title: chip1_wce_rct1_2


title: chip1_wce_clr3

status: Public on Jun 20 2017

type: SRA

city: Cold Spring Harbor

first: Robert

middle: A

last: Martienssen

state: NY

address: 1 Bungtown Rd

department: Delbruck Bldg.

country: USA

institute: Cold Spring Harbor Laboratory

library_source: genomic

data_processing:
Obtained reads were quality filtered using Trimmomatic and aligned to the S. pombe genome assembly ASM294v2.21 using Bowtie v2.1.0 and local alignment, with multi-mappers randomly distributed. All read counts were normalized to reads per million (RPM) using total library size. ChIP enrichment was calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads. Quantification at individual features was performed by intersecting reads with the feature of interest.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Coverage of ChIP enrichment calculated as the log2 of the ratio of normalized IP reads to normalized input (whole cell extract) reads in bigWig format.

molecule: genomic DNA

organism: Schizosaccharomyces pombe

growth_protocol: All yeast strains were cultured in YES (yeast exact with supplements) media at 30 °C.

extract_protocol: Cells were spheroplasted by zymolyase at 37°C and then sonicated using a bioruptor for 8 cycles (30s ON 60s OFF). For each IP, 500-750 ug of chromatin were used with 3 to 5 ul antibody. 1 ng of DNA purified from ChIP experiments was made into libraries by using NEB enzymes. In brief, DNA was end-repaired by T4 DNA polymerase, Klenow fragment and T4 DNA PNK. “A” bases were added to the 3’ end of end-repaired DNA fragment with Klenow 3’ to 5’ exo minus and dATP. Barcoded Truseq adaptors (Illumina) were ligated to DNA fragments using quick ligase at 25°C. Five PCR cycles were performed prior to size selection. After size selection, purified DNA was PCR amplified with 6 to 12 cycles (Kapa HiFi HotStart ready mix). Barcoded libraries were pooled and sequenced on Illumina HiSeq platform.

treatment_protocol: Yeast cells were grown to a concentration of ~1 X 10^7 cells/ml, then fixed in 1% formaldehyde at 25°C for 20 min. Fixation was stopped by adding glysine to a final concentration of 0.125 M, and cells were washed twice in 1XPBS then stored in -80°C until all strains were harvested.

tag: strain

tag: chip antibody

value: whole cell extract


title: chip1_h3k9me2_rct1rrm

value: H3K9me2 (Upstate 07-441)


title: scler_ht280_C10

city: PHILADELPHIA

first: Andrew

last: Vaughan

state: United States

address: 3800 Spruce Street

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
bcl2fastq 1.8.4 was used to separate out the data for each single cell using unique barcode combinations from the Nextera XT preparation and to generate *.fastq files.
paired reads were aligned against hg19 using bowtie2-2.2.3 and tophat-2.0.13
Fragments Per Kilobase of transcript Per Million mapped reads (FPKM) values were computed using cufflinks-2.2.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample.

molecule: total RNA

organism: Homo sapiens

source_name: scleroderma patient

extract_protocol:
Cells were loaded into the Fluidigm C1 microfluidic platform, where single cells were captured. Lysis of single cells, reverse-transcription of mRNA into cDNA as well as preamplification of cDNA occured within the microfluidic device using reagents provided by Fluidigm as well as the SMARTer Ultra Low RNA kit for Illumina (Clontech). External RNA spike-in transcripts (ERCC spike-in Mix, Ambion) were added to all single cell lysis reactions.
Libraries were prepared using Illumina Nextera XT kit per illumina's protocols.

treatment_protocol: Tissue was mechanically and enzymatically disaggregated using dispase.  Single cells were then stained with antibodies and flow sorted.

tag: cell type

value: lung epithelial cells

tag: facs purification

value: live, CD45-, Epcam+, HTII-280+


title: chip1_h3k9me2_rct1_2


title: chip1_h3k9me2_clr3


title: scler_ht280_B3


title: scler_ht280_B6


title: small RNA sequencing 11H129

city: Heidelberg

first: Christian

last: Rohde

address: Im Neuenheimer Feld 410

country: Germany

institute: Heidelberg University

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA BclToFastq was used to export fastq files
Illumina adapter sequences were removed using Cutadapt
Reads were mapped using Bowtie2 and further processed to BAM format using samtools
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Regions with a BLAST hit were further aggregated calculating the mean of the average coverages and further normalized to the total number of mapped reads by the identified hit name.
Genome_build: hg19
Supplementary_files_format_and_content: processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.

source_name: human acute myeloid leukemia

extract_protocol: Total RNA was extracted with the Qiagen miRNeasy kit and 500 ng was subject to library preparation using the Illumina Truseq small RNA kit. Molecules with the size of 40-200 nt were purified from a gel before sequencing.

tag: diagnosis

value: acute myeloid leukemia (AML)

tag: tissue

value: leukemia blast cells


title: small RNA sequencing 10H056


title: small RNA sequencing 10H161


title: small RNA sequencing 05H094


title: small RNA sequencing 05H181


title: scler_ht280_B2


title: scler_ht280_B10


title: small RNA sequencing 09H115


title: scler_ht280_B1


title: small RNA sequencing 05H050


title: scler_ht280_A8


title: small RNA sequencing 03H041


title: scler_ht280_A6


title: small RNA sequencing 03H116


title: scler_ht280_B8


title: chip1_h3k9me2_wt


title: scler_ht280_A5


title: small RNA sequencing 11H009


title: small RNA sequencing 10H101


title: small RNA sequencing 11H006


title: scler_ht280_A2


title: small RNA sequencing 05H149


title: small RNA sequencing 02H053


title: scler_ht280_A12


title: small RNA sequencing 11H095


title: small RNA sequencing 06H135


title: small RNA sequencing 06H028


title: scler_ht280_A10


title: U937_MIG

description: small RNA sequencing

data_processing:
Basecalls were performed using on-instrument real time analysis (RTA) on an Illumina HiScan-SQ
CASAVA BclToFastq was used to export fastq files
Illumina adapter sequences were removed using Cutadapt
Reads were mapped using Bowtie2 and further processed to BAM format using samtools
Regions with coverage were called from mapped reads using the bedtools genomeCoverageBed algorithm
Sequences from the extracted regions were compiled to a consensus sequence which was subject to BLAST against a custom small RNA database. Regions with a BLAST hit were further aggregated calculating the mean of the average coverages and further normalized to the total number of mapped reads by the identified hit name.
Genome_build: hg19 for human samples and mm10 for mouse samples
Supplementary_files_format_and_content: Each processed file contains a column for the identified small nucleolar RNA (snoRNA) elements and the normalized average coverage for the respective sample.

source_name: human leukemia cell line U937

value: human cell line retrovirally transduced with empty vector


title: small RNA sequencing 04H112


title: U937_AML1.ETO

description: small RNA sequencing

value: human cell line retrovirally transduced with AML1-ETO


title: scler_ht280_A1


title: small RNA sequencing 11H142


title: IgG RIP replicate 2

data_processing:
SnoRNA-seq reads were trimmed using the cutadapt software (version 1.6). Trimmed reads were aligned to human genomes (hg19) with bowtie2 (version 2.2.4).
Specific binding was identified based on peak-calling strategy using the program Piranha. Peaks were called between IgG and RIP sample groups.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include genomic region of the peaks and reads per million values.

growth_protocol: Kasumi-1 cells stablly expressing V5-tagged AES were cultured in RPMI-1640 medium with 20% of FBS.

extract_protocol:
TRIzol
Sequencing libraries were constructed from total RIP RNA using the TruSeq™ small RNA sample prep kit v2 (Illumina) according to the instructions of the manufacturer. Before sequencing the libraries were size selected to 40-200 insert size.

treatment_protocol: 1×107 Kasumi-1 cells stably expressing V5-tagged AES were rinsed with ice cold PBS. Cells were resuspended in 1 ml RIP buffer. RIP were performed with Anti-V5 (Abcam, ab9116), anti-DDX21 (Novus Biologicals BP100-1781) or control (Abcam, ab46540G).

tag: antibody

value: control IgG (Abcam, ab46540G)


title: DDX21 RIP replicate 3

source_name: Kasumi-1 cells stablly expressing V5-tagged AES

value: anti-DDX21 (Novus Biologicals BP100-1781)


title: IgG RIP replicate 1


title: DDX21 RIP replicate 2


title: DDX21 RIP replicate 1


title: AES RIP

value: Anti-V5 (Abcam, ab9116)


title: Kasumi-1 cell line with shRNA against DDX21 shDDX21

description: Human AML snoRNA expression

source_name: human leukemia cell line Kasumi-1

tag: sample type


title: Kasumi-1 cell line control shLuc

description: Human AML snoRNA expression

value: Kasumi-1 cell line control


title: Kasumi-1 cell line control Shctr

description: Human AML snoRNA expression


title: Kasumi-1 cell line with shRNA against human AES ShAES

description: Human AML snoRNA expression


title: norm_ht280_H4

source_name: normal lung donor #2


title: Primary diagnosis 133-001

source_name: Density centrifuged bone marrow

value: Primary diagnosis

tag: chemotherapy response

value: Bad response

tag: npm1 mutation

tag: molecular risk group


title: norm_ht280_H6


title: Primary diagnosis 121-009

value: good response

value: yes

value: Intermediate


title: norm_ht280_H3


title: small RNA sequencing 09H043


title: Primary diagnosis 121-008

value: No


title: Primary diagnosis 121-007


title: norm_ht280_H2


title: norm_ht280_H12


title: norm_ht280_H9


title: Primary diagnosis 120-001


title: norm_ht280_H8


title: Primary diagnosis 120-002


title: Primary diagnosis 121-005

value: Good


title: norm_ht280_G8

value: lung epithelial cells


title: Primary diagnosis 118-001


title: Primary diagnosis 118-002


title: norm_ht280_H7

value: live, CD45-, Epcam+, HTII-280+


title: Primary diagnosis 114-001


title: Primary diagnosis 109-006


title: norm_ht280_G7


title: Primary diagnosis 088-001


title: Primary diagnosis 080-003


title: Primary diagnosis 074-002


title: Primary diagnosis 080-002


title: norm_ht280_G5


title: Primary diagnosis 057-026


title: norm_ht280_G4


title: norm_ht280_G6


title: Primary diagnosis 057-029


title: Primary diagnosis 057-021


title: Primary diagnosis 057-016


title: Primary diagnosis 057-019


title: norm_ht280_G3


title: Primary diagnosis 057-017


title: Primary diagnosis 057-013


title: norm_ht280_G2


title: norm_ht280_G9


title: Primary diagnosis 057-011


title: norm_ht280_G12


title: Primary diagnosis 057-008


title: Primary diagnosis 057-005


title: norm_ht280_G10


title: Primary diagnosis 053-009


title: norm_ht280_G1


title: Primary diagnosis 053-005


title: Primary diagnosis 043-008


title: norm_ht280_F9


title: Primary diagnosis 043-007


title: norm_ht280_F8


title: Primary diagnosis 043-004


title: Primary diagnosis 043-006


title: Primary diagnosis 036-005


title: Primary diagnosis 036-004


title: Primary diagnosis 036-001


title: norm_ht280_F7


title: Primary diagnosis 035-003


title: norm_ht280_F4


title: norm_ht280_F5


title: Primary diagnosis 017-003


title: Primary diagnosis 017-001


title: norm_ht280_F3


title: Primary diagnosis 014-007


title: Primary diagnosis 016-002


title: Primary diagnosis 053-010


title: Primary diagnosis 014-006


title: norm_ht280_F2


title: norm_ht280_F12


title: Primary diagnosis 014-002


title: Primary diagnosis 014-003


title: norm_ht280_F10


title: Primary diagnosis 014-005


title: Primary diagnosis 009-006


title: Primary diagnosis 009-009


title: norm_ht280_F1


title: norm_ht280_F6


title: Primary diagnosis 009-003


title: Primary diagnosis 009-002


title: Primary diagnosis 005-012


title: Primary diagnosis 035-001


title: Primary diagnosis 005-010


title: Primary diagnosis 005-011


title: norm_ht280_E9


title: norm_ht280_E8


title: norm_ht280_E7


title: Primary diagnosis 053-006


title: Primary diagnosis 005-009


title: Primary diagnosis 005-008


title: Primary diagnosis 005-005


title: norm_ht280_E6


title: Primary diagnosis 005-007


title: norm_ht280_E4


title: Primary diagnosis 005-002


title: Primary diagnosis 014-001


title: Primary diagnosis 005-003


title: Primary diagnosis 003-004


title: norm_ht280_E2


title: norm_ht280_E12


title: Primary diagnosis 003-003


title: Primary diagnosis 003-001


title: norm_ht280_E10


title: srna2_wt_2

description: small RNA

data_processing:
Obtained reads were quality filtered using Trimmomatic and aligned to the S. pombe genome assembly ASM294v2.21 using Bowtie v2.1.0 and local alignment, with multi-mappers randomly distributed. Only reads between 15 and 36 nucleotides were used for the analysis. Read counts were normalized to reads per million (RPM) using total library size. Reads mapping to the sense strands of tRNA and rRNA were discarded before producing genome browser pileups.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Normalized read coverage (RPM) per strand in bigWig format.

extract_protocol: Small RNA libraries were constructed by NEBNext multiplex Small RNA library prep kit (NEB E7300) following manufacturer's protocol. Libraries were further size selected (125-160 bp) by Blue Pippin machine (Sage Science). Barcoded libraries were pooled and sequenced on Illumina MiSeq platform.


title: srna2_rrp6_2

description: small RNA


title: srna2_wt_1

description: small RNA


title: norm_ht280_E1


title: norm_ht280_D9


title: srna2_rct1rrm_rrp6_1

description: small RNA


title: srna2_rct1rrm_2

description: small RNA


title: srna2_rct1_rrp6_2

description: small RNA


title: srna2_rct1_2

description: small RNA


title: srna2_rct1rrm_1

description: small RNA


title: norm_ht280_D7


title: norm_ht280_D6


title: srna1_wt

description: small RNA


title: norm_ht280_D5


title: srna1_clr3

description: small RNA


title: srna1_rct1_clr3

description: small RNA


title: norm_ht280_D12


title: norm_ht280_D3


title: srna1_rct1_1

description: small RNA


title: norm_ht280_C9


title: srna2_rrp6_1

description: small RNA


title: norm_ht280_C6


title: srna1_rct1_2

description: small RNA


title: norm_ht280_D1


title: norm_ht280_C4


title: srna2_rct1_rrp6_1

description: small RNA


title: norm_ht280_B6


title: srna2_rct1rrm_rrp6_2

description: small RNA


title: norm_ht280_C3


title: norm_ht280_B7


title: norm_ht280_C1


title: norm_ht280_B5


title: norm_ht280_B2


title: norm_ht280_B4


title: norm_ht280_D4


title: norm_ht280_D2


title: srna2_rct1_1

description: small RNA


title: norm_ht280_B12


title: norm_ht280_B10


title: norm_ht280_A9


title: norm_ht280_A7


title: norm_ht280_C5


title: norm_ht280_A6


title: norm_ht280_A4


title: norm_ht280_A3


title: norm_ht280_A5


title: norm_ht280_A12


title: norm_ht280_A2


title: norm_ht280_C12


title: norm_ht280_A10


title: norm_alpha6_H12

source_name: normal lung donor #1

value: live, CD45-, Epcam+, HTII-280-, integrin alpha6+


title: norm_alpha6_H9


title: norm_alpha6_H1


title: norm_alpha6_G7


title: norm_alpha6_G10


title: norm_alpha6_G9


title: norm_alpha6_F7


title: norm_alpha6_G6


title: norm_alpha6_F2


title: norm_alpha6_F10


title: norm_ht280_B1


title: norm_alpha6_E8


title: norm_alpha6_D8


title: norm_alpha6_D11


title: norm_alpha6_E1


title: norm_alpha6_B9


title: norm_alpha6_C9


title: norm_alpha6_C10


title: hu_IPF_HTII280_8

source_name: idiopathic pulmonary fibrosis patient


title: norm_alpha6_C1


title: norm_alpha6_H2


title: norm_alpha6_B8


title: norm_alpha6_A9


title: hu_IPF_HTII280_66


title: hu_IPF_HTII280_55


title: hu_IPF_HTII280_61


title: hu_IPF_HTII280_57


title: norm_alpha6_E2


title: hu_IPF_HTII280_53


title: hu_IPF_HTII280_52


title: hu_IPF_HTII280_50


title: hu_IPF_HTII280_5


title: hu_IPF_HTII280_48


title: hu_IPF_HTII280_38


title: hu_IPF_HTII280_32


title: hu_IPF_HTII280_43


title: norm_alpha6_F8


title: hu_IPF_HTII280_27


title: hu_IPF_HTII280_42


title: hu_IPF_HTII280_26


title: hu_IPF_HTII280_56


title: hu_IPF_HTII280_24


title: hu_IPF_HTII280_4


title: hu_IPF_HTII280_19


title: hu_IPF_HTII280_11


title: hu_IPF_HTII280_18


title: hu_IPF_HTII280_21


title: Tdrd9 -/-;P0;MILI IP;piRNAs

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

country: Switzerland

institute: University of Geneva

description:
MILI IP
RR301-RR306.csv
RR303_mult

data_processing:
Reads were sorted into individual libraries based on the barcodes, the 3′ adapter sequences were removed and mapped to the mouse genome (mm9). The software used for processing the data (genomic coordinates etc) from the raw data files are in-house tools developed by the Sachidanandam lab (Olson et al., 2008). Only reads perfectly matching the genome were kept for further analysis.
To analyze the reporter piRNA production, the reads were sorted into individual libraries based on the barcodes and the 3′ adapter sequences were clipped from the reads using cutadapt (DOI:http://dx.doi.org/10.14806/ej.17.1.200). Reads of at least 15 nucleotides were then aligned to the DsRed2-LoxP-piRNAsites-in-LacZ-LoxP-SV40pA reporter sequence (Homolka et al,2016;PMID:26669262) using bowtie (Langmead et al., 2009) allowing no mismatches.
Genome_build: Reads were mapped to mm9 or the artificial DsRed2 reporter sequence.
Supplementary_files_format_and_content: The files contain the comparison of abundances of reads mapped to the genome or mapping of the reads to DsRed2 reporter (Homolka et al,2016;PMID:26669262)

organism: Mus musculus

source_name: testis

extract_protocol:
Testicular RNAs present in endogenous MILI, MIWI2, MIWI and MVH complexes were isolated using indicated antibodies.
Sequencing libraries  were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Cat No:E7300) according to manufacturer instructions. The synthesized libraries were resolved on agarose gel and fragments of around 120 bp (corresponding to piRNAs) and around 150-300bp (longer RNAs) were separately sequenced on Illumina HiSeq platform (EMBL Heidelberg Gene core facility).

treatment_protocol: Mvh KI allele was created by single nucleotide mutation in the exon 16 that changes the encoded amino acid (E446Q) within the helicase catalytic motif (DEAD →DQAD). Mvh null allele was created by deletion of exon 16 in the gene. Tdrd9 KI allele was created by a point mutation (E257Q) in the ATPase motif (DEVH→DQVH). Tdrd9 null allele was created by deletion of exons 3 to 5. DsRed2 reporter mouse was already described (Homolka et al,2016;PMID:26669262).

tag: genotype

tag: developmental stage

tag: ip antibody

value: MILI (mouse monoclonal) (Reuter et al., 2009;PMID:19465913)

tag: rna

value: piRNAs


title: hu_IPF_HTII280_14


title: Tdrd9 KI/KI;P0;MIWI2 IP;piRNAs

description:
MIWI2 IP
RR301-RR306.csv
RR305_mult

value: MIWI2 (rabbit polyclonal) (Pandey et al., 2013;PMID:24067652)


title: hu_IPF_HTII280_20


title: hu_IPF_HTII280_13


title: Tdrd9 +/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR301-RR306.csv
RR301_mult


title: Tdrd9 +/KI;P0;MIWI2 IP;piRNAs

description:
MIWI2 IP
RR301-RR306.csv
RR304_mult


title: Tdrd9 -/-;P0;MIWI2 IP;piRNAs

description:
MIWI2 IP
RR301-RR306.csv
RR306_mult


title: MVH +/+;adult;MVH IP;longer RNAs

description:
MVH IP
JW9-JW24.csv
JW24_mult

value: MVH +/+

value: adult

value: MVH (Abcam, ab13840)

value: longer RNAs


title: Tdrd9 KI/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR301-RR306.csv
RR302_mult


title: DK_ht280_H9

source_name: dyskeratosis congenita patient


title: DK_ht280_H7


title: MVH +/KI;adult;MVH IP;longer RNAs;rep3

description:
MVH IP
JW9-JW24.csv
JW23_mult

value: MVH +/KI


title: MVH +/KI;adult;MVH IP;longer RNAs;rep1

description:
MVH IP
JW9-JW24.csv
JW21_mult


title: DK_ht280_G9


title: DK_ht280_G7


title: DK_ht280_G5


title: MVH +/-;adult;MILI IP;longer RNAs

description:
MILI IP
JW9-JW24.csv
JW20_mult

value: MVH +/-


title: MVH +/KI;adult;MILI IP;longer RNAs

description:
MILI IP
JW9-JW24.csv
JW19_mult


title: MVH +/-;adult;MIWI IP;longer RNAs

description:
MIWI IP
JW9-JW24.csv
JW18_mult

value: MIWI (rabbit polyclonal) (Reuter et al.,2011;PMID:22121019)


title: DK_ht280_G2


title: MVH +/KI;adult;MIWI IP;longer RNAs

description:
MIWI IP
JW9-JW24.csv
JW17_mult


title: hu_IPF_HTII280_1


title: DK_ht280_G1


title: MVH +/KI;adult;MVH IP;piRNAs;rep3

description:
MVH IP
JW9-JW24.csv
JW15_mult


title: DK_ht280_F6


title: MVH +/+;adult;MVH IP;piRNAs

description:
MVH IP
JW9-JW24.csv
JW16_mult


title: MVH +/KI;adult;MVH IP;piRNAs;rep2

description:
MVH IP
JW9-JW24.csv
JW14_mult


title: DK_ht280_F4


title: DK_ht280_F5


title: DK_ht280_F1


title: MVH +/KI;adult;MVH IP;piRNAs;rep1

description:
MVH IP
JW9-JW24.csv
JW13_mult


title: MVH +/-;adult;MILI IP;piRNAs

description:
MILI IP
JW9-JW24.csv
JW12_mult


title: MVH +/KI;adult;MILI IP;piRNAs

description:
MILI IP
JW9-JW24.csv
JW11_mult


title: MVH +/-;adult;MIWI IP;piRNAs

description:
MIWI IP
JW9-JW24.csv
JW10_mult


title: DK_ht280_F12


title: DK_ht280_E8


title: DK_ht280_H11


title: DK_ht280_E6


title: MVH +/KI;adult;MVH IP;longer RNAs;rep2

description:
MVH IP
JW9-JW24.csv
JW22_mult


title: MVH +/KI;adult;MIWI IP;piRNAs

description:
MIWI IP
JW9-JW24.csv
JW9_mult


title: DK_ht280_E5


title: DK_ht280_G3


title: DK_ht280_E4


title: MVH +/KI;P0;MIWI2 IP;longer RNAs

description:
MIWI2 IP
RR374-RR383.csv
RR383_mult


title: MVH +/-;P0;MIWI2 IP;longer RNAs

description:
MIWI2 IP
RR374-RR383.csv
RR382_mult


title: DK_ht280_E3


title: MVH -/KI;P0;MILI IP;longer RNAs

description:
MILI IP
RR374-RR383.csv
RR381_mult

value: MVH -/KI


title: DK_ht280_E2


title: MVH +/-;P0;MILI IP;longer RNAs

description:
MILI IP
RR374-RR383.csv
RR379_mult


title: MVH +/KI;P0;MILI IP;longer RNAs

description:
MILI IP
RR374-RR383.csv
RR380_mult


title: DK_ht280_D9


title: DK_ht280_D8


title: MVH +/KI;P0;MIWI2 IP;piRNAs

description:
MIWI2 IP
RR374-RR383.csv
RR378_mult


title: MVH +/-;P0;MIWI2 IP;piRNAs

description:
MIWI2 IP
RR374-RR383.csv
RR377_mult


title: DK_ht280_D7


title: DK_ht280_D6


title: DK_ht280_D4


title: MVH +/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR374-RR383.csv
RR375_mult


title: MVH -/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR374-RR383.csv
RR376_mult


title: DK_ht280_D2


title: DK_ht280_D3


title: DK_ht280_D1


title: DK_ht280_C5


title: DK_ht280_D11


title: DK_ht280_C8


title: Rosa26-pi reporter;MVH +/-;P0;MILI IP;longer RNAs

description:
MILI IP
RR394_mult


title: Rosa26-pi reporter;MVH -/KI;P0;MILI IP;longer RNAs

description:
MILI IP
RR397_mult


title: Rosa26-pi reporter;MVH +/KI;P0;MILI IP;longer RNAs

description:
MILI IP
RR396_mult


title: Rosa26-pi reporter;MVH -/-;P0;MILI IP;piRNAs

description:
MILI IP
RR391_mult

value: MVH -/-


title: MVH +/-;P0;MILI IP;piRNAs

description:
MILI IP
RR374-RR383.csv
RR374_mult


title: DK_ht280_C4


title: Rosa26-pi reporter;MVH +/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR392_mult


title: Rosa26-pi reporter;MVH -/KI;P0;MILI IP;piRNAs

description:
MILI IP
RR393_mult


title: DK_ht280_C2


title: Rosa26-pi reporter;MVH +/-;P0;MILI IP;piRNAs

description:
MILI IP
RR390_mult


title: DK_ht280_C3


title: DK_ht280_C11


title: DK_ht280_B7


title: DK_ht280_B4


title: DK_ht280_B3


title: DK_ht280_B5


title: DK_ht280_B2


title: Rosa26-pi reporter;MVH -/-;P0;MILI IP;longer RNAs

description:
MILI IP
RR395_mult


title: DK_ht280_A6


title: DK_ht280_A4


title: DK_ht280_A2


title: DK_ht280_A11


title: DK_ht280_A1


title: ND-75-i rep2

city: Boston

first: Wei

last: Song

email: rocwsong@gmail.com, songw@whu.edu.cn

state: Massachusetts

address: 77 Ave Louis Pasteur, NRB 336

department: Department of Genetics

institute: Harvard Medical School

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Drosophila  genome (flybase genome annotation version r5.51) using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
FPKM values were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: Flybase genome annotation version r5.51
Supplementary_files_format_and_content: csv files include FPKM values for each Sample .

organism: Drosophila melanogaster

source_name: Fat body

extract_protocol:
In each replicate, 10 fat bodies were dissected out from both dMef2-Gal4/UAS-white-RNAi (Con) and dMef2-Gal4/UAS-ND-75-RNAi (ND-75-i) 3rd instar larvae. Total RNAs were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tag

value: yw

tag: development stage

value: 3rd instar larval fat body

tag: age

value: 110h after egg laying

tag: genotype/variation


title: 36C: Yki RNAi tails 24hpa replicate C

city: Portland

first: Bret

middle: J

last: Pearson

state: OR

address: 3181 SW Sam Jackson Park Rd., BRB Room 305

department: Pediatrics

institute: Oregon Health and Science University

description: 3 RNAi feeds, irradiated at 15 days post-feeding, amputated (or collected intact) 24hrs post-irradiation, and RNA-extracted at appropriate timepoint

data_processing:
Base calls and demultiplexing was performed with Illumina bcl2fastq version 1.8.3
Untrimmed reads were aligned to the transcritpome associated with BioProject 215411 using the program Bowtie2 version 2.2.4.  Raw counts were extracted from resulting SAM files and normalized to the number of mapped reads to calculate Counts Per Million reads (CPM).
Wound-induced genes were determined by comparing the control(RNAi) regenerating time points (6, 12, and 24 hours post amputation) to intact animals by the DEseq2 test using RNAseq raw counts. This procedure includes normalization and differentiation expression tests. A total of 440 transcripts were differentiatially upregulated between the regenerating time points to intact animals with a [FC] > 2, FDR < 0.05 and >1 count per million (CPM).
To identify whether these 440 wound-induced genes that were upregulated in yki(RNAi), yki(RNAi) tail fragments were compared pair-wise to their corresponding control(RNAi) regenerating time point by DEseq2. This procedure generated a total of 32 differentially expressed transcripts.
Genome_build: NCBI BioProject PRJNA215411  SmedASXL_transcripts_20130210.nt

organism: Schmidtea mediterranea

source_name: Wildtype animals

growth_protocol: The clonal strain of Schmidtea mediterranea, CIW4, was grown in a milli-Q-based salt solution on beef liver.  Organisms were starved for 1 week prior to tissue collection.

extract_protocol:
All tissue samples were RNA extracted in Trizol reagent, and RNA quality was analyzed on a bioanalyzer.  RNA samples were library prepped using Illumina's Truseq Library preps, which included polyA selection.
Illumina TruSeq library prep kit with v4 chemistry.

treatment_protocol: Animals were fed 3 times control(RNAi) or yki(RNAi) every 3 days. After 15 days in high salt treatment (details in methods), animals were irradiated at 60Gy and were amputated at 24 hours post-irradiation. RNA was extracted from >8 irradiated intact animals, and from 15 irradited tail fragments at 6, 12, and 24 hours post amputation. In total, 24 samples (2 RNAi conditions with 4 time points, biologically replicated 3 times) were sequenced to a depth of 20 million reads.

tag: strain

value: Asexual CIW4

value: Tail fragments only

tag: treatment

value: Yki RNAi


title: 34A: Yki RNAi tails 24hpa replicate A


title: GM_19 scNOMe-seq Control

city: Chicago

first: Sebastian

last: Pott

state: Il

address: 920 58th Street

department: Human Genetics

institute: University of Chicago

description: bisulfite converted DNA

data_processing:
reads were trimmed to remove low quality bases and 6 bp were clipped from the 5prime end of each read to avoid mismatches introduced by amplification, in the case of GM12878 cells 6 bp were clipped from either end. Only reads that remained longer than 20 bp were kept for further analyses. these processing steps were performed using trim_galore version 0.4.0 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the following settings: trim_galore --quality 30 --phred33 --illumina --stringency 1 -e 0.1 --clip_R1 6 --gzip --length 20 --output_dir outdir Sample.fastq.gz
sequencing data was aligned to the in silico bisulfite converted human genome assembly hg38 using Bismark aligner v0.15 (Krueger, F., Kreck, B., Franke, A. & Andrews, S. R. DNA methylome analysis using short bisulfite sequencing data. Nat Meth 9, 145–151 (2012).) with default settings (bismark --fastq --prefix SamplePrefix --output_dir output_dir --non_directional --phred33-quals --score_min L,0,-0.2 --bowtie2 genome.index trimmed.fastq.gz). Reads were aligned in single end modus with each read of a paired-end read aligned separately
Coverage and methylation status of all cytosines was extracted using bismarkmethyl extract (bismark_methylation_extractor -s --ignore 6 --output outdir --cytosine_report --CX --genome_folder path_to_genome SampleAligned.bam).
Coverage files were used to extract the methylation status of cytosines specifically in GpC and CpG di-nucleotides using the coverage2cytosine script in Bismark. The resulting files contained the coverage and methylation information at individual GpC and CpG di-nucleotides. Cytosines in ambiguous GCG positions were removed from the coverage files. Regions covered by a read with more than 3 unconverted cytosines in non-CpG and non-GpC context were removed from further analyses as well.
Genome_build: hg38
Supplementary_files_format_and_content: GpC and CpG coverage files <chr><start><stop><%methylation><count methylated><total count> counts above 1 are a reflection of redundant reads that were not removed due to sequencing error or different length (after clipping)

source_name: lymphoblast cell line

growth_protocol: GM12878 and K562 cells were obtained from Coriell and ATCC, respectively. GM12878 were grown in RPMI medium 1640 (Gibco), supplemented with 2mM L-Glutamine (Gibco), and Penicilin and Streptavidin (Pen Strep, Gibco), and 15% fetal bovine serum (FBS, Gibco). K562 were grown in RPMI medium 1640 of the same composition but with 10% FBS.

extract_protocol:
Between 2 M and 5 M cells were collected by centrifuging the cell suspension for 5 min at 500x g. Cells were washed once with 1x PBS, resuspended in 1 ml lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2) and incubated for 10 min on ice. IGEPAL CA-630 (Sigma) was added to a final concentration of 0.025% and cell suspension was transferred to a 2 ml Dounce homogenizer. Nuclei were released by 15 strokes with the pestle. Success of lysis was confirmed by inspection under a light microscope. Nuclei were pelleted at at 4C and washed twice with cold lysis buffer without detergent. One million nuclei were resupended in reaction buffer to yield 100 ul with a final concentration of 1x GpC MTase buffer (NEB), 0.32 mM S-Adenosylmethionine (SAM) (NEB). 50 ul of GpC methyltransferase (4U/ul)) from M.CviPl (NEB)were added. The suspension was carefully mixed before incubation for 8 min at 37C after which another 25 ul of enzyme and 0.7 ul of 32mM SAM were added for an additional 8 min incubation at 37C. To avoid disruption of nuclei incubation was stopped by adding 750 ul of 1x PBS and pelleting the nuclei at 800 xg. Supernatant was removed and nuclei were resuspended in 500 ul 1x PBS containing Hoechst 33342 DNA dye (NucBlue Live reagent, Hoechst). Nuclei were kept on ice until sorting. Nuclei were sorted at the Flow Cytometry core at the University of Chicago on a BD FACSAria or BD FACSAria Fusio equipped with a 96-well-plate holder. To obtain individual and intact nuclei gates were set to exclude aggregates and debris, and to include cells with DNA content corresponding to cells in G1 phase of the cell cycle to maintain similar DNA content per cell and to remove potential heterogeneity attributable to cell cycle. Cells were sorted into individual wells pre-filled wth 19 ul of 1x M-Digestion buffer (EZ DNA Methylation Direct Kit, Zymo Research) containing 1mg/ml Proteinase K. Following collection, the plates were briefly spun to collect droplets that might formed during handling. Nuclei were lysed by incubating the samples at 50C for 20 min in a PCR cycler. DNA was subjected to bisulfite conversion by adding 130 ul of freshly prepared CT Conversion reagent (EZ DNA Methylation Direct Kit, Zymo) to the lysed nuclei. Conversion was performed by denaturing the DNA at 98C for 8 min followed by 3.5 hrs incubation at 65C. DNA isolation was performed using the EZ DNA Methylation Direct Kit (Zymo Research) following the manufacturer’s instruction with the modification that the DNA was eluted in only 8 ul of elution buffer.
Libraries were prepared using the Pico Methyl-seq Library prep Kit (Zymo Research) following the manufacturer’s instruction for low input samples. Specifically, the random primers were diluted 1:2 before the initial pre-amplification step and the first amplification extended to a total of 10 amplification cycles. Libraries were amplified with barcoded primers allowing for multiplexing. The sequences can be found in supplementary material, primers were ordered from IDT. The purification of amplified libraries was performed using Ampure beads, using a 1:1 ratio of bedas and libraries. Concentration and size distribution of the final libraries was assessed on an Bioanalyzer (Agilent). Libraries with average fragment size above 150bp were pooled and sequenced.

tag: cell line

tag: enzyme


title: 32B: Control RNAi tails 24hpa replicate B

tag: tissue

value: Control RNAi


title: 35B: Yki RNAi tails 24hpa replicate B


title: 28A: Yki RNAi tails 12hpa replicate A


title: 31A: Control RNAi tails 24hpa replicate A


title: Con rep2


title: 33C: Control RNAi tails 24hpa replicate C


title: 27C: Control RNAi tails 12hpa replicate C


title: Con rep1


title: 30C: Yki RNAi tails 12hpa replicate C


title: DK_ht280_B11

tag: cell type

value: lung epithelial cells

tag: facs purification

value: live, CD45-, Epcam+, HTII-280+


title: DK_ht280_A7


title: 29B: Yki RNAi tails 12hpa replicate B


title: 25A: Control RNAi tails 12hpa replicate A


title: GM_17 scNOMe-seq Control

description: bisulfite converted DNA


title: 26B: Control RNAi tails 12hpa replicate B


title: GM_18 scNOMe-seq Control

description: bisulfite converted DNA


title: GM_16 scNOMe-seq Control

description: bisulfite converted DNA


title: 24C: Yki RNAi tails 6hpa replicate C


title: GM_15 scNOMe-seq Control

description: bisulfite converted DNA


title: GM_14 scNOMe-seq Control

description: bisulfite converted DNA


title: ND-75-i rep1


title: DK_ht280_A12


title: GM_13 scNOMe-seq Control

description: bisulfite converted DNA


title: 21C: Control RNAi tails 6hpa replicate C


title: 20B: Control RNAi tails 6hpa replicate B


title: 18C: Yki RNAi intacts replicate C

value: Intact animals


title: 17B: Yki RNAi intacts replicate B


title: GM_11 scNOMe-seq Sample

description: bisulfite converted DNA

value: GpC Methyltransferase M.CviPl (NEB)


title: 19A: Control RNAi tails 6hpa replicate A


title: GM_10 scNOMe-seq Sample

description: bisulfite converted DNA


title: GM_9 scNOMe-seq Sample

description: bisulfite converted DNA


title: GM_8 scNOMe-seq Sample

description: bisulfite converted DNA


title: 15C: Control RNAi intacts replicate C


title: GM_7 scNOMe-seq Sample

description: bisulfite converted DNA


title: GM_5 scNOMe-seq Sample

description: bisulfite converted DNA


title: 14B: Control RNAi intacts replicate B


title: GM_6 scNOMe-seq Sample

description: bisulfite converted DNA


title: 23B: Yki RNAi tails 6hpa replicate B


title: GM_3 scNOMe-seq Sample

description: bisulfite converted DNA


title: hrde-2(gg517)_l4440_dsRNA_rep3

city: Worcester

first: George

last: Spracklin

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

description:
hrde2_l4440
Small RNA-seq
Processed data file: read_counts.xlsx

data_processing:
Remove 5' barcode (custom script) and 3' barcode (fastX toolkit: fastx_clipper).
Map reads to WS220 genome and annotation.
A custom Python script was used to generate histogram at single nucleotide level.
Read counts were generated by htseq-count 0.6.1.
Genome_build: WS220
Supplementary_files_format_and_content: read_counts.xlsx: Read counts combined into single Excel file.

organism: Caenorhabditis elegans

source_name: Whole animals, hrde-2 mutant, l4440 dsRNA

growth_protocol: C. elegans grown at 20°C.

extract_protocol:
Small RNAs were enriched with a mirVana miRNA Isolation Kit (Ambion, AM1560).
2ug of small RNAs were cloned using a 5'-mono-phosphate independent small RNA protocol as previously described by Gent et al. 2009. Libraries were multiplexed with a 4nt 5' barcode and a 6nt 3' barcode and pooled for HTS on a NextSeq500 (Biopolymers Facility, HMS).

treatment_protocol: Exposed to l4440 or oma-1 dsRNA.

tag: strain/background

value: whole animal

value: adult

tag: food source

value: l4440 dsRNA

tag: 5' barcode

value: CGTC

tag: 3' adapter

value: CTGTAGCCAGCATCAAT


title: hrde-2(gg517)_l4440_dsRNA_rep1

tag: developmental stage


title: 13A: Control RNAi intacts replicate A


title: 22A: Yki RNAi tails 6hpa replicate A


title: GM_4 scNOMe-seq Sample

description: bisulfite converted DNA


title: GM_2 scNOMe-seq Sample

description: bisulfite converted DNA


title: hrde-2(gg517)_l4440_dsRNA_rep2


title: GM_12 scNOMe-seq Sample

description: bisulfite converted DNA


title: GM_1 scNOMe-seq Sample

description: bisulfite converted DNA


title: hrde-2(gg517)_oma-1_dsRNA_rep1

description:
hrde2_oma
Small RNA-seq
Processed data file: read_counts.xlsx

source_name: Whole animals, hrde-2 mutant, oma-1 dsRNA

value: oma-1 dsRNA


title: hrde-2(gg517)_oma-1_dsRNA_rep2


title: hrde-2(gg517)_oma-1_dsRNA_rep3


title: VPS13-D716H_sam37del

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

data_processing:
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8, For pair-end sequencing, treat as single-end
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
log2 ratio of mutants vs wt were used
Genome_build: sacCer3
Supplementary_files_format_and_content: FPKM

organism: Saccharomyces cerevisiae

source_name: BY4741 Background

growth_protocol: Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.

extract_protocol:
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or KAPA stranded mRNA-Seq Kits following the manufacturer’s protocol

tag: genotype

value: VPS13-D716H, sam37-delta


title: wild-type_l4440_dsRNA_rep3

description:
wt_l4440
Small RNA-seq
Processed data file: read_counts.xlsx

source_name: Whole animals, control, l4440 dsRNA

value: AGCG


title: 16A: Yki RNAi intacts replicate A


title: wild-type_l4440_dsRNA_rep2


title: wild-type_l4440_dsRNA_rep1


title: wild-type_oma-1_dsRNA_rep3

description:
wt_oma
Small RNA-seq
Processed data file: read_counts.xlsx

source_name: Whole animals, control, oma-1 dsRNA


title: Aft1-1up


title: VPS13-D716H_mmm1del

value: VPS13-D716H, mmm1-delta


title: wild-type_oma-1_dsRNA_rep2


title: VPS13-D716H


title: wild-type_oma-1_dsRNA_rep1


title: mmm1del_rep2


title: WT_rep2

value: WT


title: F3V3

city: Pullman

first: Michael

last: Skinner

state: WA

address: Abelson 507

department: SBS

institute: WSU

data_processing:
Basic read quality was verified using summaries produced by FastQC
The reads for each sample were mapped to the rat (Rattus norvegicus) genome using Bowtie2
The mapped read files were then converted to sorted BAM files using SAMtools
The MEDIPS R package was used to calculate differential coverage between sample groups. To identify DMR, the reference genome was broken into 100 bp windows. The edgeR Pvalue was used to determine the relative difference between the two sample groups for each genomic window. Windows with an edgeR P value less than 1e-4 were considered DMR. The DMR edges were extended until no genomic window with an edgeR P value less than 0.1 remained within 1000 bp of the DMR.
The DMR that included at least one genomic window with an edgeR P value < 1e-4 were then selected for further analysis and annotated.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: The results of the edgeR analysis in CSV format. This includes raw read counts for each genomic window as well as the calculated p-value and other summary values.

organism: Rattus norvegicus

growth_protocol: Female and male rats of an outbred strain Hsd:Sprague Dawley (Harlan) at about 70 and 100 days of age were fed ad lib with a standard rat diet and ad lib tap water for drinking. To obtain time-pregnant females, the female rats in proestrus were pair-mated with male rats. The sperm-positive (day 0) rats were monitored for diestrus and body weight. The gestating female rats treated were designated as the F0 generation. The offspring of the F0 generation rats were the F1 generation. Non-littermate females and males aged 70-90 days from F1 generation of control or vinclozolin lineages were bred to obtain F2 generation offspring. The F2 generation rats were bred to obtain F3 generation offspring. Individuals were maintained for 12 months and euthanized for sperm collection.

extract_protocol:
The epididymis was dissected free of connective tissue, a small cut made to the cauda and placed in 5 ml of F12 culture medium containing 0.1% bovine serum albumin for 10 minutes at 37°C and then kept at 4ºC to immobilize the sperm.  The epididymal tissue was minced and the released sperm centrifuged at 13, 000 x g and stored in fresh NIM buffer at -20C until processed further. One hundred ul of human sperm suspension were used, then 820uL DNA extraction buffer and 80ul 0.1M DTT added. The sample was incubated at 65C for 15 minutes. Following the incubation 80 ul proteinase K (20 mg/ml) were added and the sample was incubated at 55C for 2 hours under constant rotation. Then 300 ul of protein precipitation solution (Promega Genomic DNA Purification Kit, A795A) were added, the sample mixed thoroughly and incubated for 15 min on ice. The sample was centrifuged at 13,500 rpm for 20 minutes at 4C. One ml of the supernatant was transferred to a 2 ml tube and 2 ul of glycoblue and 1 ml of cold 100% isopropanol were added. The sample was mixed well by inverting the tube several times then left in -20C freezer for at least one hour. After precipitation the sample was centrifuged at 13,500 rpm for 20 min at 4C. The supernatant was taken off and discarded without disturbing the (blue) pellet. The pellet was washed with 70% cold ethanol by adding 500ul of 70% ethanol to the pellet and returning the tube to the freezer for 20 minutes. After the incubation the tube was centrifuged for 10 min at 4C at 13,500 rpm and the supernatant discarded. The tube was spun again briefly to collect residual ethanol at bottom of tube and then as much liquid as possible was removed with gel loading tip. Pellet was air-dried at RT until it looked dry (about 5 minutes). Pellet was then resuspended in 100 ul of nuclease free water. Equal amounts of DNA from three individual sperm samples were used to produce three DNA pools per lineage and employed for methylated DNA immunoprecipitation (MeDIP).
The MeDIP pools were used to create libraries for next generation sequencing (NGS) using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (San Diego, CA) starting at step 1.4 of the manufacturer’s protocol to generate double stranded DNA. After this step the manufacturer’s protocol was followed.

treatment_protocol: On days 8 through 14 of gestation, the F0 females were administered daily intraperitoneal injections of vinclozolin (100 mg/kg BW/day) or dimethyl sulfoxide (vehicle). Treatment lineages are designated ‘control’ or vinclozolin lineages.

value: Hsd:Sprague Dawley

tag: maternal treatment

value: Vinclozolin exposed

tag: generation

value: Sperm


title: F3V2


title: WT_celanYPD_BPS

extract_protocol:
BPS were add to firnal 100 uM in clean YPD and treat for 4 hours
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or KAPA stranded mRNA-Seq Kits following the manufacturer’s protocol

treatment_protocol: Yeast cells were grown in clean YPD to exponential phase


title: WT_celanYPD


title: F3C3

value: Control


title: F3V1


title: mmm1del_rep1


title: mdm34del_rep1


title: WT_rep1


title: F3C2


title: F3C1


title: F1V2


title: F1V3


title: F1V1


title: F1C3


title: F1C1


title: F1C2


title: sam37del


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU4)

city: Hilo

first: Monika

last: Frazier

state: HI

address: 200 West Kawili Street

department: Tropical Conservation Biology and Environmental Science

institute: University of Hawaii at Hilo

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU4

data_processing:
Signal intensities are converted to individual base calls during a run using the system's Real Time Analysis (RTA) software. Sample de-multiplexing is performed using Illumina's CASAVA 1.8.2 software suite.
Trimmomatic (version 0.32) was used to quality filter raw reads. Parameters: WINSIZE=5; WINCUTOFF=20; LEADING=20; TRAILING=20; MINLEN=50
Trinity (version trinityrnaseq_r20140413p1) default parameters were used to construct de novo metatranscriptome assembly using in silico normalized reads (50X coverage; Trinity default settings).
RSEM and edgeR were used to calculate abundance statistics (TPM and FPKM) using default Trinity  (trinityrnaseq_r20140413p1) perl scripts for gene expression analysis.
Homolog identification using BlastP (version 2.2.23+) and Inparanoid (version 4.1) along with GC-content analysis was utilized to identify the subset of transcripts that are of coral (Montipora capitata) origin.
Supplementary_files_format_and_content: Metatranscriptome_denovoassembly.fasta is a fasta file containing the de novo assembled metatranscriptome of the Montipora capitata holobiont.
Supplementary_files_format_and_content: Metatranscriptome_qualityfiltered.fasta is a fasta file containing the quality-filtered metatranscriptome of the Montipora capitata holobiont.
Supplementary_files_format_and_content: Montiporacapitata_transcriptome.fasta is a fasta file containing the subset of transcripts from the metatranscriptome that were identified as originating from the coral host (Montipora capitata).
Supplementary_files_format_and_content: Metatranscriptome_qualityfiltered_genes_FPKM.tsv is a tab-delimited text file with TMM normalized FPKM abundance values assessed at the gene (unigene) level for the quality-filtered metatranscriptome. This data was utilized to assess differential gene expression at the metatranscriptome level.
Supplementary_files_format_and_content: Metatranscriptome_denovoassembly_isoforms_TPM.tsv is a tab-delimited text file with raw read count abundance values assessed at the isoform (transcript) level for the entire metatranscriptome.  This data was utilized to conduct multidimensional scaling analysis at the metatranscriptome level.
Supplementary_files_format_and_content: Montiporacapitata_transcriptome_genes_FPKM.tsv is a tab-delimited text file with TMM normalized FPKM abundance values assessed at the gene (unigene) level for the coral (Montipora capitata) transcriptome subset. This data was utilized to assess differential gene expression at the coral transcriptome level.
Supplementary_files_format_and_content: Montiporacapitata_transcriptome_isoforms_TPM.tsv is a tab-delimited text file with raw read count abundance values assessed at the isoform (transcript) level for the coral (Montipora capitata) transcriptome subset.  This data was utilized to conduct multidimensional scaling analysis at the coral transcriptome level.
Supplementary_files_format_and_content: Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv  is a tab-delimited text file with raw read count abundance values assessed at the isoform (transcript) level for the entire metatranscriptome for samples collected at the Kiholo site.

organism: coral metagenome

source_name: Coral tissue

extract_protocol:
Total RNA was extracted from ~0.1g tissue powder using a combination of TRIzol reagent (Life Technologies) and the RNeasy Mini Kit (Qiagen). TRIzol was added to sample tubes (1ml per 0.1g tissue) and tubes were incubated for 5min at room temperature. Samples were then centrifuged at 12,000g at 4˚C for 10min, and the supernatant transferred to an RNase-free 1.5ml tube. Chloroform (Sigma-Aldrich) was added (0.2ml per 1ml TRIzol), the samples were shaken vigorously for 20–30 seconds, and then incubated at room temperature for 3 minutes. Samples were then centrifuged at 18,000g at 4˚C for 18 minutes. The top layer of aqueous solution was transferred to an RNase-free tube and an equal volume of 200 proof molecular grade ethanol (Sigma-Aldrich) was added. RNA was purified using the RNeasy Mini Kit with a 25min DNA digestion step (Qiagen RNase-free DNase Set) and eluted in 60µl DEPC-treated water (Omega). RNA quality and quantity was determined using the Qubit RNA Broad Range Assay Kit (Life Technologies) and Agilent RNA 6000 Nano Kit (Agilent), and RNA aliquots were stored at –80˚C.
mRNA is purified from approximately 500ng of total RNA with oligo-dT beads and sheared by incubation at 94C.  Following first-strand synthesis with random primers, second strand synthesis is performed with dUTP for generating strand-specific sequencing libraries.  The cDNA library is then end-repaired, and A-tailed, adapters are ligated and second-strand digestion is performed by Uricil-DNA-Glycosylase. Indexed libraries that meet appropriate cut-offs for both are quantified by qRT-PCR using a commercially available kit (KAPA Biosystems) and insert size distribution determined with the LabChip GX. Samples with a yield of ≥0.5 ng/ul are used for sequencing.

tag: site

value: Waiopae, Hawaii

tag: tissue type

value: Unaffected

tag: coral colony number

value: Diseased 4

tag: coral colony health state

value: Diseased (growth anomaly)


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU2)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU2

value: Diseased 2


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU3)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU3

value: Diseased 3


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU5)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU5

value: Diseased 5


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU1)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU1

value: Diseased 1


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH5)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH5

value: Healthy

value: Healthy 5


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH3)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH3

value: Healthy 3


title: m_6hps_2

city: Bad Nauheim

first: Shih-Lei

middle: Ben

last: Lai

state: Hessen

address: Ludwigstraße 43

department: Developmental Genetics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
Read quality trimming with Trimmomatic version 0.33 (java -jar trimmomatic-0.33.jar PE ... LEADING:3 TRAILING:3 SLIDINGWINDOW:5:15 CROP:500 MINLEN:30)
Mapping of reads versus zebrafish genome assembly 10 (Danio rerio GRCz10) and medaka assembly 1 (Oryzias latipes MEDAKA1) using STAR 2.4.0a (--outFilterMismatchNoverLmax 0.1)
Read counting per gene with featureCounts 1.4.5-p1 from the Subread package using default parameters
Raw gene counts for both organisms were joined to a common matrix based on gene homology (BioMart) resulting in 15292 genes
The common matrix of gene counts was normalized with DESeq
Genome_build: Danio rerio GRCz10, Oryzias latipes MEDAKA1
Supplementary_files_format_and_content: The tab-delimited text file (matrix.txt) contains DESeq normalized counts for all homologous genes

organism: Oryzias latipes

source_name: Ventricle

growth_protocol: Zebrafish were raised and handled in compliance with local animal welfare legislation and maintained according to standard protocols (zfin.org). All animals were maintained at 28 °C in a re-circulating system and fish at >6 months of age were used in the experiment.

extract_protocol:
For RNA-seq, RNA was isolated from medaka and zebrafish ventricles using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.  RNA and library preparation integrity were verified with a BioAnalyzer 2100 (Agilent) or LabChip Gx Touch 24 (Perkin Elmer).
500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol (Illumina).

treatment_protocol: WT zebrafish (AB strain) and medaka (Cab strain) from 6-9 month old with similar body size were anethesized and operated (untouched, sham operation, or cryoinjurd) as previously described (Gonzalez-Rosa et al., 2011, Chablais et al., 2011, Schnabel et al., 2011).  Fish were recovered after operation, and lived until specified time points of sample collection.

tag: hours/days after injury

tag: operation

value: sham operation


title: m_6hps_1


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH6)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH6

value: Healthy 6


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH2)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH2

value: Healthy 2


title: m_0h_2

value: 0h = untreated


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH1)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH1

value: Healthy 1


title: m_6dpci_2

value: cryoinjury


title: m_0h_1


title: Unaffected coral tissue from Waiopae, Hawaiʻi (Mcap_WU6)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WU6

value: Waiopae, Hawaii

value: Diseased 6


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA5)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA5

value: Affected


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA6)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA6

value: Diseased (growth anomaly)


title: m_6dps_1


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA2)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA2

value: Diseased 2


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA3)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA3

value: Diseased 3


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA1)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA1


title: m_3dpci_2


title: m_3dpci_1


title: m_6dps_2


title: Healthy coral tissue from Waiopae, Hawaiʻi (Mcap_WH4)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WH4

value: Healthy 4


title: m_3dps_2


title: m_2dpci_2


title: Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU3)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KU3

value: Kiholo, Hawaiʻi

value: Unaffected

value: Diseased 8


title: Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU2)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KU2

value: Diseased 7


title: m_2dpci_1


title: Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH8)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KH8

value: Healthy

value: Healthy 9


title: m_3dps_1

value: sham operation


title: Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH2)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KH2

value: Healthy 8


title: m_2dps_1


title: m_2dps_2


title: Healthy coral tissue from Kiholo, Hawaiʻi (Mcap_KH1)

description:
Montipora capitata holobiont
Coral tissue sample from a healthy M. capitata colony
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KH1

value: Healthy 7


title: m_6hpci_2

value: cryoinjury


title: m_6dpci_1


title: Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA5)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KA5

value: Diseased 9


title: m_6hpci_1


title: Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA2)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KA2


title: Affected coral tissue from Kiholo, Hawaiʻi (Mcap_KA3)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KA3


title: Affected coral tissue from Waiopae, Hawaiʻi (Mcap_WA4)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled directly from a growth anomaly lesion.
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_qualityfiltered_genes_FPKM.tsv
Metatranscriptome_denovoassembly_isoforms_TPM.tsv
Montiporacapitata_transcriptome_genes_FPKM.tsv
Montiporacapitata_transcriptome_isoforms_TPM.tsv
Mcap_WA4

value: Waiopae, Hawaii

value: Diseased 4


title: nitroxyl-treated [Nit3]

status: Public on Jun 19 2017

city: Bloomington

first: David

middle: Peter

last: Giedroc

state: IN

address: 212 S. Hawthorne Drive

department: Chemistry

institute: Indiana University

description:
countstable.txt.gz
Nit3

data_processing:
Bases were called using the Illumina HCS
Sequencing reads were trimmed using Trimmomatic (version 0.33; 1) with the following parameters: ILLUMINACLIP:adapter.fa:2:20:6 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:20 MINLEN:35.
The trimmed reads were mapped on to the Staphylococcus aureus subsp. aureus str. Newman genome using bowtie2 (version 2.1 with default parameters; 2).
Read counts for genes and intergenic intervals were calculated using a custom perl script. Resulting gene/interval counts were used to conduct differential expression analysis using the program DESeq2 algorithm (3) with default parameters.
Calprotectin data quality was checked with FastQC and QC3. Alignment was performed by TopHat. Gene quantification (FPKM) was done using Cufflinks. Differential expression analysis was carried out using Cuffdiff from the Cufflinks package.
Genome_build: AP009351.1
Supplementary_files_format_and_content: raw counts of sequencing reads for the features of interest including genes and intergenic regions for each fastq file; intergenic regions are identified as follows Inter.<molecule>.<strand>.<basepair_begin>.<basepair_end>

organism: Staphylococcus aureus

source_name: Exponentially grown cells

growth_protocol: Overnight starter cultures of S. aureus strain Newman were grown in TSB medium overnight and used to inoculate 15mL cultures in Hussain−Hastings−White modified (HHWm) minimal media (Toledo-Arana et al., 2005) supplemented with 0.5 mM thiosulfate and 0.5 mM methionine at a starting OD600 = 0.02. All cultures were grown in loosely capped 50mL Falcon tubes at 37°C with shaking at 200 rpm, until a final OD600 of 0.2.

extract_protocol:
Following growth to OD600=0.2, 5mL aliquots of cells were pelleted and resuspended in 1mL TriReagent (Molecular Research Center), then lysed with 0.1mm silica beads in a bead beater (MP Bio). RNA was extracted by adding 200 uL chloroform, mixing, and centrifuging. The aqueous layer was extracted and added to one volume of 70% ethanol. RNA purification was completeted using the RNeasy minikit (Qiagen).
A total of 1 μg of RNA was used to make stranded, rRNA-delpeted RNAseq libraries using the ScriptSeq Complete (Bacteria) kit (then from Epicentre, now Illumnia Cat. # BB1206).
Sequencing was performed using an Illumina HiSeq2000 instrument with a read length of 1 × 50 nucleotides. Image analysis was done by the Illumina HCS.

treatment_protocol: Angeli's salt was handled under an inert atmosphere and resuspened in 0.01 M NaOH in a septacap tube immediately prior to use. Concentration was verified by measuring UV absorbance at 237 nm (ex. coef. = 6100, see https://www.caymanchem.com/product/82230). Nitroxyl treatment was achieved by adding 0.15mM angeli's salt when the OD600 reached 0.2.

tag: strain

value: Newman

tag: genotype/variation

value: WT

tag: treatment

value: angeli's salt.


title: nitroxyl-treated [Nit2]

description:
countstable.txt.gz
Nit2


title: Unaffected coral tissue from Kiholo, Hawaiʻi (Mcap_KU5)

description:
Montipora capitata holobiont
Coral tissue sample from a M. capitata colony affected by the disease growth anomaly.  Tissue sampled from an apparently healthy area of the colony (not growth anomaly lesion tissue).
Metatranscriptome_denovoassembly.fasta
Metatranscriptome_qualityfiltered.fasta
Montiporacapitata_transcriptome.fasta
Metatranscriptome_denovoassembly_isoforms_TPM_kiholo.tsv
Mcap_KU5

value: Diseased (growth anomaly)


title: DcstR [4CsR2]

description:
countstable.txt.gz
4CsR2

value: DcstR


title: DcstR [4CsR3]

description:
countstable.txt.gz
4CsR3


title: DcstR [4CsR1]

description:
countstable.txt.gz
4CsR1


title: nitroxyl-treated [Nit1]

description:
countstable.txt.gz
Nit1


title: sulfide-treated [HS3]

description:
countstable.txt.gz
HS3

treatment_protocol: Na2S was added to the cultures at a ﬁnal concentration of 0.2 mM when the OD600 reached 0.2.

value: sodium sulfide


title: WT unstressed (control for sulfide, nitroxyl, DcstR) [C1]

description:
countstable.txt.gz
C1


title: WT unstressed (control for sulfide, nitroxyl, DcstR) [C3]

description:
countstable.txt.gz
C3


title: sulfide-treated [HS2]

description:
countstable.txt.gz
HS2


title: sulfide-treated [HS1]

description:
countstable.txt.gz
HS1


title: WT unstressed (control for sulfide, nitroxyl, DcstR) [C2]

description:
countstable.txt.gz
C2


title: 100-59_exp_2 MSM after engaging in CRAI <24 hours prior

city: Atlanta

first: Gregory

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Illumina Casava1.8.2 software used for basecalling and demultiplexing.
Reads were mapped to hg19 genome assembly with the STAR (v2.4.0g1) aligner args: --outFilterMultimapNmax 1 --outFilterType BySJout --outSJfilterReads Unique --sjdbGTFfile refGene.gtf --outFilterIntronMotifs RemoveNoncanonicalUnannotated
Per sample annotated transcript models were quantitated with Cufflinks (v2.1.1) args: -G refGene.gtf
Sample transcript models were merged with Cuffmerge (v2.1.1)
FPKM (Fragments per kilobase of exon per million reads mapped) abundance estimates and differential expression was calculated with Cuffdiff (v2.1.1)
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] tab delimited text file containing FPKM for each sample (in columns) and each annotated transcript (in rows).

extract_protocol:
Total RNA was purified using RNAeasy Mini Kit (Qiagen). Standard quality control steps were included to determine total RNA quality using Agilent 2100 Bioanalyzer (RNA integrity number (RIN) >8.5; Eukaryote Total RNA nano Kit, Agilent, USA)
Libraries were prepared using the Illumina TruSeq mRNA protocol. Libraries were validated by microelectrophoresis, quantified, pooled and clustered on Illumina TruSeq v3 flowcell.  Clustered flowcell was sequenced on an Illumina HiSeq 1000 in 100-base single-read reactions.

tag: experimental group

value: exp

tag: visit

tag: tissue

value: rectal biopsy


title: 100-67_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-19_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-57_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-55_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-45_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-47_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-65_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-17_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-37_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-39_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-7_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-65_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-3_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-1_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-47_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-67_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-5_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-39_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-45_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-55_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-53_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-53_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-37_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-25_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-57_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-25_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-15_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-9_exp_2 MSM after engaging in CRAI <24 hours prior


title: 100-7_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-1_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-5_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-59_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-17_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-49_con_2 Control visit 2

value: con


title: 100-51_con_2 Control visit 2


title: 100-27_con_2 Control visit 2


title: 100-3_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-15_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-21_con_2 Control visit 2


title: 100-31_con_2 Control visit 2


title: 100-11_con_2 Control visit 2


title: 100-29_con_2 Control visit 2


title: 100-61_con_1 Control visit 1


title: 100-63_con_1 Control visit 1


title: 100-51_con_1 Control visit 1


title: 100-49_con_1 Control visit 1


title: 100-29_con_1 Control visit 1


title: 100-35_con_1 Control visit 1


title: 100-33_con_1 Control visit 1


title: 100-21_con_1 Control visit 1


title: 100-13_con_1 Control visit 1


title: 100-11_con_1 Control visit 1


title: 100-35_con_2 Control visit 2


title: 100-19_exp_1 MSM after abstaining from CRAI >72 hours


title: 100-33_con_2 Control visit 2


title: siCtrl batch2

city: Bridgewater

first: Wencheng

last: Li

state: NJ - New Jersey

institute: PTC Therapeutics

description:
processed data file:
3READS+.batch2.pA.read.counts.siStarPAP.txt

data_processing:
Data analysis for 3’READS or 3'READS+.  3’READS or 3'READS+ reads were mapped to the human genome (hg19) using bowtie2 (local mode). Uniquely mapped reads (with MAPQ score > 10) that had at least two additional 5’ Ts not aligned to genome (presumably derived from the poly(A) tail) were named pA site supporting (PASS) reads and were used to calculate pA isoform expression. pA isoforms expressed below 5% of all isoforms of a gene were discarded.  Significantly regulated APA events were identified by the Significance Analysis of Alternative Polyadenylation (SAAP) method [Li et al., 2015].
Genome_build: hg19
Supplementary_files_format_and_content: 3READS.pA.read.counts.txt, 3READS.pA.read.counts.siPAPag.txt, and 3READS+.batch2.pA.read.counts.siStarPAP.txt contain information of gene symbol, pA coordinates, read number of pAs in different 3'READS samples. "pA_type" is pA type based on location of a pA. "pAid" has information of chromosome, strand and coordinates (based on hg19).

source_name: Control knockdown batch 2

growth_protocol: Human embryonic kidney (HEK) 293 cells were obtained from American Type Culture Collection (ATCC). The cell culture conditions were performed as previously described (Li et al. 2012).

extract_protocol:
Total RNA was subjected to 1 round of poly(A) selection using the Poly(A)PuristTM MAG kit (Ambion), followed by fragmentation using the RNA fragmentation kit (Ambion).
Deep sequencing of mRNA was based on the 3’ region extraction and deep sequencing (3’READS) method (Hoque et al. 2013) or 3'READS+ method (Zheng et al., 2016). For 3'READS, poly(A)-containing RNA fragments were isolated using the MyOne streptavidin C1 beads (Invitrogen) coated with a 5’ biotinylated chimeric U5T45 oligo (Sigma) at room temperature for 1 hr in the binding buffer (10 mM Tris-HCl pH 7.5, 150 mM NaCl, 1 mM EDTA), followed by washing with the washing buffer (10 mM Tris-HCl pH7.5, 1 mM NaCl, 1 mM EDTA, 10% Formamide). RNA bound to the beads was digested with RNase H (5U in 50 μl reaction volume) at 37 °C for 1 hr, which removed the poly(A) sequence and eluted RNA from the beads. Eluted RNA fragments were purified by Phenol:Chloroform extraction and Ethanol precipitation, followed by phosphorylation of the 5' end with T4 kinase (NEB). Phosphorylated RNA was then purified by the RNeasy kit (Qiagen) and was sequentially ligated to a 5’-adenylated 3’ adapter (5’-rApp/NNNNGATCGTCGGACTGTAGAACTCTGAAC/3ddC) with the truncated T4 RNA ligase II (Bioo Scientific) and to a 5’ adapter (5’-GUUCAGAGUUCUACAGUCCGACGAUC) by T4 RNA ligase I (NEB). The resultant RNA was reverse-transcribed to cDNA with Superscript III (Invitrogen), followed by 12 cycles of PCR amplification with Phusion high fidelity polymerase (NEB). cDNA libraries were sequenced on an Illumina Hiseq 2000 sequencer.

treatment_protocol: The transfections of the siRNAs were performed as previously described (Li et al. 2012).

tag: cell line

tag: cell condition

value: knockdown control

tag: library protocol


title: siPAPag

source_name: PAPa and PAPg knockdown

value: knockdown


title: rheumatoid arthritis tissue 150

city: Spring House

first: Alice

last: Walsh

state: PA

address: Welsh & McKean Roads

department: Immunology

institute: Janssen R&D

data_processing:
Reads were trimmed for adaptors and sequence quality. The average number of clusters (post-trimming) per sample was 89 million.
Trimmed reads were aligned to human b37.3 reference genome using the STAR v2.4 aligner (Dobin et al., 2013).
Aligned reads were quantified using RSEM v1.2.14 algorithm (Li and Dewey, 2011) with UCSC transcriptome model (accessed on 03/17/2014) that included lincRNAs from Ensembl v75. This transcriptome model has a total of 34495 genes and 88933 isoforms
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited processed data matrix file contains feature counts for all samples and features

source_name: synovial biopsy

extract_protocol:
Total RNA was extracted from RA synovial samples and the quality of all RNA samples was evaluated using an Agilent Bioanalyzer
Sequencing libraries were prepared using TruSeq Stranded Total RNA RiboZero protocol from Illumina. Libraries were pooled and sequenced with an Illumina HiSeq 2000 with paired-end 100 bp flow cells. Raw read quality was evaluated using FastQC.

tag: Sex

value: F

tag: age

tag: disease

value: Rheumatoid arthritis (established)

tag: acpa positivity

value: Negative


title: rheumatoid arthritis tissue 145


title: rheumatoid arthritis tissue 144


title: rheumatoid arthritis tissue 147


title: rheumatoid arthritis tissue 148

value: M


title: rheumatoid arthritis tissue 152


title: rheumatoid arthritis tissue 151


title: rheumatoid arthritis tissue 149


title: rheumatoid arthritis tissue 140


title: rheumatoid arthritis tissue 143

value: Positive


title: siStarPAP batch2

source_name: StarPAP knockdown batch 2


title: rheumatoid arthritis tissue 142


title: rheumatoid arthritis tissue 141


title: 100-31_con_1 Control visit 1


title: rheumatoid arthritis tissue 137


title: rheumatoid arthritis tissue 135


title: rheumatoid arthritis tissue 139


title: rheumatoid arthritis tissue 138


title: rheumatoid arthritis tissue 134


title: rheumatoid arthritis tissue 132


title: rheumatoid arthritis tissue 129


title: 100-27_con_1 Control visit 1


title: rheumatoid arthritis tissue 146


title: rheumatoid arthritis tissue 136


title: rheumatoid arthritis tissue 131


title: rheumatoid arthritis tissue 128


title: rheumatoid arthritis tissue 130


title: rheumatoid arthritis tissue 133


title: rheumatoid arthritis tissue 127


title: rheumatoid arthritis tissue 124


title: rheumatoid arthritis tissue 125


title: rheumatoid arthritis tissue 126


title: rheumatoid arthritis tissue 122


title: rheumatoid arthritis tissue 118


title: rheumatoid arthritis tissue 120


title: rheumatoid arthritis tissue 121


title: rheumatoid arthritis tissue 119


title: rheumatoid arthritis tissue 113


title: rheumatoid arthritis tissue 117


title: rheumatoid arthritis tissue 115


title: rheumatoid arthritis tissue 116


title: rheumatoid arthritis tissue 112


title: rheumatoid arthritis tissue 114


title: rheumatoid arthritis tissue 111


title: rheumatoid arthritis tissue 110


title: WT unstressed (CP control) [WT_untreated_3]

description:
WT_vs_WTCP.counts.txt.gz
WT_untreated_3

growth_protocol: or RNAseq of calprotectin (CP)-treated cultures, bacteria were cultured overnight in Chelex-treated RPMI plus 1% casamino acids supplemented with 1 mM MgCl2, 100 μM CaCl2, and 1 μM FeSO4.  These samples were then back diluted 1 to 100 into growth media containing 38% TSB/ 72% calprotectin buffer (20 mM Tris, pH 7.5, 100 mM NaCl, 3 mM CaCl2, 10 mM β-mercaptoethanol), supplemented with 1 µM Zn and 1 µM Mn.  The bacteria were grown to exponential phase OD600 of (0.25-0.4) in the presence and absence of 960 µg/mL CP.

extract_protocol:
These cells were pelleted, resuspended in LETS buffer (0.1 M LiCl, 10 mM EDTA, 10 mM TrisHCl, 1% SDS), vortexed with acid-washed glass beads (Sigma-Aldrich) for 4 min and incubated for 5 min at 55°C. The resulting solution was subjected to extraction by TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. The RNA was then concentrated by ethanol precipitation and quantified via absorbance spectroscopy.
A total of 2 μg of RNA was processed using the Epicentre Gram-Positive rRNA kit (RZPB10106). After depletion, the Illumina Stranded Total RNA protocol was used to generate indexed cDNA libraries.
Libraries were pooled and sequenced at PE75 on the HiSeq2500. The raw sequencing reads were processed through CASAVA for FASTQ conversion and demultiplexing.

treatment_protocol: The bacteria were grown to exponential phase OD600 of (0.25-0.4) in the absence of CP.


title: CP-treated [WT_CP_2]

description:
WT_vs_WTCP.counts.txt.gz
WT_CP_2

treatment_protocol: The bacteria were grown to exponential phase OD600 of (0.25-0.4) in the presence of 960 µg/mL CP.

value: calprotectin


title: rheumatoid arthritis tissue 105


title: rheumatoid arthritis tissue 106


title: rheumatoid arthritis tissue 109


title: rheumatoid arthritis tissue 104


title: rheumatoid arthritis tissue 103


title: CP-treated [WT_CP_3]

description:
WT_vs_WTCP.counts.txt.gz
WT_CP_3

value: Newman


title: rheumatoid arthritis tissue 107


title: rheumatoid arthritis tissue 102


title: rheumatoid arthritis tissue 108


title: CP-treated [WT_CP_1]

description:
WT_vs_WTCP.counts.txt.gz
WT_CP_1

value: WT


title: WT unstressed (CP control) [WT_untreated_2]

description:
WT_vs_WTCP.counts.txt.gz
WT_untreated_2


title: rheumatoid arthritis tissue 100


title: WT unstressed (CP control) [WT_untreated_1]

description:
WT_vs_WTCP.counts.txt.gz
WT_untreated_1


title: rheumatoid arthritis tissue 123


title: rheumatoid arthritis tissue 96


title: rheumatoid arthritis tissue 99


title: rheumatoid arthritis tissue 97


title: MAT2A-ChIP_2

city: Kyoto

first: Shuntaro

last: Ikeda

address: Kitashirakawa Oiwake-cho, Sakyo-ku

department: Graduate School of Agriculture

country: Japan

institute: Kyoto University

data_processing:
Sequencing reads, which were filtered to remove adapter sequence using Illumina bcl2fastq2 (Illumina), were aligned to the bovine genome (Bos_taurus_UMD_3.1.1/bosTau8, Jun. 2014) using Bowtie (version 1.1.2) and peak calling was performed by using the Model-based Analysis of ChIP-Seq (MACS, version 1.4.2) to generate bed files.
Genome_build: bosTau8
Supplementary_files_format_and_content: Bed files containing information about called peaks: the name of the chromosome, the starting and ending positions of the feature in the chromosomes, the name of the BED lines, and scores.

organism: Bos taurus

source_name: blastocysts

growth_protocol: Bovine blastocysts were in vitro produced by in vitro fertilization (IVF) and further cultured in mSOF up to day 8 (IVF = day 0).

extract_protocol:
ChIP for small cell numbers was performed with True MicroChIP kit (Diagenode) according to the manufacturer’s instruction with some modifications. Bovine blastocysts were in vitro produced. At 192 h post insemination, approximately 110 blastocysts per culture were collected and crosslinked for 10 min with 1% formaldehyde in PBS containing 20 mM Na-butyrate (PBS-NaBu) and then quenched with 125 mM glycine for 10 min. The blastocysts were washed with PBS-NaBu containing protease inhibitor cocktail (PBS-NaBu-PIC), transferred into a 1.5-ml tube with a small volume of PBS-NaBu-PIC, and stored at -80°C until total of approximately 670 blastocysts were obtained by replicating the procedure six times. The approximately 670 blastocysts were resuspended in Lysis Buffer and the lysate was mixed with PBS-NaBu-PIC. The sample was sonicated to shear chromatin using a Bioruptor UCD-250 for 20 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 10 min at 14,000 x g and the supernatant (330 μl) was transferred to a new tube and mixed with 330 µl of ChIP Buffer. The 660-µl sample of sheared chromatin was divided into 20 µl as ‘Input’ and two aliquots of 320 µl. The latter two aliquots were mixed with 5 µg of  anti-MAT2A monoclonal antibody (ab86424, Abcam) or mouse IgG2B isotype control (MAB004, R&D Systems) as a negative control (IgG control), respectively and incubated for 16 h at 4°C with rotation at 40 rpm. Protein A-coated magnetic beads (20 µl) were added to the sample, which was then rotated at 40 rpm for 2 h at 4°C. The DNA was eluted from the immunoprecipitate, decrosslinked, and subsequently purified with MicroChIP DiaPure columns (Diagenode). The same DNA purification method was also applied to the Input sample and resulted in 10 µl each of DNA sample (Input, MAT2A-ChIP, and IgG control).
The DNA samples were processed to library preparation for next-generation sequencing (NGS) by using MicroPlex Library Preparation kit v2 (Diagenode) following the manufacturer’s instruction. After cluster generation using Illumina cBot (Illumina), sequencing was performed on HiSeq2500 (Illumina) as 100 base (single read).

treatment_protocol: The culture media (mSOF) were supplemented with 5% (v/v) fetal calf serum on day 3 to increase blastocyst yield.

value: blastocysts

tag: source

value: in vitro produced

tag: day of in vitro culture after ivf

value: day 8

tag: chip-antibody

value: anti-MAT2A (Abcam ab86424, Lot:GR241473-1)


title: Input_2


title: IgG control_1

value: IgG2B isotype control (R&D Systems MAB004, Lot:NZ1014071)


title: rheumatoid arthritis tissue 95


title: MAT2A-ChIP_1


title: rheumatoid arthritis tissue 94


title: Input_1


title: rheumatoid arthritis tissue 93


title: HESC_CO_2

city: New York

first: Shuibing

last: Chen

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq v2.17 was used for base calling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt with parameters "-O 5 -m 45 -q 10"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11.
Gene abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: hESC derived organoids

growth_protocol: hESCs were subjected to a 3 day activin endoderm differentiation, followed by 4 days of posterior endoderm differentiation in the presence of CHIR and FGF4 (COs) or WNT3A (SIOs). After that they were grown in matrigel beads for 4 weeks adding CHIR(COs) or noggin and R-spondin1 (SIOs), EGF and B27 as a supplement .

extract_protocol:
organoids were obtained by dislodging the matrigel beads pipetting up and down. Then, total RNA was extracteed with the Absolutely RNA nanoprep Agilent kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: hESC derived organoids

value: wt

tag: time in culture

value: 4 weeks


title: rheumatoid arthritis tissue 91


title: rheumatoid arthritis tissue 92


title: rheumatoid arthritis tissue 101


title: HESC_SIO_2

tag: genotype/variation


title: rheumatoid arthritis tissue 90


title: rheumatoid arthritis tissue 88


title: rheumatoid arthritis tissue 89


title: HESC_SIO_1


title: rheumatoid arthritis tissue 98


title: FAP8_CO_2

source_name: FAP8_iPSC derived Colonic organoids

growth_protocol: iPSCs were subjected to a 3 day activin endoderm differentiation, followed by 4 days of posterior endoderm differentiation in the presence of CHIR and FGF4. After that they were grown in matrigel beads for 4 weeks adding CHIR, EGF and B27 as a supplement.

value: APC-/+

value: iPSC derived colonic organoids


title: FAP9_CO_1

source_name: FAP9_iPSC derived Colonic organoids

value: APC mutations


title: IgG control_2


title: rheumatoid arthritis tissue 86

value: F

value: Rheumatoid arthritis (established)


title: HESC_CO_1


title: rheumatoid arthritis tissue 87

value: Positive


title: FAP8_CO_1


title: WT_CO_2

source_name: WT_iPSC derived Colonic organoids


title: rheumatoid arthritis tissue 83


title: rheumatoid arthritis tissue 85


title: rheumatoid arthritis tissue 82

value: M


title: rheumatoid arthritis tissue 81


title: WT_CO


title: rheumatoid arthritis tissue 84


title: HESC_SIO_4

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for low-quality sequences and adapter sequences by using cutadapt with parameters "-O 5 -m 45 -q 10"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

growth_protocol: hESCs were subjected to a 3 day activin endoderm differentiation, followed by 4 days of posterior endoderm differentiation in the presence of CHIR and FGF4. After that they were grown in matrigel beads for 4 weeks adding CHIR, EGF and B27 as a supplement for samples MCH1 and 2. Samples MCW1 & 2 were differentiated according to the protocol publisjed by Spence et al. Nature 2011.

tag: origin

tag: genotype


title: HESC_SIO_3


title: HESC_CO_4

source_name: hESC derived Colonic organoids

value: hESC derived Colonic organoids


title: JU1421 female control

city: Hong Kong

first: Runsheng

address: To Yuen Building, 31 To Yuen Street, City University of Hong Kong

country: Hong Kong

institute: City University of Hong Kong

data_processing:
Illumina MiSeq with v2 chemistry and software MCS v2.3.0.3 used for basecalling
Sequenced reads were trimmed for adaptor sequence and low-quality sequence using Trimmomatic, then mapped to to C. briggsae genome (cb4) using CLC genomic workbench 8.0. The genome sequence and gene GFF annotation files were obtained from WormBase (WS250). The cutoff for C. nigoni reads are at least 85% similarity and 80% length while for C. birggsae reads, the cutoff are 90% similarity and 85% length. To de novo annotate putative TEs, RepeatMolder was run with the genome of C. nigoni (cn1, this study) and C. briggsae genome (cb4) as an input, respectively using default parameters. The consensus sequences of TEs produced were used as input to RepeatMasker to annotate all the possible TE loci over the two genomes. RMblast was used in the two annotation pipelines to align genome sequence against possible TEs. For the TE quantification, we mapped all reads from mRNAs against the consensus sequences of as described above using CLC genomic workbench 8.0, with a cutoff of at least 75% similarity and 75 % length.
The unique reads mapped to each genes were then counted with CLC genomic workbench 8.0. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated with R package edgeR.
Genome_build: cb4
Supplementary_files_format_and_content: tab-delimited text files include unique reads mapped values for each sample

organism: Caenorhabditis nigoni

source_name: whole worm

extract_protocol:
300 young adult females were picked for mRNA extraction for each sample for C. briggsae (AF16) and C. nigoni (JU1421).
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual

tag: strain

tag: Stage

value: young adult female

value: wild type


title: rheumatoid arthritis tissue 80


title: rheumatoid arthritis tissue 79


title: rheumatoid arthritis tissue 78


title: FAP9_CO_0

data_processing:
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for low-quality sequences by using fastq_quality_trimmer in the FASTX toolkit with parameters "-t 10 -l 45"; then mapped to the UCSC hg19 human reference genome using tophat v2.0.11 with default parameters.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: hg19
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, RPKM values of each sample, for each gene

source_name: FAP-iPSC derived Colonic organoids

growth_protocol: hESCs or iPSCs were subjected to a 3 day activin endoderm differentiation, followed by 4 days of posterior endoderm differentiation in the presence of CHIR and FGF4. After that they were grown in matrigel beads for 4 weeks adding CHIR, EGF and B27 as a supplement.

value: FAP-iPSC derived colonic organoids


title: WT_CO_0

source_name: control-iPSC derived Colonic organoids

value: control-iPSC derived Colonic organoids


title: rheumatoid arthritis tissue 74


title: rheumatoid arthritis tissue 70

value: Negative


title: rheumatoid arthritis tissue 69


title: rheumatoid arthritis tissue 77


title: rheumatoid arthritis tissue 67


title: rheumatoid arthritis tissue 63


title: rheumatoid arthritis tissue 73


title: rheumatoid arthritis tissue 71


title: rheumatoid arthritis tissue 76


title: rheumatoid arthritis tissue 68


title: H1_CO

source_name: H1 hESC derived Colonic organoids

value: H1 hESC derived Colonic organoids


title: rheumatoid arthritis tissue 66


title: rheumatoid arthritis tissue 75


title: rheumatoid arthritis tissue 58


title: rheumatoid arthritis tissue 62


title: rheumatoid arthritis tissue 72


title: rheumatoid arthritis tissue 61


title: rheumatoid arthritis tissue 59


title: rheumatoid arthritis tissue 57

value: Rheumatoid arthritis (early)


title: HESC_CO_3

value: wt


title: rheumatoid arthritis tissue 55


title: rheumatoid arthritis tissue 56


title: rheumatoid arthritis tissue 53


title: rheumatoid arthritis tissue 65


title: rheumatoid arthritis tissue 51


title: rheumatoid arthritis tissue 64


title: rheumatoid arthritis tissue 50


title: rheumatoid arthritis tissue 47


title: rheumatoid arthritis tissue 44


title: rheumatoid arthritis tissue 49


title: rheumatoid arthritis tissue 45


title: rheumatoid arthritis tissue 46


title: rheumatoid arthritis tissue 43


title: rheumatoid arthritis tissue 48


title: rheumatoid arthritis tissue 42


title: rheumatoid arthritis tissue 41


title: rheumatoid arthritis tissue 36


title: rheumatoid arthritis tissue 35


title: rheumatoid arthritis tissue 39


title: rheumatoid arthritis tissue 38


title: rheumatoid arthritis tissue 34


title: rheumatoid arthritis tissue 37


title: rheumatoid arthritis tissue 33


title: rheumatoid arthritis tissue 30


title: rheumatoid arthritis tissue 28


title: rheumatoid arthritis tissue 29


title: rheumatoid arthritis tissue 54


title: rheumatoid arthritis tissue 52


title: rheumatoid arthritis tissue 26


title: rheumatoid arthritis tissue 25


title: rheumatoid arthritis tissue 24