title: IRF1_WT_LPS_4h

description: Chromatin IP against IRF1

value: BMDM cells (7th day of differentiation)

value: LPS 10ng/ml for 4 hours


title: Not IBD Male (CCFA_Risk_042)

status: Public on Jan 30 2015

type: SRA

city: Cincinnati

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

country: USA

institute: Cincinnati Children's Hospital Medical Center

description:
CCFA_Risk_042
Male diagnosed at age 12 with not IBD.

library_source: transcriptomic

data_processing:
Illumina HiSeq 2000 for sequencing.
Reads were aligned using TopHat, using hg19 as the reference genome and mapping reads per kilobase per million mapped reads (RPKM) as output.
RPKM were normalized using the DESeq algorithm using Avaids NGS software, where normalized counts were log2-transformed and base-lined to the median expression of control samples.
Normalized expression values were baselined to the median of all samples.
We removed all transcripts that did not have at least 5 RPKM in at least 5 different samples.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Tab-delimited text files contain normalized and baselined RPKM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: Ileal biopsy in treatment-naïve patient, not IBD

growth_protocol: Ileal biopsies were stored in RNAlater at -80C.

extract_protocol:
RNA was isolated using the Qiagen AllPrep RNA/DNA Mini Kit, RNA quality and concentration were measured by Agilent Bioanalyzer 2100 using the RNA 6000 Nano Assay.
RNA sequencing (RNA-seq) libraries were prepared using the Illumina TruSeq RNA preparation kit and sequenced on the Illumina HiSeq 2000 with single-end 50-bp reads (Illumina, San Diego, CA).

tag: tissue

value: Ileal biopsy

tag: Sex

value: Male

tag: age at diagnosis

tag: paris age

tag: diagnosis

value: Not IBD

tag: l2 type

tag: histopathology

tag: deep ulcer


title: Not IBD Male (CCFA_Risk_041)

description:
CCFA_Risk_041
Male diagnosed at age 4.833333333 with not IBD.


title: STAT2_WT_LPS_2h

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

description: Chromatin IP against STAT2

library_source: genomic

data_processing:
Reads pooled: Sample 19 and Sample 20; Sample 21 and Sample 22; Sample 24 and Sample 25; Sample 26 and Sample 27; Sample 28 and Sample 29.
Reads quality filtered according to the Illumina pipeline.
Reads were mapped to the mouse mm9 genome using Bowtie 0.12.7 (PMID: 19261174). All reads with a unique match to the genome with two or fewer mismatches were retained.
Peak calling was performed using MACS 1.4 (PMID 18798982) with default parameters and --gsize=2.72e9, --tsize=36. Each IP was compared to input DNA derived from BMDM (GSM487453).
Genome_build: mm9 (NCBI Build 37)
Supplementary_files_format_and_content: *-peaks.bed: list of the peaks called by MACS having -10*log10(pvalue) >= 100

molecule: genomic DNA

organism: Mus musculus

source_name: Primary bone marrow-derived macrophages (BMDM)

growth_protocol: Bone marrow cells isolated from C57BL/6 or BXH2/TyJ mice were plated in 10 cm plates in 5ml of BM-medium (high glucose DMEM supplemented with 20% low endotoxin fetal bovine serum, 30% L929-conditioned medium, 1% glutamine, 1%, Pen/Strep, 0.5% Sodium Pyruvate, 0.1% β-mercaptoethanol). Cultures were fed with 2.5 ml of fresh medium every two days.

extract_protocol: Cells were fixed in 1% formaldehyde for 10min.  Lysate was immunoprecipitated with 5-10ug of antibody. Antibodies were pre-bound overnight to 50-100ul of G protein-coupled paramagnetic beads in PBS/BSA 0.5%. Beads were then added to lysates (the preclearing step was omitted) and incubation was let to proceed overnight. Beads were washed 6 times in a modified RIPA buffer (50mM Hepes pH 7.6, 500mM LiCl, 1mM EDTA, 1% NP-40, 0.7% Na-deoxycholate) and once in TE containing 50mM NaCl. DNA was eluted in TE containing 2% SDS and crosslinks reversed by incubation overnight at 65ºC. DNA was then purified by Qiaquick columns (Qiagen) and quantified using PicoGreen (Invitrogen). ChIP DNA was prepared for HiSeq 2000 Illumina sequencing using a standard protocol consisting in blunting, addition of dA overhangs, ligation of Illumina adapters, selection on gel and PCR with index primers. A mixture of T4 DNA polymerase, DNA polymerase I and T4 kinase was used according to manufacturer’s instruction. Library preparation is carried out on SPRIworks Fragment Library System.

treatment_protocol: Macrophages were subjected to different treatment (see individual samples for details)

tag: strain

tag: cell type

tag: antibody

value: STAT2 (santa crus, sc-950)

tag: treatment

value: LPS 10ng/ml for 2 hours


title: Not IBD Female (CCFA_Risk_039)

description:
CCFA_Risk_039
Female diagnosed at age 15.33333333 with not IBD.

value: Female


title: STAT2_WT_LPS_4h

description: Chromatin IP against STAT2


title: No DOX Sample 3

city: New Haven

first: Christopher

middle: J

last: Cheng

state: CT

address: 55 Prospect St

institute: Yale University

data_processing:
Illumina TruSeq mRNA sequencing (50 bp paired end, 25 million reads per sample) and alignment performed by Expression Analysis
Abundance estimation performed by Expression Analysis using RSEM
DESeq was used to first estimate size factors and dispersions, and then identify differentially expressed genes.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file including differential gene expression analysis for 2 groups (foldChange = DOX/No-DOX)

source_name: tumor with miR-155 overexpression

extract_protocol:
Tumor tissue was dispersed into a single cell suspension and red blood cells were lysed. Total RNA was extracted from the remaining cells using the hybrid Trizol and RNeasy protocol.
High quality total RNA (Agilent 2100 Bioanalyzer RIN value greater than 7) was sent to Expression Analysis for library preparation using Ribozero kit and standard Illumina protocols.

treatment_protocol: DOX administered via grain-based mouse chow with 2.3mg/kg of doxycycline

value: NCr nude

tag: injected with

value: splenic cells from diseased mir-155LSLtTA mice

tag: treated with

value: subcutaneous tumor


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_040)

description:
CCFA_Risk_040
Female diagnosed at age 9.166666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

source_name: Ileal biopsy in treatment-naïve patient, CD

value: CD

value: iCD

value: Macroscopic inflammation

value: No


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_037)

description:
CCFA_Risk_037
Male diagnosed at age 10.5 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Yes


title: STAT2_WT_LPS_UT

description: Chromatin IP against STAT2

value: No treatment


title: No DOX Sample 1


title: Not IBD Male (CCFA_Risk_036)

description:
CCFA_Risk_036
Male diagnosed at age 10.5 with not IBD.


title: Not IBD Male (CCFA_Risk_038)

description:
CCFA_Risk_038
Male diagnosed at age 8.666666667 with not IBD.


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_049)

description:
CCFA_Risk_049
Female diagnosed at age 10.08333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_048)

description:
CCFA_Risk_048
Male diagnosed at age 7.666666667 with CD characterized with Macroscopic inflammation and deep ulcer.


title: No DOX Sample 2


title: DOX Sample 3

source_name: tumor with miR-155 withdrawal

value: DOX for 16 hours before harvest


title: Not IBD Male (CCFA_Risk_035)

description:
CCFA_Risk_035
Male diagnosed at age 11.5 with not IBD.


title: Not IBD Male (CCFA_Risk_034)

description:
CCFA_Risk_034
Male diagnosed at age 7.75 with not IBD.


title: DOX Sample 2


title: Not IBD Male (CCFA_Risk_033)

description:
CCFA_Risk_033
Male diagnosed at age 9.333333333 with not IBD.


title: Not IBD Female (CCFA_Risk_031)

description:
CCFA_Risk_031
Female diagnosed at age 12.5 with not IBD.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_032)

description:
CCFA_Risk_032
Female diagnosed at age 8.666666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: DOX Sample 1


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_030)

description:
CCFA_Risk_030
Male diagnosed at age 10.75 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: MEF_RNASeq_rep3

city: NEW YORK

first: Thiago

middle: Y

last: Oliveira

state: New York

address: 1230 YORK AVE

department: Immunology, Virology and Microbiology

institute: The Rockefeller University

data_processing:
alignment: aligned against mm9 with tophat 1.3.2 using known splice sites from RefSeq
Basecalling: Illumina RTA 1.9.35
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie requiring unique alignment (-m 1)
RNA-Seq reads were aligned using tophat requiring unique alignment
Uniquely aligned reads in ChIP-seq dataset were analyzed by SICER using an expectation value E of 0.05 in a random background model
Wiggle files for pol2 were generated using 50nt binned raw read densities limiting to a max. redundancy of 5, scaled in RPKM
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuffdiff software
Genome_build: mm9
Supplementary_files_format_and_content: wig; tab-delimited text file include FPKM

source_name: primary MEFs

growth_protocol: B lymphocytes were stimulated with LPS and IL4 and incubated for 72h

extract_protocol:
RNA was prepared using Illumina's protocol. ChIP-Seq was performed as described. In brief, cells were fixed with 1% paraformaldehyde at 37°C for 10 minutes followed by sonication. Chromatin fragments were then immunoprecipitated with antibodies specific for serine 5-phosphorylated RNA Polymerase II (Abcam).
Libraries were prepared according to Illumina's instructions

value: Mouse Embryonic Fibroblast (MEF)

tag: genotype

value: wild type CreERT2


title: MEF_RNASeq_rep2


title: activatedB_wt_RNASeq_rep3

source_name: in vitro activated B cells

value: Splenocyte (B lymphocytes)


title: Not IBD Female (CCFA_Risk_028)

description:
CCFA_Risk_028
Female diagnosed at age 16.91666667 with not IBD.

value: Ileal biopsy

value: Not IBD


title: activatedB_wt_RNASeq_rep2


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_027)

description:
CCFA_Risk_027
Female diagnosed at age 10.33333333 with CD characterized with Macroscopic inflammation and deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_047)

description:
CCFA_Risk_047
Female diagnosed at age 15.83333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_025)

description:
CCFA_Risk_025
Female diagnosed at age 6.333333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: activatedB_wt_RNASeq_rep1


title: IRF1_WT_LPS_UT

description: Chromatin IP against IRF1

value: BMDM cells (7th day of differentiation)

value: IRF1 (santa cruz, sc-640)


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_026)

description:
CCFA_Risk_026
Male diagnosed at age 5.08 with CD characterized with Macroscopic inflammation and No Deep Ulcer

source_name: Ileal biopsy in treatment-naïve patient

value: Male

value: no


title: activatedB_wt_polII_chip-seq

data_processing:
alignment: aligned against mm9 with bowtie 0.12.8 (--best --all --strata -m1 -n2 -l36)
Basecalling: Illumina RTA 1.9.35
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie requiring unique alignment (-m 1)
RNA-Seq reads were aligned using tophat requiring unique alignment
Uniquely aligned reads in ChIP-seq dataset were analyzed by SICER using an expectation value E of 0.05 in a random background model
Wiggle files for pol2 were generated using 50nt binned raw read densities limiting to a max. redundancy of 5, scaled in RPKM
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cuffdiff software
Genome_build: mm9
Supplementary_files_format_and_content: wig; tab-delimited text file include FPKM

tag: chip antibody

value: serine 5-phosphorylated RNA Polymerase II (Abcam)


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_024)

description:
CCFA_Risk_024
Male diagnosed at age 4.5 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: CD


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_023)

description:
CCFA_Risk_023
Female diagnosed at age 10.16666667 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Female

value: iCD


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_022)

description:
CCFA_Risk_022
Female diagnosed at age 10.83333333 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Macroscopic inflammation


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_029)

description:
CCFA_Risk_029
Female diagnosed at age 10.83333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: No


title: BXH2_IFN_60m

description:
IFN-genes.fpkm_tracking
IFN-gene_exp.diff

data_processing:
Reads were quality filtered according to the Illumina pipeline
Reads were mapped to the mouse mm9 genome and transcripts using TopHat 1.3.1 (PMID: 19289445), allowing up to two mismatches and with a mean distance between pairs (-r) of 120bp
Transcripts abundance and differentially expressed genes were obtained using Cufflinks 1.2.1 (PMID: 20436464)
Genome_build: mm9 (NCBI Build 37), transcripts from Mus Musculus Ensembl Build 63
Supplementary_files_format_and_content: *.fpkm_tracking list the absolute value of expression (FPKM), *.diff list the statistics for differential expression compared to the untreated (refer to http://cufflinks.cbcb.umd.edu/manual.html for details)

extract_protocol: Total RNA was extracted from 5x106 cells using RNAeasy kit (Qiagen). Libraries were prepared from 1-2 µg of RNA, after oligo-dT selection, using the TruSeq RNA sample preparation kit (Illumina).

value: IFNb (100 U/ml) for 60 minutes


title: WT_IFN_30m

value: IFNb (100 U/ml) for 30 minutes


title: BXH2_IFN_30m


title: MEF_polII_chip-seq

value: Mouse Embryonic Fibroblast (MEF)


title: Not IBD Female (CCFA_Risk_020)

description:
CCFA_Risk_020
Female diagnosed at age 10.75 with Not IBD

value: not IBD


title: BXH2_IFN_UT

value: No treatment


title: Not IBD Female (CCFA_Risk_019)

description:
CCFA_Risk_019
Female diagnosed at age 15 with not IBD.

value: Ileal biopsy


title: WT_IFN_60m


title: WT_IFN_UT


title: MEF_RNASeq_rep1

value: wild type CreERT2


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_017)

description:
CCFA_Risk_017
Male diagnosed at age 13.25 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Yes


title: BXH2_LPS_4h

description:
LPS-genes.fpkm_tracking
LPS-gene_exp.diff

value: BMDM cells (7th day of differentiation)

value: LPS (10 ng/ml) for 4 hours


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_016)

description:
CCFA_Risk_016
Male diagnosed at age 15.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: Male


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_018)

description:
CCFA_Risk_018
Female diagnosed at age 16.08 with CD characterized with Macroscopic inflammation and No Deep Ulcer

source_name: Ileal biopsy in treatment naïve patient

value: no


title: BXH2_LPS_2h

value: LPS (10 ng/ml) for 2 hours


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_015)

description:
CCFA_Risk_015
Male diagnosed at age 13.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: CD


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_013)

description:
CCFA_Risk_013
Male diagnosed at age 9.25 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: iCD


title: WT_LPS_4h


title: CD Male with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_021)

description:
CCFA_Risk_021
Male diagnosed at age 10.33333333 with CD characterized with Macroscopic inflammation and deep ulcer.

value: Macroscopic inflammation


title: Not IBD Female (CCFA_Risk_014)

description:
CCFA_Risk_014
Female diagnosed at age 9 with not IBD.

value: Female

value: Not IBD


title: WT_LPS_2h


title: CD Female with Microscopic inflammation and No Deep Ulcer (CCFA_Risk_012)

description:
CCFA_Risk_012
Female diagnosed at age 13.91666667 with CD characterized with Microscopic inflammation and no deep ulcer.

value: cCD

value: Microscopic inflammation

value: No


title: H3K27Ac_BXH2_IFN_60m

description: Chromatin IP against H3K27Ac

value: H3K27Ac (Abcam, ab4729)

value: IFNbeta for 60 minutes


title: STAT1_WT_LPS_2h

description: Chromatin IP against STAT1

value: STAT1 (santa cruz, sc-592)

value: LPS 10ng/ml for 2 hours


title: WT_LPS_UT

value: BMDM cells (7th day of differentiation)

value: No treatment


title: Not IBD Male (CCFA_Risk_010)

description:
CCFA_Risk_010
Male diagnosed at age 10.33333333 with not IBD.

value: Ileal biopsy

value: Male


title: Not IBD Male (CCFA_Risk_011)

description:
CCFA_Risk_011
Male diagnosed at age 10.83333333 with not IBD.


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_009)

description:
CCFA_Risk_009
Female diagnosed at age 9 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_007)

description:
CCFA_Risk_007
Male diagnosed at age 14.33333333 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with No Microscopic or Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_008)

description:
CCFA_Risk_008
Male diagnosed at age 11.41666667 with CD characterized with normal and no deep ulcer.

value: Normal


title: H3K27Ac_BXH2_IFN_UT

description: Chromatin IP against H3K27Ac


title: H3K27Ac_BXH2_IFN_30m

description: Chromatin IP against H3K27Ac

value: IFNbeta for 30 minutes


title: CD Female with Macroscopic inflammation and Deep Ulcer (CCFA_Risk_006)

description:
CCFA_Risk_006
Female diagnosed at age 15.75 with CD characterized with Macroscopic inflammation and deep ulcer.

value: CD

value: iCD

value: Yes


title: H3K27Ac_WT_IFN_60m

description: Chromatin IP against H3K27Ac


title: H3K27Ac_WT_IFN_UT

description: Chromatin IP against H3K27Ac


title: H3K27Ac_BXH2_LPS_4h

description:
Chromatin IP against H3K27Ac
Reads pooled: Sample 28 and Sample 29

value: LPS 10ng/ml for 4 hours


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_005)

description:
CCFA_Risk_005
Female diagnosed at age 10.16666667 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: Female

value: Macroscopic inflammation


title: BXH2_LPS_UT


title: H3K27Ac_BXH2_LPS_2h

description:
Chromatin IP against H3K27Ac
Reads pooled: Sample 26 and Sample 27


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_004)

description:
CCFA_Risk_004
Male diagnosed at age 14.58333333 with CD characterized with Macroscopic inflammation and no deep ulcer.

value: No


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_003)

description:
CCFA_Risk_003
Female diagnosed at age 12.5 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: CD Male with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_002)

description:
CCFA_Risk_002
Male diagnosed at age 14.41666667 with CD characterized with Macroscopic inflammation and no deep ulcer.


title: H3K27Ac_BXH2_LPS_UT

description:
Chromatin IP against H3K27Ac
Reads pooled: Sample 24 and Sample 25

value: H3K27Ac (Abcam, ab4729)


title: H3K27Ac_WT_LPS_4h

description: Chromatin IP against H3K27Ac


title: rhesus_monkey_spleen

city: Beijing

first: Jia-Yu

last: Chen

address: No.5 Yiheyuan Road Haidian District

department: Institute of Molecular Medicine

country: China

institute: Peking University

data_processing:
raw reads were aligned by Tophat v1.2.0
only uniquely-mapped reads are retained
RPKM values were calculated by in-house perl scripts
Genome_build: rheMac2
Supplementary_files_format_and_content: RhesusBase1 Transcript ID, Ensembl Gene ID, RPKM Values, Number of Mapped Reads, Total Length of Exon, The Gene Locus

molecule: polyA RNA

organism: Macaca mulatta

source_name: spleen

extract_protocol:
Total RNA was extracted from rhesus monkey tissues using the Trizol method and analyzed by an Agilent 2100 bio-analyzer (Agilent Technologies). Poly (A)-positive RNA was purified with the Dynabeads mRNA purification kit (Invitrogen) from 5μg of total RNA with high quality (RNA integrity number >7.5), following the manufacturer's instructions.
A strand-specific RNA-Seq library preparation on the basis of the incorporation of deoxy-UTP was performed.

value: spleen

tag: gender

value: male

tag: library type

value: strand-specific, dUTP protocol


title: CD Female with Macroscopic inflammation and No Deep Ulcer (CCFA_Risk_001)

description:
CCFA_Risk_001
Female diagnosed at age 15.25 with CD characterized with Macroscopic inflammation and no deep ulcer.

tag: tissue

tag: Sex


title: H3K27Ac_WT_LPS_2h

description:
Chromatin IP against H3K27Ac
Reads pooled: Sample 21 and Sample 22

value: BMDM cells (7th day of differentiation)

value: LPS 10ng/ml for 2 hours


title: DNase1_seq L006 rep1

city: west Haven

first: Mauris

middle: Chukwudebelu

last: Nnamani

address: 300 heffernan drive B31-ABC/rm269

department: Systems Biology institute, EEB

description:
Replicate 1
Results: DNaseI_80%Union(hg19).bed

data_processing:
Basecalls performed using CASAVA 1.8.2 according to the manufacturer’s protocols
Sequence reads were aligned to the Homo Sapiens reference genome (hg19) using using the ultra-fast short DNA sequence aligner Bowtie2
reads mapping and peak calling we used the Model-based Analysis of ChIP-Seq (MACS, coupled with PeakSplitter as described for analyzing histone modification markers
Genome_build: hg19
ChIP-Seq data was processed using a two-sample analysis model where both a ChIP sample and a negative control (input) were sequenced for each biological sample
Supplementary_files_format_and_content: files of .bed and .wig for each ChIP sample and .bed for DNase1_seq sample.  Files labeled by sample name.

source_name: dESC Tissue Culture

growth_protocol: Human endometrial stromal cells (dESC) were grown in phenol red free DMEM, supplemented with 5% charcoal-stripped calf-serum, 1% antibiotic/antimycotic (ABAM), and 1x ITS+.

extract_protocol:
cells were harvested, resuspended and chemically cross-linked in suspension by the addition of 1% fresh formaldehyde with 10 minutes incubation at room temperature on a rotator. Cross-linking was quenched and cells were harvested by centrifugation and washed twice in cold PBS. Nuclei were expected and Sonication was performed using a Misonix S4000 sonicator with 431A cup horn.  Fragment size between 200bp and 500bp was obtained and confirmed by gel electrophoresis.
DNA library preparation and high-throughput sequencing were performed on an Illumina HiSeq 2000 sequencing system following the protocol recommended by Illumina for sequencing Chromatin immunoprecipitated DNA samples.  Sequencing was done for each biological replicates at 1 x 75bp strand specific, and 2 x75bp for DNase1-seq  by the Yale Center for Genome Analysis

treatment_protocol: At 80% confluency, cells were decidualized with the addition of 0.5 mM 8-Br-cAMP (Sigma) and 1mM medroxyprogesterone acetate (Sigma) to the cell culture media for 48-72 hours. Deciduaization of the dESC was confirmed by monitoring the expression of prolactin (PRL), which is only expressed in decidualized dESC, by RT-qPCR

value: Decidualized DSC

tag: passages

tag: chip antibody / digestive enzyme

value: DNAse I (Roche cat#04716728001)


title: DNase1_seq rep2

description:
Replicate 2
Results: DNaseI_80%Union(hg19).bed


title: DNase1_seq L002 rep1


title: STAT1_BXH2_IFN_60m

description: Chromatin IP against STAT1

value: STAT1 (santa cruz, sc-592)

value: IFNbeta for 60 minutes


title: Input Chromatin rep2

description: replicate 2

value: Input Chromatin


title: STAT1_BXH2_IFN_30m

description: Chromatin IP against STAT1

value: IFNbeta for 30 minutes


title: STAT1_BXH2_IFN_UT

description: Chromatin IP against STAT1

value: No treatment


title: H3K27Ac_WT_LPS_UT

description:
Chromatin IP against H3K27Ac
Reads pooled: Sample 19 and Sample 20


title: H3K27Ac_WT_IFN_30m

description: Chromatin IP against H3K27Ac


title: Input Chromatin rep1

description: replicate 1


title: H3k4me3_ChIP-seq rep2

description:
replicate 2
Results: h3k4me3_peaks.bed
Results: h3k27ac_diff_75bp_unique_macs_output_treat_afterfiting_all.wig

value: H3k4me3 (Invitrogen cat# 49-1005)


title: H3k27ac_ChIP-seq rep2

description:
replicate 2
Results: h3k27ac_peaks.bed
Results: h3k27ac_diff_75bp_unique_macs_output_treat_afterfiting_all.wig

value: H3k27ac (Millipore cat# 200551)


title: STAT1_WT_IFN_60m

description: Chromatin IP against STAT1


title: STAT1_WT_IFN_30m

description: Chromatin IP against STAT1


title: H3k4me3_ChIP-seq rep1

description:
replicate 1
Results: h3k4me3_peaks.bed
Results: h3k27ac_diff_75bp_unique_macs_output_treat_afterfiting_all.wig


title: STAT1_WT_IFN_UT

description: Chromatin IP against STAT1


title: Input Chromatin 36bp rep2

description: replicate 2


title: PU1_BXH2_LPS_UT

description: Chromatin IP against PU.1

value: PU.1 (in-house rabbit polyclonal anti-mouse PU.1 1-100aa)


title: PU1_BXH2_LPS_4h

description: Chromatin IP against PU.1

value: LPS 10ng/ml for 4 hours


title: PU1_BXH2_LPS_2h

description: Chromatin IP against PU.1


title: H3k4me3_36bp_ChIP-seq rep2

description:
replicate 2
Results: h3k4me3_peaks.bed
Results: h3k4me3_macs_output_treat_afterfiting_all.wig


title: PU1_WT_LPS_4h

description: Chromatin IP against PU.1


title: H3k4me3_36bp_ChIP-seq rep1

description:
replicate 1
Results: h3k4me3_peaks.bed
Results: h3k4me3_macs_output_treat_afterfiting_all.wig


title: PU1_WT_LPS_2h

description: Chromatin IP against PU.1


title: PU1_WT_LPS_UT

description: Chromatin IP against PU.1


title: IRF8_BXH2_LPS_4h

description: Chromatin IP against IRF8

value: IRF8 (in-house rabbit polyclonal anti-mouse IRF8 146-162aa)


title: IRF8_BXH2_LPS_2h

description: Chromatin IP against IRF8


title: IRF8_BXH2_LPS_UT

description: Chromatin IP against IRF8


title: IRF8_WT_LPS_4h

description: Chromatin IP against IRF8


title: IRF8_WT_LPS_2h

description: Chromatin IP against IRF8


title: P3-027A

city: St. Louis

first: Muhammad Farooq

last: Rai

state: MO

address: 660 S. Euclid Ave.

department: Orthopaedic Surgery

institute: Washington University School of Medicine

data_processing:
Basecalling with Casava version 1.8.2
Raw reads were aligned to Ensembl GRch38.76 and adapters were trimmed with STAR version 2.0.4b
Gene counts of uniquely aligned unambigously mapped readsto Ensembl gene ID's were extracted with Subread:featureCounts version 1.4.5 from the aligned BAM files.
Genome_build: Ensembl GRch38.76
Supplementary_files_format_and_content: Text delimitted file containing raw counts of uniquely aligned unambiguous reads to Ensembl Gene IDs

source_name: Anterior cruciate liagment

extract_protocol:
Total RNA was extracted using TRIzol-chloroform method followed by purification using Minispin columns (Qiagen)(45). Total RNA concentrations were obtained using NanoDrop spectrophotometer (NanoDrop Technologies) and quality was determined by Agilent 2100 Bioanalyzer (Agilent Technologies).
Library preparation was performed with 10 ng of total RNA. All samples were DNAseq treated to remove residual DNA and ds-cDNA was prepared using the SeqPlex RNA kit (Sigma-Aldrich) per manufacturer’s protocol. cDNA was then blunt ended, an A base added to the 3’ ends, and then Illumina sequencing adapters were ligated to the ends. Ligated fragments were then amplified for 12 cycles using primers incorporating unique index tags. Fragments were sequenced on an Illumina HiSeq-2500 using single reads extending 50 bases, targeting 30M read per sample.

value: Anterior cruciate liagment


title: P3-012A


title: H3k27ac_ChIP-seq rep1

description:
replicate 1
Results: h3k27ac_peaks.bed
Results: h3k27ac_diff_75bp_unique_macs_output_treat_afterfiting_all.wig


title: P3-011A


title: FACS_GFP-S10-1135744

city: St Louis

first: Winnie

middle: W

last: Pong

address: 660 S. Euclid Avenue

department: Department of Neurology

description:
FACS GFP biological replicate 3
S10

data_processing:
Basecalls performed using CASAVA version 1.8.2
SPIA adapter sequence aligned and trimmed from raw sequence reads using FAR 2.17 with command line parameters : --adapter CTTTGTGTTTGA --trim-end left --adaptive-overlap yes --format fastq --write-lengthdist yes --nr-threads 4 --min-overlap 7 --max-uncalled 150 --min-readlength 25
Aligned with TopHat 2.0.4, Bowtie 2.0.0-beta7 and Ensembl 67 annotation (-G param)
FPKM calculated per sample with Cufflinks 2.0.2  and Ensembl 67 annotation with -G param
Genome_build: mm9
Supplementary_files_format_and_content: 47040_gene_fpkm.tsv is a tab delimited file with columns for gene ID and the normalized expression values per sample name
*diff.txt files are tab delimited files of differential gene expressions of the various samples, as analyzed by cufflinks software

source_name: microglia

growth_protocol: not applicable

extract_protocol:
Total RNA was isolated from snap-frozen flow sorted cell pellets using TRIzol-chloroform extraction and from LCM samples using a proteinase K acid-phenol isolation. RNA was resuspended in 10µl Ambion Nuclease-free water (Life Technologies) and DNAse treated (Ambion TURBO DNA-free Kit)
For cDNA synthesis, we added 5µl of isolated RNA into the Ovation® RNA-Seq method.  500ng cDNA was fragmented using covaris shearing and processed for Illumina library construction with the Illumina paired-end LT indexing protocol as previously published (Mardis et al., 2009; Govindan et al., 2012). Each library was sequenced on the Illumina HiSeq or MiSeq, generating between 15-22Mbp per lane.
RNA-Seq (300-500bp size fractionation): cDNA samples were constructed into Illumina libraries according to the manufacturer’s protocol (Illumina Inc, San Diego, CA) with the following modifications:  1) DNA was fragmented using Covaris S2 DNA Sonicitor using the following condtions: Duty Cycle: 5, Intensity: 4, Cycles/Burst: 200, Time: 90sec (Covaris, Inc. Woburn, MA).  Fragment sizes ranged between 100 and 500bp.  2) Illumina adapter-ligated DNA was amplified in a single 50ml PCR for five cycles.  3) Solid Phase Reversible Immobilization (SPRI) bead cleanup was used to purify the PCR and select for 300-500bp fragments.   We added 0.8 volumes of the AmpureXP solution (preformulated with polyethylene glycol and sodium chloride) to size select DNA molecules greater than 300 bp.  The size-fractioned cDNA was washed three times with 750 µl of 70% ethanol, the beads were dried, and the cDNA library was eluted off the beads by adding 20µl 10 mM Tris-HCl (pH 8.0).  The size-fractioned libraries were assayed using the Agilent BioAnalyzer High Sensitivity DNA chips.

treatment_protocol: For FACS samples, tissue was dissociated, enriched by Percoll gradient, and cells were flow sorted.  For LCM samples, dissected brainstem slices were fixed briefly in paraformaldehyde, then snap frozen for cryosectioning and capture.

tag: microglia isolation method

value: FACS

value: brain

tag: age

value: 6 weeks

value: F


title: FACS_GFP-S9-1135743

description:
FACS GFP biological replicate 2
S9

value: M


title: FACS_WT-S6--1135740

description:
FACS WT biological replicate 2
S6


title: P3-008A


title: P3-005A


title: IRF8_WT_LPS_UT

description: Chromatin IP against IRF8

value: BMDM cells (7th day of differentiation)


title: Input Chromatin 36bp rep1

description: replicate 1

value: Decidualized DSC


title: FACS_WT-S5-1135739

description:
FACS WT biological replicate 1
S5


title: P3-007A


title: LCM_GFP-S1-22689-1

description:
LCM GFP biological replicate 1
S1

value: LCM


title: LCM_GFP-S3-22690-2

description:
LCM GFP biological replicate 3
S3


title: LCM_GFP-S4-22691-8

description:
LCM GFP biological replicate 4
S4


title: LCM_GFP-S2-22835-3

description:
LCM GFP biological replicate 2
S2


title: FACS_WT-S7-1135741

description:
FACS WT biological replicate 3
S7


title: mRNA-Seq data from pregnant platypus endometrium

city: Chicago

first: Vincent

middle: J.

last: Lynch

address: 920 E. 58th Street

department: Human Genetics

institute: The University of Chicago

description: mRNA

data_processing:
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were mapped to appropriate ENSEMBL Gene builds using bowtie with parameters allowing two mismatches and discarding reads that mapped to more than one gene. Uniquely mapped reads for each gene were counted.
Genome_build: OANA5 (Platypus)
Supplementary_files_format_and_content: Platypus.txt contains mapped mRNA-Seq data as the number of unique reads (Gene_Count) that map to ENSEMBL genes (Ensembl_Gene_ID) and the associated gene name for each ENSEMBL gene (Associated_Gene_Name).

organism: Ornithorhynchus anatinus

source_name: Pregnant platypus endometrium

extract_protocol:
Qiagen RNeasy followed by on-column DNase treatment.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: pregnant endometrium


title: P3-025A


title: MBD7-5-Myc-ChIP-rep2

status: Public on Jan 29 2015

city: West Lafayette

first: Jian-Kang

last: Zhu

state: IN

address: 625 Agriculture Mall Dr.

department: Department of Horticulture and Landscape Architecture

institute: Purdue University

data_processing:
The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with bowtie2 (Langmead and Salzberg, 2012)  allowing mapping of up to 10 different genomic sites with parameter “-k 10 --no-mixed --no-discordant -I 0 -X 1000”
To remove potential PCR duplicates, rmdup from SAMtools (Li et al., 2009) was used
featureCounts (Liao et al. 2014) was used to get the fragment numbers in the processed file with parameter "-p -O"
Genome_build: TAIR10
Supplementary_files_format_and_content: TAIR10 genome was divided into 1-kb bins with an overlap of 500 bp and featureCounts (Liao et al. 2014) was used to get the fragment numbers in the each bin with parameter "-p -O".

organism: Arabidopsis thaliana

growth_protocol: Plants were grown at 23°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 1% glucose.

extract_protocol:
The ChIP-seq was performed as previously described (Wierzbicki et al., 2008). In brief, 3 g of 14-day-old seedlings was collected, placed in 35 ml of 1% formaldehyde PBS buffer, and then fixed by vacuum for 2 min followed by another 8 min. After glycine was added, samples were subjected to a vacuum for 5 min to stop the fixation. Samples were washed three times with sterile water and then ground into powder with liquid nitrogen. Nuclei were extracted with Honda buffer. The nuclei solution was sonicated to break genomic DNA into ~500-bp fragments. After centrifugation, supernatants were removed and used for immuno-precipitation. Dynabeads (Invitrogen, cat# 10003D) were used for pre-clearing and antibody binding. The antibodies were c-Myc Mouse Monoclonal Antibody (Invitrogen R950-25).
The libraries were prepared using the NuGen Ovation Ultralow Library Systems and were sequenced in the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, SIBS, CAS (Shanghai, China) with Illumina HiSeq2500.

tag: genotype/variation

value: proMBD7::gMBD7:4xMYC transgenic

value: Seedlings

value: c-Myc Mouse Monoclonal Antibody

tag: chip antibody vendor

value: Millipore

tag: chip antibody cat.#


title: MBD7-5-Myc-ChIP-rep1


title: P3-017A


title: MBD7-5-Input-rep1


title: idm3-3_MethylC-Seq 2

description: treated with bisulfite

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

source_name: Seedlings

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

value: seedling


title: 35S-SUC2-Myc-ChIP-rep1

value: WT

value: Invitrogen


title: 35S-SUC2-Myc-ChIP-rep2


title: 35S-SUC2-Input-rep2


title: FACS_GFP-S8-1135742

description:
FACS GFP biological replicate 1
S8


title: 35S-SUC2-Input-rep1


title: Input sample

city: Stanford

first: Kun

last: Qu

state: CA

address: 269 Campus Dr. CCSR 2150

department: Dermatology

institute: Stanford University

description: RNA - fragmented

data_processing:
Raw reads were uniquely mapped to reference genome (hg19) using TopHat (version 1.1.3) allowing maximum one mismatch.
RPKM and winscore of each 100bp sliding window along the transcriptome is calculated using in-house generated script
Genome_build: hg19
Supplementary_files_format_and_content: tab separated txt file with winscore

source_name: mouse embryonic stem cells

growth_protocol: GM12878 cells were grown under typical cell culture conditions, in RPMI media supplemented with 15% FBS. Cells collected at 600 thousand cells per ml.

extract_protocol:
RNA was extracted with TRIZOL and purified with Rneasy columns.
library generation with the dUTP strand specific protocol.

treatment_protocol: RNA was fragmented and subject to immunoprecipitation with a m6A specific antibody. A strand specific protocol was used to generate cDNA.

tag: cell type

value: lymphoblastoid

tag: cell line


title: MBD7-5-Input-rep2


title: mbd7-1_35S_MethylC-Seq

description: treated with bisulfite

extract_protocol:
Genomic DNA was extracted from 14-day-old seedlings using the Plant DNeasy Maxi Kit from Qiagen and sent to BGI (Shenzhen, China) for bisulfite treatment, library preparation, and sequencing. Bisulfite sequencing libraries were prepared using standard Illumina protocols.
The brief pipeline of BGI is as follows:
1. Fragment genome DNA to 100-300bp by Sonication.
2. DNA-end repair, 3’-dA overhang and ligation of methylated sequencing adaptors.
3. Bisulfite treatment by ZYMO EZ DNA Methylation-Gold kit.
4. Desalting, size selection, PCR amplification and size selection again.
5. Qualified library for sequencing.

tag: background

value: 35S-SUC2 background

value: mbd7-1 mutant


title: DroVir_head

city: Stockholm

first: Christos

last: Samakovlis

address: Svante Arrhenius väg 20C

department: Department of Molecular Biosciences

country: Sweden

institute: Stockholm University

data_processing:
Reads were aligned using tophat with --segment-length 20 and flybase gene models. Gene abundance was quantified using cufflinks.
Genome_build: DroVir3 (for D_virilis_genes_fpkm.txt), DroYak3 (for D_yakuba_genes_fpkm.txt)
Supplementary_files_format_and_content: Tab-delimited text files containing gene id, coordinates and FPKM values.

organism: Drosophila virilis

source_name: UCSC drosophila stock center stock no. 15010-1051.87

growth_protocol: 2-5 day old mated females heads were dissected and ground in trizol.

extract_protocol:
Total RNA was extracted according to manufacturer protocol
1 ug of total RNA was used to generated total RNA RNAseq libraries using Illumina's TruSeq Stranded Total RNA Sample Prep Kit (cat#RS-122-2201) according to manufacturer's guidelines.

value: heads

value: wild type

value: female


title: DroYak_head

organism: Drosophila yakuba

source_name: UCSC drosophila stock center stock no. 14021-0261.01


title: sel-1-intermediate-3RACE-rde3GLP4-25C-sel1-mix

city: Taipei

first: Hsin-yue

last: Tsai

address: 128 academia road sec 2, nankang

department: Institute of biological chemistry

country: Taiwan

institute: Sinica academia

description: RNA

data_processing:
reads were sorted using a barcode in the adaptor; 5' adaptor and 3' adaptor sequences were removed
sequences without adaptors were blasted to WS235 C. elegans genome using bowtie v 0.12.9
position of mapped reads were used to extract gene names from WS235 .gff files
sel-1 mRNA intermediates with nontemplated 3' nucleotides were identified using python scripts (available upon request)
Genome_build: WS235
Supplementary_files_format_and_content: tab-delimited text files include normalized values for each Sample ...

organism: Caenorhabditis elegans

source_name: gravid adult

growth_protocol: for glp-4 containing strains, worms are grown at 25C to result in graviet adult worms without germline, all the rest are grown at 20C till their adulthood

extract_protocol:
RNA was extracted using Trizol, per manufacturer's instruction
RNA libraries were prepared for sequencing using standard small RNA Illumina protocols

treatment_protocol: small RNAs were untreated or pretreated with phosphatase followed by polynucleotide kinase; sel-1 mRNA intermediates were amplified by a modified version of 3' RACE, see Tsai et al. for detail

tag: Stage

value: gravid adult

tag: duration of sel-1 rnai feeding


title: sel-1-intermediate-3RACE-GFPRDE8GLP4-25C-sel1-mix

description: RNA


title: sel-1-intermediate-3RACE-GFPRDE8D76NGLP4-25C-sel1-mix

description: RNA


title: smallRNA-CIPPNK-GFPRDE8

description: size selected small RNA


title: sel-1-intermediate-3RACE-GFPRDE8-sel1-7h

description: RNA


title: mbd7-2_CS876032_MethylC-Seq 2

description: treated with bisulfite

tag: genotype


title: smallRNA-CIPPNK-GFPRDE8D76N

description: size selected small RNA


title: WT_35S_MethylC-Seq

description: treated with bisulfite


title: smallRNA-CIPPNK-rde-8(ne3361)

description: size selected small RNA


title: m6A IP sample

description: RNA - fragmented


title: sel-1-intermediate-3RACE-GFPRDE8-sel1-1h

description: RNA


title: Col-0_MethylC-Seq 2

description: treated with bisulfite


title: sel-1-intermediate-3RACE-GFPRDE8D76N-sel1-7h

description: RNA


title: sel-1-intermediate-3RACE-GFPRDE8D76N-sel1-1h

description: RNA


title: smallRNA-CIPPNK-N2

description: size selected small RNA


title: sel-1-intermediate-3RACE-GFPRDE8D76N-sel1-3h

description: RNA


title: sel-1-intermediate-3RACE-GFPRDE8D76N-l4440

description: RNA


title: smallRNA-CIPPNK-GFPRDE8-sel1-8h

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-8h

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8-sel1-24h

description: size selected small RNA


title: sel-1-intermediate-3RACE-GFPRDE8-l4440

description: RNA


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-24h

description: size selected small RNA


title: idm3-1_35S_MethylC-Seq

description: treated with bisulfite

value: idm3-1 mutant


title: smallRNA-CIPPNK-GFPRDE8-sel1-3h

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-7h

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8-l4440

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8-sel1-1h

description: size selected small RNA


title: sel-1-intermediate-3RACE-GFPRDE8-sel1-3h

description: RNA


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-3h

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8-sel1-7h

description: size selected small RNA


title: smallRNA-direct-GFPRDE8

description: size selected small RNA


title: smallRNA-CIPPNK-GFPRDE8D76N-l4440

description: size selected small RNA


title: smallRNA-direct-GFPRDE8D76N

description: size selected small RNA


title: smallRNA-direct-rde8

description: size selected small RNA


title: RYY085

status: Public on Jan 28 2015

city: Singapore

first: Michael

last: Poidinger

address: #04-06, 8A Biomedical Grove

department: Bioinformatics

country: Singapore

institute: Singapore Immunology Network

description:
B2F
Butyric acid treatment

data_processing:
Raw sequencing reads were first mapped to the ERCC spike-in control sequences with bowtie2.
For each run, the mate distance and standard deviation were determined with Picard, and these values used to map the reads to the reference genome using TopHat.
The number of reads mapping to each transcript in the genome was counted with an in-house R script.
Reads mapping to overlapping regions between multiple transcripts were assigned to unique transcripts based on information from the uniquely mapping portion of each transcript and by assuming an additive effect in the overlapping regions.
Genome_build: Assembly 21, version s02-m05-r10
Supplementary_files_format_and_content: GSE49310_matrix.RPKM: RPKM values for all 6453 transcripts in the Candida genome and all 96 samples in the dataset.

organism: Candida albicans

source_name: Yeast cell culture, Butyric acid treatment

growth_protocol: Cells were grown in De Man, Rogosa and Sharpe (MRS) media (Sigma), supplemented with one of the indicated acids, at 37 °C in a shaking incubator at 150-200 rpm. On a daily basis, overnight cultures were relaunched into fresh media.

extract_protocol:
Yeast were centrifuged, flash frozen in liquid nitrogen, and total RNA was extraced using the hot phenol protocol.
RNA samples were subjected to cDNA synthesis using Illumina TruSeq® RNA sample preparation kit version 2 (Low-Throughput protocol) according to manufacturer’s protocol.

treatment_protocol: Overnight cultures of C. albicans were relaunched in fresh MRS medium, supplemented with hydrocholoric acid, lactic acid, acetic acid, propionic acid or butyric acid.

tag: strain

tag: treatment

value: Butyric acid (IC50)

tag: ph

tag: time point

tag: replicate

value: F


title: RYY092

description:
H2F
pH control

source_name: Yeast cell culture, pH control

value: HCl


title: RYY095

description:
L4F
Lactic acid treatment

source_name: Yeast cell culture, Lactic acid treatment

value: Lactic acid (IC50)


title: RYY093

description:
B3F
Butyric acid treatment


title: RYY087

description:
A3F
Acetic acid treatment

source_name: Yeast cell culture, Acetic acid treatment

value: Acetic acid (IC15)


title: RYY096

description:
H3F
pH control


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-1h

description: size selected small RNA


title: RYY088

description:
C2F
untreated control

source_name: Yeast cell culture, untreated control


title: RYY081

description:
C3F
untreated control


title: RYY083

description:
P2F
Propionic acid treatment

source_name: Yeast cell culture, Propionic acid treatment

value: Propionic acid (IC50)


title: RYY078

description:
L2F
Lactic acid treatment


title: RYY075

description:
L3F
Lactic acid treatment


title: RYY074

description:
P3F
Propionic acid treatment


title: RYY068

description:
P3D
Propionic acid treatment

value: D


title: RYY073

description:
A2F
Acetic acid treatment


title: smallRNA-CIPPNK-GFPRDE8D76N-sel1-4h

description: size selected small RNA


title: RYY067

description:
A2D
Acetic acid treatment


title: smallRNA-direct-N2

description: size selected small RNA


title: RYY059

description:
H3D
pH control


title: RYY062

description:
H2D
pH control


title: RYY064

description:
A3D
Acetic acid treatment


title: RYY060

description:
C2D
untreated control


title: RYY056

description:
L2D
Lactic acid treatment


title: RYY054

description:
B3D
Butyric acid treatment


title: smallRNA-CIPPNK-GFPRDE8-sel1-4h

description: size selected small RNA


title: RYY043

description:
C3C
untreated control

value: C


title: RYY038

description:
P3C
Propionic acid treatment


title: RYY036

description:
A3C
Acetic acid treatment


title: RYY047

description:
L2C
Lactic acid treatment


title: RYY041

description:
H2C
pH control


title: RYY042

description:
L3C
Lactic acid treatment


title: RYY066

description:
B2D
Butyric acid treatment


title: RYY032

description:
B3C
Butyric acid treatment


title: RYY034

description:
B2C
Butyric acid treatment


title: RYY023

description:
P2B
Propionic acid treatment

value: B


title: RYY024

description:
B3B
Butyric acid treatment


title: RYY028

description:
A2C
Acetic acid treatment


title: RYY022

description:
L2B
Lactic acid treatment


title: RYY031

description:
P2C
Propionic acid treatment


title: RYY029

description:
H3C
pH control


title: RYY020

description:
P3B
Propionic acid treatment


title: RYY019

description:
A2B
Acetic acid treatment


title: RYY049

description:
C3D
untreated control


title: RYY018

description:
H3B
pH control


title: RYY015

description:
B2B
Butyric acid treatment


title: RYY053

description:
P2D
Propionic acid treatment


title: RYY013

description:
H2B
pH control


title: RYY014

description:
L3B
Lactic acid treatment


title: RYY017

description:
C2B
untreated control


title: RYY058

description:
L3D
Lactic acid treatment


title: RYY046

description:
C2C
untreated control


title: RYY021

description:
A4B
Acetic acid treatment


title: RYY009

description:
A3B
Acetic acid treatment


title: RYY016

description:
C3B
untreated control


title: RYY094

description:
C4F
untreated control


title: RYY090

description:
L1F
Lactic acid treatment


title: RYY089

description:
H4F
pH control


title: RYY084

description:
A1F
Acetic acid treatment


title: RYY086

description:
P1F
Propionic acid treatment


title: RYY076

description:
A4F
Acetic acid treatment


title: RYY072

description:
P4D
Propionic acid treatment


title: RYY077

description:
H1F
pH control


title: RYY080

description:
B1F
Butyric acid treatment


title: RYY091

description:
C1F
untreated control


title: RYY071

description:
B1D
Butyric acid treatment


title: RYY065

description:
P1D
Propionic acid treatment


title: RYY069

description:
L4D
Lactic acid treatment


title: RYY063

description:
C4D
untreated control


title: RYY057

description:
A4D
Acetic acid treatment


title: RYY061

description:
L1D
Lactic acid treatment


title: RYY055

description:
H1D
pH control


title: RYY070

description:
A1D
Acetic acid treatment


title: RYY051

description:
B4D
Butyric acid treatment


title: RYY048

description:
H1C
pH control


title: RYY050

description:
H4D
pH control


title: RYY045

description:
B1C
Butyric acid treatment


title: RYY044

description:
H4C
pH control


title: RYY040

description:
C4C
untreated control


title: RYY079

description:
P4F
Propionic acid treatment


title: RYY082

description:
B4F
Butyric acid treatment


title: RYY037

description:
B4C
Butyric acid treatment


title: RYY035

description:
P4C
Propionic acid treatment


title: RYY033

description:
C1C
untreated control


title: RYY027

description:
L1C
Lactic acid treatment


title: RYY026

description:
P1C
Propionic acid treatment


title: RYY011

description:
H1B
pH control


title: RYY012

description:
C4B
untreated control


title: RYY008

description:
L1B
Lactic acid treatment


title: RYY007

description:
B4B
Butyric acid treatment


title: RYY006

description:
A1B
Acetic acid treatment


title: RYY005

description:
L4B
Lactic acid treatment


title: RYY004

description:
B1B
Butyric acid treatment


title: RYY039

description:
A1C
Acetic acid treatment


title: RYY002

description:
H4B
pH control


title: RYY025

description:
A4C
Acetic acid treatment


title: RYY001

description:
C1B
untreated control


title: nkd  starchy endopserm, biorep 3 (NS3)

city: Ames

first: Philip

last: Becraft

state: IA

address: Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

data_processing:
The raw sequence data were first quality checked using the FastQC software
Reads were then aligned to the B73 reference maize genome assembly V2 using the Tophat short sequence aligner
Read counts were normalized based on library sizes and analyzed for differentially expressed genes using the DESeq software (Anders and Huber, 2010).
Genome_build: Maize AGPv2
Supplementary_files_format_and_content: The processed data is a microsoft excel file that contains normalised transcript read counts of wild type (B) and nkd (N) mutant aleurone (A) and starchy endosperm (S) samples.

organism: Zea mays

source_name: endosperm

growth_protocol: Wild type (B73) and nkd mutant plants (fourth generation back cross to B73) were grown at the Iowa State University Curtiss research farm in the summer of 2012.

extract_protocol:
Total RNA was isolated from captured cells using Arcturus Picopure RNA Isolation Kit (Life Technologies, Grand Island, NY, USA). The total RNA was subjected to a T7 RNA Polymerase based linear RNA amplification strategy, using TargetAmp™ 2-Round aRNA Amplification Kit 2.0 (Epicentre Biotechnologies, Madison, WI) to generate sufficient quantity of RNA as a template for RNA sequencing.
Transcript libraries were constructed using the TruSeq RNA sample preparation kit (Illumina).
The libraries were indexed (barcoded) using specific adapter sequences and were subjected to cluster analysis and 50 base pair paired end sequencing using an Illumina HiSeq2000 machine, by the Iowa State University DNA facility. 3 flow cells were used, each containing 1 biorep of the 4 tissue types (i.e. flow cell 1 contained BA1, NA1, BS1 and NS1).

treatment_protocol: Developing kernels were harvested at 15 DAP (days after pollination) fixed in Farmers fixative and embedded in paraffin. Endosperm cell types were isolated from sections using a Laser Capture Microdissection (LCM) microscope (PixCell II LCM System, Arcturus Engineering).

value: Starchy endosperm

tag: developmental stage

value: 15 DAP (days after pollination)

value: nkd (mutant)


title: nkd  starchy endopserm, biorep 2 (NS2)


title: nkd  starchy endopserm, biorep 1 (NS1)


title: B73 starchy endopserm, biorep 3 (BS3)

value: B73 (wild type)


title: RYY030

description:
L4C
Lactic acid treatment


title: nkd Aleurone, biorep 2 (NA2)

value: Aleurone


title: nkd Aleurone, biorep 3 (NA3)


title: nkd Aleurone, biorep 1 (NA1)


title: B73 Aleurone, biorep 2 (BA2)


title: B73 Aleurone, biorep 3 (BA3)


title: Input_p13_ChIP-seq

status: Public on Jan 27 2015

city: Cheonan

first: Keunsoo

last: Kang

state: Chungnam

address: Dandae-ro 119

department: Microbiology

country: South Korea

institute: Dankook University

data_processing:
Basecalls performed using the CASAVA software.
The HiSeq 2000 sequence reads (single-end) were aligned to the mouse reference genome (mm9) using Bowtie2 (Langmead and Salzberg, Nat. Methods 2012).
Total mapped reads per sample were normalized to 10 million and converted to the bigWig files using the HOMER program (Heinz et al., Mol Cell, 2010).
Genome_build: mm9
Supplementary_files_format_and_content: The bigWig files were generated by using the HOMER program (Heinz et al., Mol Cell 2010)

source_name: Mammary tissues

growth_protocol: We mated Ezh2f/f mice (Ezhkova et al., 2011; Wang et al., 2010) with the control transgenic mouse line A (Wagner et al., 1997) in order to generate mice with mammary-specific deletion of Ezh2. Genotyping was confirmed by PCR using DNAs from ear clips. All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.

extract_protocol:
Frozen-stored mammary tissues from p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Antibodies against EZH1 (gift from Sartorelli, Mousavi et al. Mol. Cell 2012), EZH2 (Diagenode, cat# C15410039 and lot# 003) and PolII (Abcam, cat# ab5408, lot# GR106949-6) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.

tag: tissue

value: Mammary tissues

value: outbred

value: MMTV-Cre

value: Day 13 of pregnancy (p13)


title: RYY010

description:
P1B
Propionic acid treatment


title: EZH2_WT_p13_ChIP-seq

value: MMTV-Cre; WT

tag: chip antibody

value: EZH2 (Diagenode, cat# C15410039 and lot# 003)


title: EZH2_E2KO_p13_ChIP-seq

value: MMTV-Cre; E2KO


title: PolII_WT_p13_ChIP-seq

value: PolII (Abcam, cat# ab5408, lot# GR106949-6, 5ug)


title: B73 Aleurone, biorep 1 (BA1)


title: EZH1_E2KO_p13_ChIP-seq

value: EZH1 (gift from Sartorelli, Mousavi et al. Mol. Cell 2012)


title: Adult Tie2 endothelial cells

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

country: United Kingdom

institute: IGMM MRC Human Genetics Unit

description:
GUDMAP: 21834
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21834)

data_processing:
Genome build: mm9
Data Processing: Samples were aligned to the mm9 genome using TopHat v1.4.1. Known junctions from the RefSeq database were provided to TopHat with the -G option.
The generation of RPKM data was carried out using GeneSpring 12.6 -GX-NGS-PA (Agilent Technologies). Read density (nRPKM) in GeneSpring NGS is computed as the normalized read count (DESeq) per kilo base of exon model per Million reads. This is similar to the standard RPKM used in the literature except that it is computed on the normalized read count rather than on the raw read count.
Data file format and content: Excel spreadsheet including RPKM values for each Sample in Series.

source_name: Adult kidney endothelial cells Tie2-FACS

extract_protocol:
Total RNA was isolated from cells using the MicroRNAeasy kit (Qiagen).  Briefly,  FACS isolated cells were collected in 200ul of RLT buffer (provided by manufacturer).   The cells were quickly frozen on dry-ice and allowed to thaw on ice.  After the cells were thawed, 50ul of SDS-lysis buffer  (50mMTric-HCL pH 7.4/0.05%SDS) was added, the cells were vortexed and an equal volume of 70% ETOH was added.  The cells were voxtexed,  placed on a Qiagen column, and centrifuged for 1 min at 10,000rpm.  The column was washed by adding 350ul of RW1 and centrifuged for 1 min at 10,000rpm.  The extracted RNA was then subject to a 15 minute on-column DNAse digest following the manufacturers protocol.  After DNase digestion, the column was rinsed with a series of washes including: 350ul of RW1, 500ul RPE and 500ul of 80% ETOH.  After the washes, the column was centrifuged at 10,000 rpm for 5 mins to ensure the removal of residual ETOH.  The RNA was eluted by adding 16ul of RNAse-free H20 and incubated at room temperature for 2 mins.  The Qiagen column was placed into a 1.5ml eppendorf tube and centrifuged at 10,000 rpm for 1 min to collect the RNA.
2ng of total RNA was amplified using the Ovation RNA-Seq System v2 (NuGEN #7102).  The libraries were prepared with the Nextera DNA Sample Preparation kit (Illumina Technologies). 50 ng of cDNA was suspended in Tagment DNA  Buffer and tagmentation (fragmentation and tagging with the adaptors) was performed with the Nextera enzyme (Tagment DNA Enzyme) and incubating at 55C for 5 mins. Tagged and fragmented cDNA was purified with DNA Clean & Concentrator-5 (Zymo Research).  The libraries were prepared by PCR with Nextera PCR Master Mix, PCR Primer Cocktail and 2 Nextera Indexes (N7XX, and N5XX) according to the following program: one cycle at 98 C for 30 s, 5 cycles of 98C for 10s, 63C for 30s, 72C for 3min. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq 2500 following the manufacturers protocols.

treatment_protocol: Mice are euthanized by standard carbon dioxide asphyxiation. Dissect & isolate kidneys in ice-cold PBS. Use a razor blade, bisect kidneys length-wise (Cut on top of a tissue culture dish lid). After bisection, cut away the medullary region (to enrich for cortical region ie. glomeruli). Mince remaining cortical region into a fine mush using a razorblade. Divide the minced kidney evenly into 4 equal amounts and place into 1.5ml eppendorf tubes. To each tube, add 400μl 1% collagenase A/PBS (make fresh). Incubate at 37°C for 15-20 minutes (begin triturating at 5 minutes). Triturate vigorously every 5 minutes, you may need to start with a large bore 1 ml pipette tip (cut the end of a pipette tip off with a razor blade). After incubation, add 1ml ice-cold 10% FBS/PBS. Triturate vigorously. Place a 100μM filter on a 50ml conical tube. Add digested kidneys directly onto mesh filter. Rinse the filter with 4ml of ice-cold PBS. Centrifuge tube 1800rpm for 5 minutes. Decant supernatant. Resuspend pellet in 2-3 ml ice-cold 1% FBS/PBS (contains proximal/distal tubules, glomeruli, vasculature). Triturate vigorously. Place 40μM filter on a 50ml conical tube (orange cap). Add 1 ml of cell mixture onto filter. Rinse filter with 3-4ml ice-cold PBS. Remove filter from 50ml conical and flip (turnover) filter. Rinse the filter with 4ml 1% FBS/PBS, collect the glomeruli in a 6cm dish. Place dish on ice (to allow glomeruli to settle to bottom). Under a microscope, swirl dish to collect glomeruli in the centre of the dish. Using a pipette, collect glomeruli (also will contain other large structures). Place glomeruli into 1.5ml eppendorf tube. Triturate vigorously. Re-filter using new 40μM mesh and collect the glomeruli. It usually takes 2-3X of filtering to get pure glomeruli.  (Visually inspect with microscope). After purifying the glomeruli, spin in centrifuge 2300rpm for 5 minutes. Rinse with PBS. Centrifuge 2300rpm for 5 minutes. Repeat. Re-suspend glomeruli in 200μl 0.5% Trypsin. Incubate 37°C for 10-15 minutes. Triturate vigorously every 5 minutes. Visually inspect that glomeruli are digested (single cells) using a microscope; keep incubating until glomeruli have broken apart (be careful not to over digest as cells will lyse). Add 1ml ice-cold 10% FBS/PBS. Triturate vigorously. Spin in centrifuge at 2300rpm for 5 minutes. Repeat wash 2X. Add 1ml ice-cold 1% FBS/PBS. Spin in centrifuge 2300rpm for 5 minutes. Repeat wash 2X. Resuspend in 1ml ice-cold 1% FBS/PBS. Filter using 40μM mesh, collect cells in a 6cm dish. Place the filtered cells (flow-through) into 1.5ml eppendorf tube. Spin in centrifuge 2300rpm for 5 minutes. Resuspend in 400μl 1% FBS/PBS. Filter using FACS tube (35μM). FACS - collect GFP positive cells. Collect cells into 200μl RLT/BME. Freeze at -80°C until ready to purify RNA.

tag: component sampled

value: glomerular capillary system

tag: theiler stage

tag: age

value: Adult

value: unspecified

tag: Sex

value: unknown

tag: pooled sample

value: yes

tag: pool size

value: 2 kidneys from the same mouse


title: E15.5 Tie2 endothelial cells

description:
GUDMAP: 21833
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21833)

source_name: E15.5 kidney endothelial cells Tie2-FACS

treatment_protocol: Tie2 transgenic mice are time-mated. Pregnant Tie2 transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Mince ~6 kidneys using a razorblade. Prepare non-transgenic kidneys to use as a control. Embryonic kidneys are incubated in the presence of 200μl of 0.5% trypsin for 5 minutes at 37ºC.  Triturate vigorously. Add 1ml ice-cold 10% FBS/PBS. Triturate vigorously. The dissociated cells from the kidneys are pelleted at 2300rpm for 5 minutes at 4ºC. The media is aspirated and the cell pellet is resuspended in 1ml RBC lysis buffer. Centrifuge at 2300rpm for 5 minutes. Repeat if necessary. Add 1ml ice-cold 1% FBS/PBS. Repeat wash 2X. Centrifuge at 2300rpm for 5 minutes. Resuspend in 1ml ice-cold 1% FBS/PBS (have 40μM mesh ready). Filter using 40μM mesh, collect cells into 6cm dish. Place the filtered cells (flow-through) into 1.5ml eppendorf tube. Centrifuge at 2300rpm for 5 minutes. Resuspend in 400μl 1% FBS/PBS.  Filter using FACS tube (35μM). FACS - collect GFP positive cells. Collect cells into 200μl RLT/BME.  Freeze at -80C until ready to purify RNA.

value: endothelial layer of renal vein, endothelial layer of renal artery

value: mixed background

value: both

value: 6 kidneys from the same litter


title: B73 starchy endopserm, biorep 2 (BS2)

tag: cell type

value: Starchy endosperm

value: 15 DAP (days after pollination)

value: B73 (wild type)


title: Adult MAFB podocyte cells

description:
GUDMAP: 21829
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21829)

source_name: Adult kidney visceral epithelium (syn: podocyte layer) isolated from MAFB-GFP mice

value: visceral epithelium of mature renal corpuscle


title: RYY052

description:
C1D
untreated control

value: D


title: E15.5 Hoxb7 Ureter - 2

description:
GUDMAP: 21555
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21555)

source_name: E15.5 ureter Hoxb7-FACS sample 2

treatment_protocol: E15.5 ureter regions of kidneys from Hoxb7-GFP mice were isolated in ice-cold PBS, minced into pieces, <1mm, placed into 1.5ml eppendorf tubes and 400μl of 0.05% Trypsin-EDTA was added. The collecting ducts were incubated at 37°C for 5 minutes. After digestion, the samples were triturated and 1ml of ice-cold 10%FBS/PBS was added. The samples were centrifuged at 2300rpm for 5 minutes. The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 2300rpm for 5 minutes. The supernatant was removed and the pellet resuspended in 400μl of ice-cold 1%FBS/PBS, filtered using a FACS tube (35μM) and the GFP positive cells further isolated by FACS. The cells were collected into 200μl RLT/BME and frozen at -80 C until ready to purify RNA.

value: ureter

value: ~6 kidneys


title: E15.5 Hoxb7 collecting ducts - 3

description:
GUDMAP: 21556
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21556)

source_name: E15.5 kidney ureteric tip and collecting duct isolated from Hoxb7-EGFP mice - sample 3

treatment_protocol: E15.5 cortical regions of kidneys from Hoxb7-GFP mice were isolated in ice-cold PBS, minced into pieces <1mm, placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The collecting ducts were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and the GFP positive cells were further isolated by FACS.

value: cortical collecting duct, ureteric tip

value: 5 kidneys


title: E15.5 Proximal Tubules - 2

description:
GUDMAP: 21554
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21554)

source_name: E15.5 kidney proximal tubules (LTA-positive FACS) sample 2

treatment_protocol: 1. E15.5 kidneys are dissected in ice-cold PBS.  2. The kidneys are finely minced and divided equally into 4 tubes with 200ul 0.5% Trypsin.  3. Incubate at 37C for 5 minutes, triturating vigorously.  5. After incubation, add 1ml ice-cold 10% FBS/PBS. Triturate.  6. Centrifuge at 2300rpm for 5 minutes.  7. Add 1ml RBC Lysis buffer, mix.  8. Centrifuge at 2300rpm for 5 minutes.  9. Repeat if necessary.  10. Add 1ml ice-cold 1% FBS/PBS.  11. Repeat wash 2X.  12. Centrifuge 2300rpm for 5 minutes.  13. Re-suspend in 1ml ice-cold 1% FBS/PBS.  14. Filter using 40um mesh filter.  15. Centrifuge at 2300rpm for 5 minutes.  16. Re-suspend pellet in two tubes - 1ml in each tube (one will be LTA, one will be a control).  17. Incubate tubes containing 1ml of cells for 15 minutes - one tube should be with 10uL LTA (LTA is proximal tubule specific lectin that is fluorescently labeled).  18. Spin down cells at 2300rpm for 5 minutes.  19. Re-suspend in 400ul 1% FBS/PBS.  20. FACS sort.

value: wild type

value: early proximal tubule

value: dpc

value: unspecified

tag: pool size:


title: E15.5 MAFB - Podocytes - 2

description:
GUDMAP: 21543
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21543)

source_name: E15.5 kidney podocyte cells isolated from Mafb-GFP mice - sample 2

treatment_protocol: E15.5 kidneys from MAFB-GFP mice were isolated in ice-cold PBS, minced into pieces <1mm, placed into 1.5ml eppendorf tubes and 200ul of 0.05% Trypsin-EDTA was added.  The kidneys were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 10% FBS/PBS was added.  The samples were centrifuged at 2300rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1% FBS/PBS was added and the samples were centrifuged at 2300rpm for 5 minutes.  Filter using 40uM mesh filter. Place filtered cells into 1.5ml eppendorf tube. Centrifuge 2300rpm for 5 minutes. Re-suspend in 400ul 1% FBS/PBS. Filter through a 35um mesh filter and the GFP positive cells are further isolated using FACS.

tag: genotype

value: visceral epithelium of maturing renal corpuscle, visceral epithelium of capillary loop renal corpuscle

value: yes

value: 2 kidneys


title: E15.5 Hoxb7 collecting ducts - 2

description:
GUDMAP: 21545
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21545)

source_name: E15.5 kidney ureteric tip and collecting duct isolated from Hoxb7-EGFP mice - sample 2

tag: strain

value: mixed background

value: both


title: E15.5  Hoxb7 collecting ducts -1

description:
GUDMAP: 21540
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21540)

source_name: E15.5 kidney ureteric tip and collecting duct isolated from Hoxb7-EGFP mice - sample 1

treatment_protocol: E15.5 collecting duct regions of kidneys from Hoxb7-GFP mice were isolated in ice-cold PBS, minced into pieces <1mm, placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The collecting ducts were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and the GFP positive cells were further isolated using FACS.


title: E15.5 Proximal Tubules - 3

description:
GUDMAP: 21539
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21539)

source_name: E15.5 kidney proximal tubules (LTA-positive FACS) sample 3


title: E12.5 Six2 Cap Mesenchyme

description:
GUDMAP: 21538
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21538)

source_name: E12.5 kidney cap mesenchyme Six2-FACS

treatment_protocol: The Six2-GCE mouse was used for this sort. E12.5 Six2 +/- kidneys were isolated and then dissociated into a single cell suspension using Trypsin. Following Trypsin, the cells were washed with 10% FBS/PBS and 1% PBS, ice cold, and the GFP positive cells were further isolated using FACS.

value: cap mesenchyme


title: Adult Meis1 mesangial cells

description:
GUDMAP: 21831
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21831)

source_name: Adult kidney mesangial cells isolated from Meis1-EGFP mice

value: glomerular mesangium

value: Adult

value: 2 kidneys from the same mouse


title: E15.5 Hoxb7 Ureter -1

description:
GUDMAP: 21546
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21546)

source_name: E15.5 ureter Hoxb7-FACS sample 1

value: ureter


title: PolII_E2KO_p13_ChIP-seq

value: Mammary tissues

value: outbred

value: MMTV-Cre; E2KO

value: Day 13 of pregnancy (p13)

value: PolII (Abcam, cat# ab5408, lot# GR106949-6, 5ug)


title: E15.5 MAFB - Podocytes - 3

description:
GUDMAP: 21553
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21553)

source_name: E15.5 kidney podocyte cells isolated from Mafb-GFP mice - sample 3


title: Arsenite mRNAseq, replicate 1

city: Cork

first: Pavel

middle: V

last: Baranov

state: Co. Cork

address: Western Gateway Building, UCC

department: Biochemistry and Cell Biology

country: Ireland

institute: University College Cork

description: polyA RNA

data_processing:
Alignment; Cutadapt was used to remove the 3' adapter of the reads. Reads that did not map to either the "spike-in" (ATGTACACGGAGTCGACCCGCAACGCGA) or rRNA sequences were aligned to the RefSeq catalogue  downloaded from the NCBI website on the 15 Aug 2013. The alignment was carried out with Bowtie version 1.0.0, with parameters -a -m 100 –norc (all read mappings to the positive strand were taken with exception of those with more than 100 mappings). Reads that mapped to transcripts of more than one gene or multiple times to a transcript were discarded. In order to maximise the genuine ribosome footprints aligning to the transcriptome, riboseq reads with a length typical for monosomes (29 to 35 inclusive) were used for further analysis. In the case of multiple transcript variants, among the transcripts annotated as protein coding, the one with the highest riboseq read density in control conditions was brought forward for differential expression analysis.
Transcript abundance normalisation; The raw read count data were rescaled to normalize for the differences in the total number of reads mapped with a rescale factor. For the 1st replicate the rescale factor for each sample was calculated as the difference by which the total number of mapped reads exceeds the lowest total number of mapped reads out of two conditions. This normalization was carried out independently for riboseq and mRNAseq. The 2nd replicate was sequenced on Illumina Miseq and Hiseq 2000 instruments and obtained sequence reads were aggregated. The number of “spike-in” reads were used to rescale the read counts with a similar approach as for replicate 1. The raw read count of each sample was divided using the difference of the number of “spike-in” reads from the sample in the condition exceeds the lowest number of "spike in" reads in two conditions.
Differential expression analysis; The normalized read counts of riboseq reads aligning to the coding regions (as determined by inferred locations of the A-site codons) and of mRNAseq reads aligning to the entire transcript were used for the differential expression analysis. For riboseq reads the A-site codon of the elongating ribosome was inferred to be the 17th or 18th nucleotide of the read from its 5’ end depending on the read length.The number of reads aligning to a transcript influences the accuracy of an estimated change in its expression. To take this into account and to estimate statistical significance of observed differential expression transcripts were binned based on the number of mapped reads (expression/coverage level) in one of the conditions where this value is the minimal. With the minimum expression level threshold of 2 reads, transcripts were sorted in ascending order and an arranged in bins of size 300. Each bin had transcripts with a similar numbers of mapped reads and was analysed independently. The mean and standard deviation of change in expression of the transcripts within each bin was used to determine a Z-score for each transcripts. For the remaining transcripts, of insufficient number to be binned (<300), the mean and standard deviation was obtained from the previous bin. The Z-score determined for each transcripts enabled comparison between bins.
Genome_build: n/a
Supplementary_files_format_and_content: These tab delimited csv files record the number of mapped reads that aligned the transcripts in the RefSeq catalogue after the alignment step. Each row contains the record of a transcript with first 4 columns indicating its Gene name, RefSeq accession number, its annotation classification (coding, ncRNA, rRNA,transcript,pseudo,linc) and the number of alignments. Three more columns are used for coding transcripts. These columns indicates the number of alignments to the 5'leader, the CDS and the 3'UTR. SupplementalTable1.xlsx records the results from differential gene expression for the 2nd replicate. It contains the normalised read count for four samples (RNAseq and riboseq in two conditions) for each expressed transcript. It also includes the fold change and the Z-score of differential expression of the riboseq, mRNAseq and translation efficiency

growth_protocol: Hek293T cells were grown in DMEM

extract_protocol:
Detergent lysis was performed in the dish, and after DNAse treatment sample was taken for mRNA isolation. Lysates were subjected to ribosome footprinting by RNAse I treatment. After sucrose density gradient fractionation ribosome-protected fragments were purified from 80S peak fractions. In parallel, mRNA isolated with Oligotex kit (Quiagen) was subjected to alkaline hydrolysis and fragments of the same size as ribosome protected fragments were isolated.
Library preparation was carried out as described in Ingolia et al (2012),Nature Protocols

treatment_protocol: 40 µM sodium arsenite or vehicle were added and 30 mins later cells were harvested: dishes were immediately chilled on ice and washed with PBS+cycloheximide (100 ug/ml)

tag: treatment

value: 0.5 hour arsenite

tag: rna type

value: “naked” mRNAseq

tag: cell line


title: EZH1_WT_p13_ChIP-seq

value: MMTV-Cre; WT

value: EZH1 (gift from Sartorelli, Mousavi et al. Mol. Cell 2012)


title: E15.5 Meis1 mesangial cells

description:
GUDMAP: 21832
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21832)

source_name: E15.5 kidney mesangial cells isolated from Meis1-EGFP mice

treatment_protocol: Meis transgenic mice are time-mated. Pregnant Meis transgenic mice are euthanized by standard carbon dioxide asphyxiation. All fetuses are killed by decapitation with a scalpel. Fetal kidneys are dissected from fetuses and placed in ice-cold PBS. Mince ~6 kidneys using razorblade. Prepare non-transgenic kidneys to use as a control. Embryonic kidneys are incubated in the presence of 200μl of 0.5% trypsin for 5 minutes at 37ºC. Triturate vigorously. Add 1ml ice-cold 10% FBS/PBS. Triturate vigorously. The dissociated cells from the kidneys are pelleted at 2300rpm for 5 minutes at 4ºC. The media is aspirated and the cell pellet is resuspended in 1ml RBC lysis buffer. Centrifuge at 2300rpm for 5 minutes. Repeat if necessary. Add 1ml ice-cold 1% FBS/PBS. Repeat wash 2X. Centrifuge at 2300rpm for 5 minutes. Resuspend in 1ml ice-cold 1% FBS/PBS (have 40μM mesh ready). Filter using 40μM mesh, collect cells into a 6cm dish. Place the filtered cells (flow-through) into a 1.5ml eppendorf tube. Centrifuge at 2300rpm for 5 minutes. Resuspend in 400μl 1% FBS/PBS. Filter using FACS tube (35μM). FACS - collect GFP positive cells. Collect cells into 200μl RLT/BME. Freeze at -80C until ready to purify RNA.

value: nephrogenic interstitium, glomerular mesangium of Bowmans capsule, glomerular mesangium

value: yes

value: 6 kidneys from the same litter


title: RYY003

description:
P4B
Propionic acid treatment

source_name: Yeast cell culture, Propionic acid treatment

value: Propionic acid (IC50)

tag: ph

tag: time point

tag: replicate

value: B


title: Crym P4 cDNA - Nugen

description:
GUDMAP: 21439
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21439)

source_name: P4 kidney renal vesicle Crym cDNA - Nugen

treatment_protocol: Neonatal kidneys from Tg(Crym-EGFP)GF82Gsat mice were isolated in ice-cold PBS, bisected and minced into pieces <1mm.  The minced kidneys were placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The tubes were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and isolated by FACS.

value: renal vesicle

value: unknown

value: 2 neonatal kidneys


title: Arsenite riboseq, replicate 1

description: other

value: ribosome protected fragment


title: Control riboseq, replicate 1

description: other

value: vehicle


title: E11.5 Hoxb7 ureteric trunk

description:
GUDMAP: 21534
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21534)

source_name: E11.5 kidney ureteric trunk Hoxb7-FACS

treatment_protocol: E11.5 stalk/trunk regions of kidneys from Hoxb7-GFP mice were isolated in ice-cold PBS, minced into pieces <1mm, placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The tubes were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and the GFP positive cells were further isolated using FACS

value: ureteric stalk

value: mixed background

value: both

value: 5 kidneys


title: Arsenite riboseq, replicate 2

description: other

value: 0.5 hour arsenite


title: Control mRNAseq, replicate 2

description: polyA RNA

value: “naked” mRNAseq


title: Control riboseq, replicate 2

description: other


title: wt_ph8_4

city: Jena

first: Jörg

last: Linde

address: Naumburger Str. 96 a

department: Institute for Bacterial Infections and Zoonoses

country: Germany

institute: Federal Research Institute for Animal Health - Friedrich-Loeffler-Institute

description: 50ml volume in a 250 ml shaking flask, 180rpm.pH8. single-end,not strand-specific, no PolyA-filter.

data_processing:
FASTQ files were received from GATC, Konstanz, Germany
Sequenced reads were trimmed for low-quality regions (btrim windowsize 15 average  phredscore20)
Mapping of read pairs using TopHat (v2.0.6; -G GFF ); -maxintronlength 10000) versus the genome from www.candidagenome.org. GFF was produced durign study (see publication for details)
Read counting using htseq-count (-mode union, -s no, -type CDS)
Calculation of RPKM values using raw counts, sum of totally mapped reads and sum of exon length using  GFF file
Genome_build: the genome track downloaded (in July 2013) from http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/current/ was used.
However, there has been an update meanwhile and the file has now moved to archive http://www.candidagenome.org/download/sequence/C_glabrata_CBS138/archive/C_glabrata_CBS138_version_s02-m01-r22_chromosomes.fasta.gz
The information about the version number (sXX-mYY-rZZ) are provided at: http://www.candidagenome.org/cgi-bin/reference/reference.pl?dbid=CAL0000143461
Supplementary_files_format_and_content: xls

organism: Nakaseomyces glabratus

source_name: whole organism

growth_protocol: C. glabrata was routinely cultivated on YPD agar or in broth at 37°C. Candida glabrata was grown in standard nutrient-rich medium, ph4, ph8 and in nitrosative stress (GSNO) conditions. After harvesting RNA, paired-end and strand-specific RNA-Seq was performed on three biological replicates after PolyA filtering respectively. Additionally, a fourth replicate without filtering was sequenced single-end and not strand-specific..

extract_protocol:
Cells  were collected by centrifugation and stored in RNA later until RNA extraction.  Total RNA was isolated using the hot acidic phenol chloroform method. RNA quality was determined with a Bioanalyzer RNA 6000 Nano LabChip Kit (Agilent Technologies) according to the manufacturer's protocol. RNA concentration was determined with a Nanodrop ND1000 (Peqlab)
tagged random primed cDNA libraries were prepared from fragmented polyA-RNA using standard illumina protocols

treatment_protocol: For the pH treatment, C. glabrata was cultivated in M199 pH4 for 14-16 hours. Cells were harvested and cultured under the same condition again. 1x106 cells/ ml were harvested and transfered to fresh M199 pH4 or pH8 for 60 minutes. Cells were harvested and stored in RNAlater prior to RNA isolation. For the GNSO treatment (nitrosative stress) C. glabrata was grown in YPD medium at 37°C and 180 rpm for 14-16 h. 1X106 cells/ml were resuspended in 50 ml of normal YPD or YPD containong 0.6M GNSO (Sigma) for 60 minutes. Cells were harvested and stored in RNAlater prior to RNA isolation.

tag: growth medium

tag: incubation temperature

tag: incubation time

value: 60 minutes


title: E11.5 Hoxb7 ureteric tip/ampulla

description:
GUDMAP: 21536
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21536)

source_name: E11.5 kidney ureteric tip/ampulla Hoxb7-FACS

treatment_protocol: E11.5 tip regions of kidneys from Hoxb7-GFP mice were isolated in ice-cold PBS, minced into pieces <1mm, placed into 1.5ml eppendorf tubes and 400ul of 0.05% Trypsin-EDTA was added.  The tubes were incubated at 37C for 5 minutes.  After digestion, the samples were triturated and 1ml of ice-cold 1%FBS/PBS was added.  The samples were centrifuged at 1800rpm for 5 minutes.   The supernatant was removed, 1ml of ice-cold 1%FBS/PBS was added and the samples were centrifuged at 1800rpm for 5 minutes.  The supernatant was removed and the pellet resuspended in 400ul of ice-cold 15FBS/PBS, filtered through a 70uM mesh filter and the GFP positive cells were further isolated using FACS.

tag: component sampled

value: ureteric tip

tag: theiler stage

tag: age


title: wt_37_4

description: 50ml volume in a 250 ml shaking flask, 180rpm.Standard medium. single-end,not strand-specific, no PolyA-filter.

value: YPD


title: wt_37_3

description: 50ml volume in a 250 ml shaking flask, 180rpm.Standard medium. Paired-end,strand-specific, with PolyA-filter.


title: Crym P1 cDNA - Nugen

description:
GUDMAP: 21436
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21436)

source_name: P1 kidney cap mesenchyme Crym cDNA - Nugen

value: cap mesenchyme

tag: Sex

tag: pooled sample

value: yes

tag: pool size


title: wt_ph4_4

description: 50ml volume in a 250 ml shaking flask, 180rpm.pH4. single-end,not strand-specific, no PolyA-filter.


title: wt_37_1


title: wt_GSNO_2

description: 50ml volume in a 250 ml shaking flask, 180rpm.Nitrosative stress. Paired-end,strand-specific, with PolyA-filter.

value: YPD + 0.6M GSNO


title: Adult Proximal Tubules - 1

description:
GUDMAP: 21529
(http://www.gudmap.org/gudmap/pages/ngd_submission.html?id=GUDMAP%3A21529)

source_name: Adult kidney proximal tubules (LTA-positive FACS)

treatment_protocol: 1. Adult kidneys were bisected and the medullary region was cut away.  2. The kidneys were finely minced and divided equally into 4 tubes with 400ul 1% Collagenase A in PBS (freshly made).  3. Vortex.  4. Incubate at 37C for 15-20 mins, triturating vigorously beginning at 5 mins.  5. After incubation, add 1ml ice-cold 10% FBS in PBS. Triturate.  6. Filter using 100uM filter and rinse with 4ml ice-cold PBS - collect flow through.  7. Centrifuge at 1800rpm for 5 mins - decant supernatant.  8. Re-suspend in 2-3ml ice-cold 1% FBS/PBS (contains proximal/distal tubules, glomeruli, vasculature).  9. Triturate vigorously.  10. Filter using 40uM filter  and rinse with 4ml of ice-cold 1% FBS in PBS - save flow-through.  11. Spin down flow through at 1800rpm for 5 mins - re-suspend in 2ml 1% FBS (divided into 2 1.5ml tubes).  12. Perform RBC lysis if necessary - wash 3X in 1% FBS/PBS to remove RBC lysis buffer.  13. Perform brief trypsinization.  14. Add 1ml 10% FBS/PBS - triturate.  14. Spin down cells (1800rpm for 5 mins) - re-suspend in 2ml 1% FBS/PBS (2 tubes each with 1ml).  15. One tube will  be the control - not treated with LTA and one tube will be incubated with 10ul LTA for 15 mins. (LTA is proximal tubule specific lectin that is fluorescently labelled).  16. Spin down both tubes at 1800rpm for 5 mins.  17. Re-suspend in 400ul 1% FBS and FACS sort.

tag: genotype

value: wild type

value: renal proximal tubule

value: Adult

value: unspecified

tag: pool size:


title: wt_GSNO_3

tag: strain


title: wt_ph8_3

description: 50ml volume in a 250 ml shaking flask, 180rpm.pH8. paired-end,strand-specific, with PolyA-filter.


title: wt_ph8_2


title: wt_37_2


title: wt_ph4_3

description: 50ml volume in a 250 ml shaking flask, 180rpm.pH4. paired-end,strand-specific, with PolyA-filter.


title: B73 starchy endopserm, biorep 1 (BS1)

source_name: endosperm

tag: cell type

value: Starchy endosperm

tag: developmental stage

value: 15 DAP (days after pollination)

value: B73 (wild type)


title: wt_ph4_2


title: Control mRNAseq, replicate 1

description: polyA RNA

tag: treatment

value: vehicle

tag: rna type

tag: cell line


title: wt_ph4_1

description: 50ml volume in a 250 ml shaking flask, 180rpm. pH4. paired-end,strand-specific, with PolyA-filter.

tag: growth medium


title: Arsenite mRNAseq, replicate 2

description: polyA RNA


title: wt_GSNO_1

tag: incubation temperature


title: wt_ph8_1

tag: incubation time


title: Hermaphrodite stage H

status: Public on Jan 26 2015

city: Lisboa

first: Margarida

last: Rocheta

address: Tapada da ajuda

country: Portugal

institute: Instituto Superior de Agronomia

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Vitis vinifera 12X V1 whole genome using CLC Genomics Workbench.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi et al., Nat Methods 2008. In short, exons from all isoforms of a gene were merged to create contigs. The number of reads falling in the exons were counted and normalized by the size of the contig and by the size of the library.
Genome_build: Vitis vinifera (12X V1)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample.

organism: Vitis vinifera

source_name: Flower bud

extract_protocol:
The frozen buds were ground into a fine powder in liquid nitrogen and total RNA was extracted and purified with the SpectrumTMTotal RNA kit (Sigma-Aldrich, Inc, Spain) and Qiagen RNAeasy Mini Spin Columns (Qiagen, Valencia, CA, USA), respectively,according to the manufacturers’instructions. The concentration and purity of total RNA were determined using a Synergy HT Nanodrop system (Biotek, Germany), with the software Gen5TM (Biotek, Germany). The quality of the RNA was confirmed on a denaturing gel electrophoresis. For each sample, 25µg of total RNA were utilized for transcriptome sequencing
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Developmental stage H

tag: tissue

value: Flower bud

value: Domesticated

tag: gender

value: hermaphrodite


title: Hermaphrodite stage D

value: Developmental stage D


title: SL CAGE

city: Bergen

first: Eric

last: Thompson

address: Thormøhlensgt. 55

country: Norway

institute: Sars International Centre for Marine Molecular Biology

data_processing:
CAGE tags were aligned to the Oikopleura genome using bowtie version 0.12.5 with the following parameters: -t -m 1 -l 35
The 5’ coordinates of all uniquely mapping read (CAGE tag) alignments were extracted from the bowtie output to give positions of CAGE trans-splice sites (CTSSes), and the number of tags at each position was computed to give a tag count for each CTSS.
CTSSes were filtered to remove those in repeats and transposable elements using Genoscope and RepeatMasker annotations
Genome_build: 1_Assembly_reference_unmasked_v3.0.fa/ASM20953v1/ASM20955v1 (e.g. scaffold_998 = locus FN654012.1)
Supplementary_files_format_and_content: Tab-delimited table containing genomic coordinates of CAGE trans-splice sites and associated CAGE tag counts for each.

organism: Oikopleura dioica

source_name: Total RNA pooled from oocyte, 2-8cells, 1h PF, tailbud, hatched, day 2, day 3, day 4, day 5, adult male and adult female stages.

extract_protocol:
Animals were allowed to develop to the relevant development stages, anesthetized in cold ethyl 3-aminobenzoate methanesulfonate salt (MS-222) and collected by centrifigation. Total RNA was extracted from whole animals or isolated animal tissues using the Qiagen RNeasy kit
Library was constructed by DNAFORM, Yokohama City, Japan. DNAFORM prepared CAGE libraries according to the CAGE standard protocol applying a random primer for the 1st strand cDNA synthesis (Kodzius R. et al., CAGE: cap analysis of gene expression, Nat. Methods. 2006 Mar;3(3):211-22). DNAFORM modified the protocol in such a way that it yields DNA fragments for direct sequencing on an Illumina GAII Genome Analyzer and they omitted the 5’ linker ligation step and used the sequence of the splice leader for direct priming of 2nd strand cDNA synthesis. DNA concentration and purity were confirmed using an Agilent Bioanalyzer.

value: Mixed

value: Whole animal/embryos


title: Pol1YA,rnh201.1

city: Research Triangle Park

first: Scott

middle: Alexander

last: Lujan

state: NC

address: 101 T.W. Alexander Drive

department: LMG/LSB

institute: NIEHS

description: Sample 27

data_processing:
Library strategy: Ribo-seq
Base calling and generation of FASTQ files performed by Illumina Hiseq standard pipeline
Reads trimmed for adapter sequence using cutadapt 1.2.1, discarding pairs with one or both reads shorter than 15 nt, additional base trimmed to allow paired-end mapping with bowtie
Align end 1 to index of oligos used during library prep, exclude successful pairs from further analysis (bowtie 0.12.8 -k1 -v2)
Align remaining pairs to L03 reference genome (bowtie 0.12.8 -m1 -v2 -X10000)
Align end 1 of unmapped pairs to L03 reference genome (bowtie 0.12.8 -m1 -v2)
Retain 5' end only for all single- and paired-end unique alignments, shift 1 base upstream and combine
Combine all technical replicates
Genome_build: L03 reference v2 (see supplementary files)
Supplementary_files_format_and_content: bedGraph, count of Ribo-seq 5' ends per position

organism: Saccharomyces cerevisiae

growth_protocol: Yeast strains were grown to mid log phase (OD600=0.6) at 30°C in YPDA medium supplemented with 0.25 mg/ml adenine

extract_protocol:
DNA was isolated using the MasterPure™ Yeast DNA Purification Kit (Epicentre) without RNase A treatment.
Ribo-seq was performed by hydrolyzing one μg of genomic DNA with 0.3 M KOH for 2 hours at 55°C. Following ethanol-precipitation, the DNA fragments were treated for three minutes at 85°C, phosphorylated with 10 units of 3´-phosphatase-minus T4 polynucleotide kinase (New England Biolabs) for 30 minutes at 37°C, heat inactivated for 20 minutes at 65°C and purified using HighPrep™ PCR beads (MagBio). Phosphorylated products were treated for three minutes at 85°C, ligated to oligo ARC140 (Supplementary Table 1) overnight at room temperature using 10 units of T4 RNA ligase, 25% PEG8000 and 1 mM CoCl3(NH3)6, and purified using HighPrep™ PCR beads (MagBio) . Ligated products were treated for 3 minutes at 85°C. The second strand was synthesized using four units of T7 DNA polymerase (New England Biolabs). The ARC76/ARC77 adapter was annealed to the second strand for five minutes at room temperature and purified using HighPrep™ PCR beads (MagBio). Libraries were PCR amplified using primer ARC49 and primer ARC79 or ARC84 to ARC107, using KAPA HiFi Hotstart ReadyMix (KAPA Biosystems). Libraries were then purified using HighPrep™ PCR beads (MagBio) and pooled for sequence analysis. Paired-end sequencing was performed on a HiSeq2500 sequencer (Illumina) or MiSeq to identify the location of the 5´-DNA ends generated by alkaline hydrolysis.

value: pol1-Y869A rnh201-delta


title: Pol1YA,rnh201.2

description: Sample 28


title: Pol1YA,rnh201.3

description: Sample 29


title: Pol3LG,rnh201.2

description: Sample 26

value: pol3-L612G rnh201-delta


title: Pol3LG,rnh201.1

description: Sample 25


title: Pol2MG,rnh201.3 b

description: Sample 23

value: pol2-M644G rnh201-delta


title: Pol2MG,rnh201.1 b

description: Sample 21


title: Pol2ML,rnh201.2 b

description: Sample 20

value: pol2-M644L rnh201-delta


title: Pol2ML,rnh201.1 a

description: Sample 19


title: Pol3LM,rnh201.1 b

description: Sample 17

value: pol3-L612M rnh201-delta


title: Hermaphrodite stage G

value: Developmental stage G


title: Pol3LM,rnh201.2 a

description: Sample 18


title: Pol1LM,rnh201 b

description: Sample 16

value: pol1-L868M rnh201-delta


title: Pol3LG.2

description: Sample 11


title: Pol1YA.2

description: Sample 13


title: Pol1YA.1

description: Sample 12


title: Rnh201.1 a

description: Sample 14


title: Pol3LG.1

description: Sample 10


title: Pol2MG.3 a

description: Sample 9


title: Pol2MG.2 b

description: Sample 8


title: Pol2MG.1 a

description: Sample 7


title: Pol1LM b

description: Sample 5


title: Pol2ML.2 b

description: Sample 4


title: Pol2MG,rnh201.4 b

description: Sampe 24


title: Pol2ML.1 a

description: Sample 3


title: Pol3LM b

description: Sample 6


title: Pol2MG,rnh201.2 a

description: Sample 22


title: Male WT stage H

organism: Vitis vinifera subsp. sylvestris

value: wild type

value: male


title: WT.1 a

description: Sample 1

source_name: WT

value: WT


title: WT.2 b

description: Sample 2


title: Male WT stage G