATG


title: MARSseqA_ATAGCG


title: NC-P-38

description: Sample 133


title: MARSseqA_ACCAAC


title: NC-P-47

description: Sample 141


title: NC-P-36

description: Sample 131


title: NC-P-37

description: Sample 132


title: MARSseqA_AACTTG


title: NC-P-33

description: Sample 128


title: NC-P-34

description: Sample 129


title: NC-P-35

description: Sample 130


title: NC-P-32

description: Sample 127


title: CELseq2B_TCTGAG

description: Library preparations were performed with CEL-seq2 on the Fluidigm C1, as described in Hashimshony et al. 2016


title: CELseq2B_TCTGCA


title: CELseq2B_TCGATC


title: NC-P-6

source_name: plasma


title: CELseq2B_TCGAAG


title: NC-P-31

description: Sample 126


title: CELseq2B_TCGACA


title: NC-P-5


title: CELseq2B_TCCTAG


title: NC-P-65

description: Sample 159


title: NC-P-3


title: CELseq2B_TGTCGA


title: NC-P-39

description: Sample 134


title: CELseq2B_GTTGCA


title: CELseq2B_TCACAG


title: MARSseqA_AATGTT


title: MARSseqA_AACGCA


title: CELseq2B_GTGATC


title: CELseq2B_GTCTAG


title: CELseq2B_GTGACA


title: NC-P-30


title: NC-P-26


title: NC-P-25


title: NC-P-29


title: CELseq2B_GTACTC


title: NC-P-27


title: NC-P-22


title: NC-P-23


title: NC-P-21


title: CELseq2B_CTAGTG


title: CELseq2B_CTCAGA


title: CELseq2B_CTCATG


title: NC-P-20


title: CELseq2B_CTAGGA


title: CELseq2B_CTTCGA


title: NC-P-18


title: CELseq2B_CATGCA


title: CELseq2B_CAGATC


title: NC-P-16


title: NC-P-17


title: CELseq2B_CATGTC


title: NC-P-24


title: MARSseqA_CATAGC


title: NC-P-15


title: CELseq2B_AGTGTC


title: CELseq2B_CACTAG


title: LC-P-9


title: NC-P-13


title: NC-P-14


title: NC-P-12


title: CELseq2B_AGGATC


title: CELseq2B_AGTGCA


title: NC-P-2


title: gfD1

city: Beijing

first: Fei

last: Gao

address: 27 Zhongguancun South Street

country: China

institute: Minzu University of China

data_processing:
Library strategy: PARE-Seq
Raw sequencing reads were obtained  using Illumina’s  Pipeline  v1.5  software following  sequencing  image  analysis  by  Pipeline  Firecrest Module  and  base-calling  by  Pipeline  Bustard  Module.
Get some degradome data (RNAseq reads from 5' ends of uncapped RNAs, where the 1st nt of the read represents the in vivo 5' end), free from adapter sequences, etc.
Map the degradome reads to the appropriate transcriptome using appropriate thresholds.
Filter the mapped data, if required. Summarize  the  mapped  degradome  data  into  a  "degradome  density  file"  using  script  'CleaveLand3_map2dd.pl'. Generate small RNA / mRNA alignments using 'targetfinder.pl'.
Compare the degradome density file to the target predictions, and output significant hits using script 'CleaveLand3_analysis.pl'. Generate "t-plots" of the targets using script 'CleaveLand3_t- plotter.pl'.
Genome_build: de novo

molecule: polyA RNA

organism: Ammopiptanthus mongolicus

source_name: leaves and roots

growth_protocol: The seeds of Ammopiptanthus mongolicus were collected from Zhongwei city, Ningxia autonomous district, China. The seeds were sown in pots and germinated in an incubator. After one week, the seedlings were transplanted to the growth chambers and grown at 22°C with 16 h of light per day.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) from leaves and roots of A. mongolicus seedlings following the manufacturer’s procedure.
The library was constructed according to the method described previously [Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol 2008,26:941-946].

value: leaves; roots


title: CELseq2B_AGCTTC


title: CELseq2B_AGCTCA


title: CELseq2B_AGCTAG


title: CELseq2B_CATGAG


title: LC-P-6


title: LC-P-7


title: CELseq2B_AGACTC


title: NC-P-9


title: NC-P-7


title: LC-P-5


title: LC-P-8


title: CELseq2B_ACTCTG


title: LC-P-4


title: NC-P-8


title: CELseq2B_ACTCGA


title: CELseq2B_ACGTTG


title: LC-P-3


title: LC-P-30


title: LC-P-27


title: CELseq2B_ACGTGA


title: LC-P-22


title: LC-P-10


title: CELseq2B_ACGTAC


title: LC-P-21


title: LC-P-19


title: LC-P-20


title: CELseq2B_ACCATG


title: CELseq2B_ACAGTG


title: NC-P-1


title: LC-P-17


title: LC-P-29


title: CRC-P-8


title: LC-P-16


title: LC-P-28


title: LC-P-18


title: LC-P-26


title: LC-P-2


title: CELseq2A_TGTCGA


title: NC-P-19


title: LC-P-15


title: LC-P-25


title: CRC-P-6


title: LC-P-13


title: LC-P-1


title: LC-P-14


title: LC-P-11


title: LC-P-12


title: CRC-P-5


title: CRC-P-9


title: CRC-P-30


title: CRC-P-4


title: CELseq2A_TCGATC


title: CRC-P-29


title: CRC-P-28


title: CRC-P-3


title: CRC-P-7


title: CELseq2A_TGTCAC


title: LC-P-23


title: CRC-P-27


title: CRC-P-26


title: CELseq2A_TGCATG


title: CRC-P-2


title: CELseq2A_TCACAG


title: CRC-P-24


title: CRC-P-25


title: CRC-P-23


title: CELseq2A_GTGACA


title: CRC-P-10


title: CRC-P-1


title: CELseq2A_GTCTCA


title: CRC-P-20


title: CELseq2A_TCTGCA


title: CELseq2A_GTCTAG


title: CRC-P-22


title: CRC-P-19


title: CELseq2A_GTACTC


title: CRC-P-16


title: CELseq2A_TCCTAG


title: CRC-P-17


title: CELseq2A_GTACCA


title: CRC-P-18


title: CRC-P-12


title: CELseq2A_GTACAG


title: CRC-P-13


title: CELseq2A_CTTCGA


title: CELseq2A_CTGTGA


title: CRC-P-11


title: CELseq2A_CTAGGA


title: CELseq2A_CTAGTG


title: CRC-P-21


title: CELseq2A_CATGCA


title: CELseq2A_CTCATG


title: CELseq2A_CATGAG


title: CELseq2A_CTGTAC


title: CELseq2A_CAGATC


title: CRC-P-14


title: CELseq2A_AGTGTC


title: CELseq2A_AGGATC


title: CELseq2A_AGTGCA


title: CELseq2A_AGCTTC


title: CELseq2A_AGACTC


title: CELseq2A_CACTAG


title: CELseq2A_CTAGAC


title: CRC-P-15


title: CELseq2A_ACTCTG


title: CELseq2A_ACGTGA


title: CELseq2A_ACGTTG


title: CELseq2A_ACGTAC


title: CD31, rep2

city: Bronx

first: Paul

middle: S

last: Frenette

state: NY

address: 1301 Morris Park Avenue , Room 101

department: Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research

institute: Albert Einstein College of Medicine

data_processing:
RNA-Seq data generated from Illumina HiSeq 2500 were processed following a recently developed reproducible pipeline (Wang Z and Ma’ayan A, F1000Res. Vol.5. 2016). Briefly, paired-end sequencing reads were aligned to mouse genome mm10 using Spliced Transcripts Alignment to a (STAR) (Dobin A, et al., Bioinformatics, 29(1), 2013).
We next used featureCount (Liao Y et al., Bioinformatics, 30(7), 2014) to assign aligned reads to genes.
Genome_build: mm10

source_name: bone marrow cell

extract_protocol:
Total RNA from sorted cells was extracted using the RNAeasy Plus Micro kit (Qiagen).
Complementary DNA was generated using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech Laboratories) from 1ng of total RNA. Nextera XT DNA Sample preparation Kit (Illumina) was used for preparation of DNA libraries.

tag: developmental stage

value: adult

tag: cell type

value: bone marrow endothelial cell

tag: cell population


title: LepR-cre, rep1

value: bone marrow stromal cell


title: LepR-cre, rep2


title: Microoxic_rep2

city: Sydney

first: Miguel

middle: A

last: Hernández-Prieto

state: NSW

address: Macleay Building A12

department: School of life and environmental sciences

country: Australia

institute: University of Sydney

data_processing:
Raw data was processed using Rockhopper java based software with default parameters for paired-end sequencing files
Genome_build: Acaryochloris marina MBIC11017
Supplementary_files_format_and_content: Expression_data.xlsx (Differential expression values); Processed_Data_elbiologo.xlsx (Expression in RPKM for all detected transcripts)

organism: Acaryochloris marina MBIC11017

source_name: RNA

growth_protocol: Acaryochloris marina MBIC11017 was routinely kept in a culture room at 27°C under 15–30 µmol photons•m˗2•s˗1 of cool white light. Sterilized K+ES (artificial seawater), buffered with 25 mM TES at pH 8.0 was used as the culture medium for all three treatment groups. To make sure photosynthesis was not limited by CO2, NaHCO3 was dissolved in a small volume of autoclaved media, and injected into the enclosed culture flasks every two days (yielding an initial concentration of 0.375 mM). The initial cell density of all culture groups was adjusted to an optical density at 750 nm of 0.2. The cultures were shaken on an orbital flat-bed shaker at ~90 rpm.

extract_protocol:
Acaryochloris cultures were harvested after five days from all three different treatments. The harvested cell pellets were mixed with TRIzol (TRIzol® Reagent, Life Technologies, Australia), and frozen immediately using liquid nitrogen. They were stored at ˗80°C for at least 60 min. The frozen samples were thawed in a water bath of 37°C, and spun down at 16,000×g for 5 min to eliminate cellular debris. This supernatant was mixed at a volume ratio of 4:1, with chloroform and spun down at 16,000×g for 10 min at 4°C. The upper layer, containing RNA and DNA, was carefully transferred to a new tube, without disturbing the white middle layer of solid components. The RNA was precipitated by addition of an equal volume of isopropanol and incubated at ˗20°C for at least 45 min. RNA pellets were washed with 70% (v/v) ethanol and the DNA removed using the Baseline-ZERO™ DNase kit (Epicentre, WI, USA), following the manufacturer's instructions. Prior to RNA quality assessment, the absence of DNA was confirmed by polymerase chain reaction (data not shown).
The quality of RNA was assessed on a 2100 Bioanalyzer (Agilent Technologies, CA, USA), using a RNA 6000 Nano RNA Kit (Agilent Technologies) to obtain an RNA integrity number of >8.0. Transcripts corresponding to rRNAs (5S, 16S and 23S) were reduced from the samples with a Ribo-Zero Kit (Epicentre), following the manufacturer's instructions. The remaining RNA was mixed with the fragmentation buffer, the RNA was fragmented into short fragments. Then cDNA was synthesized using random hexamers and the RNA fragments as templates. Short fragments were purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments were connected with adapters. After agarose gel electrophoresis, the suitable fragments were selected for PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System were used in quantification and qualification of the sample library. At last, the library could be sequenced using Illumina HiSeqTM 2000. Further processing, including quality assessment, was undertaken prior to RNAseq analysis by Beijing Genomics Institution, China.

treatment_protocol: Cultures under normal O2 levels were inoculated in 1-l Erlenmeyer glass flask containing 500 ml of medium, capped with a cotton stopper that permitted gas exchange. Thus, the O2 concentration of the gas phase inside the bottle was similar to atmospheric levels ~21% (v/v).  Microoxic conditions were achieved by using a 500-ml two-necked round-bottom flask sealed tightly by a rubber stopper. Cultures were vacuumed, and refilled with pure nitrogen gas (99.95% purity) to ensure normal atmospheric pressure. We repeated this process several times, yielding a final O2 concentration of <0.2% inside the sealed culture flask. To maintain a microoxic condition, a positive pressure was created by bubbling nitrogen through the culture.  A similar set-up was used for hyperoxic conditions, with the exception that pure O2 gas was used to refill the flask after vacuuming. Because the cells generate O2 under illumination, ongoing input of O2 gas to maintain the high-oxygen concentration was not required. However, to avoid pressure build-up, the flask was re-vacuumed and refilled with O2 gas every 48 h, as described above. The O2 concentration inside the flask remained within the range of 65–75% (v/v) during the experiment.

tag: treatment

value: microoxic


title: Hyperoxic_rep1

value: hyperoxic


title: Hyperoxic_rep2


title: NG2-cre, rep1


title: Microoxic_rep1


title: Myh11-creER, rep2


title: CELseq2A_CTCAGA


title: Control_rep2

description: Control

value: control


title: Control_rep3

description: Control


title: LNCaP GIPZ Input

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description: input

data_processing:
Reads were aligned to the hg19 reference human genome using bwa v0.6.1
Peak-calling by HOMER v4.1
Genome_build: hg19
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: prostate tumor

growth_protocol: Cell lines were maintained in RPMI supplemented with 10% FBS.

extract_protocol:
Chromatin in nuclear fraction were sheared to 200-500bp using an ultrasonic sonicator (Misonix), Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antisera.  DNA was then uncrosslinked from protein, purified and sequenced using Illumina Genome Analyzers followig protocols recommended by the manufacturer.
Libraries were prepared according to Illumina's instructions.

treatment_protocol: LNCaP cells stably expressing doxycycline inducible NOV were treated with water (Ctrl) or doxycycline (NOV) for 2-3days before fixation by 1% formaldehyde.

value: LNCaP

tag: genotype

value: input

tag: antibody

value: none (input)


title: Myh11-creER, rep1


title: LNCaP_NOV AR ChIP-seq

description: Chromatin IP against AR

value: NOV

value: AR (santa cruz, sc-815X, lot K0713)


title: Control_rep1

description: Control


title: PG_DMSO_2

status: Public on Feb 18 2017

city: Seattle

first: David

middle: A. C.

last: Beck

state: WA

address: Benjamin Hall IRB, Rm 440, UW Box 355014

department: ChemE & eScience Institute

institute: University of Washington

description: Porphyromonas gingivalis control with DMSO

data_processing:
Reads were mapped to the ATCC33277 genome with BWA (0.7.4-r385).
The SAM alignments were sorted into BAM files with SAMTools (0.1.19-44428cd).
The reads were attributed to specific transcripts using htseq-count (0.5.4p5) under the intersection-nonempty mode.
Genome_build: ATCC33277
Supplementary_files_format_and_content: Tab separated values, one column for each sample with the reads mapped counts for each transcript as the rows.

organism: Porphyromonas gingivalis

source_name: Pg cells_DMSO

growth_protocol: Pg cells were grown anaerobically in trypticase soy broth supplemented with yeast extract, haemin, and menadione to mid log phase

extract_protocol:
Lysates were abtained by homogenizing in a tissue lyser in the presence of TRIzol and cleaned using Zymo Research RNA Clean and Concentrator columns
Libraries were made from total RNA using Illumina's Truseq RNA Sample prep kit V2

treatment_protocol: Cells were resuspended in vehicle plus pABA or vehicle alone for 18 hours

value: control with DMSO


title: PG_PABA_1

description: Porphyromonas gingivalis treated with pABA in DMSO

source_name: Pg cells_PABA

value: treated with pABA in DMSO


title: PG_PABA_2


title: CD31, rep1


title: PG_DMSO_1


title: NG2-cre, rep2


title: DoxLPS_HERIT_2of2

city: Stony Brook

first: Laurie

last: Krug

address: 130 Life Sciences Bldg

department: Molecular Genetics and Microbiology

institute: Stony Brook University

data_processing:
Reads with Phred score <20 towards the ends or length < 20 were removed using Trimmomatic
Read mapping was done using Salmon version 0.7.2 with k-mer length 19 and VBEM with 30 bootstrap samples. This provided transcript level quantification results.
Mapped reads to each transcript were summed and normalized for transcript length and library size using tximport. For the virus, all exons from a gene were merged to give a single transcript. The cds bed file was used for this and has slight modifications of the current NC_001826.2 annotation of the murine gammaherpesvirus genome.
Fold change of replicate TPM to average TPM was final output for Cluster and Silhouette analysis
Genome_build: mm10, cds_NC_001826.4.bed (bed file for the herpesvirus transcriptome)
Supplementary_files_format_and_content: TPMs, fold change

growth_protocol: HE-RIT cells are MHV68+ latent B cell lines derived from A20-HE2.1 cells. A20-HE-RIT were maintained in RPMI 1640 supplemented with 10% FBS, 100 U/mL of penicillin, 100 mg/mL of streptomycin, and 50 mM 2-mercaptoethanol at 37°C in 5% CO2, 300 μg/mL of hygromycin B sulfate, 300 μg/mL G418, and 2 μg/mL puromycin (Invivogen).

extract_protocol:
RNA was prepared by column purification (Qiagen RNeasy mini) and DNaseI digested. The sequencing library was prepared by BGI Americas (Cambridge, MA). In brief, polyA mRNA was isolated from total RNA using poly (T) oligo-attached magnetic beads.
The mRNA was fragmented and first-strand cDNA was generated using random hexamers, followed by second-strand cDNA synthesis and cDNA purification. The synthesized cDNA was subjected to end-repair and 3’ adenylated, followed by adaptor ligation, purification, and PCR amplification. The library was validating on the Agilent Technologies 2100 Bio-analyzer and the ABI StepOnePlus Real-Time PCR System

treatment_protocol: HE-RIT cells were treated with 5 µg/ml doxycyline (Dox) or a lower 0.5 µg/ml Dox in combination with 10 ng/ml LPS for 24 h.

value: HE-RIT

tag: herpesvirus

value: murine gammaherpesvirus 68

value: doxycycline and lipopolysaccaride


title: Sample_P28wtRetina1.sorted

city: Bethesda

first: Hong

last: Liu

state: MD

address: 9000 Rockville Pike

department: NIDDK

institute: NIH

data_processing:
The conversion from bcl to fastq was performed using bcl2fastq software, version 2.17.1.14 from Illumina.
Chastity filtering has been applied, and alignment was done using BBMap version 36.02 to the mm9 reference genome.
Reads Per Kilobase of transcript per Million mapped reads of library size (RPKM) were calculated by RNAseq analysis software in Genomatix.
Expression of each gene was represented by its RPKM value, which was calculated by Locus-based expression analysis (union of exons for all loci, i.e. gene bodies) in Genomatix platform.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file includes RPKM values for each gene at different retinal stages

source_name: Retina

extract_protocol:
Fresh retinas were dissected in cold 1xPBS, and total RNA was extracted using Trizol reagent. Dynabeads was used to purify the mRNA for NGS-library construction
Double-strand cDNA library was synthesized from purified mRNA by using Invitrogen Double-strand cDNA Synthesis kit. After fragmentation, cDNA library samples were constructed into sequencing libraies by using Illumina True-seq ChIP DNA prep kit.

tag: age

value: wild type


title: Dox_HERIT_1of2

value: doxycycline


title: DoxLPS_HERIT_1of2


title: Mock_HERIT_2of2

value: no treatment


title: Sample_P14retinaWT.sorted


title: Sample_P3retinaWT.sorted


title: LNCaP_Ctrl AR ChIP-seq

description: Chromatin IP against AR

value: Ctrl


title: FOP_3

city: Shanghai

first: Kunshan

address: 389 Xincun Road

department: Stem cell Translational Research center

institute: Tongji Hospital, Tongji University

data_processing:
Clean reads were aligning to hg19 with TopHat2 (Kim et al., 2013). Gene expression levels were estimated by Cufflinks (Ghosh and Chan 2016). Genome DNA sequence and gene annotation were download from iGenome (ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Homo_sapiens/UCSC/hg19/Homo_sapiens_UCSC_hg19.tar.gz).
Genome_build: hg19
Supplementary_files_format_and_content: CSV format file which contained gene expression level (FPKM) of each sample.

source_name: human PBMC

extract_protocol:
PBMCs were isolated and total RNA was extracted by TRIzol.
Standard TruSeq mRNA library construction protocol was applied to construct cDNA library.

tag: disease

value: Fibrodysplasia Ossificans Progressiva

value: PBMC


title: FOP_1


title: FOP_2


title: EHEC in LB Experiment 2 [RNA-Seq]

city: Freising

first: Klaus

last: Neuhaus

address: Weihenstephaner Berg 3

department: Core Facility Microbiome/NGS

institute: Technische Universität München

data_processing:
Illumina fastq files were submitted to the galaxy pipeline => grooming => mapping to NC_002655 using bowtie2 (default but seed 19 nt & zero mismatches within seed)
Genome_build: NC_002655
Supplementary_files_format_and_content: Reads, RPKM, and RCV mapped to NC_002655 (RCV = Ribosomal Coverage Value = RPKM-footprint over RPKM-transcription)

organism: Escherichia coli O157:H7 str. EDL933

source_name: biomass collected in the transition between exponential to stationary phase

growth_protocol: LB medium, 180 rpm shaking, at 37°C, between exponential and stationary phase

extract_protocol:
Trizol for RNAseq, gradient centrifugation => RNase digestions => Trizol => gel extraction for RIBOseq
Truseq Small RNA
ligation, rt-PCR, PCR

tag: growth media

value: LB medium


title: EHEC in LB Experiment 2 [RIBO-Seq]

data_processing:
Library strategy: RIBO-seq
Illumina fastq files were submitted to the galaxy pipeline => grooming => mapping to NC_002655 using bowtie2 (default but seed 19 nt & zero mismatches within seed)
Genome_build: NC_002655
Supplementary_files_format_and_content: Reads, RPKM, and RCV mapped to NC_002655 (RCV = Ribosomal Coverage Value = RPKM-footprint over RPKM-transcription)


title: EHEC in LB Experiment 1 [RIBO-Seq]


title: CTRL_1

value: normal


title: CTRL_2


title: CTRL_3


title: Sample_P1wtRetina1.sorted

tag: strain


title: Sample_E16.5wtRetina1.sorted


title: Monocyte-derived Macrophages (Unexposed)

status: Public on Feb 17 2017

city: Cambridge

first: Alex

last: Shalek

state: MA

address: 77 Masachusetts Ave

department: Chemistry

institute: Massachusetts Institute of Technology

description: MTB.txt

data_processing:
Illumina bcl2fastq2.17.1.14 was used to generate fastqs from bcl files
STAR was used to align data to app
Aligned reads were collapsed to cell barcodes and UMIs using DropSeq Tools
See Sample_Processing_Pipeline.txt, for information regarding demultiplexing and alignment of each of the fastq files.
Digitial Gene Expression matrices were generated using DropSeq Tools
Genome_build: hg19/mm10 (Species Mixing1 and Species Mixing 2)
Genome_build: hg19 (PBMC, HEK, and MTB experiments)
Supplementary_files_format_and_content: [SpeciesMixing1_HumanUMI.txt] Filtered UMI DGE Matrix, Human Transcripts Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_MouseUMI.txt] Filtered UMI DGE Matrix, Mouse Transcripts Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_HumanReads.txt] Filtered Reads DGE Matrix, Human Reads Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing1_MouseReads.txt] Filtered Reads DGE Matrix, Mouse Reads Across 250 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_HumanUMI.txt] Filtered UMI DGE Matrix, Human Transcripts Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_MouseUMI.txt] Filtered UMI DGE Matrix, Mouse Transcripts Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_HumanReads.txt] Filtered Reads DGE Matrix, Human Reads Across 331 Cells
Supplementary_files_format_and_content: [SpeciesMixing2_MouseReads.txt] Filtered Reads DGE Matrix, Mouse Reads Across 331 Cells
Supplementary_files_format_and_content: [HEK_SingleCells.txt] Filtered UMI DGE Matrix, Human Transcripts Across 1453 Single HEK293 Cells
Supplementary_files_format_and_content: [HEK_Population.txt] Filtered UMI DGE Matrix, Bead-based Population RNA-Seq of 40,000 HEK293 Cells
Supplementary_files_format_and_content: [PBMC.txt] Filtered UMI DGE Matrix, 4296 PBMC Across 6713 Genes with cell type annotations
Supplementary_files_format_and_content: [MTB.txt] Filtered UMI DGE Matrix, 4638 Macrophages with cluster and exposure annotations

organism:
Homo sapiens
Mus musculus

extract_protocol:
[Seq-Well Protocol] Samples were processed as described in Gierahn et al. Nature Methods 2017.
Detailed Protocols at Nature Protocols Exchange DOI: 10.1038

value: Monocyte-Derived Macrophage

tag: exposure

value: Unexposed Control


title: Sample_P7retinaWT.sorted


title: Dox_HERIT_2of2


title: Species Mixing 1 (HEK + 3T3)

source_name: Species Mixing 1 (HEK + 3T3)


title: muscle_Pol II_Mut

city: Illkirch

first: Shilpy

last: Joshi

address: 1 Rue laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm9 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: ChIP DNA

extract_protocol:
Hind-limb muscles from wild-type and mutant (HSA::Cre-ERT2::Tead4lox/lox , Conditional muscle-specific Tead4 knockout) mice were minced and homogenised, fixed in 1% formaldehyde for 10 min at room temperature. Cross-linking was stopped by the adding Glycine to final concentration 0.125 M. The tissue lysate was further homogenized in hypotonic buffer in order to obtain nuclei, the nuclear pellet was washed once in hypotonic buffer and then resuspended in sonication buffer. Nuclear lysates were sonicated using Covaris E220 to obtain DNA fragments <500 bp. Chromatin was pretreated with blocked protein G sepharose beads. Subsequently, samples were incubated overnight at 4°C with antibodies to AcH3K27 (Active Motif) or RNA PoI II antibody (Santa cruz). Blocked beads were then added and the mixture was incubated for 2 h at 4°C. Prot G beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA was recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.

tag: strain background

tag: genotype/variation

value: conditional muscle-specific Tead4 knockout  (HSA::Cre-ERT2::Tead4lox/lox)

tag: tissue

value: Hind-limb muscles

tag: chip antibody

value: Pol II

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #


title: Mock_HERIT_1of2

tag: cell line

value: HE-RIT


title: Input_Mut

source_name: Input


title: muscle_H3K27_Mut

value: Active Motif


title: muscle_H3K27_WT


title: muscle_Pol II_WT


title: EHEC in LB Experiment 1 [RNA-Seq]


title: muscle_Tead4_Mut

value: Aviva


title: Input_WT

value: wild type


title: S1445_healthy_VCV_057

city: Dresden

first: Peter

middle: M

last: Spieth

address: Fetscherstraße 74

department: Klinik und Poliklinik für Anästhesiologie und Intensivtherapie

institute: Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden

description: Strand-specific RNA-Seq

data_processing:
[Basecalling] Illumina CASAVA-1.8.0
[Read Alignment] BWA VN:0.5.9-r32-MPI-patch2 against rn4 transcriptome (with exon-exon junction library based on Ensembl Gene v. 67 annotation)
[Counts per feature] Reads per gene were computed using bedtools version 2.11, based on Ensembl Gene v. 67 annotation (intersectBed -f 0.55 for non-split reads, -f 1 for split reads - falling on exon-exon junctions).
[Read count normalization] The raw read counts (absolute number of reads) were normalized with the DESeq R package (v.1.8.3).
Genome_build: rn4
Supplementary_files_format_and_content: .txt file with DESeq normalized counts per gene (rows) and sample (columns)

organism: Rattus norvegicus

extract_protocol:
Lung tissue was removed, flash frozen in liquid nitrogen and RNA was harvested using Qiagen RNeasy kit. mRNA was isolated using a bead-based poly-dT selection technique  (Sera Mag Oligo(dT) beads, Thermo Scientific). Library preparation was performed using NEBnext reagents (New England Biolabs).
Total RNA was isolated and quality controlled using the Bioanalyzer (Agilent). mRNA from 1 ug total RNA was isolated using bead based poly-dT selection followed by chemical fragmentation and further processing for Illumina short read sequencing. For strand specific sequencing the dUTP method according to Parkhomchuk et al. (Parkhomchuk D, Borodina T, Amstislavskiy V, Banaru M, Hallen L, Krobitsch S, Lehrach H, Soldatov A. Transcriptome analysis by strand-specific sequencing of complementary DNA. Nucleic Acids Res. 2009 Oct;37(18):e123) was applied using the NEBnext chemistries from NEB. All samples were barcoded and sequenced as a pool using the Hiseq 2000 platform from Illumina

value: Sprague Dawley

tag: study arm

value: ventilated animals with no previous lung injury

tag: mode of ventilation

value: volume-controlled ventilation with constant tidal volumes

value: Right upper lung lobe


title: S1440_healthy_VCV_025

description: Strand-specific RNA-Seq


title: S1450_chronic_noisy_079

description: Strand-specific RNA-Seq

value: animals ventilated after chronic lung injury

value: volume-controlled ventilation with variable tidal volumes


title: S1873_control_chronic_117

description: Strand-specific RNA-Seq

value: animals 14d after induction of chronic lung injury

value: without ventilation


title: S1448_chronic_noisy_075

description: Strand-specific RNA-Seq


title: S1505_healthy_noisy_029

description: Strand-specific RNA-Seq


title: S1511_chronic_VCV_067

description: Strand-specific RNA-Seq


title: S1870_control_chronic_114

description: Strand-specific RNA-Seq


title: S1871_control_chronic_115

description: Strand-specific RNA-Seq


title: S1869_control_chronic_113

description: Strand-specific RNA-Seq


title: S1872_control_chronic_116

description: Strand-specific RNA-Seq


title: S1510_healthy_VCV_062

description: Strand-specific RNA-Seq


title: S1514_chronic_VCV_073

description: Strand-specific RNA-Seq


title: S1515_healthy_noisy_078

description: Strand-specific RNA-Seq


title: S1509_healthy_noisy_061

description: Strand-specific RNA-Seq


title: Species Mixing 2 (HEK + 3T3)

source_name: Species Mixing 2 (HEK + 3T3)

tag: cell type


title: S1447_healthy_VCV_060

description: Strand-specific RNA-Seq


title: S1512_chronic_VCV_069

description: Strand-specific RNA-Seq


title: S1451_chronic_noisy_084

description: Strand-specific RNA-Seq


title: S1205_acute_VCV_040

description: Strand-specific RNA-Seq

value: animals with ventilation after acute lung injury


title: S1203_control_blank_016

description: Strand-specific RNA-Seq

value: animals without pre-existing lung injury


title: S1443_acute_noisy_047

description: Strand-specific RNA-Seq


title: S1444_acute_noisy_050

description: Strand-specific RNA-Seq


title: S1207_acute_VCV_049

description: Strand-specific RNA-Seq


title: S1206_acute_VCV_045

description: Strand-specific RNA-Seq


title: S1208_control_blank_074

description: Strand-specific RNA-Seq


title: S1507_acute_noisy_046

description: Strand-specific RNA-Seq


title: LPS-Stimulated TLR10 Donor 4

city: Urbana

first: Nicholas

middle: J.

last: Hess

state: IL

address: B103 CLSL MC110, 601 S. Goodwin Ave

department: Microbiology

institute: University of Illinois at Urbana-Champaign

data_processing:
The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 2500 using a HiSeq Rapid SBS sequencing kit version 2
Fastq files were generated and demultiplexed with the bcl2fastq v2.17.1.14 Conversion Software (Illumina), which also trims adaptors from the reads.
Any remaining adaptors, low-quality bases (< 28 phred) and resulting reads < 30 bp were trimmed using Trimmomatic v 0.33 with parametersILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.33/adapters/TruSeq3-SE.fa:2:15:10 LEADING:28 TRAILING:28 MINLEN:30
The single end reads were aligned to NCBI s GRCh38.p2 genome using STAR (v2.5.0a); index generation was done without gene models and default parameters. The gff3 of NCBI Homo sapiens Annotation Release 107 gene models was converted gtf format using the rtracklayer package (v 1.3.4), and a custom R script, which also put the Entrez Gene IDs in their own attribute named gene_id. Alignment was done using default parameters except --sjdbOverhang 99 and --outSAMtype BAM SortedByCoordinate. Counts per gene were generated using featureCounts from the subread program (v 1.5.0) with parameters -s 2 -g gene_id -t exon.
genome build: NCBI s GRCh38.p2

source_name: LPS-Stimulated TLR10

growth_protocol: Primary human monocytes were isolated from healthy human donor blood by STEMCELL Technologies RosetteSep Monocyte Enrichment Cocktail (#15068)

extract_protocol:
Lysates were prepared according to Qiagen's Rneasy Extraction Kit Protocol
Libraries were prepared with Illumina's TruSeq Stranded mRNAseq Sample Prep Kit (Illimunia)

treatment_protocol: Monocytes were treated with 10ug/mL of either the TLR10 or isotype control antibody for 10 min before 10ng/mL of LPS was added to cells in the stimulated condition

tag: subject status

value: healthy donor

tag: subject id

value: Donor 4

value: primary human monocytes

tag: treated with

value: 10ug/mL of TLR10 antibody for 10 min

tag: stimulated with

value: 10ng/mL of LPS


title: LPS-Stimulated TLR10 Donor 3

value: Donor 3


title: Unstimulated TLR10 Donor 1

source_name: Unstimulated TLR10

value: Donor 1

value: none (unstimulated control)


title: Unstimulated TLR10 Donor 2

value: Donor 2


title: LPS-Stimulated Control Donor 4

source_name: LPS-Stimulated Control

value: 10ug/mL isotype control antibody for 10 min


title: LPS-Stimulated Control Donor 1


title: Unstimulated Control Donor 4

source_name: Unstimulated Control


title: LPS-Stimulated Control Donor 3


title: LPS-Stimulated Control Donor 2


title: Unstimulated TLR10 Donor 3


title: LPS-Stimulated TLR10 Donor 1


title: S1204_control_blank_021

description: Strand-specific RNA-Seq

value: Sprague Dawley

value: Right upper lung lobe


title: Unstimulated Control Donor 1


title: Unstimulated Control Donor 2


title: MDS-1.12_Day 17+ 500 nM 5-AzaC

city: New York

first: Samir

last: Parekh

address: 1470 Madison Ave, 5th FL, Room 202

institute: Icahn School of Medicine at Mount Sinai, New York

description: iPSC cell line from low risk MDS pateint

data_processing:
Basecalls performed using CASAVA version 1.8.2
Used Bismark to align the filtered, adapter trimmed sequence reads to the bisulfite converted to reference human genome hg19 (whole genome alignment approach) and determined the methylation context for each cytosine.
Bismark returns methylation calls for cytosines in CpG, CHG, and CHH context.
The outputs are a methylation score file for each cytosine context with columns corresponding to: the position, strand, coverage, percent cytosine, and percent thymine, and for CHG and CHH context, a column for the next base (the H).
Generated BAM file of the aligned reads using Bismark’s bismark2SAM_v5_xm.pl and SAMTOOLS.
Genome_build: hg19
Supplementary_files_format_and_content:   These are tab delimited text files that contain the locations of C's in either CpG, CHG, or CHH, context and their methylation levels. The txt file contain sites with greater than or equal to 10x coverage for CpG, CHG, and CHH contexts. The minimum read coverage cutoff for this file is 10.

growth_protocol: MDS-1.12 cells used to assess  colony formation, were collected on day 14 of hematopoietic  differentiation and treated with 0, 100 nM and 500 nM 5-AzaC every day for 3 days.

extract_protocol:
Genomic DNA was extracted using Qiagen Dneasy kit
Genomic DNA was extracted and library fragment lengths of 150-250 bp  and 250-400 bp were prepared, gel isolated and sequenced on an Illumina Hi-seq 2500.
Enhanced reduced representation bisulfite sequencing (ERRBS)

treatment_protocol: MDS-1.12 cells were collected on day 14 of hematopoietic  differentiation and treated with 0, 100 nM and 500 nM 5-AzaC every day for 3 days.

value: Bonemarrow derived iPSC cell line


title: MDS-1.12_Day 17 + 100 nM 5-AzaC

source_name: iPSC cell line from low risk MDS pateint


title: MDS-1.12_Day 17


title: MDS-1.12_Day 16


title: MDS-1.12_Day 16 + 100 nM 5-AzaC


title: LPS-Stimulated TLR10 Donor 2


title: MDS-1.12_Day 16 + 500 nM 5-AzaC


title: P25 [RNA-seq]

first: Jin

last: Gu

address: FIT Building 1-112C

department: Automation

institute: Tsinghua University

data_processing:
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
Bowtie2 and Tophat2 for pair-end read mapping
Subread for raw read counts according to gene annotations
Use size factor to normalize raw counts
Genome_build: hg19
Supplementary_files_format_and_content: tab-limited text file for size-factor normalized read counts

source_name: PVTT

extract_protocol:
Samples were treated with 1mL TRIzol reagent (Life Technologies Cat.#15596-026) according to manufacturer's instructions. Nanodrop ND-1000 was used for RNA density/purity detection. Agilent BioAnalyzer 2100 was used for RNA quality control.
rRNA depletion was conducted before RNA-seq library preparation using TruSeq Stranded Total RNA Library Prep Kit (Illumina Cat.#RS-122-2302).

value: hepatocellular carcinoma (HCC) patient

tag: patient id

tag: gender

value: male

tag: age

tag: tumor size (cm)

tag: hbv infection

value: Yes

tag: cirrhosis

value: No

value: Portal vein tumor thrombosis (PVTT)


title: P24 [RNA-seq]

tag: tissue


title: P21 [RNA-seq]


title: Unstimulated TLR10 Donor 4

value: healthy donor

value: Donor 4


title: P26 [RNA-seq]


title: P19 [RNA-seq]


title: P18 [RNA-seq]


title: P16 [RNA-seq]


title: Unstimulated Control Donor 3

value: primary human monocytes


title: P14 [RNA-seq]

value: female


title: P13 [RNA-seq]


title: P20 [RNA-seq]


title: P12 [RNA-seq]


title: P17 [RNA-seq]


title: S1508_acute_noisy_053

description: Strand-specific RNA-Seq

tag: strain

value: animals with ventilation after acute lung injury

value: volume-controlled ventilation with variable tidal volumes


title: P10 [RNA-seq]


title: P11 [RNA-seq]


title: P6 [RNA-seq]


title: P8 [RNA-seq]


title: P3 [RNA-seq]


title: P7 [RNA-seq]


title: T26 [RNA-seq]

source_name: primary tumor

value: primary tumor


title: T24 [RNA-seq]


title: T25 [RNA-seq]


title: P22 [RNA-seq]


title: T21 [RNA-seq]


title: T22 [RNA-seq]


title: T20 [RNA-seq]


title: T19 [RNA-seq]


title: T17 [RNA-seq]


title: T15 [RNA-seq]


title: P15 [RNA-seq]


title: T16 [RNA-seq]


title: T14 [RNA-seq]


title: T10 [RNA-seq]


title: T3 [RNA-seq]


title: T11 [RNA-seq]


title: T7 [RNA-seq]


title: T8 [RNA-seq]


title: N26 [RNA-seq]

source_name: adjacent normal

value: adjacent normal


title: N25 [RNA-seq]


title: N19 [RNA-seq]


title: N22 [RNA-seq]


title: N21 [RNA-seq]


title: N24 [RNA-seq]


title: N18 [RNA-seq]


title: N16 [RNA-seq]


title: N17 [RNA-seq]


title: N15 [RNA-seq]


title: T13 [RNA-seq]


title: N20 [RNA-seq]


title: N14 [RNA-seq]


title: T18 [RNA-seq]


title: N12 [RNA-seq]


title: N11 [RNA-seq]


title: T12 [RNA-seq]


title: N10 [RNA-seq]


title: N7 [RNA-seq]


title: N6 [RNA-seq]


title: N3 [RNA-seq]


title: P26 miRNA-seq

data_processing:
Real Time Analysis (RTA) and CASAVA v1.8 for base-calling
miRDeep2 for mapping (bowtie) and processing
Use size factor to normalize raw counts
Genome_build: hg19
Supplementary_files_format_and_content: tab-limited text file for size-factor normalized read counts

source_name: Portal vein tumor thrombosis (PVTT)

extract_protocol:
Samples were treated with 1mL TRIzol reagent (Life Technologies Cat.#15596-026) according to manufacturer's instructions. Nanodrop ND-1000 was used for RNA density/purity detection. Agilent BioAnalyzer 2100 was used for RNA quality control.
Total RNA was treated mirVanaTM miRNA Isolation Kit (Life Technologies Cat.#AM1560).

tag: diagnosis

value: hepatocellular carcinoma (HCC)

value: Male


title: P20 miRNA-seq


title: P25 miRNA-seq


title: P22 miRNA-seq


title: P24 miRNA-seq


title: P21 miRNA-seq


title: P19 miRNA-seq


title: P15 miRNA-seq


title: P14 miRNA-seq

value: Female


title: P13 miRNA-seq


title: P17 miRNA-seq


title: P16 miRNA-seq


title: P11 miRNA-seq


title: P12 miRNA-seq


title: N13 [RNA-seq]


title: P18 miRNA-seq


title: P3 miRNA-seq


title: N8 [RNA-seq]


title: P6 miRNA-seq


title: P10 miRNA-seq


title: T6 [RNA-seq]


title: P8 miRNA-seq


title: T25 miRNA-seq


title: T26 miRNA-seq


title: T24 miRNA-seq


title: T20 miRNA-seq


title: T21 miRNA-seq


title: T19 miRNA-seq


title: T22 miRNA-seq


title: T18 miRNA-seq


title: T15 miRNA-seq


title: T16 miRNA-seq


title: T12 miRNA-seq


title: T7 miRNA-seq


title: T11 miRNA-seq


title: T8 miRNA-seq


title: P7 miRNA-seq


title: T10 miRNA-seq


title: N22 miRNA-seq


title: N25 miRNA-seq


title: N24 miRNA-seq


title: T3 miRNA-seq


title: N18 miRNA-seq


title: N26 miRNA-seq


title: N20 miRNA-seq


title: N19 miRNA-seq


title: T14 miRNA-seq


title: N21 miRNA-seq


title: N16 miRNA-seq


title: N13 miRNA-seq


title: N11 miRNA-seq


title: N10 miRNA-seq


title: T6 miRNA-seq


title: N12 miRNA-seq


title: N17 miRNA-seq


title: N15 miRNA-seq


title: T17 miRNA-seq


title: T13 miRNA-seq


title: N3 miRNA-seq


title: N8 miRNA-seq


title: N14 miRNA-seq


title: DGCR8HET - 1

city: Milano

first: Francesco

last: Nicassio

address: Via Adamello 16

department: Center for genomic science

country: Italy

institute: Istituto Italiano di Tecnologia

description:
small RNA sequecing Illumina
DGCR8_S9810_index3

data_processing:
Data were analyzed with the IsomiRAGE tool,  a desktop application that counts the number of occurrences of small RNA molecules in a Bowtie .map alignment file.
FASTQ data of the small RNA sequencing experiment were trimmed to remove adapter sequences and aligned to custom sequence libraries listing all isoforms of small RNA molecules.
Alignment of trimmed FASTQ data was performed using Bowtie with --best and -v 0 switches and saved in .map output format.
Custom library was built using miRBASE21 database of mouse microRNAs
Genome_build: GRCm38
Supplementary_files_format_and_content: Excel Spreadsheet containing the raw counts of each IsomiR

source_name: CORTEX

extract_protocol:
Total RNA, including small species, was isolated through the miRNeasy mini kit (Qiagen).
1000 nanograms of total RNA were used to prepare Small RNA libraries following the Illumina TruSeqTM Small RNA kit instructions

tag: delelopmental stage

tag: genotype/variation

value: DGCR8 heterozygote


title: DICER KO - 1

description:
small RNA sequecing Illumina
DICER_S9810_index3

value: Dicer knock out


title: Dicer WT - 2

description:
small RNA sequecing Illumina
DICER_S9810_index2

value: Dicer wild type


title: DGCR8 WT - 1

description:
small RNA sequecing Illumina
DGCR8_S9810_index1

value: DGCR8 wild type


title: DGCR8 HET - 2

description:
small RNA sequecing Illumina
DGCR8_S9810_index4


title: DGCR8 KO - 2

description:
small RNA sequecing Illumina
DGCR8_S9810_index6

value: DGCR8 knock out


title: Dicer WT - 1

description:
small RNA sequecing Illumina
DICER_S9810_index1


title: DGCR8 WT - 2

description:
small RNA sequecing Illumina
DGCR8_S9810_index2


title: HFL-1 siTAZ #1, rep2

city: Tokyo

first: Satoshi

last: Noguchi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Respiratory Medicine

country: Japan

institute: Graduate School of Medicine, The University of Tokyo

data_processing:
BAM Alignment to Hg19 (TMAP version 3.4.1, the Torrent Mapping Alignment Program for Ion Torrent Data)
Read count analysis (HTseq version 0.6.1, Ensemble annotation)
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text file include raw read count values for each Sample

source_name: siTAZ #1

growth_protocol: Standard HFL-1 growth condition.

extract_protocol:
RNeasy mini kit (Qiagen) was used for total RNA extraction.
RNA libraries were prepared for sequencing using standard Ion Torrent protocols

treatment_protocol: Cells were transfected with siRNA, using Lipofectamine RNAiMAX (Invitrogen), according to the manufacturer’s instructions.Total RNA was extracted from HFL-1 cells 48h after transfection.

tag: cell line

tag: transfection

value: siTAZ #1


title: HFL-1 siTAZ #2, rep2

source_name: siTAZ #2

value: siTAZ #2


title: HFL-1 siTAZ #2, rep1


title: HFL-1 siTAZ #1, rep1


title: HFL-1 siNTC, rep2

source_name: siNTC

value: siNTC


title: Monocyte-derived Macrophages (Mtb Exposed, MOI=10)

description: MTB.txt

tag: cell type

value: Monocyte-Derived Macrophage

tag: exposure

value: M. tuberculosis H37rv, MOI=10


title: HFL-1 siNTC, rep1


title: DICER KO - 2

description:
small RNA sequecing Illumina
DICER_S9810_index4


title: SIRT7 RIP RNA, ribo-zero rep1

city: Ithaca

first: Jennifer

middle: K

last: Grenier

address: 526 Campus Rd

department: Biomedical Sciences

institute: Cornell University

description: SIRT7-RIP RNA

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
bowtie2 v2.2.6 (default params) was used to divide reads into 2 sets: matching and not matching rRNA (and other noncoding, non-polyA+ RNAs such as microRNAs, snoRNAs, snRNAs, etc).
tophat v2.0.13 (--no-novel-juncs --library-type fr-firststrand) was used to map non-rRNA reads to the Human hg19 reference genome (UCSC).
cuffquant (--no-novel-juncs --library-type fr-firststrand) was used to quantify transcripts based on the Human hg19 reference transcriptome (UCSC).
cuffdiff v2.2.1 (--library-type fr-firststrand) was used to call differentially expressed genes based on the Human hg19 reference transcriptome (UCSC).
Genome_build: Human hg19 (UCSC)
Supplementary_files_format_and_content: Tab delimited text files including counts, FPKM values, and p-values generated from Cuffdiff2 when corrected for multiple hypothesis testing

source_name: HEK 293T stably overexpressiong Flag-SIRT7

growth_protocol: HEK293T cells stably overexpressing Flag-tagged SIRT7 were cultured in DMEM supplemented with 10% FBS (fetal bovine serum) and penicillin-streptomycin

extract_protocol:
The total cellular RNA was extracted by TRI reagent according to manufacturer's instruction. For the extraction of total SIRT7-RIP RNA, we performed RIP (RNA immunoprecipitation) experiment. Briefly, the lysates were incubated with anti-Flag M2 affinity gel to immunoprecipitate SIRT7 ribonucleoprotein complex (RNP) . Anti-Flag beads were washed extensively and then subjected to proteinase K digestion to release RNA from SIRT7 RNP. RNA associated with SIRT7 was then extracted by standard phenol-chloroform extraction followed with ethanol precipitation. Ribosomal RNA was substracted from both input cellular RNA and SIRT7-RIP RNA during library construction with the Ribozero Gold HMR kit (Illumina).
Directional RNA-seq libraries were prepared from 25-100ng rRNA-subtracted RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).

value: HEK 293T

tag: overexpression construct

tag: passages


title: HEK Population

source_name: HEK Population


title: N7 miRNA-seq

city: Beijing

value: Yes


title: SIRT7 RIP RNA, ribo-zero rep2

description: SIRT7-RIP RNA


title: SIRT7 RIP RNA, nucleus rep2

description: SIRT7-RIP RNA, nuclear fraction

data_processing:
Illumina pipeline software v1.8 was used for base calling.
cutadapt v1.5 (-m 20 -q 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTC --match-read-wildcards) was used to trim and filter reads.
bowtie2 v2.2.6 (default params) was used to map reads matching human rRNA genes (45S, 5S, MT 12S, MT 16S).
samtools mpileup v1.3 was used to compile coverage counts per nucleotide for rRNA genes
Genome_build: NR_046235.1 (45S), NR_023363.1 (5S), NC_012920.1: gi|251831106:1671-3229 (MT 16S), gi|251831106:648-1601 (MT 12S)
Supplementary_files_format_and_content: samtools mpileup counts per position for rRNA genes (txt file)

source_name: HEK 293T stably overexpressing Flag-SIRT7

extract_protocol:
For the extraction of total SIRT7-RIP RNA, we first fractionated cell lysates into cytosolic and nuclear fractions and then performed RIP (RNA immunoprecipitation) experiment. Briefly, the lysates were incubated with anti-Flag M2 affinity gel to immunoprecipitate SIRT7 ribonucleoprotein complex (RNP) . Anti-Flag beads were washed extensively and then subjected to proteinase K digestion to release RNA from SIRT7 RNP. RNA associated with SIRT7 was then extracted by standard phenol-chloroform extraction followed with ethanol precipitation.
Directional RNA-seq libraries were prepared from 25-100ng input RNA using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs).


title: N6 miRNA-seq


title: DGCR8 KO - 1

description:
small RNA sequecing Illumina
DGCR8_S9810_index5


title: total input RNA, ribo-zero rep1

description: input


title: SIRT7 RIP RNA, nucleus rep1

description: SIRT7-RIP RNA, nuclear fraction


title: SIRT7 RIP RNA, cytosol rep1

description: SIRT7-RIP RNA, cytosolic fraction


title: SIRT7 RIP RNA, cytosol rep2

description: SIRT7-RIP RNA, cytosolic fraction


title: HEK Single cells

source_name: HEK Single cells


title: PBMC Sample

source_name: PBMC Sample

value: PBMC


title: total input RNA, ribo-zero rep2

description: input


title: PB naïve CD8SP R2 beta

city: Pasadena

first: Michael

middle: T

last: Bethune

address: 1200 E California Ave, MC147-75

department: BBE

institute: California Institute of Technology

description: focused cDNA library of TCR alpha and beta sequences

data_processing:
After demultiplexing using sample-specific barcodes, TCR rearrangements were aligned to a custom library of all human TCR germline sequences using BLAT
Best hits from alignment were identified with the psICDnaFilter utility of the BLAT suite using '-maxAligns=1 - ignoreIntrons' options
Clonotype frequencies were calculated using custom Perl scripts (available upon request)
Genome_build: Custom reference sequence library (available upon request) comprising all human TRAV, TRAJ, TRBV, TRBD, and TRBJ sequences contained in the IMGT database (http://www.imgt.org)
Supplementary_files_format_and_content: tab-delimited text files include counts and frequencies of unique clonotypes for each sample

source_name: PB

extract_protocol:
Cells were lysed in RLT buffer and RNA was extracted using Qiagen RNEasy Micro kit per manufacturer's protocol
A focused TCRαβ cDNA library was prepared using the Clontech SMARTer PCR cDNA synthesis kit according to a gene-specific modification of the manufacturer's protocols. cDNA was reamplified with a semi-nested strategy to introduce sample barcodes and 8 barcoded sample libraries (4 alpha, 4 beta) were pooled prior to Illumina adaptor ligation.

value: peripheral blood

value: Naive CD8 T cell

tag: phenotype

tag: method

value: Adult peripheral blood mononuclear cells were isolated and cells of the indicated phenotype sorted by FACS


title: PB naïve CD8SP R1 beta


title: PB naïve CD8SP R2 alpha


title: Thymus naïve CD8SP R2 alpha

source_name: Thymus

value: thymus

value: Neonatal thymocytes were isolated and cells of the indicated phenotype sorted by FACS


title: PFD-450-1FL1R1

city: Palmerston North

first: Helge

last: Dzierzon

address: Bachelar Road

department: Bioinformatics

country: New Zealand

institute: Plant and Food Research Ltd.

description:
biological rep: 1
processed data file: PFD Galaxy588.txt

data_processing:
Data was processed using the Galaxy pipeline
First sequences were trimmed (14 bp removed from the 5’ end, 5 from the 3’ end leaving about 105 bp). Data were converted to the Sanger format using FASTQ Groomer, filtered by quality and Bowtie2 run to align reads to Arabidopsis mRNA data from TAIR 10.
The status of the alignment file checked by Flagstat. Over 92 to 95% of reads were of acceptable quality. The protocol SAM/BAM to counts was then applied to count the number of aligned sequences that matched selected genes in the Arabidopsis TAIR10 database
Genome_build: TAIR10_cdna_20101214
Supplementary_files_format_and_content: Txt files tab delinated, count against arabidopsis genes

organism: Arabidopsis thaliana

source_name: Leaf tissue

growth_protocol: A. thaliana ‘Columbia’ plants were grown for 6 weeks in two controlled environment rooms at the New Zealand Controlled Environment Laboratory. After 4 weeks, the plants were uniform, with a ~50 mm diameter rosette and 13 leaves. At this stage, environmental conditions were adjusted to stress the plants. The PFD was increased in the rooms to 700 µmoles photons m-2 s-1 for 10 h photoperiod, and four levels of light using three levels of shade cloth were established (plus unshaded) providing PFDs at plant height of 100, 250, 450 and 700 µmoles m-2 s-1. The temperature were diurnal of 23°C day and 5°C night. Other conditions were the same as for the establishment period, except VPD was 0.3 kPa for the low night temperature room.

extract_protocol:
Approximately 100 mg of ground plant material were extracted using the Sigma-Aldrich Spectrum Plant Total RNA kit using the protocol described by Sigma-Aldrich. RNA was then treated with DNAse RNA quality was assessed using a Nanodrop 1000 spectrophotometer (Thermofisher Scientific) as well as a 2100 Bioanalyzer system (Agilent), using samples with a RNA integrity number > 7. Samples within a time period and treatment were randomly combined to create two replicates per treatment measured.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: After 2 weeks of growth under these conditions, destructive harvests were made over the next 48 h as described in the results. Plants were harvested at one time point over the four PFD levels (PFD treatment); plants grown at 250 µmoles m-2 s-1 were harvested over two diurnal cycles at approximately 3 h intervals (diurnal treatment); and plants were also subjected to a step change in PFD from 100 to 700 for approximately 20 h (step treatment). Depending on the treatment between four (PFD transfer and some diurnal measurements) and six (PFD response and some diurnal measurements) separate plants were harvested as replicates and processed separately for RNA extraction. RNA samples were pooled to create two biological replicates after the separate RNA extraction. Harvested rosettes were rapidly wrapped in aluminium foil and immersed in liquid nitrogen to freeze samples. Leaf samples were powdered under liquid nitrogen and were transferred to storage at- 80°C until further processing.

value: leaf

tag: ecotype

value: Columbia

tag: treatment

value: Growth light; light intensity:450; days:0.583


title: PFD-700-1FL1R1

value: Growth light; light intensity:700; days:0.583


title: PFD-250-2FL2R2

description:
biological rep: 2
processed data file: PFD Galaxy588.txt

value: Growth light; light intensity:250; days:0.583


title: PFD-700-2FL1R2


title: PFD-250-1FL2R1


title: PFD-450-2FL2R2


title: PFD-450-1FL2R1


title: Thymus naïve CD8SP R1 beta


title: PFD-250-1FL1R1


title: PFD-100-2FL2R2

value: Growth light; light intensity:100; days:0.583


title: PFD-700-2FL2R2


title: PB naïve CD8SP R1 alpha


title: PFD-100-1FL2R1


title: PFD-700-1FL2R1


title: Thymus naïve CD8SP R1 alpha


title: PFD-100-1FL1R1


title: PFD-450-2FL1R2


title: CB ATO CD8SP R1 alpha

source_name: CB ATO

value: cord blood in artificial thymic organoid

value: ATO-derived naive CD8 T cell

value: Sorted CB CD34+CD3- HSPCs were cultured in MS5-hDLL1 ATOs for 6-8 weeks followed by FACS sorting for the indicated phenotype


title: PFD-250-2FL1R2


title: Diurnal-0.916-2FL2R2

description:
biological rep: 2
processed data file: Diurnal_Galaxy590.txt

value: Diurnal serries; light intensity:250; days:0.916


title: PFD-100-2FL1R2


title: Thymus naïve CD8SP R2 beta


title: G010_Zika-2

city: Galveston

first: Ping

last: Wu

state: Texas

address: 301 University Blvd

institute: University of Texas Medical Branch

data_processing:
Illumina bcl2fastq v2.17.1.14  was used for base calling.
Human hg38 reference genome and the hg38.gtf annotation file were downloaded from iGenome. http://support.illumina.com/sequencing/sequencing_software/igenome.html
Reads were mapped to the human hg38 genome using STAR v2.5.1b with parameters (--runThreadN 10 --outSAMtype BAM Unsorted SortedByCoordinate --outSAMstrandField intronMotif --outFilterType BySJout --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMax 1000000  --alignMatesGapMax 1000000 --quantMode GeneCounts).
Differential gene expression was determined with Cufflinks v2.2.1 using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: Tab delimited text file output from cuffdiff containing FPKM values, log2 fold-change and FDR adjusted p-values.

source_name: Cell line G010, primary human fetal brain-derived neural stem cells

extract_protocol:
Total cellular RNA was extracted using  RNAqueous™ phenol-free total RNA isolation kits (Life Technologies, CA) according to the manufacturer’s recommendations
RNA sequencing libraries were generated from ~1 ug total RNA using the illumina TruSeq RNA kit v2, according to the manufacturers' directions

value: ZIKV Infected


title: G010_Zika-3

value: primary human fetal brain-derived neural stem cells


title: CB ATO CD8SP R2 beta


title: G010_Zika-1


title: CB ATO CD8SP R2 alpha


title: G010_Control-3

value: Mock Infected


title: Diurnal-0.916-2FL1R2


title: K054_Control-1

source_name: Cell line K054, primary human fetal brain-derived neural stem cells


title: K054_Control-3


title: G010_Control-1


title: G010_Control-2


title: K054_Zika-3


title: K054_Zika-2


title: Diurnal-0.625-2FL2R2

value: Diurnal serries; light intensity:250; days:0.625


title: K054_Zika-1


title: Diurnal-0.625-2FL1R2


title: K054_Control-2


title: K048_Zika-3

source_name: Cell line K048, primary human fetal brain-derived neural stem cells


title: K048_Zika-2


title: Diurnal-0.625-1FL2R1

description:
biological rep: 1
processed data file: Diurnal_Galaxy590.txt


title: K048_Zika-1


title: Diurnal-0.625-1FL1R1


title: K048_Control-2


title: K048_Control-1


title: K048_Control-3


title: Diurnal-0.375-2FL1R2

value: Diurnal serries; light intensity:250; days:0.375


title: Diurnal-0.375-2FL2R2


title: Diurnal-0.916-1FL2R1


title: deltaSnf2_rep2 (RNA-Seq)

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

data_processing:
Illumina data was processed for all samples with RTA 1.17.21.3 and CASAVA 1.8.2 from Illumina.
ChIP-seq data was aligned to sacCer2 genome from UCSC with bowtie2 (2.1.0) with -k 1.
MNase-seq paired-end data was aligned to sacCer2  with bowtie2 (2.1.0). Same-fragment reads from fragments sized between 100 and 200 were centered at their midpoint and resized to the 73 middle bases, then normalized to reads per million for the bigWig files.
RNA-seq data was aligned to sacCer2 with a gtf file from Ensembl 63 using tophat (2.0.10) with --segment-mismatches 1 -x 1 -g 1 --no-coverage-search.
Any downstream analysis and bigWig file generation was done in R.
Genome_build: sacCer2
Supplementary_files_format_and_content: bigWig files were created in all cases by reading in bam files, normalizing to reads per million by multiplying by 1 million and dividing by the total number of alignments. For RNA-seq (strand specific protocol), data was split into positive (forward) and negative (reverse) strands for the bigWIg files.

growth_protocol: Cells were grown in YPD

extract_protocol:
For RNA-seq, RNA was isolated and Ribo-depleted.
ChiP-seq, Mnase-seq, RNA-seq libraries were prepared using KAPA High Throughput Library Preparation Kit, Roche.

treatment_protocol: Cells were grown in YPD to Abs ~0.8 and crosslinked for ChIP and Mnase, harvested without crosslinking for isolating RNA

value: Snf2 deletion

tag: sample extract

value: Ribo-depleted RNA


title: taf14_rep2 (RNA-Seq)

value: Taf14 deletion


title: deltaSnf2_rep1 (RNA-Seq)


title: taf14_rep1 (RNA-Seq)


title: Diurnal-0.916-1FL1R1

value: leaf

value: Columbia


title: Diurnal-0.375-1FL1R1


title: Diurnal-0.25-2FL2R2

value: Diurnal serries; light intensity:250; days:0.25


title: Diurnal-0.375-1FL2R1


title: Diurnal-0.25-1FL1R1


title: Diurnal-0.25-2FL1R2


title: swp82_rep1 (RNA-Seq)

value: Swp82 deletion


title: rtt102_rep1 (RNA-Seq)

value: Rtt102 deletion


title: snf11_rep1 (RNA-Seq)

value: Snf11 deletion


title: rtt102_rep2 (RNA-Seq)


title: swp73_rep1 (RNA-Seq)

value: Swp73 deletion


title: swp82_rep2 (RNA-Seq)


title: snf11_rep2 (RNA-Seq)


title: swi3_rep2 (RNA-Seq)

value: Swi3 deletion


title: swp73_rep2 (RNA-Seq)


title: snf6_rep2 (RNA-Seq)

value: Snf6 deletion


title: Diurnal-0.083-2FL2R2

value: Diurnal serries; light intensity:250; days:0.083


title: Diurnal-0.083-2FL1R2


title: snf5_rep2 (RNA-Seq)

value: Snf5 deletion


title: Diurnal-0.083-1FL2R1


title: snf5_rep1 (RNA-Seq)


title: Diurnal-0.083-1FL1R1


title: snf6_rep1 (RNA-Seq)


title: Dirnal-0.75-2FL1R2

value: Diurnal serries; light intensity:250; days:0.75


title: Dirnal-0.75-2FL2R2


title: Diurnal-0.25-1FL2R1


title: 2Swp73Snf2IP (ChIP-Seq)

extract_protocol:
Yeast whole cell extract were sonicated DNA-protein complexes were isolated with Snf2-C'antibody (kind gift from Joseph Reese Pennsylvania State University: antibody raised in Reese lab) .
ChiP-seq, Mnase-seq, RNA-seq libraries were prepared using KAPA High Throughput Library Preparation Kit, Roche.

value: WCE

tag: chip antibody

value: Snf2 C' Ab (antibody raised in Reese lab)


title: 1Snf11Snf2IP (ChIP-Seq)


title: 1Swp73Snf2IP (ChIP-Seq)


title: Dirnal-0.75-1FL1R1

tag: tissue


title: 2Swp82Snf2IP (ChIP-Seq)


title: Dirnal-0.75-1FL2R1


title: 2Snf11Snf2IP (ChIP-Seq)


title: swi3_rep1 (RNA-Seq)


title: Change-2.57-1FL2R1

description:
biological rep: 1
processed data file: Change_Galaxy592.txt

value: light change; light intensity:700; days:2.57


title: 1Swp82Snf2IP (ChIP-Seq)


title: Change-2.57-2FL2R2

description:
biological rep: 2
processed data file: Change_Galaxy592.txt


title: Change-0.60-2FL2R2

value: light change; light intensity:700; days:0.6


title: 2Snf6Snf2IP (ChIP-Seq)


title: Change-0.60-1FL2R1


title: wt_rep2 (RNA-Seq)

source_name: wt

value: WT

value: Ribo-depleted RNA


title: 1Snf6Snf2IP (ChIP-Seq)


title: 1Swi3Snf2IP (ChIP-Seq)


title: Change-0.60-1FL1R1

value: leaf

value: Columbia


title: 1Snf5Snf2IP (ChIP-Seq)


title: 2Snf5Snf2IP (ChIP-Seq)


title: 2WTSnf2IP (ChIP-Seq)


title: 1WTSnf2IP (ChIP-Seq)


title: 1Snf11IN (ChIP-Seq)

value: none (input)


title: Change-2.57-2FL1R2


title: 2Snf11IN (ChIP-Seq)


title: Change-2.57-1FL1R1


title: 2Swi3Snf2IP (ChIP-Seq)


title: wt_rep1 (RNA-Seq)


title: 2Swp82IN (ChIP-Seq)

value: Swp82 deletion


title: rep2 siT1/4 D3 SPJH58

data_processing:
Base calling : Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2
Alignment : Reads were mapped to mm9 assembly of mouse genome using Tophat v2.0.10 and bowtie2 v2.1.0 aligner
Quantification of gene expression was performed using HTSeq v0.6.1 (Anders et al., 2014) using  gene annotations from Ensembl release 67.
Comparisons of interest were performed using the method proposed by Love et al (2014) and  implemented in the DESeq2 Bioconductor library (DESeq2 v1.8.1), taking into account the batch,  treatment and day effects
Genome_build: mm9
Supplementary_files_format_and_content: The processed data file is a tabulated text with the following columns : Ensembl gene id, Gene name and one column for each sample containing the normalized read counts (normalization was done using the size factors calculated with DESeq2 v1.8.1 Bioconductor package).

source_name: C2C12 cells

growth_protocol: Both C2C12  cells and primary myoblasts were transfected with control and Tead1/Tead4 siRNA and following which cells were subjected to 2% HS medium in order to differentiate.RNA was isolated from non differentiated cells 24hrs after transfection and at day 3 &day 6 of differentiation. Samples from duplicate biological replicates were subjected to RNA-seq analysis.

extract_protocol: After isolation of total cellular RNA fromthe above 24 samples, libraries of template molecules suitable for high throughput DNA sequencing were created using “TruSeq™ RNA Sample Preparation v2 Kit” (Illumina). Briefly, mRNA was purified from 2 µg of total RNA using poly-T oligo-attached magnetic beads and fragmented using divalent cations at 94°C for 8 minutes. The cleaved mRNA fragments were reverse transcribed to cDNA using random primers then the second strand of the cDNA was synthesized using DNA Polymerase I and RNase H. The double stranded cDNA fragments were blunted using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK. A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments using a Klenow fragment (3' to 5'exo minus) enzyme. The cDNA fragments were ligated to double stranded adapters using T4 DNA Ligase. The ligated products were enriched by PCR amplification (30 sec at 98°C; [10 sec at 98°C, 30 sec at 60°C, 30 sec at 72°C] x 12 cycles; 5 min at 72°C). Then surplus PCR primers were removed by purification using AMPure XP beads (Agencourt Biosciences Corporation). DNA libraries were checked for quality and quantified using 2100 Bioanalyzer (Agilent).

treatment_protocol: Total RNA was extracted using Sigma total RNA extraction kit

value: myoblasts

tag: strain


title: 2Swi3IN (ChIP-Seq)


title: 1Swp82IN (ChIP-Seq)


title: rep2 siT1/4 D6 SPJH59


title: 1Swi3IN (ChIP-Seq)


title: 2Snf6IN (ChIP-Seq)


title: rep2 siT1/4 D0 SPJH57


title: 1Swp73IN (ChIP-Seq)

value: Swp73 deletion


title: rep2 siLuc D6 SPJH56


title: rep2 siLuc D3 SPJH55


title: 1Snf6IN (ChIP-Seq)


title: 2Snf5IN (ChIP-Seq)


title: 1Snf5IN (ChIP-Seq)


title: 2WTIN (ChIP-Seq)


title: rep1 siT1/4 D0 SPJH48


title: rep1 siT1/4 D6 SPJH50


title: rep1 siT1/4 D3 SPJH49


title: 1WTIN (ChIP-Seq)


title: rep1 siLuc D6 SPJH47


title: 2Swp73IN (ChIP-Seq)


title: rep1 siLuc D0 SPJH45


title: rep2 siT1/4 D6 SPJH35

source_name: Primary myoblasts


title: rep2 siLuc D3 SPJH31


title: rep1 siT1/4 D3 SPJH25


title: rep1 siT1/4 D6 SPJH26


title: CB ATO CD8SP R1 beta

value: cord blood in artificial thymic organoid

value: ATO-derived naive CD8 T cell

value: Sorted CB CD34+CD3- HSPCs were cultured in MS5-hDLL1 ATOs for 6-8 weeks followed by FACS sorting for the indicated phenotype


title: rep1 siLuc D3 SPJH46


title: rep2 siT1/4 D3 SPJH34


title: rep2 siT1/4 D0 SPJH33


title: rep2 siLuc D0 SPJH30


title: rep1 siT1/4 D0 SPJH24


title: Change-0.60-2FL1R2


title: rep1 siLuc D3 SPJH22


title: rep1 siLuc D0 SPJH21


title: C2C12_Diff_TEAD1

data_processing:
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie -m 1 --strata --best -y -S -l  40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)

extract_protocol: ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.

treatment_protocol: C2C12 cells were harvested either in non-differentiated or differentiated state and resuspended in sonication buffer for 10 mins and then sonicated using covarys sonicator. Muscle from hind limbs of three wil-type B6 were minced and homogenised, fixed in 1% formaldehyde and incubated for 10 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in hypotonic buffer inorder to obtain nuclei, the nuclear pellet was resuspended in sonication buffer and were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with blocked protein G sepharose beads. Subsequently, samples were incubated overnight at 4°C with antibodies to AcH3K27 (Abcam, ab4729) or 7C2 RNAPII antibody. Blocked beads were then added and the mixture was incubated for 2 h at 4°C. Prot G beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.

value: myotubes

value: TEAD1 BD Biosciences


title: C2C12_ND_Input

value: No antibody


title: muscle_Tead4

source_name: muscle

value: muscle

value: TEAD4 Aviva


title: muscle_input


title: muscle_Pol II

value: Pol II


title: rep2 siLuc D0 SPJH54


title: rep2 siLuc D6 SPJH32


title: C2C12_ND_TEAD4


title: Mutant rep3

city: Taipei

first: Cheng-Yen

last: Kao

address: Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang Ming University, No.155, Sec. 2, Linong St., Beitou Dist

institute: National Yang Ming University

description:
delta_5
Processed data file: RNA-seq_Summary.xls

data_processing:
The 50-base short read sequences produced by the 5500XL SOLiD™ sequencer were first run through SOLiD Accuracy Enhancement Tool (SAET) to improve color call accuracy.
Mapped in color space using SOLiD™ LifeScope™ software version 2.5 using default parameters against the H. pylori J99 reference genome (NCBI RefSeq accession number, NC_000921.1).
The BAM file from LifeScope was performed the analysis of gene expression with Partek software package.
The gene expression from each sample was then tested separately for statistical differences using one-way ANOVA at 5% confidence level.
Gene expression of the csrA mutant compared to wild-type J99 with a fold change > 1.5-fold was selected and confirmed by RT-qPCR.
Genome_build: H. pylori J99 reference genome (NC_000921.1)
Supplementary_files_format_and_content: RNA-seq_Summary.xls

organism: Helicobacter pylori J99

source_name: csrA mutant

growth_protocol: H. pylori cells were grown on CDC plates in microaerophilic conditions for 36 h, then transferred to 100 ml Brucella broth containing 10% (v/v) horse serum at an optical density of 0.2 and incubated with shaking (180 rpm, reduce cell aggregation) for 18 h in microaerophilic conditions.

extract_protocol:
Mini Qiagen columns and a Qiagen RNeasy mini kit (Qiagen, Valencia, CA) were used for RNA extraction. Ribosomal RNA was depleted according to the manufacturer's instruction using Bacteria MinusTM Transcriptome Isolation Kit (Invitrogen Life Technologies).
The Applied Biosystems SOLiD™ Total RNA-Seq kit was used to generate the cDNA template library.

tag: strain/background

value: csrA mutant


title: H39236/TMD-8_+_1uM_ID_clone_2F6D5_L4.D702

city: Foster City

first: Li

last: Li

address: 333 Lakeside Drive

institute: Gilead Sciences

data_processing:
Clipping adapters and low-quality bases.
BWA
RSEM
edgeR
limma
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include log2(CPM) values for each Sample

growth_protocol: Idela-sensitive TMD8 clones were cultured in RPMI-1640 medium supplemented with 20% FBS, 100 U/mL penicillin, and 100 pg/mL  streptomycin (Life Technologies). Idela-resistant TMD8 clones were cultured in the same growth media but supplemented with 1 µM idelalisib.  Cultures were grown in a humidified atmosphere of 5% CO2 and 95% air at 37°C.

extract_protocol:
1 x 10^7 cells were harvested by centrifugation.  Pellets were resuspended in 1 mL of PBS, transferred to eppendorf tubes and pelleted again.  Pellets were resuspended in 150 uL of QIAGEN RLT buffer and frozen (-80'C).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Idela 1uM

value: Diffuse Large B Cell Lymphoma


title: H39236/TMD-8_+_1uM_ID_clone_3D8B9_L4.D703


title: H39236/TMD-8_DMSO_P8_clone_2C6B5_L5.D709

value: DMSO


title: H39236/TMD-8_+_1uM_ID_clone_1E6D5_L1.D712


title: Input

city: Bethesda

first: Stacie

last: Loftus

address: 49 Convent Dr

institute: National Human Genome Research Institute

data_processing:
Alignment was performed using BWA-MEM
ChIP-Seq peaks for each experimental replicate were called independently using the Model-based Analysis for ChIP-Seq (MACS v1.4.2) algorithm by applying default settings and a significance p-value threshold of 1.00e-05, except for H3K27me3 where the broad peak parameters were applied as follows: macs14 -t chip.bam -c input.bam -name = chip_output -format = BAM -gsize = mm -tsize = 50 -bw = 300 -mfold = 10,30 -nolambda -nomodel -shiftsize = 150 --pvalue=1.00e-05.
Only ChIP-Seq profiles that showed reproducible overlap between both experimental samples were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: narrowPeak (i.e., BED6+4)  file with Chip-seq peak regions and the columns represent; chrom, chromStart, chromEnd, name, score, strand, signalValue, pValue, qValue, peak and bigwig file

source_name: melan-a cells

growth_protocol: According to guidelines from Bennett et al. 1987 (PMID 3102392), cells were grown in RPMI 1640 medium supplemented with 10% fetal bovine serum (Gibco), 200 nM 12-O-tetradecanoylphorbol 13-acetate (Sigma-Aldrich, St Louis, MO, USA) and 200 pM cholera toxin (Sigma- Aldrich, St Louis, MO, USA) at 37°C in humidified air with 10% CO2.

extract_protocol:
Approximately 2 x 107 cells were harvested and crosslinked at room temperature with 1% formaldehyde for 10 minutes. Crosslinking reaction was quenched with the addition of glycine to a final concentration of 125 mM for at least 15 minutes. Crosslinked cells were lysed on ice using 1 ml low-salt ChIP buffer (150 mM NaCl, 50 mM Tris-HCl (pH 7.5), 5 mM EDTA, 0.5% NP-40, 1.0%Triton X-100) and sonicated using a Qsonica Sonicator Q500 (Newtown, CT 0647) with the following settings: 70% amplitude; 10 seconds on/20 seconds off cycles; total sonication time of 35 minutes. Sonicated samples were centrifuged and the soluble chromatin (supernatant) was used for chromatin immunoprecipiation reactions. Briefly, 200 µl of lysate (~ 2 x 106 cells) was incubated with each  antibody and immunoprecipitated chromatin was recovered using recombinant protein G beads or magnetic Dynabeads® (Invitrogen). ChIP samples were reverse crosslinked and DNA was purified using the phenol-chloroform extraction method.
Aliquots of input (total genome) and ChIP DNA obtained from two independent experiments per antibody were used for ChIP library construction and high-throughput sequencing, per Illumina protocols.

treatment_protocol: no treatments

value: Normal embryonic skin

value: Cdkn2a tm1RDp/tm1RDp

value: melanocyte

value: immortalized cell line melan-a


title: rep1 siLuc D6 SPJH23

value: myoblasts


title: TFAP2A_B1


title: H39236/TMD-8_DMSO_P8_clone_1D4C6_L5.D708


title: H39236/TMD-8_DMSO_P8_clone_1D4B7_L5.D707


title: WT rep2

department: Department of Biotechnology and Laboratory Science in Medicine

description:
J3
Processed data file: RNA-seq_Summary.xls

source_name: WT

value: wild-type


title: C2C12_Diff_TEAD4


title: Mutant rep2

description:
delta_3
Processed data file: RNA-seq_Summary.xls


title: H39236/TMD-8_+_1uM_ID_clone_4B9E6_L4.D706


title: H39236/TMD-8_+_1uM_ID_clone_1E6B6_L2.D709


title: C2C12_ND_TEAD1


title: WT rep1

description:
J1
Processed data file: RNA-seq_Summary.xls


title: H39236/TMD-8_+_1uM_ID_clone_3D8E6_L4.D704


title: H39236/TMD-8_+_1uM_ID_clone_2F6B6_L4.D701


title: TFAP2A_B2


title: 1703-CB-0017

status: Public on Feb 16 2017

city: New Brunswick

first: Caroll

last: Bagnell

state: New Jersey

address: 59 Dudley Road

department: Animal Sciences

institute: Rutgers University

data_processing:
Quality control checks on raw sequence data from each sample were performed using FastQC (Babraham Bioinformatics, London, UK). Raw reads were imported on a commercial data analysis platform Avadis NGS (Strand Scientifics, CA, USA). Adapter trimming was done to remove ligated adapters from the 3' end of the sequenced reads with only one mismatch allowed; poorly aligned 3' ends were also trimmed. Sequences shorter than 15 nucleotides in length were excluded from further analysis. Trimmed reads with low qualities (base quality score less than 30, alignment score less than 95, mapping quality less than 40) were removed. Filtered reads were used to extract and count miRNAs which were annotated with miRBase release 18 database. Reads were grouped according to their respective identifiers followed by quantification of miRNA abundance. Differentially expressed miRNAs, based on fold change (≥ ± 2.0), were identified with respect to effects of neonatal age (PND 2N versus PND 0 and PND 2R versus PND 0) and nursing (PND 2N versus PND 2R). Probability values for each differentially expressed miRNA were estimated by z-score calculations using a false discovery rate of 0.05.
Genome_build: NCBI Sscrofa10.2
Supplementary_files_format_and_content: Excel file with normalized expression values for each sample

organism: Sus scrofa

source_name: uterus

extract_protocol:
Total RNA was isolated using Rneasy kit (Qiagen) following the manufacturer's protocol.  RNA quality was assessed using Agilent Bioanalyzer and Qbit Fluorometer.
smRNA-Seq was performed at the Genomic Services Laboratory, HudsonAlpha Institute for Biotechnology. Total RNA (500 ng) from each uterine sample was used for small RNA library preparation using the NEBNext® Small RNA Library Prep Set for Illumina (New England Biolabs Inc., Ipswich, MA, USA) according to the manufacturer’s protocol. Briefly, adapters were ligated to total RNA, multiplex primers were hybridized, and reverse transcription was accomplished using SuperScript III RT (Life Technologies, Grand Island, NY, USA) for 1 hour at 50°C. Bar codes with uniquely indexed primers were attached to each cDNA library and amplified through six PCR cycles. Following PCR amplification, purification was done using the QIAquick PCR purification kit (Qiagen Inc., Valencia, CA, USA). Size selection of the libraries was then performed using a 3% dye-free agarose gel on the Pipin prep instrument (Sage Science, Beverly, MA, USA). Post size-selected miRNA library concentration was assessed using a Qubit® 2.0 Fluorometer and library quality was determined using a DNA High Sense (HS) chip on Agilent 2100 Bioanalyzer. Further library quantification was performed using the qPCR-based KAPA Biosystem Library Quantification kit (Kapa Biosystems Inc., Woburn, MA, USA). Individual sample libraries were diluted to a final concentration of 1.25 nM, equimolar amounts of each sample and were pooled prior to sequencing.  MicroRNA sequencing was performed using an Illumina HiSeq 2500 instrument (Illumina Inc., San Diego, CA, USA) at 50bp Single End (SE) condition.

treatment_protocol: Pigs were euthanized within 1 h of birth (PND 0) or at 50 h of age (PND 2N and PND 2R).  Uteri were trimmed of connective tissue, immersed in RNALater and stored at -80C until RNA extraction.

tag: breed

value: Crossbred (Landrace, Yorkshire, Duroc, Hampshire)

tag: feeding

value: no nursing

tag: age (days)

value: PND 0


title: 1703-CB-0020