title: F71_A82V_T230A_2hr

value: 2 hour stimulation with A82V/T230A M-EBOV


title: F71_A82V_T230A_1hr

status: Public on Aug 31 2017

type: SRA

city: Worcester

first: Alper

last: Kucukural

state: MA

address: 364 Plantation Street

department: Program in Molecular Medicine

country: USA

institute: UMass Medical School

library_source: transcriptomic

data_processing:
Because of their lower quality, the first and last base of all reads was trimmed, we then used trimmomatic-0.32 to trim by quality, removing 5’ or 3’ stretches of bases having average quality of less than 20 in a window size 10
Only reads longer than 36 bases were kept for further analysis. After quality trimming reads were aligned to the human ribosomal RNA using Bowtie2 v 2.2.3 with parameters -p 2 -N 1 --no-unal
All reads mapped to rRNA were discarded from further analysis. To estimate gene and isoform expression in Transcripts per Million (TPM) units and raw counts (expected_count), we used RSEM v1.2.28
Genome_build: hg19
Supplementary_files_format_and_content: tsv, read counts and tpm normalized counts

molecule: total RNA

organism: Homo sapiens

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by gradient centrifugation on Histopaque-1077 and CD14+ mononuclear cells were enriched via positive selection using anti-CD14 antibody MicroBead conjugates, according to the manufacturer’s protocol. CD14+ cells were then plated at a density of 1 to 2 x 106 cells/ml in RPMI-1640 supplemented with 5% heat inactivated human AB+ serum, 20 mM L-glutamine, 75 mM HEPES pH 7.2, 1 mM sodium pyruvate, and 1 x MEM non-essential amino acids. Differentiation of the CD14+ monocytes into dendritic cells (MDDCs) was promoted by addition of recombinant human GM-CSF and human IL-4; cytokines were produced from HEK293 cells stably transduced with pAIP-hGMCSF-co or pAIP-hIL4-co, respectively, as previously described (C. Reinhard et al., Retrovirology, 2014) with each cytokine supernatant added at a dilution of 1:100.

extract_protocol:
Qiagen RNeasy Miniplus
Nugen Ovation FFPE RNA-seq

treatment_protocol: MDDCs were seeded at 5x10^5 cells per well in 24-well plates and incubated with 100ul HIV-derived lentiviral vector pseudotyped with M-EBOV founder or A82V-containing Ebola virus glycoprotein. These challenges were performed in a total volume of 250ul culture medium. Cells were harvested at times indicated postinnoculation with virus.

tag: donor id

value: healthy donor #F71

tag: cell type

value: monocyte-derived dendritic cells (MDDCs)

tag: stimulation

value: 1 hour stimulation with A82V/T230A M-EBOV


title: F71_A82V_4hr

value: 4 hour stimulation with A82V M-EBOV


title: F71_WT_1hr

value: 1 hour stimulation with founder M-EBOV


title: F71_0hr

value: Unstimulated


title: F70_WT_4hr

value: healthy donor #F70

value: 4 hour stimulation with founder M-EBOV


title: F71_A82V_1hr

value: 1 hour stimulation with A82V M-EBOV


title: F71_A82V_T230A_6hr

value: 6 hour stimulation with A82V/T230A M-EBOV


title: F70_A82V_T230A_6hr


title: F70_WT_1hr


title: F71_A82V_2hr

value: 2 hour stimulation with A82V M-EBOV


title: F71_A82V_6hr

value: 6 hour stimulation with A82V M-EBOV


title: F70_A82V_T230A_2hr


title: F71_A82V_T230A_4hr

value: 4 hour stimulation with A82V/T230A M-EBOV


title: F70_A82V_T230A_4hr


title: F70_WT_2hr

value: 2 hour stimulation with founder M-EBOV


title: F70_WT_6hr

value: 6 hour stimulation with founder M-EBOV


title: F70_A82V_T230A_1hr


title: F70_A82V_6hr


title: F70_A82V_4hr


title: F70_A82V_2hr


title: F70_0hr


title: F71_WT_6hr


title: hippocampus, TRF2 #3

city: Bethesda

first: Eros

last: Lazzerini Denchi

state: MD

address: 9000 Rockville Pike building 37, room 2144B

institute: National Cancer Institute

description:
TRF2 depleted, replicate
Hippo_cds_exp_diff

data_processing:
CASAVA 1.8
tophat2
cufflinks
cuffdiff
Genome_build: mm10
Supplementary_files_format_and_content: cuffdiff files

organism: Mus musculus

source_name: hippocampus, TRF2

extract_protocol:
RNAeasy kit from quiagen
NEBNext Ultra

tag: strain

tag: tissue

value: hippocampus

tag: genotype/variation

value: TRF2 depleted


title: hippocampus, TRF2 #1


title: hippocampus, TRF2 #2


title: hippocampus, control #2

description:
Control replicate
Hippo_cds_exp_diff

source_name: hippocampus, control

value: control


title: hippocampus, control #1

description:
Control replicate
Hippo_cds_exp_diff


title: Cortex, TRF2 #3

description:
TRF2 depleted, replicate
Cortex_cds_exp_diff

source_name: Cortex, TRF2

value: cortex


title: hippocampus, TRF2 #4


title: Cortex, TRF2 #2


title: Cortex, control #2

description:
Control replicate
Cortex_cds_exp_diff

source_name: Cortex, control


title: Cortex, TRF2 #1


title: RhoKO1

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Removed the low quality reads; Bowtie2 was used to map RNAseq to hg19 with default parameters.
RPKM was calculated to measure the genes expression level.
DESeq2 was used to call differential expressed genes.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file include the RPKM for each gene in each sample

source_name: CD4+ T cells, RhoKO

growth_protocol: CD4+ T cells was isolated from adoptively transferred T cell mice model using CD4 T cell isolation kit (miltenyibiotec).

extract_protocol:
RNA was isolated using Qiagen RNeasy mini kit.
RNAseq libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: WT and Tet2 knockout CD4+ T cells were transduced with retrovirus encoding GFP or Flag-RhoAG17V to yield four experimental groups: WT, Tet2-/-, RhoAG17V, Tet2-/-RhoAG17V). These T cells were transferred into TCRα-/- mice for 20 weeks and then purified from spleen and lymph nodes. RNA were purified from these cells and subjected to RNA-seq library preparation.

value: CD4+ T cells

value: RhoKO


title: DKO1

source_name: CD4+ T cells, DKO

value: DKO


title: Tet2KO2

source_name: CD4+ T cells, TetKO

value: TetKO


title: RhoKO2


title: DKO2


title: WT1

source_name: CD4+ T cells, WT

value: WT


title: F70_A82V_1hr

value: healthy donor #F70

value: monocyte-derived dendritic cells (MDDCs)


title: Tet2KO1


title: WT2


title: KO_10d_U_2

city: Boston

first: Zach

last: Herbert

address: 450 Brookline Ave

department: Molecular Biology Core Facilities

institute: Dana-Farber Cancer Institute

description:
Raw_Gene_Counts.csv
Normalized_FPKM_Gene_Counts.csv

data_processing:
Illumina Bcl2fastq v2.16
Sequencing reads were aligned to mm9 reference genome using STAR (v2.5)
Raw gene counts were generated from STAR output and normalized RPKM counts were generated using cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: comma separated value files containing raw gene counts and RPKM values for all samples

source_name: KO, 10d, U, kidney

extract_protocol:
Total RNA was extracted from kidney tissue using TRIzol according to manufacturer's protocol
Libraries were constructed using Illumina TruSeq stranded mRNAseq reagents and protocol and 1ug of total RNA input

value: kidney

tag: treatment

value: unilateral ureteral obstruction (UUO)

tag: time

value: day 10


title: KO_10d_U_4


title: KO_10d_U_3


title: KO_10d_U_1


title: hippocampus, control #3

description:
Control replicate
Hippo_cds_exp_diff


title: WT_10d_U_3

source_name: WT, 10d, U, kidney


title: WT_10d_U_4


title: KO_5d_U_3

source_name: KO, 5d, U, kidney

value: day 5


title: WT_10d_U_2


title: WT_10d_U_1


title: KO_5d_U_4


title: KO_5d_U_2


title: KO_5d_U_1


title: WT_5d_U_1

source_name: WT, 5d, U, kidney


title: Cortex, control #3

description:
Control replicate
Cortex_cds_exp_diff


title: KO_N_4

source_name: KO, N, kidney

value: day 0


title: Cortex, control #1

description:
Control replicate
Cortex_cds_exp_diff


title: Cortex, control #4

description:
Control replicate
Cortex_cds_exp_diff


title: KO_N_3


title: WT_5d_U_4


title: KO_N_1


title: WT_N_1

source_name: WT, N, kidney


title: KO_N_2


title: WT_N_3


title: WT_N_2


title: Tb4-primed, -injured MI heart input  rep1

city: Oxford

first: Joaquim

middle: Miguel

last: Vieira

address: South Parks Road

department: Department of Physiology, Anatomy & Genetics

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Sequence reads were mapped with Bowtie (version 1.0.0)
Peaks were called using MACS2 (version 2.0.10)
Genome_build: mm9

molecule: genomic DNA

source_name: Heart

extract_protocol:
Lysates were clarified from sonicated nuclei and Brg1-DNA complexes were isolated with antibody.
DNA libraries were prepared with the NEBNext® Ultra DNA Library Prep Kit for Illumina according to the manufacturer’s protocol. Libraries were quantified with Qubit dsDNA HS Assay Kit (Invitrogen) and KAPA Library Quantification Kit for Illumina, and then sequenced on an Illumina NextSeq 500 instrument.

treatment_protocol: Adult C57BL/6 mice were primed with a daily intraperitoneal (i.p.) injection of Tβ4 (12 mg kg−1) or vehicle (PBS) for one week. Primed mice were subsequently given a myocardial infarction by permanent ligation of the left anterior descending  coronary artery (Day 0). Further injections of Tβ4/vehicle were given on day 0 and 2 post-surgery. Hearts were harvested at day 4 after ligation, digested, cross-linked with 1% formaldehyde at room temperature for 10 min, incubated in nuclei extraction buffer first, then in lysis buffer and sonicated. Solubilized chromatin was incubated overnight at 4°C with a specific rabbit polyclonal anti-Brg1 antibody coupled to anti-rabbit IgG Dynabeads (Invitrogen). Immunoprecipitated chromatin was then purified by standard phenol-chlorophorm extraction.

value: heart 4 days post-injury (MI)

tag: age

value: Adult (10-12 weeks postnatally)


title: Tb4-primed, -injured MI heart input rep2


title: PBS-primed, -injured MI heart input rep2


title: Tb4-primed, -injured MI heart rep2

tag: chip antibody

value: Anti-SNF2b/Brg1 (Millipore, 07-478)


title: PBS-primed, -injured MI heart rep1


title: PBS-primed, -injured MI heart input rep1


title: dpy-21(y622) (RNA)

city: Berkeley

first: Barbara

middle: J.

last: Meyer

state: CA

address: 16 Barker Hall #3204

department: MCB

institute: HHMI/UCB

data_processing:
RNA-seq libraries were sequenced with Illumina’s HiSeq 2000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further.
To remove and trim reads containing the adapter barcodes, we used cutadapt version 0.9.5 (https://cutadapt.readthedocs.org/).
Reads were aligned to the WS220 transcriptome using GSNAP version 2012-01-11. Uniquely mapping reads were assigned to genes using HTSeq version 0.5.4p3 using the union mode.
DESeq was used to calculate normalization factors and gene expression fold change and for significance testing.
Genome_build: WS220
Supplementary_files_format_and_content: processed data files contain  gene names and locations and DESeq means.   For the experimental strains, the fold change and the adjusted p-value are also included.

organism: Caenorhabditis elegans

source_name: mixed stage embryos

growth_protocol: Nematode Culture.  All strains were cultured on NG agar plates with HB101 bacteria grown in Luria Broth (LB) except as indicated for RNAi.  Growth of set-1(RNAi) and control RNAi nematodes for RNA-seq is described below.  HT115 DE3 bacteria carrying either the empty RNAi feeding library vector L4440 or the L4440 vector with the set-1 coding region were grown overnight to saturation in 5 ml cultures of LB with 100 µg ml-1 ampicillin. For both bacterial strains, two ml of saturated culture was seeded into each of 3 separate 1 L volumes of LB with 100 µg ml-1 ampicillin. The 1 L cultures were grown for 4-6 h, induced with a final concentration of 4 mM IPTG for 2 h at 37°C to produce dsRNA, and grown to saturation. Bacteria were concentrated by centrifugation at 4300´ g for 10 min, resuspended in a 1:1 (w/v) ratio with LB, and seeded (2 ml) onto 9 cm RNAi plates (NG agar with 1 mM IPTG and 100 µg ml-1 carbenicillin). Plates were allowed to dry overnight at 25°C. Synchronized populations of starved N2 L1s were placed onto two separate sets of plates with L4440 vector bacteria and three separate sets of plates with set-1(RNAi) bacteria and allowed to grow to adulthood. The resulting F0 gravid hermaphrodite populations were bleached separately, and the resulting starved L1s were transferred to independent sets of freshly prepared RNAi plates. The F1s were grown to adulthood and then bleached separately to obtain independent populations of embryos. mRNA extracted from these independently isolated sets of embryos was used for making RNA-seq libraries as described below. This set-1(RNAi) treatment caused  ~95% embryonic lethality.

extract_protocol:
RNA was extracted using a protocol described previously (Baugh,DeModena, and Sternberg, Science vol 324, pp 92-94, 2009) except that 10 µl of a 20 mg ml-1 glycogen solution was used as a carrier
Libraries were prepared from 10 µg of total RNA. PolyA+ RNA was purified using the Dynabeads mRNA purification kit (Ambion, 610-06) and fragmented using Fragmentation Reagent (Ambion, AM8740). First strand cDNA was synthesized from polyA+ RNA using the SuperScript III Reverse Transcriptase Kit (Life Technologies, 18080044) with random primers (Life Technologies, 48190-011). Second strand cDNA synthesis was performed using Second Strand Synthesis buffer, DNA Pol I, and RNase H (Life Technologies, 10812014, 18010025, 18021014). cDNA libraries were prepared for sequencing using the mRNA TruSeq protocol (Illumina).

treatment_protocol: Nematodes were grown to adulthood and then bleached  to obtain populations of embryos which were and frozen at -80°C in 1X M9 buffer


title: WT_5d_U_2


title: dpy-21(y607) (RNA)


title: WT_5d_U_3


title: PBS-primed, -injured MI heart rep2


title: Tb4-primed, -injured MI heart rep1


title: dpy-21(y618) (RNA)


title: set-4(n4600) (RNA)


title: N2-L4440 (RNA)

description: N2 grown on L4440 as a control of RNAi


title: WT_N_4

value: control


title: ICOShiCCR6+Treg

city: Seoul

first: BYUNG-SEOK

last: KIM

address: 1 Gwanak-ro, Gwanak-gu

country: South Korea

institute: SEOUL NATIONAL UNIVERSITY

description:
Seven days after immunization
CCR6plusICOShiTreg_2(ICOShiCCR6+Treg)

data_processing:
Sequenced reads were mapped to mm10  genome using TopHat.
Normalization of the dataset was done by rescaling the read counts according to the sample medians.
Genome_build: mm10
Supplementary_files_format_and_content: text file with rescaled read count

source_name: Inguinal lymph nodes of immunized mice

extract_protocol:
CD4+ T cells were isolated from Inguinal lymph nodes by MACS sorting and then cell were further sorted by FACS ARIA II. RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard SOLiD v4 sequencing protocols

value: Inguinal lymph nodes

value: Treg

value: 6-8 week

tag: genotype


title: dpy-21(e428) (RNA)


title: RORgtKO Treg

description:
Seven days after immunization
RgflminusTreg_7(RORgt-/-Treg)

value: Rorcf/f Foxp3-YFP-Cre


title: WT Treg

description:
Seven days after immunization
RgflplusTreg_6(WTTreg)

value: Rorc+/+ Foxp3-YFP-Cre


title: D2-HD-C_BACHD-WT_D2_cells_dStr_5-6mo_M

city: Princeton

first: Jeff

last: Aaronson

state: New Jersey

address: 155 Village Boulevard, Suite 200

department: Discovery & Systems Biology

institute: CHDI

data_processing:
Illumina CASAVA 1.8.2 software used for basecalling
Genome mapped via Omicsoft OSA 4.0
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by using fastq-mcf sequence quality filter, clipping and processor with following settings for Omicsoft: Trimming  /Mode=TrimByQuality /ReadTrimQuality=2;  Options  /ParallelJobNumber=4 /PairedEnd=True /FileFormat=FASTQ /AutoPenalty=True /FixedPenalty=2 /Greedy=false /IndelPenalty=2 /DetectIndels=False /MaxMiddleInsertionSize=10 /MaxMiddleDeletionSize=10 /MaxEndInsertionSize=10 /MaxEndDeletionSize=10 /MinDistalEndSize=3 /ExcludeNonUniqueMapping=False /ReportCutoff=10 /WriteReadsInSeparateFiles=True /GenerateSamFiles=False /ThreadNumber=6 /InsertSizeStandardDeviation=40 /ExpectedInsertSize=300 /MatePair=False /InsertOnSameStrand=False /InsertOnDifferentStrand=True /QualityEncoding=Automatic /CompressionMethod=Gzip /Gzip=True /SearchNovelExonJunction=False /ExcludeUnmappedInBam=False /KeepFullRead=False /Replace=False /Platform=ILLUMINA /CompressBam=False;
Genome_build: Genome version Mouse.B37, gene models version Ensembl.R67
Supplementary_files_format_and_content: Excel files include FPKM and Count values for each Sample

source_name: BACHD-WT_Striatum_ dopamine D2 receptor-expressing neurons

extract_protocol:
Tissue specimens were removed, flash frozen on dry ice, and total RNA was harvested using the Qiagen miRNeasy kit. RNA quality and integrity were monitored via Agilent Bioanalyzer. A minimum of 3.75 ug of total RNA were used to collect enriched RNA subfractions for library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Corpus striatum

value: Wild type

tag: background strain

value: FVB/NJ

value: Medium spiny neurons

tag: cell subtype

value: dopamine D2 receptor-expressing neurons

tag: Sex

value: Male


title: N2 (RNA)


title: D1-HD-H_BACHD-hd+_D1_cells_dStr_5-6mo_M

source_name: BACHD-HD_Striatum_dopamine D1 receptor-expressing neurons

value: dopamine D1 receptor-expressing neurons


title: ICOSloCCR6-Treg

description:
Seven days after immunization
CCR6minusICOSloTreg_1(ICOSloCCR6-Treg)


title: D2-HD-H_BACHD-hd+_D2_cells_dStr_5-6mo_M

source_name: BACHD-HD_Striatum_ dopamine D2 receptor-expressing neurons


title: NaiveTreg

description:
No immunization
NaveTreg_3(NaïveTreg)

source_name: Inguinal lymph nodes of unimmunized mice


title: D1-HD-C_BACHD-WT_D1_cells_dStr_5-6mo_M

source_name: BACHD-WT_Striatum_ dopamine D1 receptor-expressing neurons


title: H2O2 rep2

city: Haifa

first: Reut

last: Shalgi

address: 1 Efron st.

department: Faculty of Medicine

country: Israel

institute: Technion

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using bowtie.
In each replicate, the number of reads in each treatment was downsampled to match the treatment with the minimum number of reads using samtools
Fragments Per Kilobase of Megabase of library size (FPKM) were calculated using Cufflinks.
Genome_build: mm9
Supplementary_files_format_and_content: abundance measurements

source_name: NIH3T3_0.2 mM H2O2 for 2 hrs

growth_protocol: NIH3T3 (mouse embryonic fibroblasts) cells were cultured in a 1:1 mix of Dulbecco’s Modified Eagle Medium and F-12 Nutrient’s mixture (both Gibco) substituted by 10% Fetal Bovine Serum (Atlanta biologicals), 1% L-glutamine (Gibco) and 1% Penicillin/Streptomycin (Sigma-Aldrich).

extract_protocol:
For preparation of nuclear-enriched RNA, cells were grown to confluency on 15 cm plates (Falcon), treated with stress, washed in PBS, scraped in PBS, Pelleted by centrifugation at 3000 x g and resuspended in 200 uL of RLB buffer (10 mM Tris, pH 7.5, 140 mM NaCl, 1.5 mM MgCl2, 0.5% Nonidet P-40, 1mM DTT and 100U/ml RNase IN (Roche). Samples were incubated on ice for 5 min and then layered over 600 ul the RLB buffer containing 24% (wt/vol) sucrose.  Samples were centrifuged at 13000 x g for 10 min at 4°C. After centrifugation, supernatants (cytoplasmic extracts) were discarded and nuclear pellets were resuspended in 200 ul buffer w. sucrose, and RNA was extracted by the addition of 1 ml Trizol. RNA (total or nuclear) was then treated with DNase RQ (Promega) using 0.5-1 units DNase/μg RNA following the manufacturer’s instructions. RNA was recovered by phenol/chloroform/isoamyl alcohol (PCA) extraction and ethanol precipitation, following standard protocols. For sequencing, RNA was subjected to additional rounds of purification by Qiagen RNaEasy kit followed by PCA.
RNA quality was assessed by NanoDrop 8000 (Thermo Scientific) and agarose gel electrophoresis. RNA quality was further established at the Yale Center for Genome Analysis (YCGA) by running an Agilent Bioanalyzer gel. Ribosomal RNA was then depleted using the Ribo-Zero Gold Kit (MRZG12324, Epicentre) and remaining RNA fragmented by incubation at 94°C. Strand-specific Libraries were prepared using Illumina reagents. Following first-strand synthesis with random primers, second-strand synthesis was performed with dUTP for generating strand-specific sequencing libraries. The cDNA library was end-repaired and A-tailed, adapters were ligated and second-strand digestion was performed by Uricil-DNA-Glycosylase. Quality of indexed libraries was validated by quantification by qRT-PCR (KAPA Biosystems) and by insert size distribution determination (LabChip GX).
Two samples were multiplexed per sequencing lane, and samples were sequenced using 75 bp paired-end sequencing on an Illumina HiSeq 2000 according to Illumina protocols. Signal intensities were converted to individual base calls during the run using the system’s Real-Time Analysis (RTA) software. Sample de-multiplexing and splitting of the paired-end reads were done using Illumina's CASAVA 1.8.2 software suite.

treatment_protocol: For stress treatments, cells were cultured at 44°C (heat shock), or in the presence of 200 mM KCl (osmotic stress), or of 0.2 mM H2O2 (oxidative stress) for 2 h if not otherwise stated. Cells were plated at 500,000 cells/well in 6-well plates, and cultured for 24 hours before treatments

tag: cell line

value: mouse embryonic fibroblasts

tag: treated with

value: 0.2 mM H2O2 (oxidative stress) for 2 hours

tag: molecule subtype

value: nuclea-eniched  RNA


title: KCl rep1

source_name: NIH3T3_200 mM KCl for 2 hrs

value: 200 mM KCl (osmotic stress) for 2 hours


title: KCl rep2


title: H2O2 rep1


title: HS rep2

source_name: NIH3T3_Heat shock for 2 hrs

value: Heat shock (44°C) for 2 hours


title: set-1(RNAi) (RNA)

description: N2 grown on set-1(RNAi)


title: HS rep1


title: UN rep2

value: none (untreated)


title: CRF0Brain24M_IF_4

city: Bonn

first: Kan

last: Xie

address: Sigmund-Freud-Str. 25

country: Germany

institute: German Center for Neurodegenerative Diseases

description: Intermittent fasted old male C57BL/6J mouse

data_processing:
Reads were adapter and quality trimmed (phred threshold of 5)
Trimmed reads were aligned with STAR
featureCounts was used with the ensembl annotation to generate counts
Genome_build: GRCm38
Supplementary_files_format_and_content: TSV, ensembl ids and counts

source_name: Brain

extract_protocol:
Whole brain was quickly isolated and snap-frozen in liquid nitrogen. RNA was extracted using RMeasy Mini Kit (Qiagen) according to manufacturer´s intructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Whole brain

value: wildtype

value: 24 months

value: male


title: CRF0Brain24M_IF_2


title: CRF0Brain24M_AL_4

description: Ad libitum fed control old male C57BL/6J mouse


title: UN rep1


title: CRF0Brain24M_AL_3


title: CRF0Brain24M_AL_2


title: CRF0Brain24M_IF_3


title: CRF0Brain24M_IF_1


title: CRF0Brain24M_AL_1


title: CRF0Brain3M_IF_3

description: Intermittent fasted young male C57BL/6J mouse

value: 3 months


title: CRF0Brain3M_AL_3

description: Ad libitum fed control young male C57BL/6J mouse


title: CRF0Brain3M_IF_2


title: CRF0Brain3M_AL_2


title: CRF0Brain3M_IF_1


title: CRF0Brain3M_AL_4


title: PolyA RNA-seq BmalKO KLA48h

city: Bunkyo

first: Yumiko

last: Oishi

state: Tokyo

address: 1-5-45, Yushima

department: Department of Cellular and Molecular Medicine

country: Japan

institute: Tokyo Medical and Dental University

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using  RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study.
Genome_build: mm9

molecule: polyA RNA

source_name: mouse BMDM

growth_protocol: Mouse thioglycollate-elicited macrophages and bone marrow-derived macrophages were isolated from male 6- to 9-weeks old C57BL/6J (Charles River laboratories) and Arntl-/- mice. Cells are cultured in RPMI-1640 medium containing 10% FCS. M-CSF (20ug/ml) was added for BMDM culture medium for 6 days.

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles.
RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA.  RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA).  Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA)
Reads were aligned to mm9 genome using default parameter for RNA-star.  Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.

treatment_protocol: Mouse macrophages are treated with bacterial lipopolysaccharide (LPS) or Kdo2-Lipid A,chemically defined substructure of  LPS specifically recognized by Toll-like receptor 4  for indicated time.

value: bone marrow-derived macrophage

value: KLA 48h


title: PolyA RNA-seq WT KLA48h


title: CRF0Brain3M_AL_1


title: PolyA RNA-seq WT KLA0h

value: KLA 0h


title: PolyA RNA-seq WT KLA6h

value: KLA 6h


title: PolyA RNA-seq BmalKO KLA24h

value: KLA 24h


title: PolyA RNA-seq BmalKO KLA0h


title: PolyA RNA-seq BmalKO KLA6h


title: PolyA RNA-seq WT KLA24h


title: WT1

first: Jae-Hyung

last: Lee

address: 26 Kyungheedae-ro, Dongdaemun-gu

institute: Kyung Hee University

description: Wild-type, replicate 1

data_processing:
Illumina Casava software used for basecalling.
The sequencing raw reads were mapped onto the mouse genome reference mm10 using GSNAP (version 2013-11-27). Uniquely and properly mapped read pairs were used for further analysis.
Expression levels of genes, the RPKM (reads per kilobase of exon per million mapped reads) measure was calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample

source_name: Control, wild-type

extract_protocol:
Total RNA was extracted from mouse hippocampal tissues using TRIzol (Invitrogen).
Poly(A) mRNA was isolated and fragmented using Illumina Truseq RNA Sample Prep Kit with poly-T oligo-attached magnetic beads. The adaptor-ligated library was size-selected by band excision after agarose gel electrophoresis and purified using QIAquick gel extraction kit (Qiagen).

treatment_protocol: Eight to fifteen weeks old male LSD1 knock-in (KI) and wild type (WT) littermates were used for behavioral experiments. Mice were housed on a 12 h light/dark cycle in standard laboratory cages, and the behavioral experiment was performed during light phase of the cycle. Food and water were provided ad libitum. The Institutional Animal Care and Use Committee (IACUC) of Seoul National University approved the animal protocols.

value: wild-type

value: hippocampus

tag: gender


title: KI2

description: LSD1 knock-in, replicate 2

source_name: Experiment, LSD1 knock-in

value: LSD1 knock-in


title: KI1

description: LSD1 knock-in, replicate 1


title: WT2

description: Wild-type, replicate 2


title: PMG-GSKJ4-LPS-3

city: Ansan

first: Young Gyu

last: Chai

state: Gyeonggi-do

address: 55 Hanyangdaehak-ro

department: Molecualr & Life Science

institute: Hanyang Univ.

data_processing:
Illumina CASAVA v1.8.2 software was used for basecalling.
To avoid low-quality data, we clipped and trimmed the reads using Trimmomatic (v0.33)
For the analysis of differentially expressed genes,  quality controlled FASTQ files were alignment to mus musculus UCSC mm10 reference genome sequence using the STAR (version 2.5.1) aligner software. The differential gene expressed values of each sample were calculated by the DESeq2 Bioconductor package.
The number of reads mapped to gene ID features were counted using STAR.
Genome_build: Mus musculus UCSC mm10
Supplementary_files_format_and_content: tab-delimited text files including normalized read counts for each sample

source_name: primary microglia cells

growth_protocol: PM were seeded in poly-L-lysine-coated T-75 flask in DMEM/nutrient mixture F-12 (DMEM/F12, 1:1) containing 20% FBS (catalog # 26140), 100 IU/ml penicillin and 10 µg/ml streptomycin (catalog # 15140) from Invitrogen (CA, USA). The cells were maintained in a humidified incubator with a 95% air/5% CO2 atmosphere at 37¡C. The medium was changed every 2-3 days. After two weeks in culture, mixed glial cell cultures are shaken at 150 rpm at 37¡C for 45 min, and the glial cell suspension was collected from each flask and seeded on poly-L-lysine coated cell culture plate. PM were sub-plated and used for further experiments.

extract_protocol:
RNA was extracted using RNAiso Plus (Takara Bio Inc, Shiga, Japan) and QIAGEN RNeasy¨ Mini kit (QIAGEN, Hilden, Germany) according to the manufacturerÕs protocol. For RNA-Seq, RNA libraries were created from each group using the NEBNext¨ Ultraª Directional RNA Library preparation kit from Illumina¨ (Illumina, San Diego, CA, USA). The first step in the workflow involved the removal of ribosomal RNA using the RNAMiusª Transcriptome Isolation kit (Life Technologies, Carlsbad, CA, USA).  Following purification, total RNA was fragmented into small pieces using divalent cations at elevated temperature. The cleaved RNA fragments were copied into first-strand cDNA using reverse transcriptase and random primers, followed by second-strand cDNA synthesis using DNA polymerase I and RNase H. The cDNA fragments were then processed through an end-repair reaction by the addition of a single ÔAÕ base, followed by ligation of the adapters. The products of these reactions were then purified and enriched by PCR to create the final cDNA library. The cDNA fragments were sequenced using the Illumina HiSeq2000 (101 cycles PE lane)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Murine microglial PM, were treated with GSKJ4 (10 uM), and with LPS (10 ng/ml) for 4 hrs.

tag: cell type

value: primary microglia cells

value: treated with GSKJ4 (10 uM) and LPS (10 ng/ml) for 4 hrs


title: PMG-GSKJ4-3

value: treated with GSKJ4 (10 uM) for 4 hrs


title: PMG-GSKJ4-LPS-2


title: PMG-GSKJ4-LPS-1


title: PMG-GSKJ4-2


title: PMG-GSKJ4-1


title: WT_CBX2_ChIP

first: Robert

last: Kingston

address: 185 Cambridge Street

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Alignment: BWA version 0.5.9-r16
Alignment manipulation: Samtools 0.1.18.0
Data smoothing and enrichment calculation: 'get.smoothed.tag.density' routine in spp version 1.13
Peak calling: Statistical significance of enrichment of ChIP vs. input was estimated using the negative binomial distribution, with the estimate of the mean based on the tag counts in input, and the size parameter(s) selected based on manual inspection of resulting peak calls. Adjacent enriched windows separated by 1kb or less were merged to generate a list of regions with significant enrichment.
Genome_build: mm9

growth_protocol: mESCs were cultured on irradiated MEFs in mESC media containing DMEM, supplemented with 15% FBS, 1000U/mL LIF, non-essential amino acids, GlutaMax, penincillin/ streptomycin, 2- betamercaptoethanol.

extract_protocol:
Lysates were sonicated to fragment chromatin, pre-cleared by centrifugation, and subjected to immunoprecipitation with CBX2 antibody.
Libraries were prepared as described in PMID: 23837789.

treatment_protocol: To induce CBX2 expression, cells were treated with the appropriate amounts of doxycycline (empirically determined to induce similar levels of CBX2 across the cell lines) for 48 hours before collection. The feeder MEFs were removed from mESCs using Feeder Removal MicroBeads (MACS Miltenyi Biotec, 130-095-531).  Purified mESCs were crosslinked with 1% formaldehyde at room temperature for 10 minutes.

tag: strain background

value: Embryonic stem cells

value: WT

value: CBX2 (Bethyl Laboratories Inc. A302-524A)


title: KRA_CBX2_ChIP

value: compaction mutant CBX2; KRA


title: KRA_input


title: KRA.2_+dox_rep2

data_processing:
Quality Control: PICARD, Version: 1.100, CollectRnaSeqMetrics
Alignment: Tophat version 2.0.8b
Alignment manipulation: Samtools 0.1.18.0
Feature counting: HTSeq version 0.6.0. Parameters: unstranded=TRUE, quality thresh=10, feature file=ftp.ensembl.org//pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz
Differential expression: R library edgeR, version 3.8.6
Genome_build: mm9

extract_protocol:
Total RNA was extracted from cells with Trizol, purified using Direct-zol™ RNA MiniPrep (Zymo) and DNaseI-treated. polyA RNA was purified from the RNA and made into cDNA libraries using TruSeq total RNA kit (Illumina).
Libraries were prepared as described in PMID: 23837789.

treatment_protocol: To induce CBX2 expression, cells were treated with the appropriate amounts of doxycycline (empirically determined to induce similar levels of CBX2 across the cell lines) for 48 hours before collection.    The feeder MEFs were removed from mESCs using Feeder Removal MicroBeads (MACS Miltenyi Biotec, 130-095-531).

value: KRA-CBX2 variants in Cbx2 null cells 2


title: DEA_no-dox_rep2

value: DEA-CBX2 variants in Cbx2 null cells


title: WT_input


title: DEA_+dox_rep1


title: DEA_no-dox_rep1


title: KRA.1_+dox_rep1

value: KRA-CBX2 variants in Cbx2 null cells 1


title: KRA.1_no-dox_rep2


title: KRA.1_+higher-dox_rep1


title: KRA.1_+dox_rep2


title: KRA.2_no-dox_rep1


title: KRA.2_no-dox_rep2


title: KRA.1_+higher-dox_rep2


title: KRA.2_+dox_rep3


title: WT.2_+dox_rep3

value: WT-CBX2 variants in Cbx2 null cells 2


title: WT.2_no-dox_rep3


title: KRA.1_no-dox_rep1


title: WT.2_+dox_rep1


title: DEA_+dox_rep3


title: WT.1_+dox_rep2

value: WT-CBX2 variants in Cbx2 null cells 1


title: DEA_+dox_rep2


title: WT.2_no-dox_rep2


title: KRA.2_no-dox_rep3


title: WT.2_+dox_rep2


title: WT.1_no-dox_rep2


title: WT.1_+dox_rep1


title: KRA.2_+dox_rep1


title: WT.1_no-dox_rep1


title: PDGF_K27M_DMSO_RNA-seq

city: Copenhagen

first: Faizaan

last: Mohammad

state: Choose A State

address: Ole Maaloøs vej 5 Fourth Floor

country: Denmark

institute: BRIC

data_processing:
Basecalling performed using CASAVA version 1.8.2
Raw reads trimmed using Trimmomatic v.0.32
Raw reads aligned to mm10 assembly using the STAR aligner. The STAR mm10 index was built with a RefSeq gtf file downloaded 20150119 (excluding multimapping genes).
The alignment files were converted from BED12 to BED6 format, split into + and – strand, converted to bedGraph format using bedItemOverlapCount, normalized to Reads Per Million and converted to bigwig format using bedGraphToBigWig
Genome_build: mm10
Supplementary_files_format_and_content: bigwig: standard bigwig format

growth_protocol: The cells  were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors).

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
rRNA was removed from the total RNA using RiboMinus Transcriptome Isolation Kit (Invitrogen, K1550-01) and remaining RNA was fragmented using NEBNex®t Magnesium RNA Fragmentation Module (E6150). The fragmented RNA was purified and used to make the library using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (1–12) (E7300S).

treatment_protocol: The cells were treated with either DMSO or Ezh2 inhibitor (EPZ6438, 3 uM) for 12 days.

value: DIPG cell line

value: K27M H3.3 mutant

value: DMSO


title: PDGF_K27M_EPZ_RNA-seq

value: EPZ


title: PDGF_K27M_EPZ_II_RNA-seq


title: PDGF_H3_3_DMSO_II_RNA-seq

value: wildtype


title: PDGF_H3_3_DMSO_RNA-seq


title: PDGF_H3_3_EPZ_II_RNA-seq


title: PDGF_H3_3_DMSO_IgG

data_processing:
For pre-processing and reads mapping, ChIP-seq libraries were sequenced using the Illumina Genome Analyzer platform, producing single-end 42 bp reads after removal of multiplex index sequence tags. Reads were mapped to the human (UCSC hg38) or mouse (UCSC mm10) genome assemblies using the bowtie short read aligner (version 0.12.7) and excluding all haplotype variants and random or unknown chromosomal sequences. We used the default bowtie parameters except concerning multi-mapping reads which were discarded using option "-m1".
For representation of H3K27me3 ChIP-seq profiles on selected loci, mapped reads were de-duplicated by keeping a single read in each group of reads mapping to the exact same genomic sequence. Reads were extended to a total length of 250 bp starting from the 5' end and genomic coverage was computed at base pair resolution using the UCSC Kent utilities. Coverage values were scaled according to sequencing depth and immuno-precipitation yield.
For identification of genes and CGIs associated with H3K27me3 peaks, regions locally enriched for H3K27me3 were established by the SPP peak calling program using default parameters with a z-threshold value of 8 and a custom normalization factor between H3K27me3 ChIP and IgG libraries. This normalization factor was defined according to sequencing depth and immuno-precipitation yield.

source_name: PDGF H3 3 DMSO IgG

growth_protocol: The mouse cells  as well as three human DIPG cell lines (DIPG007, DIPG012 and SF7761) were cultured on poly-D-lysine (PDL, Sigma) and laminin (Sigma) coated plates in neural stem cell medium (50% DMEM-F12, 50% neurobasal medium, N2 and B27 supplements, sodium pyruvate, glutamax, HEPES, β−mercaptoethanol, non-essential amino acids, bovine serum albumin, heparin, 100U/ml penicillin, 100 μg/ml streptomycin, human recombinant epidermal and basic fibroblast growth factors). Another human DIPG cell line (SF8628) was cultured in DMEM with 10% FBS.

extract_protocol:
Cells were cross-linked with 1% formaldehyde for 10 minutes at room temperature. Glycine was added at a final concentration of 125 mM to quench the formaldehyde. Cells were then washed twice with PBS and harvested in SDS buffer (50 mM Tris at pH 8.1, 0.5% SDS, 100 mM NaCl, 5 mM EDTA). Cells were pelleted down, resuspended in Triton-X IP buffer (100 mM Tris at pH 8.6, 0.3% SDS, 1.7% Triton X-100, and 5 mM EDTA) and the chromatin was sonicated to get the DNA fragments of <1000 bp with average DNA fragment size of 300 bp. 500 μg chromatin was used to perform chromatin immunoprecipitation (ChIP)
10 ng of ChIP DNA was used to make library using NEBNext Ultra DNA library kit for illumine (E7370; New England Biolabs) according to supplier’s instructions and the libraries were sequenced using Illumina HiSeq2500 sequencer.

value: H3 3 DMSO IgG

value: IgG


title: PDGF_H3_3_EPZ_me3

source_name: PDGF H3 3 EPZ me3

value: H3 3 EPZ me3


title: PDGF_K27M_DMSO_me3

source_name: PDGF K27M DMSO me3

value: K27M DMSO me3


title: PDGF_K27M_EPZ_me3

source_name: PDGF K27M EPZ me3

value: K27M EPZ me3


title: WT.2_no-dox_rep1

value: Embryonic stem cells


title: S2-AbdA_rep2

city: Marseille

first: Andrew

middle: J

last: Saurin

address: Campus de Luminy

country: France

institute: IBDM / CNRS

description:
RNA-Seq of S2-AbdA cells Rep2
DE_genes_upon_AbdA_expression_FDR10.xls

data_processing:
Basecalls performed using RTA (Illumina)
RNA-seq reads were aligned to the dm3 genome assembly using CASAVA 9v1.8.2) using module "eland_rna"and counts determined using theCASAVA  "variant detection and counting" module
RNA-Seq differentially expressed genes were called using edgeR using a false discovery rate (FDR) cut-off of 10%
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited (tsv) text files show raw counts of genes for each sample; XLS file shows the edgeR output of differentially expressed genes upon AbdA expression.

organism: Drosophila melanogaster

source_name: S2-HA::AbdA Cell line

growth_protocol: Cells were grown in T-flasks to a density of not more than 7x10^6 cells/ml in Schneider Medium supplemented with 10% FBS

extract_protocol:
Chromatin was prepared according to the modENCODE procedure; RNA was extracted with Qiagen Rneasy kit
DNA libraries were prepared according to Illumina's instructions; RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with 10 microMolar Copper Sulphate for 24 h prior to chromatin and RNA preparation

value: late embryo-derived cell line stably transfected with HA::AbdA

tag: strain

value: 10 microMolar Cu2SO4


title: S2_rep4

description: RNA-Seq of S2 cells Rep4

source_name: S2 Cell line

value: late embryo-derived cell line

value: wild type


title: S2-Ubx_HA-Ubx_ChIPSeq_Rep2

description:
HA ChIP-Seq of S2-Ubx cells Rep2
S2-Ubx_HA_ChIP_peaks.bed

data_processing:
Basecalls performed using RTA (Illumina)
ChIP-seq reads were aligned to the dm3 genome assembly using BWA v0.7.12 using default parameters
ChIP-Seq peak calling was performed using MACS2 (v0.7.12) using low stringency on individual replicates. Final peaks were called using an Irreproducible Discovery Rate (IDR) of 4% according to guidelines set out by the ENCODE consortium.
Genome_build: dm3
Supplementary_files_format_and_content: Bed files were prepared using MACS2 and represent peaks called in both replicates having an IDR of 4%.

source_name: S2-HA::Ubx Cell line

value: late embryo-derived cell line stably transfected with HA::Ubx

value: HA (AbCam ab9110)


title: S2-Ubx_Input

description: ChIP Input


title: S2-AbdA_Input_D_rep2

description: ChIP Input (Code D)

data_processing:
Basecalls performed using RTA (Illumina)
ChIP-seq reads were aligned to the dm3 genome assembly using BWA v0.7.12 using default parameters
ChIP-Seq peak calling was performed using MACS2 (v0.7.12) using low stringency on individual replicates. Final peaks were called using an Irreproducible Discovery Rate (IDR) of 1% according to guidelines set out by the ENCODE consortium.
ChIP-seq bigWig files of enrichment >0 were produced using spp using merged replicate bamfiles that had been randomly downsampled to have equal numbers of reads between samples from S2 cells and those from S2-HA::AbdA cell line
Genome_build: dm3
Supplementary_files_format_and_content: BigWig files were prepared using spp and show ChIP enrichment values >0; Bed files were prepared using MACS2 and represent peaks called in both replicates having an IDR of 1%.


title: S2-Ubx_HA-Ubx_ChIPSeq_Rep1

description:
HA ChIP-Seq of S2-Ubx cells Rep1
S2-Ubx_HA_ChIP_peaks.bed


title: S2-AbdA_Input_D_rep1

description: ChIP Input (Code D)


title: S2-AbdA_E(z)_ChIPSeq_Rep2

description:
E(z) ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_Ez_ChIP_peaks.bed
S2-AbdA_Ez_ChIP.bigWig

value: E(z) (SantaCruz dN-20)

tag: input dna code

value: D


title: S2_Input_B_rep1

description: ChIP Input (Code B)


title: S2-AbdA_rep1

description:
RNA-Seq of S2-AbdA cells Rep1
DE_genes_upon_AbdA_expression_FDR10.xls


title: S2_rep3

description: RNA-Seq of S2 cells Rep3


title: S2_Input_A

description: ChIP Input (Code A)


title: PDGF_K27M_DMSO_II_RNA-seq

value: DIPG cell line

value: K27M H3.3 mutant

value: DMSO


title: S2_rep2

description:
RNA-Seq of S2 cells Rep2
DE_genes_upon_AbdA_expression_FDR10.xls


title: S2_Input_B_rep2

description: ChIP Input (Code B)


title: PDGF_H3_3_DMSO_me3

source_name: PDGF H3 3 DMSO me3

value: H3 3 DMSO me3


title: S2-AbdA_E(z)_ChIPSeq_Rep1

description:
E(z) ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_Ez_ChIP_peaks.bed
S2-AbdA_Ez_ChIP.bigWig


title: S2_E(z)_ChIPSeq_Rep2

description:
E(z) ChIP-Seq of S2 cells Rep2
S2_Ez_ChIP_peaks.bed
S2_Ez_ChIP.bigWig

value: B


title: S2-AbdA_dRing_ChIPSeq_Rep2

description:
dRing ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_dRing_ChIP_peaks.bed
S2-AbdA_dRing_ChIP.bigWig

value: dRing (this study)


title: S2-AbdA_dRing_ChIPSeq_Rep1

description:
dRing ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_dRing_ChIP_peaks.bed
S2-AbdA_dRing_ChIP.bigWig


title: S2_E(z)_ChIPSeq_Rep1

description:
E(z) ChIP-Seq of S2 cells Rep1
S2_Ez_ChIP_peaks.bed
S2_Ez_ChIP.bigWig


title: S2_dRing_ChIPSeq_Rep2

description:
dRing ChIP-Seq of S2 cells Rep2
S2_dRing_ChIP_peaks.bed
S2_dRing_ChIP.bigWig


title: S2-AbdA_GAGA_ChIPSeq_Rep1

description:
GAGA ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_GAF_ChIP_peaks.bed
S2-AbdA_GAF_ChIP.bigWig

value: GAGA (modENCODE; G. Cavalli)

value: C


title: S2_GAGA_ChIPSeq_Rep2

description:
GAGA ChIP-Seq of S2 cells Rep2
S2_GAF_ChIP_peaks.bed
S2_GAF_ChIP.bigWig


title: S2_GAGA_ChIPSeq_Rep1

description:
GAGA ChIP-Seq of S2 cells Rep1
S2_GAF_ChIP_peaks.bed
S2_GAF_ChIP.bigWig


title: S2_dRing_ChIPSeq_Rep1

description:
dRing ChIP-Seq of S2 cells Rep1
S2_dRing_ChIP_peaks.bed
S2_dRing_ChIP.bigWig


title: S2-AbdA_Input_C

description: ChIP Input (Code C)


title: S2-AbdA_GAGA_ChIPSeq_Rep2

description:
GAGA ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_GAF_ChIP_peaks.bed
S2-AbdA_GAF_ChIP.bigWig


title: S2_M1BP_ChIPSeq_Rep2

description:
M1BP ChIP-Seq of S2 cells Rep2
S2_M1BP_ChIP_peaks.bed
S2_M1BP_ChIP.bigWig

value: M1BP (a gift from Dr. D. Gilmour -  Li and Gilmour (2013) EMBO J. 32(13):1829-1841)


title: S2-AbdA_M1BP_ChIPSeq_Rep1

description:
M1BP ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_M1BP_ChIP_peaks.bed
S2-AbdA_M1BP_ChIP.bigWig

value: late embryo-derived cell line stably transfected with HA::AbdA


title: S2-AbdA_M1BP_ChIPSeq_Rep2

description:
M1BP ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_M1BP_ChIP_peaks.bed
S2-AbdA_M1BP_ChIP.bigWig

value: 10 microMolar Cu2SO4


title: S2_M1BP_ChIPSeq_Rep1

description:
M1BP ChIP-Seq of S2 cells Rep1
S2_M1BP_ChIP_peaks.bed
S2_M1BP_ChIP.bigWig

value: late embryo-derived cell line


title: S2-AbdA_PolII_phosphoSer2_ChIPSeq_Rep2

description:
PolII_phosphoSer2 ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_Ser2_ChIP_peaks.bed
S2-AbdA_Ser2_ChIP.bigWig

value: Pol II Ser-2 clone 3E10 (Merck Millipore; ref 04-1571)


title: S2_rep1

description:
RNA-Seq of S2 cells Rep1
DE_genes_upon_AbdA_expression_FDR10.xls

value: wild type


title: S2-AbdA_PolII_phosphoSer2_ChIPSeq_Rep1

description:
PolII_phosphoSer2 ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_Ser2_ChIP_peaks.bed
S2-AbdA_Ser2_ChIP.bigWig


title: S2-AbdA_Rpb3_ChIPSeq_Rep2

description:
Rpb3 ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_Rpb3_ChIP_peaks.bed
S2-AbdA_Rpb3_ChIP.bigWig

value: Rpb3 (a gift from Dr. K Adelman - Gilchrist et al., (2010) Cell 143(4):540-551)


title: S2-AbdA_HA-AbdA_ChIPSeq_Rep2

description:
HA ChIP-Seq of S2-AbdA cells Rep2
S2-AbdA_HA_ChIP_peaks.bed
S2-AbdA_HA_ChIP.bigWig

value: HA (AbCam ab9110)


title: S2-AbdA_HA-AbdA_ChIPSeq_Rep1

description:
HA ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_HA_ChIP_peaks.bed
S2-AbdA_HA_ChIP.bigWig


title: TSH_FAIREseq

first: Delphine

last: Potier

address: 27 boulevard Lei Roure

institute: CRCM

data_processing:
cleaning (fastX-clipper)
mapping to Dm3/FB5 genome using bowtie2
filtering for mapping quality (minimum 4)
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: The processed files contains FAIRE-seq data in a bigwig format

source_name: eye-antennal imaginal disc

growth_protocol: All flies were raised at 25˚C on standard fly food

extract_protocol:
Head complexes were first dissected,  fixed and lysed. 100 eye-antennal discs were the uncrosslinked and sonicated, phenol chloroform extraction was used for DNA purification.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Eye-antennal discs were manually dissected from wandering third instar larvae in 1xPBS

tag: developmental stage

value: third instar wandering larvae

tag: tissue

value: eye-antennal imaginal disc

value: OptixGal4 * UASTsh


title: HTH_FAIREseq

value: OptixGal4 * UASHth


title: S2-AbdA_Rpb3_ChIPSeq_Rep1

description:
Rpb3 ChIP-Seq of S2-AbdA cells Rep1
S2-AbdA_Rpb3_ChIP_peaks.bed
S2-AbdA_Rpb3_ChIP.bigWig

tag: treatment

value: D


title: S2_Rpb3_ChIPSeq_Rep1

description:
Rpb3 ChIP-Seq of S2 cells Rep1
S2_Rpb3_ChIP_peaks.bed
S2_Rpb3_ChIP.bigWig

value: B


title: MeiShan_Rep3

city: Wen’jiang,Chengu

first: long

middle: ke

last: ren

state: Sichuan

address: Huimin road, 211#

department: 1	Institute of Animal Genetics & Breeding

country: China

institute: sichuan agriculture university

description: small RNA-seq

data_processing:
Illumina Casava1.7 software used for basecalling. All reads were counted and the identical reads were combined into a single kind. The raw reads were subjected to a series of additional strict filters (such as the digital filters of base-call quality, reads length, and sequence comparison) with acceptance criteria derived from the statistics of mammalian miRNAs in miRBase 20.0. The reads originated from pocine known classes of RNAs (i.e., mRNA; rRNA, tRNA, snRNA, and snoRNA; and repetitive sequence elements) were also filtered.In addition, to ensure higher reliability of the reported results, only the reads that were observed more than 3 times for each library were used in subsequent analyses.
To conduct differential analysis, miRNA read in each library was normalized to obtain the expression of transcripts per million (RPM).
Genome_build: Sus_scrofa (10.2); miRbase 20.0
Supplementary_files_format_and_content: identified miRNAs in each library with reads and normalized data

organism: Sus scrofa

source_name: sketetal muscle

extract_protocol:
Three unrelated 2-year old adult females for both of LargeWhite and MeiShan pigs were used in this study. Sketetal muscle were rapidly separated from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen, and stored at − 80 °C until RNA extraction.
small RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Meishan

tag: phenotype

value: Obese

value: longissimus dorsi muscle

tag: age


title: MeiShan_Rep2

description: small RNA-seq


title: LargeWhite_Rep3

description: small RNA-seq

value: Large White

value: Lean


title: S2_Rpb3_ChIPSeq_Rep2

description:
Rpb3 ChIP-Seq of S2 cells Rep2
S2_Rpb3_ChIP_peaks.bed
S2_Rpb3_ChIP.bigWig

tag: genotype

value: 10 microMolar Cu2SO4

tag: chip antibody


title: TSH_RNAseq

description:
mRNA extracted from total RNA
RNA4

data_processing:
cleaning (fastX-clipper -M15)
mapping to D. melanogaster genome using TopHat2.0 (default parameters)
quantification of gene expression measures with HT-Seq count (option -str=no) using D. melanogaster gene annotation release 5.45 from FlyBase
Genome_build: Drosophila melanogaster FB5
Supplementary_files_format_and_content: RNAseq samples: tophat2 alignments in bigwig format and ht-seq counts on Drosphila FB5.45 annotation

extract_protocol:
RNA was extracted with the RNAqueous micro kit (Ambion)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Wandering 3rd instar larvae were dissected in PBS to extract the tissues of interest (50 eye-antennal discs per sample)


title: HTH_TSH_cross_RNAseq

description:
mRNA extracted from total RNA
RNA3

value: OptixGAL4 * UASHth * UASTsh (stock)


title: HTH_TSH_RNAseq

description:
mRNA extracted from total RNA
RNA2

value: OptixGAL4 * UAS Hth * UASTsh


title: WT_RNAseq

description:
mRNA extracted from total RNA
RNA1

value: UAS-GFP


title: Pre-plasmablast RNA-Seq, rep2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: 3'-RNAseq amplified from 1ng RNA

data_processing:
Adaptor removal, mapping and abundance measurement were performed as described in GSE63266. All reads were processed by cutadapt v1.11 with the "-c -e 0.1 -q 20 -n 2 -O 1 -m 30 -a CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -g CTCGAGGGCGCGCCGGATCCATATACGCCTTGGCCGTACAGCAG -a AAAAAAAAAAAAAAAAAAAA" option.
Reads with 30 bases and longer were mapped onto mouse mm10 genome and reference genes using  tophat v1.4.1/bowtie 1.0.1 with the "--no-coverage-search" option. Abundance measurement was performed using cufflinks-2.2.0 using the “--compatible-hits-norm”, “--no-length-correction” and “--library-type fr-secondstrand” options and mm10 reference gene annotations with extended TTSs.
Abundance of ERCC spike-in transcripts were counted separately from bam files produced by tophat.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include RPM values for each Sample

source_name: prePB

growth_protocol: Purified B cells were  cultured in RPMI-1640 medium (Wako) supplemented with 10% FBS, 55 mM 2- mercaptoethanol, 10 mM HEPES, 1 mM sodium pyruvate, 100 units/mL penicillin, and 100 μg/mL streptomycin (GIBCO)

extract_protocol:
After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 positive and CD138 negative cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

treatment_protocol: Purified B cells were  stimulated with recombinant IL-4 (2 ng/mL; Peprotech) and LPS (10 ng/mL; Sigma) for 3 days

value: Homozygous EGFP-knocked-in at the N terminus of BLIMP1 (EGFP-BLIMP1)

tag: cell sorting

value: FACS (GFP+, CD138-)


title: Pre-plasmablast RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: HTH_TSH_FAIREseq

value: third instar wandering larvae


title: MeiShan_Rep1

description: small RNA-seq


title: Blast cells RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

source_name: Blast

extract_protocol:
After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 and CD138 negative cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (GFP-, CD138-)


title: PDGF_H3_3_EPZ_RNA-seq

tag: cell line

value: DIPG cell line

value: wildtype

value: EPZ


title: B cell RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

source_name: B cell

extract_protocol:
Spleen was dissected from 8-10 week-old EGFP-BLIMP1 mice. To remove red blood cells, the cell suspension was subjected to ammonium chloride lysis buffer (0.15M ammonium chloride, 1.0mM potassium bicarbonate and 0.1mM EDTA), washed with PBS supplemented with 0.1% BSA, and filtered with cell strainer.  The cell suspension was then incubated with rat anti-CD45R/B220 antibody conjugated with PE (BD Biosciences). CD45R/B220 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.


title: S2_HA_Ctrl_ChIPSeq_Rep1

description:
Negative control HA ChIP-Seq of S2 cells Rep1
S2_HA_ChIP.bigWig

value: late embryo-derived cell line

value: wild type

value: HA (AbCam ab9110)

value: A


title: HTH_RNAseq

description:
mRNA extracted from total RNA
RNA5

value: eye-antennal imaginal disc

value: OptixGal4 * UASHth


title: P6_Photoreceptor precursor_CD73+ RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Retinal tissues (P6) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). The cell suspension was stained with rat anti-CD73 (ecto-5`-nucleotidase) antibody conjugated with APC (BioLegend) . CD73 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (CD73+)


title: Plasmablast RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

source_name: PB

extract_protocol:
After 3 days of stimulation, cells were harvested and incubated with rat anti-CD138 (Syndecan-1) antibody conjugated with APC. BLIMP1 and CD138 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (GFP+, CD138+)


title: LargeWhite_Rep1

description: small RNA-seq

value: Large White

value: Lean

value: longissimus dorsi muscle


title: Plasmablast RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

value: Homozygous EGFP-knocked-in at the N terminus of BLIMP1 (EGFP-BLIMP1)


title: LargeWhite_Rep2

description: small RNA-seq


title: P4_Photoreceptor precursor_CD73+ RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Retinal tissues (P4) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). The cell suspension was stained with rat anti-CD73 (ecto-5`-nucleotidase) antibody conjugated with APC (BioLegend) . CD73 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.


title: B cell RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: Blast cells RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: P10_Photoreceptor precursor_CD73+ RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Retinal tissues (P10) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). The cell suspension was stained with rat anti-CD73 (ecto-5`-nucleotidase) antibody conjugated with APC (BioLegend) . CD73 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.


title: P4_Photoreceptor precursor_CD73+ RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: P4_Photoreceptor precursor_GFP+CD73- RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Retinal tissues (P4) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). The cell suspension was stained with rat anti-CD73 (ecto-5`-nucleotidase) antibody conjugated with APC (BioLegend) . BLIMP1 positive and CD73 negative cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (GFP+)


title: P4_Photoreceptor precursor_GFP+CD73- RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: P6_Photoreceptor precursor_CD73+ RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: P14_intestinal epithelium RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications.  The intestine (P14) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed. Then the intestine was open by cutting longitudinally through the lumen The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible.  The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min.  After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA].  After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane.  Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS.  The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells.  The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min.  After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 negative and EpCAM positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (EPCAM+)


title: P3_intestinal epithelium RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications.  The intestine (P3) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed. Then the intestine was open by cutting longitudinally through the lumen The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible.  The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min.  After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA].  After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane.  Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS.  The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells.  The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min.  After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 negative and EpCAM positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.


title: P10_Photoreceptor precursor_CD73+ RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: E16.5_Embryonic intestinal epithelium RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Intestinal epithelium were isolated as described (Gracz et al., 2012) with minor modifications.  The intestine (E16.5) from caudal half of duodenum to the ileocecal junction of EGFP-BLIMP1 mice were dissected, and the surrounding connective tissues and vessels were gently removed.  The isolated intestine were placed in the 1.5 ml eppendorf tube containing ice-cold PBS and cut into small pieces as fine as possible.  The intestine fragments were then transferred to 10 ml Falcon tube containing dissociation reagent ♯1 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA, 75 μL of 1 M (1.5 mM) DTT] and placed on ice for 20min.  After the incubation, dissociation reagent ♯1 was replaced with dissociation reagent ♯2 [47 mL PBS, 3 mL of 0.5 M (30 mM) EDTA].  After 10 min incubation at 37 °C, the tube that contained intestine was shaken by hand for 30 sec to release epithelium from the basement membrane.  Dissociated cells were washed by removing supernatant and re-suspending cells in 10 mL PBS with 10% FBS.  The cells were collected by centrifugation and then re-suspended in 10 mL DMEM containing 8-mg Dispase (GIBCO), which digested cell–cell junction proteins and dissociated the whole epithelium to single cells.  The cells were then incubated in a water bath for 10 min at 37°C with vigorous shaking every 2 min.  After adding 10 % FBS, the cell suspension was passed through the cell strainer to remove large undissociated clumps of cells and connective tissues. BLIMP1 and EpCAM positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

value: FACS (GFP+, EPCAM+)


title: P3_intestinal epithelium RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: P14_intestinal epithelium RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: E16.5_Embryonic intestinal epithelium RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: P0_Photoreceptor precursor_GFP+ RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA

extract_protocol:
Retinal tissues (P0) were dissociated from eye balls of EGFP-BLIMP1 mice and the incubation with 0.1 % trypsin and 1 mM EDTA in PBS at 37 °C for 10 min.  Trypsin was then inactivated by adding equal volume of PBS/10% FBS supplemented with 0.1mg/mL DNaseI (Sigma). BLIMP1 positive cells were purified with FACS. Total RNAs from collected cells were extracted with RNeasy Micro Kit (QIAGEN, 74004) according to the manufacture's instruction.
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.


title: 09 SH-SY5Y

city: Mainz

first: Holger

last: Herlyn

address: Anselm-Franz-von-Bentzel-Weg 5

department: Institute of Organismic and Molecular Evolution

institute: University of Mainz

data_processing:
Barcoded RNA-seq libraries were clustered on the cBot using the Truseq PE cluster kit V3 using 10 pM and 2 x 50 bps were sequenced on the Illumina HiSeq 2500 using a Truseq SBS V3 kit (50 cycles).
The raw output data of the HiSeq was preprocessed according to the Illumina standard protocol. This includes filtering for low quality reads and demultiplexing.
Sequence reads were aligned to the reference genomic sequence (hg19).
The alignment coordinates were compared to the exon coordinates of the UCSC transcripts and for each transcript the counts of overlapping alignments were recorded.
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq_primate_FOXP2.xls containing read counts for single genes in alternatively transfected SH-SY5Y cells (two biological replicates, each)

growth_protocol: Parental SH-SY5Y neuroblastoma cells (ATCC no. CRL-2266) were grown in DMEM containing 15% FCS, 1% Pen-Strep. Stably transfected cells were cultivated in selection medium supplemented with 600 µg/ml geneticin (G 418; PAA; optimized concentration according to toxicity testing). Efficiency and persistence of transfection were monitored in cell lines carrying pcDNA3-eGFP constructs by fluorescence microscopy and through ECL Western blotting using anti-eGFP (mouse monoclonal IgG, cat 11814460001, Roche; peroxidase conjugated sheep anti-mouse IgG, NA931V, GE healthcare).

extract_protocol:
Total RNA was extracted using Illumina´s TruSeq RNA Sample Preparation Kit.
Barcoded mRNA-seq cDNA libraries were prepared from 600 ng of total RNA. mRNA was isolated using Oligo(d)T magnetic beads. Isolated mRNA was fragmented using divalent cations and heat and converted into cDNA using random primers and SuperScriptII (Invitrogen), followed by second strand synthesis. cDNA was end repaired, 3’ adenylated and single T-overhang Illumina multiplex specific adapters were ligated to the cDNA fragments, followed by an enrichment PCR. All cleanups were done using Agencourt AMPure XP magnetic beads.

treatment_protocol: Cells were stably transfected with linearized empty plasmid or pcDNA3-FOXP2 (isoform I) constructs, using Amaxa Cell Line Nucleofector V Kit (Lonza). This was done twice, thus generating two biological replicates per condition (A, B).

value: neuroblastoma cells

tag: transfection state

value: Rhesus monkey FOXP2 cDNA

tag: biological replicate

value: B


title: 07 SH-SY5Y

value: human FOXP2 cDNA


title: d2 PGCLC RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA

source_name: d2 PGCLC

growth_protocol: Transfected ESCs were maintained under 2i+LIF condition and adapted to a feeder-free condition prior to induction. EpiLC differentiation was performed as reported previously (Hayashi et al., Cell, 2011).

extract_protocol:
BV positive cells were purified with FACS. Total RNA was extracted using Qiagen RNeasy according to manufacturer's instruction
RNA-seq libraries were prepared according to Nakamura et al., 2015, GEO:  GSE63266.

treatment_protocol: Ck-PGCLCs were induced by BMP4 (500 ng/ml), BMP8A (500 ng/ml), SCF (100 ng/ml), LIF (1000 U/ml) and EGF (50 ng/ml) as previously described (Hayashi et al., Cell, 2011)

value: Blimp1-mVenus, stella-ECFP, Rosa26-rtTA

value: FACS (BV+)


title: 05 SH-SY5Y

value: common chimpanzee FOXP2 cDNA

value: A


title: 10 SH-SY5Y


title: 06 SH-SY5Y

value: empty expression vector (pcDNA-3)


title: 03 SH-SY5Y

value: white-tufted ear marmoset FOXP2 cDNA


title: 04 SH-SY5Y


title: 01 SH-SY5Y


title: P0_Photoreceptor precursor_GFP+ RNA-Seq, rep2

description: 3'-RNAseq amplified from 1ng RNA


title: d2 PGCLC RNA-Seq, rep1

description: 3'-RNAseq amplified from 1ng RNA


title: mutant control replicate 2

city: St. Louis

first: Mark

middle: M

last: Voigt

state: MO

address: 1402 S Grand Blvd

department: Pharmacology and Physiology

institute: Saint Louis University

description:
foxd3-/- genetic background
mutant.txt
control foxd3-2

data_processing:
Read alignment used STAR ver 2.0.04b
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.5.
Transcript counts were produced by Sailfish version 0.6.3.
Sequencing performance was assessed for total number of aligned reads, total number of uniquely aligned reads, genes and transcripts detected, ribosomal fraction, known junction saturation and read distribution over known gene models with RSeQC version 2.3.
All gene-level and transcript counts were imported into the R/Bioconductor package EdgeR and TMM normalized to adjust for differences in library size.
Generalized linear models with robust dispersion estimates were created to test for gene/transcript level differential expression. The fit of the trended and tagwise dispersion estimates were then plotted to confirm proper fit of the observed mean to variance relationship where the tagwise dispersions are equivalent to the biological coefficients of variation of each gene. Differentially expressed genes and transcripts were then filtered for those having fold-changes (FC) > 1.2 together with false-discovery rate (FDR) adjusted p-values less than or equal to 0.05. R/Bioconductor package “gplots” was used to generate heatmaps. The differentially expressed zebrafish genes in each condition were transferred to their human orthology by using the PANTHER classification system (http://pantherdb.org/genes/index.jsp), then GO enrichment analysis was performed in ToppGene suite, with the p-value cut-off < 0.05 (B&H corrected).
Genome_build: Danio rerio Zv9 assembly from Ensembl
Supplementary_files_format_and_content: wt.txt and mutant.txt report gene counts RPKMs

organism: Danio rerio

source_name: head

extract_protocol:
Heads of 4 dpf larvae exposed to 10 mM MET for either 0, 2 or 5 hours were dissected using a small scalpel, with 8 heads pooled per sample. Each sample was then homogenized in 250 mL of TRIzol (Life Technologies), and total RNA extracted. The RNA samples were then treated with DNase and column purified using a Qiagen RNEasy mini kit (Qiagen, Inc.). Biological triplicates (8 heads per replicate) were prepared for each condition.
RNA purity and integrity was determined using an Agilent Bioanalyzer 2100, and only those samples having a RIN > 8.7 were used. For library construction, 1 μg total RNA was used for each wild-type replicate and 0.35 μg for the mutant replicates. The total RNA samples were depleted of rRNA using the Ribo-Zero protocol (Epicentre). cDNA was synthesized, blunt ended, an A base added to the 3’ ends and then had Illumina sequencing adapters ligated. cDNA fragments were then amplified for 12 cycles using primers incorporating unique index tags.

treatment_protocol: For treated samples, 4 dpf larvae were exposed to 10 mM metronidazole in fish water for either 2 hrs or 5 hrs.

value: 4 dpf

value: larvae

tag: genotype/variation

tag: agent

value: control

value: head


title: mutant 5 hr treatment replicate 1

description:
foxd3-/- genetic background
mutant.txt
foxd3-5-1

value: metronidazole

tag: time

value: 5 hr


title: mutant control replicate 3

description:
foxd3-/- genetic background
mutant.txt
control foxd3-3


title: 54-1.DM.control_kd

city: Seattle

first: Qing

last: Feng

state: WASHINGTON

address: 1100 Fairview Ave. N., Fred Hutchinson Cancer Research Center

department: Public Health and Basic Science devisions

institute: FRED HUTCH CANCER RESEARCH Center

data_processing:
Illumina CASAVA software was used for basecalling and sample de-multiplexing.
Reads were mapped to the hg19 human genome assembly using Bowtie v1.0.0 and RSEM v1.2.4. RSEM was modified to call Bowtie  with the -v 2 mapping strategy. RSEM was then invoked with the arguments --bowtie-m 100 --bowtie-chunkmbs 500 --calc-ci --output-genome- bam on the gene annotation file.
Genome_build: hg19
Supplementary_files_format_and_content: Text files with RSEM-based expression estimates for coding and non-coding RNA transcripts.

source_name: skeletal myoblast cell line

growth_protocol: Human myoblasts (54-1 cells) were cultured in high serum growth media for proliferation below 60% confluence, and induced to differentiate in low serum differentiation media when the cells reached 99% confluence. The growth media was F-10 media-based (Gibco), and contained 20% fetal bovine serum (Gibco), 1% penicillin/streptomycin (Gibco), rhFGF(10 ng/mL, Promega), and dexamethasone (1 µM, Sigma). The differentiation media was also F-10 media-based (Gibco), and contained 1% horse serum (Gibco), 1% penicillin/streptomycin (Gibco), insulin (10 µg/mL, Sigma), and transferrin (10 µg/mL, Sigma).

extract_protocol:
RNA was extracted from cultured cells using Trizol and Qiagen RNeasy columns
The Illumina TruSeq RNA Sample Prep Kit was used with 2-4 ug of total RNA for the construction of sequencing libraries. The protocol was modified to select DNA fragments in the 100-400bp range using bead selection. Samples were multiplexed using Illumina barcodes to run four samples per sequencing lane.

treatment_protocol: siUPF1 (Dharmacon, ON-TARGETplus siRNA J-011763-07) and siControl (Dharmacon, ON-TARGETplus negative control siRNA D-001810-03) were transfected with Lipofectamine RNAiMAX (Life Technologies). For transfection in a six-well plate format, 10nM of siRNA and 6 µl of Lipofectamine RNAiMAX was added on top of cells at 60% confluence in each well. The cells would reach 99% confluence in two days and then be ready for differentiation.

tag: cell type

value: skeletal myoblast

value: control siRNA

tag: time point

value: Differentiation media day2


title: mutant control replicate 1

description:
foxd3-/- genetic background
mutant.txt
control foxd3-1

tag: developmental stage


title: wild-type 5 hr treatment replicate 1

description:
AB wild-type genetic background
wt.txt
met_5_1

value: AB wild-type

tag: tissue


title: wild-type 5 hr treatment replicate 3

description:
AB wild-type genetic background
wt.txt
met_5_3


title: 54-1.DM.upf1_kd

tag: treatment

value: UPF1 siRNA


title: wild-type 5 hr treatment replicate 2

description:
AB wild-type genetic background
wt.txt
met_5_2


title: wild-type 2 hr treatment replicate 2

description:
AB wild-type genetic background
wt.txt
met_2_2

value: 2 hr


title: wild-type 2 hr treatment replicate 1

description:
AB wild-type genetic background
wt.txt
met_2_1


title: wild-type control replicate 2

description:
AB wild-type genetic background
wt.txt
control_2


title: wild-type 2 hr treatment replicate 3

description:
AB wild-type genetic background
wt.txt
met_2_3


title: 08 SH-SY5Y

value: neuroblastoma cells

value: B


title: mutant 5 hr treatment replicate 2

description:
foxd3-/- genetic background
mutant.txt
foxd3-5-2


title: 02 SH-SY5Y

value: human FOXP2 cDNA

value: A


title: wild-type control replicate 1

description:
AB wild-type genetic background
wt.txt
control_1


title: mutant 5 hr treatment replicate 3

description:
foxd3-/- genetic background
mutant.txt
foxd3-5-3


title: ChIP-seq p65 WT KLA48h

description: formaldehyde cross-linked

data_processing:
For ChIP-Seq and RNA-Seq samples, reads were aligned to the mm9 genome using  RNA-Star. Aligned read files were analyzed with HOMER (http://homer.salk.edu/homer/) to find peaks, calculate RPKM from the gene bodies of RefSeq genes, perform motif-  and  other analyses in the study.
Genome_build: mm9

source_name: mouse BMDM

extract_protocol:
ChIP-Seq: Sequencing libraries were prepared from collected DNA by using NEB next Ultra DNA library prep kit for Illumina. Libraries were PCR-amplified for 12-15 cycles and sequenced on a Hi-Seq 1500 (Illumina) for 51 cycles.
RNA-Seq: PolyA-tagged RNA was pulled down with oligo-dT magnetic beads from total RNA.  RNA-seq libraries were multiplexed and prepared according to the manufacturer's protocol (NEB cat#E7530, Ipswich, MA).  Libraries were paired-ended sequenced on a HiSeq 2000 sequencer (Illumina, San Diego, CA)
Reads were aligned to mm9 genome using default parameter for RNA-star.  Aligned reads read files were analyzed with HOMER (http://homer.salk.edu/homer/) to calculate RPKM from the gene bodies of RefSeq genes, perform motif analysis in the study. Reads counts were normalized using DESeq2.

tag: strain

value: bone marrow-derived macrophage

value: KLA 48h


title: ChIP-seq p65 WT KLA4h

description: formaldehyde cross-linked

value: KLA 4h


title: Input for BmalKO

description: formaldehyde cross-linked

value: KLA 0h


title: ChIP-seq Bmal1 LPS4h

description: formaldehyde cross-linked

source_name: mouse peritoneal macrophage

value: peritoneal macrophage

value: LPS 4h


title: ChIP-seq p65 WT KLA12h

description: formaldehyde cross-linked

value: KLA 12h


title: ChIP-seq p65 WT KLA0h

description: formaldehyde cross-linked


title: ChIP-seq p65 BmalKO KLA8h

description: formaldehyde cross-linked

value: KLA 8h


title: ChIP-seq p65 BmalKO KLA24h

description: formaldehyde cross-linked

value: KLA 24h


title: ChIP-seq H3K27Ac WT KLA48h

description: formaldehyde cross-linked


title: ChIP-seq p65 BmalKO KLA4h

description: formaldehyde cross-linked


title: wild-type control replicate 3

description:
AB wild-type genetic background
wt.txt
control_3

value: 4 dpf

value: larvae

value: control

value: head


title: ChIP-seq H3K27Ac WT KLA4h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac BmalKO KLA48h

description: formaldehyde cross-linked


title: ChIP-seq p65 BmalKO KLA12h

description: formaldehyde cross-linked


title: ChIP-seq p65 BmalKO KLA48h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac WT KLA24h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac WT KLA8h

description: formaldehyde cross-linked


title: Input for WT

description: formaldehyde cross-linked


title: ChIP-seq Bmal1 LPS0h

description: formaldehyde cross-linked

value: LPS 0h


title: ChIP-seq H3K27Ac WT KLA12h

description: formaldehyde cross-linked


title: ChIP-seq p65 BmalKO KLA0h

description: formaldehyde cross-linked


title: ChIP-seq Bmal1 LPS24h

description: formaldehyde cross-linked

value: LPS 24h


title: ChIP-seq H3K27Ac BmalKO KLA24h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac BmalKO KLA4h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac BmalKO KLA12h

description: formaldehyde cross-linked


title: ChIP-seq p65 WT KLA8h

description: formaldehyde cross-linked


title: ChIP-seq p65 WT KLA24h

description: formaldehyde cross-linked


title: ChIP-seq H3K27Ac BmalKO KLA8h

description: formaldehyde cross-linked


title: OSS_147_RNA_siPIWI

city: BOSTON

first: NELSON

middle: C

last: LAU

address: 72 E Concord St K219, Dept of Biochemistry

department: Biochemistry and Cell Biology

institute: Boston University Chobanian & Avedisian School of Medicine

data_processing:
Illumina Nextseq 500 on instrument base calling
FastX initial quality score trimming and filtering of reads against structural RNAs, microRNAs, viral RNAs
Mapped to the Drosophila melanogaster reference genome, build Dm3 / Release 5, with Bowtie, allowing up to 2 mismatches
For just the 146_NUN set (siGFP, siPIWI, siPAF1 and siPIWI+siPAF1), a "jackpot" reads filter was applied to remove any sequences whose read count was greater than 50 reads.
SAM file of reads counted against RefSeq database of all Drosophila transcripts, counts per locus region and both strands measured
Genome_build: Drosophila melanogaster genome build Release 5.1, Dm3
Supplementary_files_format_and_content: text file tab-delimited tables of read counts mapped to refseq transcripts

growth_protocol: OSS cells were cultured in a customly assembled media comprised of fly extract, M13 media, FBS, insulin, and glutathione.  See the full protocol from Lau et al, Genome Res, 2009.

extract_protocol:
Total RNA from NUN pellets or cytoplasm lysates were extracted with the Tri-reagent protocol of Chomzcynski and and Sacchi, 1987.
New Englad Bioloabs, NEBNext Ultra Directional RNA Library Prep Kit for Illumina.
Eight libraries with different barcodes were multiplexed in each sequencing run.  Separation of sequences by different barcodes was conducted during the on-instrument base-calling.

treatment_protocol: For each experiment, 500 pmoles siRNAs were electroporated into a 10cm plate of OSS cells using Amaxa kit V (program D013), and cells were cultured for 6 days before harvesting.

value: OSS

value: ovarian follicle cell culture

tag: sirna knockdown of

value: PIWI

tag: rna extracted from

value: cytoplasm lysates


title: OSS_147_RNA_siGFP

value: GFP negative control


title: ChIP-seq H3K27Ac WT KLA0h

description: formaldehyde cross-linked

value: bone marrow-derived macrophage

value: KLA 0h


title: OSS_147_NUN_siPIWI_siPAF1

value: both PAF1 and PIWI

value: NUN pellets


title: OSS_147_RNA_siPAF1


title: OSS_147_RNA_siPIWI_siPAF1


title: OSS_147_NUN_siGFP


title: OSS_146_RNA_siPAF1


title: OSS_147_NUN_siPAF1


title: OSS_146_RNA_siPIWI_siPAF1


title: OSS_146_RNA_siPIWI


title: OSS_147_NUN_siPIWI


title: 19_Pang_input_bTP039

city: Boston

first: Ting

last: Pang

address: 4 Blackfan Circle

department: MBIB

institute: Harvard Medical School

description: genomic DNA, input sample (no antibodies)

data_processing:
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Bacillus subtilis PY79 (NCBI Reference Sequence: NC_022898.1) independently using CLC genomics workbench 8.0 (Qiagen), and exported .csv file.
Genome_build: NC_022898.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. Column1 - genome position, column2 - number of reads at each genome position.

organism: Bacillus subtilis PY79

source_name: Bacillus subtilis PY79

growth_protocol: Cells were grown in defined rich medium (CH) (Harwood and Cutting 1990, Molecular Biological Methods for Bacillus ) at 37°C with aeration. For the strains harboring a Pspank_noc_his fusion, isopropyl ß-d-thiogalactopyranoside  (IPTG, 0.5mM) was added >5 generations prior to harvest.

extract_protocol:
ChIP-seq experiments were performed using anti-His6 (Genscript) antibodies according to previous publications (Graham et al, 2014 PMID 24829297; Wang et al, 2015 PMID 26253537).
Standard library construction protocol was used for Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol:
Cells were growing in CH medium at 37˚C, IPTG was added to a final concentration of 0.5 mM;, fixed by 3% formaldehyde for 30min at room temperature
Cells were grown to OD600 = 0.25 and incubated with 3% formaldehyde for 30 min at room temperature. Formaldehyde was quenched and the cells washed, and lysed

tag: growth protocol

value: CH, 37˚C

tag: genotype

value: PY79 {delta}noc::tet ycgO::Pspank- Bsnochis (spec)


title: 18_Pang_input_bRB73

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
Cells were grown to OD600 = 0.4 and incubated with 3% formaldehyde for 30 min at room temperature. Formaldehyde was quenched and the cells washed, and lysed

value: PY79 {delta}noc::tet

tag: chip antibody


title: 16_Pang_ChIPHis6_bTP041

description: ChIP using anti-His6 Genscript) antibodies

value: PY79 {delta}noc::tet ycgO::Pspank-Sanochis (spec)


title: 17_Pang_input_PY79

treatment_protocol:
Cells were growing in CH medium at 37˚C, fixed by 3% formaldehyde for 30min at room temperature
Cells were grown to OD600 = 0.25 and incubated with 3% formaldehyde for 30 min at room temperature. Formaldehyde was quenched and the cells washed, and lysed

value: wild type B. subtilis PY79


title: OSS_146_NUN_siPIWI_siPAF1

tag: cell line


title: 15_Pang_ChIPHis6_bTP039


title: OSS_146_RNA_siGFP


title: 14_Pang_ChIPHis6_bRB73


title: OSS_146_NUN_siPIWI


title: dpy-21(e428) (ChIP)

first: Barbara

last: Meyer

address: 16 Barker Hall #3204

institute: HHMI/UCB

description: Crosslinked chromatin for ChIP-Seq

data_processing:
To analyze the ChIP-Seq data, a hybrid reference genome was built by combining the C. elegans genome version WS230 and the largest 70 contigs in the C. tropicalis genome version WS230. 50-bp single end reads from ChIP and input libraries were then mapped to the hybrid genome using Bowtie version 1.1.1 (Langmead et al. 2009), allowing up to two mismatches in the seed region and only retaining reads uniquely mapped to the hybrid genome.
The reads mapped to the C. elegans genome were then extracted and sorted using SAMtools version 0.1.19 (Li et al. 2009).
The H4K20me1 read coverage in the C. elegans genome was calculated by normalizing the read number in each 50 bp bin to the total read number using the bamCoverage function in deepTools version 2.5.0.1 (Ramirez et al. 2014)
The H4K20me1 ChIP-Seq enrichment profile of each sample was generated by calculating the ratios between read coverage scores in each ChIP dataset and corresponding input dataset using bwCompare function in deepTools.
To directly compare the H4K20me1 levels between experimental replicates and different genotypes, a spike-in normalization factor was calculated for each ChIP-Seq dataset. The number of reads mapped to C. elegans and C. tropicalis genome in ChIP and corresponding input data were calculated. The normalization factor was then calculated as (C. elegans ChIP / C. tropicalis ChIP) / (C. elegans Input / C. tropicalis Input).  To correct the H4K20me1 ChIP-Seq enrichment with spike-in, we multiplied the read coverage for each ChIP dataset by the normalized factor and then compared it with the corresponding input. The genome-wide spike-in corrected log2 enrichment profiles were generated using the bwCompare function in deepTools.
Genome_build: ce11
Supplementary_files_format_and_content: The processed data files are in bigWig format. These files are the genome-wide spike-in corrected log2 enrichment profiles for each ChIP dataset compared to its corresponding input generated using the bwCompare function in deepTools.

source_name: mixed stage embryos

growth_protocol: Embryos were collected as in Crane et al. (2015).

extract_protocol:
The embryo extract was prepared and the immunoprecipitation was perfromed as in Kruesi et al. (2013). For each sample, 6 μg of H4K20me1 antibody was used for 2 mg embryo extract.
The library construction was performed as in Kruesi et al. (2013).

treatment_protocol: As the spike-in control, C. Tropicalis (TY5752) embryos were mixed with each C. elegans sample at 1: 6.5 weight ratio. The embryos were fixed for 15 min at room temperature with 2% (w/v) formaldehyde prepared by diluting 16% (w/v) formaldehyde (polysciences 18814-10) in 1x M9 buffer.


title: 13_Pang_ChIPHis6_PY79


title: OSS_146_NUN_siPAF1


title: treatment3

city: Beijing

first: Luyao

last: Zhao

address: No.12 Southern Street of Zhongguancun

department: Chinese Academy of Agricultural Sciences

data_processing:
Illumina HiSeq 2500 reads were trimmed and clipped for quality control.
Read quality was checked for each sample using FastQC v0.10.1.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol (RefSeq release 2013-5-10).

organism: Capra hircus

source_name: muscle

extract_protocol:
Take 25 ~ 50mg sample in liquid nitrogen and ground to a powder，transfer all powder to a 2 ml RNase-free tube with some small balls，and immediately add the appropriate amount of lysates. The centrifuge tube into the tissue sample crusher for further crushing to fully lyse the cells and release the RNA.
A total amount of 3 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Ractopamine was orally given to goats every morning at 1 mg/kg (body weight) in the experimental group before feeding for 28 consecutive days (dosing days). Then, ractopamine was not fed for 21 consecutive days (withdrawal days) until the end of the experiment.

tag: stain

value: Cashmere Goats

value: Longissimus dorsi muscle

tag: age

value: 2 months


title: OSS_146_NUN_siGFP

value: OSS


title: treatment2


title: dpy-21(y607) (ChIP)

city: Berkeley

description: Crosslinked chromatin for ChIP-Seq


title: control


title: treatment1


title: N2 (Hi-C)

description: Cross linked N2 DNA for Hi-C

data_processing:
HI-C libraries were sequenced with Illumina’s HiSeq 4000 platform. Reads were required to have passed the CASAVA 1.8 quality filtering to be considered further.
Reads were mapped to genome assembly ce11, binned at 50 kb, and iteratively corrected as previously described (Imakaev et al., 2012) using scripts derived from those available at https://bitbucket.org/mirnylab/hiclib.
To quantitatively identify TADs and examine the strength of TAD boundaries, we calculated the insulation scores from Hi-C interaction data binned at 50 kb and performed boundary calling using a previously described method (Crane et al., 2015).
To correct for the experimental variations in the overall decay of chromatin contacts with genomic distance, we transformed the Hi-C interaction data into Z-scores using a previously described LOWESS method (Imakaev et al., 2012).
To calculate the scaling of the contact probability, we plotted contact probability as a function of genomic separation and used the contact probability between 500 kb and 7 Mb to calculate the scaling factor for chromosome X, combined autosomes, and combined all chromosomes in wild-type and dpy-21(y607 JmjC) mutant replicates.
Genome_build: ce11
Supplementary_files_format_and_content: The '.matrix' files are the  tab separated matrix files of normalized counts. The '.Zscore.matrix' files are the Zscore matrices.  The '.insulation' files are the insulation scores calculated from the '.matrix' files.

growth_protocol: Embryos were collected and nuclei were isolated as in Crane et al. (2015).

extract_protocol:
DNA was purified as in Rao et al. (2014) and sheared in a 130 µl microTUBE (Covaris, 520045) using an S2 Covaris (Covaris 520045) for 55s with duty cycle 10%, intensity 4, and 200 cycles/burst. 300-500bp fragments were selected as in Rao et al. (2014), except that 40 µl of AMPure XP beads were used for the second size selection step. Biotinylated fragments were pulled down according to Rao et al. (2014) and Dynabeads were washed in 100 ul 1X End-It DNA End-Repair Kit (Lucigen, ER81050) End-Repair buffer. Beads were resuspended in 100 µl of End-Repair Mix (10 µl 10X End-Repair buffer, 10 µl 2.4mM dNTP mix, 10 µl 10mM ATP, 2 µl End-Repair enzyme mix, 68 µl water) and incubated at room temperature for 45 min with gentle rotation.
A-tailing and adapter ligation were performed as in Rao et al. (2014) using 2 µl NEXTflex DNA Barcode (Bioo Scientific, 514101). To avoid PCR inhibition, the beads were divided between seven 50 µl PCRs and amplified for 4-6 cycles using Phusion polymerase (Thermo Fischer Scientific, F-530L) and NEXTflex Primer Mix (Bioo Scientific, 514107-48). The final library was purified according to Rao et al. (2014). To verify successful Hi-C, 1 µl of the library was cloned using a Zero Blunt TOPO PCR cloning kit (Life Technologies, 450245), and 20-50 colonies were amplified and sequenced. If at least 50% of the fragments contained informative ligations, the library was sequenced using 100 bp paired end reads on a HiSeq4000 platform. A step-by-step version of this protocol will be available on our website.

treatment_protocol: Nuclei (1.5 x 108) were resuspended in 50 µl of 0.5% SDS and incubated at 62°C for 5-10 min. SDS was quenched as in the in situ Hi-C protocol of Rao et al. (2014). Then 25 μl of 10X DpnII Buffer and 2 µl (100 U) of DpnII (NEB R0543M) were added, and chromatin was digested overnight at 37°C with rotation. DpnII was inactivated, restriction fragment overhangs were filled in, and ligation was performed as in Rao et al. (2014), except that the following recipe was used for the ligation master mix: 13 μl 1 U/μl T4 DNA Ligase (Life Technologies 15224-090), 240 μl 5X T4 DNA ligase buffer, 100 μl 10% Triton X-100, 12 μl 10mg/ml Bovine Serum Albumin, 535μl water.

tag: tag


title: S2_PolII_phosphoSer2_ChIPSeq_Rep2

description:
PolII_phosphoSer2 ChIP-Seq of S2 cells Rep2
S2_Ser2_ChIP_peaks.bed
S2_Ser2_ChIP.bigWig

source_name: S2 Cell line

extract_protocol:
Chromatin was prepared according to the modENCODE procedure; RNA was extracted with Qiagen Rneasy kit
DNA libraries were prepared according to Illumina's instructions; RNA libraries were prepared for sequencing using standard Illumina protocols

value: late embryo-derived cell line

value: wild type

value: 10 microMolar Cu2SO4

value: Pol II Ser-2 clone 3E10 (Merck Millipore; ref 04-1571)

tag: input dna code

value: B


title: dpy-21(y607) (Hi-C)

description: Cross linked dpy-21(y607) DNA for Hi-C


title: 12_Pang_WGS_aTP510

data_processing:
Library strategy: WGS-Seq
Reads from each end of a DNA fragment were represented in each of the two FASTQ files generated by Illumina paired-end sequencing.
We mapped reads in each FASTQ file back to the genome of Staphylococcus aureus NCTC8325 genome (NCBI Reference Sequence NC_007795.1) independently using CLC genomics workbench 8.0 (Qiagen), and exported .csv file. Three prophage regions(1463618 - 1508580, 1923408 - 1967011, 2031911 - 2074632) were removed manually from samples 1-10, to match the RN4220 genome.
Genome_build: NC_007795.1
Supplementary_files_format_and_content: Files ending with .csv: comma-separated values files of ChIP-seq results. Column1 - genome position, column2 - number of reads at each genome position.

organism: Staphylococcus aureus subsp. aureus NCTC 8325

growth_protocol: Cells were grown in tryptic soy broth (TSB)or LB 0.5% NaCl medium  at 37°C with aeration. For the strains harboring a Ptet-noc_his fusion, anhydrotetracycline (aTc, 100 ng/ml) was added >5 generations prior to harvest.

extract_protocol:
Whole genome sequencing was performed according to Baym et al PMID: 26000737.
Standard library construction protocol was used for Illumina Miseq (ChIP-seq). Illumina Truseq indexes were used.

treatment_protocol: Samples 7-10 were treated with 2ug/ml PC190723 at OD600 ~0.13 for 0.5h (samples 7-8) or 1.5h (samples 9-10 ) before harvesting. All cells were harvested at OD600 = 0.4.

tag: derivative strain

tag: growth condition

value: LB 0.5% NaCl medium , 37˚C

tag: drug treatment

value: HG003 {delta}noc::spec {delta}rbd::kan


title: N2 (ChIP)

description: Crosslinked chromatin for ChIP-Seq


title: S2_PolII_phosphoSer2_ChIPSeq_Rep1

description:
PolII_phosphoSer2 ChIP-Seq of S2 cells Rep1
S2_Ser2_ChIP_peaks.bed
S2_Ser2_ChIP.bigWig


title: 11_Pang_WGS_HG003

source_name: Staphylococcus aureus subsp. aureus NCTC 8325

value: wild type HG003


title: 10_Pang_WGS_aTP977_1.5hPC19

value: TSB, 37˚C

value: RN4220 {delta}noc::spec


title: 13_Pang_WGS_aTP518

value: HG003 {delta}noc::spec {delta}rbd::kan {delta}naCA352V


title: 09_Pang_WGS_RN4220_1.5hPC19

value: wild type RN4220