title: singles-SU353-LSC-160209-82

description: Sample 178


title: singles-SU353-LSC-160209-83

status: Public on Jul 30 2016

type: SRA

city: Cambridge

first: Jason

middle: Daniel

last: Buenrostro

state: MA

address: 415 Main Street

country: USA

institute: Broad Institute

description: Sample 179

library_source: genomic

data_processing:
library strategy: scATAC-seq
Adapter sequences were trimmed from FASTQs using custom python scripts to enable mapping fragments with sequences containing adapters. Paired-end reads were aligned to hg19 or mm10 using BOWTIE2 using the parameter –X2000 allowing fragments of up to 2 kb to align. Duplicates were removed using PICARD tools. Reads were subsequently filtered for alignment quality of >Q30 and were required to be properly paired. Reads mapping to the mitochondria, unmapped contigs and chromosome Y were removed and not considered.
Genome_build: hg19
Supplementary_files_format_and_content: All samples supplied as a count table for all called regulatory elements.

molecule: genomic DNA

organism: Homo sapiens

source_name: LSC

extract_protocol:
Single cells were captured using the C1 Single-Cell Auto Prep IFC microfluidic chips. Cells were permeabilized and accessible fragments were captured using 20 µL of Tn5 transposition mix (1.5x TD buffer, 1.5 µL transposease (Nextera DNA Sample Prep Kit, Illumina), 1x C1 Loading Reagent with low salt (Fluidigm), and 0.15% NP40) at 30 minutes at 37°C.
In a 96-well plate, 10 µL of harvested libraries were amplified in 50 µL PCR for an additional 14 cycles (1.25 µM custom Nextera dual-index PCR primers (Supplementary Table 1) in 1x NEBnext High-Fidelity PCR Master Mix) using the following PCR conditions: 72°C for 5min; 98°C for 30 s; and thermocycling at 98°C for 10 s, 72°C for 30 s, and 72°C for 1 min. The PCR products were pooled creating a final volume of ~4.8 mL. The pooled library was purified on a single MinElute PCR purification column (Qiagen) yielding libraries at an approximate concentration of ~1 µM. Libraries were quantified using qPCR prior to sequencing.

tag: cell type

value: acute myeloid leukemia, leukmeia stem cell

tag: doner id


title: singles-SU353-LSC-160209-75

description: Sample 171


title: singles-SU353-LSC-160209-79

description: Sample 175


title: singles-SU353-LSC-160209-73

description: Sample 169


title: singles-SU353-LSC-160209-84

description: Sample 180


title: singles-SU353-LSC-160209-71

description: Sample 167


title: singles-SU353-LSC-160209-74

description: Sample 170


title: singles-SU353-LSC-160209-69

description: Sample 165


title: singles-SU353-LSC-160209-77

description: Sample 173


title: singles-SU353-LSC-160209-72

description: Sample 168


title: singles-SU353-LSC-160209-81

description: Sample 177


title: singles-SU353-LSC-160209-70

description: Sample 166


title: singles-SU353-LSC-160209-78

description: Sample 174


title: singles-SU353-LSC-160209-80

description: Sample 176


title: singles-SU353-LSC-160209-67

description: Sample 163


title: singles-SU353-LSC-160209-63

description: Sample 159


title: singles-SU353-LSC-160209-65

description: Sample 161


title: singles-SU353-LSC-160209-62

description: Sample 158


title: singles-SU353-LSC-160209-61

description: Sample 157


title: singles-SU353-LSC-160209-85

description: Sample 181


title: singles-SU353-LSC-160209-87

description: Sample 183


title: singles-SU353-LSC-160209-60

description: Sample 156


title: singles-SU353-LSC-160209-58

description: Sample 154


title: singles-SU353-LSC-160209-57

description: Sample 153


title: singles-SU353-LSC-160209-68

description: Sample 164


title: singles-SU353-LSC-160209-66

description: Sample 162


title: singles-SU353-LSC-160209-50

description: Sample 146


title: singles-SU353-LSC-160209-54

description: Sample 150


title: singles-SU353-LSC-160209-51

description: Sample 147


title: singles-SU353-LSC-160209-49

description: Sample 145


title: singles-SU353-LSC-160209-52

description: Sample 148


title: singles-SU353-LSC-160209-44

description: Sample 140


title: singles-SU353-LSC-160209-64

description: Sample 160


title: singles-SU353-LSC-160209-55

description: Sample 151


title: singles-SU353-LSC-160209-42

description: Sample 138


title: singles-SU353-LSC-160209-45

description: Sample 141


title: singles-SU353-LSC-160209-53

description: Sample 149


title: singles-SU353-LSC-160209-56

description: Sample 152


title: singles-SU353-LSC-160209-48

description: Sample 144


title: singles-SU353-LSC-160209-43

description: Sample 139


title: singles-SU353-LSC-160209-39

description: Sample 135


title: singles-SU353-LSC-160209-38

description: Sample 134


title: singles-SU353-LSC-160209-40

description: Sample 136


title: singles-SU353-LSC-160209-41

description: Sample 137


title: singles-SU353-LSC-160209-37

description: Sample 133


title: singles-SU353-LSC-160209-59

description: Sample 155


title: singles-SU353-LSC-160209-35

description: Sample 131


title: singles-SU353-LSC-160209-47

description: Sample 143


title: singles-SU353-LSC-160209-36

description: Sample 132


title: singles-SU353-LSC-160209-34

description: Sample 130


title: singles-SU353-LSC-160209-32

description: Sample 128


title: singles-SU353-LSC-160209-31

description: Sample 127


title: singles-SU353-LSC-160209-33

description: Sample 129


title: singles-SU353-LSC-160209-28

description: Sample 124


title: singles-SU353-LSC-160209-30

description: Sample 126


title: singles-SU353-LSC-160209-27

description: Sample 123


title: singles-SU353-LSC-160209-25

description: Sample 121


title: singles-SU353-LSC-160209-26

description: Sample 122


title: singles-SU353-LSC-160209-21

description: Sample 117


title: singles-SU353-LSC-160209-29

description: Sample 125


title: singles-SU353-LSC-160209-24

description: Sample 120


title: singles-SU353-LSC-160209-23

description: Sample 119


title: singles-SU353-LSC-160209-46

description: Sample 142


title: singles-SU353-LSC-160209-17

description: Sample 113


title: singles-SU353-LSC-160209-16

description: Sample 112


title: singles-SU353-LSC-160209-18

description: Sample 114


title: singles-SU353-LSC-160209-15

description: Sample 111


title: singles-SU353-LSC-160209-19

description: Sample 115


title: singles-SU353-LSC-160209-20

description: Sample 116


title: singles-SU353-LSC-160209-11

description: Sample 107


title: singles-SU353-LSC-160209-13

description: Sample 109


title: singles-SU353-LSC-160209-14

description: Sample 110


title: singles-SU353-LSC-160209-6

description: Sample 102


title: singles-SU353-LSC-160209-10

description: Sample 106


title: singles-SU353-LSC-160209-5

description: Sample 101


title: singles-SU353-LSC-160209-7

description: Sample 103


title: singles-SU353-LSC-160209-9

description: Sample 105


title: singles-SU353-LSC-160209-12

description: Sample 108


title: singles-SU353-LSC-160209-8

description: Sample 104


title: singles-SU353-LSC-160209-4

description: Sample 100


title: singles-SU353-LSC-160209-3

description: Sample 99


title: singles-SU353-LSC-160209-1

description: Sample 97


title: singles-SU353-Blast-160205-96

description: Sample 96

source_name: Blast

value: acute myeloid leukemia, blast cell


title: singles-SU353-LSC-160209-2

description: Sample 98


title: singles-SU353-Blast-160205-95

description: Sample 95


title: singles-SU353-Blast-160205-94

description: Sample 94


title: singles-SU353-Blast-160205-93

description: Sample 93


title: singles-SU353-Blast-160205-91

description: Sample 91


title: singles-SU353-Blast-160205-92

description: Sample 92


title: singles-SU353-Blast-160205-88

description: Sample 88


title: singles-SU353-Blast-160205-87

description: Sample 87


title: singles-SU353-Blast-160205-90

description: Sample 90


title: singles-SU353-Blast-160205-89

description: Sample 89


title: singles-SU353-Blast-160205-86

description: Sample 86


title: singles-SU353-Blast-160205-84

description: Sample 84


title: singles-SU353-Blast-160205-85

description: Sample 85


title: singles-SU353-Blast-160205-82

description: Sample 82


title: singles-SU353-Blast-160205-81

description: Sample 81


title: singles-SU353-Blast-160205-79

description: Sample 79


title: singles-SU353-Blast-160205-83

description: Sample 83


title: singles-SU353-Blast-160205-80

description: Sample 80


title: singles-SU353-Blast-160205-76

description: Sample 76


title: singles-SU353-Blast-160205-73

description: Sample 73


title: singles-SU353-Blast-160205-77

description: Sample 77


title: singles-SU353-Blast-160205-71

description: Sample 71


title: singles-SU353-Blast-160205-75

description: Sample 75


title: singles-SU353-Blast-160205-74

description: Sample 74


title: singles-SU353-Blast-160205-70

description: Sample 70


title: singles-SU353-Blast-160205-69

description: Sample 69


title: singles-SU353-Blast-160205-68

description: Sample 68


title: singles-SU353-Blast-160205-65

description: Sample 65


title: singles-SU353-Blast-160205-66

description: Sample 66


title: singles-SU353-Blast-160205-67

description: Sample 67


title: singles-SU353-Blast-160205-63

description: Sample 63


title: singles-SU353-Blast-160205-64

description: Sample 64


title: singles-SU353-Blast-160205-58

description: Sample 58


title: singles-SU353-Blast-160205-59

description: Sample 59


title: singles-SU353-Blast-160205-61

description: Sample 61


title: singles-SU353-Blast-160205-60

description: Sample 60


title: singles-SU353-Blast-160205-78

description: Sample 78


title: singles-SU353-Blast-160205-57

description: Sample 57


title: singles-SU353-Blast-160205-54

description: Sample 54


title: singles-SU353-Blast-160205-50

description: Sample 50


title: singles-SU353-Blast-160205-49

description: Sample 49


title: singles-SU353-Blast-160205-47

description: Sample 47


title: singles-SU353-Blast-160205-48

description: Sample 48


title: singles-SU353-Blast-160205-62

description: Sample 62


title: singles-SU353-Blast-160205-72

description: Sample 72


title: singles-SU353-Blast-160205-56

description: Sample 56


title: ZF4-18d30dRNA3

city: Shanghai

first: Junfang

last: Zhang

address: Huchenghuan Road 999

department: College of fishery and life science

country: China

institute: Shanghai Ocean University

description: RNATotalInfo.txt

library_source: transcriptomic

data_processing:
Illumina Casava1.7 software was used for basecalling.
The fastx-toolkit program was used to filter off low quality sequences from raw sequencing data.
Sequences were aligned with Zebrafish genome(ZR9/danRer7) downloaded from iGenome using Bowtie2.
MeDIP-seq peaks were called with the Model-based Analysis of MeDIP-Seq (MACS) software with default parameters with alignment results.
The three peak sets generated by MACS were merged using Bedtools for peaks with at least 1bp overlap to get a reference peak set (REF) for following analysis.
Genome_build: ZR9/danRer7
Supplementary_files_format_and_content: .txt

molecule: total RNA

organism: Danio rerio

source_name: embryonic fibroblast cells

growth_protocol: The zebrafish embryonic fibroblast cell line ZF4 was purchased from the American Type Culture Collection (ATCC CRL 2050; Driever and Rangini, 1993).  The cells were grown at 28 °C, 5% CO2, in Dulbecco's modified Eagle's medium/F12 nutrient mix (DMEM/F12) supplemented with 10% FBS, 1% l-glutamine, 100 u/ml penicillin, 100 μg/ml streptomycin.  For cold treatment, cells were grown at 18 °C, 5% CO2, in the same medium for up to 30 days.  All cell culture medium components were purchased from Gibco BRL Life Technologies Ltd (USA).

extract_protocol: For MeDIP-seq, genomic DNAs were isolated and sonicated. End repair, adenylation, adapter ligation, methylated DNA enrichment and methylated DNA library construction were all performed with The NEXTflex™ Methyl -Seq 1 Kit (BIOO LIFE SCIENCE PRODUCTS, Cat No. 5118-01 ) according to the manufacturer’s instruction. For RNA-seq, total RNA was isolated using TRlzol reagent (Invitrogen life Technologies).

value: fibroblast cell line

tag: growth

value: cultured at 18°C for 30 days

tag: treatment

value: cold treatment for 30 days


title: singles-SU353-Blast-160205-44

description: Sample 44


title: ZF4-18d30dRNA2

description: RNATotalInfo.txt

treatment_protocol: For cold treatment, cells were grown at 18 °C, 5% CO2, in the same medium for up to 30 days.


title: ZF4-18d30dRNA1

description: RNATotalInfo.txt


title: singles-SU353-Blast-160205-46

description: Sample 46


title: singles-SU353-Blast-160205-43

description: Sample 43


title: singles-SU353-LSC-160209-22

description: Sample 118


title: singles-SU353-Blast-160205-41

description: Sample 41


title: singles-SU353-Blast-160205-42

description: Sample 42


title: ZF4-18d5dRNA3

description: RNATotalInfo.txt

value: cultured at 18°C for 5 days

value: cold treatment for 5 days


title: ZF4-18d5dRNA2

description: RNATotalInfo.txt


title: singles-SU353-Blast-160205-45

description: Sample 45


title: singles-SU353-Blast-160205-55

description: Sample 55


title: singles-SU353-Blast-160205-53

description: Sample 53


title: singles-SU353-Blast-160205-39

description: Sample 39


title: ZF4-28dRNA3

description: RNATotalInfo.txt

value: normal cultured(28°C)

value: control


title: singles-SU353-Blast-160205-38

description: Sample 38


title: singles-SU353-Blast-160205-52

description: Sample 52


title: ZF4-28dRNA2

description: RNATotalInfo.txt


title: singles-SU353-Blast-160205-51

description: Sample 51


title: singles-SU353-Blast-160205-40

description: Sample 40


title: ZF4-28dRNA1

description: RNATotalInfo.txt


title: Input DNA

description:
Input DNA for MeDIP-seq
MeDIPallInfo.txt


title: ZF4-18d30dMeDIP

description:
Three replica of MeDIP DNA were pooled together for sequencing
MeDIPallInfo.txt


title: singles-SU353-Blast-160205-35

description: Sample 35


title: singles-SU353-Blast-160205-34

description: Sample 34


title: ZF4-18d5dRNA1

description: RNATotalInfo.txt


title: singles-SU353-Blast-160205-33

description: Sample 33


title: singles-SU353-Blast-160205-36

description: Sample 36


title: singles-SU353-Blast-160205-37

description: Sample 37


title: ZF4-28dMeDIP


title: singles-SU353-Blast-160205-32

description: Sample 32


title: singles-SU353-Blast-160205-30

description: Sample 30


title: singles-SU353-Blast-160205-29

description: Sample 29


title: singles-SU353-Blast-160205-28

description: Sample 28


title: singles-SU353-Blast-160205-24

description: Sample 24


title: singles-SU353-Blast-160205-22

description: Sample 22


title: singles-SU353-Blast-160205-21

description: Sample 21


title: singles-SU353-Blast-160205-20

description: Sample 20


title: singles-SU353-Blast-160205-17

description: Sample 17


title: singles-SU353-Blast-160205-25

description: Sample 25


title: singles-SU353-Blast-160205-27

description: Sample 27


title: singles-SU353-Blast-160205-18

description: Sample 18


title: singles-SU353-Blast-160205-14

description: Sample 14


title: singles-SU353-Blast-160205-15

description: Sample 15


title: ZF4-18d5dMeDIP


title: singles-SU353-Blast-160205-12

description: Sample 12


title: singles-SU353-Blast-160205-13

description: Sample 13


title: singles-SU353-Blast-160205-10

description: Sample 10


title: singles-SU353-Blast-160205-11

description: Sample 11


title: singles-SU353-Blast-160205-8

description: Sample 8


title: singles-SU353-Blast-160205-9

description: Sample 9


title: singles-SU353-Blast-160205-7

description: Sample 7


title: singles-SU353-Blast-160205-6

description: Sample 6


title: singles-SU353-Blast-160205-4

description: Sample 4


title: singles-SU353-Blast-160205-16

description: Sample 16


title: singles-SU353-Blast-160205-31

description: Sample 31


title: singles-SU353-Blast-160205-3

description: Sample 3


title: singles-SU353-Blast-160205-26

description: Sample 26


title: singles-SU353-Blast-160205-2

description: Sample 2


title: singles-SU353-Blast-160205-23

description: Sample 23


title: singles-SU353-Blast-160205-19

description: Sample 19


title: singles-SU353-Blast-160205-1

description: Sample 1


title: Sus3_WSTF.bam

city: New York

first: Eric

last: Nestler

state: NY

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

data_processing:
CASAVA 1.8 /usr/local/bin/configureBuild.pl -id Aligned/Sample_Coc_4_WSTF_Lib -od BAM/Sample_Coc_4_WSTF_Lib -ref /genomes/Mus_musculus/UCSC/mm9/Sequence/Chromosomes/ --targets sort bam
IGV Tools 2.3.57 igvtools count Coc_4_WSTF.bam Coc_4_WSTF.tdf mm9
diffReps 1.54 diffReps.pl -tr ${T[@]} -co ${C[@]} --btr ${TI[@]} --bco ${CI[@]} --nproc 8 -gn ${GENOME_DIFFREPS} --re diffReps_results_WSTF_coc.txt -me nb -pval 1e-4 --nsd 2
pipeline on github: https://github.com/ny-shao/pipelines_for_ChIP-seq_analysis/tree/master/Differential_enrichment_detection/diffReps
Genome_build: mm9
Supplementary_files_format_and_content: bam

organism: Mus musculus

source_name: nucleus accumbens

growth_protocol: C57BL/6J male mice (7– 8 weeks old; Jackson Laboratory) were housed at constant temperature (23°C) on a 12 h light/dark cycle with ad libitum access to food and water.

extract_protocol:
For each ChIP-sequencing (ChIP-seq) replicate, bilateral 14 Ga NAc punches were pooled from five to 10 mice. Tissue was lightly fixed to cross-link DNA with associated proteins and the material was further sheared using a Bioruptor to obtain mostly 100–300 bp fragments and immunoprecipitated.
Immunoprecipitated DNA were prepared for ChIP-seq using an Illumina kit according to the manufacturer’s instructions. Each experimental condition was analyzed with independent biological triplicates. Amplification and size selection were confirmed with a BioAnalyzer. The resulting libraries were sequenced on an Illumina HiSeq 2500 with 100 bp read length.

treatment_protocol: Intraperitoneal cocaine administration: Cocaine hydrochloride (Sigma-Aldrich) was dissolved in sterile 0.9% saline (w/v). Daily saline or cocaine (20 mg/kg, i.p.) injections were administered in the animals’ home cages. Chronic social defeat stress (CSDS): performed exactly as described previously (Berton et al., 2006; Krishnan et al., 2007).

tag: strain

value: Susceptible

tag: antibody

value: WSTF, abcam ab51256


title: Sus1_WSTF.bam


title: Res1_WSTF.bam

value: Resilient


title: Res3_WSTF.bam


title: Sus2_WSTF.bam


title: Res2_WSTF.bam


title: Con2_WSTF.bam

value: Normal control


title: Sal_6_WSTF.bam

value: Saline


title: Con1_WSTF.bam


title: Sal_5_WSTF.bam


title: Sal_4_WSTF.bam


title: Con3_WSTF.bam


title: Coc_4_WSTF.bam

value: Cocaine


title: Coc_6_WSTF.bam


title: singles-SU353-Blast-160205-5

description: Sample 5


title: miRNA-seq Th0

city: Shanghai City

first: li

last: cao

address: 800 Xiangyin Road

department: Department of neurobiology

institute: second military medical university

data_processing:
The small RNA sequence reads were pre-processed using FASTXToolkit (fastx_toolkit-0.0.13.2; http://hannonlab.cshl.edu/fastx_toolkit/commandline.html), excluding low-quality reads (ambiguous N, quality < 10 nt, and length <18 nt) as well as 3′ adapter, 5′adapter and poly(A) sequences.
Further annotation analyses were performed using the commercial software CLC Genomic Workbench 5.5. Briefly, the resulting clean reads were aligned against various databases, including ncRNA, piRNA, and Rfam, allowing a maximum mismatch of 2 nt to remove noncoding RNA, such as rRNA, tRNA, snRNA, and snoRNA.The remaining sequences were analyzed by BLAST Mus musculus search against Sanger miRBase (version 21.0).
We standardize the miRNA-sequence data, procedures were shown as below: (1)Normalize the expression of miRNA in 2 libraries to get the expression of transcript per million (TPM). Normalization formula: Normalized expression = Actual miRNA count/Total count of clean reads×1000000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include Reads counts and TPM values for each Sample

source_name: Th0 cells

growth_protocol: Naive CD4+CD62L+ helper T cells were isolated using the Mice CD4+CD62L+ T Isolation KitⅡ(Miltenyi). Sorted mouse T cells were also cultured in RPMI 1640 containing 10% foetal bovine serum (Gibco).

extract_protocol:
Total RNA was extracted from Th0 or Th17 cells using a mirVanamiRNA Isolation Kit (Ambion, USA). RNA quality was evaluated with a BioAnalyzer 2100 system (Agilent Technologies, USA).
Small RNAs had linkers ligated to them and bar-coded cDNAs were prepared using a TruSeq Small RNA Sample Prep Kit (Illumina, USA) following the manufacturer’s instructions. Individual libraries were analyzed for the presence of linked cDNA at the appropriate size (140-150 bp) as determined by the BioAnalyzer. Subsequently, the amplified cDNA constructs were purified from agarose gel in preparation for sequencing analysis using the Illumina HiSeq 2500 platform (Illumina, CA, USA) according to the manufacturer’s instructions at the Shanghai Biotechnology Corporation.

treatment_protocol: Anti-CD28 (1 μg/ml, BD), anti-IL-4 (5 μg/ml, BD) and anti-IFN-γ (5 μg/ml, BD) were added to the control group, which was defined as the Th0 cells. For Th17 induction, anti-CD28 (1 μg/ml, BD), anti-IL-4 (5 μg/ml, BD), anti-IFN-γ (5 μg/ml, BD), anti-IL-2 (5 μg/ml, BD), anti-IL-12 (5 μg/ml, BD), TGF-β (2 ng/ml, R&D), IL-6 (40 ng/ml, R&D), IL-1β (10 ng/ml, R&D) and IL-23 (40 ng/ml, R&D) were added, and cells were cultured for 6-7 days before further analysis.

tag: tissue

value: spleen

tag: gender

value: female


title: siDROSHA_rep1

city: Philadelphia

first: Ian

middle: M

last: Silverman

state: Pennsylvania

address: 433 South University Ave, Room 104

department: Biology

institute: University of Pennsylvania

description: siDROSHA_v_siSCR_DESeq_gencode.all.symbol.txt

data_processing:
Reads were trimmed with Cutadapt, mapped with Tophat2, and gene expression was quantified using HTseq (Trapnell et al. 2009; Martin 2011; Anders et al. 2015). DEseq2 was used perform differential expression analysis (Love et al. 2014).
Genome_build: hg19
Supplementary_files_format_and_content: [*gencode_counts.txt] Gene Counts - number of reads mapped to ensemble gene IDs.
Supplementary_files_format_and_content: [*DESeq_gencode.all.symbol.txt] DESeq2 Output - differential expression analysis of RNA-seq data

molecule: polyA RNA

source_name: HEK293T Cell

growth_protocol: HEK293T cells were grown to 70-80% confluence in 15cm tissue cultures plates with DMEM media supplemented with 10% FBS and 1x pen/strep at 37°C and 5% CO2.

extract_protocol:
Total RNA was purified from the HEK293T cell cultures (miRNeasy; Qiagen, Valencia, CA). Poly(A)+ RNA was isolated using oligo dT beads (Life Technologies, Frederick, MD).
RNA was fragmented for 7 minutes using Fragmentation Reagent (Life Technologies, Waltham, MA).  mRNA-seq libraries were then generated using the Illumina mRNA-seq kit (illumina, San Diego, CA).

treatment_protocol: To knockdown endogenous levels of Dgcr8 or Drosha, we performed two sequenctial siRNA transfections 48 hours apart. To transfect these cells, we combined 45 pmol of siRNAs (22.5 pmol siRNA-1 and 22.5 pmol siRNA-2), 125 mL Opti-MEM (Life Technologies), and 6 mL Lipofectamine 2000 (Life Technologies) per reaction. Reactions were incubated at room temperature for 20 minutes. During this incubation, we seeded 6.0x105 HEK293T cells per replicate in two wells of a 6-well plate (3.0x105 cells/well) in 2 mL media. We then added the siRNA mixture to each well dropwise, and allowed cells to incubate at 37ºC in 5% CO2 for 48 hours. After 48 hours we repeated the transfection, harvesting the two wells per replicate (~1.2x105 cells) and dividing them into four wells in a 6-well plate. We treated each well with 45 pmol of siRNAs, and allowed them to incubate at 37ºC in 5% CO2 for another 48 hours. Cells were then pooled and washed with PBS prior to storage at -80ºC.

tag: cell line

tag: transfection

value: siDROSHA


title: siDROSHA_rep2


title: RNA-Seq cytokinin (BAP)

city: Seoul

first: TAEYOUNG

last: UM

address: Daehak-dong, Gwanak-gu

department: College of Agriculture Sciences

country: South Korea

institute: SEOUL NATIONAL UNIVERSITY

description: AnnoOnly_FPKM_from_all_samples_in_TAIR10.gene.txt

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to arabidopsis genomic DNA reference(Tair10) using bowtie aligner.
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using a protocol from TRAPNELL, Cole, et al., Nature protocols, 2012.
Genome_build: arabidopsis genomic DNA reference (Tair10)

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Plants were grown in 1/2 MS solid media with or without hormones for 7 days.

extract_protocol:
Total RNA was extracted using RNeasy plant mini-prep kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For hormone treatment, 10 uM MeJA, 50nM CK (BAP) or 10uM MeJA/50nM CK was supplied to 1/2 MS solid media.

tag: ecotype

tag: organ

value: Roots

tag: age

value: 7 day old

value: CK (50nM)


title: miRNA-seq Th17

source_name: Th17 cells


title: RNA-Seq MeJA-CK

value: 10uM MeJA/50nM CK


title: A3_small RNA-seq

city: Anyang

first: Du

last: Xiongming

state: Henan

address: 38# Huanghe Avenue

institute: Institute of cotton research of CAAS

data_processing:
After removal of low-quality reads and adapter sequences from the Solexa sequencing reads, unique sequences of 17–35 nt were used for further analysis.
First, the unique sequences were queried against ribosomal and transfer RNAs from tRNAdb (http://trna.bioinf.uni-leipzig.de/DataOutput/Search), SILVArRNA (http://www.arb-silva.de/), and NONCODE v3.0 (http://www.noncode.org/NONCODERv3/; plant database only, single-nt mismatches allowed) databases to obtain matching rRNA, tRNA, snRNA, and snoRNA sequences.
Any small RNA sequences having exact matches to these sequences were removed from the analysis. The remaining unique small RNA sequences were then BLASTn-searched against the conserved plant miRNAs in the miRBase database (miRBase 19.0; www.mirbase.org/) to identify conserved miRNAs. Only perfectly matched sequences were considered to be conserved miRNAs.
miRNA expression abundance in each library was calculated as RPM (reads per million) according to the formula RPM = mapped reads × 106 / total reads. Calculation of P-values for comparing the miRNA expression between salt-treated samples and the control sample was based on previously established methods(Audic S et al.,1997)

organism: Gossypium hirsutum

source_name: China

growth_protocol: The seeds of upland cotton, Ari971, wild type (G. hirsutum cv.) and its dwarf mutant (Ari1327) and tall-culm mutant (Ari3697) were surface sterilized in 30% H2O2 for three hours, washed with distilled water for three times, and then soaked in distilled water for one day at room temperature. Sterilized seeds were grown and maintained in pots in a greenhouse at a day/night temperature of 28/22°C with a 14-h photoperiod.

extract_protocol:
Total RNA was purified from stem apexes of three samples (Ari971, Ari1327 and Ari3697) using Trizol reagent (Invitrogen) according to the manufacturer’s protocols. Equal amounts of RNA from Ari971, Ari1327 and Ari3697 were pooled for transcriptome and small RNA libraries construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At the fifth true leaf stages, stem apexes of wild type and mutant seedlings were harvested and immediately frozen in liquid nitrogen and stored at -80°C until further use.

tag: genotype

value: tall-culm mutant Ari3697 (A3)

value: stem apexes

tag: developmental stage

value: At the fifth true leaf stages


title: A9_mRNA-seq

data_processing:
The raw image data was transformed by base-calling into sequence data and stored in fastq format. To control for the influence of error rate in the Solexa data results, quality pretreatment of the raw data was performed: the sliding window method was first used to remove low-quality fragments (quality threshold = 20, error rate = 1%, window size = 5 bp, and length threshold = 35 bp), followed by removal of partial (<35 bp) sequences containing “N” from the reads.
After filtering of low-quality and dirty raw reads, transcriptome de novo assembly was carried out using the paired-end assembly method as implemented in Trinity (http://trinityrnaseq.sourceforge.net/; trinityrnaseq_r2012-10-05) [123]. After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.

value: wild type Ari971 (A9)


title: A3_mRNA-seq


title: A9_small RNA-seq


title: A1_small RNA-seq

value: dwarf mutant Ari1327 (A1)


title: siDGCR8_rep2

description: siDGCR8_v_siSCR_DESeq_gencode.all.symbol.txt


title: RNA-Seq Control


title: MEF_SON_I

city: Mashhad

first: Moein

last: Farshchian

address: Vakilabad Highway

department: Department of Biology,Faculty of Science,

country: Iran

institute: Ferdowsi University of Mashhad

description: Cells infected with Stella, Oct4, Nanos2  Lerntivirus

data_processing:
Cluster detection and base calling were performed using RTAv1.13 and quality of reads assessed with CASAVA v1.8.1 (Illumina)
Mapping aginst themouse genome (GRCm38) using tophat version 2.0.11 with the options -r 180  -mate-std-dev 80 -b2-sensitive -no-novel-juncs -no-coverage-search -a 5 -p 10 -library-type fr-unstranded and using known exon junctions (Ensembl release 75).
Gene expression was determined with HTSeq version 0.5.3p3 with the annotation location obtained from Ensembl release 75. Differential expression was calculated using the R package DESeq2. Genes with 2 fold-change (+/-) and adjusted p-value (FDR) less than 0.05 were considered as differentially expressed. For endogenous retroviral (ERV) analysis the reads were mapped to the mouse genome (mm10) using STAR 2.4.0j with --outFilterMultimapNmax 1, keeping only uniquely mapping reads, allowing for up to 3 mismatches per read.  ERV expression was quantified using featureCounts (The subread package) with RepBase (v16.08) annotations.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include mRNA Count files from Htseq containing the raw reads counts per samples
Supplementary_files_format_and_content: tab-delimited text files include ERV counts of  Control_a (GFP replicate1) Control_b (GFP replicate2) Treated_a (SON replicate1) Treated_b (SON replicate2)

source_name: mouse embryonic fibroblast

growth_protocol: DMEM supplemented with10% FBS, 1X Pen/Strep, 1X non-essential amino acid, 1X L-glutamine (Basal MEF medium)

extract_protocol:
Total RNA extracted with TriPure (Roche) according to manufacture protocol
1 µg of RNA samples with the TruSeq mRNA kit v2 (Illumina). Size and concentration of sequencing libraries were determined with DNA-chip (Bioanalyser 2100, Agilent) and the concentrations adjusted to 8pM.

treatment_protocol: MEFs at passage 2 were transduced with lentiviruses of GFP and Stella-Oct4-Nanos2 (SON) and 72hrs post infection cell selected with 2 μg/ml puromycin for 4 days, after positive selection puromycin was removed and culturing continued for 21 days.

value: MEF passage 2

value: BALB/c

tag: infection

value: Stella, Oct4, Nanos2  Lentivirus


title: Coc_5_WSTF.bam

value: WSTF, abcam ab51256


title: S12_F1

city: Wenzhou

first: Wang

last: hui

state: Zhejiang

address: Wenzhou Medical University Chashan Campus  Chashan University Town, Wenzhou,  Zhejiang Province

description:
Sample 3
Zebrafish (AB strain) were purchased from a local supplier.

data_processing:
Briefly, the raw reads were subjected to the Illumina pipeline filter (Solexa 0.3), and then the dataset was further processed with an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 20.0 by BLAST search to identify known miRNAs and novel 3p- and 5p-derived 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 identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining 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 we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12); (2) number of base pairs in the stem region of the predicted hairpin (>=16); (3) cutoff of free energy (kCal/mol <=15); (4) length of hairpin (up and down stems + terminal loop >=50); (5) length of hairpin loop (<=20); (6) number of nucleotides in one bulge in mature region (<=8); (7) number of biased errors in one bulge in mature region(<=4); (8) number of biased bulges in mature region (<=2); (9) number of errors in mature region (<=7); (10) number of base pairs in the mature region of the predicted hairpin (>=12); and (11) percent of mature in stem (>=80).
For normalized abundance measurements, a modified global normalization is used to correct copy numbers among different samples. Basic assumptions and procedures involved in this method are:
1. There is a subset of sequences of a significant number that do not change significantly across all samples.
2. In sequencing measurements, experimental condition variations may lead to copy-number reading variations. However, in each sample run, the reading variations occur in the same proportion to all sequences. This assumption permits the use of a single correction factor for all sequences in a sample.
Genome_build: Zv9 (ftp://ftp.ensembl.org/pub/release-66/fasta/danio_rerio/dna/)
Supplementary_files_format_and_content: Table8.2_S12_F1vsS6_F1vsCON_F1.xlsx indicates the differential expression between two DKA-exposure treatments (6.25 and 12.5 mg/L treatments) and control.
Supplementary_files_format_and_content: Table8.6_S12_F1vsS6_F1.xlsx indicates the differential expression between 6.25 mg/L and 12.5 mg/L DKA-exposure treatments.
Supplementary_files_format_and_content: Table8.7_S6_F1vsCON_F1.xlsx indicates the differential expression between 6.25 mg/L DKA-exposure treatment and control.
Supplementary_files_format_and_content: Table8.8_S12_F1vsCON_F1.xlsx indicates the differential expression between 12.5 mg/L DKA-exposure treatment and control.

source_name: F1 zebrafish, 7-dpf, F0 12.5 mg/L DKA exposure

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analyzed by Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Approximately 1 μg of total RNA was used to prepare small RNA library according to protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, USA). Then, we performed the single-end sequencing (36 bp) on an Illumina HiSeq 2500 at the LC-BIO (Hangzhou, China) following the vendor’s recommended protocol.

treatment_protocol:
Adult wild type zebrafish (AB strain) were purchased from a local supplier. Embryos at 6 hpf were exposed to control and two DKA treatments (6.25 and 12.5 mg/L) composed of a mix of the six DKA species listed below with equal weight concentrations and equal volumes of each DKA species. After 90 days of DKA exposure, F1-zebrafish at 7-dpf for each group (control and two DKA-exposure treatments) were collected.
Certified DKA reference standards were sourced from Amresco (Solon, OH, USA) and used as received: ofluoxacin (CAS No. 82419-36-1, purity of 99%), ciprofloxacin (85721-33-1, 99%), enrofloxacin (93106-60-6, 99%), doxycycline (24390-14-5, 99%), chlortetracycline (64-72-2, 95%) and oxytetracycline (79-57-2, 99%).

tag: strain/background

value: AB

tag: genotype/variation

value: WT

tag: f0 treatment

value: 12.5 mg/L DKA exposure for 90 days

value: F1 whole body

tag: f1 developmental stage


title: MEF_GFP_II

description: Cells infected with control Lerntivirus

tag: cell type

value: control Lerntivirus


title: MEF_SON_II

tag: strain


title: siLUC_rep2

description:
siDGCR8_v_siSCR_DESeq_gencode.all.symbol.txt
siDROSHA_v_siSCR_DESeq_gencode.all.symbol.txt

value: siLUC


title: S6_F1

institute: Wenzhou Medical University Chashan Campus  Chashan University Town, Wenzhou,  Zhejiang Province

description:
Sample 2
Zebrafish (AB strain) were purchased from a local supplier.

source_name: F1 zebrafish, 7-dpf, F0 6.25 mg/L DKA exposure

value: 6.25 mg/L DKA exposure for 90 days


title: A1_mRNA-seq


title: siDGCR8_rep1


title: CON_F1

description:
Sample 1
Zebrafish (AB strain) were purchased from a local supplier.

source_name: F1 zebrafish, 7-dpf, F0 0 mg/L DKA exposure

value: 0 mg/L DKA exposure for 90 days


title: HEK293T miRNA-seq

description: AGO-associated (20-25 nt)

data_processing:
The first 20 nts of the 3’ adapter sequence CTGTAGGCACCATCAATAGA was used to trim adapter sequence from the raw reads using cutadapt (v1.4.2).  Identical reads were collapsed but clone information was retained to reduce computational time. Trimmed reads were sequentially mapped to miRBase (v20) and RefSeq annotated spliced transcript models (hg19 or mm10, downloaded on 06082015), with a two-stage alignment strategy with Bowtie2 and EMBOSS-WATER. First, Bowtie2 was used to map the 5’ regions of reads to either miRbase (v20) primary miRNA sequences with a 50nt extension on the 3’ end or RefSeq annotated spliced transcript models. For pre-miRNA-seq, the first 35 nts were used in the initial alignment step, whereas 18 nts were used for miRNA- and smRNA-seq.  Following bowtie2 alignment, reads were extended by local alignment with EMBOSS-WATER (with parameters: -gapopen 10.0 -gapextend 0.5). Multimapped reads were partially resolved by selecting the longest, highest scoring alignments. Missmatches detected at the 3’ ends of reads were considered as non-templated additions and analyzed separately. We filtered unmapped reads from pre-miRNA-seq on known rRNA, snoRNA, snRNA, tRNA, mitochondrial transcripts, and repeat-masked sequences before mapping to RefSeq.
Genome_build: hg19,mm10
Supplementary_files_format_and_content: Relative Mappings: Relative mappings and non-templated additions
Supplementary_files_format_and_content: Bed Plus: Bed coordinates and genic classification

extract_protocol:
Pre-miRNA-seq and miRNA-seq was performed as previously described [18]. Briefly, HEK293T cells were lysed in RSB 200 (20 mM Tris-HCl pH 7.4, 200 mM NaCl, 2.5 mM MgCl2, 0.5% NP-40) supplemented with 0.2 U/μl RNaseIn  (Promega) and 1tab/10ml of protease inhibitor cocktail (Roche) with 1-3 10s bursts of sonication. Cleared lysates were incubated with agarose protein G beads (Life Technologies) conjugated to 12μg of AGO 2A8 antibody or 3 μl of non-immune serum (NIMS) per 1 ml of lysate. Conguated beads were incubated with lysate for 1.5 h at 4°C on nutator and washed 4X with lysis buffer. 500 μl of trizol was added to washed beads and vortexed for 30 s. 150 μl of chloroform was added and the reaction and vortexed for 30 s followed by 20 m of centrifugation at 16,000 g.  The supernatant was transferred to a new tube with 300 μl of isopropanol and 15 μg of glycogen. Pellets were recovered and RNA was dephosphorylated with phosphatase and labeled with T4 polynucleotide kindase and λ-p32-ATP.
5’ end radiolabeled RNA from AGO-IPs were resolved on a 15% denaturing PAGE gel with 7M urea. Gel slices from 20-25 nt (miRNA-seq) and 50-80 nt (pre-miRNA-seq) were recovered and ligated to miRCat 3’ Linker (IDT) with T4 RNA Ligase 2 Truncated (NEB). Ligation products were resolved on a 15% PAGE gel with 7 M urea, size selected and repurified.  Reverse transcription was performed and product was purified on a 10% PAGE gel and repurified.  cDNA was circularized using CircLigase I and PCR amplified.  PCR amplicons were gel purified on a 3% Metaphor Gel, size selected and a second round of PCR was peformed.  Product was again size selected, repurified and submitted for sequenceing.

tag: fraction

value: AGO-associated (20-25 nt)


title: siLUC_rep1


title: MEF_GFP_I

description: Cells infected with control Lerntivirus


title: HEK293T pre-miRNA-seq

description: pre-miRNA-seq

value: AGO-associated (50-80 nt)


title: Trisomic, Fibroblast, Male, 21 Year old, replicate 1

status: Public on Jul 29 2016

city: Aurora

first: Ahwan

last: Pandey

state: CO

department: Pharmacology

institute: University of Colorado Anschutz Medical Center

description:
shRNA cassette
M21YR_T21_14D_1

data_processing:
Library strategy: shRNA-seq
Basecalls performed using bcl2fastq_v1.8.4 with the following options (--mismatches 1 fastq-cluster-count 0 )
Samples were demultiplex using fastx_barcode_splitter in fastx_0.0.13.2 allowing 2 mismatches
FASTQC v0.11.2 was used to determine sequence quality
Seqeunces were trimmed using fastx_trimmer in fastx_0.0.13.2 with the following options (-Q33 -f 22 -l 42)
Trimmed sequences were mapped with Bowtie2 v2.2.3 using the following options (--phred33 --end-to-end --very-sensitive-local)
Genome_build: Human TRC 1/1.5 + Kinase
Supplementary_files_format_and_content: Tab delimited text files containing raw shRNA counts for each sample

source_name: Fibroblast

growth_protocol: Cells were passaged in DMEM with 10% FBS

extract_protocol:
DNeasy Kit from Qiagen
Custom; shRNA amplicon

treatment_protocol: Cells were transduced with pLKO.1 kinome library and propagated for 2 weeks

tag: condition

value: Trisomic

value: Male

value: 21 Year old

tag: batch


title: Trisomic, Fibroblast, Female, 19 Year old, replicate 2

description:
shRNA cassette
F19YR_T21_14D_2

tag: gender

value: Female

value: 19 Year old


title: Trisomic, Fibroblast, Female, 19 Year old, replicate 1

description:
shRNA cassette
F19YR_T21_14D_1


title: Trisomic, Fibroblast, Female, 14 Year old, replicate 3

description:
shRNA cassette
F14YR_T21_14D_3

value: 14 Year old


title: RNA-Seq Methyl jasmonate (MeJA)

value: Roots

value: 7 day old

tag: treatment

value: MeJA (10uM)


title: Trisomic, Fibroblast, Male, 1 Year old, replicate 2

description:
shRNA cassette
M1YR_T21_14D_2

value: 1 Year old


title: Trisomic, Fibroblast, Male, 1 Year old, replicate 3

description:
shRNA cassette
M1YR_T21_14D_3


title: Trisomic, Fibroblast, Male, 2 Year old, replicate 2

description:
shRNA cassette
M2YR_T21_14D_2

value: 2 Year old


title: Trisomic, Fibroblast, Male, 2 Year old, replicate 3

description:
shRNA cassette
M2YR_T21_14D_3


title: Trisomic, Fibroblast, Male, 1 Year old, replicate 1

description:
shRNA cassette
M1YR_T21_14D_1


title: Trisomic, Fibroblast, Female, 3 Day old, replicate 3

description:
shRNA cassette
F3DA_T21_14D_3

value: 3 Day old


title: Trisomic, Fibroblast, Female, 3 Day old, replicate 2

description:
shRNA cassette
F3DA_T21_14D_2


title: Trisomic, Fibroblast, Male, 21 Year old, replicate 2

description:
shRNA cassette
M21YR_T21_14D_2


title: Disomic, Fibroblast, Male, 20 Year old, replicate 1

description:
shRNA cassette
M20YR_D21_14D_1

value: Disomic

value: 20 Year old


title: Disomic, Fibroblast, Male, 20 Year old, replicate 2

description:
shRNA cassette
M20YR_D21_14D_2


title: Disomic, Fibroblast, Male, 19 Year old, replicate 1

description:
shRNA cassette
M19YR_D21_14D_1


title: Disomic, Fibroblast, Female, 11 Year old, replicate 2

description:
shRNA cassette
F11YR_D21_14D_2

value: 11 Year old


title: Disomic, Fibroblast, Female, 11 Year old, replicate 1

description:
shRNA cassette
F11YR_D21_14D_1


title: Disomic, Fibroblast, Male, 19 Year old, replicate 2

description:
shRNA cassette
M19YR_D21_14D_2


title: Disomic, Fibroblast, Male, 20 Year old, replicate 3

description:
shRNA cassette
M20YR_D21_14D_3


title: Disomic, Fibroblast, Female, 11 Year old, replicate 3

description:
shRNA cassette
F11YR_D21_14D_3


title: Disomic, Fibroblast, Female, 2 Year old, replicate 3

description:
shRNA cassette
F2YR_D21_14D_3


title: Disomic, Fibroblast, Female, 2 Year old, replicate 1

description:
shRNA cassette
F2YR_D21_14D_1


title: Disomic, Fibroblast, Female, 2 Year old, replicate 2

description:
shRNA cassette
F2YR_D21_14D_2


title: Trisomic, Fibroblast, Female, 19 Year old, replicate 3

description:
shRNA cassette
F19YR_T21_14D_3


title: Disomic, Fibroblast, Male, 19 Year old, replicate 3

description:
shRNA cassette
M19YR_D21_14D_3


title: Trisomic, Fibroblast, Female, 14 Year old, replicate 2

description:
shRNA cassette
F14YR_T21_14D_2


title: Disomic, Fibroblast, Female, 2 Day old, replicate 3

description:
shRNA cassette
F2DA_D21_14D_3

value: 2 Day old


title: Disomic, Fibroblast, Male, 1 Year old, replicate 1

description:
shRNA cassette
M1YR_D21_14D_1


title: Disomic, Fibroblast, Female, 2 Day old, replicate 1

description:
shRNA cassette
F2DA_D21_14D_1


title: Disomic, Fibroblast, Female, 2 Day old, replicate 2

description:
shRNA cassette
F2DA_D21_14D_2


title: Trisomic, Fibroblast, Male, 2 Year old, replicate 1

description:
shRNA cassette
M2YR_T21_14D_1


title: Trisomic, Fibroblast, Female, 14 Year old, replicate 1

description:
shRNA cassette
F14YR_T21_14D_1


title: Case 2

city: Bari

first: Alberto

last: L'Abbate

address: via Orabona 4

department: Department of Biology

country: Italy

institute: University of Bari

data_processing:
In order to identify fusion transcripts, the reads were analyzed by means ChimeraScan. It is implemented with Bowtie aligner. We run Chimerascan with the default options
Genome_build: hg19
Supplementary_files_format_and_content: BEDPE custom format defined for BEDTools. They contain informations about chimeric genes identified by Chimerascan (5' and 3' partner, start/end chromosomes position, split reads, etc)

source_name: bone marrow

extract_protocol:
Total RNA was extracted from each AML sample using TRIZOL reagent (Invitrogen)
Libraries were prepared according to Illumina TruSeq Stranded Total RNA kit

value: bone marrow

tag: diagnosis

value: AML M2

tag: tumor stage

value: progression


title: Case 1

value: CMML

value: onset


title: NP_16_25

city: Easter Bush

last: Ioannidis

state: Midlothian

address: Easter Bush Veterinary Campus

department: Developmental Biology

country: United Kingdom

institute: The Roslin Institute

description: Oestrous cycle, Day 16

data_processing:
sRNAbench, v05/14
sRNAbench adapter trimming, v05/14, adapter = TGGAATTCTCGGGTGCCAAGG
sRNA bench mapping, v05/14, bowtie v0.12.9, 1 mismatch allowed, seed length 19, -n, -m 40 (bowtie parameter)
sRNAbench, v05/14, standard data normalisation (RPMM)
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: A single processed data file is provided, "processed_data.xlsx". The file consists of two spreadsheets, "Raw reads" which includes the raw reads obtained after analysis using sRNAbench , and "Normalised reads" which includes the normalised data (reads per million mapped, RPMM).

organism: Bos taurus

source_name: Plasma_Oestrous cycle, Day 16

extract_protocol:
RNA was extracted from 1.05 mL of plasma using TRIzol LS (Life Technologies, USA), following the manufacturer’s protocol. During the RNA extraction protocol, glycogen (180 μg; Sigma-Aldrich, USA) was added to each sample to facilitate the precipitation of RNA, and an exogenous miRNA control, syn-cel-miR-39-3p (0.25 fmol; Qiagen, NL), was spiked into each sample. RNA was re-suspended in 30 μL of RNase-free water and used immediately or frozen at -80 °C.
Small-RNA libraries were prepared using the Illumina TruSeq small-RNA sample preparation kit (Illumina, USA) following the manufacturer’s protocol. Libraries were submitted to 36-base single-end sequencing using the Illumina HiSeq 2000 platform.

tag: subject

tag: day

tag: tissue

value: plasma

tag: Sex

value: female


title: NP_16_22

description: Oestrous cycle, Day 16


title: NP_16_35

description: Oestrous cycle, Day 16


title: mut 1

city: San Francisco

first: Divya

last: Punwani

state: CA

address: 555 Mission bay blvd south

department: Pediatrics

institute: University of California San Francisco

data_processing:
FASTQC  (check quality) 0.63
FAST groomer 1.04
BWA for illumina (MAP the reads to the genome) 1.2.3
MACS2 callpeak  (Peak identification: Enrichement fold 2.5, FDR:0.05) 2.1.0.20151222.0
IDR (To identified peaks between replicates, FDR:0.05) 2012
Genome_build: hg38, Dec 2013

source_name: CD34+ hematopoietic stem cells

growth_protocol: Grown in X-vivo 15 medium, supplemented with human SCF, Flt3L, TPO and IL-3 for 14 days

extract_protocol:
Diagenode ChIP-seq kit
University of California, Davis Genomics Core

treatment_protocol: Transduced with lentivirus

tag: source

value: peripheral blood mobilized stem cells

tag: passages

value: primary stem cells cultured for 14 days

tag: antibody

value: anti-FLAG M2 (Sigma-Aldrich, Catalog no. F3165)

tag: transduction

value: lentivirus expressing FLAG-tagged mutant BCL11B and GFP


title: NP_16_18

description: Oestrous cycle, Day 16


title: GFP 2

value: GFP lentivirus


title: WT 1

value: lentivirus expressing FLAG-tagged WT BCL11B and GFP


title: WT 2


title: mut 2


title: Disomic, Fibroblast, Male, 1 Year old, replicate 2

description:
shRNA cassette
M1YR_D21_14D_2

value: Disomic

value: Male

tag: age

value: 1 Year old


title: NP_08_35

description: Oestrous cycle, Day 8

source_name: Plasma_Oestrous cycle, Day 8


title: NP_08_25

description: Oestrous cycle, Day 8


title: NP_08_34

description: Oestrous cycle, Day 8


title: NP_08_22

description: Oestrous cycle, Day 8


title: GFP 1


title: NP_08_20

description: Oestrous cycle, Day 8


title: NP_08_21

description: Oestrous cycle, Day 8


title: NP_08_16

description: Oestrous cycle, Day 8


title: NP_00_35

description: Oestrous cycle, Day 0

source_name: Plasma_Oestrous cycle, Day 0


title: NP_08_18

description: Oestrous cycle, Day 8


title: NP_00_22

description: Oestrous cycle, Day 0


title: NP_16_34

description: Oestrous cycle, Day 16


title: NP_00_25

description: Oestrous cycle, Day 0


title: NP_00_21

description: Oestrous cycle, Day 0


title: NP_16_21

description: Oestrous cycle, Day 16


title: NP_00_16

description: Oestrous cycle, Day 0


title: NP_16_20

description: Oestrous cycle, Day 16


title: NP_16_16

description: Oestrous cycle, Day 16


title: NP_00_20

description: Oestrous cycle, Day 0


title: NP_00_18

description: Oestrous cycle, Day 0


title: PTTH 3 hr

city: Edmonton

first: Kirst

last: King-Jones

state: Alberta

address: 11455 saskatchewan driver

department: Biological Sciences

country: Canada

institute: University of Alberta

data_processing:
Illumina CASAVA (version 1.8.0) software was used for basecalling.
The low quality base pairs were truncated by removing the first 5 base pairs and last 35 base pairs of the sequences for a total of 60 base pairs.
The sequence libraries were mapped to the Silkworm genome, build 2.0 (downloaded from http://www.silkdb.org) using TopHat.
Bam files were indexed using the samtools suite so that the mappings could be visualized by using IGV tools.
Genome_build: Silkworm genome, build 2.0 (downloaded from http://www.silkdb.org)

organism: Bombyx mori

source_name: prothoracic gland

growth_protocol: Bombyx mori racial hybrid larvae (Mulberry Farms, Fallbrook, CA) were grown at 25ºC on an artificial diet and staged after the final (fourth) larval ecdysis.

extract_protocol:
Total RNA was extracted by using the TRIzol Reagent (Invitrogen) and RNeasy Mini Kit (Qiagen).  The frozen PGs were homogenized in 500 microliter of TRIzol Reagent and incubated at room temperature for five minutes before adding 350 microliter of buffer RLT (QIAGEN) containing 1% beta-mercaptoethanol.  Samples were vortexed and 100 microliter of chlorophorm was added before spinning at 12,000 rpm for 15 min at 4ºC.  The aqueous phase was removed and RNA was isolated according to the instruction of RNeasy Mini Kit.
RNA sequencing libraries were prepared according to specifications by the University of Minnesota’s Biomedical Genomics Center (BMGC) using the Paired-end mRNA-Seq 8-Sample Prep Kit (Illumina).

treatment_protocol: The PGs were dissected rapidly and pre-incubated in 100 microliter of Grace’s Insect Medium (Gibco) for 30 minutes.  After pre-incubation, each gland of the pair was transferred into 100 microliter of the same medium with or without 10 nM PTTH (gift from Hiroshi Kataoka, University of Tokyo, Japan). The PGs were incubated at room temperature for either one or three hours. After incubation, PGs were immediately placed at -80ºC until RNA extraction.

tag: strain

value: Racial hybrid from Mulberry Farms, Fallbrook, CA

tag: developmental stage

value: Day 4 fifth instar larvae

value: 3 hr incubation with 10 nM PTTH


title: PTTH 1 hr

value: 1 hr incubation with 10 nM PTTH


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 2)

city: Boston

first: Alex

last: Ng

address: 77 Avenue Louis Pasteur Rm 233

department: Genetics

institute: Harvard Medical School

data_processing:
Basecalls performed by NextSeq 500 RTA 2.4.11
mRNA reads were aligned to mm10 using STAR 2.4.0j
Quantification and differential expression were computed using Cufflinks/Cuffdiff/Cuffnorm 2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: Excel file documenting FPKMs and statistical tests

source_name: Lymph nodes

extract_protocol:
Total RNA was isolated using TRIzol and polyA mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation (E7490L)
mRNA were prepared for sequencing using NEBNext Ultra Directional RNA Library Prep Kit (E7420L)

value: Lymph nodes


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 1)


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 3)


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 3)


title: Control 1 hr

value: 1 hr incubation


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 1)


title: Control 3 hr

value: 3 hr incubation


title: Lymph Nodes TurboRFP (control, biological replicate 3)


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 3)

source_name: Muscle

value: Muscle


title: Lymph Nodes TurboRFP (control, biological replicate 1)


title: Lymph Nodes TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 2)


title: Lymph Nodes TurboRFP (control, biological replicate 2)


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 1)


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 3)


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 1)


title: NP_00_34

description: Oestrous cycle, Day 0

value: plasma

value: female


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn, Fst, Pd-l1, Cd47 (biological replicate 2)


title: mESC_unstranded_RNASeq

first: Jin-Wu

last: Nam

address: Seongdong-Gu Hangdang-dong

department: Department of Life Science

institute: Hanyang University

data_processing:
Illumina Casava1.8 sotfware used for basecalling.
To check RNA-seq data quality, RNA-seq reads were mapped to the mm9 genome assembly using Bowtie (version 1.0.0) with default parameters.
We calculate mismatch rates across the mapped read positions.
If the raw read end(s) had a mismatch rate higher than 10%, they were trimmed off using Seqtk (version 1.0-r31).
The tirmmed reads with Phred base qulaity ≦ 20 were filtered using Sickle (version 1.200).
The remaining reads were mapped to the mm9 genome assembly using Tophat (veriosn 2.0.6) with paramters "-i 52 -I 240764 --min-segment-intron 52 --max-segment-intron 240764 -g 5".
Base transcriptome assemblies were performed using Cufflinks (version 2.1.1) with defeault parameters for mapped reads.
Genome_build: mm9
Supplementary_files_format_and_content: gtf files were generated using Cufflinks (version 2.1.1).

source_name: Embryonic stem cells

growth_protocol: mES cells were cultured in regular media containing 15% FBS, 1% PEN/STREP, 1% glutamine, 1% NEAA, and LIF. For mES cell maintenance, dishes were coated with 0.2% gelatin and irradiated CF1 mouse embryonic fibroblasts were plated as a confluent layer of feeder cells. mES cells were seeded at a density of 50,000 cells/6-well plate and were split every 2-3 days.

extract_protocol:
RNA from mES cells was extracted using an RNeasy kit (Qiagen, USA). Polyadenylated RNA was isolated using Oligo dT beads (Invitrogen, USA).
Illumina Truseq stranded and unstranded mRNA library prep kits (Illuminca, USA) were used for deep sequencing library preparation from 6ug of total RNA according to the manufacturer's protocol.

tag: cell type

value: Embryonic stem cells

tag: genotype

value: wild type

tag: library type

value: Illumina Truseq unstranded library


title: Striatal MSN nuclei, Pol II

first: Josefa

last: Sullivan

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Sequences were aligned with Bowtie v0.12.7 allowing for less than 2 mismatches in 36 bp.
Uniquely mapped reads were used for peak finding using MACS v1.4 and CCAT v3.0
Genome_build: mm9

source_name: Striatal MSN nuclei

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 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 15 cycles. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq following the manufacturer's protocols.

value: Medium spiny neuron

value: 8 weeks

value: Pol II (Abcam AB5408)


title: Muscle TurboRFP, AAV9-Cas9-VPR-gRNAs Mstn and Fst (biological replicate 2)


title: mESC_stranded_RNASeq

value: Illumina Truseq stranded library


title: Striatal MSN nuclei, input


title: Muscle TurboRFP (control, biological replicate 3)


title: Striatal MSN nuclei, H3k27ac

value: H3k27ac (Abcam AB4729)


title: Muscle TurboRFP (control, biological replicate 2)


title: Striatal MSN nuclei, H3k27me3

value: H3k27me3 (Millipore 07-449)


title: Muscle TurboRFP (control, biological replicate 1)


title: DP16 replicate 2 [P2_rep2]

description:
polyA RNA from LSK cells
P2_rep2

data_processing:
FASTQC v0.11.2 was used to determine sequence quality
fastqc-mcf was used to trim low quality bases, adapters and N content from 3’ end (<q10). Removed reads that were shorter than 30bp after trimming
Reads were mapped using Tophat2 (v2.0.13) with the following options (--b2-sensitive --keep-fasta-order --no-coverage-search --max-multihits 10 --library-type fr-firststrand)
Reads with MAPQ > 10 were kept using Samtools (v0.1.19)
Reads were coordinate sorted and duplicates were marked using Picard (v1.129)
Raw count data was generated using HTSeq (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon –idattr=gene --mode=intersection-nonempty)
Genome_build: mm10
Supplementary_files_format_and_content: Tab delimited text files containing raw gene counts for each sample

extract_protocol:
RNA was prepared using the RNeasy Kit from Qiagen
Libraries were prepared using the Truseq Stranded Kit from Illumina

tag: condition

tag: batch

value: A


title: DP16 replicate 2 [P1_rep2]

description:
polyA RNA from LSK cells
P1_rep2


title: DP16 replicate 1 [P2_rep1]

description:
polyA RNA from LSK cells
P2_rep1


title: DP16 replicate 1 [P3_rep1]

description:
polyA RNA from LSK cells
P3_rep1


title: DP16 replicate 1 [P1_rep1]

description:
polyA RNA from LSK cells
P1_rep1


title: Normal, replicate 2 [N3_rep2]

description:
polyA RNA from LSK cells
N3_rep2

value: Normal


title: Normal, replicate 1 [N3_rep1]

description:
polyA RNA from LSK cells
N3_rep1


title: Normal, replicate 1 [N2_rep1]

description:
polyA RNA from LSK cells
N2_rep1


title: Nfib_Mycl_3_Tumor_RNaseq

city: Amsterdam

first: Anton

last: Berns

state: Amsterdam

address: Plesmanlann 121

department: Division of Molecular Genetics

country: Netherlands

institute: NKI

data_processing:
RNAseq: Tophat single end - Steps performed: link, align, count, bamqc, QCstrandness, eset. Readlength: 65bp. Tophat version: 2.1, Bowtie version: 1.0.0, Samtools version: 0.1.19, Reference: Mus_musculus.GRCm38.dna.primary_assembly
RNAseq : DEseq2
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count values for each Sample

source_name: primary lung tumor-derived cells_Nfib overexpression

growth_protocol: mouse Nfib was overexpressed in mouse small cell lung cancer cell lines for RNAseq analysis

extract_protocol:
Genomic DNA was extracted from fresh frozen mouse small cell lung tumor samples
RNA libraries were prepared for sequencing using standard Illumina TruSeq RNA Sample Prep protocol

value: lung

value: primary mouse SCLC

value: invCAG-Mycl-Luc; Rb1-/- ; Trp53 -/-

tag: background strain

value: FVB/n; 129/Ola


title: Normal, replicate 2 [N1_rep2]

description:
polyA RNA from LSK cells
N1_rep2


title: Normal, replicate 2 [N2_rep2]

description:
polyA RNA from LSK cells
N2_rep2


title: Nfib_Mycl_4_Tumor_RNaseq


title: Nfib_Mycl_3_Control_RNaseq

source_name: primary lung tumor-derived cells_empty vector


title: Nfib_Mycl_2_Tumor_RNaseq


title: Nfib_Mycl_2_Control_RNaseq


title: JS172_3if3e

city: La Jolla

first: Dieter

last: Wolf

address: 10901 North Torrey Pines Road

department: Tumor Initiation & Maintenance Program

institute: Sanford-Burnham-Prebys Medical Discovery Institute

data_processing:
alignment to the tRNA, rRNA; Bowtie 1.1.0
alignment the unaligned reads to S. pombe genome; TopHat 1.4.1
Duplicated remove; samtools
generation of normalized abundance measurements; Partek Genomics Suite 6.0
Supplementary_files_format_and_content: txt file, summarization results, including the raw counts and normalized abundance measurements

organism: Schizosaccharomyces pombe

source_name: Mutant Replicate 2

growth_protocol: Cells were grown to an OD of 0.8 - 1.0 in standard yeast extract medium containing adenine and uracil (YES media).

extract_protocol:
Total RNA was extracted by phase separation using RNA-BeeTM (Amsbio) and chloroform, and precipitated in isopropanol. RNA was further purified using the RNeasy Mini Kit (Qiagen), performing an on-column DNase digestion. The quality of total RNA was assessed by the Agilent Bioanalyzer (Agilent Technologies).
Total RNA samples were treated with RiboMinus Eukaryotic kit (Invitrogen) to deplete rRNA. The rRNA-depleted sample was subjected to enzymatic fragmentation using RNase III from the SOLiD Total RNA-Seq kit. The purified fragmented RNA was then ligated with SOLiD adaptors on both ends and served as templates for cDNA synthesis. The cDNA libraries were constructed and purified twice using AMPure beads to ensure complete capture and size-selection of desired cDNA. The cDNA was PCR amplified and sequenced on the SOLiD 4 platform.

tag: strain genotype

value: h- int6::kanMX6 ura4-D18 leu1-32


title: JS172_WT

source_name: Wildtype Replicate 2


title: Nfib_Mycl_1_Tumor_RNaseq


title: Nfib_Mycl_1_Control_RNaseq


title: MCF10A-attached

city: Worcester

first: Victoria

middle: E

last: Pedanou

address: 364 Plantation St Room 670A

institute: Umass Medical School

data_processing: Sequence reads were obtained and mapped to the human (hg18) genomes using the Illumina Genome Analyzer Pipeline. All reads uniquely mapped with two or fewer mismatches were retained for subsequent analysis

organism: synthetic construct

growth_protocol: attached cells are grown under normal cell culture conditions, detached cells are grown with the same media supplemented with 1% methyl cellulose and plated on poly-HEMA coated plates

extract_protocol:
Genomic DNA preparation
PCR
identify shRNA region from retroviruses integrated in genomic DNA with primers that target the shRNA region

treatment_protocol: detached (on poly-HEMA coated plates) for 10 days

value: MCF10A, attached


title: JS167_eif3e

source_name: Mutant Replicate 1


title: MCF10A-detached

value: MCF10A, suspension


title: Striatal MSN nuclei, H3k4me3

value: H3k4me3 (Abcam AB8580)


title: DP16 replicate 2 [P3_rep2]

description:
polyA RNA from LSK cells
P3_rep2


title: kidney mac 3

status: Public on Jul 28 2016

first: Jeffrey

last: Zhao

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

description:
s_PBS_003__s_PBS
sorted kidney macrophages from mouse #3

data_processing:
The output data (FASTQ files) were mapped to the target genome using the rnaStar aligner that maps reads genomically and resolves reads across splice junctions.
HTSeq v0.5.4 is used for feature counting.
DESeq (v1.18.0) is used for the normalization of count table. R3.1.2 is used as the processing platform.
Genome_build: mm9
Supplementary_files_format_and_content: txt files, normalized count tables, 2 technical replicates were merged per biological sample

source_name: kidney

growth_protocol: C57BL6/J were injected i.v. with PBS. Kidneys were isolated 1 hour after injection.

extract_protocol:
Kidneys were digested in Dnase, collagenaseD, dispase for 30min at room temperature
SMART-seq V4 (Clonetech) ultra low input RNA kit was used for library preparation. 10 ng of amplified cDNA was used to prepare Illumina hiseq libraries with the Kapa DNA library preparation chemistry (Kapa Biosystems) using 8 cycles of PCR.

tag: agent

value: PBS


title: kidney mac 2

description:
s_PBS_002__s_PBS
sorted kidney macrophages from mouse #2


title: kidney mac 1

description:
s_PBS_001__s_PBS
sorted kidney macrophages from mouse #1


title: Normal, replicate 1 [N1_rep1]

description:
polyA RNA from LSK cells
N1_rep1


title: P12_Cd73P_WT

city: Minato-ku, Tokyo

first: Sumiko

last: Watanabe

address: 4-6-1 Shirokane-dai

department: Institute of Medical Science

country: Japan

institute: University of Tokyo

data_processing:
bcl2fastq-1.8.4 used for basecalling with default parameters
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using TopHat (v2.0.8b) with the option (--coverage-search --max-multihits 50)
fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using CuffLinks (v2.1.1) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Retina

growth_protocol: SPF with normal feeding

extract_protocol:
total RNA was extracted using RNeasy Plus Micro Kit (Qiagen), and RNA quality was confirmed using a 2100 Bioanalyzer (Agilent Technologies)
The first-strand cDNA was synthesized using random primers and SuperScript II (Invitrogen), and the second-strand cDNA was synthesized using RNaseH and DNA pol I (Illumina). Illumina GA sequencing adaptors were ligated to the cDNA ends. Double-stranded cDNA was size-fractionated by 6% PAGE, and cDNAs of 200 bp were recovered. cDNAs were amplified by 15 PCR cycles using Phusion DNA Polymerase (Finnzymes). Thirty-six-base-pair single-end-read RNA Seq tags were generated using an Illumina GA sequencer according to the standard protocol.

value: wildtype

tag: tissue

value: retina

value: postnatal day 12

tag: cd73 status

value: positive


title: P12_Cd73N_WT

value: negative


title: P12_Cd73P_Ezh2-cKO


title: P2_Cd73N

data_processing:
CASAVA-1.8.2 (for samples by Illumina HiSeq 2000) and bcl2fastq-1.8.4 (for samples by Illumina HiSeq 2500) used for basecalling with default parameters
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using TopHat (v2.0.8b) with the option (--coverage-search --max-multihits 50)
fragments per kilobase of exon per million mapped fragments (FPKM) was calculated from the aligned reads by using CuffLinks (v2.1.1) with the default option
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

value: postnatal day 2


title: P2_Cd73P


title: P8_Cd73N_input

data_processing:
CASAVA-1.8.2 (for samples by Illumina HiSeq 2000) and bcl2fastq-1.8.4 (for samples by Illumina HiSeq 2500) used for basecalling with default parameters
The sequence reads were aligned to the mouse reference genome assembly (NCBI37/mm9) using Bwa (v0.6.2) with default parameters.
The output bam files were converted to bedgraph files using Bedtools (v2.16.2)
Supplementary_files_format_and_content: bedgraph files were generated using Bedtools (v2.16.2). Scores represent the depth at each genome position.

extract_protocol:
Sonicated cell extract was incubated with antibody and DynaBeads. DNA was extracted and purified by QIAquick PCR purification kit.
ChIP-seq libraries were suquenced using HiSeqplatfom.

value: ICR

value: postnatal day 8


title: Nfib_Mycl_4_Control_RNaseq

value: lung


title: P5_Cd73P_H3K4me3

value: postnatal day 5


title: P8_Cd73N_H3K27me3


title: P5_Cd73P_H3K27me3


title: P2_Cd73N_H3K4me3


title: P5_Cd73N_H3K4me3


title: P5_Cd73N_H3K27me3


title: P8_Cd73N_H3K4me3


title: BT474 Persister rep 3

first: Matthew

last: Hangauer

institute: UC San Francisco

data_processing:
Casava 1.8 was utilized to make basecalls and generate FASTQ files.
FASTQ files were aligned to hg18 using TopHat v2.0.6, allowing only uniquely aligned reads (-g 1 option).
Aligned reads were analyzed using CuffDiff v2.0.2, with quartile normalization and -compatible-hits-norm options. Read were aligned to a GTF file containing coordinates for all human RefSeq NM and NR genes. The GTF file was downloaded from the UCSC Table Browser and converted into a CuffDiff readable format using Cuffcompare as described in the Cufflinks manual.
Genome_build: hg18
Supplementary_files_format_and_content: Tab-delimited text file containing CuffDiff output. Includes Gene ID, RefSeq ID, Parental FPKM, Persister FPKM, q_value and foldchange.

source_name: BT474 cells

growth_protocol: BT474 cells were maintained in RPMI medium supplemented with penicillin, streptomycin and 10% FBS. Cells were grown in 15 cm tissue culture plates (Corning).

extract_protocol:
Total RNA was isolated using Trizol (Life Technologies) from 2 million cells per replicate. RNA integrity was assessed using an Agilent RNA 6000 Nano kit which was assayed on an Agilent 2100 Bioanalyzer. All RNA samples had a measured RNA Integrity Number (RIN) > 9.3.
Library construction was performed by the UC Davis Genome Center using the non-strand specific Illumina TruSeq RNA Library Preparation kit following the manufacturer's protocol. Sequencing was performed on an Illumina HiSeq 2000 instrument with multiplexed samples spread across 5 lanes for each sample.

treatment_protocol: BT474 persister cells were derived by treating 75% confluent BT474 cells with 2 uM lapatinib for 9 days, with fresh lapatinib-containing media (0.01% DMSO) added every 3 days. BT474 parental cells were cultured simultaneously in 0.01% DMSO without lapatinib.

tag: cell line

tag: tissue of origin

value: breast

tag: number of cells

value: 2 million


title: JS167_WT

source_name: Wildtype Replicate 1


title: BT474 Parental rep 2


title: BT474 Persister rep 2


title: BT474 Persister rep 1


title: Pcgf6_ChIP seq_Abcam_repeat_2

first: Tariq

last: Rana

state: California

address: 9500 Gilman Drive

institute: University of California San Diego

data_processing:
Base calling was conducted using the Illumina pipeline
Sequencing reads were aligned to mouse mm9 genome assembly using Bowtie (version 0.1.2.7.). Parameter: bowtie -S -t -q -p 4 -m 1 -n 2 -l 32 -e 3001.
Peak calling was performed using MACS. Parameter: default.
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-Seq peaks in Bed and Bigwig

growth_protocol: CCE cells were cultured in mouse ESC medium (DMEM with 15% fetal bovine serum, nonessential amino acids, L-glutamine, monothioglycerol, and 1000 U/ml LIF).

extract_protocol:
Nuclear extracts were prepared using cell extraction buffers and sonication. Specific histone-DNA complexes were isolated using Pcgf6 antibodies.
Pcgf6-bound genomic DNA was extracted and amplified using an Illumina Library Prep Kit (Illumina, IP-202-1012).

treatment_protocol: CCE cells were cross-linked with disuccinimidyl glutarate and paraformaldehyde

value: CCE

tag: passages

tag: chip antibodies

value: Pcgf6 (Abcam, ab48010)


title: RNA-Seq-Dox+_2

city: Portland

first: Jae

middle: W

last: Lee

state: OR

address: 3181 SW Sam jackson Rd

institute: Oregon Health & Science University

data_processing:
Basecalls was performed using CASAVA software of Illumina
RNA-seq reads were aligned to the mm9 genome assembly using tophat2
The mapped reads were counted using HTSeq
Differential gene expression analysis was performed by Deseq
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited txt file were produced by Deseq

source_name: A172LoxP ESC line

growth_protocol: Chx10-ESCs were generated from the A172LoxP ESC line (Iacovino et al., 2011).

extract_protocol:
Total RNA was extracted using RNeasy Mini kit (Qiagen) and reverse transcription was performed using SuperScript III (Invitrogen).
Libraries were prepared according to the Illumina TruSeq protocol, validated using the bioanalyzer and real-time PCR, and then sequenced on the Illumina HiSeq 2000

treatment_protocol: For MN differentiation assays, Chx10-ESC aggregates (embryoid bodies, EBs) were treated with all trans retinoic acid (0.5 μM) and a Shh agonist purmorphamine (1 μM; Calbiochem) for two days, and then cultured with either doxycycline (2 μg/mL) or vehicle for additional two to three days before the analyses.

value: Chx10-ESC-derived motor neurons

tag: treatment

value: Dox Positive


title: BT474 Parental rep 1


title: Pcgf6_ChIP seq_Abcam_repeat_1


title: Input


title: Pcgf6_ChIP seq_SC_repeat_2

value: Pcgf6 (Santa Cruz, sc-160649)


title: P12_Cd73N_Ezh2-cKO

tag: age


title: Pcgf6_ChIP seq_SC_repeat_1


title: Chx10_Input

data_processing:
Basecalls was performed using CASAVA software of Illumina
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
The peak calling was conducted with MACS software
MEME-ChIP Suite (Bailey et al., 2009; Machanick and Bailey, 2011) and TOMTOM algorithm (Gupta et al., 2007) was used for motif analysis
Genome_build: mm9
Supplementary_files_format_and_content: bed files were generated by MACS

extract_protocol:
Cell lysates were sonicated and the DNA complexes were precipitated with rabbit anti-Chx10.
Libraries were prepared according to the Illumina TruSeq protocol, validated using the bioanalyzer and real-time PCR, and then sequenced on the Illumina HiSeq 2000

tag: cell type

tag: chip-antibody


title: mutant 1

first: Lori

last: Sussel

address: 1775 Aurora Ct.

institute: University of Colorado

data_processing:
RTA (Illumina) was used for base calling
bcl2fastq (version 1.8.4) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-files include FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: csv-file includes DeSeq analysis for all samples

source_name: Colon

extract_protocol:
2 cm of the colon (as measured after the caecum) were dissected, stored in RNAlater (Ambion) and total RNA was isolated using QIAGEN RNeasy Midi kits. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mixed

tag: rnaseq id

value: RNASeq ID:DB002

tag: developmental stage

value: adult, 6 weeks

tag: genotype

value: Nkx2.2flox/flox; Villin-Cre/+

value: Colon


title: mutant 2

value: RNASeq ID:DB003


title: RNA-Seq-Dox+_1


title: RNA-Seq-Dox-_2

value: Dox Negative


title: RNA-Seq-Dox-_1


title: control 1

value: RNASeq ID:DB001


title: Fungal keratitis

city: Madurai

first: Bharanidharan

last: Devarajan

state: Tamil Nadu

address: 1,Anna nagar

department: Bioinformatics

country: India

institute: Aravind Medical Research Foundation

data_processing:
Raw data from the deep sequencing was obtained in the FASTQ format. Adaptor and low quality reads were discarded using our perl script, allowing no mismatches for adaptor identification
The sequencing data were further aligned to Homo sapiens hg19 genome reference allowing for one mismatch using bowtie1 aligner (Langmead et al., 2009) in the sRNAbench tool (Barturen et al., 2014). Next, this tool identified the validated miRNAs from the miRBase (release 20) (Kozomara A and Griffiths-Jones S 2011).
For differential expression analysis, miRNAs with same isoMIRs were considered together and less represented miRNAs (0.01% of the total reads) were eliminated from analysis. Further, the analysis was performed using NOISeq R package on the quantile normalized reads (Bioconductor 2.14 with R version 3.1.0). The method of NOISeq applied was NOISeqsim, which assumes no replicates for the experimental conditions.
The variable expression of miRNAs between patients and controls was considered significant when the fold change was >2 and the probability score was>0.9.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files

source_name: cornea

extract_protocol:
The flash frozen corneal tissue (using liquid nitrogen) was grinded to a powder with liquid nitrogen in a prechilled mortar and pestle sitting in a bed of dry ice, total RNA was isolated using mirVana miRNA isolation kit following the frozen tissue, and extremely hard tissues protocol provided in the kit. Libraries were sequenced in a Single Read 50 base run , using TruSeq SR Cluster Kit v3-cBot- HS (Catalog#GD-401-3001) for cluster generation on cBot and TruSeq SBS Kit v3-HS (Catalog# PE-401-3002) for sequencing on the Illumina HiSeq1000 platform
Small RNA libraries were prepared for sequencing using Illumina standard protocols

value: cornea

tag: disease state

value: fungal keratitis


title: control


title: Chx10_ChipSeq

value: rabbit anti-Chx10


title: control 2

value: RNASeq ID:DB004


title: mutan t3 [LS048]

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-files includse FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: csv-file includes DeSeq analysis for all samples; Differentially expressed gene analysis

source_name: Duodenum

extract_protocol:
2 cm of the duodenum (as measured from the stomach) were dissected, stored in RNAlater (Ambion) and total RNA was isolated using QIAGEN RNeasy Midi kits. Libraries were prepared from total RNA (RIN>8) with the TruSeq RNA prep kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: adult mice, 6 weeks

value: Duodenum

value: mixed background


title: control 2 [LS040]

value: Nkx2.2flox/+; Rosa26Tomato/+


title: control 3 [LS042]


title: mutant 1 [LS044]


title: mutant 2 [LS045]


title: mutant 2 [LS031]

data_processing:
RTA (Illumina) was used for base calling
CASAVA (version 1.8.2) was used for converting BCL to fastq format, coupled with adaptor trimming
Reads were mapped  to a reference genome (Mouse: UCSC/mm9) using Tophat (Trapnell C et al 2009 Bioinformatics) (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
Relative abundance (aka expression level) of genes and splice isoforms was determined using cufflinks (Trapnell C et al 2010 Nature Biotech) (version 2.0.2) with default settings.
Differentially expressed genes were calculated using Deseq (Anders S et al 2010 Genome Biology).
Genome_build: mm9
Supplementary_files_format_and_content: csv-files includse FPKM values for all genes/isoforms in a sample
Supplementary_files_format_and_content: txt-file includes DeSeq analysis for all samples; Differentially expressed gene analysis

value: Nkx2.2flox/SD; Villin-Cre/+


title: control 1 [LS039]


title: mutant 1 [LS030]


title: mutant 3 [LS032]


title: control 3 [LS025]

value: WT


title: control 2 [LS024]


title: ag-10 fhy3-68 rep2

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-seq reads were aligned to the Ler-0 genome assembly using tophat version 2.0.14 with the default parameters
The read counts of the genes were calculated by HTSeq version 0.6.1p1. The read counts were normalized and converted to Reads Per Megabase of library size (RPM) by edgeR version 3.10.0.
Genome_build: Ler-0
Supplementary_files_format_and_content: tab-delimited text files include RPM values for each sample

source_name: Inflorescence

extract_protocol:
Lysates were clarified from ground flower tissue and total RNA were isolated with RNA extract kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Inflorescence containing stage 8 and younger flowers

tag: Stage

value: flower


title: ag-10 fhy3-68 rep1

tag: tissue


title: fhy3-68 rep2


title: control 1 [LS023]


title: fhy3-68 rep1


title: mutant 3 [LS018]


title: mutant 2 [LS016]

value: Nkx2.2flox/flox; Villin-Cre/+


title: ag-10 rep2


title: ag-10 rep1


title: ler rep2

value: Ler


title: mutant 1 [LS015]


title: control 3 [LS010]


title: control 2 [LS008]


title: input

data_processing:
Basecalls performed using CASAVA version 1.8
ChIP-seq reads were aligned to the No-0 genome assembly using bowtie2 version 2.2.3 with the default parameters
peaks were called using MACS version 1.4.2 with the following setting: effective genome size (1.18e+08), band width (300), model fold (10,30), pvalue cutoff (1.00e-05)
Genome_build: No-0 genome assembly
Supplementary_files_format_and_content: bed files were generated using MACS version 1.4.2; Scores represent -10*log10(pvalue)

growth_protocol: plants were grown in greenhouse under LD (16h light/8h dark).Inflorescence of  35S:3FLAG-FHY3-3HA fhy3-4 containing stage 8 and younger flowers were harvested for ChIP-seq analysis.

extract_protocol:
Lysates were clarified from sonicated nuclei and FHY3-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303).

tag: chip antibody


title: FHY3 ChIP-seq1

value: Sigma-Aldrich, A2220


title: control 1 [LS007]


title: FHY3 ChIP-seq2


title: P8_Cd73N

tag: background strain

value: retina

value: postnatal day 8

tag: cd73 status

value: negative


title: P5_Cd73N

value: postnatal day 5


title: H3K4me3-shJARID1D_ChIP-Seq_rep2

city: Memphis

first: JIE

last: Lv

state: TN

address: 262 Danny Thomas Place

department: Department of Computational Biology

institute: St Jude Children's Research Hospital

description: Processed data file: H3K4me3-shJARID1D.bgsub.Fnor.wig

data_processing:
Illumina Casava1.7 software used for basecalling.
Total read numbers of ChIP-Seq samples without spike-in control are normalized to be 25 million, and ChIP-Seq samples with spiked-in Control are normalized according to the number of spiked-in Drosophila melanogaster chromatin.
ChIP-seq reads were aligned to the hg19 genome assembly using bowtie v1.1.2 with parameters -p 8 -m 1 --chunkmbs 512 --best
ChIP-Seq peaks were called using DANPOS2 v2.2.2 with the following parameters: --smooth_width 0 -e 1 --frsz 200 --extend 200 --pheight 1e-50 --extend_pheight 1e-20
RNA-Seq reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 genome assembly using tophat v2.0.12 with parameters --mate-std-dev 200 -p 8 -r 203
The number of fragments that originated from each gene in each sample is estimated using cuffdiff with default parameters. Then, the differentially expressed genes based on read counts are inferred using edgeR R package v3.12.0.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: For RNA-Seq data, tab-delimited text file (genes.count_tracking.txt) includes raw counts of reads, RPKM values for each gene of each sample.
Supplementary_files_format_and_content: For ChIP-Seq data, wig files showing the average signal density across genome are generated using DANPOS2 v2.2.2.

source_name: DU145 cells, shJARID1D, H3K4me3 ChIP

growth_protocol: DU145 were cultured in High Glucose Dulbecco's Modified Eagle's Medium supplemented with L-glutamine, sodium bicarbonate, pyridoxine.HCI, sodium pyruvate and 10% fetal bovine serum.

extract_protocol:
ChIP with reference exogenous genome (ChIP-Rx) was performed to compare H3K4me1 and H3K4me3 levels in shLuciferase, shJARID1D or shZMYND8 DU145 human prostate cancer cells. Drosophila melanogaster chromatin and Drosophila-specific H2Av antibody were spiked-in to each ChIP reaction as a minor fraction. Cells were cross-linked with 1% formaldehyde at room temperature for 10 min and then lysed and sonicated to fragment genomic DNA sizes to 200-500 bp. Chromatin samples were incubated with specific antibodies overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads. The bound fractions were washed with low salt, high salt, LiCI wash buffer and TE buffer. Reverse-crosslinking of the eluted DNA were carried out at 67℃ for 8 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR purification kit.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: JARID1D knockdown DU145 cells.

tag: cell line

value: prostate cancer cell line

tag: tissue derivation

value: prostate; derived from brain metastatic site

value: H3K4me3 (Millipore, 07-473, lot 2664283), Drosophila-specific H2Av (Active Motif, 61686, lot 18815002)


title: H3K4me3-shZMYND8_ChIP-Seq _rep2

description: Processed data file: H3K4me3-shZMYND8.bgsub.Fnor.wig

source_name: DU145 cells, shZMYND8, H3K4me3 ChIP

treatment_protocol: ZMYND8 knockdown DU145 cells.


title: E18

value: embryonic day 18


title: shZMYND8_RNA-Seq_rep1

description: Processed data file: genes.count_tracking.txt

source_name: DU145 cells, shZMYND8

extract_protocol:
Total RNAs were extracted using RNeasy kits (Qiagen), which were used for RNA-seq experiments.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: shZMYND8_RNA-Seq_rep2


title: H3K4me1-shZMYND8_ChIP-Seq_rep2

description: Processed data file: H3K4me1-shZMYND8.bgsub.Fnor.wig

source_name: DU145 cells, shZMYND8, H3K4me1 ChIP

value: H3K4me1 (Abcam, ab8895, lot GR251663-1), Drosophila-specific H2Av (Active Motif, 61686, lot 18815002)


title: shJARID1D_RNA-Seq_rep1

source_name: DU145 cells, shJARID1D


title: shControl_RNA-Seq_rep1

source_name: DU145 cells, shLuciferase

treatment_protocol: Control shLuciferase DU145 cells.

value: shLuciferase


title: H3K4me3-shControl_ChIP-Seq_rep2

description: Processed data file: H3K4me3-shControl.bgsub.Fnor.wig

source_name: DU145 cells, shLuciferase, H3K4me3 ChIP


title: P8_Cd73P_input

value: ICR

value: positive


title: shControl_RNA-Seq_rep2


title: E15

value: embryonic day 15


title: P5_Cd73P


title: H3K4me1-shJARID1D_ChIP-Seq_rep2

description: Processed data file: H3K4me1-shJARID1D.bgsub.Fnor.wig

source_name: DU145 cells, shJARID1D, H3K4me1 ChIP


title: shJARID1D_RNA-Seq_rep2


title: P8_Cd73P_H3K27me3


title: Ler rep1

value: Inflorescence containing stage 8 and younger flowers

value: flower


title: H3K4me3-shJARID1D_ChIP-Seq_rep1


title: P5_Cd73P_input


title: H3K4me1-shControl_ChIP-Seq_rep2

description: Processed data file: H3K4me1-shControl.bgsub.Fnor.wig

source_name: DU145 cells, shLuciferase, H3K4me1 ChIP


title: H3K4me1-shJARID1D_ChIP-Seq_rep1


title: P8_Cd73P

source_name: Retina


title: H3K4me3-shZMYND8_ChIP-Seq _rep1


title: P2_Cd73P_input

value: postnatal day 2


title: H3K4me1-shZMYND8_ChIP-Seq_rep1


title: H3K4me3-shControl_ChIP-Seq_rep1


title: Input-shJARID1D

description: Processed data file: Input-shJARID1D.uniq.wig

source_name: DU145 cells, shJARID1D, input


title: P2_Cd73P_H3K4me3


title: H3K4me1-shControl_ChIP-Seq_rep1


title: P2_Cd73N_input


title: P2_Cd73N_H3K27me3


title: P8_Cd73P_H3K4me3


title: cat2shr 24h photorespiratory stress rep1

city: Gent

first: Patrick

last: Willems

address: Technologiepark 927

department: PSB

country: Belgium

institute: Ghent University

description:
catshr-24H-I_S22
Stress (24h photorespiratory stress) sample cat2xshr
Three-week-old seedlings (shoot tissue)

data_processing:
Adapter sequences and low quality base-pairs (Q < 20) were trimmed using Trim Galore (v0.3.3, http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/), retaining high-quality reads of at least 50 bp length.
Quality-filtered reads were aligned to the TAIR10 Arabidopsis reference genome using the spliced aligner TopHat2 (v2.1.0)
The number of reads per gene was quantified using featureCounts function as implemented in the Subread package v1.4.6
Genome_build: Arabidopsis TAIR10
Supplementary_files_format_and_content: Table containing gene counts for all 24 samples as delivered by featureCounts

source_name: cat2shr 24h photorespiratory stress

growth_protocol: Plants were grown in Petri dishes (150×25 mm; Becton-Dickinson) on full-strength MS agar-solidified medium supplemented with 1% (w/v) sucrose, 100 mg/L myo-inositol, 0.5 mg L‑1 nicotinic acid, 0.5 mg/L pyridoxine, and 1 mg/L thiamine at 21°C and LD conditions (16 h light [100 μmol m−2 s−1]/8 h dark).

extract_protocol:
RNA was extracted using a combination of TRIzol and RNeasy Kit (Qiagen) according to the manufacturers’ instructions.
Library preparation and sequencing was performed at the VIB Nucleomics Core (www.nucleomics.be). Sequencing libraries were constructed with using the TruSeq Stranded mRNA Library Preparation Kit (Illumina).

treatment_protocol: After 21 days of growth, the MicroporeTM surgical tape (3M) that sealed the plates was replaced by two layers of Parafilm M (Bemis) to restrict gas exchange. Plants were transferred to a continuous light regime.

value: seedling

value: shoot

tag: ecotype

tag: genotype/variation

tag: stress

value: photorespiratory stress


title: shr 24h photorespiratory stress rep3

description:
shr-24H-III_S21
Stress (24h photorespiratory stress) sample shr
Three-week-old seedlings (shoot tissue)

source_name: shr 24h photorespiratory stress

tag: age

value: shr


title: ZMYND8_ChIP-Seq_rep2

description: Processed data file: ZMYND8.bgsub.Fnor.wig

source_name: DU145 cells, untreated, ZMYND8 ChIP

extract_protocol:
DU145 prostate cells were cross-linked with 1% formaldehyde at room temperature for 10 min and then lysed and sonicated to fragment genomic DNA sizes to 200-500 bp. Chromatin samples were incubated with specific antibodies overnight at 4℃. The protein-DNA complexes were immobilized on protein A/G beads. The bound fractions were washed with low salt, high salt, LiCI wash buffer and TE buffer. Reverse-crosslinking of the eluted DNA were carried out at 67℃ for 8 hours. After RNase A and protease K digestion, DNA fraction was purified using PCR purification kit.
ChIP DNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Normal DU145 cells.

tag: cell type

tag: treatment


title: ZMYND8_ChIP-Seq_rep1


title: Input-shZMYND8

description: Processed data file: Input-shZMYND8.uniq.wig

source_name: DU145 cells, shZMYND8, input


title: shr 24h photorespiratory stress rep1

description:
shr-24H-I_S19
Stress (24h photorespiratory stress) sample shr
Three-week-old seedlings (shoot tissue)


title: Input_ZMYND8_rep1

description: Processed data file: ZMYND8_input.Fnor.wig

source_name: DU145 cells, untreated, input


title: Input_ZMYND8_rep2


title: cat2shr 24h photorespiratory stress rep2

description:
catshr-24H-II_S23
Stress (24h photorespiratory stress) sample cat2xshr
Three-week-old seedlings (shoot tissue)


title: Input_JARID1D_rep2

description: Processed data file: JARID1D_input.Fnor.wig


title: Input_JARID1D_rep1


title: shr 24h photorespiratory stress rep2

description:
shr-24H-II_S20
Stress (24h photorespiratory stress) sample shr
Three-week-old seedlings (shoot tissue)


title: JARID1D_ChIP-Seq_rep2

description: Processed data file: JARID1D.bgsub.Fnor.wig

source_name: DU145 cells, untreated, JARID1D ChIP


title: P5_Cd73N_input

value: retina

value: postnatal day 5

value: negative


title: cat2 24h photorespiratory stress rep3

description:
cat-24H-III_S18
Stress (24h photorespiratory stress) sample cat2
Three-week-old seedlings (shoot tissue)

source_name: cat2 24h photorespiratory stress


title: JARID1D_ChIP-Seq_rep1

value: prostate cancer cell line

value: prostate; derived from brain metastatic site


title: Input_DNA

description: Processed data file: input.Fnor.wig


title: cat2 24h photorespiratory stress rep2

description:
cat-24H-II_S17
Stress (24h photorespiratory stress) sample cat2
Three-week-old seedlings (shoot tissue)


title: Input-shControl

description: Processed data file: Input-Control.uniq.wig

source_name: DU145 cells, shLuciferase, input


title: Col-0 24h photorespiratory stress rep3

description:
Col-24H-III_S15
Stress (24h photorespiratory stress) sample Col-0
Three-week-old seedlings (shoot tissue)

source_name: Col-0 24h photorespiratory stress

value: wt


title: P2_Cd73P_H3K27me3


title: H3K4me1_ChIP-Seq_rep2

description: Processed data file: H3K4me1.bgsub.Fnor.wig

source_name: DU145 cells, untreated, H3K4me1 ChIP


title: Col-0 24h photorespiratory stress rep2

description:
Col-24H-II_S14
Stress (24h photorespiratory stress) sample Col-0
Three-week-old seedlings (shoot tissue)


title: Col-0 24h photorespiratory stress rep1

description:
Col-24H-I_S13
Stress (24h photorespiratory stress) sample Col-0
Three-week-old seedlings (shoot tissue)


title: H3K4me3_ChIP-Seq

description: Processed data file: H3K4me3.bgsub.Fnor.wig

source_name: DU145 cells, untreated, H3K4me3 ChIP


title: cat2shr 0h photorespiratory stress rep3

description:
catshr-0H-III_S12
Control sample cat2xshr
Three-week-old seedlings (shoot tissue)

source_name: cat2shr 0h photorespiratory stress

value: control


title: H3K4me1_ChIP-Seq_rep1


title: cat2shr 0h photorespiratory stress rep2

description:
catshr-0H-II_S11
Control sample cat2xshr
Three-week-old seedlings (shoot tissue)


title: shr 0h photorespiratory stress rep2

description:
shr-0H-II_S8
Control sample shr
Three-week-old seedlings (shoot tissue)

source_name: shr 0h photorespiratory stress


title: shr 0h photorespiratory stress rep3

description:
shr-0H-III_S9
Control sample shr
Three-week-old seedlings (shoot tissue)