title: NCDS001120

value: Lung


title: Cut_and_Run_CTCF_7_5min_(20160401_PS_HsDm_CTCF_7_5)

status: Public on Dec 30 2016

type: SRA

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 7.5 min digestion time on ice

library_source: genomic

data_processing:
Genome_build: UCSC hg19
Genome_build: FlyBase r6.06
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to dm6 version of  the D.melanogaster genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed). 4. We counted the properly paired reads from the D.melanogaster alignments. 5. We used the bedtools 2.21.0 genomecov command with a scaling factor of (hg19 genome size/number of mapped fragments to hg19) create a normalized human track file (Supplementary file .stdnorm.bedgraph). 6. We used the bedtools 2.21.0 genomecov command with a scaling factor of (10000/number of fragments mapped to D.melanogaster) to create a normalized human track file (Supplementary file .spikenorm.bedgraph).

molecule: genomic DNA

organism: Homo sapiens

source_name: Chromatin immunocleavage and release

extract_protocol:
Cut_and_Run_human.rtf
PMID 25827087

tag: cell line

value: human K562 cells


title: NCDS001121

city: Cambridge

first: Hugues

last: Bernard

state: MA

address: 35 Landsdowne St.

department: Molecular Pathology

institute: Millennium: The Takeda Oncology company

library_source: transcriptomic

data_processing:
OSA v4 (http://omicsoft.com/osa) was used to align the reads to the Dog genome (CanFam3.1) and to MiRBase (v.21) [44] allowing for two mismatches and excluding any reads that aligned to greater than 10 genomic locations
Expression levels were quantified by counting the number of reads aligned to mature miRNA region
Genome_build: Dog genome (CanFam3.1)

molecule: total RNA

organism: Canis lupus familiaris

source_name: Skeletal Muscle:  Quadraceps

extract_protocol:
Total RNA was isolated by Asuragen from tissue homogenate with KingFisher Pure RNA Tissue Kit (Thermo Scientific).
Isolation of miRNA from 50 μM tissue samples used a lysis buffer (RLT [Qiagen] + 1% β  mercaptoethanol) and a rotor-stator homogenizer
A TruSeq Small RNA Library Kit (Illumina) was used for library construction of dog miRNA

treatment_protocol: No Treatment

tag: tissue

value: Skeletal Muscle: Quadraceps

tag: treatment

value: Untreated

tag: breed

value: Beagle

tag: prep type

value: Qiagen RNeasy_96

tag: Sex

value: Male


title: SCZ rep15

city: Sydney

first: Susan

last: Corley

state: NSW

address: D26, Kensignton Campus

department: Biotechnology & Biomolecular Sciences

country: Australia

institute: UNSW

description: processed data column: T11

data_processing:
RNA libraries sequenced on theSOLiDv4 platform (Life Technologies, Carlsbad, CA, USA)
Sequenced reads werer mapped to the human genome (hg19) using TopHat2 (v 2.0.4) calling the Bowtie aligner (v 0.12.8) using the default parameters.
HTSeq-count (Python package HTSeq, python v 2.7.3) was used to generate counts of reads uniquely mapped to annotated genes using the Ensembl annotation file GRCh37.66_chr.gtf
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with read count for each sample.

source_name: DLPFC

extract_protocol:
Tissue from dorsal lateral prefrontal cortex (DLPFC) was pulverized over dry ice. Approximately 300 mg was weighed while frozen and stored at 80°C until extraction. Total RNA was extracted with TRIzol Reagent (Invitrogen Life Science, Cat. No. 15596-018, Mount Waverley, Victoria), using a polytron. Total RNA pellets were re-suspended in DEPC treated water. The yield of total RNA was then analysed using a spectrophotometer (Nanodrop ND-1000, Thermo Scientific). Total RNA was not further purified through a column. The quality of extracted total RNA was determined by high resolution capillary electrophoresis using the Agilent Bioanalyzer 2100.
Twelve micrograms of RNA from each of the samples was used in creation of the library for sequencing. RNA was DNase treated using TURBO DNA-free (Ambion, Austin TX, USA) before the depletion of ribosomal RNA using the Ribominus kit (Invitrogen, Carlsbad, CA, USA). The resulting RNA was fragmented and the SOLiD library prepared using the Total RNA-Seq kit (Invitrogen). Quality control of the library was assessed by size (480% and within 200--300 bp) using a bioanalyser.
Samples were run with four individuals per slide on the SOLiDv4 (Life Technologies, Carlsbad, CA, USA). Reads were unpaired and 50nt in length. Average reads per individual were 135 355 990 (±32 081 820) and did not differ between diagnostic groups.

value: Post-mortem brain (DLPFC) tissue

tag: condition

value: SCZ

tag: batch


title: SCZ rep14

description: processed data column: T13


title: SCZ rep16

description: processed data column: T43


title: SCZ rep13

description: processed data column: T4


title: Cut-and-Run_Mot1_5s_Total_(20161123_SH_ScDm_Mot15s_1107)

description:
Cut-and-Run Mot1 5 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1

data_processing:
Genome_build: YeastBase V64
Genome_build: FlyBase r6.06
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options "-F STDFQ -a -r Random -o SAM" to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC.  2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to release 6.06 (Jul 2015) of D.melanogaster genomic sequence obtained from FlyBase. This release corresponds to release dm6 from UCSC.  3. We extracted properly paired reads from both alignments (Supplementary files .bed.gz .DM.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 10000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).

organism: Saccharomyces cerevisiae

tag: cell type

value: yeast


title: Cut_and_Run_CTCF_4min_(20160414_PS_HsDm_CTCF_4m)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 4 min digestion time at room temp

data_processing:
Genome_build: UCSC hg19
Genome_build: FlyBase r6.06
1. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the paired-end 25bp reads to hg19 of Homo sapiens genomic sequence obtained from UCSC. 2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to dm6 version of  the D.melanogaster genomic sequence obtained from UCSC. 3. We extracted properly paired reads from Homo sapiens alignments to generate a bed files <chr> <start> <stop> <length> (Supplementary file .bed). 4. We counted the properly paired reads from the D.melanogaster alignments. 5. We used the bedtools 2.21.0 genomecov command with a scaling factor of (10000/number of fragments mapped to D.melanogaster) to create a normalized human track file (Supplementary file .spikenorm.bedgraph).


title: Cut_and_Run_CTCF_2min_(20160414_PS_HsDm_CTCF_2m)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 2 min digestion time at room temp


title: NCDS001118

source_name: Heart

value: Heart


title: Cut-and-Run_Mot1_3m_Total_(20161123_SH_ScDm_Mot13m_1107)

description:
Cut-and-Run Mot1 3 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1


title: Cut-and-Run_Mot1_20s_Total_(20161123_SH_ScDm_Mot120s_1107)

description:
Cut-and-Run Mot1 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1


title: Cut_and_Run_CTCF_1min_(20160414_PS_HsDm_CTCF_1m)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 1 min digestion time at room temp


title: SCZ rep11

description: processed data column: T12


title: NCDS001119

source_name: Testis

value: Testis


title: NCDS001117

source_name: Liver

value: Liver


title: Cut_and_Run_CTCF_disrupted_(20160315_PS_HsDm_CTCF_expl_UB)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF disrupted nuclei @37C


title: SCZ rep10

description: processed data column: T35


title: Cut-and-Run_Mot1_1m_Total_(20161123_SH_ScDm_Mot11m_1107)

description:
Cut-and-Run Mot1 1 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1


title: Cut_and_Run_CTCF_10million_(20160315_PS_HsDm_CTCF_10)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 10 million cells @37C


title: NCDS001116

source_name: Colon

value: Colon


title: SCZ rep9

description: processed data column: T42


title: NCDS001115

source_name: Pancreas

value: Pancreas


title: Cut-and-Run_Mot1_10m_Total_(20161123_SH_ScDm_Mot110m_1107)

description:
Cut-and-Run Mot1 10 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Mot1


title: SCZ rep8

description: processed data column: T63


title: Cut_and_Run_CTCF_2_5million_(20160315_PS_HsDm_CTCF_2_5)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 2.5 million cells @37C


title: Cut-and-Run_H2A_X-link_3m_Total_(20160916_SH_ScDm_H2Apx3m825)

description:
Cut-and-Run H2A cross-linked 3 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: NCDS001114

source_name: Ileum

value: Ileum


title: Cut_and_Run_CTCF_0_6million_(20160315_PS_HsDm_CTCF_0_6)

description:
experiment: anti CTCF Millipore 07-729
Cut-and-Run CTCF 0.6 million cells @37C


title: Cut-and-Run_H2A_X-link_20s_Total_(20160916_SH_ScDm_H2Apx20s825)

description:
Cut-and-Run H2A cross-linked 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: NCDS001113

source_name: Jejunum

value: Jejunum


title: SCZ rep7

description: processed data column: T32


title: SCZ rep12

description: processed data column: T15


title: Cut-and-Run_H2A_X-link_1m_Total_(20160916_SH_ScDm_H2Apx1m825)

description:
Cut-and-Run H2A cross-linked 1 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: SCZ rep6

description: processed data column: T34


title: Cut-and-Run_H2A_X-link_10m_Total_(20160916_SH_ScDm_H2Apx10m825)

description:
Cut-and-Run H2A cross-linked 10 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: SCZ rep5

description: processed data column: T61


title: NCDS001110

source_name: Brain

value: Brain


title: NCDS001112

source_name: Duodenum

value: Duodenum


title: SCZ rep4

description: processed data column: T25


title: Cut-and-Run_H2A_500s_(20160909_SH_ScDm_H2_500s0829)

description:
Cut-and-Run H2A 500 second digestion time
experiment: 3xFLAG-tagged H2A


title: NCDS001109

source_name: Thymus

value: Thymus


title: ZNFKD_exp3

city: La Jolla

first: Bruce

last: Hamilton

state: CA

address: 9500 Gilman Dr.

department: Medicine

institute: UC San Diego

description: Sample 6

data_processing:
Illumina CASAVA-1.8.2 software used for basecalling.
Reads were aligned to the hg19 genome assembly using STAR version 2.3.1f with parameters --genomeDir hg19 –runThreadN 8 …
Reads of genes were counted using HOMER software (Mol Cell 2010, 38(4):576-589) followed analysis with edgeR package in R
for bedGraph file, reads were mapped to hg19 using STAR 2.3.1f, and the bed files were made based on the mapping information with HOMER software command “makeTagDirectory” with -flip option and followed by “makeUCSCfile”.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file reports Total Tags

source_name: Daoy cell line

extract_protocol:
RNA was harvested using Trizol reagent. mRNA were purified with Dynabeads® mRNA Purification Kit (Cat#61006).
RNA libraries were prepared for sequencing using strand specific dUTP protocols.(nature methods 2010, 7(9):  709-715)

treatment_protocol: Daoy cells were cultured in DMEM supplemented with 10% fetal bovine serum. Daoy cells were flow sorted after infected with virus for 5days.

value: brain/cerebellum

value: cerebellar medulloblastoma

value: Daoy

tag: genotype/variation

value: ZNF423 knockdown


title: ZNFKD_exp2

description: Sample 5


title: control_exp3

description: Sample 3

value: control


title: ZNFKD_exp1

description: Sample 4


title: SCZ rep3

description: processed data column: T22

value: Post-mortem brain (DLPFC) tissue

value: SCZ


title: Cut-and-Run_H2A_500s_Total_(20160909_SH_ScDm_H2_500A0829)

description:
Cut-and-Run H2A 500 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A

value: yeast


title: NCDS001108

source_name: Kidney

value: Kidney

value: Untreated

value: Beagle

value: Qiagen RNeasy_96

value: Male


title: control_exp2

description: Sample 2


title: Cut-and-Run_H2A_2500s_(20160909_SH_ScDm_H2_2500s0829)

description:
Cut-and-Run H2A 2500 second digestion time
experiment: 3xFLAG-tagged H2A


title: NCDS001107

value: Skeletal Muscle: Quadraceps


title: SCZ rep2

description: processed data column: T5


title: control_exp1

description: Sample 1


title: NCDS001106

source_name: Lung

value: Lung


title: Cut-and-Run_H2A_20s_Total_(20160909_SH_ScDm_H2_20A0829)

description:
Cut-and-Run H2A 100 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: NCDS001105

value: Testis


title: Cut-and-Run_H2A_20s_2_(20160909_SH_ScDm_H2_20s0829)

description:
Cut-and-Run H2A 20 second digestion time
experiment: 3xFLAG-tagged H2A


title: Control rep18

description: processed data column: T58

value: Control


title: NCDS001104

value: Heart


title: NCDS001103

value: Liver


title: Control rep15

description: processed data column: T26


title: Cut-and-Run_H2A_100s_(20160909_SH_ScDm_H2_100s0829)

description:
Cut-and-Run H2A 100 second digestion time
experiment: 3xFLAG-tagged H2A


title: Control rep14

description: processed data column: T85


title: Cut-and-Run_H2A_100s_Total_(20160909_SH_ScDm_H2_100A0829)


title: Cut-and-Run_Cse4_X-link_3m_Total_(20160916_SH_ScDm_Cse4px3m825)

description:
Cut-and-Run Cse4 cross-linked 3 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Cut-and-Run_Cse4_X-link_20s_Total_(20160916_SH_ScDm_Cse4px20s825)

description:
Cut-and-Run Cse4 cross-linked 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Control rep17

description: processed data column: T9


title: Control rep13

description: processed data column: T37


title: Control rep12

description: processed data column: T56


title: Cut-and-Run_Cse4_X-link_1m_Total_(20160916_SH_ScDm_Cse4px1m825)

description:
Cut-and-Run Cse4 cross-linked 1 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Control rep11

description: processed data column: T7


title: Cut-and-Run_Cse4_500s_(20160909_SH_ScDm_Cs_500s0829)

description:
Cut-and-Run Cse4 500 second digestion time
experiment: 3xFLAG-tagged Cse4


title: Bisulfite Nonvascular

city: Davis

first: Gina

middle: Marie

last: Turco

address: University of California, Davis

institute: UC Davis

data_processing:
RNA-Sequence data was aligned with TopHat using the phytozome Sorghum bicolor (BTx623) genome containing mitochondria and chloroplast sequences as the reference genome under default parameters. Differential expression was determined with the R package EdgeR which normalized the data and ran a genewise exact test. Genes with an FDR value less than or equal to 0.05 and a positive log fold change were considered specific to that sample. Read per kilobase per million (RPKM) were categorized into four groups based on quartile range where 1 delineates the lowest quartile and 4 the highest expression quartile.
Methylome paired end raw reads are filtered for poor base quality and adapters using the cutadapt program. The filtered reads are mapped using BSmap with reads having minimum of 75 bps length. The Smithlab DNA Methylation Data Analysis Pipeline (MethPipe) was used for identification of CpG, CHG and CHH methylated regions and removal of regions of PCR overamplication. Methylation counts were then merged for each of the 3 replicates.  True methylated cytosines were identified using a binomial test that was applied to each cytosine. The spike in control was used to determine the error rate and the FDR was set to <0.01.
Genome_build: Sorghum bicolor (BTx623) genome
Supplementary_files_format_and_content: Processed RNA-Seq datasets contain gene name, RPKM replicates for 3 samples, logFC, logCPM, pvalue from EdgeR t-test, and FDR pvalue determined by EdgeR.
Supplementary_files_format_and_content: Methylomes are in bed format for potential context of methylation (CG,CHG, CHH) with the chromosome, region,  strand, context, pecentage of reads methylated, total reads mapping to that region. These files have been processed with BSmap and filtered for potental PCR duplicates

organism: Sorghum bicolor

source_name: Bisulfite Nonvascular

extract_protocol:
For all experiments carried out in this manuscript, Sorghum bicolor (L.) Moench (BTx623) seeds were separated into three biological replicates prior to germination under sterile conditions at ( 28C for N/NV LCM) while maintained in a 16/8 light/dark cycle for 3 days. For whole root and whole shoot transcriptomes RNA was isolated using TRIzol reagent (Life Technologies) according to the manufacturer's instructions followed by DNase treatment using RQ1 enzyme (Promega). Whole root and whole shoot methylomes were prepared from DNA extracted using a method modified from that of Shure. Briefly, powdered tissue that had been ground in N2 was resuspended in an extraction buffer containing 8 M urea, 350 mM NaCl, 50 mM Tris-HCI (pH 7.5), 20 mM EDTA and 2% sarcosyl prior to  phenol chloroform extraction and precipitation with isopropanol. DNA was collected by centrifugation and cleaned following resuspension in TE with ammonium acetate/isopropanol precipitation. Precipitated DNA was collected by centrifugation rinsed with 75% ethanol and resuspended in TE.
For root vascular and non-vascular nucleic acid preps Sorghum tissue was prepared for laser capture microdissection (LCM) as described. Shoots and roots were separated prior to fixation in EEA. Samples were dehydrated through an ethanol series prior to embedding in paraplast X-tra. 8-10 micron sections were mounted on PEN membrane slides (Leica) and vascular and nonvascular tissue were separated using the LCM setup described. For RNA extraction a RNAqueous-Micro Kit (Ambion) was used and for DNA extraction a QIAamp Micro DNA kit (Qiagen).
For whole root and whole shoot RNA-seq, mRNA was purified from 1µg of total RNA using magnetic beads containing poly-T oligos. LCM RNA-seq libraries were prepared by removing rRNA from 10-50ng of total RNA using Ribo-Zero™ rRNA Removal Kit (Epicentre). For both whole shoot/root and LCM captured material, stranded cDNA libraries were generated using Illumina Truseq Stranded RNA LT kit (Illumina). mRNA was fragmented using divalent cations and high temperature. The fragmented RNA was reversed transcribed using random hexamers and SSII (Invitrogen) followed by second strand synthesis.  The fragmented cDNA was treated with end-repair, A-tailing, adapter ligation, and 10 cycles of PCR (for whole root/shoot) or 15 cycles of PCR (for LCM captured material).  qPCR was used to determine the concentration of the libraries. Libraries were sequenced on the Illumina Hiseq.
Whole root and whole shoot methylomes were generated from 1ug of DNA which was sheared to 500bp using the covaris LE220 (Covaris).  DNA fragments smaller than 200bp were removed using SPRI beads (Beckman Coulter).  The fragments were treated with end-repair, A- tailing, and ligation of methylated Illumina adapters (Illumina) using an Illumina library creation kit (KAPA biosystems).  The adaptor ligated DNA were bisulfite treated using EZ DNA Methylation Lightning Kit (Zymo Research), converting the non-methylated nucleotides from Cytosines to Uracil. The converted DNA was enriched with 10 cycles of PCR to generate the final library. qPCR was used to determine the concentration of the libraries. Libraries were sequenced on the Illumina Hiseq. Vascular and non-vascular root methalomes were generated in the same manner, but  from 100ng of Laser Capture Microdissection DNA which was sheared to 700bp. Removal of < 200 bp fragments, end-repair, A- tailing, adaptor ligation and bisulphide conversion were as described for whole root/shoot. The converted DNA was enriched with 12 cycles of PCR to generate the final library.

tag: strain

value: (L.) Moench BTx623

tag: age

value: 3 days after germination

value: Nonvascular

tag: genotype

value: wild type


title: SCZ rep1

description: processed data column: T2

value: Post-mortem brain (DLPFC) tissue

value: SCZ


title: Bisulfite Vascular

source_name: Bisulfite Vascular

value: Vascular


title: Control rep10

description: processed data column: T30


title: Control rep19

description: processed data column: T46


title: Cut-and-Run_Cse4_2500s_(20160909_SH_ScDm_Cs_2500s0829)

description:
Cut-and-Run Cse4 2500 second digestion time
experiment: 3xFLAG-tagged Cse4

source_name: Chromatin immunocleavage and release

value: yeast


title: Control rep9

description: processed data column: T86

source_name: DLPFC


title: Cut-and-Run_H2A_2500s_Total_(20160909_SH_ScDm_H2_2500A0829)

description:
Cut-and-Run H2A 2500 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged H2A


title: Bisulfite Root

source_name: Bisulfite Root

value: Root


title: Control rep8

description: processed data column: T40


title: Control rep16

description: processed data column: T28


title: RNASeq Nonvascular [AGTTCC_N]

description: processed data file: vascular_nonvascular.txt

source_name: RNASeq Nonvascular


title: Cut-and-Run_Cse4_20s_(20160909_SH_ScDm_Cs_20s0829)

description:
Cut-and-Run Cse4 20 second digestion time
experiment: 3xFLAG-tagged Cse4


title: Control rep7

description: processed data column: T20


title: RNASeq Nonvascular [AGTCAA_N]


title: Control rep6

description: processed data column: T29


title: Cut-and-Run_Cse4_20s_Total_(20160909_SH_ScDm_Cs_20A0829)

description:
Cut-and-Run Cse4 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Cut-and-Run_Cse4_100s_(20160909_SH_ScDm_Cs_100s0829)

description:
Cut-and-Run Cse4 100 second digestion time
experiment: 3xFLAG-tagged Cse4


title: Cut-and-Run_Cse4_X-link_10m_Total_(20160916_SH_ScDm_Cse4px10m825)

description:
Cut-and-Run Cse4 cross-linked 10 minute digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: RNASeq Nonvascular [GCCAAT_N]


title: Control rep5

description: processed data column: T88


title: RNASeq Vascular [CTTGTA_V]

source_name: RNASeq Vascular


title: Control rep4

description: processed data column: T17


title: Cut-and-Run_Abf1_4s_Total_(20160909_SH_ScDm_Ab_4A0829)

description:
Cut-and-Run Abf1 4 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Cse4_500s_Total_(20160909_SH_ScDm_Cs_500A0829)

description:
Cut-and-Run Cse4 500 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Cut-and-Run_Cse4_100s_Total_(20160909_SH_ScDm_Cs_100A0829)

description:
Cut-and-Run Cse4 100 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Control rep3

description: processed data column: T47


title: Bisulfite Shoot

source_name: Bisulfite Shoot

value: Shoot


title: Control rep2

description: processed data column: T68


title: Control rep1

description: processed data column: T18


title: RNASeq Vascular [ACAGTG_V]


title: RNASeq Shoot [GCCAAT_s]

description: processed data file: root_shoot.txt

source_name: RNASeq Shoot


title: RNASeq Shoot [CAGATC_s]

description: processed data file: root_shoot.txt


title: Cut-and-Run_Abf1_4s_3_(20160909_SH_ScDm_Ab_4s0829)

description:
Cut-and-Run Abf1 4 second digestion time
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Cse4_2500s_Total_(20160909_SH_ScDm_Cs_2500A0829)

description:
Cut-and-Run Cse4 2500 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Cse4


title: Cut-and-Run_Abf1_20s_Total_(20160909_SH_ScDm_Ab_20A0829)

description:
Cut-and-Run Abf1 20 second digestion time Ampure selected Total
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_20s_(20160909_SH_ScDm_Ab_20s0829)

description:
Cut-and-Run Abf1 20 second digestion time
experiment: 3xFLAG-tagged Abf1


title: RNASeq Shoot [ACTTGA_s]

description: processed data file: root_shoot.txt


title: RNASeq Root [TAGCTT_r]

description: processed data file: root_shoot.txt

source_name: RNASeq Root


title: Cut-and-Run_Reb1_128s_2_(20160718_SH_ScDm_Reb1_128s630)

description:
Cut-and-Run Reb1 128 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1

data_processing:
Genome_build: YeastBase V64
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options "-F STDFQ -a -r Random -o SAM" to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC.  2. We extracted properly paired reads (Supplementary file .bed.gz). 3. We separated mapped fragments into two length categories, 21-120bp and 151-max bp. 4. We counted  the number of reads mapped to each base pair in the two length categories and normalized the counts by computing the fraction of total counts at each base pair and multiplying by the size of the yeast genome (Supplementary files .21-120.bedgraph.gz and .151-max.bedgraph.gz).


title: Cut-and-Run_Reb1_64s_(20160718_SH_ScDm_Reb1_64s_0426)

description:
Cut-and-Run Reb1 64 second digestion time
experiment: 3xFLAG-tagged Reb1


title: RNASeq Root [GGCTAC_r]

description: processed data file: root_shoot.txt


title: RNASeq Vascular [TGACCA_V]


title: RNASeq Root [GATCAG_R]

description: processed data file: root_shoot.txt


title: Cut-and-Run_Reb1_32s_2_(20160718_SH_ScDm_Reb1_32s0630)

description:
Cut-and-Run Reb1 32 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Reb1_8s_2_(20160718_SH_ScDm_Reb1_8s0630)

description:
Cut-and-Run Reb1 8 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Reb1_16s_2_(20160718_SH_ScDm_Reb1_16s0630)

description:
Cut-and-Run Reb1 16 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Abf1_128s_2_(20160718_SH_ScDm_Abf1_128s630)

description:
Cut-and-Run Abf1 128 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_64s_2_(20160718_SH_ScDm_Abf1_64s0630)

description:
Cut-and-Run Abf1 64 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Reb1_1s_2_(20160718_SH_ScDm_Reb1_1s0630)

description:
Cut-and-Run Reb1 1 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Reb1_4s_2_(20160718_SH_ScDm_Reb1_4s0630)

description:
Cut-and-Run Reb1 4 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Reb1_2s_2_(20160718_SH_ScDm_Reb1_2s0630)

description:
Cut-and-Run Reb1 2 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Cut-and-Run_Abf1_4s_2_(20160718_SH_ScDm_Abf1_4s0630)

description:
Cut-and-Run Abf1 4 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_8s_2_(20160718_SH_ScDm_Abf1_8s0630)

description:
Cut-and-Run Abf1 8 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_64s_(20160628_SH_ScDm_Abf1_64s_0426)

description:
Cut-and-Run Abf1 64 second digestion time
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_16s_2_(20160718_SH_ScDm_Abf1_16s0630)

description:
Cut-and-Run Abf1 16 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Cut-and-Run_Abf1_32s_2_(20160718_SH_ScDm_Abf1_32s0630)

description:
Cut-and-Run Abf1 32 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Sample 8_RNAseq control rep2

city: Okayama

first: Hisao

last: Moriya

address: Tsushima-naka 3-1-1, Kita-Ku

department: Research Core for Interdisciplinary Sciences

country: Japan

institute: Okayama University

data_processing:
Basecalls performed using Illumina Casava 1.8 software
Removing adaptor sequences from library using fastx_clipper
Splitting reads by barcode using fastx-split
rRNA alignment using bowtie2 v2.0.6
Alignment of rRNA-depleted reads to yeast transcriptome using TopHat v2.0.7
Extracting mapped reads using samtools
Depleting duplicated reads using custom scripts
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: Text files (*.txt) contain following information in three columns: (1) systematic gene names; (2) position of coding sequence, amino acid, used for counting read; (3) reads counts.

source_name: RNAseq control

growth_protocol: Yeast cells BY4741 expressing POP5-TAP from a single genomic locus and carrying pTOWug2-836 or pTOWug2-POP5 were grown in 150 mL of SC-Ura at 30 °C with vigorous shaking. These cells were grown from an initial OD600 of approximately 0.2 to OD600 around 0.7, and the cells were then harvested by vacuum filtration.

extract_protocol:
Extracts were prepared as previously described (Ingolia et al., 2009, Science, PMID: 19213877), except that the frozen cells were pulverized with a mixer mill at 30 Hz.
The total amount of RNA in the extracts was quantified using RiboGreen (Invitrogen), and then, 50 ng of total RNA was diluted to 300 µL with the lysis buffer. The sample was subjected to preparation of ribosome footprints according to a previously described method (Ingolia et al., 2012, Nat Protoc, PMID: 22836135). Briefly, total RNA was treated with RNase I (Epicentre), and then the ribosomal pellet was collected by sucrose cushion centrifugation. RNA was recovered from the pellet with TRIzol (Life Technologies) and purified with Direct-zol RNA MiniPrep (Zymo), followed by isopropanol precipitation. RNA-seq libraries were generated using TruSeq Standard Total RNA Library Prep Kit (Illumina) from total RNA prepared as described above.

treatment_protocol: The cell pellet was immediately immersed in a 50-mL conical tube filled with liquid nitrogen and 2 mL of lysis buffer [10 mM Tris-HCl (pH 7.0), 10 mM Tris-HCl (pH 8.0), 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 200 µg/mL cycloheximide, 25 U/mL Turbo DNase (Invitrogen)] was dripped into the tube.

value: BY4741 POP5-TAP

tag: plasmid

tag: medium

value: SC-Ura


title: Sample 7_RNAseq control rep1


title: Cut-and-Run_Abf1_2s_2_(20160718_SH_ScDm_Abf1_2s0630)

description:
Cut-and-Run Abf1 2 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Sample 6_RNAseq experiment rep2

source_name: RNAseq experiment


title: Cut-and-Run_Abf1_1s_2_(20160718_SH_ScDm_Abf1_1s0630)

description:
Cut-and-Run Abf1 1 second digestion time, biological replicate
experiment: 3xFLAG-tagged Abf1


title: Sample 5_RNAseq experiment rep1


title: Sample 4_Ribosome footprints control rep2

data_processing:
library strategy: ribosome profiling
Basecalls performed using Illumina Casava 1.8 software
Removing adaptor sequences from library using fastx_clipper
Splitting reads by barcode using fastx-split
rRNA alignment using bowtie2 v2.0.6
Alignment of rRNA-depleted reads to yeast transcriptome using TopHat v2.0.7
Extracting mapped reads using samtools
Depleting duplicated reads using custom scripts
Read quantitation using custom scripts
Genome_build: sacCer3
Supplementary_files_format_and_content: Text files (*.txt) contain following information in three columns: (1) systematic gene names; (2) position of coding sequence, amino acid, used for counting read; (3) reads counts.

source_name: Ribosome footprints control


title: Cut-and-Run_H2A_3m_(20160706_SH_ScDm_H2A3m61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 3 minute digestion time

data_processing:
Genome_build: YeastBase V64
Genome_build: FlyBase r6.06
1. We used Novoalign 2.08.03 (http://www.novocraft.com) with options "-F STDFQ -a -r Random -o SAM" to map paired-end 25bp reads to release V64 (Feb 2011) of the S.cervisiae genomic sequence obtained from YeastBase. This release corresponds to release sacCer3 from UCSC.  2. We used Bowtie2 2.2.5 with options "--local --very-sensitive-local --no-unal --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map the same paired-end 25bp reads to release 6.06 (Jul 2015) of D.melanogaster genomic sequence obtained from FlyBase. This release corresponds to release dm6 from UCSC.  3. We extracted properly paired reads from both alignments (Supplementary files .SC.bed.gz .DM.bed.gz). 4. We used the bedtools 2.17.0 genomecov command with a scaling factor of 1000/(number of fragments mapped to D.melanogaster) to create a normalized yeast track file (Supplementary file .bedgraph.gz).


title: Cut-and-Run_H2A_3mN_(20160706_SH_ScDm_H2A3mN61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 3 minute digestion time with 2M NaCl extraction


title: Cut-and-Run_Reb1_64s_2_(20160718_SH_ScDm_Reb1_64s0630)

description:
Cut-and-Run Reb1 64 second digestion time, biological replicate
experiment: 3xFLAG-tagged Reb1


title: Sample 1_Ribosome footprints experiment rep1

source_name: Ribosome footprints experiment


title: Cut-and-Run_Cse_3m_(20160706_SH_ScDm_Cse3m61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 3 minute digestion time


title: Cut-and-Run_H2A_1mN_(20160706_SH_ScDm_H2A1mN61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 1 minute digestion time with 2M NaCl extraction


title: Sample 2_Ribosome footprints experiment rep2


title: Cut-and-Run_H2A_1m_(20160706_SH_ScDm_H2A1m61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 1 minute digestion time


title: Cut-and-Run_Cse_1m_(20160706_SH_ScDm_Cse1m61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 1 minute digestion time


title: Cut-and-Run_H2A_20s_(20160706_SH_ScDm_H2A20s61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 20 second digestion time


title: Cut-and-Run_Cse_1mN_(20160706_SH_ScDm_Cse1mN61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 1 minute digestion time with 2M NaCl extraction


title: Cut-and-Run_H2A_20sN_(20160706_SH_ScDm_H2A20sN61416)

description:
experiment: 3xFLAG-tagged H2A
Cut-and-Run H2A 20 second digestion time with 2M NaCl extraction


title: Cut-and-Run_Cse_20s_(20160706_SH_ScDm_Cse20s61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 20 second digestion time


title: Cut-and-Run_Cse_20sN_(20160706_SH_ScDm_Cse20sN61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 20 second digestion time with 2M NaCl extraction


title: Cut-and-Run_Reb1_16s_(20160517_SH_ScDm_Reb1_16s0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 16 second digestion time


title: Cut-and-Run_Reb1_2s_(20160517_SH_ScDm_Reb1_2s_0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 2 second digestion time


title: Cut-and-Run_Reb1_4s_(20160517_SH_ScDm_Reb1_4s_0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 4 second digestion time


title: Cut-and-Run_Reb1_8s_(20160517_SH_ScDm_Reb1_8s0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 8 second digestion time


title: Cut-and-Run_Abf1_128s_(20160517_SH_ScDm_Abf1128s0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 128 second digestion time


title: Cut-and-Run_Reb1_128s_(20160517_SH_ScDm_Reb1128s0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 128 second digestion time


title: H3K4me3 ChIP-seq-2

city: Hershey

first: chunhua

last: song

state: PA

address: 500 University Drive

department: Pediatrics

institute: Pennsyvania  State University College of Medicine

data_processing:
ChIP-seq reads were aligned to the HG19 genome assembly with pipeline CASAVA 1.7 using ELANDv2 or CASAVA-1.8.2 using ELANDv2e.
For WDR5 and H3K4me3 ChIP-seq data, the bed files are made from a BAM file created from the CASAVA pipeline, which contains uniquely mapping reads as described above. The FASTQ under this pipeline is Phred33 or Phred64
They were filtered to exclude tags that do not align uniquely to the hg19 genome, tags that do not pass filter, tags that contain Ns, and tags that contain more than 2 mismatches.
MACS was used for peak calling of WDR5 and H3K4me3. Parameters lpcut = 3 and c = 2 were selected for WDR5and w = 5 for H3K4me3 and H3K27me3 datasets, respectively. Other parameters remain in default to run the program. Peaks with FDR ≤ 0.05 and Log2FC ≥ 1 were selected for further analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The final processed files are all in txt format. Each file contains peaks for a sample.

source_name: THP-1 leukemia cells

growth_protocol: 10% FBS RPMI1640 + A/P + b-ME in 5% CO2, 37°C, change media every 2-3 days, cell density in  2x10^5 to 1x10^6

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the ChIP-seq DNA Sample Kit . Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 18 cycles and library fragments of 200-400bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The resulted library was validated by using Agilent Technologies 2100 Bioanalyzer. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer (Illumina GA2) following the manufacturer's protocols.

value: acute myeloid leukemic cells

tag: antibody

tag: cell culture condition

value: 10% FBS RPMI1640 in 5% CO2, 37°C


title: H3K4me3 ChIP-seq-1

source_name: RS 4;11 leukemia cells

tag: cell line


title: WDR5 ChIP-seq-2

value: acute lymphoblastic leukemia cells


title: Sample 3_Ribosome footprints control rep1


title: Cut-and-Run_Abf1_8s_(20160517_SH_ScDm_Abf1_8s0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 8 second digestion time


title: Cut-and-Run_Abf1_32s_(20160517_SH_ScDm_Abf1_32s0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 32 second digestion time


title: Cut-and-Run_Reb1_32s_(20160517_SH_ScDm_Reb1_32s0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 32 second digestion time


title: WDR5 ChIP-seq-1


title: Cut-and-Run_Reb1_1s_(20160628_SH_ScDm_Reb1_1s_0426)

description:
experiment: 3xFLAG-tagged Reb1
Cut-and-Run Reb1 1 second digestion time


title: Cut-and-Run_Abf1_4s_(20160517_SH_ScDm_Abf1_4s_0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 4 second digestion time


title: skin rep2 RNA

city: Innsbruck

first: Mirjana

last: Efremova

address: Innrain 80-82

country: Austria

institute: Medical University of Innsbruck

description:
processed data file:
wt_rag_normalized_counts.txt

data_processing:
The sequencing reads were preprocessed through a quality control pipeline consisting of adapter removal with Cutadapt  and quality trimming with Trimmomatic  to remove bases with bad quality scores and reads shorter than 22 nucleotides. The quality trimmed reads were mapped to the mm10 reference genome using a two-step alignment method; alignment with STAR followed by alignment of the unmapped reads with Bowtie2. From the reads that mapped to multiple locations in the genome only the primary alignment was retained. Reads that mapped to ribosomal RNA locations in the genome were removed from further analysis using the split_bam.py script from the quality control package RSeQC. Gene-specific read counts were calculated using HTSeq-count. The R package DESeq2 was used for generating normalized counts.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each Sample

organism: Mus musculus

source_name: skin

extract_protocol: Total RNA was extracted, quality validated with the Agilent Bioanalyzer, and submitted to Lexogen 3’ QuantSeq library preparation, following the manufacturers instructions (Lexogen, Vienna Biocenter, Austria). Resulting libraries were sequenced with the Ion ProtonTM System.

tag: strain background

value: 8- to 12-week-old

tag: time point

value: day 23


title: Cut-and-Run_Cse_3mN_(20160706_SH_ScDm_Cse3mN61416)

description:
experiment: 3xFLAG-tagged Cse4
Cut-and-Run Cse4 3 minute digestion time with 2M NaCl extraction


title: H9-iMSC_Frozen_1h_SGC

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

data_processing:
Base calling was performed with the Illumina CASAVA 1.9 pipeline
QC was performed on the FASTQ files using RSeQC software (http://rseqc.sourceforge.net/)
The paired end reads were aligned by TopHat 12.0.6
Gene counts were generated using HTseq (http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Raw counts and RPKM values for each gene per sample

source_name: H9-iMSC Frozen 1h SGC

extract_protocol:
RNA for RNA-Seq was isolated using the miRNeasy mini kit (Catalog # 217004, Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols


title: skin rep1 RNA


title: H9-iMSC_Frozen_1h_DMSO

source_name: H9-iMSC Frozen 1h DMSO


title: H9-iMSC_Frozen_0h_DMSO

source_name: H9-iMSC Frozen 0h DMSO


title: Hippocampus_High-CPF_smRNA11

city: Ft. Detrick

first: Christine

last: Baer

state: MD

address: 568 Doughten Drive

department: Environmental Health Program

institute: Excet, Inc. / USACEHR

data_processing:
Basecalling performed using CASAVA version 1.8.2
Adaptor sequences were trimmed from the reads using the Cutadapt v1.2 package.  Adaptor-trimmed reads with Q-score >20 and a length of 16-24 bases were aligned to the rat genome build UCSC Baylor 3.4/rn4 (Nov 2004) using bowtie with parameters -p 4 -q -n 1 -l 15 -e 80 -m 5 --best --strata.
Aligned reads were mapped to miRBase seuqnces (release 19) using Partek Genomics Suite version 6.6.   Reads were assigned to mature miRNA sequences using a modified E/M algorith in Partek Genomics Suite and reads per million mapped miRNA (RPM) were calculated for each miRNA feature.
Genome_build: rn4
Supplementary_files_format_and_content: Tab-delimited text files including RPM values for each sample.

organism: Rattus norvegicus

source_name: Hippocampus_10 mg/kg/day CPF

growth_protocol: All animals used in this study were housed and maintained in the animal facilities at WIL Research Laboratories, LLC (Ashland, OH) that are fully accredited by the Association for Assessment and Accreditation of Laboratory Animal Care International (AAALAC International). Research was conducted in compliance with the Animal Welfare Act, and other Federal statutes and regulations relating to animals and experiments involving animals and adheres to principles stated in the Guide for the Care and Use of Laboratory Animals (National Research Council 2011). Nine-week old Long Evans (LE) male rats were received from Charles River Laboratories, Inc. (Raleigh, NC) and acclimated for at least ten days. The animals were housed individually in suspended stainless steel wire mesh cages in a humidity and temperature-controlled room (50% ± 20% and 25 °C) with a 12-hour (h) light/12-h dark cycle (lights on at 0600). Rats were provided ad libitum access to rodent chow (Certified Rodent LabDiet 5002, PMI Nutrition International, LLC, St. Louis, MO) and reverse-osmosis treated water throughout the study. Individual body weights were recorded twice weekly.

extract_protocol:
Total RNA including small non-coding RNA was isolated from the CA1 region of rat hippocampus using miRNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Small RNA libraries were constructed using the TruSeq small RNA library preparation kit (Illumina, San Diego, CA) according to the manufacturer’s recommended protocol.  1 ug of total RNA were ligated to 3’ and 5’ adaptors containing bases targeting small RNAs and sequencing primer sequences, respectively.  The enrichment of adaptor-ligated small RNA molecules was achieved by reverse transcription followed by limited-cycle polymerase chain reaction.  Sample-specific barcode tags were incorporated into the small RNA libraries during the PCR process.  The quality and concentration of newly constructed libraries were assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Small RNA libraries constructed from the same type of tissue were pooled together in equimolar amounts and separated on 6% Novex Tris-Borate-EDTA gels (Life Technologies, Grand Island, NY) for size selection.  Gel-purified sequencing libraries were quantified using KAPA Library Quantification Kit (Kapa Biosystems, Woburn, MA).  Small RNA sequencing libraries were sequenced on the Illumina HiScanSQ according to the manufacturer's protocols.

treatment_protocol: Rats were 11 weeks old at the initiation of dosing, and individual body weights ranged from 350 g to 450 g. Two CPF formulations (3 or 10 mg/kg b.w./day) and the vehicle control (peanut oil) were administered by subcutaneous (s.c.) injection for 21 consecutive days (study days 0 - 20), approximately 24 h apart. Fear conditioning testing was conducted for cohort A animals on the study day 20. Cohort B animals were not subjected to behavioral assessments. Fear conditioning training was given to the animals on day 19, approximately 24 h prior to contextual and cued memory assessments. A freezing response was used as a measure of cue and context-based learning.

value: Long Evans

tag: gender

value: male

value: 14 wk

tag: administered with

value: 10 mg/kg b.w./day chlorpyrifos (CPF) for 21 days

tag: tissue

value: Hippocampus

tag: molecule subtype

value: small RNA


title: H9-iMSC_Frozen_2h_SMC

source_name: H9-iMSC Frozen 2h SMC


title: Cut-and-Run_Abf1_2s_(20160517_SH_ScDm_Abf1_2s_0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 2 second digestion time

source_name: Chromatin immunocleavage and release


title: Hippocampus_High-CPF_smRNA10


title: Hippocampus_High-CPF_smRNA9


title: MC38 2 RNA

source_name: tumor cells

value: day 0


title: H9-iMSC_Fresh_1h_Media

source_name: H9-iMSC Fresh 1h Media


title: MC38 1 RNA


title: H9-iMSC_Fresh_1h_DMSO

source_name: H9-iMSC Fresh 1h DMSO


title: Hippocampus_High-CPF_smRNA8


title: Hippocampus_High-CPF_smRNA7


title: IgG2b rep2 RNA

description:
processed data file:
aPDL1_IgG2b_normalized_counts.txt

value: wild type

value: day 14


title: IgG2b rep1 RNA


title: Cut-and-Run_Abf1_16s_(20160517_SH_ScDm_Abf1_16s0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 16 second digestion time

value: yeast


title: Twin Pair5-2

first: Kai

last: Wang

address: 401 Terry Ave N

institute: Institute for Systems Biology

data_processing:
All mapped reads were normalized to reads per million then convert to log 2 values.
If a log 2 value of a miRNA was above the average value of all miRNAs, we defined this miRNA as detectable.
A detectable miRNA that was present in at least 70% of samples analyzed was defined as “present miRNA” in the sample set.
Supplementary_files_format_and_content: The reads were mapped against human miRNA database (miRBASE ver)

source_name: plasma

extract_protocol:
After centrifugation, plasma aliquots were frozen at -70 °C
The sequencing libraries were constructed using the Illumina Small RNA sample prep kit and were analyzed on Illumina HiSeq 2000 platform with single end 50 nucleotide read length.

treatment_protocol: Blood was drawn from the forearm vein after an overnight fast into EDTA tubes and immediately placed on ice.

tag: storage time

value: 41 yrs

tag: twin pair id

tag: baseline age

tag: age at death


title: aPDL1 rep3 RNA

tag: genotype/variation

tag: age


title: Hippocampus_High-CPF_smRNA6

tag: strain


title: Hippocampus_High-CPF_smRNA5


title: Twin Pair5-1


title: IgG2b rep3 RNA


title: H9-iMSC_Fresh_0h

source_name: H9-iMSC Fresh 0h


title: Hippocampus_High-CPF_smRNA4


title: H9-iMSC_Frozen_1h_SGI

source_name: H9-iMSC Frozen 1h SGI


title: Cut-and-Run_Abf1_1s_(20160628_SH_ScDm_Abf1_1s_0426)

description:
experiment: 3xFLAG-tagged Abf1
Cut-and-Run Abf1 1 second digestion time

tag: cell type


title: Hippocampus_High-CPF_smRNA3


title: aPDL1 rep2 RNA


title: Twin Pair4-1


title: aPDL1 rep1 RNA


title: Hippocampus_High-CPF_smRNA2


title: Twin Pair3-2


title: RAG1 day23 rep3 RNA


title: Twin Pair2-2


title: RAG1 day23 rep2 RNA


title: RAG1 day23 rep1 RNA


title: Hippocampus_Control_smRNA11

source_name: Hippocampus_vehicle control

value: vehicle control (peanut oil)  for 21 days


title: Twin Pair2-1


title: RAG1 day13 rep3 RNA

value: day 13


title: Twin Pair1


title: WT day46 rep3 RNA

value: day 46


title: Hippocampus_Control_smRNA9


title: Hippocampus_Control_smRNA8


title: RAG1 day13 rep2 RNA


title: Hippocampus_Control_smRNA7


title: RAG1 day13 rep1 RNA


title: Twin Pair4-2


title: Hippocampus_Control_smRNA5


title: WT day46 rep2 RNA


title: Hippocampus_Control_smRNA4


title: Twin Pair3-1


title: WT day46 rep1 RNA


title: KK_RWPE1_H3K36me3_fullmedia_Hg_rep2

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College street

department: Princess Margaret Cancer Centre

country: Canada

institute: University Health Network

description: processed data file: KK_RWPE1_H3K36me3_combinedreps_MACS14_peaks.bed

data_processing:
fastq files are raw reads generated from Casava v1.8.2.
Bowtie 2  was used to align reads to the reference Hg19 genome.
MACS 1.4 was used to call peaks with a p-value threshold of 10(exp)-5 and excluding duplicate read fragments
Genome_build: Hg19
Supplementary_files_format_and_content: Bed files correspond to the called peaks files from MACS1.4 after aligning to hg19 using Bowtie 2

source_name: normal prostate epithelial cells immortalized with HPV18

growth_protocol: RWPE-1 cells were cultured in Keratinocyte serum free media (Gibco cat# 17005-042) with bovine pituitary extract (0.05 mg/ml) and EGF (5 ng/ml) supplemented

extract_protocol:
The genomic DNA was extracted following Dnase digestion (Dnase), Chromatin Immunoprecipitation following sonication (H3K27ac, H3K27me3, H3K36me3, H3K4me1, H3K4me3) or simply following sonication (Input).
Libraries were constructed using the Rubicon Thruplex FD kit (Rubicon cat# R40048) according to the manufacturer's recommended protocol

tag: passage

tag: antibody/enzyme


title: KK_RWPE1_H3K4me3_fullmedia_Hg_rep1

description: processed data file: KK_RWPE1_H3K4me3_combinedreps_MACS14_peaks.bed

tag: cell line


title: KK_RWPE1_H3K4me1_fullmedia_Hg_rep2

description: processed data file: KK_RWPE1_H3K4me1_combinedreps_MACS14_peaks.bed


title: KK_RWPE1_H3K4me3_fullmedia_Hg_rep2


title: KK_RWPE1_H3K4me1_fullmedia_Hg_rep1


title: WT day23 rep3 RNA

tag: strain background


title: Hippocampus_Control_smRNA3


title: KK_RWPE1_H3K36me3_fullmedia_Hg_rep1


title: Hippocampus_High-CPF_smRNA1


title: Hippocampus_Control_smRNA2


title: Hippocampus_Control_smRNA10


title: KK_RWPE1_H3K27me3_fullmedia_Hg_rep2

description: processed data file: KK_RWPE1_H3K27me3_combinedreps_MACS14_peaks.bed

value: H3K27me3 (Diagenode, pAb-069-050, lot A1821D)


title: WT day23 rep2 RNA

value: 8- to 12-week-old

tag: time point


title: Hippocampus_Control_smRNA6

tag: gender


title: Hippocampus_Control_smRNA1

tag: administered with


title: WT day23 rep1 RNA

value: day 23


title: KK_RWPE1_H3K27me3_fullmedia_Hg_rep1


title: Non infected stems

city: Thiverval Grignon

first: Julie

last: Gervais

address: Avenue Lucien Brétignières

department: BIOGER

country: France

institute: INRA

description: RNA-seq pilot project

data_processing:
The sofwtware CLC worckbench v7.5.1 (Qiagen, Venlo, Netherlands) was used for data processing.
Sequenced reads were trimmed with the following parameters: ambiguous limit: 2, quality limit: 0.05, maximum number of nucleotides in reads: 50, minimum number of nucleotides in reads: 15. Short reads were discarded.
Reads were mapped on the genomes of L. maculans and B. napus with the following parameters: maximum number of mismatches allowed: 2, minimum lenght fraction: 0.80, Minim fraction of similarity: 0.8, unspecific match limit: 30
Expression values of fungal genes was measured with the RPKM.
Genome_build: Brassica napus (annotation release:100) (Chalhoub et al., 2014)
Genome_build: Leptosphaeria maculans JN3 (Rouxel et al., 2011)
Supplementary_files_format_and_content: Text files include RPKM (Reads Per Kilobase of exon per Megabase) values and number of aligned reads for each fungal gene.

organism: Brassica napus

source_name: Stem

growth_protocol: Plants were grown in grown chambers at 16°C (night) and 24°C (day), with a 12h photoperiod.

extract_protocol:
Total RNA was extracted from infected cotyledon and stem tissues, using the TRIzol reagent (Invitrogen,Cergy Pontoise, France) according to the manufacturer’s protocol. Total RNA was treated with DNase I RNase-Free (New England Biolabs, Ipswich, MA, U.S.A.).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: l.maculans strain

tag: brassica napus cultivar

value: Eurol

tag: inoculation protocol

value: Adult plants of the susceptible cultivar Eurol were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off at 1 cm from the leaf insertion and 10µl of water was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 24 days after inoculation stem tissues were sampled.


title: Non infected cotyledons

description: RNA-seq pilot project

source_name: Cotyledons

value: Darmor-bzh

value: Ten days-old seedling of the susceptible cultivar Darmor-bzh were inoculated with 10µl of water at a needle puncture. Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 7 days after infection,  cotyledons were sampled.


title: Hippocampus_High-CPF_mRNA5

data_processing:
Basecalling performed using CASAVA version 1.8.2
Pre-processed FASTQ reads were filtered based on sequence base quality scores (Q > 20) using the PRINSEQ package.  Quality-filtered reads were trimmed for 50 bases from the 3' end; only the 50 bases from the 5' end were used for alignment.  Trimmed reads were aligned to the rat genome RGSC Rnor_5.0/rn5 build (March 2012) using TopHat v2.0 with default parameters.
Read counts were normalized to the total number of reads per kilo-base of transcript per million mapped reads (RPKM) and summarized to the gene level using a modified E/M algorithm in Partek Genomics Suites v6.6
Genome_build: rn5
Supplementary_files_format_and_content: Tab-delimited text files including RPKM values for each sample.

molecule: polyA RNA

extract_protocol:
Total RNA including small non-coding RNA was isolated from the CA1 region of rat hippocampus using miRNeasy kit (Qiagen, Valencia, CA) according to the manufacturer’s protocol.
Thirteen rat hippocampus RNA samples were selected from a CPF treatment group (10 mg/kg b.w./day CPF, n=6) or a vehicle control group (n=7). Total RNAs were processed for RNA-seq using the TruSeq RNA sample prep kit v2 (Illumina, San Diego, CA) according to the manufacturer’s protocol (Illumina, San Diego, CA). The rat hippocampus RNA libraries were clustered onto a TruSeq V3 flowcell, and subjected to a 100-cycle single read run (1x100 cycles) on Illumina HiScanSQ sequencing instrument according to the protocols described by the manufacturer (Illumina, San Diego, CA).

treatment_protocol: Rats were 11 weeks old at the initiation of dosing, and individual body weights ranged from 350 g to 450 g. Two CPF formulations (3 or 10 mg/kg b.w./day) and the vehicle control (peanut oil) were administered by subcutaneous (s.c.) injection for 21 consecutive days (study days 1 - 20), approximately 24 h apart.

value: Long Evans

value: male

value: 14 wk

value: 10 mg/kg b.w./day chlorpyrifos (CPF) for 21 days

tag: tissue

value: Hippocampus


title: KK_RWPE1_H3K27ac_fullmedia_Hg_rep2

description: processed data file: KK_RWPE1_H3K27ac_combinedreps_MACS14_peaks.bed


title: KK_RWPE1_H3K27ac_fullmedia_Hg_rep1


title: KK_RWPE1_DNase_fullmedia_Hg_rep1

description: Dnase-seq

value: Dnase (NEB M0303L)


title: Hippocampus_High-CPF_mRNA4


title: Hippocampus_High-CPF_mRNA3


title: KK_RWPE1_Input_fullmedia_Hg_rep1


title: No-antibody control 4

city: Stanford

first: Douglas

last: Porter

address: 269 Campus Drive

department: Dermatology

institute: Stanford

data_processing:
PCR duplicates were removed using a random barcode.
The first 9 nucleotides of the read (the sample barcode and random barcode) were removed.
Reads were mapped to the C. Elegans WS235 genome using STAR v 2.4.2 and parameters --alignIntronMax 1000 --alignSJoverhangMin 100 --alignSJDBoverhangMin 15  --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outFilterScoreMin 20 --readMapNumber -1 --outReadsUnmapped Fastx --outSAMstrandField intronMotif
Reads with MAPQ below 20 were removed.
Reads were assigned to genes using HTSeq. Peaks were called by custom CLIP-seq processing scripts by random read permutation.
Genome_build: WS235
Supplementary_files_format_and_content: Processed data files are the number of reads assigned to each gene.

organism: Caenorhabditis elegans

source_name: C. elegans bearing a FLAG tagged FOG-3 integrated into the genome in a single copy

growth_protocol: iCLIP was performed on C. elegans grown to L4 on plates.

extract_protocol:
Cells were lysed by ball milling, and libraries prepared by the iCLIP method.
iCLIP

tag: antibody

value: No-antibody control


title: No-antibody control 3


title: Hippocampus_High-CPF_mRNA2


title: Hippocampus_High-CPF_mRNA1


title: Hippocampus_Control_mRNA5

value: vehicle control (peanut oil)  for 21 days


title: Hippocampus_Control_mRNA7


title: Hippocampus_Control_mRNA6


title: FOG-3 3

value: Flag


title: FOG-3 4


title: No-antibody control 1


title: FOG-3 2


title: No-antibody control 2


title: FOG-3 1


title: Hippocampus_Control_mRNA3


title: Hippocampus_High-CPF_mRNA6


title: BMSC_3_CytoD+CK

value: bone marrow-derived mesenchymal stem cells (BMSCs)

tag: treated with

value: CytochalasinD and CK666 for 24hrs


title: BMSC_3_CytoD

value: CytochalasinD for 24hrs


title: Hippocampus_Control_mRNA4


title: BMSC_3_Ctr1

value: none (control)


title: Hippocampus_Control_mRNA2


title: BMSC_2_CK

value: CK666 for 24hrs


title: BMSC_3_CK


title: BMSC_2_CytoD+CK


title: BMSC_2_CytoD


title: BMSC_2_Ctrl


title: BMSC_1_CytoD+CK


title: BMSC_1_CytoD


title: BMSC_1_CK


title: BMSC_1_Ctrl


title: Hippocampus_Control_mRNA1


title: 5B6epid_1029

city: Olsztyn

first: Barbara

last: Gawrońska-Kozak

address: ul. Tuwima 10

country: Poland

institute: Polish Academy of Sciences

data_processing:
Sequenced fragments were aligned to the mouse NCBI37/mm9 SAGE reference sequence using SOLiD™ SAGE™v1.10 software, Life Technologies.
Raw counts were used as input for differential expression analysis using GeneSifter, Geospiza, Inc.
Differentially expressed genes met a fold-change of > or =1.5 between experimental groups and a p-value or Benjamini-Hochberg adjusted p-value of 0.05.
Biological pathway analysis was performed with DAVID bioinformatics platform provided by National Institute of Allergy and Infectious Diseases (http://david.abcc.ncifcrf.gov/home.jsp)
Genome_build: mouse NCBI37/mm9
Supplementary_files_format_and_content: Excel format table of median normalized counts

source_name: Epidermis

growth_protocol: The B6 mice were bred and housed in a temperature- and humidity-controlled room (22 ± 2°C and 30–70%, respectively) with a 12-h light/12-h dark cycle at the Pennington Biomedical Research Center, Baton Rouge, LA and at the Institute of Animal Reproduction and Food Research of Polish Academy of Sciences, Olsztyn, Poland. Twelve-week-old female and male B6 mice were caged together and the presence of a vaginal plug indicated possible pregnancy and the embryonic age of fetus was designated as gestational day 0.5 (E1). Embryos were collected at embryonic day E14 and E18.

extract_protocol:
Total RNA from each sample was isolated using Trizol (Invitrogen, Carlsbad, CA). Total RNA samples passing Agilent RIN greater than 7 were prepared for sequencing.
Total RNA samples were prepared for sequencing using the SOLiD™ SAGE Kit using 500 ng input according to the manufacturer’s protocol. Emulsion PCR and SOLiD sequencing, SAGE-sequencing of 35 bp tags, 30 base pairs in a single direction, were performed according to manufacturer’s instructions for the SOLiD™ 3 System (Life Technologies).
SOLiD SAGE Kit with Barcoding Adaptor Module (#4452811) and SOLiD RNA Barcode Kit (#4427046)

treatment_protocol: Pregnant mice were anesthetized by intraperitoneal injections of ketamine (45mg/kg) and xylazine (3 mg/kg). The maternal abdominal wall was shaved and cleansed with 70% ethanol. An abdominal midline incision was made to expose the uterus. The fetuses were removed from uterine cavity. Under the dissecting microscopy (10 x magnification, Zeiss, Germany), individual fetuses were immediately killed by decapitation and the full-thickness dorsal skin of fetus was excised with micro-scissors. The skin samples were immediately snap-frozen in liquid nitrogen for subsequent RNA isolation

tag: background strain

tag: strain name

tag: genotype

value: wild type

value: Epidermis

value: 6 week old


title: 5Nudeskin_1002

department: Institute of Animal Reproduction and Food Research

source_name: Skin

value: B6.Cg-Foxn1 nu (Nude)

value: Skin

tag: age


title: 5Nudeskin_1001


title: 5Nudeepid_1027


title: 5Nudeepid_1028


title: 5B6epid_1031


title: 5B6epid_1032


title: 5Nudeskin_1003


title: 5Nudeskin_1000


title: 5B6skin_997


title: 5Nudeskin_999


title: 5B6skin_992


title: 5Nudeepid_1026


title: 18B6skin_991

value: embryonic day E18


title: 18B6skin_990


title: 5Nudeskin_998


title: 18B6skin_989


title: 18B6skin_988


title: 18B6skin_987


title: 5B6epid_1030


title: 14B6skin_983

value: embryonic day E14


title: 14B6skin_984


title: 18B6skin_986


title: 5Nudeepid_1025


title: 5B6skin_995


title: 14B6skin_982


title: 5B6skin_993


title: 14B6skin_981


title: Non inoculated stems rep2

description: validation RNA-seq project

value: Darmor-bzh

value: Adult plants of the susceptible cultivar Darmor-bzh were inoculated 22 days after sowing at the three leaves development stage. The petiole of the second leaf was cut off just under the leaf blade and 10µl of water was placed over the wound.Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 14 days after inoculation stem tissues were sampled.


title: 5B6skin_996


title: Non inoculated cotyledons rep2

description: validation RNA-seq project

value: Ten days-old seedling of the susceptible cultivar Darmor-bzh were inoculated with 10µl of water at a needle puncture. Inoculated plants were incubated in darkness for 48h at room temperature under saturated humidity, and then transferred to a growth chamber at 16°C (night) and 24°C (day), with a 12h photoperiod. 7 days after infection,  cotyledons were sampled.


title: R-3 (OD600 1.5)

city: Kuala Lumpur

first: Jia-Yi

last: Tan

address: University of Malaya

country: Malaysia

institute: University of Malaya

data_processing:
Rockhopper (assembly and generation of raw counts)
DESeq (differential expression, graphical visualization)
Genome_build: NZ_CP009706
Supplementary_files_format_and_content: tab-delimited text files include raw counts, normalized counts and expression for each sample

organism: Hafnia alvei

source_name: Fish paste

growth_protocol: LBB, 30°C, OD 1.5

extract_protocol:
RNA extraction: QIAamp RNA mini kit, RNAProtect
ScriptSeq

treatment_protocol: Replacement knockout of quorum sensing genes

tag: strain


title: Mycelium in vitro rep2

description: validation RNA-seq project

organism: Plenodomus lingam

source_name: Axenic culture


title: I-1 (OD600 1.5)


title: 5B6skin_994


title: R-1 (OD600 1.5)


title: I-2 (OD600 1.5)


title: WT-1 (OD600 1.5)

value: Wild type


title: WT-3 (OD600 1.5)


title: WT-2 (OD600 1.5)


title: R-2 (OD600 1.5)


title: Input rep2

status: Public on Dec 29 2016

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

description: Input rep2

data_processing:
Reads were mapped to reference genome using bowtie2.
Peaks were identified using SICER.
Coverage files were generated by genomecov form BEDTools.
Genome_build: TAIR10
Supplementary_files_format_and_content: BedGraph

organism: Arabidopsis thaliana

source_name: Seedlings

extract_protocol: The libraries were prepared using the NuGen Ovation Ultralow Library Systems and were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.

value: none, Input


title: 14B6skin_980


title: Mycelium in vitro rep1

description: validation RNA-seq project


title: HDP2 IP rep2

description: HDP2 IP rep2

value: anti-FLAG (SIGMA, cat#F1804)


title: I-3 (OD600 1.5)


title: Non inoculated stems rep1

description: validation RNA-seq project


title: HDP2 IP rep1

description: HDP2 IP rep1


title: idm1-06299

data_processing:
Reads were mapped to TAIR10 using BRAT-BW v2.0.1 with parameters -m 2 -i 0 -a 1000
Copy-duplicates were remove using remove-dupl command of BRAT-BW
acgt-count command of BRAT-BW was used to count mapped Cs and Ts at each cytosine of forward and reverse strands of the reference
Genome_build: TAIR10
Supplementary_files_format_and_content: The wig files give methylation level for all Cs(three contexts) with depth >= 4. Methylation level of each cytosine base was calculated according to number of converted and unconverted C mapped at that position ( unconverted_C / ( converted_C+ unconverted_C ) ).

extract_protocol: The genomic DNA was extracted from 1 gram of 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen. And 5 µg of gDNA was used for library construction using Illumina’s standard DNA methylation analyses protocol and the TruSeq DNA sample preparation kit. The samples were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.

tag: genotype/variation

value: idm1 mutant (SALK_06299)


title: 14B6skin_985


title: Col-0

value: WT


title: Non inoculated cotyledons rep1

description: validation RNA-seq project


title: Input rep1

description: Input rep1


title: hdp1-T2


title: hdp1-T1


title: hdp2-2-2


title: hdp2-2-1


title: 23-1_rep1

data_processing:
Read were aligned to reference genome using TopHat.
TDF files were generated by IGVTools
Genome_build: TAIR10
Supplementary_files_format_and_content: TDF files with read coverage

extract_protocol: Total RNAs of were isolated by Trizol reagent (Invitrogen), and were treated with DNase I (Ambion) to remove DNA. mRNAs were enriched with Oligo (dT)-conjugated magnetic beads and were then sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) for library preparation and Illumina sequencing.


title: WTSUC2_rep2


title: WTSUC2_rep1


title: 23-1_rep2


title: 56-1_rep1


title: hdp2-1 MethylC-Seq

extract_protocol: The bisulfite treatment, library preparation, and sequencing was done in Genomics Core, Shanghai Center for Plant Stress Biology . Bisulfite sequencing libraries were prepared using standard Illumina protocols.


title: mbd7 MethylC-Seq


title: hdp1-1 MethylC-Seq


title: 35S-SUC2_WT MethylC-Seq

value: 35S-SUC2 WT


title: cytosol mRNA in knockdown-FLII HBE

city: Guangzhou

first: Kezhi

last: Chen

state: Guangdong

address: Huangpu Avenue

department: Institute of life and health engineering

country: China

institute: Jinan University

description: cytosol mRNA in knockdown-FLII HBE

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were obtained and mapped to thehuman mRNA reference sequence (RefSeq) for GRCh37/hg19 in UCSC genome browser by using FANSe2 mapping algorithm with the options –L78 –S8 –I0 –E9 –B1.The reads mapped to splice variants of one gene were summed.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: txt files include RPKM values and read counts of each gene for each sample

source_name: cytosol mRNA in knockdown-FLII HBE

growth_protocol: Human H1299 and HBE cells (Cell Resource Center, Institute of life science Chinese Academy of Sciences, Shanghai, China) were cultured in Dulbecco’s modified Eagle medium (DMEM, Gibco BRL, Grand island, NY) supplemented with 10% fetal bovine serum (PAA Laboratories, Weike Biochemical Reagent, Shanghai, China), 1% penicillin/streptomycin (Genom, China) at 37°C in a humidified atmosphere containing 5% CO2.

extract_protocol:
The RNC extraction was performed as described by Esposito et al. (18) with modifications. In brief, cells were pre-treated with 100 mg/ml cycloheximide for15 min, followed by pre-chilled phosphate buffered saline washes and addition of 2 ml cell lysis buffer [1%Triton X-100 in ribosome buffer (RB buffer) [20mM HEPES-KOH(pH=7.4), 15 mM MgCl2, 200 mM KCl, 100 mg/ml cycloheximide and 2 mM dithiothreitol]. After 30-min ice-bath, cell lysates were scraped and transferred to pre-chilled 1.5 ml tubes. Cell debris was removed by centrifuging at 13200 g for 10 min at 4°C. Supernatants were transferred on the surface of 20 ml of sucrose buffer (30%sucrose in RB buffer). RNCs were pelleted after ultra-centrifugation at 185 000 g for 5 h at 4°C. RNC-RNA was purified using Trizol method.
Libraries were prepared according to NEBNext® mRNA Library Prep Master Mix Set for Illumina®.

treatment_protocol: H1299 cells were transfected with either empty pCMV-N-Flag or pCMV-N-Flag-FLII vectors using Lipofectamine 2000. Lentiviral shRNA vectors targeting human FLII were utilized for stable knockdown in HBE cells.

value: lung

tag: cell type

value: Epithelial lung cell

tag: cell line

value: HBE

tag: passage


title: idm1-9 MethylC-Seq


title: nuclear mRNA in knockdown-FLII HBE

description: nuclear mRNA in knockdown-FLII HBE

source_name: nuclear mRNA in knockdown-FLII HBE


title: cytosol mRNA in NC HBE

description: cytosol mRNA in NC HBE

source_name: cytosol mRNA in NC HBE


title: hdp2mbd7 MethylC-Seq


title: nuclear mRNA in NC HBE

description: nuclear mRNA in NC HBE

source_name: nuclear mRNA in NC HBE


title: nuclear mRNA in overepress-FLII H1299

description: nuclear mRNA in overepress-FLII H1299

source_name: nuclear mRNA in overepress-FLII H1299


title: nuclear mRNA in overepress-vector H1299

description: nuclear mRNA in overepress-vector H1299

source_name: nuclear mRNA in overepress-vector H1299


title: cytosol mRNA in overepress-FLII H1299

description: cytosol mRNA in overepress-FLII H1299

source_name: cytosol mRNA in overepress-FLII H1299


title: RNC in overexpress-FLII H1299

description: RNC-bound mRNA of in overexpress-FLII H1299


title: RNC in NC HBE

description: RNC-bound mRNA of RNC in NC HBE

source_name: RNC-bound mRNA of RNC in NC HBE


title: RNC in overexpressed-vector H1299

description: RNC-bound mRNA in overexpressed-vector H1299


title: RNC in knockdown-FLII HBE

description: RNC-bound mRNA of RNC in knockdown-FLII HBE


title: mRNA in knockdown-FLII HBE

description: mRNA in knockdown-FLII HBE

source_name: mRNA in knockdown-FLII HBE


title: cytosol mRNA in overepress-vector H1299

description: cytosol mRNA in overepress-vector H1299

source_name: cytosol mRNA in overepress-vector H1299


title: mRNA in NC HBE

description: mRNA in NC HBE

source_name: mRNA in NC HBE


title: 56-1_rep2


title: Subject_14_V5_2

city: New York

first: Chenyi

last: Xue

state: NY

institute: Columbia University

description: FFAME_PUFA_pre_LPS_vs_post_LPS_gene_exp.diff.gz

data_processing:
Base calling was done by RTA v1.13.48.0
Sequence reads were aligned to hg19 genome using STAR with default options.
Alignment was filtered using the following specifications: 1) read was uniquely mapped, 2) reads from the same pair were mapped to the same chromosome with expected orientations and mapping distance between the read pair was < 500,000 bp
Fragments Per Kilobase of exon per Million reads mapped (FPKM) was estimated by Cufflinks 2.1.1. Differential expression was tested by Cuffdiff with options "-u --max-bundle-frags 50000000".
Genome_build: hg19
Supplementary_files_format_and_content: DIFF files were obtained from Cuffdiff output.
Supplementary_files_format_and_content: FFAME_placebo_pre_vs_post_treatment_gene_exp.diff contains differential expression result in placebo group before and after placebo treatment. Annotation included mRNAs from RefSeq and lincRNAs combined in Ballantyne et al. Human Molecular Genetics (2016)
Supplementary_files_format_and_content: FFAME_PUFA_pre_vs_post_treatment_gene_exp.diff contains differential expression result in PUFA group before and after n-3 PUFA treatment. Annotation included mRNAs from RefSeq and lincRNAs combined in Ballantyne et al. Human Molecular Genetics (2016)
Supplementary_files_format_and_content: FFAME_placebo_pre_LPS_vs_post_LPS_gene_exp.diff contains differential expression result in placebo group after treatment/before LPS vs. after LPS. Annotation included mRNAs from RefSeq and lincRNAs combined in Ballantyne et al. Human Molecular Genetics (2016)
Supplementary_files_format_and_content: FFAME_PUFA_pre_LPS_vs_post_LPS_gene_exp.diff contains differential expression result in PUFA group after treatment/before LPS vs. after LPS. Annotation included mRNAs from RefSeq and lincRNAs combined in Ballantyne et al. Human Molecular Genetics (2016)

source_name: Gluteal subcutaneous adipose tissue

extract_protocol:
RNA from adipose tissue biopsies was extracted using the RNeasy total RNA kit (Qiagen Inc., Valencia, CA). Extracted RNA samples underwent quality control (QC) assessment using the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
Using a minimum of 300ng input RNA, Poly-A libraries were prepared using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina, San Diego, CA) per standard protocols. The prepared libraries were sequenced on an Illumina HiSeq 2000 at the UPenn Next Generation Sequencing Core (NGSC). We sequenced samples at a depth of 6 samples per lane, which generated ~30 million 2×101 bp paired-end reads per sample.

value: Adipose

tag: treatment

value: n-3 PUFA

tag: time

value: Post-LPS


title: mRNA in overepress-vector H1299

description: mRNA in overepress-vector H1299

source_name: mRNA in overepress-vector H1299


title: Subject_13_V5_2


title: Subject_12_V5_2


title: Subject_11_V5_2


title: Subject_10_V5_2


title: mRNA in overepress-FLII H1299

description: mRNA in overepress-FLII H1299

source_name: mRNA in overepress-FLII H1299


title: Subject_7_V5_2


title: Subject_6_V5_2

description: FFAME_placebo_pre_LPS_vs_post_LPS_gene_exp.diff.gz

value: Placebo


title: Subject_4_V5_2


title: Subject_9_V5_2


title: Subject_3_V5_2


title: Subject_1_V5_2


title: Subject_12_V5_1

description:
FFAME_PUFA_pre_vs_post_treatment_gene_exp.diff.gz
FFAME_PUFA_pre_LPS_vs_post_LPS_gene_exp.diff.gz

value: Post-treatment Pre-LPS


title: Subject_13_V5_1


title: Subject_14_V5_1


title: Subject_9_V5_1


title: Subject_10_V5_1


title: Subject_2_V5_2


title: Subject_11_V5_1


title: Subject_7_V5_1


title: Subject_8_V5_1


title: Subject_5_V5_1

description:
FFAME_placebo_pre_vs_post_treatment_gene_exp.diff.gz
FFAME_placebo_pre_LPS_vs_post_LPS_gene_exp.diff.gz


title: Subject_3_V5_1


title: Subject_8_V5_2


title: Subject_4_V5_1


title: Subject_6_V5_1


title: Subject_14_V2

description: FFAME_PUFA_pre_vs_post_treatment_gene_exp.diff.gz

value: Pre-treatment


title: Subject_13_V2


title: Subject_1_V5_1


title: Subject_10_V2


title: Subject_5_V5_2


title: Subject_12_V2


title: Subject_9_V2


title: Subject_8_V2


title: Subject_11_V2


title: Subject_5_V2

description: FFAME_placebo_pre_vs_post_treatment_gene_exp.diff.gz


title: Subject_4_V2


title: Subject_2_V2


title: YL1

city: Beijing

first: Bo

last: Zhang

address: No. 2 Yuanmingyuan West Road, College Animal Science & Technology, China Agriculture University, Beijing

institute: China Agricultural University

description:
processed data file: TL_FPKM.txt
processed data file: expression all_FPKM.txt

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for more than 2 Ns, more than half of the base’s qualities were less than 10 and reads with less than 20 bp ,and the adapters from all reads, then mapped to Sscrofa10.2.72 whole genome using bowtie v0.12.5 and Tophat (version:2.0.9) and two mismatches were allowed for 100 bp reads in each alignment.
Numbers of fragment reads per kilobase of exon region in a gene per million mapped reads (FPKM) analyzed by Cufflink (version: 2.1.1) were used as the value of normalized gene expression
Differential expression analyses of four comparsion groups (TH vs.YH, TH vs.TL, YH vs.YL and TLvs.YL.) were performed using the DESeq R package (1.10.1)
Genome_build: Sscrofa10.2.72
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: Yorkshire raised at lowland

extract_protocol:
Hearts were removed, flash frozen on liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 3 ug of total RNA for the construction of sequencing libraries.
mRNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Yorkshire

value: heart

value: 6 months

tag: Sex

value: male


title: Subject_3_V2


title: YH2

description:
processed data file: YH_FPKM.txt
processed data file: expression all_FPKM.txt

source_name: Yorkshire pigs raised at highland


title: YH1


title: Subject_1_V2


title: TL2

source_name: Tibetan pigs raised at lowland

value: Tibetan


title: Subject_2_V5_1


title: TH1

description:
processed data file: TH_FPKM.txt
processed data file: expression all_FPKM.txt

source_name: Tibetan pigs raised at highland


title: TH2


title: RSUY031_methylome

city: Sao Paulo

first: Joao

middle: C

last: Setubal

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Biochemistry

country: Brazil

institute: University of Sao Paulo

data_processing:
Library strategy: DNA methylation analysis with PacBio sequencing reads
Reads were assembled using RS_HGAP_Assembly.2 protocol from SMRT Analysis 2.3
Motif detection was performed using RS_Modification_and_Motif_analysis.1 protocol from SMRT Analysis using QV threshold of 30
Genome_build: GCA_001299555.1
Supplementary_files_format_and_content: Positions represent methylated motifs on the genome

organism: Ralstonia solanacearum

source_name: genomic DNA from Ralstonia solanacearum UY031 at stationary phase

growth_protocol: R. solanacearum strain UY031 was routinely grown in rich B medium (10 g/l bactopeptone, 1 g/l yeast extract and 1 g/l casaminoacids)

extract_protocol:
Genomic DNA was extracted from a bacterial culture grown to stationary phase to avoid over-representation of genomic sequences close to the origin of replication
P5-C3 chemistry, quality control was performed with DUGSIM

treatment_protocol: Twelve ml of a culture grown for 16 h at 30 °C and shaking at 200 rpm (OD600 = 0.87) were used to extract DNA with Blood & Cell Culture DNA Midi kit (Qiagen), following manufacturer’s instructions for gram-negative bacteria. DNA concentration and quality were measured in a Nanodrop (ND-8000 8-sample spectrophotometer)


title: TL1


title: 8h_IgG_P5

status: Public on Dec 28 2016

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

description: 8 hours after activation of Cll cells from patient p5 with IgG (control)

data_processing:
Reads were demultiplexed the reads into the different samples
Reads were aligned to the hg19 genome built using Tophat (v2.0.10)
Read counting to Refseq genes was done with HTseq-count (version 0.6.1p1)
Differential expression analysis was performed with DESeq2 (1.6.3)
Genome_build: hg19
Supplementary_files_format_and_content: Excel file includes the normalized counts, log fold change, p-value and FDR

source_name: Cll cells

growth_protocol: B cells were obtained from CLL patients using a RosettSep antibody mixture.

extract_protocol:
mRNA from primary human CLL cells was isolated using PerfectPure RNA Cultured Cell Kit (5 Prime, Hamburg, Germany), according to the manufacturer’s instructions.
Libraries  were  constructed  from total  RNA  using  the  Illumina TruSeq  RNA  Sample  Preparation  v2  (Cat.  number: RS-122-2002,  Illumina,  Inc,  CA,   U.S.A) according  to  the  manufacturer's  instructions

treatment_protocol: Cells were activated with either CD74 Ab or IgG control Ab

tag: diagnosis

value: CLL

tag: patient age

tag: patient sex

value: Male

tag: disease level

value: Binet B

tag: activation ab

value: isotype control antibody

tag: activation time

value: B cells


title: 8h_IgG_P3

description: 8 hours after activation of Cll cells from patient p3 with IgG (control)

value: Female

value: Binet A


title: 2h_IgG_P6

description: 2 hours after activation of Cll cells from patient p6 with IgG (control)


title: Subject_7_V2

tag: tissue

value: Adipose

value: n-3 PUFA


title: 8h_CD74_P5

description: 8 hours after activation of Cll cells from patient p5 with CD74

value: CD74 (C-16; Santa Cruz Biotechnology)


title: 2h_CD74_P6

description: 2 hours after activation of Cll cells from patient p6 with CD74


title: Subject_6_V2

value: Placebo


title: 8h_CD74_P3

description: 8 hours after activation of Cll cells from patient p3 with CD74


title: 2h_IgG_P3

description: 2 hours after activation of Cll cells from patient p3 with IgG (control)


title: 8h_CD74_P6

description: 8 hours after activation of Cll cells from patient p6 with CD74


title: YL2

tag: age


title: p4_CD74_Input_2

description: input for p4_CD74_H3K27Ac.fastq

data_processing:
Reads were demultiplexed
Adapters were trimmed using the cutadapt tool
The reads were aligned uniquely to the human genome (hg19)
Bound regions were detected using MACS2 (version 2.0.10.20131216)
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS2 peaks

extract_protocol:
Lysates were clarified from sonicated cells and protein-DNA complexes were isolated with antibody.
In-house ChIP-Seq protocol, Libraries were evaluated by Qubit and TapeStation. Sequencing libraries were constructed with barcodes to allow multiplexing of y samples on one lane.

tag: patient number

tag: chip ab

value: Input

tag: activation


title: 2h_CD74_P3

description: 2 hours after activation of Cll cells from patient p3 with CD74

tag: cell type


title: 2h_CD74_P5

description: 2 hours after activation of Cll cells from patient p5 with CD74


title: p4_CD74_H3K27Ac

description: processed data file: p4_CD74_activation_H3K27Ac_versus_input.bed

value: H3K27Ac (abcam ab4729)


title: p7_CD74_H3K27Ac

description: processed data file: p7_CD74_activation_H3K27Ac_versus_input.bed


title: p6_IgG_Input

description: input for p6, activation with IgG, H3K4Me2 and H3K4Me3

value: IgG


title: p6_IgG_H3K4Me3

description: processed data file: p6_IgG_activation_H3K4Me3_versus_input.bed

value: H3K4Me3 (Millipore, 07-473)


title: 8h_IgG_P6

description: 8 hours after activation of Cll cells from patient p6 with IgG (control)


title: p6_CD74_H3K4Me3

description: processed data file: p6_CD74_activation_H3K4Me3_versus_input.bed


title: p3_IgG_H3K4Me3

description: processed data file: p3_IgG_activation_H3K4Me3_versus_input.bed


title: p6_CD74_Input

description: input for p6 with CD74 activation,  H3K4Me2 and H3K4Me3


title: p3_IgG_Input

description: input for p3, activation with IgG, H3K4Me2 and H3K4Me3


title: p3_IgG_H3K4Me2

description: processed data file: p3_IgG_activation_H3K4Me2_versus_input.bed

value: H3K4Me2 (abcam ab32356)


title: p3_CD74_Input

description: input for p3, activation with CD74, H3K4Me2 and H3K4Me3


title: p3_CD74_H3K4Me3

description: processed data file: p3_CD74_activation_H3K4Me3_versus_input.bed


title: p3_CD74_H3K4Me2

description: processed data file: p3_CD74_activation_H3K4Me2_versus_input.bed


title: p3_CD74_CD74

description: processed data file: p3_CD74_activation_CD74_versus_input.bed

value: CD74 (BD Bioscience 555317)


title: p4_b_CD74_CD74

description: processed data file: p4_CD74_activation_CD74_versus_input.bed

value: CLL


title: 2h_IgG_P5

description: 2 hours after activation of Cll cells from patient p5 with IgG (control)

value: Male


title: p2_CD74_Input

description: input for p2_a_CD74_CD74.fastq and p2_b_CD74_CD74.fastq

value: Binet B


title: p2_a_CD74_CD74

description: processed data file: p2_CD74_activation_CD74_versus_input.bed


title: p4_CD74_Input_1

description: input for p4_a_CD74_CD74.fastq and p4_b_CD74_CD74.fastq


title: p4_a_CD74_CD74


title: p1_b_CD74_CD74

description: processed data file: p1_CD74_activation_CD74_versus_input.bed


title: p1_a_CD74_CD74


title: p1_CD74_Input

description: input for p1_a_CD74_CD74.fastq and p1_b_CD74_CD74.fastq


title: p2_b_CD74_CD74


title: chilling-treated

city: Hangzhou

first: Xu

last: shengchun

address: Deshengzhonglu

department: Institute of Vegetables

data_processing:
To identify known and novel miRNAs, a data processing procedure was conducted with some modification suited for plant in hairpin prediction provided by LC Sciences Service 31,46. Briefly, all of the raw reads were firstly subjected to the Illumina pipeline filter, and then processed by ACGT101-miR program (LC Sciences, Houston, Texas, USA) to fil-ter out adapter sequences, low-quality and low copy reads, as well as common RNA families (rRNA, tRNA, snRNA, snoRNA). Subsequently, filtered sequences with 18-25 nt in length were compared to miRNA database, miRBase 20.0 (http://www.mirbase.org/) by BLASTn search to identify the known miRNAs. Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identied as known miRNAs. The unique sequences mapping to the other arm of known specific species precur-sor hairpin opposite to the annotated matu-re miRNA-containing arm were considered to be novel 5p’ or 3p’ derived miRNA candidates. The remain-ing sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 20.0 by BLAST search, and the mapped pre-miRNAs were further blasted against the specific species genomes to determine their genomic locations. The above two were defined as known miRNAs.
Then, the unmapped sequences were subjected to blast against the soybean genome to identify novel miRNAs and predicated stem-loop hair-pin secondary structures by using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The criteria for secondary structu-re predic-tion was as described by previous studies 46, including: (1) the miRNA located in one arm of the folded stem-loop hair-pin secondary structu-re, (2) less than 12 nt in one bulge and more than 16 base pairs in the stem region of the predicted  hair-pin, (3) less than 20 nt in length of hair-pin loop and more than 50 nt in length of to-tal hair-pin, (4) no more than 4 nt and two biased er-rors in one bulge, (5) less than two biased bulges and 4 mismatches, as well as more than 12 base pairs in mature region, (6) more than 80% of mature region in stem, (7) predicted secondary structu-re had higher negative minimal folding energy (MFE) and minimal free folding energy indexes (MFEI).
To investigate the differentially expressed miRNAs between chilling stress and control li-brar-ies, each identified miRNAs read count was normalized to the total number of miRNA reads in each given sample and multiplied by a million (RPKM). The p value (≤ 0.001) and absolute value of log2Ratio (≥1), indicating the ra-tio of RPKM values for the chilling treated and control libraries, were used to judge the significance of gene expression differences 47
Identification and classifi-cation of categories of the sliced miRNA targets were processed according to the CleaveLand 3.0 pipeline 27. The sliced-target transcripts were grouped in-to five categories. Category ‘0’ is defined as > 1 raw read at the posi-tion, with abundance at a posi-tion equal to the maximum on the transcript, and with only one maximum on the transcript. Category ‘1’ is described as > 1 raw read at the posi-tion, with abundance at the posi-tion equal to the maximum on the transcript, and more than one maximum posi-tion on the transcript. Category ‘2’ includes > 1 raw read at the posi-tion, and abundance at the posi-tion less than the maximum but higher than the median for the transcript. Category ‘3’ comprised the transcripts with > 1 raw read at the posi-tion, and  abundance at the posi-tion equal to or less than the median for the transcript; and category ‘4’ showed only one raw read at the posi-tion. All of the candidate target transcripts were performed to gene ontology (GO) analysis by using the AgriGO toolkit 49.
Genome_build: Gmax_275_Wm82.a2.v1
Supplementary_files_format_and_content: expression data of miRNA and differential analysis results, and targets prediction results for all detected miRNAs; xls format.  Table S1.xls contains known miRNAs, Table S3.xls contains novel miRNAs and Table S5.xls contains the predicted miRNA targets.

organism: Glycine max

growth_protocol: The experiments were conducted in the Institute of Vegetables, Zhejiang Academy of Agricultural Sciences. Vegetable soybean ‘Taiwan 75’ was planted in pots at a photosynthetic photon flux density (PPFD) of 600 μmol m-2 s-1 with a photoperiod of 12 h, temperatures of 25 °C (day) and 17 °C (night), and a humidi-ty between 50% and 85%. At the one true-leaf stage, the plants were transferred to 4 °C for chilling stress with the same growth conditions as the control. Relative growth rate (RGR) 44 and MDA content 9 were determined for each of the chilling treatments at 3 h, 6 h, 9 h, 12 h, 24 h and 36 h and the control. At 24 h, there were significant differences in both RGR and MDA content between chilling treatment and the control (Figure S1). Therefore ten pots (10 plants) each for 24-h chilling treatment and the control were prepared for small RNA sequencing and qRT-PCR vali-dation.

extract_protocol:
Leaves of three replicates with 24h chilling treatment and control were collected, respectively, and stored at -80 °C. For Solexa sequencing, three replicates were pooled together from chilling treatment and control, respectively. Total RNA was extracted separately with TRIzol reagent (Invitrogen, USA) according to the manufacturer’s instructions. RQ1 RNase-Free DNase (Promega, USA) was used to remove genomic DNA contamination. The total RNA quantity and purity were analysis by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA).
About 1 μg of total RNA were used to construct small RNA library following the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Then we performed the single-end sequencing on an Illumina Hiseq2500 at the LC-BIO (Hangzhou, China) following a recommended protocol 45.A degradome li-brary was constructed from vegetable soybean leaves to predict the potential target mRNAs following the methods described previously by German et al.48. The purified cDNA li-brary was used for cluster genera-tion on Il-lumina’s Cluster Station and then sequenced on Il-lumina Hiseq 2500 following vendor’s in-struction for running the in-strument. Raw sequencing reads were obtained using Il-lumina’s Pipeline v1.5 software.

tag: cultivar

value: Taiwan 75

tag: developmental stage

value: At the one true-leaf stage

value: 24h chilling treatment

value: leaf


title: p7_CD74_Input

description: input for p7_CD74_H3K27Ac.fastq

value: B cells


title: XSCD1dgd

institute: Zhejiang Academy of Agricultural Sciences

description: degradome sequencing

value: 10 days after pollination

tag: treatment

value: pooled chilled and control leaves


title: control

value: control without chilling treatment


title: ASH1 Rep1

city: Chiyodaku

first: Yujiro

last: Tanaka

state: Tokyo

address: 2-3-10 Kandasurugadai

department: School of Biomedical Science

institute: Tokyo Medical and Dental University

data_processing:
Alignment to hg19 by BWA.
MACS14 peak detection software with p-value 1x10^-7.
Statistical analysis by Genomatix suite, CLC Main Workbench, Galaxy portal, and ngs.plot.
Gene ontology analysis by DAVID server.
Genome_build: GRCh38 (hg19)
Supplementary_files_format_and_content: WIG, BED (peak calls)

growth_protocol: K562 cells were cultured in DMEM with 10% fetal calf serum.

extract_protocol:
Approximately 1x108 K562 cells were fixed by 10% formaldehyde in 50 mM Hepes-KOH, pH7.5, 100 mM NaCl, 1 mM EDTA, ph8.0, 0.5 mM EGTA, pH8.0 for 10 min at room temperature, quenched by one tenth volume of 2.5 M Glycine, rinsed sequentially with LB1 (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100), LB2 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, pH8.0), and resuspended in LB3 (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1 mM EDTA, pH8.0 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine) containing Protease Inhibotor Cocktail (Roche). Cell suspension was then sonciated by Covaris S2 Acoustic Solbilyzer with Duty Cycle 20%, Intensity 5, Cycles per Burst 200, and 20-30 cycles. Lysates were cleared by centrifugation, and immunoprecipitated with anti-ASH1 antibodies fixed on Dynabeads M-280 sheep anti-rabbit/mouse IgG (Invitrogen), washed with LiCl buffer (100 mM Tris-HCl, pH7.5, 500 mM LiCl, 1% NP-40, 1% Na-Deoxycholate) and then with TE, and eluted in 1% SDS, 0.1 M NaHCO3. After overnight de-crosslinking, DNA was purified with PCR Cleanup column (QIAGEN). Fragment sizes were checked by 2100 BioAnalyzer (Agilent).
Sequencing libraries were constructed using ChIP-Seq Sample Prep Kit (Illumina) according to the manufacture's protocol.

tag: cell line

value: leukemia cell line K562

tag: chip antibody

value: anti-ASH1 (made in-house)

tag: chip antibody batch


title: lncOL1KO_rep2

city: Cincinnati

first: Richard

last: Lu

state: OH

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mm10 whole genome using Tophat using default options
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks with default options. Outputs from Cufflinks are provided as supplementary files as a tab-delimited text file. Differential gene expression analysis was performed using Cuffdiff.
Genome_build: mm10
Supplementary_files_format_and_content: [.txt] tab-delimited text files include FPKM values of all UCSC_mm10 annotated genes and differential gene expression analysis

source_name: mouse primary oligodendrocyte

growth_protocol: primary mouse oligodendrocyte precursor cells are  differentiated for one day with T3

extract_protocol:
total RNA was harvested using Trizol reagent
Libraries were prepared according to Illumina's instructions accompanying Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001)

value: Primary oligodendrocyte

tag: genotype

tag: strain

value: mixed background


title: Ctrl_rep1

value: lncOL1+/+, lncOL1+/-