title: lambda validation

data_processing:
lambda_stage5_1-3.pileup; genome build: UCSC dm3
Read calling and alignment. Illumina raw data were  processed with Illumina's Pipeline 1.3.2, skipping the first two cycles (corresponding to the portion of the HpyCH4III recognition site that was left after restriction digestion) to facilitate cluster identification. The first 9 nucleotides of each read, corresponding to the C in the adapter following the HpyCH4III site and the first 8 bases of the random primer, showed higher error rates than the remaining 25 nucleotides and were trimmed prior to sequence alignment. Paired reads were aligned to the  drosophila reference genome assembly (version dm3 from the UCSC Genome Bioinformatics site, using all the chromosomes except Uextra) using Novoalign v2.07.06 run in bisulfite mode. Novoalign was run with the following options: -t 90 -h 120 -r A 3 -k; these options allow a set of paired reads to align with up to (approximately) 3 mismatches over the combined length of the two reads, and report up to 3 alignments for reads generating more than one optimal alignment. The forward (CT) and reverse (GA) stands of DNA become non-complementary following bisulfite conversion. Novoalign in bisulfite mode  can align bisulfite treated sequences against a reference genome in a single pass that aligns against both CT and GA in-silico indexed reference sequences.    Identification of methylated cytosines. Unconverted (methylated) cytosines will be read as 'C' if the sequence is derived from the CT strand, and as 'G' if the sequence is derived from the GA strand. Conversely, a 'C' from the GA strand and a 'G' from the CT strand correspond to a guanine in the reference sequence and must be ignored in the analysis. The loss of complementarity following bisulfite conversion makes it possible to determine if a methylated cytosine is on the CT or the GA strand. This is important if methylated sequences are asymmetric (i.e. non-CG methylation). To determine if a sequence alignment is derived from the CT or GA strand, we implemented the following decision tree: 1- if an alignment  has only CT or GA mismatches, it is assigned to the respective strand if the corresponding number of CT or GA mismatches is at least 2; otherwise, the read is considered ambiguous and further processed in step 3; 2- if an alignment has both CT and GA mismatches, it is assigned to the strand that has at least a 2-fold excess of one type of mismatch; otherwise, the read is considered ambiguous and further processed in step 3; 3- if an ambiguous alignment is primary and in a proper pair, the strand assignment of the mate pair is transferred to the ambiguous read; otherwise the ambiguous alignment is discarded; 4- alignments that are primary, in a proper pair, and not containing an ambiguous strand assignment, are checked for consistent strand assignment (i.e.: both mate pairs are assigned to the same strand). If the assignment is inconsistent, the pair is discarded.    Generation of "medip-bis_PE-tr9_d2_CT-PE.pileup" and "medip-bis_PE-tr9_d2_GA-PE.pileup" files: following strand assignment of all alignments, we calculated pileup files for the CT and GA strands from their respective alignments files. We used a modified pileup program that does not ignore  any reads in the alignment: reads with multiple alignments and reads not mapped in proper pair are included in the output. We identified methylated cytosines on the CT and GA strands separately, by counting (from the pileup files)  how many alignments contained either a 'C' or a 'T' at C positions on the CT strand, and  how many alignments contained either a 'G' or an 'A' at G positions on the GA strand. From here onwards we refer to C positions on the CT strand and G positions on the GA strand as “methylated cytosines”.  Identification of methylated regions.  We first selected cytosines with strong evidence of methylation by retaining only those methylated cytosines at which at least three alignments had an unconverted C and the ratio of C-containing alignments over the sum of C- and T-containing alignments was greater than 0.1. These criteria remove cytosines with methylation supported by only one or two reads or where the vast majority of the reads do  not support the presence of methylation. It is likely that these filtering steps remove cytosines with low levels of methylation.Generation of "box25_d2_AG_count_3_ratio_0.1.bed"  and "box25_d2_TC_count_3_ratio_0.1.bed" files: we used all methylated cytosines passing the filter above to identify regions of high methylation. We divided the genome into segments of 25 nucleotides and counted how many methylated cytosines were within each segment. Segments without any methylated cytosine were discarded, and contiguous segments with at least one methylated cytosine were merged. Finally, we retained for analysis only segments in which the underlying alignments contained at least 25 methylated cytosines.
Read calling and alignment of bisulfite PCR sample.  Sequence reads were aligned to a reference sequence consisting of the regions that were targeted for amplification using Novoalign v2.07.11 run in bisulfite mode with the -g200 option.  After bisulfite conversion, PCR amplifies one of the two DNA strands (labeled 'CT' and 'GA'), the one against which the PCR primers are designed. Only reads aligning against the correct DNA strand were further processed. We used a modified pileup program (that retains reads with multiple alignments) to determine the degree of methylation at all cytosines. Cytosine positions at which the total count of converted and unconverted cytosines was less than 90% where discarded as potentially polymorphic.
We used the sequences from the lambda phage to asses the efficiency of bisulfite conversion.

organism: Lambdavirus lambda

source_name: virus

value: cl857 Sam7


title: HB27Δago-3

status: Public on Feb 17 2014

type: SRA

city: Wageningen

first: daan

middle: christianus

last: swarts

address: Dreijenplein 10

department: Agrotechnology and Food Sciences Group

country: Netherlands

institute: Wageningen UR

description:
Linker has barcode AGTTCC
RNA-seq, BaseClear B.V., The Netherlands

library_source: transcriptomic

data_processing:
Linkers removed by BaseClear B.V., The Netherlands
Reads mapped on Thermus thermophilus HB27 chromosome AND Thermus thermophilus HB27 pTT27 megaplasmid using Rockhopper
Relative expression of genes calculated by comparing averages of total counts for each gene
Genome_build: AE017221 and AE017222
Supplementary_files_format_and_content: Text file with counts per annotated gene. Relative expression of genes in each strain calculated using averages of counts.

molecule: total RNA

organism: Thermus thermophilus HB27

source_name: Cells

growth_protocol: OD600=0.5 --> RNA isolation

extract_protocol:
miRVana isolation kit (Ambion)
Libraries were prepared using standard illumina protocols

treatment_protocol: Cells harvested by centrifugation

tag: genotype

value: ago ko

tag: temperature

tag: strain


title: Rosa late (orange/red) ommochrome, rep 2

status: Public on Feb 15 2014

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2300 Biological Sciences III

department: Developmental & Cell Biology

country: USA

institute: University of California Irvine

description: Sample 20

data_processing:
Each dataset was filtered with Khmer (parameters: -C 20 -k 20 -N 4 -x 2e9 ) to even out coverage, remove redundant reads and to remove reads with sequencing errors.
Replicates of each developmental stage of each color morph were pooled and assembled into developmental stage transcriptomes using Oases v.1.2.03 with hash lengths ranging from 29 to 61 bp.
The developmental stage transcriptomes were consolidated using CD-HIT-EST of CD-HIT package v.4.5.7 (parameters: ) into a reference transcriptome. All transcripts longer than 1 Kb were kept for subsequent analyses.
#1 mate of the paired-end reads were mapped to the reference transcriptome using Bowtie v.0.12.7 (parameters: -aS --offrate 1 -e 200) and transcript expression levels were obtained using eXpress v.1.0.0 (default options).
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for the indicated samples (no measurements for samples 1,8,11,17)

molecule: polyA RNA

organism: Junonia coenia

source_name: Hind wings

growth_protocol: A population of J. coenia from Durham, North Carolina (35°59’19”N, 78°54’26”W) was reared in incubators, and fed a standard artificial diet (Nijhout 1980). Two sets of conditions known to induce alternative color morphs in North Carolina populations (Smith 1991) were applied: 21°C with 8 hr light per day for short/cool day conditions, and 27°C with 16 hr light for long/warm day conditions.

extract_protocol:
Total RNA was extracted from wing tissues using RNeasy Mini Kit - spin column protocol (QIAGEN, Valencia, CA).
TURBOtm DNase treatment (Life Technologies, Grand Island, NY) was then used to degrade contaminating DNA and mRNA was purified from the total RNA using the Oligotex mRNA Mini Kit (QIAGEN, Valencia, CA). The Ovation® RNA-seq system (NuGEN, San Carlos, CA) was used to prepare double stranded cDNA from mRNA and this cDNA product was then purified with QIAquick PCR purification columns (QIAGEN, Valencia, CA). The purified double stranded cDNA was sheared by a Covaris Ultrasonicator to 300bp lengths. The EncoreTM NGS Multiplex System I (NuGEN, San Carlos, CA) was used for final library preparation. Multiplexed libraries were sequenced as 75 bp paired-end Illumina reads or 100 bp paired-end Illumina reads.

treatment_protocol: Hindwings from four developmental stages were sampled for both color morphs.The four stages sampled include imaginal disks from fifth instar larvae, pre-pigment pupa, early (yellow) ommochrome development, and late (orange/red) ommochrome development). To preserve mRNA quality, wings were rapidly dissected into RNAlater (Life Technologies, Grand Island, NY), incubated for ~24h at 4oC to allow the solution to permeate tissues, and then stored at -80oC until mRNA extraction.

tag: tissue

value: hind wings

tag: developmental stage

value: late (orange/red) ommochrome


title: HB27-1

description:
Linker has barcode CCGTCC
RNA-seq, BaseClear B.V., The Netherlands

value: wt


title: Rosa early (yellow) ommochrome, rep 3

description: Sample 18

value: early (yellow) ommochrome


title: Rosa early (yellow) ommochrome, rep 1

description: Sample 16


title: Rosa early (yellow) ommochrome, rep 2

description: Sample 17


title: Linea late (orange/red) ommochrome, rep 2

description: Sample 10


title: Rosa 5th instar larvae, rep 2

description: Sample 12

value: 5th instar larvae


title: Rosa 5th instar larvae, rep 1

description: Sample 11


title: Rosa pre-pigment pupa, rep 2

description: Sample 15

value: pre-pigment pupa


title: HB27Δago-1

description:
Linker has barcode TTAGGC
RNA-seq, BaseClear B.V., The Netherlands


title: Linea early (yellow) ommochrome, rep 1

description: Sample 6


title: Rosa 5th instar larvae, rep 3

description: Sample 13


title: Linea pre-pigment pupa, rep 2

description: Sample 5


title: Linea early (yellow) ommochrome, rep 3

description: Sample 8


title: Linea early (yellow) ommochrome, rep 2

description: Sample 7


title: HB27-3

description:
Linker has barcode GGCTAC
RNA-seq, BaseClear B.V., The Netherlands


title: Linea 5th instar larvae, rep 3

description: Sample 3


title: Linea 5th instar larvae, rep 2

description: Sample 2


title: c587-gal4>UASt-HA::Lsd1_input

city: Dallas

first: Michael

last: Buszczak

state: Texas

address: 5323 Harry Hines Boulevard

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

library_source: genomic

data_processing:
Image scanning and basecalls were performed using BioScope (v. 1.2.1)
ChIP-seq reads were aligned to dm3 geneome assembly using BioScope (v. 1.2.1)
Mapped reads were filtered to remove low quality, ambiguous and redundant reads
Peaks were called using the FindPeaks module in the Homer software tool
Genome_build: dm3
Supplementary_files_format_and_content: Processed data files contains LSD1 peak coordinates in BED format

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Escort cells and early follicle cells

growth_protocol: Ovaries expressing the HA-tagged Lsd1 transgene in specific cell populations under control of two different gal4-drivers were dissected from 3-7 day old females

extract_protocol:
Lysates were clarified from sonicated samples and the Lsd1-DNA complexes were isolated using an anti-HA antibody
Libraries were prepared according to SOLiD 5500 instructions accompanying the ChIP-seq kit with barcoding beta protocol. AMPure® XP beads were used in this protocol. Briefly, DNA was end-repaired using a combination of 5X reaction buffer, dNTP mix (10mM), end polishing enzyme 1 and 2, and nuclease free water included in the kit. Binding and washing of end-paired DNA was performed using AMPure® XP beads and 70% ethanol respectively. Then, the end-paired DNA was eluted with elution buffer included in the kit. Then,  the 5500 barcoded adaptors were liagted to the DNA and purified using 70% ethanol. Purified adaptor ligated DNA was PCR amplified for 10-15cycles. Amplified DNA was purified and ~1μL of purified amplified product was run on a 2% E-Gel® EX Gel to confirm the removal of any primer dimers.This product was quantified using qPCR. Following qPCR quantitation, the SOLiD™ ChIP-Seq fragment library was subjected to templated bead preparation.

tag: epitope

value: Hemagglutinin (HA)

tag: chip antibody

value: rabbit-HA antibody (Abcam)

tag: cell type

value: Escort cells and early follicle cells


title: Linea 5th instar larvae, rep 1

description: Sample 1


title: c587-gal4>UASp-HA::Lsd1_input


title: Input_control

city: Austin

first: Bum-Kyu

last: Lee

state: TX

address: 2506 Speedway Stop A5000

institute: University of Texas at Austin

description: Input

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to mouse hg18 genome using BWA version 0.5.9-r16.
Peaks were called using  a Parzen window based algorithm (LEE et al, 2011. Nucleic Acis Res. 39(9):3558-73).
Genome_build: hg18
Supplementary_files_format_and_content: tab-delimited text files include information regarding chromosome, peak start, peak end, peak score, and peak center for each peak

organism: Homo sapiens

source_name: CAL-1 plasmacytoid dendritic cells

growth_protocol: The human CAL-1 plasmacytoid dendritic cell line was grown RPMI media supplemented with 10% FBS and 2mM L-Glutamine.  Media was changed every 2-3 days.

extract_protocol:
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution. Immunoprecipitated DNA was sequenced using Illumina sequencers.
Pull-downed DNA was applied for generation of sequencing libraries using the NEB ChIP-seq library prep. kit (E6200L ) following by manufacturer’s instructions.

value: plasmacytoid dendritic cell

value: preimmune rabbit IgG (Bethyl Labs P120-101)


title: BCL11A_ChIPSeq

description: Chromatin IP against BCL11A

value: Anti-BCL11a polyclonal (Bethyl Labs BL1797)


title: c587-gal4>UASt-HA::Lsd1


title: hh-gal4>UASt-HA::Lsd1_input

source_name: Cap cells and terminal filament cells

value: Cap cells and terminal filament cells


title: c587-gal4>UASp-HA::Lsd1


title: hh-gal4>UASp-HA::Lsd1


title: hh-gal4>UASt-HA::Lsd1


title: Rosa late (orange/red) ommochrome, rep 1

description: Sample 19


title: hh-gal4>UASp-HA::Lsd1_input


title: Rosa pre-pigment pupa, rep 1

description: Sample 14


title: Linea late (orange/red) ommochrome, rep 1

description: Sample 9


title: SEQC_Utr_F_104_2

status: Public on Feb 14 2014

city: Shanghai

first: Leming

last: Shi

address: 2005 Songhu Road

department: School of Life Sciences

country: China

institute: Fudan University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rn4 whole genome using TopHat v2.0.4 with default parameters
Alignment results were then processed using Cufflinks v2.0.2 for gene and transcript quantification with default parameters. For samples with 2~3 technical replicates, average FPKM (Fragment Per Kilobase per Million mapped reads) values were used.
Genome_build: rn4
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample

organism: Rattus norvegicus

source_name: Uterus

growth_protocol: Male and female (unsynchronized) Fisher 344 rats obtained from NCTR's animal breeding colony were fed the NIH-31 diet (ad libitum) and housed under AAALAC- approved conditions with a 12-hr light/dark cycle (0600 - 1800). Rats were housed two per cage in standard polycarbonate cages with hardwood chip bedding maintained at 23 degrees C with a relative humidity of ~50%. Animals were sacrificed at 2, 5, 6, 8, 15, 21, 52, 78 and 104 weeks-of-age. Rats were treated according to the NCTR Institutional Animal Care and Use Committee guidelines.

extract_protocol:
Each whole organ was individually ground (mortar and pestle, under continuous liquid N2 chilling) into a fine powder prior to RNA extraction, with the exception of liver, spleen, and gastrocnemius muscle for which approximately 100 mg was ground. Ground organ tissue was stored at -80ºC. Total RNA was extracted from approximately 30 mg of ground tissue by using the miRNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, including treatment with DNase.
RNA libraries were prepared for sequencing using an rRNA depletion protocol using the Ribo-Zero Nonmagnetic Kit (Epicentre) coupled with the Illumina TruSeq RNA-Seq library protocol using TruSeq RNA Sample Preparation Kit (Illumina).

value: Fisher 344

value: Uterus

tag: Sex

value: F

tag: developmental stage (week)


title: SEQC_Utr_F_021_3


title: SEQC_Utr_F_006_4


title: SEQC_Utr_F_021_1


title: SEQC_Utr_F_006_3


title: Linea pre-pigment pupa, rep 1

description: Sample 4


title: SEQC_Utr_F_104_4


title: SEQC_Utr_F_021_4


title: SEQC_Utr_F_006_1


title: SEQC_Utr_F_021_2


title: SEQC_Utr_F_002_2


title: SEQC_Utr_F_006_2


title: SEQC_Utr_F_002_3


title: SEQC_Utr_F_002_4


title: SEQC_Tst_M_104_4

source_name: Testes

value: Testes

value: M


title: SEQC_Utr_F_002_1


title: SEQC_Tst_M_104_3


title: SEQC_Tst_M_021_4


title: SEQC_Tst_M_021_1


title: SEQC_Tst_M_021_2


title: SEQC_Tst_M_021_3


title: SEQC_Tst_M_104_1


title: SEQC_Utr_F_104_1


title: SEQC_Utr_F_104_3


title: SEQC_Tst_M_006_3


title: SEQC_Tst_M_006_2


title: SEQC_Tst_M_006_4


title: SEQC_Tst_M_006_1


title: SEQC_Tst_M_002_4


title: SEQC_Tst_M_002_3


title: SEQC_Tst_M_002_2


title: SEQC_Thm_M_104_3

source_name: Thymus

value: Thymus


title: SEQC_Thm_M_104_1


title: SEQC_Thm_M_104_4


title: SEQC_Thm_M_021_3


title: SEQC_Tst_M_104_2


title: SEQC_Tst_M_002_1


title: SEQC_Thm_M_021_4


title: SEQC_Thm_M_021_1


title: SEQC_Thm_M_006_4


title: SEQC_Thm_M_006_2


title: SEQC_Thm_M_021_2


title: SEQC_Thm_M_006_3


title: SEQC_Thm_M_002_4


title: SEQC_Thm_M_006_1


title: SEQC_Thm_F_104_4


title: SEQC_Thm_M_002_1


title: SEQC_Thm_M_002_2


title: SEQC_Thm_M_002_3


title: SEQC_Thm_F_104_3


title: SEQC_Thm_F_104_1


title: SEQC_Thm_F_006_3


title: SEQC_Thm_F_006_2


title: SEQC_Thm_M_104_2


title: SEQC_Thm_F_021_3


title: SEQC_Thm_F_021_4


title: SEQC_Thm_F_021_2


title: SEQC_Thm_F_006_1


title: SEQC_Thm_F_021_1


title: SEQC_Thm_F_002_4


title: SEQC_Thm_F_002_3


title: SEQC_Thm_F_002_2


title: SEQC_Spl_M_104_4

source_name: Spleen

value: Spleen


title: Sample 25_batch 40

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
NOTE: Experiment was paired-end, but read2 was used to read cell and molecule barcodes only. This information was appended to the fastq entry header.
Additional details about experimental design are available as supplementary data at the foot of Series GSE54006.

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Single cell pool-barcode and well-barcode-RMT were extracted from the first and second end of the read (paired-end reads), respectively, and added to  the fastq header, under the "barcode" field, delimited by a hyphen, i.e. POOL_BARCODE-WELL_BARCODE-RMT, where "NNNNNN" was used as a place holders if pool barcode was not used.
Reads were separated by POOL_BARCODE:WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
The umitab.txt  file contains ~4,590 sample data columns. Each of these samples corresponds to a single cell transcriptome profile. They are distributed among the 28 raw data files. Each such raw data file contains reads corresponding to between 96 and 192 single cells. In the umitab.txt file, each column/cell name begins with a pool (batch) number. Each pool corresponds to one of the 28 raw data files.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files contain mRNA molecule count values for each single cell; Rows represent gene symbols of UCSC-known genes. Underscore delimited row names correspond to known gene entries with non-unique gene symbol. Columns represent single-cell measurements and named as BATCH-ID_CELL-ID. Batch details can be found in the sample description.

organism: Mus musculus

source_name: dendritic cell-enriched single cell-sorted splenocytes_PBS

growth_protocol: 12 to 15 weeks-old mice housed at the Weizmann Institute animal facility

extract_protocol:
Each mouse was euthanized and spleen removed, homogenized to single cell suspension, red cells removed by selective lysis, and for all samples except for samples 11 and 12, the cell suspensions were enriched for CD11c-positive cells with anti-mouse CD11c antibodies coupled to magentic beads and the MACS system.
single cell RNA-seq for gene expression quantitation: 3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science

treatment_protocol: For samples 13 to 28, mice were injected with 1 µg LPS (samples 15, 16, 19, 20, 23, 24, 27 and 28) or PBS (phosphate buffered saline; control mouse; samples 13, 14, 17, 18, 21, 22, 25 and 26) 2 hours before splen extraction (2h treatment).

value: spleen

value: mouse dendritic cell-enriched single cell-sorted splenocytes

tag: selection marker

tag: treatment

value: IP injection of PBS (control) 2h before extraction


title: Sample 24_batch 39

source_name: dendritic cell-enriched single cell-sorted splenocytes_LPS

value: IP injection of LPS, 2h before extraction


title: Sample 26_batch 41


title: SEQC_Thm_F_002_1


title: Sample 28_batch 43


title: Sample 23_batch 38


title: SEQC_Spl_M_104_2


title: SEQC_Thm_F_104_2


title: Sample 22_batch 37


title: Sample 21_batch 36


title: SEQC_Spl_M_104_3


title: SEQC_Spl_M_021_4


title: SEQC_Spl_M_104_1


title: SEQC_Thm_F_006_4


title: Sample 20_batch 35


title: SEQC_Spl_M_021_3


title: Sample 27_batch 42


title: Sample 19_batch 34


title: Sample 18_batch 33


title: SEQC_Spl_M_021_2


title: Sample 17_batch 32


title: SEQC_Spl_M_006_4


title: SEQC_Spl_M_021_1


title: SEQC_Spl_M_006_2


title: SEQC_Spl_M_006_3


title: Sample 15_batch 30


title: Sample 14_batch 29


title: SEQC_Spl_M_006_1


title: Sample 13_batch 28


title: Sample 12_batch 14

source_name: dendritic cell-enriched single cell-sorted splenocytes

value: [NK1.1+ TCRb-neg CD19-neg] or [Gr1+ CD11b+ TCRb-neg CD19-neg NK1.1-neg]


title: Sample 10_batch 12


title: Sample 11_batch 13

value: [CD19+ TCRb-neg B220+] or [CD19+ TCRb-neg B220-neg]


title: SEQC_Spl_M_002_4


title: Sample 9_batch 11

value: CD11c+ CD8+ CD86-neg


title: SEQC_Spl_M_002_1


title: SEQC_Spl_F_104_4


title: SEQC_Spl_F_104_3


title: SEQC_Spl_M_002_3


title: SEQC_Spl_F_104_1


title: Sample 8_batch 8

value: CD11c+ CD8-neg CD4+ ESAM+


title: Sample 6_batch 5


title: SEQC_Spl_F_104_2


title: Sample 7_batch 7

value: CD11c+ CD8-neg CD317+


title: Sample 5_batch 4


title: Sample 16_batch 31


title: SEQC_Spl_F_021_2


title: Sample 4_batch 3


title: Sample 2_batch 1


title: SEQC_Spl_F_021_1


title: Sample 3_batch 2


title: SEQC_Spl_F_021_3


title: SEQC_Spl_F_006_4


title: SEQC_Spl_F_006_3


title: Sample 1_batch 0


title: Acute Sal Rep3

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Basecalls performed using CASAVA
Adapter (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) sequences were removed from 3' end by fastx.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat with options --frag-bias-correct and --multi-read-correct. Novel transcript assembly was not attempted.
Differential analysis was performed by Cuffdiff. An FDR<10% was used as cutoff.
Genome_build: Ensembl NCBIM37.62
Supplementary_files_format_and_content: acute_gene.diff file produced by Cuffdiff is a tab-delimited text file that contains the differential analysis information for each item tested.

source_name: NAc dissection from 3-5 animals

extract_protocol:
following trizol RNA isolation protocol
Illumina RNA seq library prep kit

tag: passages

value: 8-10 weeks

value: Repeated saline I.P. injection for 1w as control


title: SEQC_Spl_M_002_2

value: Fisher 344


title: Acute Sal Rep2


title: SEQC_Spl_F_006_2

value: F


title: Acute Coc Rep3

value: Repeated saline I.P. injection for 6 days followed by cocaine I.P. injection for 1 day at 20mg/kg


title: SEQC_Spl_F_002_3


title: Acute Sal Rep1


title: SEQC_Spl_F_002_4


title: SEQC_Spl_F_006_1


title: Acute Coc Rep2


title: Acute Coc Rep1


title: SEQC_Spl_F_002_2


title: SEQC_Spl_F_021_4


title: SEQC_Spl_F_002_1


title: SEQC_Msc_M_104_4

source_name: Muscle

value: Muscle

value: M


title: SEQC_Msc_M_104_3


title: H3K4me1 ChIP-seq Sal Rep3

data_processing:
Basecalls performed using CASAVA
ChIP-seq reads were aligned to the mm9 genome assembly using Illumina ELAND with default configurations
Uniquely aligned reads were kept and further filtered with PCR redundancy (See Supplemental for details).
Differential sites were found by diffReps (http://code.google.com/p/diffreps/) with window size 200bp and step size 20bp. An FDR<10% was used as cutoff.
genome build: mm9
processed data files format and content: diffReps output is a tab-delimited text file which contains information for each differential site. Each differential site is also annotated by its proximity to genes or heterochromatic regions.
processed data files format and content: BED files contain six columns that represent uniquely aligned, PCR redundancy removed alignments. Columns 4 and 5 are not used.
processed data files format and content: bigWig files are binary representation of wiggle files (http://genome.ucsc.edu/goldenPath/help/bigWig.html). They are converted from the BED files above using the BedTools (https://code.google.com/p/bedtools/).

extract_protocol:
Crosslink with 1% formaldehyde for 10 min and pool 20 NAc for one replicate. Homogenize and sonicate by using bioruptor.
Antibodies were all ChIP grade from Abcam. Around ten nanograms of input DNA or pull-down DNA was used for sequencing library prep following the instructions of Illumina’s ChIP-seq sample prep kit (cat#IP-102-1001). In brief, DNA fragment overhangs were converted into phosphorylated blunt ends, using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. An “A” base was then added to the DNA fragments to enable ligation to the adapters, which have a single “T” overhang. The constructed library was then run on a 2% agarose gel and size selected between 175-300 bp. Lastly, gel-extracted DNA was further enriched by PCR and run on a bioanalyzer to validate size distribution and concentration.

value: nucleus accumbens

tag: chip antibody vendor/catalog

value: Abcam Cat#ab1012


title: DNA input4

extract_protocol: Crosslink with 1% formaldehyde for 10 min and pool 20 NAc for one replicate. Homogenize and sonicate by using bioruptor.  Antibodies were all ChIP grade from Abcam. Around ten nanograms of input DNA or pull-down DNA was used for sequencing library prep following the instructions of Illumina’s ChIP-seq sample prep kit (cat#IP-102-1001). In brief, DNA fragment overhangs were converted into phosphorylated blunt ends, using T4 DNA polymerase, Klenow polymerase, and T4 polynucleotide kinase. An “A” base was then added to the DNA fragments to enable ligation to the adapters, which have a single “T” overhang. The constructed library was then run on a 2% agarose gel and size selected between 175-300 bp. Lastly, gel-extracted DNA was further enriched by PCR and run on a bioanalyzer to validate size distribution and concentration.


title: H3K4me1 ChIP-seq Sal Rep2


title: SEQC_Msc_M_104_2


title: H3K4me1 ChIP-seq Coc Rep2

value: Repeated cocaine I.P. injection for 1w at 20mg/kg


title: SEQC_Msc_M_104_1


title: SEQC_Msc_M_021_4


title: H3K4me1 ChIP-seq Coc Rep1


title: SEQC_Msc_M_021_3


title: H3K4me1 ChIP-seq Coc Rep3


title: SEQC_Msc_M_021_1


title: SEQC_Msc_M_006_3


title: SEQC_Msc_M_006_4


title: H3K27me3 ChIP-seq Sal Rep1

value: Abcam Cat#ab6002


title: H3K27me3 ChIP-seq Coc Rep2


title: H3K27me3 ChIP-seq Coc Rep1


title: H3K27me3 ChIP-seq Coc Rep3


title: SEQC_Msc_M_002_3


title: SEQC_Msc_M_002_2


title: SEQC_Msc_M_002_1


title: H3K27me3 ChIP-seq Sal Rep2


title: SEQC_Msc_F_104_4


title: mRNA-seq Sal Rep2

description: all *.diff files from Cufflinks

data_processing:
Basecalls performed using CASAVA
Adapter (AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG) sequences were removed from 3' end by fastx.
RNA-seq reads were aligned to the mm9 genome assembly using Tophat with options --frag-bias-correct and --multi-read-correct. Novel transcript assembly was not attempted.
Differential analysis was performed by Cuffdiff. An FDR<10% was used as cutoff.
Genome_build: mm9
Supplementary_files_format_and_content: A GTF file contains the structures of the transcripts assembled by Cufflinks.
Supplementary_files_format_and_content: Each .diff file produced by Cuffdiff is a tab-delimited text file that contains the differential analysis information for each item tested. The "sample_1" and "sample_2" refer to "saline_treated" and "cocaine_treated", respectively.

extract_protocol: Brain samples were homogenized in Trizol and processed according to the manufacturer's instructions. RNA was purified with RNeasy Micro columns and Bioanalyzer confirmed that the RNA RINs were >8.0. Four µg of total RNA were used for mRNA library construction following instructions of Illumina mRNA sample prep kit (cat#RS-100-0801). In brief, the poly-A containing mRNA was purified using poly-T oligo-attached magnetic beads. The mRNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA Polymerase I and RNaseH. These cDNA fragments went through an end repair process, the addition of a single 'A' base, and then ligation of the adapters. These products were gel purified and enriched with PCR to create the final cDNA libraries. The library constructs were run on the bioanalyzer to verify the size and concentration before sequencing on the Illumina HiSeq2000 machine at Mount Sinai's Genomic Core facility.


title: SEQC_Msc_F_104_2


title: mRNA-seq Sal Rep1

description: all *.diff files from Cufflinks


title: H3K4me1 ChIP-seq Sal Rep1


title: mRNA-seq Sal Rep3

description: all *.diff files from Cufflinks


title: H3K27me3 ChIP-seq Sal Rep3


title: SEQC_Msc_F_104_3


title: SEQC_Msc_F_021_4


title: mRNA-seq Coc Rep3

description: all *.diff files from Cufflinks


title: SEQC_Msc_M_021_2


title: SEQC_Msc_F_104_1


title: mRNA-seq Coc Rep2

description: all *.diff files from Cufflinks


title: SEQC_Msc_F_021_2


title: SEQC_Msc_F_021_1


title: SEQC_Msc_M_006_1


title: SEQC_Msc_F_021_3


title: SEQC_Msc_M_006_2


title: SEQC_Msc_M_002_4


title: SEQC_Msc_F_006_4


title: SEQC_Msc_F_006_3


title: SEQC_Msc_F_002_4


title: SEQC_Msc_F_006_2


title: SEQC_Msc_F_002_1


title: SEQC_Lvr_M_104_2

source_name: Liver

value: Liver


title: SEQC_Lvr_M_104_1


title: SEQC_Lvr_M_021_3


title: SEQC_Lvr_M_021_4


title: SEQC_Lvr_M_021_2


title: SEQC_Lvr_M_021_1


title: SEQC_Lvr_M_006_3


title: SEQC_Lvr_M_006_4


title: SEQC_Lvr_M_002_3


title: SEQC_Lvr_M_006_1


title: SEQC_Lvr_M_002_4


title: SEQC_Lvr_M_002_2


title: SEQC_Lvr_M_006_2


title: mRNA-seq Coc Rep1

description: all *.diff files from Cufflinks


title: SEQC_Lvr_F_104_3


title: SEQC_Lvr_F_104_1


title: SEQC_Lvr_F_104_4


title: SEQC_Lvr_F_104_2


title: SEQC_Msc_F_002_3


title: SEQC_Lvr_F_021_4


title: SEQC_Lvr_F_021_3


title: SEQC_Lvr_M_104_4


title: SEQC_Msc_F_002_2


title: SEQC_Lvr_F_021_2


title: SEQC_Lvr_M_104_3


title: SEQC_Lvr_F_006_4


title: SEQC_Lvr_F_006_3


title: SEQC_Lvr_F_021_1


title: SEQC_Lvr_F_006_2


title: SEQC_Lvr_F_002_4


title: SEQC_Lvr_F_002_3


title: SEQC_Lng_M_104_4

source_name: Lung

value: Lung


title: SEQC_Lvr_F_002_1


title: SEQC_Lvr_M_002_1


title: SEQC_Lng_M_104_3


title: SEQC_Lvr_F_002_2


title: SEQC_Lng_M_021_1


title: SEQC_Lng_M_104_1


title: SEQC_Lng_M_104_2


title: SEQC_Lng_M_021_4


title: SEQC_Lng_M_021_2


title: SEQC_Lng_M_006_3


title: SEQC_Lng_M_006_2


title: SEQC_Lng_M_002_3


title: SEQC_Lng_M_006_1


title: SEQC_Lng_M_002_2


title: SEQC_Lng_M_006_4


title: SEQC_Lng_F_104_3


title: SEQC_Lng_F_104_4


title: SEQC_Lng_M_002_4


title: SEQC_Msc_F_006_1


title: SEQC_Lng_M_002_1


title: SEQC_Lng_F_104_2


title: SEQC_Lng_F_021_4


title: SEQC_Lvr_F_006_1


title: SEQC_Lng_F_021_2


title: SEQC_Lng_F_021_3


title: SEQC_Lng_F_104_1


title: SEQC_Lng_M_021_3


title: SEQC_Lng_F_006_3


title: SEQC_Lng_F_002_4


title: SEQC_Lng_F_006_1


title: SEQC_Lng_F_006_2


title: SEQC_Lng_F_002_2


title: SEQC_Lng_F_002_3


title: SEQC_Lng_F_002_1


title: SEQC_Kdn_M_104_2

source_name: Kidney

value: Kidney


title: SEQC_Kdn_M_104_4


title: SEQC_Kdn_M_104_3


title: SEQC_Kdn_M_021_4


title: SEQC_Kdn_M_021_3


title: SEQC_Kdn_M_104_1


title: SEQC_Kdn_M_021_2


title: Fe_Front.TAB-Seq (paired-end)

city: Beijing

first: Yuexi

last: Tan

state: Beijing

address: 1 Qinghua Yuan, Haidian Dist.

institute: Tsinghua University

description:
Data are processed without other results.
TAB-seq

data_processing:
Base calling is performed by CASAVA_v1.8.2
Alignment is performed by Bismark v0.7.6
Convert alignment results to information of each base of reference sequence, using SAMTools mpileup v0.1.18 (r982:295)
Calculate modification p-value of each site using R (version 2.14.2) function dbinom(), then assess FDR using Benjamini-Hochberg method
Genome_build: hg19
Supplementary_files_format_and_content: mC/hmC modification level of each site

source_name: Fetal brain prefrontal cortex tissue

extract_protocol:
Qiagen Blood & Cell Culture DNA Kits following the manufacture’s instructions
The DNA sample for MethylC-Seq was the same batch of sheared genomic DNAs with spike-in controls for TAB-Seq without the glucosylation and oxidation preparation. Both DNA samples for TAB-Seq and MethylC-Seq (0.5 ~ 1 μg) were end repaired, A-tailed, and ligated to methylated adaptors using Illumina TruSeq Sample Preparation Kits following the manufacturer’s instructions. Then ligated fragments were bisulfite converted using the the MethylCode kit (Invitrogen). Bisulfite-treated DNA was separated into three reactions for PCR-amplification using PfuTurbo Cx Hotstart DNA polymerase (Agilent Technologies) for 7 cycles, yielding three independent libraries for the same biological sample. Final libraries were purified with 1× AMPure XP beads then sequenced using Illumina Hiseq 2000.

value: Brain prefrontal cortex

value: Fetus (22-week-old)

value: Male


title: SEQC_Kdn_M_006_4


title: Ad_Front.TAB-Seq

description:
Data are processed based on Ad_Front.MethylC-Seq results.
TAB-seq

source_name: Adult brain prefrontal cortex tissue

value: Adult (42-year-old)

value: Female


title: SEQC_Kdn_M_021_1

value: Fisher 344


title: Ad_Front.MethylC-Seq

description: MethylC-seq


title: SEQC_Kdn_M_006_1


title: SEQC_Kdn_M_006_3


title: SEQC_Lng_F_021_1

value: F


title: SEQC_Lng_F_006_4


title: Fe_Front.TAB-Seq (single)

description: TAB-seq


title: SEQC_Kdn_M_006_2


title: SEQC_Kdn_M_002_3


title: SEQC_Kdn_F_104_4


title: SEQC_Kdn_M_002_1


title: SEQC_Kdn_M_002_4


title: SEQC_Kdn_F_104_1


title: SEQC_Kdn_F_021_4


title: SEQC_Kdn_F_104_2


title: SEQC_Kdn_M_002_2


title: SEQC_Kdn_F_021_3


title: SEQC_Kdn_F_021_2


title: SEQC_Kdn_F_021_1


title: SEQC_Kdn_F_006_3


title: SEQC_Kdn_F_006_4


title: SEQC_Kdn_F_006_1


title: SEQC_Kdn_F_002_4


title: SEQC_Kdn_F_002_3


title: pse_st12_M_3

city: Davis

first: Susan

middle: E.

last: Lott

state: CA

address: 2320 Storer Hall

department: Evolution and Ecoloty

institute: University of California, Davis

description:
pse.data.all.autonorm.txt (total RPKM)
pse.allele.spec.txt (allele specific RPKM)

data_processing:
Illumina CASAVA_v1.8.0 software used for base calling
Mapping with Bowtie, Tophat to both D. miranda and D. pseudoobscura genomes
Transcript abundances determined with Cufflinks
total RPKM renormalized to total autosomal read number (autosomes shared in both species)
allele specific counts per gene constructed as described in paper
Genome_build: D. pseudoobscura, Flybase 2.25. D. miranda, NCBI DroMir 1.0
Supplementary_files_format_and_content: RPKM values, .txt files

organism: Drosophila pseudoobscura

source_name: embryo

growth_protocol: Embryos were collected from crosses of 3-7 day old females, dechorionated, imaged using a compound microscope with DIC, and collected into Trizol and ruptured at the desired stage

extract_protocol:
Standard Trizol extraction method, with the exception of using a large amount of reagent (1 mL) relative to the expected amount of extracted total RNA (~150ug), for ease of use
Illumina TruSeq kits and protocols

value: embryo

tag: maternal genotype

value: Flagstaff 14

tag: paternal genotype

tag: illumina index


title: pse_st12_M_2

value: M


title: pse_st12_F_3


title: pse_st12_F_2


title: pse_st10_M_3


title: SEQC_Kdn_F_002_1


title: SEQC_Hrt_M_104_4

source_name: Heart

value: Heart


title: SEQC_Kdn_F_002_2


title: pse_st10_M_2


title: SEQC_Hrt_M_104_3


title: SEQC_Kdn_F_104_3


title: pse_st10_M_1


title: pse_st10_F_3


title: SEQC_Hrt_M_104_1


title: SEQC_Hrt_M_104_2


title: pse_st10_F_1


title: pse_st10_F_2


title: SEQC_Hrt_M_021_4


title: SEQC_Kdn_F_006_2


title: SEQC_Hrt_M_021_3


title: pse_st8to9_M_2


title: SEQC_Hrt_M_021_2


title: pse_st8to9_M_3


title: pse_st12_M_1


title: SEQC_Hrt_M_021_1


title: pse_st8to9_M_1


title: SEQC_Hrt_M_006_4


title: pse_st12_F_1


title: pse_st8to9_F_2


title: pse_st8to9_F_3

tag: notes

value: bad sample


title: SEQC_Hrt_M_006_2


title: SEQC_Hrt_M_006_3


title: pse_st8to9_F_1


title: SEQC_Hrt_M_006_1


title: SEQC_Hrt_M_002_4


title: pse_st7_M_3


title: pse_st7_M_1


title: SEQC_Hrt_M_002_3


title: pse_st7_M_2


title: pse_st7_F_3


title: pse_st7_F_2


title: SEQC_Hrt_M_002_1


title: SEQC_Hrt_F_104_2


title: SEQC_Hrt_F_104_4


title: SEQC_Hrt_M_002_2


title: SEQC_Hrt_F_104_3


title: SEQC_Hrt_F_104_1


title: pse_st7_F_1


title: SEQC_Hrt_F_021_3


title: pse_latest5_M_2


title: SEQC_Hrt_F_021_4


title: pse_latest5_F_3


title: pse_latest5_F_2


title: pse_latest5_M_3


title: pse_latest5_F_1


title: SEQC_Hrt_F_021_1


title: pse_midst5_M_3


title: pse_midst5_M_2


title: SEQC_Hrt_F_006_3


title: pse_midst5_M_1


title: SEQC_Hrt_F_006_4


title: pse_midst5_F_3


title: SEQC_Hrt_F_006_1


title: pse_midst5_F_2


title: pse_midst5_F_1


title: SEQC_Hrt_F_002_3


title: pse_st4_M_3


title: SEQC_Hrt_F_002_2


title: pse_latest5_M_1


title: pse_st4_M_2


title: SEQC_Hrt_F_021_2


title: pse_st4_M_1


title: SEQC_Brn_M_104_3

source_name: Brain

value: Brain


title: pse_st4_F_3


title: pse_st4_F_2


title: pse_st4_F_1


title: SEQC_Brn_M_104_4


title: SEQC_Hrt_F_002_1


title: SEQC_Brn_M_104_2


title: SEQC_Brn_M_104_1


title: pse_st2_5

value: possibly unfertilized


title: pse_st2_6


title: SEQC_Hrt_F_006_2


title: SEQC_Brn_M_021_2


title: pse_st2_3


title: SEQC_Brn_M_021_4


title: SEQC_Brn_M_021_3


title: SEQC_Hrt_F_002_4


title: pse_st2_4


title: pse_st2_2


title: SEQC_Brn_M_021_1


title: SEQC_Brn_M_002_4


title: SEQC_Brn_M_006_1


title: SEQC_Brn_M_006_4


title: SEQC_Brn_M_006_2


title: pse_st2_1


title: mir_st2_2

description:
mir.data.all.autonorm.txt (total RPKM)
mir.allele.spec.txt (allele specific RPKM)
mir.neoY.allele.spec.txt (allele specific neo-Y)

organism: Drosophila miranda


title: SEQC_Brn_M_002_2


title: mir_st2_3


title: mir_st12_M_3


title: SEQC_Brn_F_104_2


title: SEQC_Brn_M_002_1


title: mir_st2_1


title: SEQC_Brn_F_104_1


title: SEQC_Brn_F_021_4


title: SEQC_Brn_F_021_2


title: SEQC_Brn_F_104_3


title: mir_st12_M_1


title: SEQC_Brn_F_021_3


title: mir_st12_F_1


title: mir_st12_M_2


title: SEQC_Brn_F_006_4


title: SEQC_Brn_F_006_3


title: mir_st10_M_3


title: SEQC_Brn_M_006_3


title: mir_st12_F_2


title: mir_st12_F_3


title: SEQC_Brn_F_021_1


title: SEQC_Brn_F_006_1


title: SEQC_Brn_F_006_2


title: mir_st10_F_3


title: SEQC_Brn_M_002_3


title: mir_st10_M_1


title: mir_st10_M_2


title: SEQC_Brn_F_002_4


title: SEQC_Brn_F_104_4


title: SEQC_Brn_F_002_3


title: SEQC_Brn_F_002_2


title: SEQC_Adr_M_104_4

source_name: Adrenal

value: Adrenal


title: mir_st8to9_M_3


title: SEQC_Brn_F_002_1


title: mir_st8to9_M_2


title: mir_st8to9_M_1


title: mir_st8to9_F_2


title: mir_st8to9_F_1


title: SEQC_Adr_M_104_1


title: SEQC_Adr_M_021_4


title: DNA input3

description: mixed 6 input reps

value: nucleus accumbens

value: Repeated saline I.P. injection for 1w as control


title: mir_st7_M_3


title: SEQC_Adr_M_021_3


title: mir_st7_M_2


title: SEQC_Adr_M_021_2


title: mir_st10_F_1


title: SEQC_Adr_M_104_3


title: SEQC_Adr_M_021_1


title: SEQC_Adr_M_006_4


title: RNA Pol II ChIP-seq Sal Rep3

value: RNA Pol II

value: Abcam Cat#ab5408


title: mir_st7_M_1


title: SEQC_Adr_M_006_3


title: SEQC_Adr_M_104_2


title: RNA Pol II ChIP-seq Sal Rep2


title: mir_st10_F_2

value: intersex

value: is X/X neo-X/neo-Y


title: RNA Pol II ChIP-seq Sal Rep1


title: DNA input2


title: SEQC_Adr_M_006_2


title: mir_st7_F_2


title: mir_st7_F_1


title: SEQC_Adr_M_006_1


title: RNA Pol II ChIP-seq Coc Rep3

value: Repeated cocaine I.P. injection for 1w at 20mg/kg


title: mir_st8to9_F_3


title: RNA Pol II ChIP-seq Coc Rep2


title: mir_latest5_M_3


title: SEQC_Adr_M_002_4

value: Fisher 344


title: mir_latest5_M_1


title: SEQC_Adr_M_002_3


title: SEQC_Adr_M_002_2


title: RNA Pol II ChIP-seq Coc Rep1


title: H3K9me2 ChIP-seq Sal Rep3

value: Abcam Cat#ab1220


title: mir_latest5_M_2

value: embryo


title: H3K9me3 ChIP-seq Coc Rep3

description:
Complement GSE24850
diff.k9m3.res.annotated

value: Millipore #CS200604


title: mir_latest5_F_3

value: F


title: SEQC_Adr_M_002_1

value: M


title: mir_st7_F_3

value: unusually low heterozygosity on Chr. 4


title: H3K9me2 ChIP-seq Sal Rep2


title: SEQC_Adr_F_104_4


title: mir_latest5_F_1


title: H3K9me2 ChIP-seq Coc Rep3


title: SEQC_Adr_F_104_3


title: mir_latest5_F_2


title: H3K9me2 ChIP-seq Sal Rep1


title: mir_midst5_M_3


title: SEQC_Adr_F_104_2


title: mir_midst5_M_2


title: SEQC_Adr_F_104_1


title: H3K9me2 ChIP-seq Coc Rep2


title: H3K9me2 ChIP-seq Coc Rep1


title: mir_midst5_M_1


title: mir_midst5_F_3


title: SEQC_Adr_F_021_3


title: mir_st4_M_3


title: SEQC_Adr_F_021_2


title: mir_midst5_F_1


title: SEQC_Adr_F_006_3


title: SEQC_Adr_F_021_1


title: SEQC_Adr_F_006_2


title: mir_st4_F_3


title: SEQC_Adr_F_006_1


title: mir_st4_F_2


title: miR-17-5p

city: Herston

first: Nicole

last: Cloonan

state: Queensland

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Basecalling performed with SOLiD Analysis Tools (SAT) v3.5.
Reads were mapped to the human genome (GRCh37) using the X-MATE pipeline with the parameters: max_multimatch=2; recursive_maps =50.5.0,45.5.0,40.5.0,35.3.0,30.3.0,25.1.1; run_rescue=false; map_ISAS=false;
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Positive and negative strand bedGraph files were generated as a part of the X-MATE output; Scores represent the number of times a nucleotide was seen in the aligned data.

source_name: HEK293T transfected with miR-17-5p duplex

growth_protocol: Cells were grown in DMEM and 5% CO2 at 37oC; passaged routinely at 80% confluencey by splitting 1 in 5.

extract_protocol:
Cells were lysed in hypotonic lysis buffer (10mM KCl, 1.5mM MgCl2,10mM Tris-Cl pH 7.5, 5mM DTT, 0.5% NP-40,60U/ML SUPERase•In (Ambion) and 1X Complete Mini protease inhibitor (Roche)). Cell debris was cleared by centrifugation (≥10,000g at 4º C for 2 minutes). The supernatant was transferred to a clean tube, and NaCl was added to a final concentration of 1M. 25μL of myOne C1 Dynabeads (Invitrogen) were pre-blocked with 1μg/μL BSA and 1μg/uL yeast tRNA (Invitrogen), and incubated with the supernatant for 30 minutes at room temperature. Beads were then washed with hypotonic lysis buffer and 1M NaCl before RNA extraction using an RNeasy Kit (Qiagen) according to manufacturer's instructions.
Total RNA was depleted of rRNA (Ribominus Kit, Invitrogen) to select mRNA. The enriched mRNA was fragmented by digestion with RNaseIII (Ambion), and purified on a Microcon YM30 column (Microcon). Fragmented mRNA was used to generate libraries as specified in the Whole Transcriptome Analysis Kit (Ambion) protocol for mRNA.

treatment_protocol: 200 pmoles of synthetic biotin-labelled miR-17-5p duplex were transfected into 4 x 10^6 HEK293T cells using HiPerFect Transfection Reagent (Qiagen). Cells were incubated for 24 hours.

tag: cell line

tag: duplex


title: H3K36me3 ChIP-seq Sal Rep2

tag: tissue

tag: strain

value: Abcam Cat#ab9050


title: SEQC_Adr_F_002_3


title: SEQC_Adr_F_002_4


title: H3K36me3 ChIP-seq Coc Rep3


title: mir_st4_F_1


title: H3K36me3 ChIP-seq Sal Rep1


title: mir_st2_6


title: SEQC_Adr_F_021_4


title: SEQC_Adr_F_002_2


title: H3K36me3 ChIP-seq Coc Rep2


title: mir_midst5_F_2


title: SEQC_Adr_F_002_1


title: D92_WM_Stem

status: Public on Feb 13 2014

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

description: small RNA

data_processing:
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and removing it from the read.
After the seqeunces are trimmed, sequences are counted with excluding any sequences shorter than 16bp. Counting is the process of compressing a file of reads by listing reads uniquely together with a number representing how many times it occurred in the file.
Supplementary_files_format_and_content: Txt files include counts of reads.

organism: Glycine max

source_name: Stem

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated days after flowering or mg fresh weight. Immature cotyledons were dissected by hand from seed coats.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and ethanol precipitation. Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
smRNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed by the Keck Center (University of Illinois) using Illumina Genome Analyzer II and Illumina HiSeq 2000.

tag: cultivar

value: Williams, PI548631

tag: Stage

value: 10 Day Seedling

tag: preservation

value: lyophilized

tag: purification


title: mir_st2_5

tag: Sex


title: mir_st2_4


title: H3K36me3 ChIP-seq Coc Rep1

value: nucleus accumbens

tag: chip antibody


title: D34_WM_ImCot_100_300mg

description: small RNA

source_name: Immature Cotyledon

value: 100-300mg fresh seed weight


title: mir_st4_M_2


title: H3K36me3 ChIP-seq Sal Rep3

tag: treatment

value: Repeated saline I.P. injection for 1w as control


title: SEQC_Adr_F_006_4

value: Adrenal

tag: developmental stage (week)


title: mir_st4_M_1


title: D112_WM_ImCot_5_6mg_BR2

description: small RNA

value: 5-6mg fresh seed weight


title: D93_WM_Uni

description: small RNA

source_name: Unifoliate


title: D101_75_100SC_BR2

description: small RNA

data_processing:
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and removing it from the read.
After the seqeunces are trimmed, sequences are counted with excluding any sequences shorter than 16bp. Counting is the process of compressing a file of reads by listing reads uniquely together with a number representing how many times it occurred in the file.
Supplementary_files_format_and_content: Fasta files include counts of reads.

source_name: seed coat

growth_protocol: Plants were grown in optimal greenhouse conditions. Tissues were harvested at stated days after flowering or mg fresh weight. Whole seeds were divided by hand into cotyledons and seed coats.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and a ethanol precipitation. Sequencing was performed by the Keck Center (University of Illinois) using an Illumina Genome Analyzer II or an Illumina HiSeq 2000.
smRNA libraries were prepared for sequencing using standard Illumina protocols. Sequencing was performed by the Keck Center (University of Illinois) using Illumina Genome Analyzer II and Illumina HiSeq 2000.

tag: developmental stage

value: 75-100mg fresh weight

value: seed coat


title: D100_50_75SC_BR2

description: small RNA

value: 50-75mg fresh weight


title: D103_200_300SC_BR2

description: small RNA

value: 200-300mg fresh weight


title: D54_200_300SC_BR1

description: small RNA


title: D105_300_400YSC_BR2

description: small RNA

value: 300-400mg fresh weight


title: D99_25_50SC_BR1

description: small RNA

value: 25-50mg fresh weight


title: D96_22_24DAF_BR2

description: small RNA

source_name: whole seed

value: 22-24 days after flowering

value: fresh frozen

value: whole seed


title: D97_5_6SC_BR2

description: small RNA

value: Williams, PI548631

value: 5-6mg fresh weight


title: D95_12_14DAF_BR2

description: small RNA

value: 12-14 days after flowering


title: D51_12_14DAF_BR1

description: small RNA


title: D52_22_24DAF_BR1

description: small RNA


title: D53_4DAF_BR1

description: small RNA

value: 4 days after flowering


title: M2_72h_rep3_miRNAseq

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

data_processing:
Basecalls were performed using CASAVA software version 1.8
Sequencing reads were retrieved as FASTQ files and then demultiplexed
Adapter sequences were trimmed from each read using Flicker 3.0 (Illumina)
Trimmed reads were mapped to hairpin and mature human miRNAs deposited in miRBase version 19 using the short read aligner Bowtie 0.12.9 (Langmead et al., 2009) with no mismatches allowed
The number of reads mapping to a specific miRNA sequence were counted within Partek Genomics Suite version 6.6 (PGS)
The dataset was normalized (NORM) by using the statistical software R package DESeq (Anders and Huber, 2010) and miRNAs having less than one normalized read count in all unpolarized macrophage (M0) samples were excluded
The read counts were transformed (TRANSF) into log2 counts per million (cpm) and were divided by the corresponding library size (in millions) by using the R package limma (Smyth, 2005)
The R package sva (Johnson et al., 2007) was used to perform a batch removal (BR) for the random factors date and donor. Then miRNAs having less than one transformed read count in all samples of the same condition were excluded
Differentially expressed miRNAs between macrophages polarized with IFNγ (M1), IL-4 (M2) or with the combination of TNFα, PGE2 and P3C (TPP) were determined against M0 by using the R package limma (Smyth, 2005) with a p-value of 0.05 as well as an absolute fold change of 2 as cutoffs
Finally, for each condition a set of uniquely differentially expressed miRNAs was determined, which was then sorted by the transformed expression values.
Genome_build: miRBase version 19

source_name: peripheral blood

growth_protocol: For differentiation primary human monocytes into M0 macrophages, cells were cultivated for 3 days in RPMI1640 medium + 10%FCS + Pen/Strep + 500IU/ml rhGM-CSF

extract_protocol:
5x106 -2x107 MΦ were harvested and total RNA including small RNAs was isolated.
Small RNA libraries were generated from 1 μg total RNA with the TruSeq Small RNA Sample Preparation Kit (Illumina). After successful ligation of 3’ and 5’ adapters to RNA molecules, RNA was reverse-transcribed using SuperScript II reverse transcriptase (Invitrogen). cDNA was amplified by 11 PCR cycles with high-fidelity Phusion Polymerase (Finnzymes). cDNA with the size of miRNAs plus ligated adapters was purified on a pre-cast 6% Tris/Borate/EDTA polyacrylamide gel electrophoresis gel (Invitrogen).

treatment_protocol: To further polarize macrophages into different subtypes the following stimuli were used: M1 (3days 500IU/ml rhGM-CSF + 200IU/ml rhIFNy); M2 (3days 500IU/ml rhGM-CSF + 1000IU/ml rhIL-4); TPP (3days 500IU/ml rhGM-CSF + rhTNFα (800 IU/ml), Pam3CSK4 (P3C, 1 µg/ml), prostaglandine E2 (PGE2, 1 µg/ml).

tag: cell type

value: monocyte derived macrophages

tag: initial differentiation

value: GM-CSF

tag: activation stimuli

tag: time

tag: donor

value: Donor 12

tag: date

value: Date 5


title: TPP_72h_rep3_miRNAseq


title: D94_4DAF_BR2

description: small RNA

tag: tissue


title: M1_72h_rep3_miRNAseq

value: IFNg


title: TPP_72h_rep2_miRNAseq

value: Donor 10

value: Date 4


title: M0_0h_rep11_miRNAseq


title: D91_WM_Shtp

description: small RNA

source_name: Shoot tip

value: 10 Day Seedling

value: lyophilized


title: D55_WM_ImCot_5_6mg_BR1

description: small RNA

value: 5-6mg fresh seed weight


title: M2_72h_rep1_miRNAseq

value: Donor 11


title: M2_72h_rep2_miRNAseq


title: M1_72h_rep2_miRNAseq


title: M1_72h_rep1_miRNAseq


title: M0_0h_rep10_miRNAseq


title: M0_0h_rep9_miRNAseq

value: Donor 9

value: Date 3


title: D98_10_25SC_BR1

description: small RNA

value: Williams, PI548631

value: 10-25mg fresh weight

value: seed coat


title: D56_5_6SC_BR1

description: small RNA

value: 5-6mg fresh weight


title: M0_0h_rep7_miRNAseq

value: monocyte derived macrophages

value: Donor 7


title: M0_0h_rep6_miRNAseq

value: GM-CSF

value: Donor 6

value: Date 2


title: M0_0h_rep5_miRNAseq

value: Donor 5


title: M0_0h_rep3_miRNAseq

value: Donor 3

value: Date 1


title: M0_0h_rep2_miRNAseq

value: Donor 2


title: M0_0h_rep4_miRNAseq

value: Donor 4


title: M0_0h_rep1_miRNAseq

value: Donor 1


title: TPP_72h_rep1_miRNAseq

value: Donor 11

value: Date 4


title: H3K4me3_M0_Macro_ChIPSeq

description:
raw file: B06PDABXX_human_CAGATC_M0_H3K4me3_SR.fastq.gz
raw file: 6300DAAXX_human_CAGATC_M0_H3K4me3_SR.fastq.gz
raw file: C00G9ABXX_human_CAGATC_M0_H3K4me3_SR.fastq.gz

data_processing:
Basecalls performed using CASAVA software version 1.7 (for histone datasets) and 1.8 (for PU.1 datasets)
ChIP-seq reads were aligned to the NCBI Build 36 (hg18) genome assembly using ELAND (Illumina Pipeline) at its default setting and were exported in .bam file format
Genome_build: NCBI36

extract_protocol:
Fixed or unfixed chromatin out of primary human macrophage lysates was sheared and histone-DNA or TF-DNA complexes isolated with antibody.
Multiplex DNA libraries of both H3K4me3 as well as PU.1 bound DNA were generated using Illumina’s ChIP-Seq Sample Preparation Kit (Illumina; # IP-102-1001) and the Multiplexing Sample Preparation Oligonucleotide Kit (Illumina; # PE-400-1001) using approximately 10 ng DNA following the manufacturer’s instructions. Briefly, purified DNA ends were repaired using PNK and Klenow enzyme, followed by treatment with Klenow exo minus polymerase to generate a protruding 3′ A base used for adaptor ligation. Next, size selection of libraries was performed as follows: DNA libraries were agarose gel purified, DNA fragments with approximately 220 bp size excised and eluted using QIAquick Gel Extraction kit (Qiagen). After subsequent adapter ligation to the repaired ends, an amplification step was performed for 5 cycles with PCR primers 1.1 and 2.1 (Illumina; # IP-102-1001). During a second 13 cycles amplification step multiplex PCR primers were added to the DNA libraries to construct multiplex sequencing libraries. For PU.1 DNA libraries multiplex PCR primers were added directly after adapter ligation to the amplification mix and 18 cycles of amplification were performed. After amplification steps DNA was purified.

treatment_protocol: To further polarize macrophages into different subtypes the following stimuli were used: M1 (3days 500IU/ml rhGM-CSF + 200IU/ml rhIFNy); M2 (3days 500IU/ml rhGM-CSF + 1000IU/ml rhIL-4); TPP (3days 500IU/ml rhGM-CSF + Pam3CSK4 (P3C, 1 µg/ml) + prostaglandine E2 (PGE2, 1 µg/ml) + TNFa (800 IU/ml))


title: H3K4me3_M2_Macro_ChIPSeq

description:
raw file: B06PDABXX_human_GATCAG_M2_H3K4me3_SR.fastq.gz
raw file: 6300DAAXX_human_GATCAG_M2_H3K4me3_SR.fastq.gz
raw file: C00G9ABXX_human_GATCAG_M2_H3K4me3_SR.fastq.gz


title: H3K4me3_M1_Macro_ChIPSeq

description:
raw file: B06PDABXX_human_ACTTGA_M1_H3K4me3_SR.fastq.gz
raw file: 6300DAAXX_human_ACTTGA_M1_H3K4me3_SR.fastq.gz
raw file: C00G9ABXX_human_ACTTGA_M1_H3K4me3_SR.fastq.gz

value: IFNg, 72h


title: H3K4me3_TPP_Macro_ChIPSeq

description:
raw file: B06PDABXX_human_TAGCTT_TPP_H3K4me3_SR.fastq.gz
raw file: 6300DAAXX_human_TAGCTT_TPP_H3K4me3_SR.fastq.gz
raw file: C00G9ABXX_human_TAGCTT_TPP_H3K4me3_SR.fastq.gz

value: TNFa+PGE2+P3C, 72h


title: PU.1_M1_Macro_ChIPSeq

description: raw file: D118TACXX_human_CGATGT_M1_PU1_SR_001.fastq.gz

value: anti PU.1 (Santa Cruz Biotechnology, sc-352X, lot D2011)


title: Control_55

city: Cantanhede

first: Jacek

middle: Dariusz

last: Marzec

address: Biocant Park

country: Portugal

institute: CoLAB AccelBio

description: PB from healthy donor

data_processing:
GS Run Processor application provided with 454 Sequencing Software v2.6 was used for basecalling.
Barcoded sequence reads were trimmed for barcode-adaptor sequences and assigned to appriopriate sample.
Methylation status of each CpG site was determined by aligning reads to the germline sequence using character-based user interface version of QUMA program (quantification tool for methylation analysis; http://quma.cdb.riken.jp). The percent identity score was normalized to the reads length. After alignment, sequence reads were filtered according to the following quality control: for the sequencing quality reads with < 90% identity score or > 10 mismatches were removed. For bisulfite conversion control, a lower limit of conversion efficiency was set to 95% and no more than 5 unconverted cytosines in CpH (non-CpG) sites were allowed. The percentage of methylation at each CpG site was calculated based on the number of sequences containing methylated CpGs versus the total number of sequences analysed.
Genome_build: hg19
Supplementary_files_format_and_content: Wiggle Track Format (WIG) files: display scores indicating methylation level of covered CpG sites
Supplementary_files_format_and_content: Matrix table containing methylation status for each CpG site (0 - unmethylated; 100 - fully menthylated; NA - not determined). First and second columns indeicate chromosome and genomic position of single CpG site. Subsequent columns contain methylation status for indivifual samples

source_name: Peripheral Blood

extract_protocol: Genomic DNA was bisulfite converted using EZ DNA Methylation kit. Libraries were prepared according to Roche 454 instructions for amplicon sequencing. Briefly, bisulfite converted DNA was amplified with specific primers containing the adapters for the Roche 454 sequencer, purified with AMPure beads, quantified with Quant-iT Picogreen dsDNA assay kit and loaded into 16x platforms. Libraries were sequenced on the Roche 454 sequencer following the manifacture's protocols

value: Peripheral Blood

tag: cytogenetic group

value: PB from healthy donor


title: PU.1_M2_Macro_ChIPSeq

description: raw file: D118TACXX_human_TTAGGC_M2_PU1_SR_001.fastq.gz

value: monocyte derived macrophages


title: Control_52

description: Bone Marrow Mono Cells cryoamp, Lonza

source_name: Bone Marrow Mononuclear Cells

value: Bone Marrow Mononuclear Cells

value: BM-MNC from healthy donor


title: IgG_M1_Macro_ChIPSeq

description:
raw file: D118TACXX_human_GCCAAT_M1_IgG_SR_001.fastq
raw file: D118TACXX_human_GCCAAT_M1_IgG_SR_002.fastq

value: GM-CSF

value: Rabbit IgG (Millipore, 12-370)


title: IgG_M2_Macro_ChIPSeq

description: raw file: D118TACXX_human_CAGATC_M2_IgG_SR_001.fastq.gz


title: Control_57

description: PB from healthy donor


title: Control_46

description: BM from healthy donor

source_name: Bone Marrow

value: Bone Marrow

value: BM from healthy donor


title: Control_54

description: PB from healthy donor


title: Control_53

description: Bone Marrow Mono Cells cryoamp, Lonza


title: Control_51

description: Non infiltrated BM from Non-hodgkin's lymphoma

value: BM from Non-hodgkin's lymphoma


title: Control_45

description: BM from healthy donor


title: Control_50


title: M0_0h_rep8_miRNAseq

value: Donor 8

value: Date 3


title: AML_38

description: AML with t(8;21)

value: t(8;21) diagnosis


title: APL_33

description: AML with t(15;17)

source_name: Leukapheresis

value: Leukapheresis

value: t(15;17) diagnosis


title: AML_40

description: AML with inv(16)

value: inv(16) diagnosis


title: AML_41

description: AML with inv(16)


title: Control_56

description: PB from healthy donor


title: AMPL_CR_32

description: complete remission of AML with t(15;17)

value: t(15;17) complete remission


title: APL_35

description: AML with t(15;17)

value: Peripheral Blood


title: AML_42

description: AML with inv(16)


title: APL_29

description: AML with t(15;17)


title: APL_31

description: AML with t(15;17)


title: APL_CR_28

description: complete remission of AML with t(15;17)


title: APL_CR_26/32

description: complete remission of AML with t(15;17)

source_name: Bone Marrow/Bone Marrow

value: Bone Marrow/Bone Marrow


title: APL_CR_28/32

description: complete remission of AML with t(15;17)


title: AML_23

description: AML with Normal Karyotype (NK)

value: Normal Karyotype (NK) diagnosis


title: AML_CR_22

description: complete remission of AML with NK

value: Normal Karyotype (NK) complete remission


title: AML_CR_24

description: complete remission of AML with NK


title: APL_27

description: AML with t(15;17)


title: AML_19

description: AML with Normal Karyotype (NK)


title: AML_21

description: AML with Normal Karyotype (NK)


title: AML_17

description: AML with Normal Karyotype (NK)


title: APL_15

description: AML with t(15;17)


title: APL_13

description: AML with t(15;17)


title: AML_CR_18/20

description: complete remission of AML with NK


title: APL_CR_16

description: complete remission of AML with t(15;17)


title: APL_11

description: AML with t(15;17)


title: APL_CR_10/16

description: complete remission of AML with t(15;17)

source_name: Bone Marrow/Peripheral Blood

value: Bone Marrow/Peripheral Blood


title: APL_CR_10

description: complete remission of AML with t(15;17)


title: AML_37

description: AML with t(8;21)


title: AML_39

description: AML with t(8;21)


title: APL_9

description: AML with t(15;17)


title: APL_CR_8

description: complete remission of AML with t(15;17)


title: APL_5

description: AML with t(15;17)


title: APL_3

description: AML with t(15;17)


title: APL_1

description: AML with t(15;17)


title: APL_7

description: AML with t(15;17)


title: APL_CR_6/12/14

description: complete remission of AML with t(15;17)

source_name: Bone Marrow/Bone Marrow/Bone Marrow

value: Bone Marrow/Bone Marrow/Bone Marrow


title: APL_CR_2/4/8

description: complete remission of AML with t(15;17)

source_name: Peripheral Blood/Peripheral Blood/Bone Marrow


title: APL_25

description: AML with t(15;17)


title: MF3_DNaseSeq

city: Durham

first: Yoichiro

last: Shibata

state: NC

address: 101 Science Dr

department: Inst. of Genome Sciences and Policy

institute: Duke University

data_processing:
Illumina CASAVA 1.3 software used for single-end basecalling.
Sequenced reads were trimmed to the first 20bp to remove adaptor sequence using custom scripts, and masked for low-complexity or low-quality sequence, then mapped to the samples native whole genome (hg19 for human, panTro2 for chimpanzee and rheMac2 for macaque) using BWA version 0.6.1-r104 with default indexing (index -a bwtsw) and aln parameters (aln -t 8) to create alignment SAI files.
SAM files were created from the SAI files using bwa samse with default parameters, then filtered for alignments with greater than 4 mismatches using custom scripts.
The SAM files (after filtering for mismatches >4) were converted to BAM format using "samtools view", then sorted via chromosome using "samtools sort", then converted to BED format using "bedtools bamtobed".
Sharp sequence pileups introduced by PCR amplification artifacts or potential misalignments were filtered out to reflect a maximum acceptable read count for a peaks region based on a Poisson distribution.
Each 20-mer alignment of chimpanzee and macaque species were converted to a human genome coordinate using LiftOver (Hinrichs AS, et al. 2006. Nucleic Acids Res 34: D590–598) using a minMatch setting of 0.80.
Custom scripts were used to pull out the exact bp positions that were cut by DNaseI (ExactCuts.bigWig in hg19 space for all species).
Genome_build: hg19, panTro2, rheMac2
Supplementary_files_format_and_content: bigWig format (hg19)

organism: Macaca mulatta

source_name: Skin fibroblast cells

growth_protocol: We obtained two cell types from Coriell Cell Repositories for this study: skin fibroblast cells and lymphoblastoid cell lines (LCLs). Primary skin fibroblast cells from three human, three chimpanzee, and three macaque individuals. LCLs, which are B cells immortalized with Epstein-Barr Virus, were obtained from the same three human and three chimpanzee individuals that fibroblasts were isolated from. EBV does not reliably transfect macaque lymphocyte cells, so matched macaque LCLs cells were not available for this study. Importantly, other recent genome-wide studies that used macaque LCLs were of B-Lymphocyte cells transformed with rhesus herpes papio virus, a close relative of human EBV. Cells from all species were grown in standard growth media. Fibroblast growth media consisted of Gibco's MEM (10370-021), L-Glutamine (25030-081), Pen/Strep (15140-122), and 10% FBS (Hyclone SH30070). LCLs growth media consisted of Gibco's RPMI (21870) media with L-Glutamine, Pen/Strep, and 15% FBS. We harvested ~35 million cells for DNase analysis.

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

value: Primary Dermal Fibroblast

tag: biopsy site

value: skin, upper arm

tag: coriell catalog #


title: input DNA (Kd)

city: New Haven

first: Andrew

middle: Zhuo

last: Xiao

state: CT

address: 10 Amistad St

department: Genetics

institute: Yale Stem Cell Center

data_processing:
Basecalls performed using CASAVA from Illumina
ChIP-seq and Input DNA reads were aligned to the mm9 genome assembly using BOWTIE version 0.12.5 with the following configurations: -v 1 -m 1 --best -S
Aligned unique genomic location reads (sam file) transfer to bed file
Peaks (or blocks) were called (vs. Input DNA), or compared (Knockdown vs. wildtype H3K9Me3 ChIP) using R-seg following -mode 2 (or -mode 3) and default setting, except that bin size is set to 5Kb.
The  differentially enriched/devoid domains whose size are more than 100Kb or less than 10Kb are filtered out.
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraph files were generated from R-seg (mode 2 or mode 3).   The "scores" mean  HMM domain scores; The input DNA samples files  only contain the Bowtie alighment results.

source_name: Rif1 knockdown ESCs

growth_protocol: ESCs were growing on feeder-free plates following the standard  mouse ESC culture condition.

extract_protocol:
Cells were fixed and chromatin was extracted after sonication for ChIP experiments using H3K9me3 antibody. Genomic DNA was used as input DNA.
Libraries were prepared according to Illumina's standard protocol.

value: mouse ESCs

tag: genotype

value: Rif1 knowckdown


title: MF1_DNaseSeq


title: MF1_DGE-seq

data_processing:
library strategy: DGE-seq (Digital Gene Expression)
Illumina CASAVA 1.3 software used for single-end basecalling.
Sequenced reads were trimmed to the first 16bp to remove adaptor sequence using custom scripts, then 4 bp sequences accounting for the NlaIII cut site (CATG) were added to the 3'-end to construct a 20 mer final sequence length. Next, reads were masked for low-complexity or low-quality sequence, then mapped to the samples native whole genome (hg19 for human, panTro2 for chimpanzee and rheMac2 for macaque) using BWA version 0.6.1-r104 with default indexing (index -a bwtsw) and aln parameters (aln -t 8) to create alignment SAI files.
SAM files were created from the SAI files using bwa samse with default parameters, then filtered for alignments with greater than 4 mismatches using custom scripts.
The SAM files (after filtering for mismatches >4) were converted to BAM format using "samtools view", then sorted via chromosome using "samtools sort", then converted to BED format using "bedtools bamtobed".
Using custom scripts, we compared the DGE-seq sequence counts that aligned to exonic regions within each species' native sequence alignment.
Genome_build: hg19, panTro2, rheMac2
Supplementary_files_format_and_content: Tab delimited txt file, comprised of a matrix of 16 columns by 19233 rows.  First column is the gene name, followed by 15 columns of sequence read counts that fell within an exon of each individual gene.  There are 3 biological replicates of human fibroblast (hf), chimpanzee fibroblast (cf), macaque fibroblast (qf), human LCLs (hl), and chimpanzee LCLs (cl), ordered respectively from left to right.

growth_protocol: We obtained two cell types from Coriell for this study: skin fibroblast cells and lymphoblastoid cell lines (LCLs). Primary skin fibroblast cells from three human, three chimpanzee, and three macaque individuals. LCLs, which are B cells immortalized with Epstein-Barr Virus, were obtained from the same three human and three chimpanzee individuals that fibroblasts were isolated from. EBV does not reliably transfect macaque lymphocyte cells, so matched macaque LCLs cells were not available for this study. Importantly, other recent genome-wide studies that used macaque LCLs were of B-Lymphocyte cells transformed with rhesus herpes papio virus, a close relative of human EBV. Cells from all species were grown in standard growth media. Fibroblast growth media consisted of Gibco's MEM (10370-021), L-Glutamine (25030-081), Pen/Strep (15140-122), and 10% FBS (Hyclone SH30070). LCLs growth media consisted of Gibco's RPMI (21870) media with L-Glutamine, Pen/Strep, and 15% FBS. We harvested ~35 million cells for DNase assays and 5 million for RNA DGE-seq expression analysis.

extract_protocol:
Standard Trizol extraction protocol followed by Qiagen's DNase treatment and column purification protocol.
Illumina's DGE library protocol.


title: input DNA (Ctrl)

source_name: Control ESCs

value: wild type


title: MF2_DGE-seq


title: MF3_DGE-seq


title: H3K9me3_ChIPSeq (Ctrl)

value: Abcam ab8898


title: H3K9me3_ChIPSeq (Kd)


title: iPSC_A

city: Tokyo

first: Yasuhiro

last: Yamada

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

department: Department of Molecular Pathology

country: Japan

institute: University of Tokyo

description: The mice are basically F1 genetic background between 129 and C57BL/6. However, tumor samples may contain some ICR genome as well because they were harvested from chimeric mice.

data_processing:
Removed low quality reads by using FastX toolkit
Trimed terminus of reads by using NGSQCToolkit
Mapping of the reads was perfomed by using Bismark and Bowtie2
Methylation call was performed by using bismark methylation extractor
RRBS analysis provides us DNA methylation data with "a single base" resolution, so BEDGRAPH start and end coordinates are identical.
Genome_build: mm9
Supplementary_files_format_and_content: bedGraph columns: <chromosome> <start position> <end position> <methylation percentage> <count methylated> <count unmethylated>

source_name: iPS cells

extract_protocol:
PureLink Genomic DNA mini kit (invitrogen)
gDNA was digested by MspI. After purification, libraries were constructed by TruSeq DNA sample prep kit. Bisulfite treatment was perfomed by EZ DNA methylation-GOLD kit (ZYMO) after the adapter ligation.

tag: strain

value: iPS


title: KT_E

source_name: kidney tumor

value: kidney tumor


title: iPSC_B


title: KT_D


title: KT_C


title: KT_B


title: KT_A


title: NK_C

source_name: kidney

value: normal kidney


title: NK_B


title: NK_A


title: ESC_B

source_name: ES cells

value: ES


title: D19_WM_Root

description: small RNA

source_name: Root

tag: cultivar

value: Williams, PI548631

tag: Stage

value: 10 Day Seedling

tag: preservation

value: lyophilized

tag: purification


title: MF2_DNaseSeq


title: D18_WM_Gcot

description: small RNA

source_name: Germinated Cotyledon


title: D28_300_400YSC_BR1

description: small RNA

source_name: seed coat

tag: developmental stage

value: 300-400mg fresh weight

value: seed coat


title: D33_75_100SC_BR1

description: small RNA

value: 75-100mg fresh weight


title: Runx2_day9_ChIP-Seq

city: Burlington

first: Jonathan

middle: AR

last: Gordon

state: VT

address: 89 Beaumont Ave Given E209

department: Biochemistry

institute: University of Vermont

data_processing:
Basecalls performed using CASAVA version 1.6
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie (version 0.12.8) with seed length of 28 base, allowing upto 2 mismatches in the seed.
Read densities and regions of statistically significant enrichment (“peaks”) were determined using MACS (Model-Based Analysis of ChIP-Seq, version 1.4.1) [2] using default settings. Peaks of ChIP-seq enrichment with p < 10-10, relative to input, were considered significant and included in subsequent analyses.
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using MACS (version 1.4.1); Scores represent reads per 10 million reads.

source_name: matrix-depositing MC3T3-E1 subclone 4 cells at day 9

growth_protocol: The calvaria-derived preosteoblast cell line MC3T3-E1 (Subclone 4) was obtained from ATCC and maintained in ascorbic acid-free alpha-MEM (Hyclone) supplemented with 10% fetal bovine serum (FBS; Hyclone), 2 mM L-glutamine, 100 U/ml of penicillin and 100 µg/ml streptomycin (Pen/Strep, Invitrogen). To induce osteogenic differentiation, complete alpha-MEM was supplemented with 280 μM ascorbic acid and 10 mM beta-glycerophosphate (Sigma Aldrich). Cells were maintained at 37C in a humidified 5% CO2 environment and media replaced every 2-3 days for the duration of all experiments.

extract_protocol:
Lysates were obtained from sonicated nuclei and Runx2-DNA complexes were isolated with Runx2 antibody (M70).
Libraries of purified DNA were generated using Illumina SR adapters (Illumina) following manufacturer’s manual, and were selected for the inserted fragments of 200 ± 50 bp, and sequenced 36 bases on an Illumina Genome Analyzer II.

tag: cell type

value: matrix-depositing osteoblast

tag: passages

tag: chip antibody

value: Runx2 antibody (M70, Santa Cruz Biotechnologies, Inc.)


title: Input DNA

source_name: matrix-depositing MC3T3-E1 subclone 4 cells


title: HL3_DNaseSeq

source_name: Lymphoblastoid cell line

value: Lymphoblastoid

value: blood, peripheral vein


title: HF2_DNaseSeq

value: Primary Dermal Fibroblast

value: skin, unspecified


title: Runx2_day28_ChIP-Seq

source_name: mineralizing MC3T3-E1 subclone 4 cells at day 28

value: mineralizing osteoblast


title: HL1_DNaseSeq


title: HF3_DNaseSeq

value: skin, upper arm


title: HF2_DGE-seq


title: HF1_DNaseSeq


title: HL2_DGE-seq


title: HF3_DGE-seq


title: HL1_DGE-seq


title: HF1_DGE-seq


title: AML 18

description: monoclonal antibody to precipitate 5 methyl cytosine

data_processing:
Illumina Casava1.4 software used for basecalling.
Alignment: Sequence reads were obtained and mapped to the human genome (build 36, March 2006) using the 'Bowtie' (http://bowtie-bio.sourceforge.net/index.shtml) software with parameters  '-n 2 -l 28 -e 70 -I 0 -X 250 -a' for pair-end alignment and '-n 2 -l 28 -e 70' for single-end alignment
DNA Methylation: Absolute DNAm states were inferred from alignment of raw reads using the Batman algorithm (Down et al., Nat Biotech 2008)
Genome_build: NCBI36/hg18
Supplementary_files_format_and_content: Wiggle Track Format (WIG) files: display density graphs of raw signal representing the aligned read density; generated with MEDIPS R package (http://www.bioconductor.org/help/bioc-views/release/bioc/html/MEDIPS.html) using genomic window of 50bp and read extension of 400bp.
Supplementary_files_format_and_content: General Feature Format (GFF) files: tab-delimited files generated with Bayesian tool for methylation analysis (Batman) (Down et al., Nat Biotech 2008); each line in the file represents genomic window of 100bp (chromosome in 1st column, start and stop positions in 4th and 5th columns, respectively) with estimated absolute methylation level represented as a score between 0 and 1 (indicating unmethylated and methylated state, respectively) in the 6th column.

source_name: peripheral blood

growth_protocol: Mononuclear cells (MNCs), derived from the white blood cells of the peripheral blood of relapse trisomy 8 acute myeloid leukemia patients, were separated by Ficoll and cryopreserved.

extract_protocol: The quantified dsDNA MeDIP library was prepared for sequencing over Illumina flow cell. Preparation for sequencing includes firstly, DNA denaturation by NaOH solution and further diluted in HT1 buffer (tris buffer) to end into 4 PM concentration solution ready to be put over the flow cell. Secondly, the “cluster generation” step, which is processed by adding a mixture of unlabelled nucleotides and DNA polymerase to the ssDNA library, which will attach to the primer sequences present inside the surface of the flow cell.  The result is initiating the amplification of each fragment through a ‘bridge amplification’ reaction, which is unique to Illumina and subsequently generation of millions of clusters; each one represents a single fragment of MeDIP library. The average insert size of paired-end libraries was 200 bp and the standard deviation was of 20 bp. Illumina GAII, with the criteria of 1.4-pipeline software and 2.4-system control software (SCS) can produce 180.000-270.000 clusters/tile

treatment_protocol: Genomic DNA was extracted from AML by Qiagen kit, then the DNA sonicated by Sonic vibracel. The DNA frament will be blunt ended by adding klenow enzme and T4 polynucleotide kinase. 7.5 micrograms of monoclonal antobody (Diagenode 1 micro/micrL) is added to at least 4 micrograms of DNA for 2 hours at 4 C with slow rotation. 40 µl of magnetic Dynabeads (Dynabeads M-280 sheep anti-Mouse IgG, Invitrogen) are prewashed with 1ml 1XIP buffer and collected with a magnetic rack. Dynabeads are added to the DNA sample and incubated for 2 hours at 4 C with slow rotation. Dynabeads are collected using a magnet and washed with 750 µl 1X IP buffer for three times. To release the immunoprecipitated DNA, Dynabeads are resuspended in 200 µl digestion buffer and 5 µl of Proteinase Kinase (10mg/ml). The suspension is incubated for 2 hours at 55C with shaking to avoid the sedimentation of the beads. After the incubation, the sample is divided in 2 separate tubes and purified by Zymo DNA Clean and Concentrator-5 kit (using 700 µl binding buffer) in 20 µl EB. 10 µl MeDIP and 10 ng of input DNA are subjected to limited PCR (LM PCR) using primers provided from Illumina for paired end library preparation. For size selection, 15 µl of MeDIP is run over 2% low melting temperature gel. MeDIP is excised from gel in the range of 250-300 bp and eluted in 30 µl EB using Qiagen Gel Extraction kit.

tag: cytogenetic

value: trisomy 8 (relapse)

tag: sample type

value: DNA of AML patient

tag: disease state

value: AML

value: mononuclear cell

tag: medip antibody

value: 5-methyl cytosine

tag: medip antibody manufacturer

value: Diagenode


title: HL2_DNaseSeq

tag: biopsy site


title: AML 17


title: AML 19


title: ESC_A

value: ES


title: iCLIP experiment with FLAG antibody, biological repl. 1

city: Giessen

first: Lee-Hsueh

last: Hung

state: Hessen

address: Heinrich-Buff-Ring 58

institute: University of Giessen

data_processing:
Basecalls performed using CASAVA version 1.4
Sequence from .fq file were mapped to hg19 genome sequence. The first unique mapped position is defined as cross link site of the protein, and assembled in .bed file.
Mapping detail refered to König et al. iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 2010 Jul;17(7):909-15. PMID: 20601959
Genome_build: hg19
Supplementary_files_format_and_content: .bed files represent cross-link sites

source_name: HeLa

growth_protocol: HeLa cells were grown in Dulbecco's Modified Eagle Medium (DMEM; supplemented with 10% fetal calf serum) in 15-cm cell culture dishes at 37°C with 5% CO2.

extract_protocol: Following reverse transcription of the purified RNA with a primer that introduces a BamHI-site and additional linker sequence, cDNAs were separated by denaturing gel electrophoresis, and three different size regions were selected and gel-purified. In order to add a linker sequence to the 3’ end, the cDNAs were self-ligated using an ssDNA-specific circligase, and linearized again by BamHI, following annealing of a short oligonucleotide to form a double-stranded restriction site. CLIP tags were amplified by PCR, and subjected to Solexa high-throughput sequencing. For experimental details, see: König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM & Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909–915.

treatment_protocol: HeLa cells were irradiated with UV-light at 254 nm to crosslink proteins to nucleic acids. Following cell lysis, RNA was trimmed to an appropriate size by limited RNase I treatment. The hnRNP L protein was immunoprecipitated by a monoclonal antibody and immobilized Protein A under stringent washing conditions, and 2’,3’-cyclic phosphates were removed using the polynucleotide phosphatase. This facilitated ligation of a 3’ RNA linker, which is blocked by puromycin at its 3’ end to prevent self-ligation. For detection of the protein-bound RNA, it was radioactively labeled at its 5’ end. Neutral-pH denaturing gel-electrophoresis was performed, followed by transfer to a nitrocellulose membrane. The RNA/protein complexes were visualized by autoradiography, and a region above the expected molecular weight of hnRNP L, was cut from the membrane. The crosslinked RNA was released by digestion of hnRNP L protein using Proteinase K. For experimental details, see: König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM & Ule J (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909–915.

tag: cell line

value: HeLa

value: ANTI-FLAG M2

tag: chip antibody manufacturer

value: Sigma-Aldrich

tag: chip antibody catalog #

tag: chip antibody lot #


title: iCLIP experiment with hnRNPL antibody, biological repl. 1

value: Anti-hnRNP-L


title: iCLIP experiment with hnRNPL antibody, biological repl. 3


title: iCLIP experiment with hnRNPL antibody, biological repl. 2


title: iCLIP experiment with FLAG antibody, biological repl. 2


title: iCLIP experiment with FLAG antibody, biological repl. 3


title: CF2_DNaseSeq

organism: Pan troglodytes

tag: coriell catalog #


title: Runx2_day0_ChIP-Seq

source_name: proliferating preosteoblast MC3T3-E1 subclone 4 cells at day 0

value: preosteoblast

tag: strain

value: Runx2 antibody (M70, Santa Cruz Biotechnologies, Inc.)


title: CL3_DNaseSeq

value: Lymphoblastoid

value: blood, peripheral vein


title: CF3_DNaseSeq

source_name: Skin fibroblast cells

value: Primary Dermal Fibroblast

value: skin, unspecified


title: CL2_DNaseSeq


title: CF1_DNaseSeq


title: HL3_DGE-seq


title: CF3_DGE-seq


title: CL1_DNaseSeq


title: CF2_DGE-seq


title: CL2_DGE-seq


title: CL1_DGE-seq


title: CF1_DGE-seq


title: MCF7_Hypoxia_32h_microRNAseq_rep1

city: Oxford

first: Carme

last: Camps

address: Roosevelt Drive

country: United Kingdom

institute: Wellcome Trust Centre for Human Genetics/ U. of Oxford

description: Total RNA containing short RNA fraction

data_processing:
Small RNA sequencing data were processed from raw FASTQ files and analysed using the Kraken pipeline (http://www.ebi.ac.uk/research/enright/software/kraken)
The 3' adaptors were stripped using Kraken tools and according the following criteria: 12-nt alignment stretch with no more than 2 mismatches and no gaps.
The reads were filtered for low-complexity regions and the remaining reads were size-selected for 18-26nt, all using Kraken tools. A file with unique reads and their corresponding counts was generated for each sample.
The final processed unique reads were mapped to the human genome (hg19 based on Ensembl v64) using bowtie 0.12.7 allowing for two mismatches and using the best alignment stratum option. Reads mapped to more than 20 loci were discarded. Mapped reads were classified and counted based on genomic annotations (RNAs, coding genes, pseudogenes and repeats) obtained from Ensembl v64. For reads mapping to multiple loci, counts were divided by total number of reads.
For differential expression of miRNAs, the overlap between mapped reads and human mature miRNAs (based on miRBase v17) was found using the function findOverlaps available in the Bioconductor GenomicRanges package (http://www.bioconductor.org/packages/2.10/bioc/html/GenomicRanges.html). The normalization and differential expression was performed with Bioconductor edgeR package v2.3.57 using both common and tagwise dispersion. The significant differentially expressed miRNAs were determined by an adjusted P value <0.05 based on the Benjamini and Hochberg multiple testing correction.
Genome_build: hg19 based on Ensembl v64 and miRBase (human, v17)
Supplementary_files_format_and_content: Normalised counts using the TMM method of edgeR package from Bioconductor

source_name: MCF-7 cells

growth_protocol: MCF-7 cells were grown in Dulbecco's Modified Eagle Medium supplemented with 10% fetal bovine serum and 2mmol/L of L-glutamine.

extract_protocol:
RNA was extracted from cells using the miRVana miRNA isolation kit (Ambion) in accordance with the prescribed protocol provided with the kit. RNA quality was assessed after extraction using Agilent bioanalyser.
Libraries were prepared from the 20 to 30 nucleotide RNA fraction according to the Illumina DGE-small RNA sample preparation protocol (v1.5). The 20 to 30 nucleotide RNA fraction was isolated from 2µg of total RNA after being run in a 15% urea-TBE gel (Invitrogen) for 1h at 200V. The RNA contained on the excised band was eluted in 300µl of 0.3M NaCl by 4h of constant rotation at room temperature. The elute was separated from the gel debris using a Spin-X-column (Thermo Fisher Scientific) and RNA was precipitated by adding 750µl of 100% ethanol and 3µl of glycogen (1mg/ml) and incubating for 30 minutes at -80˚C. The precipitated RNA was centrifuged at 14,000 rpm for 25 minutes at 4˚C, washed with 75% ethanol, air dried and resuspended in 5µl of RNAse-free water. This material was used to prepare miRNA sequencing libraries using the DGE-small RNA sample preparation kit (v1.5) from Illumina and according to the protocol provided with the kit.

treatment_protocol: Exposure of cell cultures to hypoxia (1% oxygen) was undertaken in an In vivo2 Hypoxia Work Station (Ruskin Technologies) in parallel with cells maintained in normoxic conditions (21% oxygen). Cells were recovered after 16h, 32h and 48h of exposure to hypoxia.

tag: treatment

value: 1 percent Oxygen

tag: time


title: MCF7_Hypoxia_48h_microRNAseq_rep1

description: Total RNA containing short RNA fraction


title: MCF7_Hypoxia_48h_microRNAseq_rep2

description: Total RNA containing short RNA fraction


title: MCF7_Hypoxia_16h_microRNAseq_rep1

description: Total RNA containing short RNA fraction


title: MCF7_Hypoxia_16h_microRNAseq_rep2

description: Total RNA containing short RNA fraction


title: MCF7_Normoxia_microRNAseq_rep2

description: Total RNA containing short RNA fraction

value: 21 percent Oxygen


title: MCF7_Normoxia_microRNAseq_rep1

description: Total RNA containing short RNA fraction


title: Input1 Sample 8

status: Public on Feb 12 2014

city: Ames

first: Jorgen

last: Johansen

state: Iowa

address: MBB3142, Iowa State Univeristy

department: BBMB

institute: Iowa State Universtiy

data_processing:
ChIP-seq reads were aligned to the dm3(BDGP5.72) Drosophila genome assembly using  Bowtie V0.12.7
SAMtools  V0.1.18  and BEDtools V2.14.3 were used to sort and transfer files.
peaks were called using SICER V1.1  with the following setting: 200 bp window size, 200 bp gap size, and an effective genome size of 72% of the Drosophila genome

source_name: Salivary Glands

growth_protocol: Salivary gland cells were isolated from wild type and JIL-1 null mutant 3rd instar larvae of Drosophila Melanogaster

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions

tag: cell type

value: Salivary Gland Cells

tag: developmental stage

value: Third instar larvae

value: Wild Type


title: Z2_input Sample 7


title: H3K9me2_Z2 Sample 6

tag: chip antibody

value: Abcam Anti-Histone H3 (di methyl K9) antibody [mAbcam 1220]


title: H3K9me2_WT Sample 5


title: H3S10ph_AM Sample 4

value: Active Motif Histone H3S10ph antibody (pAb) #39253


title: H3S10ph_CS Sample 3

value: Cell signalling Phospho-Histone H3 (Ser10) (D2C8) XP® Rabbit mAb


title: CL3_DGE-seq


title: 5C9_2 Sample 2

value: JIL-1 monoclonal antibody 5C9


title: 5C9_1 Sample 1


title: D7C

first: liang

last: zhang

address: 1230 york Avenue

department: fuchs

institute: the Rockefeller University

data_processing:
Galaxy Webtools: Groomer data, based on MM9 female ref genome
Galaxy Webtools: Trimming 3 nt from each end of all reads
Galaxy Webtools: Filter Fastq, filtering any reads with any base quality <20
Galaxy Webtools: Tophat mapping, all default settings, use MM9 female as refer genome
Galaxy Webtools: Cufflink transcript analysis, all default settings, use MM9_gene.gtf from the MM9 data base as reference annotation. Use refmrna.fa file from the MM9 database for bias correction
Genome_build: MM9
Supplementary_files_format_and_content: Tabular file, content including: tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage status FPKM FPKM_conf_lo FPKM_conf_hi

source_name: miR-125b addicted tumor initiating cells Off Dox day 7, replicate 3

growth_protocol: For Histone-H2BGFP expression in DTG tumor cells, the U6 promoter was deleted in the PLKO-PGK-H2B-GFP vector {Beronja, 2010 #68}throughNdeI-AgeI digestion, Quick Blunting Kit treatment (NEB), and self-ligation. The resulting PLNA-PGK-H2BGFP plasmid was packaged into lentivirus and used to infect ~1x106freshly sorted α6hiβ1hi DTG tumor cells. After 30 min, cells were then extensively washed and immediately engrafted onto backskins of Nude mice by intradermal transplantation. GFP+α6hiβ1hicells were FACS-isolated from resulting tumors and then serially transplanted as above

extract_protocol:
Total RNAswere extracted from the FACS-sorted cells using the miRNeasy Mini Kit (Qiagen) according to the vender’s protocol.
RNA samples were submitted to the Genomics Resources Core Facility of the Weill Cornell Medical College for library construction using IlluminaTruSeq Stranded mRNA Sample Prep Kit and then sequencing using Illumina HiSeq2000.

treatment_protocol: For RNA seq analysis of the miR-125b addicted tumor regression process, H2BGFP labeled DTG tumor cells were intradermally engrafted onto backskins of Nude mice (1x104cells/site). Tumors were allowed to grow to ~1cm diameter. Mice were then taken Off Dox by transferring them to regular food {Zhang, 2011 #96} for 0, 4, 7 days. GFP+α6hiβ1hiwere then FACS-isolated from the tumors. Two or three independent replicates were collected for each time point.

value: Day 7

tag: genetic background

value: FVB


title: D7A

source_name: miR-125b addicted tumor initiating cells Off Dox day 7, replicate 1


title: D4B

source_name: miR-125b addicted tumor initiating cells Off Dox day 4, replicate 2

value: Day 4


title: D7B

source_name: miR-125b addicted tumor initiating cells Off Dox day 7, replicate 2


title: WDR5_F266A_RIPseq_IP_rep2

city: Stanford

first: Kun

last: Qu

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: library strategy: RIP-seq

data_processing:
Sequencing reads were mapped to the mouse genome using TopHat (version 1.1.3) (Trapnell et al., 2009). Each sample generated 13.6 to 51.1 million mapped sequences, recorded in BAM/SAM format.
A non-redundant mm9 transcriptome was assembled from UCSC RefSeq genes, UCSC genes, and predictions from (Ulitsky et al., 2011) and (Guttman et al., 2011). Gene expression in the form of log2d RPKM was calculated.
Genome_build: mm9
Supplementary_files_format_and_content: The processed file is in txt format with RPKMs.

source_name: embryonic stem cells

growth_protocol: Embryonic stem cells were cultured under standard feeder-free conditions with LIF supplementation.

extract_protocol:
RIPiT was performed as described previously (Singh et al., 2013) with the following modifications. WDR5 tagged constructs contained a FLAG and HA epitope which were used for sequential purification of WDR5 bound RNAs. No RNaseI elution step was included. Full length WDR5 bound RNAs were isolated by Trizol extraction and first converted into dsDNA with a NuGen Ovation v2 kit. This dsDNA was converted into a deep sequencing library using the NEBNext ChIP-seq Library Prep Kit from NEB. WDR5 empty represents ESCs infected with a lentivirus containing no tagged WDR5. WDR5 wild type represents ESCs infected with a lentivirus containing a FLAG-HA tagged WDR5 wild type sequence expression construct. WDR5 F266A represents ESCs infected with a lentivirus containing a FLAG-HA tagged WDR5 mutated at position F266 (to an alanine) expression construct.
The isolated RNA was DNase treated and purified using Qiagen miRNeasy columns.
For sequencing libraries we first amplified the RNA with the NuGEN Ovation v2 kit and then followed Illumina’s protocol.

treatment_protocol: Formaldehyde crosslinked RIP-seq was carried out as previously described (Yong et al. 2010)

value: embryonic stem cells

tag: infection

value: 129/B6 F1 hybrid

value: Anti-FLAG-M2 Affinity Gel (Sigma, Cat# A2220) and Anti-HA Agarose (Pierce, Cat# 26181)


title: WDR5_F266A_RIPseq_IP_rep1

description: library strategy: RIP-seq

value: lentivirus containing a FLAG-HA tagged WDR5 mutated at position F266 (to an alanine)


title: D4A

source_name: miR-125b addicted tumor initiating cells Off Dox day 4, replicate 1


title: D0B

source_name: miR-125b addicted tumor initiating cells Off Dox day 0, replicate 2

value: Day 0


title: MCF7_Hypoxia_32h_microRNAseq_rep2

description: Total RNA containing short RNA fraction

value: 1 percent Oxygen


title: D0A

source_name: miR-125b addicted tumor initiating cells Off Dox day 0, replicate 1


title: WDR5_wildtype_RIPseq_IP_rep2

description: library strategy: RIP-seq

value: lentivirus containing a FLAG-HA tagged WDR5 wild type


title: WDR5_wildtype_RIPseq_IP_rep1

description: library strategy: RIP-seq


title: WDR5_F266A_RIPseq_Input

description: library strategy: RIP-seq


title: WDR5_empty_RIPseq_IP_rep1

description: library strategy: RIP-seq

value: lentivirus containing no tagged WDR5


title: WDR5_wildtype_RIPseq_Input

description: library strategy: RIP-seq


title: Input2 Sample 9

value: Salivary Gland Cells

value: Third instar larvae