title: Control VMB RNA-Seq

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
Control_VMB.txt: mm9

value: 3 month old mice


title: Ch_Yn07-147__Pt_FP_18

status: Public on Sep 04 2012

type: SRA

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing: Reads were aligned to the genome and RefSeq using bfast.  Up to one mismatch was allowed.  Only reads that aligned to one genomic location were used.

molecule: total RNA

organism: Pan troglodytes

source_name: chimp, frontal pole

extract_protocol: RNA extracted using Qiagen Rneasy kit; library made using Illumina DpnII protocol

tag: brain region

value: frontal pole

tag: isolate


title: 3hs1_FL_498524

city: Rehovot

first: Gilad

last: Landan

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute of Science

description:
4C PCR product
library strategy: 4C-Seq

library_source: genomic

data_processing:
Processing of sequenced 4C-seq reads is performed using a special purpose computational analysis pipeline, 4Cseqpipe, which can be downloaded along with a detailed manual at: http://compgenomics.weizmann.ac.il/tanay/?page_id=367 .
Briefly, sequenced reads are mapped to a pre-built database of restriction fragment locations and fragment end sequences, representing a reduced genome defined by the primary and secondary restriction enzymes.
Mapping takes into account fragment end uniqueness and mappability, and utilizes base-calling qualities to partially apportion reads according to mismatch probabilities.
Dense genomic profiles are created for four distinct classes of fragment ends by linear interpolation of mapped reads.
One interpolated profile is selected and the three other profiles are quantile-normalized to match its distribution. Resulting profiles are combined by direct summation, resulting in a coverage profile.
Finally, medians of normalized coverage, as well as 20th and 80th percentiles, are calculated for sliding windows ranging from 2kb to 50kb in size.
Genome_build: mm9
Supplementary_files_format_and_content: ID.nearcis.norm.median.scales – Median of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns:
column 1 – the starting coordinate of the 1kb bin
column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin
column 3 – the 80th percentile of values in the window
column 4 – the 20th percentile of values in the window
column 5-148 – as columns 2-4, but with linearly increasing window size, going up to 50kb

molecule: genomic DNA

organism: Mus musculus

source_name: Fetal liver

growth_protocol: 10-12 14.5 dpc embryo livers were resuspended in DMEM supplemented with 10% FCS. The equivalent of two fetal livers (approximately 4 × 10^7 cells) was diluted to 50 ml with DMEM (10% FCS).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with a primary restriction enzyme and subsequently ligated under dilute conditions. After reversal of the cross inks the DNA is purified and treated with the second restriction enzyme. After a second re-ligation step the sample is purified and a 4C inverse PCR is perfomed using primers annealing to the viewpoint fragment-end of interest. Primers contain non-annealing dangles with Illumina adapter sequences, allowing immediate sequencing of purified PCR products.

treatment_protocol: cells were cross-linked using 2% formaldehyde for 10 minutes at room temperature in PBS (10% FCS)

tag: strain

tag: developmental stage

value: fetal

tag: tissue

value: liver

tag: 1st restriction enzyme

value: DpnII

tag: 2nd restriction enzyme

tag: viewpoint

value: beta-globin 3' HS-1


title: hbb_FB_692

description:
4C PCR product
library strategy: 4C-Seq

source_name: Fetal brain

growth_protocol: 10-12 14.5 dpc embryo brains were resuspended in DMEM supplemented with 10% FCS. The equivalent of four fetal brains (approximately 4 × 10^7 cells) was diluted to 50 ml with DMEM (10% FCS).

value: brain

value: beta-globin Hbb-b1 promoter


title: sat_es_1563

description:
4C PCR product
library strategy: 4C-Seq

source_name: Embryonic stem cells

growth_protocol: Mouse ES (mES) cells were grown in buffalo rat liver cell-conditioned medium combined with DMEM GlutaMAX (Gibco) containing 15% fetal bovine serum (Invitrogen), leukemia inhibitory factor (LIF), 2-β-mercaptoethanol, and non-essential amino acids.

value: IB10/E14 cell line

value: embryonic stem cells

value: NlaIII

value: Satb1 promoter


title: hbb_FL_489510

description:
4C PCR product
library strategy: 4C-Seq


title: hs2_FL_532553

description:
4C PCR product
library strategy: 4C-Seq

value: beta-globin HS-2


title: hs26_FB_693

description:
4C PCR product
library strategy: 4C-Seq

value: alpha-globin HS-26


title: hba_FB_691

description:
4C PCR product
library strategy: 4C-Seq

value: alpha-globin Hba-a1 promoter


title: hs26_FL_570

description:
4C PCR product
library strategy: 4C-Seq


title: hba_FL_656

description:
4C PCR product (1/16 template)
library strategy: 4C-Seq


title: Paraquat VMB RNA-Seq

city: New York

first: Seema

last: Gollamudi

state: New York

address: 525 East 68th Street A501

department: Neurology and Neuroscience

institute: Weill Cornell Medical College

data_processing:
RPKM: Sequence reads were obtained and mapped to the mouse ResSeq transcript sequence (June 2010 release) using BWA with default parameters. Read counts were then normalized using the RPKM approach (Mortazavi et al, 2008).
Genome Build:
PQ_VMB.txt: mm9

source_name: Brain

extract_protocol: mRNA libraries were prepared according to Illumina's instructions accompanying the mRNA-Seq sample preparation kit (part number:1004814).  Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: 3 month old C57Bl6 mice were administered pesticides using subcutaneous alzet pumps for one week. After one week the mice were harvested and ventral mid brain and striatum collected for RNA isolation. RNA was purified followed by qualitative and quantitative analysis.

tag: age

value: Ventral mid brain (VMB)

tag: treatment

value: Paraquat


title: NP_RESTko_Suz12_biological_replicate_b

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Suz12 ChIP in RESTko NP cells

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome Build:
MmNP_RESTko_Suz12_b.mm9-mmV02-aln2.w100m100.wig: mm9

source_name: Suz12 ChIP in RESTko NP cells

growth_protocol: RESTwt and RESTko (Black Agouti 129) embryonic stem cells were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments were performed as described before (M. Weber et al., Nat Genet 39, 457 (Apr, 2007), starting with 70 µg of chromatin and 5 µg of anti-Suz12. The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols. ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/40 of ChIP or 1:100 diluted Input DNA per PCR reaction. Primers sequences are available upon request.

tag: background strain

value: Black Agouti 129

tag: genotype/variation

value: RESTko

tag: cell type

value: Neuronal Progenitor (NP) Cells

tag: antibody


title: NP_RESTko_Suz12_biological_replicate_a

description: Suz12 ChIP in RESTko NP cells

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome Build:
MmNP_RESTko_Suz12_a.mm9-mmV02-aln2.w100m100.wig: mm9


title: hba_FL_487508

description:
4C PCR product
library strategy: 4C-Seq

value: fetal

value: liver


title: NP_RESTwt_Suz12_biological_replicate_b

description: Suz12 ChIP in wildtype NP cells

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome Build:
MmNP_RESTwt_Suz12_b.mm9-mmV02-aln2.w100m100.wig: mm9

source_name: Suz12 ChIP in wildtype NP cells

value: RESTwt


title: NP_RESTwt_Suz12_biological_replicate_a

description: Suz12 ChIP in wildtype NP cells

data_processing:
2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.
Genome Build:
MmNP_RESTwt_Suz12_a.mm9-mmV02-aln2.w100m100.wig: mm9


title: Adiponectin_KO

city: Cambridge

first: Qingqing

last: Liu

address: 9 Cambridge Center

institute: Whitehead Institute

data_processing:
reads were aligned to mm9 using tophat with parameters --segment-length 18 --segment-mismatches 1, -G Ensembl NCBIM37.62 gtf
gene level abundance in Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated with cuffdiff with parameters -u -b -M rRNA.gtf
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values

source_name: liver

extract_protocol: Mice were fasted overnight before euthanization. Liver tissues from WT or adiponectin KO male mice (n = 9-10) at 12 weeks of age were harvested and subjected to total RNA extraction using an RNeasy Plus Mini Kit (Qiagen, Valencia, CA).  Total RNA from nine to ten mice of the same strain was pooled together as one biological sample. The mRNA sequencing samples were prepared using the Illumina sample preparation protocol (RS-930-1001, Illumina, Inc. San Diego, CA).

value: 12 weeks

tag: genotype

value: Adipoq-/-


title: sat_thy_683

description:
4C PCR product
library strategy: 4C-Seq

source_name: Adult thymus

growth_protocol: 1 adult thymus was resuspended in DMEM supplemented with 10% FCS. Approximately 4 × 10^7 cells were diluted to 50 ml with DMEM (10% FCS).

value: adult

value: thymus

value: DpnII

value: Satb1 promoter (-6kb)


title: hs2_FB_694

description:
4C PCR product
library strategy: 4C-Seq

value: brain

value: beta-globin HS-2


title: Input

description: Chromatin Input (sonicated)

data_processing: 2007 M. musculus genome assembly (mm9) was used as a basis for all analyses. Low-complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). Alignments to the M. musculus genome were performed by the software bowtie (Langmead et al. 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches.

source_name: Embryonic Stem Cells (ESCs) wildtype

growth_protocol: Wild-type (129Sv-C57Bl/6) and RESTko (Black Agouti 129) embryonic stem cells were cultured and differentiated as previously described (M. Bibel, J. Richter, E. Lacroix, Y. A. Barde, Nat Protoc 2, 1034 (2007))

extract_protocol: ChIP experiments were performed as described before (C.M. Koch et al., Genome Res 17, 691 (Jun, 2007)) or (M. Weber et al., Nat Genet 39, 457 (Apr, 2007)), starting with 70 µg of chromatin and 5 µg of anti-REST or anti-H3K27me3, respectively. The ChIP libraries were prepared with the Illumina ChIP-Seq DNA Sample Prep Kit (Cat# IP-102-1001) according to Illumina’s instructions and sequenced on the Genome Analyzer 2 following the manufacturer’s protocols. ChIP-real time PCR was performed using SYBR Green chemistry (ABI) and 1/40 of ChIP or 1:100 diluted Input DNA per PCR reaction. Primers sequences are available upon request.

value: wild type

value: Embryonic Stem Cells (ESCs)

value: anti-REST (Santa Cruz, #H-290)


title: NP_REST_biological_replicate_a

description: REST ChIP in wildtype NP cells

source_name: Neuronal Progenitor (NP) Cells wildtype


title: ES_RESTko_H3K27me3_biological_replicate_a

description: K27me3 ChIP in RESTko ES cells

source_name: Embryonic Stem Cells (ESCs) RESTko

value: RESTko (Black Agouti 129)

value: anti-H3K27me3 (Millipore,#07-449)


title: NP_RESTko_H3K27me3_biological_replicate_a

description: K27me3 ChIP in RESTko NP cells

source_name: Neuronal Progenitor (NP) Cells RESTko

value: RESTko

value: Neuronal Progenitor (NP) Cells


title: ES_RESTko_H3K27me3_biological_replicate_b

description: K27me3 ChIP in RESTko ES cells


title: ES_REST_biological_replicate_c

description: REST ChIP in wildtype ES cells


title: ES_REST_biological_replicate_a

description: REST ChIP in wildtype ES cells


title: NP_REST_biological_replicate_b

description: REST ChIP in wildtype NP cells


title: ES_REST_biological_replicate_b

description: REST ChIP in wildtype ES cells


title: Hu_4924_ca_57

organism: Homo sapiens

source_name: human, caudate nucleus

value: caudate nucleus


title: WT


title: Hu_4640_ca_59


title: Hu_4548_ca_60


title: NP_REST_biological_replicate_c

description: REST ChIP in wildtype NP cells


title: Hs1570

city: Atlanta

first: Jia

last: Zeng

state: GA

address: Georgia Institute of Technology

department: School of Biology

institute: Georgia Institute of Technology

data_processing:
Basecalls performed using CASAVA version 1.8.2
All Cs were converted to Ts both in the reads and in the reference genomes, then aligned the converted reads to the converted reference genomes using the Bowtie algorithm. If multiple reads have identical external coordinates, we only retained the reads with the highest mapping quality. Besides, we  allowed up to two mismatches per read.
The output of the mapping reulsts were convert to BAM format. We used the samtools and custom perl scripts to get the base-pair resolution methylation maps.
Genome_build: GRCh37/HG19 for human, and CGSC2.1/panTro2 for chimpanzee.
Supplementary_files_format_and_content: methylation_CG.gff files are tab-delimited text files that include fractional methylation values for each Sample.
Supplementary_files_format_and_content: methylation_nonCG.gff files are tab-delimited text files that contain the base-pair resolution methylation  map for the cytosines in non-CpG context.

extract_protocol: BS-seq libraries for Illumina sequencing were custom-constructed from ~1 μg of genomic DNA which was fragmented by sonication, end repaired and ligated to custom-synthesized methylated adapters. Adaptor-ligated libraries were subjected to two successive treatments of sodium bisulfite conversion using the EpiTect Bisulfite kit. Five to ten ng of bisulfite-converted libraries was PCR amplified with the following condition: 2.5 U of ExTaq DNA polymerase (Takara), 5 μl of 10X Extaq reaction buffer, 25 μM dNTPs, 1 μl Primer 1.1, 1 μl Primer 2.1 (50 μl final). The thermocyling was as follows: 95°C  3 min, then 14-16 cycles of 95°C 30 sec, 65°C 30 sec and 72°C 60 sec. The enriched libraries were purified twice with SPRI method using AMPure beads.

value: prefrontal cortex

tag: organism

value: Human

tag: Sex

value: Male


title: Hu_1905_ca_56

tag: brain region


title: Hu_813_FP_47

source_name: human, frontal pole

value: frontal pole

tag: isolate


title: NP_RESTko_H3K27me3_biological_replicate_b

description: K27me3 ChIP in RESTko NP cells

tag: strain


title: Hu_1903_FP_48


title: Hu_4548_hi_45

source_name: human, hippocampus

value: hippocampus


title: Hu_1029_FP_49


title: Hu_4598_hi_43


title: Hu_1905_hi_40


title: Hu_4593_ca_55


title: HA-Ago3 R→ K IP control

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX54

data_processing:
Illumina CASAVA software used for basecalling
A custom pipeline was used to convert sequencing reads from FASTQ to FASTA, clip the adapter sequences of smallRNA reads, map the reads to the respective genomes using exact-match suffix array based method and annotate the mapped reads for further analysis.
NCBI BLASTALL was used to map the transposons to the mapped reads.
Genome_build: mm9 for mouse, bombyx mori genome (GenBank Assembly ID: GCA_000151625.1; Assembly Name: ASM15162v1; BioProject Accession: PRJDA20217)
Supplementary_files_format_and_content: Tab-delimited text (.txt) file includes reads that mapped to the genome (mm9 for mouse and  bombyx mori genome (GenBank Assembly ID: GCA_000151625.1; Assembly Name: ASM15162v1; BioProject Accession: PRJDA20217)), chromosome, start, stop, annotation and their frequencies.

organism: Bombyx mori

source_name: Bombyx mori, BmN4 cells

extract_protocol: Detailed protocol can be found in Xiol et al. 2012. Briefly, small RNAs from immunoprecipitated proteins were extracted by phenol-choroform and purified through 15% urea-PAGE. Libraries were prepared using NEB Kit E6120S. For polyA+ and total small RNA libraries, total RNA was extracted from cells using Trizol and purified by mRNA isolation kit (Invitrogen) and 15% urea-PAGE respectively. Libraries were prepared using NEB kit E6120S.

tag: cell line

tag: treatment protocol

value: Control

tag: treatment time

value: control

tag: rip antibody

value: Anti-HA (Reuter et al. 2009, Nat. Struct. Molec. Biol.)

tag: barcode

value: ACTA


title: HA-Ago3 R→ K IP GA

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX55

value: Geldanamycin

value: 2 days

value: CGGA


title: Hu_4593_hi_39


title: Strand-specific polyA+ RNAseq, GA

description:
PolyA+ RNA
Library: JX37

molecule: polyA RNA

value: 24 hours


title: Hu_4924_hi_41


title: Hu_4598_FP_54


title: HA-Ago3 IP GA

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX32


title: HA-Ago3 IP control

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX31


title: Ago3 IP control, short RNAs (12-20nt)

description:
small RNAs from protein immunoprecipitation (Ago3)
Library: JX66

value: Anti-Ago3 (Xiol et al. 2012, Mol. Cell)

value: GTAA


title: Ago 3 IP GA, piRNAs

description:
small RNAs from protein immunoprecipitation (Ago3)
Library: JX21

value: 4 days


title: HA-Ago3 ADH IP control

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX50

value: TACA


title: Hu_4548_FP_52


title: Ago3 IP GA, ping-pong by-product #1

description:
small RNAs from protein immunoprecipitation (Ago3)
Library: JX22

value: ACGC


title: Ago3 IP Control

description:
small RNAs from protein immunoprecipitation (Ago3)
Library: JX20


title: Siwi IP Control

description:
small RNAs from protein immunoprecipitation (Siwi)
Library: JX18

value: Anti-Siwi (Xiol et al. 2012, Mol. Cell)


title: Hu_4640_hi_42


title: HA-Ago3 ADH IP GA

description:
small RNAs from protein immunoprecipitation (HA-Ago3)
Library: JX51


title: Hu_1134_FP_46


title: Siwi IP GA

description:
small RNAs from protein immunoprecipitation (Siwi)
Library: JX19


title: Ago3 IP GA, ping-pong by-product #2

description:
small RNAs from protein immunoprecipitation (Ago3)
Library: JX46


title: ser2p_r2

city: Barcelona

first: David

last: Rossell

address: Baldiri Reixac 10

country: Spain

institute: IRB Barcelona

data_processing:
Reads were aligned to the dm3 genome with Bowtie 0.12.5, setting the parameters -n 2 -m 1
Peaks were called with Bioconductor htSeqTools package, using functions enrichedRegions and enrichedPeaks succesively
Genome_build: dm3
Supplementary_files_format_and_content: bed files with "aligned" in the file name contain aligned reads as returned by Bowtie.
Supplementary_files_format_and_content: Peaks were called with Bioconductor.

organism: Drosophila melanogaster

source_name: wing imaginal discs

growth_protocol: CantonS or lidk06801;act5Cgal4>lid RNAi larvae were grown at 25ºC until they became wall-climbing third instar larvae.

extract_protocol: Discs were crosslinked in 1.8% formaldehyde solution and sonicated. DNA-protein complexes were immunoprecipitated with anti-PolIIS5P (ab5131) or anti-PolIIS2P (ab5095)  antibodies. Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 40 (H3K4me3) and 36 (LID) nucleotides on the Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: LID RNAi strain was obtained from NIG-FLY and it was combined with lidk06801. For every sample, around 800 wing imaginal discs were dissected in PBS

value: LID RNAi mutant

tag: developmental stage

value: third instar larvae

tag: tissue

value: wing imaginal discs

tag: chip antibody

value: POLIISER2 [anti-PolIIS2P]

tag: antibody vendor

value: Abcam

tag: antibody catalog number


title: ctrl_ser2p_r2

tag: genotype/variation

value: none (control)


title: ser5p_r2

value: POLIISER5 [anti-PolIIS5P]


title: ctrl_ser5p_r2


title: Strand-specific polyA+ RNAseq, control

description:
PolyA+ RNA
Library: JX36

value: Control

value: control


title: Total small RNAs (14-33nt) P0 Fkbp6 Het

description:
Purified small RNAs
Library: JX56

source_name: Mouse testis, P0

tag: age

value: testis

value: Fkbp6 +/-


title: MIWI2 IP E18 Tdrd1 Het

description:
small RNAs from protein immunoprecipitation (Miwi2)
Library: MR16

source_name: Mouse testis, E18

value: Tdrd1 +/-

value: Anti Miwi2 (de Fazio et al. 2011, Nature)


title: Total small RNAs (14-33nt) P0 Fkbp6 KO

description:
Purified small RNAs
Library: JX57

value: Fkbp6 -/-


title: Gu4_1

city: PARIS

first: sophie

last: lemoine

address: 46 rue d'Ulm

department: Biologie

country: France

institute: Ecole Normale Supérieure

data_processing:
Base Calling using Illumina platform
Before read mapping, we trimmed polyN read tails, removed reads with a length lower or equals to 11 bases and discarded reads with quality mean lower or equals to 12.
We aligned from the 4 samples a total of 48334923 bp single end reads produced from the Illumina GAII device using the SOAP2 software (version 2.20) (Li et al., 2009).The mapping tool was configured to return all alignment hits by setting the seed length to 28 bp. In addition we authorized with SOAP2 up to 5 mismatches with 2 in the seed.
Before expression estimation, alignments from reads that matches more than one time on the reference genome were removed
In addition, we searched for new transcripts by combining the Gu4 and Gu5 reads and identifying regions of the genome with a minimum coverage of at least 3 reads/nucleotides (with at least one read in three independent samples) for a stretch of at least 100 nucleotides.
To compute gene expression abundance, we used Candida albicans GFF genome annotation from assembly 21 together with the annotation file for new transcripts and we counted all overlapping regions between alignments and listed exons.
Genes differentially expressed between Gu5 and Gu4 strains were identified applying two different methodologies available in the R programming language, i.e. DESeq (Anders and Huber, 2010) and edgeR (Robinson et al., 2010). Default parameters were used and genes with p-value lower than 0.01 with the two methods were finally selected for further analysis
Genome_build: Candida albicans Ca21 (Nov 2009)
Supplementary_files_format_and_content: .txt files contain read counts

organism: Candida albicans

source_name: Gu4 strain was described in Franz et al., 1999

growth_protocol: Cells were grown in YPD rich medium (2% glucose, 1% bactopeptone, 1% yeast extract) at 30 oC for 48 hrs.

extract_protocol: Twenty ml of exponentially growing (OD=0.6-0.7) Gu4 or Gu5 cells were flash frozen in 30ml of cold ethanol, centrifuged for 5 minutes at 3000g, washed with sterile water and centrifuged again. The cell pellets were stored at -80°C. RNA were extracted using the RNeasy kit (Qiagen), with DNAse treatment. The RNA quality was checked on a bioanalyzer Nanochip (Agilent).Strand non-specific cDNA libraries (mRNA-Seq 8-Sample Prep Kit) were prepared according to manufacturer’s instructions (Illumina).

tag: drug response


title: MILI IP E18 Tdrd1 Het

description:
small RNAs from protein immunoprecipitation (Mili)
Library: MR13

value: Anti-Mili (Reuter et al. 2009, Nat. Struct. Molec. Biol.)


title: MILI IP E18 Tdrd1 KO

description:
small RNAs from protein immunoprecipitation (Mili)
Library: MR14

value: Tdrd1 -/-


title: Gu4_2


title: Gu5_1

source_name: Gu5 strain was described in Franz et al., 1999

value: Fluconazole-resistant clinical isolate


title: Hs813

source_name: Brain

value: prefrontal cortex

tag: organism

value: Human

tag: Sex

value: Male


title: Gu5_2


title: Hs1832


title: couR mutant

status: Public on Sep 01 2012

city: Seattle

first: Somsak

last: Phattarasukol

state: WA

address: 1705 NE Pacific St., HSC K-327

department: Microbiology

institute: University of Washington

description:
YO9
cDNA from RNA.

data_processing:
Xpression was used for filtering and trimming reads.
Xpression called BWA to align reads against the R. palustris strain CGA009 genome (BX571963.1).
Xpresssion was used for quantifying, normalizing and visualizing read counts.
DESeq was used for identifying differentially expressed genes.
Genome_build: gi|39748133
Supplementary_files_format_and_content: Bed files were generated for each sample.

organism: Rhodopseudomonas palustris CGA009

source_name: bacterial cells, couR mutant

growth_protocol: Cells were grown anaerobically in light in photosynthetic medium plus 10 mM succinate at 30C until an OD660 = 0.5 was reached; cells were pelleted, flash frozen, and stored at -80C until processed for RNA extraction.

extract_protocol: Total RNA was purified from frozen cell pellets using a miRNeasy Mini Kit following the manufacturer's instructions. RNA was treated with TURBO DNase and purified with an RNeasy MinElute Cleanup Kit. The construction of the cDNA library was performed as described previously (Armour et. al., 2009 (PMID 19668204)). Briefly, first-strand cDNA synthesis was carried out using first-strand NSR (Not-So-random) primer mix and SuperScript III enzyme. RNA template was then removed by RNase H. Second-strand synthesis was carried out with exo- Klenow fragment and second-strand NSR primer mix. After PCR amplification, double-stranded DNA was purified using a QIAquick PCR Purification Kit.

tag: strain/background

tag: genotype

value: couR mutant


title: wild-type (2)

description:
YO2
cDNA from RNA.

source_name: bacterial cells, WT

value: wild-type

tag: strain


title: HP1a -/- 2

city: St. Louis

first: Nicole

middle: Christina

last: Riddle

state: MO

address: 1 Brookings Dr.; CB1137

department: Biology

institute: Washington University

data_processing:
Alignment: Tophat
Gene level expression: Cufflinks
Genome_build: R5.32
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample

source_name: third instar larvae

growth_protocol: Fly stocks were maintained on standard cornmeal media at 25ºC with 70% humidity. Mutant 3rd instar larvae lacking HP1a were recovered from a cross of flies carrying the Su(var)205^04 allele over a GFP balancer to flies carrying the Su(var)205^05 allele over a GFP balancer by selecting for lack of GFP.

extract_protocol: Total RNA was isolated from third instar larvae using Trizol according to the manufacturer's recommendations.  rRNA-depleted cDNA libraries suitable for Illumina sequencing were prepared and sequencing was carried out by the Genome Technology Access Center (GTAC) at Washington University according to standard protocols.  Following are the index sequences used and the samples they correspond to.  CCATCAT HP1a -/- 1; CCGATTA OR 2; CTTGGAA OR 1; TAACAAG HP1a -/- 2.

value: third instar larvae


title: wild-type (1)

description:
YO1
cDNA from RNA.


title: WT2

value: wildtype - Oregon R


title: MILI IP P0 Fkbp6 Het

description:
small RNAs from protein immunoprecipitation (Mili)
Library: JX44

value: ACTA


title: MILI IP  P0 Fkbp6 KO

description:
small RNAs from protein immunoprecipitation (Mili)
Library: JX45

value: CGGA


title: MILI IP  P10 Fkbp6 KO

description:
small RNAs from protein immunoprecipitation (Mili)
Library: JX24

source_name: Mouse testis, P10

value: testis


title: MILI IP P10 Fkbp6 Het

description:
small RNAs from protein immunoprecipitation (Mili)
Library: JX23

value: Fkbp6 +/-


title: H3K36me3_minusRA

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD

description: ChIP on H3K36me3

data_processing: The image analysis and base calling were performed by using Illumina's Genome Analysis pipeline. The sequencing reads were aligned to the human genome UCSC build hg18 by using Bowtie and the read counts on each gene were computed by using BedTools.

source_name: Ntera2 cells

growth_protocol: Ntera2 cells were cultured in MEMalpha medium with 10% FBS.

extract_protocol: The libraries were constructed following Illumina's Chip-Seq sample preparation kit.

treatment_protocol: The H3K36me3 antibody was provided by Abcam (Cat. # ab9050). The cells were treated with 10 uM all-trans RA for 48 hours, and then lysed and subject to standard ChIP preparation procedure. 2 ug of antibodies were used to precipitate the samples.

tag: cell type

tag: antibody

tag: vendor

value: Abcam (Cat. # ab9050)

tag: treatment

value: no retinoic acid


title: SB1

city: Worcester

first: Craig

last: Mello

state: MA

address: 368 Plantatoin Street, Suite AS5-2047

department: Program in Molecular Medicine

institute: University of Massachusetts Medical School

description: control Reporter 1

data_processing:
Samples are prepared using ligation dependent method with 5' linker containing 4nt barcode and 3' linker added to the RNA, and single-end 36nt sequence was obtained using illumina genome analyzer. A custom PERL script is used to de-barcode the sample and remove the 3' linker CTGTAG and beyond. If the read does not contain the complete 3' linker, as represented by CTGTAG, then CTGTA/CTGT/CTG/CT at the very 3' end is removed only once to account for the incomplete 3' linker. RNA at least 17 nt was used in the following analysis.
use bowtie 0.12.7 with parameter v 3 -a --best --strata -m 400 and allow 1 mutation if the RNA size is 19-21, 2 mutations if the size 22-24, 3 mutations if the size is 25 or bigger.
The sample is normalized to 5 million of non-structural reads and the reads of an individual RNA are distributed evenly to all the genomic loci matched
A custom PERL pipeline is used to perform the post-bowtie analysis, including summarizing, making gff, drawing scatter plot, grouping reads, etc
Genome browse 1.70 plus custom perl script are used to visualize the RNA matched
Genome_build: Wormbase WS215
Supplementary_files_format_and_content: Fasta format sequence with id containing the RNA number matched to the genome and transgene (The 'x' and the number following  are the RNA counts and the number before the x is the id)

organism: Caenorhabditis elegans

source_name: control Reporter 1

growth_protocol: Grown on plate with OP50 at 20C. Harvest when worms become gravid adults

extract_protocol:
Small RNAs of 18-40nt were gel purified from a 15% polyacrylamide 7M Urea Gel, along with 20 picomoles of RNA standard (18- and 40-nt) in separate lanes. To make the RNA clonable at the 5' end, either CIP/PNK or TAP treatment is required during cloning, as indicated in the paper. Ethidium Bromide staining was used to visualize the RNA standards. A gel fragment was excised from the sample lanes in the migration range between the two standards. RNA was eluted from the gel fragment in (0.3M NaCl-TE pH7.5) solution overnight and ethanol-precipitated with 20mg of glycogen as the carrier. The gel purified RNA and 1µM of each standard were incubated with 10µM of 3’-end linker, 1 Unit/µl of SuperRNaseIN, 10% DMSO and 3 Units/µl T4 RNA ligase (Takara) in 10µl ligation buffer (50mM Tris-Cl pH7.5, 10mM MgCl2,10mg/mL BSA, 10mM DTT).  The 3’ ligated products were gel purified, eluted, precipitated and then incubated with 10µM of 5’ adapter oligonucleotide with 4nt barcode at the 5' end, 1 Unit/µl SuperRNaseIN (Ambion) and 3 Units/µl of T4 RNA ligase in ligation buffer (50mM Tris-HCI pH7.5), 10mM MgCI2, 10mM DTT, 1mM ATP) and 10% DMSO. The ligated products were gel purified and reverse transcribed in a standard 20µl reaction (SuperScript III, Invitrogen). The cDNA was amplified by PCR and purified in a 8% acrylamide gel. PCR products generated for all the samples were sequenced on a Solexa sequencing platform (Illumina, Inc.) and single-end 36 nt reads were obtained.
small RNA cloning, 5' and 3' ligation dependent.

treatment_protocol: normal growth condition

tag: strain background

value: control Reporter 1

value: gravid adult

tag: 5' barcode

value: TGAC


title: GH21U

description: 21U-RNA Reporter 1

source_name: 21U-RNA Reporter 1

value: 21U-RNA Reporter 1

value: CAGT


title: sRNAs from Contig 22226.0 IES1+ strain backcrossed to wild-type strain at 19 hr

city: Princeton

first: Wenwen

last: Fang

state: NJ

address: 323 Guyot Hall, Washington Rd

department: EEB

institute: Princeton University

description: CTGATC; AAGCTA

data_processing:
The raw sequencing data from a control Illumina lane were first filtered by requiring the presence of sequences "TCACGATCAGATCTC" or "TCACTAGCTTATCTC" (15bp sequences with barcodes inside) in the read. This filtered fastq file is provided here as the raw file.  Then 3’ adapter is trimmed by requiring a perfect 15bp match to “TGGAATTCTCGGGTG” (the 5'-end of the 3' adapter). Reads that contain “N” or shorter than 18bp were discarded. The remaining reads were collapsed using FASTX Tool kit Collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and those that contain telomeric sequences “CCCCAAAACCCC” or “GGGGTTTTGGGG” were removed. The non-redundant, telomere-reads removed dataset was provided here as the processed fasta file. The SHiMP output of the reads mapping against Contig22226.0 MAC and MIC contigs are provided as processed datafiles, after removing those mappings with more than two mismatches.
Genome_build: not applicable
Supplementary_files_format_and_content: not applicable

organism: Oxytricha trifallax

source_name: Oxytricha mating cells

extract_protocol: Total RNA at ~19 hr was directly used for library construction following ng Illumina® TruSeq™ Small RNA Sample Preparation protocol with two different barcodes, and these two libraries were sequenced together as a partial control lane on Illumina HiSeq 2000.

treatment_protocol: Contig22226.0 IES1+ strain was obtained by injection of Contig22226.0 IES1-containing piRNA in the mating pairs of wild-type strains JRB310 and JRB510.  The clonal line of Contig22226.0 IES1+ was mated with wild-type JRB510, and total RNA was extracted at ~19 hr post mixing.

value: Contig22226.0 IES1+ strain backcrossed to wild-type parental strain at 19 hr

tag: time


title: H3K36me3_plusRA

description: ChIP on H3K36me3

treatment_protocol: Ntera2 cells were treated with 10uM all-trans RA for 48 hours. The H3K36me3 antibody was provided by Abcam (Cat. # ab9050). The cells were treated with 10 uM all-trans RA for 48 hours, and then lysed and subject to standard ChIP preparation procedure. 2 ug of antibodies were used to precipitate the samples.

value: with retinoic acid


title: control RNAi rep3

city: Stanford

first: Eric

middle: L

last: Van Nostrand

address: 279 Campus Drive B341

department: Developmental Biology

institute: Stanford University

description: 3' end enriched poly-A RNA

data_processing:
Basecalls were performed using CASAVA 1.7.0 from Illumina
Reads with 10 or more consecutive A's or T's were removed as likely amplification artifacts, and remaining reads were mapped to the Wormbase reference WS215 genome and transcriptome using Bowtie version 0.12.7, with the options “-a --best --strata -v 2” to obtain all genomic position(s) to which the read mapped with the least number mismatches (up to 2 allowed)
To determine expression for each transcript in the WS215 Wormbase annotation, we counted the number of reads that uniquely mapped to the sense strand (i.e., they did not map equally well elsewhere in the genome).
Genome_build: WS215 (genome + annotated transcripts)
Supplementary_files_format_and_content: Tab-delimited file contains read density (per million uniquely mapped reads) for all annotated WS215 genes.

source_name: whole day 4 adult worms

growth_protocol: Three independent biological replicate batches of approximately ~10,000 sterile hermaphrodites of the sterile TJ1060 (fem-15(b26); spe-9(hc88)) strain were grown at the non-permissive (25°C) temperature until the first day of adulthood, at which point half were placed on plates seeded with unc-62 RNAi and half on empty vector RNAi. The worms were then grown for 3 days at 20°C, after which poly-A-purified RNA was isolated

extract_protocol: RNA was isolated by Trizol extraction followed by phenol-chloroform purification. poly-A-purified RNA was then isolated using the Qiagen Oligotex Mini kit, and 3’ end enriched RNA-seq libraries were prepared in accordance with the 3’SEQ method. 400ng of mRNA was heat sheared for 7.5 minutes at 850C to obtain 200-500bp fragments, and barcoded oligo-dT primers were used to generate cDNA for mRNA fragments located at the 3’ end of transcripts. After second strand synthesis, adaptors were ligated to the 5’ end, and PCR primers (including the barcode sequence) were used in order to enable multiplexed sequencing. The three replicate libraries from worms grown on unc-62 RNAi were then pooled and sequenced in a single flow-cell lane on the Illumina single-end 36bp HiSeq 2000 platform, with the three libraries from worms grown on control RNAi pooled and sequenced in an additional lane.

tag: RNAi

value: empty vector control RNAi

tag: tissue

value: whole worms


title: flagprg1da4

description: prg-1 mutant rescued by flag::prg-1 (583A)

source_name: flag::prg-1 (D583A); prg-1

value: N2::prg-1 mutant

tag: genotype/variation

value: flag::prg-1 (D583A); prg-1

value: ATCA


title: unc-62 RNAi rep1

description: 3' end enriched poly-A RNA

value: unc-62 RNAi


title: unc-62 RNAi rep2

description: 3' end enriched poly-A RNA


title: sx922

description: prg-1 mutant

source_name: prg-1 mutant

value: prg-1 mutant

tag: age

value: GCTG


title: control RNAi rep2

description: 3' end enriched poly-A RNA


title: flagprg11

description: prg-1 mutant rescued by flag::prg-1 (WT)

source_name: flag::prg-1 (WT); prg-1

value: flag::prg-1 (WT); prg-1


title: N2

description: wild-type

source_name: wild-type

value: wild-type


title: WT1

value: wildtype - Oregon R

tag: developmental stage

value: third instar larvae


title: Otiwi1 RNA-ChIP at 30 hr post-mixing

description:
small RNA sequencing
piRNA_30hr
barcode: GCCAAT

data_processing:
The raw sequencing data were first barcode-splitted by using Barcode Splitter (version1.0.0) on Princeton Galaxy web sever (the splitted files are provided here as raw file).Then 3’ adapter is trimmed by requiring a perfect 21bp match to “TGGAATTCTCGGGTGCCAAGG”. Reads that contain “N” or shorter than 18bp were discarded. The remaining reads were collapsed using FASTX Tool kit Collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and those that contain telomeric sequences “CCCCAAAACCCC” or “GGGGTTTTGGGG” were removed. The non-redundant, telomere-reads removed datasets were provided here as the processed data files. SHRiMP mapping output files after removing those mappings with more than two mismatches are also provided as processed data files.
The genome fasta file used for mapping: http://trifallax.princeton.edu/cms/databases/data-files/otiwi1_manuscript_relevant/master-genome-for-pirna-mapping/view

organism: Sterkiella histriomuscorum

extract_protocol: Otiwi1 ChIPed RNAs were directly used for library construction following ng Illumina® TruSeq™ Small RNA Sample Preparation protocol with different barcodes for each sample.

treatment_protocol: Wildtype strains of JRB310 and JRB510 were mated and cells were crosslinked with 1% formaldehyde at time point indicated and used in IP experiments.

value: mating cells

value: 30 hr post-mixing of opposite mating types

tag: sample composition

value: 90% of the cells are late exconjugants, 9% are mating pairs, the rest are vegetative cells and cysts.

tag: rip antibody

value: Otiwi1 antibody (Abcam, cat# ab12337, lot#868987)


title: sRNAs from Oxytricha conjugation at 20 hr

data_processing:
The raw sequencing data from one Illumina lane are provided here as the raw file.  3’ adapter is trimmed by requiring a perfect 15bp match to “ATCTCGTATGCCGTC” (the 5'-end of the 3' adapter). Reads that do not contain the adapter sequence, or contain “N”, or shorter than 18bp were discarded. The remaining reads were collapsed using FASTX Tool kit Collapser (http://hannonlab.cshl.edu/fastx_toolkit/index.html), and those that contain telomeric sequences “CCCCAAAACCCC” or “GGGGTTTTGGGG” were removed. The non-redundant, telomere-reads removed dataset was provided here as the processed fasta file.
Genome_build: not applicable
Supplementary_files_format_and_content: not applicable

extract_protocol: 10 microgram of total RNA extracted at 20hr post mixing was directly used for library construction following Illumina® Small RNA  v1.5 Sample Preparation guide.

treatment_protocol: Wild-type Oxytricha strains JRB310 and JRB510 were mixed to induce conjugation, and total RNA was extracted using TRIzol at 20hr post mixing.

value: At 20 hr post mixing of different mating types


title: HP1a -/- 1


title: Otiwi1 RNA-ChIP at 12 hr post-mixing

description:
small RNA sequencing
piRNA_12hr
barcode: CGATGT

value: 12 hr post-mixing of opposite mating types

value: 90% of the cells are in pairing stage, and not exconjugant was observed. The rest are vegetative cells.


title: Otiwi1 RNA-ChIP at 19 hr post-mixing

description:
small RNA sequencing
piRNA_19hr
barcode: ACTTGA

value: 19 hr post-mixing of opposite mating types

value: 90% of the cells are early exconjugants, less than 10% were mating pairs. The rest are vegetative cells.


title: control RNAi rep1

description: 3' end enriched poly-A RNA

value: empty vector control RNAi

value: whole worms


title: Cells growing under nitrogen fixing conditions

city: Nijmegen

first: Huub

last: Op den Camp

address: Heyendaalseweg 135

country: Netherlands

web_link: http:// http://www.ru.nl/microbiology/

institute: Radboud University Nijmegen

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Methylacidiphilum fumariolicum SolV genome using the CLCBio Workbench
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using CLCBio Workbench
Genome_build: European Nucleotide Archive (ENA) accession numbers CAHT01000001 to CAHT01000109
Supplementary_files_format_and_content: Excel file with Gene GenBank identifier, Gene length, Gene name, and Unique reads, RPKM value for the 3 different conditions

source_name: Chemostat culture

extract_protocol: Total cell RNA was extracted from cells collected from the 3 different cull cultures with the RiboPure-Bacteria Kit (Ambion) in accordance with the manufacturer’s instructions. An additional DNase I treatment was performed (provided within the RiboPure-Bacteria Kit). RNA quality was checked by agarose-gel electrophoresis, and the RNA concentration was measured with a Nanodrop ND-1000 spectrophotometer (Isogen Life Science). First-strand cDNA was generated with RevertAid H Minus M-MuLV Reverse Transcriptase (Fermentas Life Sciences), in accordance with the manufacturer’s protocol. Second-strand cDNA synthesis was performed with RNase H (Fermentas Life Sciences) and DNA polymerase I (Fermentas Life Sciences) in accordance with the manufacturer’s protocol. Purification of the double-stranded DNA for sequencing was performed with the Qiaquick PCR Purification Kit (Qiagen) in accordance with the manufacturer’s instructions. For sequencing the samples were prepared in accordance with the manufacturer’s protocol (Illumina). Subsequent sequencing was conducted on a genome Analyser II (Illumina).

value: SolV

value: nitrogen fixing conditions


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_diffProtD_3hr_Timecourse

status: Public on Aug 31 2012

first: ENCODE

last: DCC

address: 300 Pasteur Dr

institute: ENCODE DCC

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

value: M

tag: antibody antibodydescription

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

tag: antibody targetdescription

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

tag: treatment description

value: 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

value: Timecourse

tag: age description

value: Embryonic day 0 (stem cell)

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid

tag: replicate

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_diffProtD_7hr_Timecourse

tag: lab

tag: lab description

tag: datatype

tag: datatype description

tag: antibody

tag: treatment

value: 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: age

tag: strain


title: Cells growing at μmax

source_name: Batch culture

value: SolV

value: growing at μmax


title: unc-62 RNAi rep3

description: 3' end enriched poly-A RNA

tag: RNAi

value: unc-62 RNAi

tag: genotype

tag: tissue

value: whole worms


title: Arabidopsis thaliana Microspore

city: Cold Spring Harbor

first: Joseph

last: Calarco

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

institute: Cold Spring Harbor Laboratory

data_processing:
Bases were called using CASAVA (version 1.6.0 and version 1.8.2)
Paired end reads were mapped using Bismark Bisulfite Read Mapper and Methylation caller (version: v0.4.10) (Krueger et al 2012) using the default settings and bowtie as the underlying genome mapper.
Bismark's  Methylation_extractor was used to extract the methylation status at each cytosine on each read.
The number of unmethylated and methylated bases per locus were collated and percent methylation per locus was calculated as: percent methylation = number of methylated bases / (number of methylated bases + number of unmethylated bases).
Genome_build: Arabidopsis thaliana TAIR10
Supplementary_files_format_and_content: GFF format. Column one: chromosome, column two: source (corrosponding author), column three: feature (methylation context), column four: start position, column five: end position, column six: score (percent of methylated reads), column seven: strand, column eight: frame (not relevant set to '.'), column nine: attributes (number of Cs and Ts called at locus).

organism: Arabidopsis thaliana

source_name: Purified microspores

growth_protocol: All samples were grown with standard long day arabidopsis growth contidions, 16 hour long days at 24C (Weigel and Glazebrook 'Arabidopsis A laboratory Manual' 2002).

extract_protocol: Genomic DNA was isolated from approximately 600,000 sperm cells, 300,000 vegetative nuclei and 1,000,000 microspores isolated by FACS (Borges et al., 2012) and fragmented by Covaris in 10mM Tris-HCl, pH 8.0. Fragments were end repaired, A-tailed and ligated to methylated Illumina adaptors. Ligated fragments were bisulfite treated using the EZ DNA Methylation-Gold Kit (Zymo), and PCR enriched with Expand High-Fidelity Polymerase (Roche). Amplified fragments of 340-360bp were size selected by gel extraction, and sequenced on an Illumina GAII platform as paired end 50 nt (PE50) reads.

treatment_protocol: Purified DNA was treated with Sodium Bisulphite during library production (Zymo Sciences DNA methylation Gold Kit).

tag: ecotype

value: developing pollen

tag: cell type

value: FACS-purified microspores


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_diffProtD_24hr_Timecourse

value: PSU-m

value: Hardison - Penn State University

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell

tag: cell organism

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

value: M

tag: antibody antibodydescription

tag: antibody targetdescription

tag: antibody vendorname

tag: antibody vendorid

tag: treatment description

value: 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

tag: age description

tag: control

tag: control description


title: Olig2_ChIP-seq

city: Dallas

first: Qing

middle: Richard

last: Lu

address: 5323 Harry Hines Boulevard

institute: UT southwestern medical center

data_processing:
ChIP-seq reads were aligned to the rn4 genome assembly using the GERALD.pl script from the Illumina CASAVA 1.7.0 software package.
Peaks were called using MACS version 1.40 with default settings.
Peaks were annotated using CisGenome software.
Genome_build: rn4
Supplementary_files_format_and_content: Wig files were generated using MACS using default parameters.

organism: Rattus norvegicus

source_name: primary oligodendrocytes, Olig2 ChIP

growth_protocol: Differentiating oligodendrocytes (1X10^7 cells) were harvested from purified rat oligodendrocyte progenitor cells (OPCs) cultured in oligodendrocyte differentiation medium for 3 days.

extract_protocol: Chromatin preparation, ChIP, DNA purification, and library preparation for Illumina sequencing were performed using a ChIP-Seq DNA Prep Kit (Illumina) according to the manufacturer's instructions.

tag: strain

value: Sprague-Dawley

value: differentiating oligodendrocytes

tag: differentiation stage

value: 70 hours of in vitro differentiation

tag: chip antibody

tag: antibody vendor

value: Abcam

tag: antibody catalog number


title: Otiwi1 RNA-ChIP at 23 hr post-mixing

description:
small RNA sequencing
piRNA_23hr
barcode: TGACCA

tag: cell type

value: mating cells

tag: developmental stage

value: 23 hr post-mixing of opposite mating types

tag: sample composition

value: 80% of the cells are early exconjugants, less than 10% are mating pairs. The rest are vegetative cells and cysts.

tag: rip antibody

value: Otiwi1 antibody (Abcam, cat# ab12337, lot#868987)


title: d0h_small RNA-seq

city: Stockholm

first: Johan

last: Reimegård

state: Solna

address: Tomtebodavägen 23A

country: Sweden

institute: Science for Life Laboratories

data_processing:
Remove adaptersequence using in-house program (available upon request)
Map reads to the genome sequence
Remove reads that are not 21 nt
Remove reads that map to more than 10 locations
Remove reads that likely come from siRNAs
Remove reads where the surrounding sequence does not correspond to a potential pre-miRNA structure
Supplementary_files_format_and_content: the count of the miRNA and their sequence

organism: Dictyostelium discoideum

source_name: single-cells

growth_protocol: Cell were grown in HL5 liquid media (0h) and developed in PDF buffer on nitrocellulose filters (16h and 24h)

extract_protocol: Total RNA was isolated using TRIzol. Small RNA was enriched using FlashPAGE (Ambiont). The SOLiD Small RNA Expression system (Applied Biosystems) was used for preparation of cDNA and multiplexing and subsequently sequenced using the SOLiD technology.

value: 0 hour single cells


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_Timecourse

tag: lab

value: PSU-m

tag: lab description

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

tag: antibody

tag: antibody antibodydescription

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

tag: antibody targetdescription

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

value: Santa Cruz Biotech

tag: treatment

value: No special treatment or protocol applies

value: Timecourse

tag: age

value: Embryonic day 0 (stem cell)

value: Input

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid

tag: replicate

tag: strain description

value: Strain 129, has widely available embryonic stem cells


title: d24h_small RNA-seq

source_name: developing multicellular cells

tag: strain

tag: cell type

value: 24 hour developing multicellular cells


title: d16h_small RNA-seq

value: 16 hour developing multicellular cells


title: PSU_RnaSeq_G1E-ER4_diffProtD_3hr_paired-end (superseded by GSE90214)

description:
****************************
GSM995538 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90214
****************************

extract_protocol: For more information, see http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=mm9&g=wgEncodePsuRnaSeq

tag: lab

tag: lab description

value: Hardison - Penn State University

value: RnaSeq

value: Sequencing analysis of RNA expression

value: mouse

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

tag: treatment description

value: 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

value: paired-end

tag: age description

tag: readtype

tag: readtype description

value: Paired 99 nt directed reads


title: Cells growing under oxygen limitation

value: SolV

value: oxygen limitation


title: PSU_RnaSeq_G1E-ER4_diffProtD_24hr_paired-end (superseded by GSE90215)

description:
****************************
GSM995539 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90215
****************************

value: PSU-m

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

tag: cell sex

value: 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

value: Embryonic day 0 (stem cell)


title: Ch_Y06-147__Pt_ca_24

first: Genevieve

last: Konopka

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

data_processing: Reads were aligned to the genome and RefSeq using bfast.  Up to one mismatch was allowed.  Only reads that aligned to one genomic location were used.

source_name: chimp, caudate nucleus

extract_protocol: RNA extracted using Qiagen Rneasy kit; library made using Illumina DpnII protocol

tag: brain region

value: caudate nucleus

tag: isolate


title: Ma_Y04-05__Ryd-1_FP_1

organism: Macaca mulatta

source_name: macaque, frontal pole

value: frontal pole


title: PSU_RnaSeq_FVLstem_paired-end (superseded by GSE90208)

description:
****************************
GSM995535 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90208
****************************

source_name: FVLstem

value: FVLstem

value: Friend virus infected murine CD34+,CD133+,Kit+,Sca1+ Leukemia stem cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). #PROVISIONAL

value: B

tag: treatment

value: No special treatment or protocol applies

tag: age

value: Adult between 8-10 weeks #PROVISIONAL

tag: replicate

tag: strain

value: BALB/cJ

tag: strain description

value: A common inbred strain of laboratory mouse. #PROVISIONAL


title: PSU_RnaSeq_Erythrobl_paired-end (superseded by GSE90207)

description:
****************************
GSM995533 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90207
****************************

source_name: Erythrobl

tag: lab

tag: lab description

value: Hardison - Penn State University

value: RnaSeq

value: Sequencing analysis of RNA expression

value: Erythrobl

value: mouse

value: Erythroblast, ter119+ cells from liver

tag: treatment description

tag: labexpid

value: Embryonic day 14.5

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_RnaSeq_G1E-ER4_diffProtD_30hr_paired-end (superseded by GSE90216)

description:
****************************
GSM995541 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90216
****************************

value: PSU-m

tag: datatype

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

value: paired-end

tag: age description

value: Embryonic day 0 (stem cell)

tag: readtype

tag: readtype description

value: Paired 99 nt directed reads

value: Strain 129, has widely available embryonic stem cells


title: Control ChIP-seq

source_name: primary oligodendrocytes, control ChIP

value: Sprague-Dawley

tag: cell type

value: differentiating oligodendrocytes

tag: differentiation stage

value: 70 hours of in vitro differentiation

tag: chip antibody

value: control IgG

tag: antibody vendor

value: Abcam

tag: antibody catalog number


title: PSU_RnaSeq_G1E-ER4_paired-end (superseded by GSE90213)

description:
****************************
GSM995532 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90213
****************************

value: Hardison - Penn State University

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

tag: cell organism

value: mouse

tag: cell description

tag: cell sex

tag: treatment

value: No special treatment or protocol applies

tag: age


title: PSU_RnaSeq_FVprogenitor_paired-end (superseded by GSE90209)

description:
****************************
GSM995534 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90209
****************************

source_name: FVprogenitor

tag: lab

value: PSU-m

tag: lab description

value: FVprogenitor

value: Friend virus infected murine CD34-,CD133-,Kit+,Sca1+ progenitor cells. Strains which can be used to generate the cells must carry the Fv2 sensitive allele (Fv2s). #PROVISIONAL

value: B

tag: treatment description

tag: labexpid

value: Adult between 8-10 weeks #PROVISIONAL

tag: replicate

tag: strain

value: BALB/cJ

tag: strain description

value: A common inbred strain of laboratory mouse. #PROVISIONAL


title: PSU_RnaSeq_G1E-ER4_diffProtD_7hr_paired-end (superseded by GSE90212)

description:
****************************
GSM995531 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90212
****************************

tag: datatype

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

value: paired-end

tag: age description

value: Embryonic day 0 (stem cell)

tag: readtype

tag: readtype description

value: Paired 99 nt directed reads

value: Strain 129, has widely available embryonic stem cells


title: PSU_RnaSeq_G1E_paired-end (superseded by GSE90210)

description:
****************************
GSM995536 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90210
****************************

value: Hardison - Penn State University

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

value: Gata1- erythroid progenitor


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_diffProtD_30hr_Timecourse

value: PSU-m

value: ChipSeq

value: Chromatin IP Sequencing

tag: cell organism

value: mouse

tag: cell description

tag: antibody

tag: antibody antibodydescription

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

tag: antibody targetdescription

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

value: Timecourse

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid


title: PSU_ChipSeq_G1E-ER4_Input_Timecourse

tag: lab

tag: lab description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

value: M

tag: antibody description

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

tag: age

value: Embryonic day 0 (stem cell)

tag: replicate

tag: strain

tag: strain description


title: PSU_RnaSeq_MEL_DMSO_2.0pct_single (superseded by GSE93476)

description:
****************************
GSM995526 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93476
****************************

source_name: MEL

value: Hardison - Penn State University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell

value: MEL

tag: cell organism

tag: cell description

value: Leukemia (K562 analog)

value: 5 d with 2% Dimethyl sufloxide (DMSO) (Weissman)

value: single

value: immortalized

tag: age description

value: Immortal cells

tag: readtype

tag: readtype description

value: Single 45 nt reads

value: Unknown

value: Unknown strain origin


title: PSU_RnaSeq_Megakaryo_paired-end (superseded by GSE90217)

description:
****************************
GSM995537 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90217
****************************

source_name: Megakaryo

tag: lab

value: PSU-m

tag: lab description

value: Megakaryo

value: mouse

value: Megakaryocyte

tag: cell sex

value: B

value: paired-end

value: Embryonic day 14.5

value: Paired 99 nt directed reads

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_RnaSeq_MEP_paired-end (superseded by GSE90218)

description:
****************************
GSM995525 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90218
****************************

source_name: MEP

value: Hardison - Penn State University

value: RnaSeq

value: Sequencing analysis of RNA expression

value: MEP

value: mouse megakaryocyte erythroid progenitor cells with lineages CD16/32 and CD34-

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

value: Adult 5 weeks

value: A substrain of C57BL/6


title: PSU_RnaSeq_G1E-ER4_diffProtD_14hr_paired-end (superseded by GSE90211)

description:
****************************
GSM995527 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90211
****************************

value: PSU-m

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

tag: age

value: Embryonic day 0 (stem cell)

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_Megakaryo_TAL1_(SC-12984)

value: ChipSeq

value: Chromatin IP Sequencing

value: Megakaryo

value: mouse

value: Megakaryocyte

value: B

tag: antibody

tag: antibody antibodydescription

value: goat polyclonal antibody; epitope mapping at the C-terminus of TAL1 of human origin, recommended for detection of TAL1 of mouse, rat and human origin. Antibody Target:TAL1

tag: antibody targetdescription

value: TAL1 (also designated SCL) is a serine phosphoprotein and basic helix-loop-helix transcription factor known to regulate embryonic hematopoiesis.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: Embryonic day 14.5

tag: control

value: Input

tag: control description

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: controlid

tag: strain


title: PSU_ChipSeq_G1E-ER4_Input_diffProtD_14hr_Timecourse

value: PSU-m

value: Hardison - Penn State University

tag: datatype

tag: datatype description

tag: cell

tag: cell organism

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: antibody description

value: Timecourse

tag: age description

tag: replicate

tag: strain description


title: PSU_ChipSeq_G1E-ER4_GATA1_(SC-265)_diffProtD_14hr_Timecourse

tag: lab

tag: lab description

tag: cell sex

value: M

tag: antibody

tag: antibody antibodydescription

value: rat monoclonal antibody raised against mouse recombinant GATA1; recommended for detection of GATA1 of mouse, rat and human origin. Antibody Target:GATA1

value: GATA1 is erythroid-specific and is responsible for the regulated transcription of erythroid genes.

tag: treatment

tag: treatment description

value: 14 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

tag: age

value: Embryonic day 0 (stem cell)

value: Strain 129, has widely available embryonic stem cells


title: PSU_ChipSeq_G1E-ER4_Input_diffProtD_30hr_Timecourse

tag: datatype

value: ChipSeq

tag: datatype description

value: Chromatin IP Sequencing

value: mouse

value: 30 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: control

tag: control description

tag: controlid

tag: strain


title: PSU_ChipSeq_G1E-ER4_Input_diffProtD_3hr_Timecourse

tag: cell

tag: cell organism

tag: cell description

tag: antibody description

value: 3 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: age description

tag: replicate


title: PSU_ChipSeq_Megakaryo_FLI1_(sc-356)

tag: lab

tag: lab description

value: Megakaryo

value: Megakaryocyte

tag: cell sex

value: B

tag: antibody

tag: antibody antibodydescription

value: FLI1 (C-19) is an affinity purified rabbit polyclonal antibody raised against a peptide mapping at the C-terminus of FLI1 of mouse origin.

tag: antibody targetdescription

value: Fli1 (Friend leukemia virus integration 1) is a member of a family of genes identified on the basis of their homology to the v-Ets oncogene isolated from the E26 erythoblastosis virus.

tag: antibody vendorname

value: Santa Cruz Biotech

tag: antibody vendorid

value: Embryonic day 14.5

value: Input

tag: strain description

value: Multipurpose mouse used for safety testing, aging studies, surgical models and pseudopregnancy.


title: PSU_ChipSeq_G1E-ER4_Input_diffProtD_7hr_Timecourse

value: PSU-m

value: Hardison - Penn State University

tag: datatype

tag: datatype description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

value: M

value: Control signal which may be subtracted from experimental raw signal before peaks are called.

tag: treatment

tag: treatment description

value: 7 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

value: Timecourse

tag: age

tag: control

tag: control description

tag: controlid


title: PSU_RnaSeq_MEL_single (superseded by GSE93475)

description:
****************************
GSM995528 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93475
****************************

tag: lab

tag: lab description

value: RnaSeq

value: Sequencing analysis of RNA expression

tag: line

value: MEL

tag: cell organism

value: mouse

tag: cell description

value: Leukemia (K562 analog)

value: No special treatment or protocol applies

value: single

value: immortalized

value: immortalized cell line

tag: readtype

tag: readtype description

value: Single 45 nt reads

tag: replicate

tag: strain

value: Unknown

value: Unknown strain origin


title: Sample 12_whole transcriptome (RNA-seq)

middle: S

last: Takahashi

address: 5323 Harry Hines Blvd., NA4.118

department: HHMI, Neuroscience

institute: University of Texas Southwestern Medical Center

data_processing:
Sequence reads were mapped to the mouse genome (NCBI m37/mm9) with Applied Biosystems BioScope v1.3 to create Wig and BigWig files for visualization on the UCSC Genome Browser.
Wig files were normalized to display uniquely mapped reads per 10 million total number of  reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigWig

source_name: whole transcriptome (RNA-seq)

growth_protocol: Male C57BL/6J at 8-12 weeks of age were housed in light-tight boxes and entrained to LD12:12 conditions. After a minimum of 7 days, animals were transferred to constant darkness (DD) conditions. Thirty-six hours after DD, liver samples (N=3 mice) were collected every 4 hrs.

extract_protocol:
RNA was isolated from livers using Trizol reagent according to the manufacturer’s instructions (Life Technologies).
10 μg of total RNA pooled from three mice (individual mouse RNA samples with RIN values of 8-9) was depleted of ribosomal RNAs using RiboMinus Eukaryote Kit for RNA-seq according to the manufacturer’s instructions (Life Technologies).
The removal of ribosomal RNAs was confirmed on a Bioanalyser Pico Chip (Agilent). Sequencing libraries were constructed using SOLiD Total RNA-seq Kit (Life Technologies) with a modification below.
A total of 1 μg of rRNA-depleted total RNA was fragmented in the 30 μl of T4 PNK buffer for 18 min at 95°C and placed on ice immediately.
Fragmented RNA was phosphorylated by adding 2 μl of T4 PNK and 1 mM ATP for 60 min at 37°C and purified by RiboMinus Concentration module (Life Technologies) prior to the adaptor ligation.

tag: strain background

tag: gender

value: male

tag: genotype/variation

value: wild-type

tag: tissue

value: liver

tag: time

tag: molecule subtype

value: rRNA depleted total RNA


title: Sample 9_whole transcriptome (RNA-seq)


title: Sample 8_whole transcriptome (RNA-seq)


title: Sample 10_whole transcriptome (RNA-seq)


title: Sample 11_whole transcriptome (RNA-seq)


title: Sample 7_whole transcriptome (RNA-seq)


title: Sample 5_whole transcriptome (RNA-seq)


title: Sample 2_whole transcriptome (RNA-seq)


title: Sample 6_whole transcriptome (RNA-seq)


title: Sample 1_whole transcriptome (RNA-seq)


title: Sample 3_whole transcriptome (RNA-seq)


title: Sample 138_Input DNA for H3K36me3/K79me2 ChIP-seq #2

data_processing:
Sequence reads were mapped to the mouse genome (NCBIm37/mm9) with Applied Biosystems BioScope v1.3.
In order to adjust for differences in sequencing depth among time samples, the sequence reads were “down sampled” to the lowest number of the uniquely mapped reads with duplicates among the six time points for each ChIP factor.
PCR duplicates were removed using Picard MarkDuplicates.
Genome_build: mm9
Supplementary_files_format_and_content: The .bw files show the sequence read density across the mm9 mouse genome. The bed files show where the transcription factors or histone marks bind.

extract_protocol:
The immunoprecipitated DNA fragments were repaired by the End-It DNA End Repair Kit (Epicentre Biotechnology) according to the manufacturer’s instructions. The end-repaired ChIP DNA fragments  ere purified by MinElute Reaction Cleanup Kit (Qiagen) and eluted in 20 μl in EB buffer.
The resulting DNA fragments were ligated with P1 and P2 adaptors for the Applied Biosystems SOLiD system for 20 min at room temperature using the Quick Ligase Kit (NEB), followed by purification using the MinElute Reaction Cleanup Kit (Qiagen).
The purified, adaptor-ligated ChIP DNA fragments were run on 5% native polyacrylamide gel electrophoresis (PAGE) for an in-gel PCR reaction. A gel slice containing 175–200 bp adaptor-ligated ChIP DNA fragments (corresponding to 115-140 bp genomic gment sizes) was cut and shredded.
PCR Platinum Supermix (100 μl, Invitrogen), 50 pmol of PCR primers with barcodes, 0.5 μl Taq DNA polymerase (NEB), and 0.15 μl p.f.u. Turbo DNA polymerase (Stratagene) were added into the shredded gel slice.
The adaptor-ligated ChIP DNA fragments were amplified by 14-19 cycles of in-gel PCR. After the PCR reaction, gel pieces were filtered out with a 0.45 μm filter spin column, and the amplified ChIP-seq library was purified by the MinElute PCR purification kit (Qiagen).
The library was purified by one more round of 5% PAGE. A gel slice containing 200-230 bp PCR products (110-130 bp fragment size) was cut and shredded, and the amplified library was extracted out of the gel by passive elution in elution buffer (2.5 M ammonium acetate in TE).
Gel pieces were removed with a spin column, and the resulting ChIP-seq library was purified using the QIAquick PCR purification kit (Qiagen).

value: mixture of CT0 to 20

tag: chip antibody


title: Sample 136_H3K79me2 ChIP-seq

source_name: H3K79me2 ChIP-seq

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot #


title: Sample 137_Input DNA for H3K36me3/K79me2 ChIP-seq #1


title: Sample 133_H3K79me2 ChIP-seq


title: Sample 135_H3K79me2 ChIP-seq


title: Sample 130_H3K36me3 ChIP-seq

source_name: H3K36me3 ChIP-seq


title: Sample 132_H3K79me2 ChIP-seq


title: Sample 131_H3K79me2 ChIP-seq


title: Sample 128_H3K36me3 ChIP-seq


title: Sample 126_H3K36me3 ChIP-seq


title: Sample 125_H3K36me3 ChIP-seq


title: Sample 127_H3K36me3 ChIP-seq


title: Sample 4_whole transcriptome (RNA-seq)


title: Twi12endo native 2-step IP

city: Boston

first: Mary

middle: T

last: Couvillion

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: 5' linker: ACACUCUUUCCCUACACGACGCUCUUCCGAUCU (RNA); 3' linker: (AMP)CTGTAGGCACCATCAATddC (DNA); Sequencing primer: ACACTCTTTCCCTACACGACGCTCTTCCGATCT

data_processing:
Finding the 3' end varying-length adaptor (no 5' end adaptor in the raw data, 3' end adaptor is cleaved at 36 bases); Software: Python script
i) First search for the adaptor with no mismatch, and then consecutively look for matches with 1, 2 and 3 mismatches, where mismatches are only allowed in the last 6 nucleotides, which are known to be lower quality based on quality scores per base plots
ii) For the remaining lower quality reads, search for the adaptor sequence by looking for perfect match only in the first 6 nucleotides in the adaptor
Remove reads where adaptor is not found, given the rules set in the previous steps
Remove reads where adaptor is found at less than 8 nt from the 5' end: short reads with less than 8 nucleotides were considered invalid (all removed reads are 0.89% of the original library)
Compare short reads length distribution (7%, 77%, 16%)  with the lengths distribution of the library prep (10%, 50%, 40%)
Genome_build: http://www.ncbi.nlm.nih.gov/nuccore?term=GG662205:GG663362%5BPACC%5D
Supplementary_files_format_and_content: three fastq files, text format, table style, columns: read sequence, read length, frequency observed in the library

organism: Tetrahymena thermophila

source_name: cells

growth_protocol: media: 1xSPP, 30 degrees C.

extract_protocol: ZZ-TEV-3xFLAG-Twi12 was affinity purified with IgG agarose, TEV elution, anti-FLAG resin, and FLAG peptide elution. Bound RNA was Phenol-chloroform extracted and resolved by urea-PAGE. RNA in the size range ~10-12 nt and ~18-25 nt was gel extracted and ligated to adaptors in 3 reactions (~10-12 nt, ~18-22 nt, and ~23-25 nt). Libraries were combined for Illumina sequencing.

tag: life cycle stage

value: Vegetative growth

tag: sample type

value: small RNAs associated with ZZF-tagged Twi12

tag: antibody

value: anti-Flag


title: Sample 116_H3K9ac ChIP-seq

source_name: H3K9ac ChIP-seq


title: Sample 115_H3K9ac ChIP-seq


title: Sample 117_Input DNA for H3K9ac ChIP-seq

source_name: Input DNA for H3K9ac ChIP-seq


title: Sample 114_H3K9ac ChIP-seq


title: Sample 113_H3K9ac ChIP-seq


title: Sample 109_H3K4me3 ChIP-seq

source_name: H3K4me3 ChIP-seq


title: Sample 112_H3K9ac ChIP-seq


title: Sample 108_H3K4me3 ChIP-seq


title: Sample 134_H3K79me2 ChIP-seq


title: Sample 111_H3K9ac ChIP-seq


title: Sample 104_H3K4me3 ChIP-seq


title: Sample 106_H3K4me3 ChIP-seq


title: Sample 107_H3K4me3 ChIP-seq


title: Sample 105_H3K4me3 ChIP-seq


title: Sample 129_H3K36me3 ChIP-seq


title: Sample 100_H3K4me1 ChIP-seq

source_name: H3K4me1 ChIP-seq


title: Sample 102_H3K4me1 ChIP-seq


title: Sample 103_Input DNA for H3K4me1 ChIP-seq

source_name: Input DNA for H3K4me1 ChIP-seq


title: Sample 97_H3K4me1 ChIP-seq


title: Sample 88_RNAPII-8WG16 ChIP-seq

source_name: RNAPII-8WG16 ChIP-seq

value: Covance


title: Sample 98_H3K4me1 ChIP-seq


title: Sample 99_H3K4me1 ChIP-seq


title: Sample 87_RNAPII-8WG16 ChIP-seq


title: Sample 86_RNAPII-8WG16 ChIP-seq


title: Sample 85_RNAPII-8WG16 ChIP-seq


title: Sample 84_RNAPII-8WG16 ChIP-seq


title: Sample 82_Input DNA for p300 ChIP-seq

source_name: Input DNA for p300 ChIP-seq


title: Sample 81_Input DNA for CBP ChIP-sseq

source_name: Input DNA for CBP ChIP-sseq


title: Sample 80_p300 ChIP-sseq

source_name: p300 ChIP-sseq

tag: chip antibody reference

value: custom made, epitope:residues 60-242 of human p300, host:guinea pig


title: Sample 79_p300 ChIP-sseq


title: Sample 78_p300 ChIP-sseq


title: Sample 76_p300 ChIP-sseq


title: Sample 74_CBP ChIP-seq

source_name: CBP ChIP-seq

value: monoclonal AC238 culture supernatant

value: Eckner et al., 1996, Mol Cell Biol., 16, 3454-3464


title: Sample 77_p300 ChIP-sseq


title: Sample 73_CBP ChIP-seq


title: Sample 101_H3K4me1 ChIP-seq


title: Sample 75_p300 ChIP-sseq


title: Sample 68_Input DNA for CRY1/CRY2 ChIP-seq

source_name: Input DNA for CRY1/CRY2 ChIP-seq


title: Sample 71_CBP ChIP-seq


title: Sample 69_CBP ChIP-seq


title: Sample 89_Input DNA for RNAPII-8WG16 ChIP-seq

description: Raw data files for Sample 8 [GSM982695] were also used.

source_name: Input DNA for RNAPII-8WG16 ChIP-seq


title: Sample 72_CBP ChIP-seq


title: Sample 67_CRY2 ChIP-seq

source_name: CRY2 ChIP-seq

value: Cry1/Cry2 double KO

value: custom made, epitope:residues 514-592 of mouse CRY2, host:guunea pig


title: Sample 83_RNAPII-8WG16 ChIP-seq


title: Sample 70_CBP ChIP-seq


title: Sample 66_CRY2 ChIP-seq


title: Sample 65_CRY2 ChIP-seq


title: Sample 64_CRY2 ChIP-seq


title: Sample 63_CRY2 ChIP-seq


title: Sample 59_CRY1 ChIP-seq

source_name: CRY1 ChIP-seq

value: Lee et al., 2004, Mol Cell Biol., 24, 584–594


title: Sample 62_CRY2 ChIP-seq


title: Sample 60_CRY1 ChIP-seq

value: Cry1 KO


title: Sample 58_CRY1 ChIP-seq

value: male


title: Sample 55_CRY1 ChIP-seq

value: wild-type


title: Sample 53_Input DNA for PER1/PER2 ChIP-seq

source_name: Input DNA for PER1/PER2 ChIP-seq

value: liver


title: Sample 57_CRY1 ChIP-seq


title: Sample 54_CRY1 ChIP-seq


title: Sample 56_CRY1 ChIP-seq


title: Sample 49_PER2 ChIP-seq

source_name: PER2 ChIP-seq


title: Sample 47_PER2 ChIP-seq


title: Sample 50_PER2 ChIP-seq


title: Sample 52_PER2 ChIP-seq

value: Per2 KO


title: Sample 51_PER2 ChIP-seq


title: Sample 61_CRY2 ChIP-seq


title: Sample 46_PER2 ChIP-seq


title: Sample 48_PER2 ChIP-seq


title: Sample 44_PER1 Chip-sseq

source_name: PER1 Chip-sseq


title: Sample 45_PER1 Chip-sseq

value: Per1/Per2 double KO


title: Sample 41_PER1 Chip-sseq


title: Sample 40_PER1 Chip-sseq


title: Sample 42_PER1 Chip-sseq


title: Sample 39_PER1 Chip-sseq


title: PSU_RnaSeq_CH12_single (superseded by GSE93474)

description:
****************************
GSM995540 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93474
****************************

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: line

tag: cell organism

value: mouse

tag: cell description

value: B-cell lymphoma (GM12878 analog)

tag: cell sex

value: F

tag: treatment

tag: treatment description

value: No special treatment or protocol applies

tag: labexpid

value: single

tag: age

value: immortalized

value: immortalized cell line

tag: readtype

tag: readtype description

value: Single 41 nt reads

tag: strain description

value: Derived by inbreeding from selected F2 progeny of B10.A X B10.129


title: PSU_RnaSeq_G1E_single (superseded by GSE90219)

description:
****************************
GSM995530 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE90219
****************************

tag: cell

value: Gata1- erythroid progenitor

value: M

tag: age description

value: Embryonic day 0 (stem cell)

value: Single 36 nt reads

tag: replicate

tag: strain

value: Strain 129, has widely available embryonic stem cells


title: Sample 37_Input DNA for CLOCK ChIP-seq

source_name: Input DNA for CLOCK ChIP-seq

tag: strain background

tag: genotype/variation

value: wild-type

tag: gender

value: male

tag: tissue

value: liver

tag: time

value: mixture of CT0 to 20

tag: chip antibody


title: Sample 31_NPAS2 ChIP-seq

source_name: NPAS2 ChIP-seq

tag: chip antibody reference


title: Sample 35_NPAS2 ChIP-seq


title: Sample 36_NPAS2 ChIP-seq


title: A549 shRNA SOX2

city: Tianjin

last: LI

address: 94 Weijin Road

country: China

institute: NANKAI University

data_processing:
Base calling files was generated by RTA1.12 and converted to quality and sequence files using BclConverter.
Low quality reads were trimmed and adapter sequences were clipped with the aid of a dynamic programming algorithm. Clean tags were mapped to human reference genome (hg19) using SOAPaligner.
The number of unambiguous clean tags for each gene was calculated and then normalized to TPM (number of transcripts per million clean tags).
Genome_build: hg19
Supplementary_files_format_and_content: excel file includes TPM values for each Sample

source_name: A549 cell line

extract_protocol: 4 ug total RNA from each sample was extracted by TRIzol reagent.

treatment_protocol: The A549-H1tetO-shRNA-SOX2 and its control cell A549-H1tetO-shRNA-Con were collected after 4 day's incubation with Doxycycline to induce the expression of shRNA.

tag: cell type

value: lung adenocarcinoma cell line

tag: cell line

tag: knockdown


title: Sample 34_NPAS2 ChIP-seq


title: Sample 32_NPAS2 ChIP-seq


title: PSU_RnaSeq_G1E-ER4_diffProtD_24hr_single (superseded by GSE93477)

description:
****************************
GSM995529 record metadata submitted on Aug 31 2012 may be obsolete, up to date experimental metadata was resubmitted by ENCODE DCC and is available at GSE93477
****************************

tag: lab

value: PSU-m

tag: lab description

value: Hardison - Penn State University

tag: datatype

value: RnaSeq

tag: datatype description

value: Sequencing analysis of RNA expression

tag: cell organism

value: mouse

tag: cell description

value: Gata1 restored erythroid cells, differentiation induced by estradiol (E2)

tag: cell sex

tag: treatment

tag: treatment description

value: 24 hours differentiation of G1E-ER4 cells with 10 nM beta-estradiol (Hardison)

tag: labexpid

tag: age

tag: readtype


title: Sample 29_CLOCK ChIP-sseq

source_name: CLOCK ChIP-sseq

tag: strain background

tag: genotype/variation

tag: gender

tag: tissue

tag: time

tag: chip antibody

value: CLOCK


title: Sample 30_CLOCK ChIP-sseq

value: Clock-KO

tag: chip antibody reference


title: Sample 43_PER1 Chip-sseq


title: Sample 26_CLOCK ChIP-sseq


title: Sample 25_CLOCK ChIP-sseq


title: Sample 33_NPAS2 ChIP-seq


title: Sample 28_CLOCK ChIP-sseq


title: Sample 27_CLOCK ChIP-sseq


title: Sample 24_CLOCK ChIP-sseq


title: Sample 23_Input DNA for BMAL1 ChIP-seq_2cycle

source_name: Input DNA for BMAL1 ChIP-seq_2cycle

value: mixture from CT24 to 44


title: Sample 18_BMAL1 ChIP-seq-2cycle

source_name: BMAL1 ChIP-seq-2cycle


title: Sample 21_BMAL1 ChIP-seq-2cycle


title: Sample 12_BMAL1 ChIP-seq-2cycle


title: Sample 17_BMAL1 ChIP-seq-2cycle


title: Sample 16_BMAL1 ChIP-seq-2cycle


title: Sample 14_BMAL1 ChIP-seq-2cycle


title: Sample 13_BMAL1 ChIP-seq-2cycle


title: Sample 11_BMAL1 ChIP-seq-2cycle


title: A549 shRNA Con

tag: cell type

tag: cell line

tag: knockdown


title: Sample 10_BMAL1 ChIP-seq-2cycle


title: Sample 5_BMAL1 ChIP-seq

source_name: BMAL1 ChIP-seq


title: Sample 22_Input DNA for BMAL1 ChIP-seq_2cycle

value: mixture from CT0 to 20


title: Sample 9_BMAL1 ChIP-seq-2cycle


title: Sample 7_BMAL1 ChIP-seq


title: Sample 19_BMAL1 ChIP-seq-2cycle


title: Sample 20_BMAL1 ChIP-seq-2cycle


title: Sample 1_BMAL1 ChIP-seq


title: Sample 8_Input DNA for BMAL1 ChIP-seq

source_name: Input DNA for BMAL1 ChIP-seq


title: Sample 3_BMAL1 ChIP-seq


title: Sample 6_BMAL1 ChIP-seq


title: Sample 4_BMAL1 ChIP-seq


title: Sample 15_BMAL1 ChIP-seq-2cycle


title: Sample 2_BMAL1 ChIP-seq


title: Arabidopsis thaliana Sperm Cell

source_name: Purified sperm cells

tag: ecotype

value: developing pollen

value: FACS-purified sperm cells


title: Arabidopsis thaliana Vegetative Nucleus

source_name: Purified vegetative nuclei

value: FACS-purified vegetative nuclei


title: Sample 124_Input DNA for H3K27ac ChIP-seq

source_name: Input DNA for H3K27ac ChIP-seq

value: wild-type

value: male

value: liver


title: Sample 122_H3K27ac ChIP-seq

source_name: H3K27ac ChIP-seq

tag: chip antibody vendor

value: Abcam

tag: chip antibody cat.#

tag: chip antibody lot #


title: 320 bp library

city: New York

first: Philipp

last: Drewe

address: 417 East 68th Street

department: Computational Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Alignments preformed using Palmapper v0.4 with parameters: "-M 4 -G 1 -E 4 -l 15 -L 25 -K 12 -C 35 -I 25000 -NI 2 -SA 10 -CT 10 -z 10 -S -seed-hit-cancel-threshold 10000  -report-map-read -report-spliced-read  -report-map-region -report-splice-sites 0.8 -fil  ter-max-mismatches 0 -filter-max-gaps 0 -filter-splice-region 5 -qpalma-use-map-max-len 1000 -f sam  -polytrim 40 -qpalma-prb-offset-fix -QMM 7 " And using trained splice site predictors
Genome_build: WS199
Supplementary_files_format_and_content: bed file

source_name: mixed developmental stages

extract_protocol: Total RNA (150 µg) was isolated with Trizol (Invitrogen; # 15596-018) from C. elegans (strain N2) of mixed developmental stages and then mRNA purified with the µMACS mRNA Isolation kit following the manufacturer’s instructions (Miltenyi Biotec; # 130-090-276). After mRNA integrity was confirmed on a Bioanalyzer RNA 6000 Nano Chip (Agilent technologies; # 5067-1511), the 5’ cap was removed with 10 U of Tobacco Acid Pyrophosphatase (Epicentre Biotechnologies; # T19050) in the presence of 40 U Ribonuclease inhibitor (Fermentas; # EO0381) at 37 ºC for 90 min. RNA was purified using RNAqueous Micro columns (Ambion; # AM1931) and eluted in 2 x 9 µl, following the manufacturer’s LCM protocol with a few modifications: the sample volume was brought to 100 µl using lysis buffer; 1.25 volumes of ethanol were added to the sample unless otherwise noted; and no LCM additive was used.  2 µl of fragmentation buffer (Ambion; # AM8740) was used to fragment the RNA for 90 s at 70 ºC, followed by addition of 2 µl stop buffer and brief incubation on ice. RNA was purified using RNAqueous Micro columns (Ambion; # AM1931) and eluted in 2 x 8 µl. RNA was dephosphorylated then 5’ phosphorylated as in Levin et al.18 with the exception that we added Antarctic phosphatase buffer instead of PNK buffer for rephosphorylation. RNA was purified using RNAqueous Micro columns (Ambion; # AM1931), eluted in 2 x 10 µl, ethanol precipitated (-80 ºC overnight) and resuspended in 5.2 µl of DEPC-treated water. The 3’ and 5’ adaptors (adenylated-A and B respectively) were ligated as in Levin et al.18 but using 10 U T4 RNA ligase 2 truncated (Fermentas; # M0242) and T4 RNA ligase respectively (Fermentas; # EL0021). RNA was purified using RNAqueous Micro columns (Ambion; # AM1931), precipitating with 0.8 volumes of ethanol to remove un-ligated adaptors, eluted in 2 x 10 µl, ethanol precipitated (-80 ºC overnight) and resuspended in 5 µl of DEPC-treated water.  The RevertAid FirstStrand cDNA synthesis kit was used for reverse transcription (Fermentas; # K1621). 0.5 µl small RNA RT primer (D, 100 µM) was added to the RNA and incubated at 65 ºC for 10 min. 2 µl 5x First Strand Buffer, 1 µl 10 mM dNTPs and 0.5 µl RiboLock RNase inhibitor were added. After incubation at 48 ºC for 3 min, 1 µl RevertAid was added and the reaction incubated at 42 ºC for 1 h before deactivating the enzyme at 70 ºC for 10 min. 3 cycles of PCR were used to convert the ssDNA template into dsDNA (200 µl reaction volume, 1x GC buffer, 125 nM for each PCR primer (E and F), 250 µM dNTPs, 3 % DMSO and 4 U Phusion (Finnzymes; # F-530) with thermocycling conditions of 30 s at 98 ºC, 3 cycles of 10 s at 98 ºC, 45 s at 72 ºC, then an extension of 5 min at 72 ºC). Following ethanol precipitation (-80 ºC for at least 1 h), DNA was resuspended in 10 µl water and run on a 1 % agarose gel in 1 x TAE buffer. Regions with the desired insert sizes were excised, DNA extracted using the Qiaquick gel elution kit (Qiagen; # 28704) and eluted in 30 µl EB. Test PCRs were run to determine the optimum DNA dilution for each sample. Final PCRs were run (500-1500 µl reaction volume depending on test PCR results, 10 µl RT reaction, 1x GC buffer, 12 5nM for each PCR primer (E and F), 250 µM dNTPs, 3 % DMSO and 20 U/mL Phusion (Finnzymes; # F-530) with thermocycling conditions of 30 s at 98 ºC, 17 cycles of 10 s at 98 ºC, 45 s at 72 ºC, then an extension of 5 min at 72 ºC). PCR products were ethanol precipitated (-80 ºC for at least 1 h), resuspended in 10 µL of water and run on a 1 % agarose gel in 1 x TAE buffer. Regions with the desired insert sizes were excised, DNA extracted using the Qiaquick gel elution kit (Qiagen; # 28704) and eluted in 30 µl water. Library quality and concentration were evaluated on a Bioanalyzer DNA 1000 Chip (Agilent technologies: # 5067-1504). Library concentrations were brought to 10 nM with EB supplemented with 0.1 % Tween20.

tag: strain

tag: sample type

value: 320 bp library

value: whole organism


title: 595 bp library

value: 595 bp library


title: 155 bp library

value: 155 bp library


title: Sample 123_H3K27ac ChIP-seq


title: 480 bp library

value: 480 bp library


title: Sample 120_H3K27ac ChIP-seq


title: Sample 121_H3K27ac ChIP-seq


title: Sample 96_Input DNA for RNAPII-Ser5P ChIP-seq

source_name: Input DNA for RNAPII-Ser5P ChIP-seq

value: mixture of CT0 to 20


title: Sample 119_H3K27ac ChIP-seq


title: Sample 95_RNAPII-Ser5P ChIP-seq

source_name: RNAPII-Ser5P ChIP-seq

value: Millipore


title: Sample 118_H3K27ac ChIP-seq


title: Sample 94_RNAPII-Ser5P ChIP-seq


title: Sample 92_RNAPII-Ser5P ChIP-seq


title: Sample 91_RNAPII-Ser5P ChIP-seq


title: Sample 90_RNAPII-Ser5P ChIP-seq


title: Sample 93_RNAPII-Ser5P ChIP-seq


title: ctrl_trik4_wt_rep2

status: Public on Aug 30 2012

last: Rossell

address: Baldiri Reixac 10

institute: IRB Barcelona

description: Input DNA from wild type white dm.

data_processing:
Alignment files: FASTQ files were obtained with the standard Illumina Pipeline version 1.5.1. Reads were aligned to the dm3 genome with Bowtie version 0.12.5, keeping sequences mapping to a unique location in the genome with up to 2 mismatches in the first 28 bases. We removed PCR over-amplification artifacts by only keeping the first 100 appearances of a given sequence for analysis. We removed strand-specific biases with a procedure analogous to that proposed for the MACS algorithm.

Peak files: We defined peaks using a two-step procedure. Step 1: We found enriched genomic regions showing high accumulation of sequences in the IP sample compared to the control. We selected regions with coverage above 10 and compared the proportion of reads inside/outside of each region between the IP sample and its corresponding control with a logistic regression likelihood-ratio test. We defined enriched regions as those with Benjanimi-Yekutieli adjusted P-value < 0.05. Step 2: We defined peaks as location within the enriched regions (determined in Step 1) with coverage above 50. Bioconductor software was used for all data analysis unless where otherwise specified.

source_name: wing imaginal discs, wild type, input

growth_protocol: w1118, act5Cgal4>LID RNAi or lidk06801;act5Cgal4>lid RNAi larvae were grown at 25ºC until they became wall-climbing third instar larvae.

extract_protocol: Discs were crosslinked in 1.8% formaldehyde solution and sonicated. DNA-protein complexes were immunoprecipitated with anti-LID or anti-H3K4me3 antibodies. Commercial Abcam ab8580 antibodies were used as anti-H3K4me3. Custom-made anti-LID polyclonal antibodies were raised in rabbits from GST fusion proteins containing fragments of LID, and IgGs were purified for the ChIP experiments. Libraries were prepared according to Illumina's instructions accompanying the ChIP-Seq DNA Sample Prep Kit (Part# IP-102-1001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters, which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with Illumina primers for 16 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 40 (H3K4me3) and 36 (LID) nucleotides on the Illumina Genome Analyzer II following the manufacturer's protocols.

treatment_protocol: The LID RNAi strain was obtained from NIG-FLY and it was combined with lidk06801. For every sample, around 500 wing imaginal discs were dissected in PBS.

tag: genotype

value: wild type

tag: developmental stage

value: third instar larvae

value: wing imaginal discs


title: ctrl_trik4_r2_rep2

description: Input DNA from LID RNAi knock-down dm (in a mutant background).

source_name: wing imaginal discs, LID RNAi knock-down, input

value: LID RNAi


title: trik4_wt_rep1

description: Chromatin IP against H3K4me3 in wild type white dm.

source_name: wing imaginal discs, wild type, H3K4me3 ChIP

tag: antibody vendor

tag: antibody catalog number


title: lid

description: Chromatin IP against LID from wild type white dm.

source_name: wing imaginal discs, wild type, LID ChIP

tag: tissue

value: lid

value: custom-made


title: trik4_wt_rep2


title: trik4_r2_rep2

description: Chromatin IP against H3K4me3 in LID RNAi knock-down dm (in a mutant background).

source_name: wing imaginal discs, LID RNAi knock-down, H3K4me3 ChIP


title: ctrl_trik4_wt_rep1

description: Input DNA from wild type white dm.


title: trik4_r2_rep1


title: ctrl_lid

description: Input DNA from wild type white dm.