title: Chimpanzee replicate 2

city: Durham

first: Gregory

last: Crawford

state: NC

address: 101 Science Drive

institute: Duke University

data_processing:
Due to the use of MmeI to generate DNase-seq libraries, sequencing reads were trimmed to 20 bases using a custom perl script.
Reads for each species were mapped to its native genome using Bowtie version 0.12.9 (parameters: -trim5 0 --trim3 0 -m 1 -l 20) as part of a custom two-step pipeline. In the first step (“tier 1”), reads were required to match to a unique location with no mismatches (parameter: -n 0). In the second step (“tier 2”), unmapped reads from step one were re-mapped with a relaxed mismatch parameter of one mismatch  (parameter: -n 1). Reads that mapped to multiple locations or had more than one mismatch were discarded.
Samtools version 0.1.19-44428cd was used to convert the sam files from each step to bam files, merge them into one file, and remove duplicate reads (defined as having the same chromosomal position).
Bedtools v2.17.0 was used to convert the bam files to bed files.
Reads from the non-human samples were converted from their native genome coordinates to the human hg19 genome coordinates using a three-step process that removed reads that did not have a one-to-one relationship between the genomes. In each step, read coordinates were converted from one genome to the other using the UCSC liftOver software with a minMatch parameter of 0.8, which requires that 80% of the read maps to the new genome. Note that this parameter filters only on genomic coverage, not sequence identity. In the first step, read coordinates were converted from their native genome to hg19. Read coordinates that successfully lifted to hg19 were then lifted back to the native genome. Read coordinates that did not lift back to the same coordinates on the native genome were removed. Reads that did lift back to the same coordinates were lifted back to hg19. An additional filtering step was added to ensure the reads did not map to a duplicated region. In that step, overlapping reads were merged into a region, and that region was lifted from the native genome to hg19. Regions that failed to lift uniquely to hg19 were flagged and reads that overlapped them were removed.
Because some of the samples were from males and some were from females, we removed reads that mapped or lifted over to the human X or Y chromosomes to eliminate any sex-specific bias.
Genome_build: hg19 for human, panTro4 for chimpanzee, gorGor3 for gorilla, ponAbe2 for orangutan, rheMac3 for macaque
Supplementary_files_format_and_content: bed files contain hg19 coordinates for the reads

organism: Pan troglodytes

source_name: Skin fibroblast cells

growth_protocol: Growth media consisted of Gibco's MEM (10370-021), L-Glutamine (25030-081), Pen/Strep (15140-122), and 10% FBS (Hyclone SH30070).

extract_protocol:
Cells were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations. All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106). Briefly, cells were lysed and incubated at 37¡C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).

tag: coriell id


title: 51428_DC_NESAM

status: Public on Oct 11 2019

type: genomic

city: Houston

first: Neil

middle: A.

last: Hanchard

state: TX

address: One Baylor Plaza

department: Molecular and Human Genetics

country: USA

institute: Baylor College of Medicine

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium HumanMethylation450 BeadChip using the standard Illumina protocol.

scan_protocol: Arrays were imaged using iSan.

data_processing:
GenomeStudio Methylation Module (version 1.9.0) with background correction followed by color balancing and quantile normalization with the R package lumi (version 2.22.1). Probes meeting the following criteria were omitted from subsequent analyses: internal controls (N=65), detection P-value < 0.0001 in >10% of samples (N=860), bead counts <3 in 5% of samples (N=665), sex chromosomes (N=11,288), cross-reactive (N=29,895), and containing SNPs with a minor allele frequency (MAF) >0.01 in African populations at, or within 5bp of, the single base extension (SBE) site (N=16,918 and N=5,386, respectively).
matrix processed value definition: M-value (color balanced and quantile normalized)

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: Buccal epithelial cells

label_protocol: Standard Illumina Protocol

extract_protocol: Samples were collected and extracted with the help of the Oragene Discover (OGR-250) DNA collection kit.

tag: tissue

value: Buccal epithelial cells

tag: gender

value: M

tag: sample timing

value: DC

tag: disease group

value: NESAM

tag: age

tag: nationality

value: Malawi

tag: sentrix id

tag: sentrix position

tag: diagnosis

value: child with SAM


title: 51420_DC_NESAM


title: 51419_DC_NESAM


title: 55327_DC_NESAM

value: F


title: 51416_DC_NESAM


title: 51417_DC_NESAM


title: 51418_DC_NESAM


title: 51377_DC_NESAM


title: C1(Control 1)

status: Public on Oct 12 2019

type: SRA

city: Chengdu

first: lidan

last: Xiong

address: No. 5, Gong Xing Road

country: China

institute: West China Hospital

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to human genome whole genome using featureCounts 1.5.0-p3 with parameters -Q 10 -B -C
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Garber M et al.,  Nature methods, 2011. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: human genome
Supplementary_files_format_and_content: table-delimited text files include RPKM values for each Sample

molecule: total RNA

source_name: Epidermis

extract_protocol:
RNA was extracted from tissues or cells by standard extraction method, followed by strict quality control of RNA samples, which mainly included the following three aspects. Agarose gel electrophoresis: analysis of RNA integrity and presence of DNA contamination. NanoPhotometer spectrophotometer: RNA purity was determined (OD260/280 and OD260/230 ratios). Agilent 2100 bioanalyzer: accurate detection of RNA integrity.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: HaCaT

value: Epidermis

tag: passages

value: Less than 30 passages


title: 55326_DC_NESAM


title: 51382_DC_NESAM


title: 51335_DC_NESAM


title: 55325_DC_NESAM


title: 55324_DC_NESAM


title: 51309_DC_NESAM


title: 51304_DC_NESAM


title: JMICSM430_DC_NESAM

value: Jamaica


title: 51306_DC_NESAM


title: JMICSM180_DL_NESAM

value: DL

value: health adult with history of SAM


title: 51276_DC_NESAM


title: 51308_DC_NESAM


title: 51273_DC_NESAM


title: 51253_DC_NESAM


title: 55302_DC_NESAM


title: 51415_DC_NESAM


title: 51119_DC_NESAM


title: 55300_DC_NESAM


title: 51260_DC_NESAM


title: 55306_DC_NESAM


title: 51027_DC_NESAM


title: 51057_DC_NESAM


title: 51014_DC_ESAM

value: ESAM


title: 51023_DC_NESAM


title: 51054_DC_ESAM


title: 51117_DC_NESAM


title: 51107_DC_ESAM


title: 51049_DC_NESAM


title: 51109_DC_ESAM


title: 51105_DC_NESAM


title: 51218_DC_ESAM


title: 51002_DC_ESAM


title: 51235_DC_NESAM


title: 51009_DC_NESAM


title: 51102_DC_NESAM


title: 51240_DC_NESAM


title: 51044_DC_NESAM


title: 51113_DC_ESAM


title: 51034_DC_ESAM


title: 51112_DC_NESAM


title: 51101_DC_NESAM


title: JMICSM248_DC_NESAM


title: 51050_DC_NESAM


title: 51010_DC_NESAM


title: 51039_DC_NESAM


title: 51202_DC_NESAM


title: 51001_DC_NESAM


title: 51017_DC_ESAM


title: 51016_DC_ESAM


title: 51032_DC_ESAM


title: 51040_DC_NESAM


title: 51106_DC_NESAM


title: 51248_DC_NESAM


title: 51207_DC_ESAM


title: 51103_DC_ESAM


title: 51038_DC_NESAM


title: 51230_DC_NESAM


title: 51221_DC_ESAM


title: 51035_DC_NESAM


title: 51233_DC_ESAM


title: 51234_DC_NESAM


title: 51015_DC_NESAM


title: 51037_DC_ESAM


title: 51047_DC_NESAM


title: 51249_DC_NESAM


title: 51241_DC_NESAM


title: JMICSM254_DC_NESAM


title: 51030_DC_NESAM


title: 51021_DC_NESAM


title: 51031_DC_NESAM


title: 51111_DC_NESAM


title: 51046_DC_NESAM


title: JMICSM033_DC_NESAM


title: 51389_DC_NESAM


title: 51100_DC_NESAM


title: 51242_DC_NESAM


title: JMICSM037_DC_NESAM


title: JMICSM170_DL_NESAM


title: 51094_DC_NESAM


title: 51108_DC_ESAM


title: 51127_DC_NESAM


title: JMICSM508_DC_NESAM


title: 51208_DC_NESAM


title: 51062_DC_NESAM


title: 51250_DC_NESAM


title: 51029_DC_NESAM


title: JMICSM439_DC_NESAM


title: 51403_DC_NESAM


title: 51066_DC_NESAM


title: JMICSM447_DC_NESAM


title: JMICSM032_DC_NESAM


title: 51229_DC_NESAM


title: JMICSM163_DL_NESAM


title: 51025_DC_NESAM


title: 51083_DC_NESAM


title: JMICSM490_DC_NESAM


title: JMICSM217_DL_NESAM


title: 51227_DC_NESAM


title: JMICSM142_DL_NESAM


title: 51093_DC_NESAM


title: JMICSM434_DC_NESAM


title: JMICSM214_DL_NESAM


title: JMICSM414_DL_NESAM


title: 51222_DC_NESAM


title: 51064_DC_NESAM


title: JMICSM448_DC_NESAM


title: JMICSM151_DL_NESAM


title: JMICSM127_DL_NESAM


title: JMICSM441_DL_NESAM


title: JMICSM042_DC_NESAM


title: JMICSM116_DC_NESAM


title: 51078_DC_NESAM


title: JMICSM443_DC_NESAM


title: JMICSM068_DC_NESAM


title: JMICSM252_DC_NESAM


title: JMICSM119_DC_NESAM


title: JMICSM479_DL_NESAM


title: JMICSM083_DC_NESAM


title: JMICSM502_DC_NESAM


title: JMICSM476_DL_NESAM


title: JMICSM346_DL_NESAM


title: JMICSM066_DC_NESAM


title: JMICSM055_DC_NESAM


title: JMICSM094_DC_NESAM


title: JMICSM394_DL_NESAM


title: JMICSM049_DC_NESAM


title: JMICSM452_DC_NESAM


title: JMICSM087_DC_NESAM


title: JMICSM309_DL_NESAM


title: JMICSM468_DC_NESAM


title: JMICSM485_DC_NESAM


title: JMICSM034_DC_NESAM


title: JMICSM005_DC_NESAM


title: JMICSM480_DL_NESAM


title: JMICSM061_DC_NESAM


title: JMICSM450_DC_NESAM


title: JMICSM463_DL_NESAM


title: JMICSM438_DC_NESAM


title: JMICSM086_DC_NESAM


title: JMICSM247_DC_NESAM


title: JMICSM292_DL_NESAM


title: JMICSM029_DC_NESAM


title: JMICSM106_DL_NESAM


title: JMICSM445_DL_NESAM


title: JMICSM368_DC_NESAM


title: JMICSM059_DC_NESAM


title: JMICSM473_DC_NESAM


title: JMICSM318_DL_NESAM


title: JMICSM056_DC_NESAM


title: JMICSM410_DL_NESAM


title: JMICSM184_DC_NESAM


title: JMICSM301_DL_NESAM


title: JMICSM228_DL_NESAM


title: JMICSM223_DL_NESAM


title: JMICSM405_DL_NESAM


title: JMICSM121_DL_NESAM


title: JMICSM283_DL_NESAM


title: JMICSM491_DC_NESAM


title: JMICSM475_DL_NESAM


title: JMICSM249_DC_NESAM


title: JMICSM202_DL_NESAM


title: JMICSM198_DL_NESAM


title: JMICSM161_DL_NESAM


title: JMICSM046_DC_NESAM


title: JMICSM436_DC_NESAM


title: JMICSM323_DL_NESAM


title: JMICSM231_DC_ESAM


title: 51048_DC_NESAM


title: 51448_DC_ESAM


title: JMICSM065_DC_ESAM


title: 51255_DC_ESAM


title: JMICSM051_DC_ESAM


title: 51414_DC_ESAM


title: 51238_DC_ESAM


title: JMICSM114_DL_ESAM


title: 51043_DC_NESAM


title: 51265_DC_ESAM


title: 51412_DC_ESAM


title: 51385_DC_ESAM


title: 51272_DC_ESAM


title: 55305_DC_ESAM


title: 51404_DC_ESAM


title: 51258_DC_ESAM


title: 55304_DC_ESAM


title: 51305_DC_ESAM


title: 51383_DC_ESAM


title: 51274_DC_ESAM


title: JMICSM423_DC_ESAM


title: 51266_DC_ESAM


title: 51087_DC_ESAM


title: 51264_DC_ESAM


title: 51022_DC_NESAM


title: JMICSM095_DC_ESAM


title: JMICSM093_DC_ESAM


title: JMICSM073_DC_ESAM


title: 51247_DC_NESAM


title: JMICSM362_DC_ESAM


title: JMICSM082_DC_ESAM


title: 51011_DC_ESAM


title: 51041_DC_ESAM


title: JMICSM003_DC_ESAM


title: 51045_DC_ESAM


title: 51000_DC_ESAM


title: 51211_DC_NESAM


title: 51053_DC_NESAM


title: 51224_DC_NESAM


title: 51051_DC_ESAM


title: 51115_DC_ESAM


title: JMICSM081_DC_ESAM


title: 51026_DC_ESAM


title: 51212_DC_NESAM


title: 51223_DC_NESAM


title: 51201_DC_ESAM


title: 51012_DC_NESAM


title: 51110_DC_ESAM


title: 51226_DC_NESAM


title: JMICSM465_DC_ESAM


title: 51205_DC_ESAM


title: 51006_DC_NESAM


title: 51052_DC_ESAM


title: 51114_DC_ESAM


title: JMICSM088_DC_ESAM


title: JMICSM072_DC_ESAM


title: 51203_DC_ESAM


title: JMICSM120_DC_ESAM


title: 51033_DC_ESAM


title: 51236_DC_ESAM


title: 51028_DC_NESAM


title: 51204_DC_ESAM


title: 51036_DC_ESAM


title: 51019_DC_NESAM


title: JMICSM014_DC_ESAM


title: 51232_DC_ESAM


title: 51121_DC_ESAM


title: 51213_DC_NESAM


title: 51056_DC_ESAM


title: 51225_DC_ESAM


title: 51018_DC_ESAM


title: 51116_DC_ESAM


title: 51007_DC_ESAM


title: JMICSM057_DC_ESAM


title: 51231_DC_ESAM


title: 51243_DC_ESAM


title: 51246_DC_ESAM


title: 51042_DC_ESAM


title: JMICSM111_DC_ESAM


title: 51244_DC_ESAM


title: 51003_DC_ESAM


title: 51220_DC_ESAM


title: 51024_DC_ESAM


title: 51104_DC_NESAM


title: 51020_DC_ESAM


title: rs2836411 HASMC control

city: Dunedin

first: Judith

last: Marsman

state: Otago

address: 201 Great King Street

department: Surgical Sciences

country: New Zealand

institute: University of Otago

library_source: genomic

data_processing:
Library strategy: 4C-seq
Baits were demultiplexed based on bait primer sequences up to and including the digestion site using grep, allowing 0 mismatches. Only read pairs that had the forward and reverse bait sequences in the correct orientation were selected.
Adapter sequences, and bases with a Phred quality score under 20 were then trimmed from the reads using fastq-mcf. Bait sequences up to but excluding the digestion site were trimmed from the reads using seqtk (https://github.com/lh3/seqtk).
Reads were mapped to the hg19 reference genome using Burrows-Wheeler Aligner (MEM algorithm).
Mapped reads were assigned to MseI digestion fragments using fourSig.
In the replicate samples, bait and neighbouring fragments for which the read count was high in the control (unligated) libraries were removed (includes self-ligated and uncut reads). The running mean of windows of 21 successive fragments was calculated from the read per million-normalised read counts, which was obtained using fourSig
Significant interaction calling was performed using fourSig with the following settings: window size of 3, 1000 iterations, FDR (false discovery rate) of 0.01, fdr.prob of 0.05 (which selects the top fifth percentile of interactions with a FDR < 0.01), and only included mappable fragments. Significant interactions were called for two regions: 1) the whole of chr21, and 2) within the ERG-P3 sub-domain at chr21:39,730,000-39,911,000. Significant interactions of category 1 and 2 in both replicates were overlapped using the bedIntersect tool from UCSC
Genome_build: hg19
Supplementary_files_format_and_content: For reads assigned to digestion fragments bedGraph files are provided for the read per million normalised running mean of 21 successive MseI digestion fragments for each replicate and the avarage of two replicates. For significant interactions bed files are provided for each repliacte and for the overlap between two replicates.

source_name: human aortic smooth muscle cells

growth_protocol: HUVECs were grown in EGM™-2 BulletKit™ (CC-3162, Lonza) and HASMCs were grown in SmGM™-2 BulletKit™ (CC-3182, Lonza) according to the manufacturer’s instructions.

extract_protocol:
Per library, 2.5 million cells were harvested by trypsinization to obtain a single-cell suspension, then cross-linked in 2% formaldehyde, 5% FBS and 1x PBS for 10 minutes at RT while rotating. Formaldehyde was quenched with a final concentration of 125 mM glycine for 5 minutes on ice while inverting several times. Cells were lysed (10 mM Tris pH 8.0, 10 mM NaCl, 0.2% NP-40, protease inhibitors) by resuspending in 2.5 mL ice-cold lysis buffer and incubating for 10 minutes on ice. Cell pellets were spun down, snap-frozen and stored at -80°C. A second lysis was performed in 10 mL ice-cold lysis buffer for 30 minutes on ice, followed by 10x strokes of a dounce homogeniser. Nuclei were then resuspended in ice-cold PBS and transferred to Eppendorf tubes. Pellets were resuspended in 50 µL 0.05% SDS in MQ and incubated at 60°C for 10 minutes. To quench the SDS, 153.3 µL MQ and 16.7 µL of 15% Triton X-100 (final concentration of 1.14%) was added and the suspension was incubated at 37°C for 20 minutes, while breaking up aggregates every 5 minutes by resuspending. Nuclei were digested horizontally in a total volume of 600 µL with 400 units of MseI (R0525M, New England Biolabs [NEB]) by incubating at 37°C overnight. While incubating, samples were mixed regularly by gently inverting the tube. MseI was inactivated by incubating at 65°C for 20 mins. Ligation was performed (omitted for the controls) in a total volume of 2.5 mL using 1675 units T4 DNA ligase (M0202M, NEB) by incubating at 16°C overnight at 30 revolutions per minute (rpm). Samples were proteinase K (Invitrogen) treated and reverse-crosslinked overnight at 65°C. Samples were then treated with RNase A (Thermo Scientific) at 37 °C for 30 minutes. DNA was purified by 2x phenol/chloroform extraction and ethanol precipitated.   A second digestion was performed with 25 units CviQI (R0639L, NEB) by incubating at 25°C overnight at 30 rpm. The restriction enzyme was removed via phenol/chloroform extraction followed by ethanol precipitation. A second ligation was performed in the same way as the first ligation, in a total volume of 3.5 mL using 1675 units of ligase. DNA was ethanol precipitated with 70 µg glycogen.  Digestion and ligation efficiencies were checked after each step by running aliquots on an agarose gel. DNA concentrations were measured using a Qubit® 3.0 Fluorometer (Life Technologies) and Qubit® double-stranded DNA (dsDNA) Broad Range or High-Sensitivity Assay kits (Life Technologies).  For each replicate a total of 1 µg in 5 x 25-µL reactions was amplified by PCR using Q5 Hot Start High-Fidelity 2X Master Mix (NEB). PCR products were purified twice using the QIAquick PCR Purification kit (QIAGEN) and AMPure XP beads (Agencourt).
DNA concentrations were measured using a Qubit® 3.0 Fluorometer and were run on a 2100 Bioanalyser (Agilent Technologies) using a High Sensitivity DNA Kit (Agilent Technologies). Amplicons were mixed equally based on the concentration and ratio of demultiplexed 4C baits obtained from an in-house MiSeq run. Libraries were prepared using the Thruplex Kit (Rubicon) with 10 ng of input DNA according to the manufacturer’s instructions, using 7 cycles of adapter amplification and 30 seconds of extension time. Libraries were mixed in equal concentrations and sequenced as 2 x 150-bp (paired-end) reads on a HiSeq X by Admera Health.

tag: cell type

value: HASMC

tag: rs2836411 genotype

value: TT

tag: replicate

value: control (first ligation step omitted)


title: 51090_DC_ESAM

value: Buccal epithelial cells


title: 51118_DC_ESAM

value: M


title: rs2836411 HASMC replicate 2

value: CC

value: replicate 2


title: 51085_DC_ESAM

value: DC

value: Malawi


title: rs2836411 HASMC replicate 1

value: replicate 1


title: JMICSM054_DC_ESAM

value: child with SAM


title: 51055_DC_ESAM


title: 51084_DC_ESAM


title: JMICSM148_DL_ESAM

value: F


title: 51228_DC_ESAM


title: Mouse_FO_B_4

city: Cambridge

first: Vinay

middle: S

last: Mahajan

state: MA

address: 65 Landsdowne Street

institute: Brigham and Women's Hospital

description: t123_fo.rsem.mm10.ensembl.counts.matrix.txt

data_processing:
Bcl2fastq - demultiplexing
fastqc
RSEM - alignment to mm10 genome, ENSEMBL transcriptome annotation
Genome_build: mm10 or hg38
Supplementary_files_format_and_content: count matrix; tab-delimited text file of expected counts

organism: Mus musculus

source_name: Follicular B cells

extract_protocol:
Qiagen RNAeasy kit
Smartseq2

tag: strain

tag: mouse id

value: Mouse 4

tag: genotype

value: wild-type

value: Follicular B cells


title: rs2836411 HUVEC replicate 2_C

source_name: human umbilical vein endothelial cells

value: HUVEC

value: CT

value: replicate 2_C


title: rs2836411 HUVEC control_C

value: control (first ligation step omitted)_C


title: rs2836411 HUVEC control_T

value: control (first ligation step omitted)_T


title: rs2836411 HUVEC replicate 2_T

value: replicate 2_T


title: JMICSM024_DC_ESAM

tag: tissue

value: Buccal epithelial cells

value: ESAM

value: Jamaica


title: 51065_DC_ESAM

tag: gender

value: DC


title: rs2836411 HUVEC replicate 1_C

value: replicate 1_C


title: rs2836411 HUVEC replicate 1_T

value: replicate 1_T


title: Mouse_FO_B_2

value: Mouse 2


title: Mouse_FO_B_3

value: Mouse 3


title: Mouse_FO_B_1

value: Mouse 1


title: Mouse_T3_B_3

source_name: Transitional (T3)  B cells

value: wild-type

value: Transitional (T3)  B cells


title: JMICSM069_DC_ESAM

value: F

tag: sample timing

value: child with SAM


title: Mouse_T2_B_3

source_name: Transitional (T2)  B cells


title: 51237_DC_ESAM

value: M

tag: disease group

value: Malawi


title: 51060_DC_ESAM

tag: age


title: 51391_DC_ESAM

tag: nationality


title: Mouse_T1_B_3

source_name: Transitional (T1)  B cells


title: JMICSM435_DC_ESAM

tag: sentrix id


title: JMICSM483_DL_ESAM

value: DL

tag: sentrix position

value: health adult with history of SAM


title: 51063_DC_ESAM

value: Buccal epithelial cells

tag: diagnosis


title: 51059_DC_ESAM

value: ESAM


title: Mouse_T3_B_1

value: Transitional (T1)  B cells


title: Mouse_T1_B_2

value: Transitional (T2)  B cells


title: JMICSM100_DL_ESAM

value: Jamaica


title: 51206_DC_ESAM

value: DC


title: JMICSM489_DC_ESAM


title: JMICSM105_DL_ESAM


title: Mouse_T2_B_2

value: Mouse 2


title: JMICSM285_DL_ESAM


title: JMICSM089_DC_ESAM


title: Mouse_T1_B_1


title: JMICSM117_DL_ESAM


title: D3839 mouse erythroid cells biological replicate 1

city: Oxford

first: A Marieke

last: Oudelaar

address: John Radcliffe Hospital

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

description:
Tri-C product (DNA)
3C library enriched for multi-way interactions with viewpoint fragments

data_processing:
Library strategy: 3C-seq
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
In silico restriction enzyme digestion of FASTQ file (custom scripts)
Alignment to the genome (bowtie -m 2)
Removal of PCR duplicates, mapping of reads to restriction enzyme fragments, proximity exclusion (if within ~1 kb of viewpoint) (custom scripts)
Calculation of multi-way interaction frequencies with viewpoints (custom scripts)
Processing of interaction frequencies into a contact matrix (custom scripts)
Genome_build: mm9
Supplementary_files_format_and_content: Custom combined data format (interacting restriction enzyme fragment1 \t interacting restriction enzyme fragment2 \t count \n)

source_name: Primary erythroid cells

growth_protocol: Ter-119+ erythroid cells were obtained from the spleens of female C57BL/6 mice treated with phenylhydrazine (three doses of 40 mg/g body weight given 12 hours apart; mice were sacrificed after five days).

extract_protocol:
Spleens were gently dissociated into a single cell suspension and cells were passed through a 70 μm strainer to remove clumps. For ter-119+ cell selection, cells were stained with phycoerythrin conjugated anti-ter-119 antibodies and positively selected using anti-phycoerythrin MACS beads before fixation with formaldehyde.
Tri-C combines 3C library preparation (NlaIII restriction enzyme) with oligonucleotide capture enrichment that is optimized to detect multiway interactions with viewpoints of interest, as described in detail in the Methods of the paper.

value: Ter-119+ cells

value: phenylhydrazine treated spleen

tag: Sex

value: female

tag: viewpoints analysed

value: R2, Mpg

tag: genotype/variation


title: Wild type mouse erythroid cells biological replicate 3

tag: cell type

value: Wild type


title: D3839 mouse erythroid cells biological replicate 2


title: 51396_DC_ESAM

value: F

value: child with SAM


title: Wild type mouse erythroid cells biological replicate 2


title: D3839 mouse erythroid cells biological replicate 3


title: 51080_DC_ESAM

value: M

value: Malawi


title: Wild type mouse erythroid cells biological replicate 1


title: Mouse_T3_B_2

value: wild-type


title: JMICSM373_DC_ESAM

value: Buccal epithelial cells


title: 162.4

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 1 Gilbert street

institute: Yale University

data_processing:
Basecalling was performed with Ion Torrent Suite 5.0.5
After quality control for adapter contamination and trimming, Fastq files were mapped on human genome  ( Hg19) by by combinations of Top Tophat and Bowtie2   softwares.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks 2.2.1
Genome_build: Hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was extracted using miRNeasy mini kit (Qiagen) from each core. according the manufacturer’s protocol. RNA concentration and integrity were measured by using NanoDrop ND-2000 and 2200 Tape Station
20 ng RNA input was used for library preparation by AmpliSeq™ Transcriptome Human Gene Expression kit according the manufacturer’s protocol . The cDNA was then amplified and barcoded using the Ion Xpress™ RNA-Seq Barcode 1-16 Kit (Life Technologies 4475485).  The Ion PI™ Chip Kit v2 BC (Life Technologies) 4484270) was then loaded using the Ion Chef™ System (Life Technologies 4484177) with the Ion PI™ IC 200 Kit (Life Technologies 4488377). Afterwards, the chips were run on the Ion Proton™ System for Next-Generation Sequencing (Life Technologies 4476610) using the Ion PI™ IC 200 Kit.

treatment_protocol: Following explantation, lungs were inflated to 30 cm H2O and held at 10 cm H2O pressure inflation while frozen over liquid nitrogen vapor according to previously established protocols.(12) The frozen lung was imaged using a high resolution CT scanner and cut into 2 cm thick slices along the transverse plane for sampling. Cores were systematically sampled from each slice using a 1.4 cm diameter coring drill. For this study, 2 cores were randomly selected from each of upper, mid, and lower lung regions for 6 samples per lung.

tag: disease state

value: IPF


title: 51401_DC_ESAM

value: ESAM


title: Mouse_T2_B_1

tag: strain

value: Mouse 1

value: Transitional (T1)  B cells


title: 51392_DC_ESAM

value: DC


title: JMICSM427_DC_ESAM

value: Jamaica


title: 162.15


title: 51123_DC_ESAM


title: 162.1


title: 51086_DC_ESAM


title: 51393_DC_ESAM


title: 51058_DC_ESAM


title: 147.48


title: 51081_DC_ESAM


title: 162.11


title: 147.69


title: 51061_DC_ESAM


title: 127.8


title: 147.24


title: JMICSM053_DC_ESAM


title: 51402_DC_ESAM


title: 127.4


title: 162.23


title: 51091_DC_ESAM


title: 127.29


title: 127.28


title: 51089_DC_ESAM


title: 162.12


title: 120.4


title: 51088_DC_ESAM


title: 120.23


title: 51079_DC_ESAM


title: 51390_DC_ESAM


title: 110.3


title: 110.23


title: 51394_DC_ESAM


title: 51122_DC_ESAM


title: 51126_DC_ESAM


title: 110.16


title: 51125_DC_ESAM


title: 51124_DC_ESAM


title: 110.1


title: RNA of 6-3F_L1

city: Guangzhou

first: Wenru

last: Li

address: No.100, Xianliezhong Road

institute: Institute of Microbiology, Guangdong Academy of Sciences

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads Vontaining ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, Vonsidering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008).
Genome_build: Pseudomonas aeruginosa PAO1
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Pseudomonas aeruginosa PAO1

source_name: Transcriptome of farnesol-treated P. aeruginosa PAO1

growth_protocol: Every 50 mL LB medium was inoculated exponential growth phase of P. aeruginosa PAO1, with the bacterial concentration of 1.0E8 CFU/mL.  All the three triplicate experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate at 180 rpm for 5 hours.

extract_protocol:
Cells of P. aeruginosa PAO1 were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
Strand specific library: The construct method of strand specific library is similar to that of NEB library expect that when synthesizing the second strand cDNA, dTTP is replayed by dUTP. After overhangs of the purified double-stranded cDNA are converted into blunt ends, adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure is ligated to prepare for hybridization, the second strand cDNA is digested by USER enzyme. The following step is identical with NEB library construction.

treatment_protocol: LB medium (50 mL) was inoculated with exponential growth phase P. aeruginosa PAO1 at a concentration of 108 CFU/mL. Farnesol was then added at a concentration of either 0 (control) or 0.56 mg/mL, in triplicate. All six experiment groups were incubated in a water bath shaker at 37 ºC with a shaking rate of 180 rpm for 5 h.

tag: treatment

value: 0.56 mg/mL farnesol

tag: phase

value: exponential growth phase


title: 110.12


title: 50.46


title: 50.27


title: JMICSM230_DL_ESAM

tag: tissue

value: DL

value: health adult with history of SAM


title: RNA of 6-2F_L1


title: RNA of 6-1F_L1


title: JMICSM503_DC_ESAM

tag: gender


title: RNA of 0-3F_L1

source_name: Transcriptome of control of P. aeruginosa PAO1

value: native


title: 50.25


title: 50.18


title: 50.16


title: RNA of 0-2F_L1


title: 120.11


title: 147.3


title: 25.59


title: JMICSM462_DL_ESAM

value: F

tag: sample timing


title: 120.1


title: RNA of 0-1F_L1


title: JMICSM146_DC_ESAM

tag: disease group

value: child with SAM


title: 25.47


title: JMICSM449_DC_ESAM

tag: age


title: 11.6


title: 25.15


title: 11.54


title: 25.22


title: Day16_2

city: Beijing

first: ruoyan

address: Yiheyuan street

institute: Peking University

data_processing:
Clean reads were aligned to rat reference rn19 using Tophat (version 2.1.1)
Genome_build: UCSC rn6
Supplementary_files_format_and_content: Cufflinks(cuffquant, cuffnorm version 2.2.1) were used  to aquire normalized expression matrix (FPKM) covering all the samples.

organism: Rattus norvegicus

source_name: REF cell line

extract_protocol:
Total RNA was isolated from the cell pellets with RNA extraction kit (Zymo Research, R1050)
All the RNA products were confirmed with high quality (RQN score ≥ 7.5) using the Fragment AnalyzerTM platform (Advanced Analytical Technologies, Inc).

value: cell with serum starvation for 16 days

tag: transformation


title: 25.49


title: Day16_3


title: JMICSM486_DL_ESAM

value: M

tag: nationality

tag: sentrix id


title: JMICSM126_DL_ESAM

tag: sentrix position

tag: diagnosis


title: 11.3


title: Day16_1


title: 11.18


title: 11.11


title: JMICSM492_DC_ESAM


title: Day14_3

value: cell with serum starvation for 14 days


title: 190.64


title: 190.36


title: JMICSM379_DC_ESAM

value: Buccal epithelial cells


title: Day14_2


title: Day14_1


title: 50.4

value: IPF


title: JMICSM001_DC_ESAM

value: ESAM


title: 190.22


title: JMICSM472_DC_ESAM


title: JMICSM291_DL_ESAM


title: Day12_3

value: cell with serum starvation for 12 days


title: 3.28


title: 3.16


title: Day12_1


title: JMICSM299_DL_ESAM


title: 3.45


title: 11.25


title: JMICSM460_DL_ESAM


title: Day12_2


title: 6989.1992

value: healthy donor


title: Macaque replicate 3

organism: Macaca mulatta

tag: coriell id


title: Day10_3

value: cell with serum starvation for 10 days


title: JMICSM494_DC_ESAM

value: DC

value: Jamaica


title: 6989.1971


title: JMICSM071_DC_ESAM


title: 6989.1814


title: 190.23


title: Day10_1


title: JMICSM397_DC_ESAM


title: 3.76


title: Day10_2


title: 6989.1771


title: Day8_3

value: cell with serum starvation for 8 days


title: Chimpanzee replicate 1


title: JMICSM428_DC_ESAM


title: Day8_2


title: 6989.1149


title: JMICSM498_DC_ESAM


title: Day8_1


title: Macaque replicate 2


title: Chimpanzee replicate 3


title: 6983.791


title: Day6_3

value: cell with serum starvation for 6 days


title: JMICSM469_DL_ESAM

value: DL

value: health adult with history of SAM


title: Day6_2


title: JMICSM484_DL_ESAM

value: F


title: Day6_1


title: JMICSM501_DC_ESAM

value: child with SAM


title: JMICSM107_DL_ESAM


title: Day4_3

value: cell with serum starvation for 4 days


title: 6989.1109


title: 6983.2284


title: 6983.404


title: Day4_2


title: 6983.758


title: 6983.405


title: JMICSM039_DC_ESAM


title: Day4_1


title: 6983.2283


title: Day3_3

value: cell with serum starvation for 3 days


title: JMICSM377_DL_ESAM

value: M


title: JMICSM477_DL_ESAM

value: Buccal epithelial cells


title: Day3_1


title: 6978.524


title: 6978.525


title: Day3_2


title: NC control+Pg_2

type: RNA

city: Nanjing

first: Lang

last: Lei

state: Jiangsu

address: Zhongyang Road 30, Xuanwu District

institute: Nanjing Stomatological Hospital, Medical School of Nanjing University

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide (Agilent Human 4x44K Gene Expression Microarrays v2).

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 7 out of 14 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information. The circRNA/microRNA interaction was predicted with Arraystar's home-made miRNA target prediction software. All the differentially expressed circRNAs were annotated  in detail with the circRNA/miRNA interaction information.

source_name: THP-1 cells, non-targeting scramble shRNA, Pg

label_protocol: Total RNA from each sample was linearly amplified and labeled with Cy3-UTP, the Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: THP-1 cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/streptomycin solution and 0.1% β-mercaptoethanol at 37℃ in a 5% CO2 humidified incubator.

extract_protocol: Total RNA was extracted by RNA extraction kit (Tiangen, China) after treatment with PBS or P. gingivalis for 2 hours.

treatment_protocol: Lentiviral vectors carrying CDK9 shRNA or not were transfected into THP-1 cells for 96 hours, with the assist of Envirus. Then THP-1 cells were treated with P. gingivalis or PBS.

tag: agent

value: P. gingivalis


title: NC control+Pg_1


title: JMICSM255_DL_ESAM

value: ESAM


title: NC control_3

source_name: THP-1 cells, non-targeting scramble shRNA, PBS

value: PBS


title: JMICSM041_DC_ESAM


title: JMICSM499_DC_ESAM


title: NC control_1


title: 6978.537

value: healthy donor


title: NC control+Pg_3


title: NC control_2


title: 6978.508


title: Day2_3

tag: cell type

value: cell with serum starvation for 2 days


title: LNCaP radioresistant vs. Normal

city: Dresden

first: Michael

last: Seifert

address: Fetscherstr. 74

country: Germany

institute: TU Dresden

description:
aCGH profiling
LNCaP_RR

hyb_protocol: Hybridization was done according to the manufacturer‘s instructions.

scan_protocol: Arrays were scanned using the Agilent Technologies Scanner G2505C according to the manufacturer‘s instructions.

data_processing: Feature extraction and processing of raw data were done with Agilent’s CytoGenomics Editions 2.7 (DU145) and 2.9 (LNCaP).

source_name: Radioresistant LNCaP

label_protocol: Labeling was done according to the manufacturer‘s instructions with the exception that the labeling of reference and test DNA was reversed.

growth_protocol: Prostate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection (ATCC, Manassas, VA) and cultured according to the manufacturers recommendations in a humidified 37°C incubator supplemented with 5% CO2. DU145 cells were maintained in Dulbecco's Modified Eagle's Medium (DMEM) (Sigma-Aldrich) and LNCaP cells in RPMI-1640 medium (Sigma-Aldrich) containing 10% fetal bovine serum (FBS, PAA Laboratories) and 1mM L-glutamine (Sigma-Aldrich).

extract_protocol: DNA was extracted from cell cultures and normal tumor tissue by phenol:chloroform extraction using standard protocols.

treatment_protocol: Radioresistant sub-line was generated from original (parental) DU145 or LNCaP cell line by multiple X-ray irradiations, 4Gy/dose, 1 week recovery between doses. Prior to RNA isolation cells were stained with Aldefluor kit (Stem Cell Technologies) and sorted by FACS.

tag: cell line

value: derived from LNCaP

tag: phenotype

value: radioresistant

tag: Sex

value: Male

source_name: Agilent Euro Male

value: Normal tissue


title: DU145 radioresistant vs. Normal

description:
aCGH profiling
DU145_RR

source_name: Radioresistant DU145

value: derived from DU145


title: DU145 radiosensitive vs. Normal

description:
aCGH profiling
DU145_RS

source_name: Radiosensitive DU145

value: parental DU145

value: radiosensitive


title: Day2_2


title: JMICSM031_DC_ESAM

source_name: Buccal epithelial cells

value: DC

value: Jamaica

value: child with SAM


title: LNCaP radiosensitive vs. Normal

description:
aCGH profiling
LNCaP_RS

source_name: Radiosensitive LNCaP

value: parental LNCaP


title: CDK9 shRNA+Pg_3

source_name: THP-1 cells, CDK9 shRNA, Pg


title: JMICSM453_DC_ESAM

value: Buccal epithelial cells

value: M


title: 51004_DC_ESAM

value: ESAM

value: Malawi


title: Control_3

value: cell without serum starvation


title: JMICSM048_DC_ESAM


title: JMICSM016_DC_ESAM

value: F


title: 146.193

tag: disease state

value: healthy donor


title: 146.13


title: 146.84


title: Day2_1

value: cell with serum starvation for 2 days


title: 146.116


title: JMICSM487_DC_ESAM

tag: tissue


title: Control_1


title: 3.68

value: IPF


title: JMICSM097_DL_ESAM

tag: gender

value: DL

value: health adult with history of SAM


title: 146.111


title: 6978.339


title: Macaque replicate 1

source_name: Skin fibroblast cells


title: Control_2


title: JMICSM043_DC_ESAM

tag: sample timing


title: CDK9 shRNA_2

source_name: THP-1 cells, CDK9 shRNA, PBS

value: PBS


title: 94.78


title: 146.1


title: CDK9 shRNA_1


title: JMICSM253_DC_ESAM

tag: disease group


title: JMICSM251_DC_ESAM

tag: age


title: 94.5


title: 8_Hours_2

city: Jingzhou

first: Min

last: Yao

address: Jingmi Road #266

institute: Yangtze University

description: Eight hour, synthetic miR-155 oligo-treated mouse CD5+ T-cells

data_processing:
Illumina Casava1.7 software used for basecalling.
RNA-Seq reads were mapped to Mouse reference mRNA (GRCm38) using the Bowtie1 software
Using R version 3.4.2 software to find differential genes
Genome_build: GRCm38
Supplementary_files_format_and_content: Reads count (tab deli text)

source_name: CD4+ T-cells

extract_protocol:
Total RNA were extrated by PAXgene RNA kit using the standard protocols.All samples were quantified using a NanoDrop 2000 (Thermo-Fisher Scientific, Waltham, MA, USA), and assessed with an Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). The RNA integrity number (RIN) of each sample was >8.
RNA libraries were prepared for sequencing with an Illumina Truseq RNA sample preparation kit according to the manufacturer’s protocol (Illumina, San Diego, CA, USA).

tag: treatment

value: synthetic miR-155 oligo-treated

tag: replicate

value: CD4+ T-cells


title: 8_Hours_3


title: CDK9 shRNA+Pg_1

value: P. gingivalis


title: CDK9 shRNA_3


title: Control_3

description: Zero hour, synthetic miR-155 oligo-treated mouse CD4+ T-cells


title: JMICSM250_DC_ESAM

value: DC

tag: nationality

value: Jamaica

tag: sentrix id

value: child with SAM


title: 94.27


title: JMICSM160_DC_ESAM

value: Buccal epithelial cells

value: M

tag: sentrix position

tag: diagnosis


title: Primary keratinocytes, Input_ChIPseq

city: San Diego

first: George

last: Sen

state: CA

address: 9500 Gilman Drive

institute: UCSD

description: ChIP-seq protocol

data_processing:
Raw ChIP-seq reads were aligned using bwa 0.7.13 then deduplicated using picard 2.10.6.
MACS2 (version 2.1.1) was used for call peaks in individual replicates using Input ChIP-seq as the control sample.
Peaks overlapped among all replicates were obtained using bedtools.
Genome_build: hg19
Supplementary_files_format_and_content: peaks file

source_name: Human epidermal keratinocytes

growth_protocol: Primary keratinocytes were grown on culture dishes and maintained in keratinocyte epiLIFE medium (Life technologies).

extract_protocol:
DNA was isolated with Thermo Scientific's GeneJET Gel Extraction kit
ChIP-seq libraries were prepared with TruSeq RNA Library Prep Kit (Illumina) then multiplexed

treatment_protocol: 10 million cells were crosslinked with 2mM DSG and 1% formaldehyde and used in the experiment. The ChIP experiment was done using the Lab ChIP-seq protocol

value: Neonatal foreskin

value: primary keratinocytes

tag: chip antibody


title: JMICSM159_DC_ESAM

value: F

value: ESAM


title: JMICSM074_DC_ESAM


title: 94.136

source_name: Lung

value: healthy donor


title: Control_1

tag: cell type


title: 94.137


title: Primary keratinocytes, TEAD1_ChIPseq_rep_2

description: ChIP-seq protocol


title: Primary keratinocytes, TEAD1_ChIPseq_rep_1

description: ChIP-seq protocol


title: JMICSM158_DC_ESAM


title: hi600_3

city: Cleveland

first: Maria

last: Hatzoglou

state: OH

address: 10900 Euclid Ave

department: Genetics and Genome Science

institute: Case Western Reserve University

data_processing:
Basecalling was performed using CASAVA 1.8
Raw/sequenced reads were filtered to remove reads containing adaptors, reads containing >10% bases that could not be determined, and reads with low Quality value.
Reads were mapped to the reference genome (mm10) using STAR software
Genome_build: mm10
Supplementary_files_format_and_content: Con_lo500_hi600_MEFs_processed.txt contains raw numbers of reads and FPKM for each sample.

source_name: MEF

growth_protocol: MEFs were grown on 100 mm cell culture dishes in DMEM containing 10% fetal bovine serum, 2 mM glutamine, 100 units/ml of penicillin and 100 ug/ml streptomycin. Cells were maintained at 37 degrees C and 5% CO2.

extract_protocol:
MEFs were flash frozen in liquid nitrogen and stored at -80 degrees C. Total RNA was extracted using Trizol reagent.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. The mRNA was fragmented randomly by addition of fragmentation buffer. Then first strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Double-stranded cDNA was purified using AMPure XP beads. Remaining overhangs of the purified double-stranded cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3' ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Finally, the final library is retrieved by PCR amplification and purification of PCR products by AMPure XP beads.

treatment_protocol: MEFs at approximately 80% confluence were treated with DMEM containing 200 mM sucrose (total 500 mOsm, lo500) or 300 mM sucrose (total 600 mOsm, hi600).

tag: strain

value: Mouse Embryonic Fibroblast (MEF)

tag: stress

value: 600 mOsm sucrose


title: 94.3


title: Control_2


title: Mono_CA

city: Jena

first: Christine

last: Skerka

address: Beutenbergstraße 11A

department: Infection Biology

institute: Leibniz Institute for Natural Product Research and Infection Biology

data_processing:
LCSciences: Transcripts Assembly: Firstly, Cutadapt [Martin M. Cutadapt removes adapter sequences from high-throughput sequencing reads. Embnet Journal 17 (2011)] and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 [Kim, D., Langmead, B. & Salzberg, S.L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015)] to map reads to the genome. The mapped reads of each sample were assembled using StringTie [Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015)]. Then, all transcriptomes from the samples were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie [Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015)] and Ballgown [Frazee, A.C. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat. Biotechnol. 33, 243–246 (2015)] was used to estimate the expression levels of all transcripts.
LCSciences: Different expression analysis of mRNAs: StringTie [Pertea, M. et al. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat. Biotechnol. 33, 290–295 (2015)] was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package Ballgown [Frazee, A.C. et al. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat. Biotechnol. 33, 243–246 (2015)].
Supplementary_files_format_and_content: MonoVSMono_CA_Gene_differential_expression.txt

source_name: blood derived monocytes

growth_protocol: Bicoll (15 mL, Biochrom) was overlayed by a mixture of DPBS (5 mL, Lonza) and buffy coat (30 mL), derived from healthy male donors. After centrifugation (20 min, 550 x g) the PBMC layer was washed with DPBS (5 min, 160 x g). Bicoll and wash steps were repeated twice. Afterwards the pellet was resuspended in IMDM (25 mL, Thermo Scientific) and used for overlaying Percoll (46%) (GE Healthcare Life Sciences) in IMDM. After centrifugation (20 min, 550 x g) the PBMC layer was washed with DPBS. Monocytes were selected according to the protocol of the human Pan Monocyte Isolation Kit (MiltenyiBiotec). Monocyte experiments were performed in RPMI medium with Ultraglutamin (BioWhittaker).

extract_protocol:
RNA was extracted using total RNA purification kit (NORGEN), RNA from Candida albicans treated and untreated monocytes derived from 3 different donors were equaly pooled (total 3 μg) and sequenced by LCSciences
LCSciences: RNA was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 190-200 bp. And then we performed the paired-end sequencing on an Illumina Hiseq 4000 at the (lc-bio, China) following the vendor's recommended protocol.

treatment_protocol: Isolated monocytes (1 x 106) were incubated with Candida albicans (1 x 106) in RPMI with Ultraglutamin for 1 h at 37°C.

value: blood derived monocytes

tag: agent

value: Candida albicans


title: hi600_2


title: JMICSM317_DC_ESAM


title: JMICSM349_DC_ESAM


title: 62.5

tag: disease state


title: 62.81


title: 62.96


title: lo500_3

value: 500 mOsm sucrose


title: hi600_1


title: PCD7040T1

city: New York

first: Samir

last: Parekh

state: NY

address: 1470 Madison Avenue, 5-114, Box 1079

department: Tisch Cancer Institute

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw RNA-seq data from tumor samples (CD138+ cells), in fastq format, were mapped to the reference genome (GRCh37) using STAR (v2.5).
Gene-level features were quantified by featureCounts from the Subread package (v1.5.1).
We filtered expression data to include genes with cpm (counts per million) > 1 in at least 10% of the samples.
Screening patient samples were split by PFS of 1 year, and differential expression analysis was performed using the R package DESeq2.
Variance Stabilizing Transformation was applied to DESeq2 dds output for downstream analysis.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files contain gene-level counts (featurecounts output)

molecule: polyA RNA

source_name: bone marrow CD138+ cells

extract_protocol:
RNA was isolated with the help of the Allprep DNA/RNA/Protein mini kit (Qiagen).
RNA-Seq libraries were constructed from the PolyA selected mRNA using TruSeq RNA sample preparation guide (Illumina) and submitted for the paired-end 100 base pairs sequencing on a HiSeq2500 (Illumina) by the Genomics Core Facility at the Icahn Institute Department of Genetics and Genomic Sciences, following the manufacturer's instructions.

treatment_protocol: Bone marrow was collected and CD138+ cells were selected using a RoboSep instrument (Stemcell Technologies).

tag: time point

tag: disease

value: myeloma tumor

value: CD138+ cells


title: Mono

value: DPBS


title: PCD7039T1


title: 62.46


title: 8_Hours_1

value: synthetic miR-155 oligo-treated

value: CD4+ T-cells


title: lo500_1


title: JMICSM012_DC_ESAM

tag: tissue

value: Buccal epithelial cells

tag: gender

tag: sample timing

value: DC

value: Jamaica

value: child with SAM


title: PCD7038T1


title: 62.148


title: PCD7036T1


title: JMICSM131_DC_ESAM

value: F

tag: disease group

tag: age


title: con_3

value: control


title: C3_T3

description: T1T2_T3_RN.rsem.hg38.ensembl.counts.matrix.txt

source_name: T3 B cells

value: Healhty donor 3

value: T3 B cells


title: JMICSM402_DL_ESAM

value: M

value: DL

value: ESAM

tag: nationality

value: health adult with history of SAM


title: con_2

value: Mouse Embryonic Fibroblast (MEF)


title: 62.79

value: healthy donor


title: JMICSM378_DL_ESAM

tag: sentrix id


title: PCD7034T1

value: myeloma tumor

value: CD138+ cells


title: PCD7029T1


title: JMICSM085_DC_ESAM

tag: sentrix position


title: con_1


title: lo500_2

value: 500 mOsm sucrose


title: JMICSM340_DL_ESAM

value: Buccal epithelial cells

tag: diagnosis


title: C3_T1T2

source_name: T1/T2 B cells

value: T1/T2 B cells


title: PCD7028T1


title: JMICSM279_DL_ESAM

value: Jamaica


title: JMICSM237_DL_ESAM


title: PCD7027T1


title: C2_T1T2

value: Healhty donor 2


title: PCD7026T1


title: C2_RN

source_name: Follicular B cells

value: Follicular B cells


title: JMICSM331_DL_ESAM


title: JMICSM324_DL_ESAM

value: F


title: C1_T3

value: Healhty donor 1


title: JMICSM300_DL_ESAM


title: PCD7023T1


title: PCD7019T1


title: C3_RN

value: Healhty donor 3


title: C1_RN


title: C2_T3

value: T3 B cells


title: PCD7013T1


title: JMICSM298_DL_ESAM

value: DL


title: C1_T1T2


title: JMICSM295_DL_ESAM

value: M

value: ESAM


title: PCD7008T1


title: Human replicate 2

tag: coriell id


title: PCD7009T1

tag: cell type


title: Human replicate 3


title: PCD7007T1


title: Human replicate 1


title: PCD7006T1


title: PCD7002T1


title: Caput PAX2 siRNA rep 3

first: Ann

last: Harris

institute: Case Western Reserve Uni

data_processing:
Libraries were sequenced on Illumina HiSeq2500 machines.
Data was analyzed using TopHat and Cufflinks (Trapnell et al., 2012 Nat Protoc. 7, 562-78.).
Biological processes associated with differentially expressed genes were identified using DAVID (Huang et al., 2009 Nucleic  Acids Res. 37, 1-13; Huang et al., 2009 Nat Protoc. 4, 44-57.)
Genome_build: hg19
Supplementary_files_format_and_content: Differentially expressed gene analysis

source_name: Caput Human Epididymis Epithelial Cells

extract_protocol:
Confluent adult Caput HEE cells transiently transfected with siRNA (targetting PAX2 or a non-targetting control) for 72h, were harvested for RNA extraction using TRIzol. RNA quality was confirmed by Nanodrop measurement of OD 260/280 and 260/230 ratios and stored at -800C under ethanol. 1ug RNA was used for RNA-seq library preparation.
RNA-seq libraries were prepared using the TruSeq RNA Sample Preparation Kit v2 (Low-Throughput protocol, Illumina).

value: Caput Human Epididymis Epithelial Cells


title: Caput PAX2 siRNA rep 2


title: LNCaP radiosensitive replicate 3

description: Gene expression profiling

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x GEx Hybridization Buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute at 37°C wit GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner G2505C using scan protocol Agilent G3_GX_1_color for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green)

data_processing: Quantile normalization was used to normalize the hybridization signals (gProcessedSignal). This was done separately for all DU145 and LNCaP samples to account for differences between DU145 and LNCaP.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 50 ng RNA using the One-Color Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer's recommendations

tag: cell line

value: parental LNCaP

tag: phenotype

value: Radiosensitive


title: LNCaP radiosensitive replicate 2

description: Gene expression profiling


title: LNCaP radioresistant replicate 3

description: Gene expression profiling

source_name: Radioresistant LNCaP

value: derived from LNCaP

value: Radioresistant


title: CDK9 shRNA+Pg_2

tag: agent

value: P. gingivalis


title: Caput PAX2 siRNA rep 1


title: Caput control siRNA rep 3


title: LNCaP radioresistant replicate 1

description: Gene expression profiling


title: LNCaP radioresistant replicate 2

description: Gene expression profiling


title: GTF2I inducible clone, biological replicate1 [hGTF2I_A1_T24]

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description:
SAMPLE 4
Gene expression data from mouse inducible ES stable clone

hyb_protocol: Biotinylated cRNAs were generated using the GeneChip IVT labelling kit (Affymetrix). 20µg of Biotinylated cRNA was fragmented and 10µg hybridised to the Affymetrix GeneChip Mouse Genome 430_2 array for 16hrs at 45°C using an Affymetrix GeneChip Fluidics Station 450 according to the manufacturer’ standard protocols.

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

data_processing: The data were analyzed with the Bioconductor package Affy using RMA method for normalizing and summarizing probe level intensity measurements.

label: biotin

source_name: inducible ES stable cell line grown in medium deprived of Tetracycline

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

growth_protocol: The growth of each inducible clone was performed in medium deprived of Tetracycline for 24 hours, while the control clones were grown in medium containing Tetracycline and the total RNA was extracted

extract_protocol: Total RNAs from either undifferentiated ES cells were purified by QIAshredder (Qiagen spa, Milano, Italy, catalog no. 79656) and extracted with RNeasy Protect Mini Kit (Qiagen, catalog no. 74126) using standard conditions.

value: mouse Embryonic Stem (ES)  cells

tag: genotype/variation

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD2


title: CTL, biological replicate 3 [hGTF2I_C6_T0]

description:
SAMPLE 3
Gene expression data from mouse inducible ES stable control clone

source_name: inducible ES stable cell line grown in medium containing Tetracycline


title: GTF2I inducible clone, biological replicate2 [hGTF2I_B3_T24]

description:
SAMPLE 5
Gene expression data from mouse inducible ES stable clone


title: Caput control siRNA rep 2


title: GTF2I inducible clone, biological replicate3 [hGTF2I_C6_T24]

description:
SAMPLE 6
Gene expression data from mouse inducible ES stable clone


title: LNCaP radiosensitive replicate 1

description: Gene expression profiling

source_name: Radiosensitive LNCaP


title: DU145 radiosensitive replicate 3

description: Gene expression profiling

source_name: Radiosensitive DU145

value: parental DU145


title: CTL, biological replicate 2 [hGTF2I_B3_T0]

description:
SAMPLE 2
Gene expression data from mouse inducible ES stable control clone


title: Caput control siRNA rep 1


title: CTL, biological replicate 1 [hGTF2I_A1_T0]

description:
SAMPLE 1
Gene expression data from mouse inducible ES stable control clone


title: DU145 radiosensitive replicate 1

description: Gene expression profiling


title: Tmock_IP_4

city: Zurich

first: A

last: McIntyre

address: Winterthurerstrasse 190

department: Molecular Life Sciences

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using CASAVA version 1.8.2
STAR version 2.6.1 alignment to hg38
TRIMMOMATIC (v0.36) used to trim adapters, ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:15
Peaks were called using MACS2 (v2.1.1), --nomodel --extsize 180 -g 100e6
Genome_build: hg38
Supplementary_files_format_and_content: narrowPeak format from MACS2

source_name: Huh7 liver cell line

growth_protocol: Cultured in 10 cm plates in cDMEM media

extract_protocol:
TRIzol, Dynabeads mRNA purification kit (Thermo Fisher)
Illumina Tru-seq PolyA RNA, 2 x 50

treatment_protocol: HCV PAMP: Transfected using Mirus mRNA transfection reagent, harvested at 8 hpt. TG: Treated with 500nM TG, harvested at 16 hpt.

tag: treatment

tag: antibody

value: NEB anti-m6A


title: WBSCR1 inducible clone, biological replicate3 [hWBSCR1_A4_T24]

value: inducible transgenic line overexpressing the human isorofm of the gene WBSCR1


title: Sso7D SARC-I at pH 1 - 3

city: Lincoln

first: Paul

last: Blum

state: NE

address: 1901 Vine St.

department: School of Biological Sciences

institute: University of Nebraska-Lincoln

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to SULG genome using Bowtie
Qualtiy and reproducibility between samples was determined using DeepTools multiBAMSummary, plotCorrelation and ComputeGCBias
Input DNA background was subtracted from experimental samples using DeepTools bamCompare
Data was visualized using IGV
Genome_build: SULG
Supplementary_files_format_and_content: bedgraph files showing read depth at genome locations (average of 10bp)

organism: Saccharolobus solfataricus

source_name: Crosslinked cells

growth_protocol: Cells were cultured in brock salts media with tryptone of pH 3.0 or 1.0

extract_protocol:
Crosslinked pellets were sonicated until chromatiin fragments reached 300-500bp and immunoprecipitated in triplicate using polyclonal antibody serum for Cren7 or Sso7D
Samples were blunt ended, A-tailed and ligated to barcoded adapters. Libraries were used to template PCR amplificaiton for 12 cycles, and products were quantified using a bioanalyzer. ChIP and background libraries were pooled in equimolar concentrations and submitted for Illumina HiSeq3000 sequencing, yielding about 300 million 50bp reads.

treatment_protocol: Cultures were crosslinked with formaldehyde when they reached 0.5OD(540nm), and stored at -20C as 10OD pellets.

tag: strain

value: SARC-I

tag: chip antibody

value: Sso7D polyclonal serum


title: DU145 radioresistant replicate 3

description: Gene expression profiling

source_name: Radioresistant DU145

value: derived from DU145


title: DU145 radioresistant replicate 2

description: Gene expression profiling


title: WBSCR1 inducible clone, biological replicate2 [hWBSCR1_A3_T24]


title: Tmock_IP_3


title: Sso7D SARC-I at pH 1 - 2


title: Tmock_input_2


title: DU145 radioresistant replicate 1

description: Gene expression profiling


title: Tmock_IP_2


title: Sso7D SARC-I at pH 1 - 1


title: Tmock_input_4


title: Sso7D SARC-I at pH 1 - input DNA

value: No antibody - total genomic DNA


title: WBSCR1 inducible clone, biological replicate1 [hWBSCR1_A1_T24]


title: CTL, biological replicate 3 [hWBSCR1_A4_T0]


title: CTL, biological replicate 2 [hWBSCR1_A3_T0]


title: CTL, biological replicate 1 [hWBSCR1_A1_T0]


title: HEK293T, No gRNA 3

city: Philadelphia

first: Edward

last: Lee

state: PA

address: 613A Stellar Chance Laboratories; 422 Curie Blvd

institute: University of Pennsylvania

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
Data was processed using ChAMP R package (v 2.12.4) with default parameters using BMIQ normalization; NogRNAvMethtemp_AllDMPs_ChAMP.txt contains group means (3 biological replicates) of normalizd Beta values for No gRNA contol (Control_AVG column) vs Methylation via HARDEN (Meth_AVG column) for each probe as outputted by ChAMP
ChAMP  R package (v2.12.4) was used to compute normalized Average Beta using BMIQ for each sample

label: Cy3, Cy5

source_name: HEK293T cells transfected with No gRNA plasmid+Meth template

label_protocol: Standard Illumina protocol

growth_protocol: HEK293Ts were grown in DMEM supplemented with 1X Pen/Strep and 10% FBS

extract_protocol: DNA was extracted with Qiagen Dneasy kit

treatment_protocol: Cells were transfected using Fugene 6

tag: method

value: No gRNA control


title: Sso7D SARC-I at pH 3 - 3


title: Tmock_input_1


title: Sso7D SARC-I at pH 3 - 2


title: HEK293T, Cas9+Meth 3

source_name: HEK293T cells were transfected with Cas9+gRNA+Meth template

value: Methylation via HARDEN


title: HEK293T, Mock Transfection 2

source_name: HEK293T, Mock Transfection

value: Non-transfected control


title: Sso7D SARC-I at pH 3 - input DNA


title: Sso7D SARC-I at pH 3 - 1


title: HEK293T, dCas9-DNMT3a 2

data_processing:
Data was processed using ChAMP R package (v 2.12.4) with default parameters using BMIQ normalization; dCas9ANV_vs_dCas9DNMT3a_AllDMPs_ChAMP.txt contains the group means (3 biological replicates) of  normalized Beta values for dead DNMT control (C_AVG column) vs Methylation via DNMT3a (M_AVG column) for each probe as outputted by ChAMP.
ChAMP  R package (v2.12.4) was used to compute normalized  Average Beta using BMIQ for each sample

source_name: HEK293T cells transfected with dCas9-DNMT3a

value: Methylation via DNMT3a


title: HEK293T, Mock Transfection 1


title: GTF2IRD2 inducible clone, biological replicate2 [hRD2_A4_T24]


title: HEK293T, No gRNA 1


title: HEK293T, Cas9+Meth 2


title: HEK293T, No gRNA 2


title: Sso7D SULG at pH 3 - input DNA

value: SULG


title: CTL, biological replicate 3 [hRD2_A5_T0]


title: TG_input_4

value: thapsigargin (TG; 16 hrs)


title: GTF2IRD2 inducible clone, biological replicate1 [hRD2_A3_T24]


title: GTF2IRD2 inducible clone, biological replicate3 [hRD2_A5_T24]


title: TG_input_3


title: DU145 radiosensitive replicate 2

description: Gene expression profiling

value: Radiosensitive


title: Sso7D SULG at pH 3 - 3


title: HEK293T, dCas9-DNMT-ANV 3

source_name: HEK293T cells transfected with dCas9-DNMT3a-ANV

value: Dead DNMT control


title: Tmock_input_3


title: TG_IP_3


title: Sso7D SULG at pH 3 - 2


title: HEK293T, Cas9+Meth 1


title: HEK293T, dCas9-DNMT-ANV 1


title: TG_input_2


title: Sso7D SULG at pH 3 - 1


title: HEK293T, No Transfection 1

source_name: HEK293T, No Transfection


title: CTL, biological replicate 1 [hRD2_A3_T0]

value: mouse Embryonic Stem (ES)  cells


title: HEK293T, dCas9-DNMT-ANV 2


title: HEK293T, dCas9-DNMT3a 1


title: Cren7 SARC-I at pH 1 - input DNA


title: TG_input_1


title: Cren7 SARC-I at pH 1 - 3

value: Cren7 polyclonal serum


title: TG_IP_2


title: TG_IP_1


title: GTF2IRD1 inducible clone, biological replicate3 [hRD1_D4_T24]

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD6


title: Tmock_IP_1

value: NEB anti-m6A


title: Cren7 SARC-I at pH 1 - 1


title: Pmock_IP_4


title: Cren7 SARC-I at pH 1 - 2


title: Pmock_input_4


title: HEK293T, No Transfection 2


title: HEK293T, dCas9-DNMT3a 3


title: Cren7 SARC-I at pH 3 - input DNA


title: Cren7 SARC-I at pH 3 - 3


title: CTL, biological replicate 2 [hRD2_A4_T0]

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD2


title: Cren7 SARC-I at pH 3 - 2

value: SARC-I


title: GTF2IRD1 inducible clone, biological replicate2 [hRD1_D2_T24]

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD5


title: Cren7 SARC-I at pH 3 - 1


title: Pmock_IP_2


title: Pmock_input_2


title: Cren7 SULG at pH 3 - input DNA


title: Pmock_input_1


title: Pmock_input_3


title: Cren7 SULG at pH 3 - 3


title: Pmock_IP_1


title: PAMP_input_4

value: HCV PAMP (8 hrs)


title: Cren7 SULG at pH 3 - 1


title: Cren7 SULG at pH 3 - 2


title: Pmock_IP_3


title: CTL, biological replicate 1 [hRD1_D1_T0]

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD1


title: PAMP_IP_4


title: CTL, biological replicate 2 [hRD1_D2_T0]


title: GTF2IRD1 inducible clone, biological replicate1 [hRD1_D1_T24]

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD4


title: DCL2RNA3

city: GUANGZHOU

first: HONG

last: ZHU

state: GUANGDONG

address: 723 XINGKE RD.TIANHE DISDRICT

institute: SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES

data_processing:
Raw sRNA-seq reads were firstly processed through custom perl and python scripts to remove reads containing ploy-N, adapter and low quality reads
The small RNA tags were mapped to reference sequence by Bowtie
small RNA tags were mapped to RepeatMasker, Rfam database or those types of datas from the specified species itself to  remove tags originating from protein-coding genes, repeat sequences, rRNA,tRNA, snRNA, and snoRNA
Candidate miRNAs were predicted with miREvo and mirdeep2

organism: Penicillium italicum

source_name: Spores and hyphae

growth_protocol: All the  strains were cultured on potato dextrose agar (PDA) at 25 ± 2 ℃

extract_protocol:
total RNA was extracted by using the HiPure Fungal Mini kit
Nine sRNA libraries (three DCL1RNAi, three DCL2RNAi and three wild type) were prepared with the total RNAs between the size18-30 nt by using TruSeq small RNA library kits

tag: tissue

value: Spores and hyphae


title: KO3

city: INDIANAPOLIS

first: TAREK M. (ASHKAR)(M.D.)

last: EL-ACHKAR

state: IN

address: 950 w walnut- r2 202

institute: INDIANA UNIVERSITY, DIVISION OF NEPHROLOGY

hyb_protocol: Individual labeled samples were hybridized to the Mouse Gene 2.0 ST GeneChips for 17 hours then washed and stained.

scan_protocol: Arrays were scanned with the standard protocol using Affymetrix GeneChip Command Console Software (AGCC) to generate data (CEL files)

data_processing: CEL files were imported into Partek Genomics Suite 6.6 (Partek, Inc.) for analysis. RMA (Robust multichip average ) expression values were generated for all probe sets using the RMA background correction, Quantile normalization and summarization by Median Polish. Summarized signals for each probe set were log2 transformed.

source_name: kidney S3 proximal tubule

label_protocol: Two ng of total RNA for each sample was labeled using the standard protocol for the Affymetrix WT Pico kit (Affymetrix).

extract_protocol: Arcturus Picopure kit (Aplied Biosystems)

value: kidney S3 proximal tubule

tag: genotype

value: THP -/-

tag: batch


title: KO1


title: KO4


title: DCL2RNA1


title: APUM9_OE2

city: Beaucouzé

first: Etienne

last: Bucher

address: 42 rue Georges Morel

country: France

institute: IRHS

description: APUM9_OE2 htseq-counts

data_processing:
RNA-seq reads were mapped to the TAIR10 Arabidopsis reference genome using STAR (Dobin et al., 2015)
read coverages on annotations were assessed with htseq-count
Differential gene expression was calculated using DESeq2 using two biological replicates for each line (Love et al., 2014)
Transcripts that had a adjusted p-value of less than 0.13 were counted as significantly differentially expressed
Supplementary_files_format_and_content: htseq-counts of the individual replicates and  DESeq2 output

organism: Arabidopsis thaliana

growth_protocol: Plants were imbibed with water for 6h

extract_protocol:
Total RNA was extracted from 100mg of wild-type and A9-OE imbibed Arabidopsis seeds, 6 h after imbibition following the Rapid Trisol based 2 step method by Ling Meng and Lewis Feldman (Meng and Feldman, 2010).
Trueseq RNA library

treatment_protocol: no treatment

value: APUM9 overexpression

value: imbibed seeds

tag: time point

value: 6h after imbibition


title: TG_IP_4

value: thapsigargin (TG; 16 hrs)


title: WT5

value: WT


title: KO5


title: CTL, biological replicate 3 [hRD1_D4_T0]

value: mouse Embryonic Stem (ES)  cells

value: inducible transgenic line overexpressing the human isorofm of the gene GTF2IRD3


title: WT6


title: APUM9_OE1

description: APUM9_OE1 htseq-counts


title: PAMP_input_3


title: WT4


title: DCL2RNA2


title: PAMP_IP_3

value: NEB anti-m6A


title: DCL1RNA3


title: WT3


title: DCL1RNA2


title: WT2

description: WT2 htseq-counts

value: wild type


title: WT1

description: WT1 htseq-counts


title: DCL1RNA1


title: Gorilla replicate 3

city: Durham

first: Gregory

last: Crawford

address: 101 Science Drive

institute: Duke University

data_processing:
Due to the use of MmeI to generate DNase-seq libraries, sequencing reads were trimmed to 20 bases using a custom perl script.
Reads for each species were mapped to its native genome using Bowtie version 0.12.9 (parameters: -trim5 0 --trim3 0 -m 1 -l 20) as part of a custom two-step pipeline. In the first step (“tier 1”), reads were required to match to a unique location with no mismatches (parameter: -n 0). In the second step (“tier 2”), unmapped reads from step one were re-mapped with a relaxed mismatch parameter of one mismatch  (parameter: -n 1). Reads that mapped to multiple locations or had more than one mismatch were discarded.
Samtools version 0.1.19-44428cd was used to convert the sam files from each step to bam files, merge them into one file, and remove duplicate reads (defined as having the same chromosomal position).
Bedtools v2.17.0 was used to convert the bam files to bed files.
Reads from the non-human samples were converted from their native genome coordinates to the human hg19 genome coordinates using a three-step process that removed reads that did not have a one-to-one relationship between the genomes. In each step, read coordinates were converted from one genome to the other using the UCSC liftOver software with a minMatch parameter of 0.8, which requires that 80% of the read maps to the new genome. Note that this parameter filters only on genomic coverage, not sequence identity. In the first step, read coordinates were converted from their native genome to hg19. Read coordinates that successfully lifted to hg19 were then lifted back to the native genome. Read coordinates that did not lift back to the same coordinates on the native genome were removed. Reads that did lift back to the same coordinates were lifted back to hg19. An additional filtering step was added to ensure the reads did not map to a duplicated region. In that step, overlapping reads were merged into a region, and that region was lifted from the native genome to hg19. Regions that failed to lift uniquely to hg19 were flagged and reads that overlapped them were removed.
Because some of the samples were from males and some were from females, we removed reads that mapped or lifted over to the human X or Y chromosomes to eliminate any sex-specific bias.
Genome_build: hg19 for human, panTro4 for chimpanzee, gorGor3 for gorilla, ponAbe2 for orangutan, rheMac3 for macaque
Supplementary_files_format_and_content: bed files contain hg19 coordinates for the reads

organism: Gorilla gorilla

source_name: Skin fibroblast cells

extract_protocol:
Cells were grown in culture then pelleted before immediately proceeding to DNase-seq library preparations. All DNase-Seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106). Briefly, cells were lysed and incubated at 37¡C for various times (5 min to 1 hour) and optimal DNase digestion was confirmed by pulsed field gel electrophoresis (Song L and Crawford GE. Cold Spring Harbor protocols 2010(2):pdb prot5384).
DNase-seq libraries were prepared according to (Song L, et al. Genome Res. 2011; PMID 21750106).


title: PAMP_IP_2


title: PAMP_input_2


title: WT2


title: Gorilla replicate 2


title: Orangutan replicate 3

organism: Pongo pygmaeus


title: KO2


title: CK3


title: PAMP_input_1


title: Orangutan replicate 2


title: CK2


title: Gorilla replicate 1


title: PAMP_IP_1


title: Orangutan replicate 1


title: CK1


title: SST040241L

status: Public on Oct 10 2019

city: New Haven

first: Matthew

middle: J

last: Girgenti

address: 34 Park St

institute: Yale School of Medicine

description: FACs-RNAseq

data_processing:
The reads were trimmed for quality.  The trimmed reads were aligned to the mm10 (UCSC reference mm10) reference genome using TopHat2.
Cufflinks and cuffdiff were used to generate transcript abundance estimates, and differential gene expression statistics.
The analyzed data was visualized using R and cummeRbund.  The genes were called "significantly" differentially expressed for q <= 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM Matrix

source_name: medial prefrontal cortex

extract_protocol:
To isolate interneurons with tdTomato expression, PFC was rapidly dissected placed in digestion buffer (PBS/10% Papain). Following 20 min incubation at 37ºC, digestion was stopped with FACS buffer (PBS/1% BSA), followed by gentle dissociation with a glass Dounce homogenizer (Kontes Glass Company, Vineland, NJ). Single-cell solutions were spun down at 1000 rpm for 5 minutes, re-constituted in 600 ul of FACS buffer, and filtered (40 um) into flow tube. Samples were sorted on a FACS Aria (Yale Immune Monitoring Core Facility) into lysis buffer; average yield was ~150,000 cells/sample. RNA was obtained with the Norgen Single Cell RNA Purification Kit (#51800; Norgen Biotek Corp., Thorold, Ontario, Canada).
100 ng of total mRNA was processed using the Pico RiboGone-Mammalian kit (TakaraBio, Kyoto, Japan) before cDNA synthesis.

treatment_protocol: experimental mice were exposed to chronic unpreditable stress for 14

value: FAC sorted interneurons

tag: Sex

value: male

tag: interneuron subtype

value: somatostatin

tag: exposure to stress

value: non-stress

value: medial prefrontal cortex


title: SST0-M

description: FACs-RNAseq

tag: cell type


title: SST3-M

description: FACs-RNAseq


title: SS04031RR

description: FACs-RNAseq

value: stress


title: SST1-M

description: FACs-RNAseq


title: FPVtdCUSB

description: FACs-RNAseq

value: female

value: parvalbumin


title: FSSTtdCUS1

description: FACs-RNAseq


title: SST4-M

description: FACs-RNAseq


title: SST4-F

description: FACs-RNAseq


title: SST6-F

description: FACs-RNAseq


title: SST-F

description: FACs-RNAseq


title: SS04031RL

description: FACs-RNAseq


title: SS04031R

description: FACs-RNAseq


title: SST2-F

description: FACs-RNAseq


title: SST04241LL

description: FACs-RNAseq


title: SS04031LL

description: FACs-RNAseq


title: FPVtdCUSA

description: FACs-RNAseq


title: SST1-F

description: FACs-RNAseq


title: WT1

value: kidney S3 proximal tubule


title: SST5-F

description: FACs-RNAseq


title: PV6-M

description: FACs-RNAseq


title: PV5-M

description: FACs-RNAseq


title: FSSTtdCUS2

description: FACs-RNAseq


title: FSSTtd3CUS

description: FACs-RNAseq


title: PV0-F

description: FACs-RNAseq


title: PV3-M

description: FACs-RNAseq


title: PV4-M

description: FACs-RNAseq


title: PV1-M

description: FACs-RNAseq


title: PV0-M

description: FACs-RNAseq


title: PV2-M

description: FACs-RNAseq


title: SST3-F

description: FACs-RNAseq


title: LPS_Heart_lysate_R3

city: Ann Arbor

first: Santhi

last: Ganesh

state: Michigan

address: 1150 W Medical Center Drive

department: Department of Internal Medicine

institute: University of Michigan

data_processing:
Fastq generation was performed using Illumina’s CASAVA-1.8.2 software
Alignment raw sequences using Bowtie2 (version 2.2.3)
Quantification and transcript length normalization with rSeq
Genome_build: mouse Gencode reference GRCm38.p2
Supplementary_files_format_and_content: CSV file contains read counts after rSeq processing; includes all genes in transcriptome and values represent read counts adjusted for transcript length

source_name: Heart

extract_protocol:
RNA (before/after TRAP) was isolated using the Qiagen RNeasy kit. SMARTer Ultra Low Input kit (Clontech) was used for RNA conversion (5 ng for tissue lysate, 10 ng for EC-TRAP samples).
cDNA was bead-purified and mechanically sheared to a 200-250 base pair range. End repair with T4 DNA polymerase was followed by dA-tailing using Klenow 3’ to 5’ exonuclease and adenosine triphosphate to create a 3’ adenosine overhang to promote adapter ligation. After purification, samples were linearized by PCR before being size-selected in a range of 300-350 bp using Invitrogen’s E-Gel system. Final enrichment of the adapter-modified cDNA fragments was performed by PCR using Phusion High-Fidelity DNA Polymerase.

treatment_protocol: Tissues were snap frozen after cycloheximide perfusion and mechanically dissociated, unless otherwise indicated

value: Heart

value: Tek-Cre

value: LPS

tag: isolation method

value: mechanic tissue dissociation

tag: molecule subtype

value: total mRNA


title: LPS_Heart_lysate_R2


title: LPS_Kidney_lysate_R2

source_name: Kidney

value: Kidney


title: LPS_Heart_ECTRAP_R3

source_name: Heart ECs

value: polysome-associated mRNA


title: LPS_Lung_lysate_R1

source_name: Lung

value: Lung


title: LPS_Lung_lysate_R2


title: LPS_Heart_ECTRAP_R2


title: LPS_Kidney_ECTRAP_R3

source_name: Kidney ECs


title: LPS_Kidney_lysate_R1


title: LPS_Liver_lysate_R2

source_name: Liver

value: Liver


title: Pf4_Plts_lysate_pool

source_name: Platelets

value: Platelets

value: Control

value: fresh cells


title: LPS_Lung_ECTRAP_R2

source_name: Lung ECs


title: LPS_Kidney_lysate_R3


title: LPS_Kidney_ECTRAP_R1


title: LPS_Lung_ECTRAP_R1


title: LPS_Heart_ECTRAP_R1


title: LPS_Heart_lysate_R1


title: LPS_Liver_ECTRAP_R2

source_name: Liver ECs


title: LPS_Liver_ECTRAP_R1


title: LPS_Lung_ECTRAP_R3


title: LPS_Liver_lysate_R1


title: Pf4_Plts_TRAP_pool

source_name: Platelets after TRAP


title: LPS_Liver_lysate_R3


title: LPS_Liver_ECTRAP_R3


title: LPS_Brain_lysate_R3

source_name: Brain

value: Brain


title: LPS_Brain_ECTRAP_R3

source_name: Brain ECs


title: LPS_Lung_lysate_R3


title: LPS_Brain_ECTRAP_R2


title: LPS_Brain_ECTRAP_R1


title: EnzDis_Liver_ECTRAP_R1

value: enzymatic tissue dissociation


title: LPS_Brain_lysate_R1


title: EnzDis_Liver_ECTRAP_R3


title: EnzDis_Liver_ECTRAP_R2


title: EnzDis_Liver_lysate_R3


title: EnzDis_Liver_lysate_R2


title: EnzDis_Kidney_lysate_R3


title: EnzDis_Brain_lysate_R2


title: EnzDis_Brain_ECTRAP_R2


title: EnzDis_Kidney_ECTRAP_R3


title: EnzDis_Brain_ECTRAP_R3


title: EnzDis_Liver_lysate_R1


title: EnzDis_Brain_lysate_R3


title: EnzDis_Kidney_lysate_R2


title: LPS_Brain_lysate_R2


title: BMT_Heart_ECTRAP_R1

value: Cre-negative bone marrow transplant

value: mechanic dissociation


title: BMT_Heart_lysate_R1


title: BMT_Brain_ECTRAP_R1


title: EnzDis_Kidney_lysate_R1


title: BMT_Brain_lysate_R1


title: BMT_Kidney_lysate_R1


title: LPS_Kidney_ECTRAP_R2


title: BMT_Liver_ECTRAP_R1


title: EnzDis_Brain_lysate_R1


title: BMT_Liver_lysate_R1


title: BMT_Kidney_ECTRAP_R1


title: EnzDis_Brain_ECTRAP_R1


title: EnzDis_Kidney_ECTRAP_R2


title: Paupar KD-rep2-Input

first: Ruth

middle: A

last: Singer

address: 1230 York Avenue, TSH 314

institute: The Rockefeller University

description: Input

data_processing:
Sequencing was performed using the Illumina HiSeq 2500 system according to the manufacturer’s instructions.
Reads were mapped to the reference genome (mm10) using Bowtie2 (Langmead and Salzberg, 2012) with the ‘--sensitive-local’ setting.
Peaks were called using MACS2 (Zhang et al., 2008; v 2.1.2) with reads extended by 200 bp while bypassing the standard model and a qvalue cutoff of 0.01.
Differential binding between control KD and Paupar KD samples was assessed using DiffBind (Ross-Innes et al., 2012) using default settings.
Annotation and visualization of genes nearby Pax6 binding peaks was done using ChIPseeker (Yu, Wang, and He, 2015).
Genome_build: mm10
Supplementary_files_format_and_content: bed files for all peaks

source_name: alphaTC1 cells

extract_protocol:
The ChIP-IT High Sensitivity kit (Active Motif) was used according to the kit instructions.
ChIP-seq libraries were prepared according to the instructions of the KAPA Hyper Prep kit for Illumina.

treatment_protocol: Antisense Oligonucletides against a scrambled control sequence or Paupar


title: Control KD-rep2-Input

description: Input


title: BL6_Ach_4

first: Christopher

middle: L

last: Mendias

address: 535 E 70th St

institute: Hospital for Special Surgery

data_processing:
Libraries were sequenced on Illumina HiSeq2500 using paired-end 28-8-98 protocol
Sequences were aligned to mm10 using Cell Ranger pipeline (10x Genomics)
Expression data was processed with Seurat v2.3.4 (Satija lab) using R v3.5.2 (Eggshell Igloo)
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 0)
filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
log normalization of expression data, scaling of expression data
MultiCCA to combine datasets of 4 mice
PCA dimension reduction
UMAP visualization
Genome_build: mm10
Supplementary_files_format_and_content: .txt files of metadata matrix, normalized gene expression matrix, and raw gene expression matrix

source_name: Achilles tendon

extract_protocol:
Single cell RNA sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (version 3, 10X Genomics, Pleasanton, CA, USA) following the directions of the manufacturer. Cells were loaded into the kit and RNA was isolated and processed using a Chromium Controller (10X Genomics).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: age

value: 6 weeks

value: Male


title: BL6_Ach_3


title: Paupar KD-rep1-Input

description: Input


title: Control KD-rep1-Input

description: Input


title: Control KD-rep1-Pax6

description: Pax6 ChIP


title: Control KD-rep2-Pax6

description: Pax6 ChIP


title: Paupar KD-rep1-Pax6

description: Pax6 ChIP


title: BL6_Ach_2


title: Mouse P30 SATB2 2

city: Boston

first: Ryoji

last: Amamoto

state: Massachusetts

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

data_processing:
Quality control of RNA-seq reads were performed using fastqc version 0.11.5
RNA-seq reads were clipped and mapped onto the mouse genome (Ensembl GRCm38.88) or human genome (Ensembl GRCh38.87) using STAR version 2.5 (27,28). Parameters used were as follows: --runThreadN 6 --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --outSAMattributes Standard --clip3pAdapterSeq  --quantMode TranscriptomeSAM GeneCounts
Read counts were generated by HT-seq version 0.6.1 (30). Sample parameters used were as follows: -i gene_name -s no
Genome_build: mm10
Supplementary_files_format_and_content: Text files with the read counts for every gene for each sample.

source_name: Mouse P30 SATB2

extract_protocol:
The mouse cerebral cortex was dissected and frozen. Nuclei were extracted, fixed, and immunolabeled with appropriate primary and secondary antibodies. Specific nuclear populations were FACS isolated and the RNA was extracted from the nuclei using the RecoverAll Kit.
cDNA was generated using the SMART-Seq v.4 kit. The indices were added using the Nextera XT Kit.

value: Cerebral Cortex

value: Nuclear RNA


title: Mouse P30 BCL11B 2

source_name: Mouse P30 BCL11B


title: Mouse Adult SATB2 2

source_name: Mouse Adult SATB2

value: Adult


title: Mouse P30 SATB2 1


title: Mouse P7 Nuclear 2

source_name: Mouse P7 Nuclear


title: Mouse P7 Cellular 2

source_name: Mouse P7 Cellular

value: Cellular RNA


title: Mouse P30 BCL11B 1


title: Mouse Adult BCL11B 2

source_name: Mouse Adult BCL11B


title: Paupar KD-rep2-Pax6

description: Pax6 ChIP


title: Healthy replicate 2

city: Tabriz

first: Karim

last: Hasanpur

state: East Azarbayjan

address: Jam-Jam street

department: Animal Science

country: Iran

institute: University of tabriz

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor and low-quality sequence, then mapped to Gallus_gallus-4 whole genome using tuxedo software suite
Genome_build: Gallus_gallus-4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each Sample.

organism: Gallus gallus

source_name: Right ventricule

growth_protocol: All of the chicks were mintained under normal condition until 21 days of age and then cold temperature was employed to induce ascites in almost all of the ascites susceptible chickens

extract_protocol:
Total RNA was extracted using TRIzol reagent using manufacturer instractions
PolyA enriched RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the chicks were treated with cold temperature as ascites inducing challenge started at day 21 and continued until day 54.

tag: breed

value: Iranian native meat-type chicken breed

tag: group

value: Healthy


title: Ascitic replicate 2

value: Ascitic


title: Healthy replicate 1


title: Ascitic replicate 1


title: Mouse Adult SATB2 1

tag: antibody


title: Mouse Adult BCL11B 1

tag: strain


title: EnzDis_Kidney_ECTRAP_R1

source_name: Kidney ECs

value: Kidney

value: Tek-Cre

tag: treatment

value: polysome-associated mRNA


title: BL6_Ach_1


title: Mouse P7 Nuclear 4


title: Mouse P7 Cellular 4


title: hindgut_Ednrb-FLEX_5

city: Kansas City

first: Chris

middle: W

last: Seidel

state: MO

department: Genomics

institute: Stowers Institute

description: Ednrb mutant in NCC cells

hyb_protocol: Following fragmentation, 12.5 ug of cRNA was hybridized for 16 hr at 45C on GeneChip Mouse MOE430 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 and processed with AGCC v3.0 software.

data_processing: Array intensities were processed using the RMA algorithm in R/bioconductor.

source_name: E14 hindgut cells

label_protocol: Biotinylated cRNA was prepared from 150 ng total RNA using the Ambion MessageAmpIII RNA Amplification kit, Catalog #1793.

extract_protocol: Total RNA was extracted using TRIzol, processed through an RNeasy column (QIAGEN) using the RNA clean-up protocol.

treatment_protocol: The terminal colon was dissected from the terminal colon of E14 wild type (WT), EdnrBNCC-/- (FLEX-EdnrB) and EdnrB(lacZ/lacZ) (EdnrB-/-) embryos.

value: hindgut cells

value: Ednrb-FLEX(NCC-/-)

tag: developmental stage


title: hindgut_WT_1D

tag: tissue

value: wt


title: hindgut_Ednrb-FLEX_2

description: Ednrb mutant in NCC cells

tag: genotype


title: OE_NC3

city: Jiangyin

first: Pengfei

last: Liu

state: Jiangsu province

address: NO. 163 Shoushan Road

institute: Jiangsu Jiangyin People's Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl  scripts
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Hisat2 v2.0.5 and  paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Differential expression analysis of two  conditions/groups (two biological replicates per condition) was performed using  the DESeq2 R package (1.16.1). DESeq2 provide statistical routines for  determining differential expression in digital gene expression data using a model  based on the negative binomial distribution
Gene Ontology (GO) enrichment analysis of differentially expressed genes was  implemented by the clusterProfiler R package, in which gene length bias  wascorrected. GO terms with corrected Pvalue less than 0.05 were considered  significantly enriched by differential expressed genes
Genome_build: Homo_sapiens_Ensemble_94
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: skin fibroblast cells_OE_NC

extract_protocol:
Trizol
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Overexpression vectors and interference vectors were constructed and transfected into WS1 cells respectively. After 48h culture, second-generation sequencing was arranged

tag: cell line

value: skin fibroblast cells

value: AUF1 gene Overexpression control


title: sh_NC1

source_name: skin fibroblast cells_sh_NC

value: AUF1 gene Interference control


title: sh_AUF1

source_name: skin fibroblast cells_sh_AUF

value: AUF1 gene Interference


title: sh_NC3


title: OE_NC2


title: OE_AUF2

source_name: skin fibroblast cells_OE_AUF

value: AUF1 gene Overexpression


title: hindgut_WT_1C


title: OE_AUF3


title: OE_AUF1


title: hindgut_Ednrb_41

value: Ednrb -/-


title: hindgut_Ednrb_37


title: hindgut_Ednrb_29


title: sh_AUF3

value: AUF3 gene Interference


title: sh_NC2


title: OE_NC1


title: rsa1-gim-2

city: Paris

first: Cosmin

last: Saveanu

address: 25-28 rue du docteur Roux

department: Genomes and Genetics

institute: Institut Pasteur

description: Comparison of double mutant abundance in populations containing the deletion of RSA1 compared with a reference population

hyb_protocol: Hybridization was done in Roche RapidHyb buffer

scan_protocol: Genepix 4200AL and GenePix Pro v7

data_processing: The scans were processed using GenePix Pro, v7. The values from the obtained gpr files were filtered to keep only values for spots with an SNR > 10. Next, we performed a loess normalization on groups of probes (UP/DAMP, UP/DELETION, DOWN/DAMP, DOWN/DELETION), followed by aggregation of values for each mutant and a second loess normalization on the aggregated data.

organism: Saccharomyces cerevisiae

source_name: S. cerevisiae GIM pool with RSA1 deletion

label_protocol: Cy3 and Cy5 5' tagged oligonucleotides were used to amplify the barcode region with universal primers. PCR products were then mixed, precipitated in the presence of linear poly-acrylamide and prepared for hybridization

growth_protocol: The pool of DamP strains was combined with the three different mutant strains using the GIM protocol (Decourty et al., PNAS 2008). After selection of double mutant haploid cells, the pool of haploid strains was growth for 18 generations under double antibiotic selection (G418 and nurseothricin).

extract_protocol: Genomic DNA was extracted through mechanical lysis (vortexing with glass beads). PCR amplification of the barcode region was followed by a second PCR amplification with Cy3 5' tagged oligonucleotide.

treatment_protocol: Cells in exponential growth were recovered by purification, washed once in cold water and stored at -80C until RNA or DNA extraction

value: Mix of haploid strains derived from BY4742/BY4741

source_name: S. cerevisiae reference GIM pool


title: hindgut_WT_1B


title: sh_AUF2

value: AUF2 gene Interference


title: YCC16_shL_OCT4-2, Biological Replicate 2

city: Madurai

first: Kumaresan

last: Ganesan

state: Tamil Nadu

address: School of Biological Sciences,

country: India

institute: Madurai Kamaraj University

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-OCT4 - Replicate 2

hyb_protocol: The fragmented and labelled cDNA were hybridized for 16 hr at 45°C with GeneChip® Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Scanning was done on an Affymetrix GeneChip® Scanner 3000.

data_processing: Gene level normalized expression signal intensity data of the HTA 2.0 arrays were calculated from CEL files using Gene Level-SST-RMA method which performs GCCN and SST prior to RMA in Affymetrix Expression Console (v1.4.1.46) .

source_name: shL-OCT4 transduced YCC16 gastric cancer cells - Replicate 2

label_protocol: 500 ng of total RNA was used to generate fragmented and biotin labelled sense cDNA using Ambion WT Expression kit (Affymetrix).

growth_protocol: YCC16 gastric cancer cell line were seeded in 6 well culture plates and maintained in MEM media with 10% FBS in a humidified incubator at 37˚C and 5% CO2.

extract_protocol: The total RNA was isolated from the cells using RNeasy mini kit (Qiagen) following manufacture's standard protocol. All RNA samples had both 18S and 28S bands with RIN (RNA integrity number) value as 10 and free of DNA and protein contamination.

treatment_protocol: Upon reaching 60-70% confluency, the cells were transduced with shL-NTC, shL-OCT4 and shL-RXRalpha lentiviral particles with 8µg/ml hexadimethirine bromide. Puromycin at the concentration of 2µg/ml  was used to select the positive cells after 48Hrs of transduction.

value: gastric adenocarcinoma cell line


title: rsa1-gim-1


title: YCC16_shL_OCT4-1, Biological Replicate 1

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-OCT4 - Replicate 1

source_name: shL-OCT4 transduced YCC16 gastric cancer cells - Replicate 1


title: YCC16_shL_RXRalpha-1, Biological Replicate 1

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-RXRalpha - Replicate 1

source_name: shL-RXRalpha transduced YCC16 gastric cancer cells - Replicate 1


title: YCC16_shL_RXRalpha-3, Biological Replicate 3

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-RXRalpha- Replicate 3

source_name: shL-RXRalpha transduced YCC16 gastric cancer cells - Replicate 3


title: YCC16_shL_RXRalpha-2, Biological Replicate 2

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-RXRalpha - Replicate 2

source_name: shL-RXRalpha transduced YCC16 gastric cancer cells - Replicate 2


title: YCC16_shL_OCT4-3, Biological Replicate 3

description: Gene expression data of YCC16 gastric cancer cell line transduced with shL-OCT4 - Replicate 3

source_name: shL-OCT4 transduced YCC16 gastric cancer cells - Replicate 3


title: sgP130_siCTL_350_B

first: Amy

middle: E

last: Schade

department: Medicine

institute: Brigham and Women's Hospital

data_processing:
Reads were mapped to the Hg19 genome by STAR.
HTseq was used to generate count file with gene names(53).
R package DESeq2 was used to normalize counts (mean-ratio method), calculate total reads, and determine differential gene expression(54).
MA plots were generated to display differentially expressed genes.
Principal component analysis showed sufficient clustering of biological replicates.
Genome_build: hg19
Supplementary_files_format_and_content: DESeq2 normalized reads.

source_name: Human Foreskin Fibroblasts (HFF)

extract_protocol:
Total RNA was isolated from HFFs using Qiagen RNeasy plus kit, treated with DNAse (Turbo DNA-free, Life Technologies), and quality control checked using Qubit, TapeStation, and qPCR.
Libraries were prepared using Kappa stranded mRNA Hyper Prep

value: Human Foreskin Fibroblasts (HFF)

tag: crispr-cas9 target

tag: sirna target

value: siControl

tag: doxorubicin treatment

tag: biological replicate

value: bio repeat B


title: sgP130_siCTL_350_A

tag: cell type

value: bio repeat A