title: ATACseqUCLA1hESC50k

city: Haining

first: Wanlu

last: Liu

state: Zhejiang

address: 718 East Haizhou Rd.,

department: Zhejiang University - University of Edinburgh Institute

institute: Zhejiang University

description: human embryonic stem cells (hESC)

data_processing:
ATAC-seq data was mapped using Bowtie as previously described (Pastor et al., 2018). MACS2 callpeaks tools were used to identify ATAC-seq peaks in somatic tissue, hESC, iMeLC, hPGCLC and hPGC datasets (Zhang et al., 2008). In order to identify peaks specific to one condition among different conditions, bedtools multiinter option was used with Invoke Ryan Layers's clustering algorithm applied (Quinlan and Hall, 2010).
Genome_build: hg19
Supplementary_files_format_and_content: ATACseq: bigwig tracks of ATACseq signals

source_name: 50,000 cells of primed UCLA1 hESCs

growth_protocol: hESC media: 20% knockout serum replacement (KSR) (Gibco, 10828-028), 100µM L-Glutamine (Gibco, 25030-081), 1x MEM Non-Essential Amino Acids (NEAA) (Gibco, 11140-050), 55µM 2-Mercaptoethanol (Gibco, 21985-023), 10ng/mL recombinant human FGF basic (R&D systems, 233-FB), 1x Penicillin-Streptomycin (Gibco, 15140-122), and 50ng/mL primocin (InvivoGen, ant-pm-2) in DMEM/F12 media (Gibco, 11330-032).

extract_protocol:
Cells were collected in lysis buffer (10mM Tris pH7.4, 10mM NaCl, 3mM MgCl2, 1% NP40) and spun at 500g for 10 min to collect nuclei for ATAC-seq library construction
ATAC-seq was performed using Nextera DNA library prep kit (Illumina, 15028212) as previously described (Pastor et al., 2018). Cells were collected in lysis buffer (10mM Tris pH7.4, 10mM NaCl, 3mM MgCl2, 1% NP40) and spun at 500g for 10 min. The pellet was resuspended in the transposase reaction mix (25 μL 2× Tagmentation buffer, 2.5 μL transposase and 22.5 μL nuclease-free water) and incubated at 37°C for 30 min. The samples were purified using MinElute PCR Purification Kit (Qiagen, 28006) and amplified using 1× NEBnext PCR master mix (NEB, M0541S) and 1.25 μM of custom Nextera PCR primers 1 and 2 with the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. Samples were amplified for five cycles and an aliquot of the PCR reaction was used to determine the required cycles of amplification by real-time PCR. The remaining 45 μL reaction was amplified with the determined cycles and purified with MinElute PCR Purification Kit (Qiagen, 28006) yielding a final library concentration of about 30 nM in 20 μL. Libraries were subjected to single-end 50bp sequencing on HiSeq 2000 or HiSeq 2500 sequencer with 4-6 indexed libraries per lane.

treatment_protocol: No treatment

value: primed UCLA1 hESCs

tag: passage number

value: Passage 16


title: ATACseqUCLA1hESC25k

status: Public on Dec 27 2018

type: SRA

country: China

description: human embryonic stem cells (hESC)

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: 20,000 cells of primed UCLA1 hESCs

tag: cell type


title: DIO-1d-DMSO-biological rep1

type: RNA

city: Boston

first: Umut

last: Ozcan

state: MA

address: 3 Blackfan Circle, CLS 16

department: Endocrinology

country: USA

institute: Boston Children's Hospital

hyb_protocol: Per manufacturer's protocol (Affymetrix GeneChip Hybridization, Stain and Wash kit)

scan_protocol: Scanned On an Affymetrix GCS3000 7G scanner

data_processing: Data were analyzed with Affymetrix software to normalize and background correct using RMA

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: diet-induced obese mice

label_protocol: Per manufacturer's protocol (Affymetrix Ambion WT Expression kit and GeneChip WT Terminal labeling kit)

growth_protocol: 4-week-old C57BL/6J male mice were fed with 45% high fat diet for 16 weeks

extract_protocol: Trizol extraction and subsequent purification of total RNA using QIAgen RNeasy MinElute Cleanup kit were performed according to the manufacturer's instructions.

treatment_protocol: Mice were intraperitoneally injected with DMSO for 6h, 1day or 4 days and then daily (25 ul/day)

tag: strain

tag: disease state

value: DIO

tag: gender

value: male

tag: age

tag: tissue

value: brain

tag: tissue region

value: hypothalamus

tag: treatment

value: treated with DMSO

tag: time

value: 1 day


title: CARE068B_rep

type: genomic

city: Toronto

first: Sarah

middle: J.

last: Goodman

state: ON

address: PGCRL, 686 Bay St.

department: Genetics and Genome Biology

country: Canada

institute: Hospital for Sick Children

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridized to Illumina Infinium HumanMethylation450k Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged with BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio software V2011.1 with GenomeStudio Methylation Analysis Module Version 1.9.1000 (background-subtraction, colour-correction)

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit (Qiagen) as per manufacturer’s instructions.

value: Buccal

tag: sample well

tag: plate id

tag: Sex

value: M

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: CARE038B_rep

value: F


title: CD56Dim Donor 3 H3K27ac

city: Columbus

first: Patrick

middle: Leonard

last: Collins

state: OH

address: 770 BRT,  460 W 12th Ave

department: Microbial Infection and Immunity

institute: Ohio State University

description: Ultra-low Input (100 k cells)

data_processing:
ChIP-seq reads were aligned ot the hg19 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
peaks were called using MACS2 findpeaks --broad
Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: hg19

source_name: CD56Dim natural killer cells

extract_protocol: Lysates were clarified from MNase treated nuclei and histone-DNA complexes were isolated with antibody. ATAC-seq were processed as per manufacturers instructions (Illumina FC-121-1030)

value: CD56Dim natural killer cells

tag: individual

value: Donor 3

tag: antibody

value: H3K27ac (abcam 4729)


title: DIO-6h-DMSO-biological rep3

value: 6 h


title: CD56Dim Donor 2 H3K27ac

description: Ultra-low Input (100 k cells)

tag: cell type

value: Donor 2


title: DIO-6h-DMSO-biological rep1

tag: strain


title: CARE097P

value: PBMC


title: CARE071B_rep


title: ATACseqUCLA1hESC10k

description: human embryonic stem cells (hESC)

source_name: 10,000 cells of primed UCLA1 hESCs

value: primed UCLA1 hESCs

tag: passage number


title: ATACseqUCLA1hESC3k

description: human embryonic stem cells (hESC)

source_name: 3,000 cells of primed UCLA1 hESCs

value: Passage 16


title: DIO-6h-DMSO-biological rep2

tag: disease state

value: DIO

tag: gender


title: CARE091P_rep

tag: tissue


title: CD56Dim Donor 1 H3K27ac

description: Ultra-low Input (100 k cells)

value: Donor 1


title: ATACseqUCLA1hESC1k

description: human embryonic stem cells (hESC)

source_name: 1,000 cells of primed UCLA1 hESCs


title: CD56Bright Donor 4 H3K27ac

description: Ultra-low Input (100 k cells)

source_name: CD56Bright natural killer cells

value: CD56Bright natural killer cells

value: Donor 4


title: CARE091P


title: ATACseqUW334femaleskin

description: skin cells from female 76d human embryo

source_name: skin cells from female 76d human embryo

value: skin cells from female 76d human embryo


title: ATACseqUW334femalelung

description: lung cells from female 76d human embryo

source_name: lung cells from female 76d human embryo

value: lung cells from female 76d human embryo


title: CD56Bright Donor 2 H3K27ac

description: Ultra-low Input (100 k cells)


title: A13026_pDC_UNS_2

city: marseille

first: Thien-Phong

last: Vu Manh

address: 163 avenue de Luminy

country: France

institute: CIML

hyb_protocol: Following fragmentation and end-labeling, 2 μg of cDNAs were hybridized for 16 hours at 45°C on Affymetrix GeneChip Mouse Gene 1.0 ST arrays. The chips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: The data were RMA normalized in R and Bioconductor, using the oligo package.  The file processed_data_allsamples.txt includes the log2 RMA values for the new and re-analyzed samples and is available on the series record.

source_name: bone-marrow derived

label_protocol: 50 ng of total RNA from each sample was used to synthesize biotinylated probes, except for pDCs where less material was available (35ng and 8ng), using 2 successive rounds of cRNA amplification (using the NuGEN Ovation Pico WTA System V2 Kit and the NuGEN Encore Biotin Module Kit according to NuGEN recommendations) with appropriate quality control to ensure full length synthesis.

extract_protocol: Each cell type was purified by flow cytometry and total RNA was extracted with the Qiagen RNeasy Plus Micro Kit, according to the manufacturer protocol.

tag: phenotype

value: live, CD11c+SiglecH+

value: pDC

value: bone-marrow derived


title: ATACseqUW334femaleheart

description: heart cells from female 76d human embryo


title: A13026_CD8a_UNS_2

value: live, CD11c+SIRPα-CD24high


title: A13026_pDC_UNS_1


title: CARE072P

value: F


title: CD56Bright Donor 1 H3K27ac

description: Ultra-low Input (100 k cells)

value: H3K27ac (abcam 4729)


title: A13026_CD8a_UNS_3


title: CARE055P


title: A13026_CD8a_UNS_1


title: D19-3

city: Harbin

first: hao nan

last: YU

state: Heilongjiang

address: Xiangfang District Wood Street No. 59

department: Life Science and Biotechnology Research Center

institute: Northeast Agricultural University

library_source: transcriptomic

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
Mapsplice v2.2.0 mapping to reference genome
count counting
Genome_build: chi_ref_CHIR_1.0
Supplementary_files_format_and_content: all.counts.txt

organism: Capra hircus

source_name: Liaoning Cashmere Goats

extract_protocol:
total  RNA was extracted using Trizol reagent. Ion Total RNA-seq Kit v2 (Life Technologies, USA) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard protocols of Total RNA-seq Kit v2 (Life Technologies, USA). Briefly, poly(A)-containing mRNA was purified by Dynabeads (Life technologies, USA) and subsequently fractionated into short fragments using RNase III and an Ion adaptor. The short RNA fragments was ligated with a 3’ adaptor and a 5’ adaptor.  Emulsion PCR was performed using mRNA cDNA library as the template. Then, the short mRNA fragments were reverse-transcribed and amplified to synthetize double-stranded cDNA.

treatment_protocol: Testis were collected by surgical operation and immediately frozen in liquid nitrogen,

tag: time point

value: 19 day peri-implantation

value: uterus


title: CARE045P

value: PBMC

value: M


title: CARE044P


title: D19-2


title: ATACseqUW325malePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from female 59d human embryonic gonad


title: ATACseqUW334femaleliver

description: liver cells from female 76d human embryo


title: D19-1


title: ATACseqUW323femalePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from female 91d human embryonic gonad


title: A13026_CD11b_UNS_3

value: live, CD11c+SIRPα+CD24-/low


title: ATACseqUW312femalePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from female 101d human embryonic gonad


title: CARE021P


title: hpx-2-OG1RF rep3

city: Houston

first: Yi

address: 6431 Fannin Street

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center at Houston

data_processing:
Raw data were uploaded to WWW.usegalaxy.org
Sequenced reads were cleaned using FastQC and FASTQ Groomer on usegalaxy.org, then mapped C.elegans whole genome using Tophat
Transcripts were assembled using Cufflink
Differential gene expression were analyzed using Cuffdiff and Cuffcompare
Genome_build: wbcel235
Supplementary_files_format_and_content: tabular files include  list of differentially expressed genes (FPKMs)
Galaxy341-N2-OP50-OG1RF.tabular - genes changed in N2 worms when exposed to E.faecalis OG1RF strain compared to E.Coli OP50 strain
Galaxy352-P1-OP50-OG1RF.tabular - genes changed in hpx-2 mutant worms when exposed to E.faecalis OG1RF strain compared to E.Coli OP50 strain
Galaxy363-OP50-N2-P1.tabular - genes changed in hpx-2 mutant worms compare to N2 worms when exposed  E.Coli OP50 strain
Galaxy374-OG1RF-N2-P1.tabular - genes changed in hpx-2 mutant worms compare to N2 worms when exposed  E.faecalis OG1RF strain

organism: Caenorhabditis elegans

source_name: hpx-2 CRISPR mutant

growth_protocol: NG plates for worm maintance and propogation.

extract_protocol:
L4 animals were exposed for 16 hours to the condition of interest and total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions. RNA samples were treated with Turbo DNA free kit (Applied Biosystems) to eliminate DNA contamination
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: Young Adult stage

tag: genotype

value: hpx-2 CRISPR mutant

tag: exposed to

value: E.faecalis OG1RF strain


title: A13026_CD11b_UNS_1


title: hpx-2-OG1RF rep4


title: D16-3

value: 16 day peri-implantation


title: A13026_CD11b_UNS_2


title: CARE031P

tag: sample well

tag: plate id

tag: Sex


title: ATACseqUW308malePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from male 67d human embryonic gonad


title: CARE002P

tag: age at sample collection (years)

tag: sentrix id

tag: sentrix position


title: CARE019P


title: CARE004P


title: CARE091P_rep2


title: N2-OG1RF rep4

source_name: Wild-type

value: Wild-type


title: D16-2


title: D16-1


title: ATACseqUW302malePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from male 82d human embryonic gonad

tag: cell type


title: hpx-2-OG1RF rep2


title: hpx-2-OG1RF rep1


title: CD56Bright Donor 3 H3K27ac

description: Ultra-low Input (100 k cells)

value: CD56Bright natural killer cells

tag: individual

value: Donor 3

tag: antibody


title: ATACseqUW303femalePGC

description: primordial germ cells (PGC)

source_name: cKIT/TNAP-sorted hPGCs from female 89d human embryonic gonad

tag: passage number


title: D6-3

value: 6 day peri-implantation


title: N2-OG1RF rep3


title: ATACseqUCLA2PGCLCrep1

description: primordial germ cell-like cells (PGCLCs)

source_name: hPGCLCs induced from primed UCLA2 hESCs

growth_protocol: PGCLC media: 15% KSR, 1x NEAA, 0.1mM 2-Mercaptoethanol, 1x Penicillin-Streptomycin-Glutamine (Gibco, 10378-016), 1mM sodium pyruvate (Gibco, 11360-070), 10ng/mL human LIF (Millipore, LIF1005), 200ng/mL human BMP4 (R&D systems, 314-BP), 50ng/mL human EGF (R&D systems, 236-EG) 10µM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow's MEM (GMEM) (Gibco, 11710-035).

value: hPGCLCs induced from primed UCLA2 hESCs

value: Passage 17


title: D6-2


title: ATACseqUCLA1PGCLCrep2

source_name: hPGCLCs induced from primed UCLA1 hESCs

value: hPGCLCs induced from primed UCLA1 hESCs

value: Passage 19


title: N2-OG1RF rep2


title: D6-1


title: N2-OG1RF rep1


title: him-5 [miRNA-seq]

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

institute: University of Science and Technology of China

data_processing:
Sequencing reads were mapped to reference transcriptome by Bowtie2 (version 2.1.0)
Dupilcated reads were deplited by samtools rmdup
Genome_build: ce11

source_name: whole worms

growth_protocol: Worms were grown on NGM (Nematode Growth Medium) plates seeded with OP50 at 20 ℃

extract_protocol:
RNAs from either whole worms were isolated with Trizol reagent (Invitrogen, 15596026) according to manufacturer’s instructions, then treated with RNase-free DNase I (Promega, M6101) and extracted with ethanol precipitation
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: mix stage


title: hpx-2-OP50 rep4

value: E. coli OP50 strain


title: N2_starved_mixture [miRNA-seq]


title: ATACseqUCLA2iMeLCrep2

description: incipient mesoderm-like cells (iMeLCs)

source_name: iMeLCs induced from primed UCLA2 hESCs

growth_protocol: iMeLC media: 15% KSR, 1x NEAA, 0.1mM 2-Mercaptoethanol, 1x Penicillin-Streptomycin-Glutamine (Gibco, 10378-016), 1mM sodium pyruvate (Gibco, 11360-070), 50ng/mL Activin A (Peprotech, AF-120-14E), 3µM CHIR99021 (Stemgent, 04-0004), 10µM of ROCKi (Y27632, Stemgent, 04-0012-10), and 50ng/mL primocin in Glasgow's MEM (GMEM) (Gibco, 11710-035).

value: iMeLCs induced from primed UCLA2 hESCs

value: Passage 18


title: ATACseqUCLA1PGCLCrep1


title: CARE019B

tag: tissue

value: Buccal

value: M


title: CARE072B

value: F


title: hpx-2-OP50 rep3

value: Young Adult stage

value: hpx-2 CRISPR mutant


title: ATACseqUCLA2iMeLCrep1

description: incipient mesoderm-like cells (iMeLCs)


title: N2_dauer [miRNA-seq]

value: dauer stage


title: hpx-2-OP50 rep2


title: CARE048B_rep


title: N2_embryo [miRNA-seq]

value: embryo


title: CARE067B_rep


title: DIO-1d-DMSO-biological rep2

source_name: diet-induced obese mice

tag: disease state

value: DIO

tag: gender

value: male

tag: age

value: brain

tag: tissue region

value: hypothalamus

tag: treatment

value: treated with DMSO

tag: time

value: 1 day


title: ATACseqUCLA1iMeLCrep1

description: incipient mesoderm-like cells (iMeLCs)

source_name: iMeLCs induced from primed UCLA1 hESCs

value: iMeLCs induced from primed UCLA1 hESCs


title: him-5 [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt

data_processing:
Sequencing reads were mapped to reference transcriptome by Bowtie2 (version 2.1.0)
Dupilcated reads were deplited by samtools
Genome_build: ce11

tag: developmental stage

value: mix stage


title: ATACseqUCLA2hESCrep2

description: human embryonic stem cells (hESC)

source_name: primed UCLA2 hESCs

value: primed UCLA2 hESCs


title: N2-OP50 rep4

tag: genotype

value: Wild-type

tag: exposed to

value: E. coli OP50 strain


title: N2-OP50 rep3


title: CARE093B

value: Buccal

tag: sample well

tag: plate id

tag: Sex

value: M

tag: age at sample collection (years)

tag: sentrix id


title: hpx-2-OP50 rep1

value: Young Adult stage


title: ATACseqUCLA2hESCrep1

description: human embryonic stem cells (hESC)

tag: cell type

tag: passage number

value: Passage 17


title: N2_starved_mixture [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt

tag: strain


title: CARE067B

tag: tissue

value: F

tag: sentrix position


title: N2-OP50 rep2


title: ATACseqUCLA1hESCrep2

description: human embryonic stem cells (hESC)

source_name: primed UCLA1 hESCs

value: primed UCLA1 hESCs

value: Passage 19


title: N2-OP50 rep1


title: ATACseqUCLA1hESCrep1

description: human embryonic stem cells (hESC)

value: Passage 18


title: CARE048B


title: 7SK IVT untreated A

status: Public on Dec 26 2018

city: West Haven

first: Matthew

middle: D

last: Simon

state: CT

address: 600 West Campus Dr. MIC312

department: Molecular Biophysics & Biochemistry

institute: Yale University Chemical Biology Instiute

data_processing:
FASTQ sequencing reads were trimmed with Cutadapt to remove Illumina adaptor sequences, and aligned using Bowtie2 local alignment to respective RNA target sequences.
Reverse transcription stops and mutations were identified, screened, and tallied using the previously published RTEventsCounter software (Sexton et al. 2017). Reverse transcription stop and mutation probabilities were calculated as the number of stops or mutations divided by the total number of read-through events plus stops, or the total number of observations for the nucleotide (depth). Only values from more than 100 read-throughs are eventually considered.
Human 7sk sequence was eventually brought to alignment with mouse 7sk sequence to facilitate comparison of EDC values by shifting nt 163-245 to +1 (164-246), with the original nt 247 value removed. None of these changes were in the studied stem-loop section.
Genome_build: Alignment to Mus musculus 7sk NR_030687.1, Homo sapiens 7sk NR_001445.2, or respective section intervals of Mus musculus Xist NR_001463.3 (nt 4701-5001 or 4658-5090).
Supplementary_files_format_and_content: The total tally and probability of modification-induced stop or mutation is indicated for each nucleotide in respective target RNA sequences in each experiment. The nucleotide number (1-based) in the aligned target sequence (nt), averaged alignment score (avgQual), the nucleotide identity (ref), depth, read-through (RT), and number of insertions and deletions are also included. The calculated probability values for each individual nucleotide is preceded with “iP”

source_name: In vitro transcription

growth_protocol: MEF cells were cultured in DMEM with 10% FBS (Thermo Fisher) and penicillin/streptomycin to 90% confluency in 15 cm plates.

extract_protocol:
After treatment, cells were lifted using Cell Scraper (Corning) and collected in PBS by centrifugation (3 min, 1000 rpm, 4 °C), and the supernatant was discarded. The RNA was extracted using TRIzol (Thermo Fisher) according to manufacturer’s instructions. The extracted RNA was treated with RQ1 DNase (1 h, 37 °C; Promega), and subsequently purified with phenol/chloroform extraction and ethanol precipitation.
Reverse transcription was carried out using either 2 μg (7SK) or 10 μg (Xist) of extracted RNA, and 1 pmol total of primers. The RNA/primer mix was brought up to 12 μL and incubated at 70 °C for 5 min, then 4 °C for 2 min for primer annealing. Next, 3 μL of 5X FS buffer was added for a 10 min incubation at 55 °C. Finally, 5 μL of reverse transcription mix (1 μL 5X FS buffer, 1 μL 10 mM dNTPs, 1 μL 100 mM DTT, 0.2 μL RNase OUT, 0.5 μL SuperScript III, 1.3 μL dH2O) was added and mixed before incubation at 55 °C for 45 min, followed by heat inactivation at 85 °C for 5 min. After reverse transcription, RNA was degraded by adding 0.4 μL of 5 M NaOH and incubating at 95 °C for 3 min, before neutralization with 0.4 μL of 10 M acetic acid and cooling on ice. The cDNA from reverse transcription was purified with AMPure XP beads by adding and mixing 1 volume of bead solution and 3 volumes of PEG solution (2.5 M NaCl, 20% PEG 8000) at room temperature. The mixture was let to incubate at room temperature for 15 min, before immobilizing the beads on a magnetic rack for 10 min. The beads were washed with fresh 80% ethanol twice before being dried for 10 min and eluted in 16 μL of dH2O. 3' adaptor ligation was carried out using T4 RNA Ligase I, followed by two rounds of PCR amplification, with Illumina indexes added in the second round.

treatment_protocol: Cells were washed with PBS and then incubated with respective reagent solutions. For CMC and EDC treatment, cells were incubated with 10 mL of respective concentrations of reagents (CMC: 10 mM, 30 mM, 90 mM; EDC: 100 mM, 300 mM, 1500 mM) in borate reaction buffer for 30 min at 25 °C. For glyoxal treatment, cells were incubated with 10 mL of 50 mM glyoxal solution in reaction buffer (50 mM HEPES pH 8.0, 50 mM KCl, 0.5 mM MgCl2) for 15 min at 25 °C (Mitchell et al. 2018). For DMS treatment, cells were incubated with 0.5% DMS in PBS (5 min, 25 °C) before removing DMS solution and quenching with three washes of wash buffer (50 mM Tris pH 7.5, 100 mM NaCl, 3 mM MgCl2, 40 mM β-mercaptoethanol). No-treatment control plates were incubated with PBS.

tag: rt-primer set

value: 7SK primer set

tag: probing treatment

value: Untreated


title: CARE068B


title: 7SK IVT untreated B


title: 7SK IVT 100mM EDC B

value: 100mM EDC, 20 min


title: N2_embryo [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt

value: embryo


title: 7SK IVT 100mM EDC A


title: CARE044B


title: 7SK IVT 10mM CMC A

value: 10mM CMC, 20 min


title: 7SK IVT 10mM CMC B


title: Donor C M2 Total MBD-Seq

city: Baltimore

first: Elizabeth

last: Jaffee

state: MD

address: 1650 Orleans St

institute: Johns Hopkins University

description:
promoter_normCounts.csv
intragenic_normCounts.csv

data_processing:
Illumina's CASAVA 1.8.2 was used to convert BCL files to FASTQ files
rsem-1.2.29 was used to align the reads to hg19 reference genome.
samtools 0.1.19 (rmdup functionality) was used to remove duplicated alignments.
bedtools 2.24.0 (multicov function) was used to compute the per-base genome coverage.
Methylation peaks were identified using methylation peak Finder (methFinder) in promoter regions (+5kbp and -2kbp of TSS) using user-defined read depth threshold
Methylation peaks were compiled into a master list
bedtools 2.24.0 (multicov function) was used to compute the coverage of each methylation site for all samples.
DESeq2 was used for differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: csv files containing normalized counts for each sample

source_name: PBMCs

extract_protocol:
DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen).
Sonicated genomic DNA (target modal size 200-500 bp) was enriched for methylated DNA using the EpiMark Methylated DNA Enrichment Kit (New England Biolabs) according to manufacturer’s protocol. A matched unenriched total input fraction was also analyzed for each sample. The enriched methylated and total input fractions were then subjected to NGS library preparation using the Thruplex library preparation kit (Rubicon).

tag: individual

value: Donor C

value: M2-polarized macrophages


title: Donor D M2 Total MBD-Seq

value: Donor D


title: Donor D M1 Total MBD-Seq

value: M1-polarized macrophages


title: CARE021B

value: Buccal


title: Donor B M2 Total MBD-Seq

value: Donor B


title: Donor C M1 Total MBD-Seq


title: CARE045B

value: M


title: CARE088B


title: N2_dauer [lncRNA-seq]

description:
lncRNA
lncRNA_RPKM.txt

value: dauer stage


title: CARE031B


title: Donor B M1 Total MBD-Seq


title: CARE071B

value: F


title: Donor D M2 Enriched MBD-Seq


title: Donor C M1 Enriched MBD-Seq


title: Donor C M2 Enriched MBD-Seq


title: Donor B M2 Enriched MBD-Seq


title: Donor B M1 Enriched MBD-Seq


title: Donor A M2 Total MBD-Seq

value: Donor A


title: Donor D M1 Enriched MBD-Seq


title: CARE004B


title: Donor D M2 RNA-Seq

description:
normCounts.csv
D_M2_count

data_processing:
Illumina's CASAVA 1.8.2 was used to convert BCL files to FASTQ files
rsem-1.2.29 was used to align the reads to hg19 reference genome and to generate gene expression levels.
rsem count output was used as input for DESeq2 differential gene expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: csv file containing normalized counts for each sample

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) and genomic DNA was digested with TURBO DNase (Ambion).
Libraries were prepared using the TrueSeq Stranded Total RNA kit (Illumina).


title: Donor D M1 RNA-Seq

description:
normCounts.csv
D_M1_count


title: Donor A M1 Enriched MBD-Seq


title: Donor C M1 RNA-Seq

description:
normCounts.csv
C_M1_count


title: Donor C M2 RNA-Seq

description:
normCounts.csv
C_M2_count


title: Donor B M1 RNA-Seq

description:
normCounts.csv
B_M1_count


title: Donor B M2 RNA-Seq

description:
normCounts.csv
B_M2_count


title: CARE002B


title: CARE097B


title: Donor A M2 RNA-Seq

description:
normCounts.csv
A_M2_count


title: ATACseqUCLA1iMeLCrep2

description: incipient mesoderm-like cells (iMeLCs)

value: iMeLCs induced from primed UCLA1 hESCs

value: Passage 19


title: Donor A M1 Total MBD-Seq


title: CARE091B


title: CARE055B


title: T47D-TRPS1siRNA-rep1_1

city: Nanjing

first: liming

last: chen

state: Jiangsu

address: Qixiaqu wenyuanlu 1hao

department: college of life science

institute: Nanjing Normal University

data_processing:
Basecalls performed using CASAVA 1.8
All reads were trimmed of adapters and sequencing quality lower than 20
The ChIPseq reads were aligned to hg38 with bwa 0.7.12-r1039
The RNAseq reads were aligned to hg38 with STAR1.5.2
The aligned ChIPseq replicates were converted to bam and merged as one bam file and peaks were called with Macs2 2.1.1
The RNAseq aligned reads were counted for each gene with htseq 0.9.0
Genome_build: hg38
Supplementary_files_format_and_content: bed format for the ChIPseq peaks file
Supplementary_files_format_and_content: tab-deliminated txt file for the abundance measureament of RNAseq

growth_protocol: T47D cell were cultured in Roswell Park Memorial Institute medium-1640 (RPMI-1640) (Life Technologies) supplemented with 10% FBS and 1% penicillin-streptomycin solution (Life Technologies), with 10 cm dish (typically 1-2 × 107cells) .

extract_protocol:
For the chip-seq: Libraries were prepared according to Illumina's instructions. Briefly, cells were crosslinked with 1% paraformaldehyde for 10 min at room temperature, quenched with glycine, and fixed chromatin was sonicated and immunoprecipitated with specific antibodies.RNA –seq: The total RNA was extracted with the RNeasy kit (Promega).
For the chip-seq:Libraries were prepared with Illumina’s ChIP-Seq sample prep kit for next-generation sequencing.For the RNA –seq:  Followed by library preparation and next-generation sequencing.

treatment_protocol: siRNAs against TRPS1, CHD4 and control siRNA(GenePharma) were transfected into T47D cells for 72h using Lipofectamine RNAiMAX reagent(Invitrogen) .

tag: cell line

tag: sirna

value: TRPS1 knock down


title: T47D-TRPS1siRNA-rep2_1


title: CARE038B


title: T47D-controlsiRNA-rep2_1

description: T47D_control-TRPS1_htcount.txt, T47D_control-CHD4_htcount.txt

value: control


title: T47D-TRPS1-rep2

tag: antibody

value: TRPS1 ChIP antibody


title: T47D-input-rep2


title: T47D-controlsiRNA-rep1_1


title: T47D-CHD4siRNA-rep1_1

value: CHD4 knock down


title: T47D-CHD4siRNA-rep2_1


title: T47D-TRPS1-rep1


title: T47D-input-rep1


title: si-ctrl_PARN

city: Kansas City

first: Peter

last: Baumann

state: MO

institute: Stowers Institute for Medical Research

description: RNAi knockdown

data_processing:
The library samples si-ctrl PARN, si-PARN, si-ctrl RRP40 and si-RRP40 were sequenced on the Illumina HiSeq using RapidSeq-250bp single-end reads. The library samples si-ctrl RRP6 DIS3 and si-RRP6 were sequenced on the Illumina HiSeq using RapidSeq-250bp paired-end reads, however only the forward reads were used for analysis. The samples were quantified by Qubit and Bioanalyzer and mixed equally . The samples were multiplexed and split between two lanes.
Raw reads were filtered for the presence of the hTR gene-specific primer sequence allowing up to 2 mismatches and 3’ RACE adapter sequence. There were 0.7 to 1.0 million reads per sample after filtering.
Reads were binned and counted based on their hTR sequence. The counts were normalized to library size.
Supplementary_files_format_and_content: Percentages of hTR forms per sample.

source_name: HeLa

growth_protocol: HeLa cells were cultured in Dulbecco’s modified eagle medium (Life  Technologies 11995-065) containing 10% fetal bovine serum (Sigma) at 37°C, 5% CO2. Technologies 11995-065) containing 10% fetal bovine serum (Sigma) at 37°C, 5% CO2.

extract_protocol:
Cells were washed once with Dulbecco’s phosphate-buffered saline and  collected in Trizol reagent (Ambion, Life Technologies) according to manufacturer’s  instructions, followed by treatment with DNase I (New England Biolabs) at 37°C for 30  min. RNA was extracted with phenol/chloroform equilibrated with 50 mM NaOAc (pH  5.0) and ethanol precipitated.
Library preparation was modified from the protocol  published by Goldfard  and Cech (Goldfarb and Cech 2013). The samples were sequenced on a Illumina HiSeq using RapidSeq-250bp reads.

treatment_protocol: HeLa cells were treated with 40 nM siRNA against PARN for 72 hours using Dharmafect I (Dharmacon). In the case of RRP6 and RRP40, HeLa cells were treated with 20 nM siRNA against RRP6 or RRP40 for 48 hours twice.

tag: treatment

value: si-ctrl PARN


title: si-RRP6

description: RNAi knockdown


title: si-RRP40

description: RNAi knockdown


title: BD46

city: new york

first: Brahma

last: Kumar

state: New York

address: 50 haven ave

institute: Columbia University

data_processing:
RNA-Seq reads were aligned to hg19 with Tophat with default parameters
HTSeq was used to obtain gene read counts.
DESeq2 was used to normalize the read counts for library size difference correction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts and DESeq2-normalized counts for each sample

source_name: Spleen

growth_protocol: Human tissues were obtained from deceased organ donors at the time of organ acquisition for clinical transplantation through an approved research protocol and MTA with LiveOnNY, the organ procurement organization for the New York metropolitan area. All donors were free of chronic disease and cancer, were Hepatitis B, C, and HIV-negative. Tissues were collected after the donor organs were flushed with cold preservation solution and clinical procurement process was completed. Isolation of tissues from organ donors does not qualify as “human subjects” research, as confirmed by the Columbia University IRB as tissue samples were obtained from brain-dead (deceased) individuals. Demographic and clinical data were extracted from summaries prepared by LiveOnNY. For isolation of blood from living volunteers, blood was drawn via venipuncture from consented volunteers, as approved by the Columbia University IRB. A list of donors and individuals from whom samples were obtained for this study is presented in Table S4.

extract_protocol:
Lyphocyte suspensions were enriched for T cells using the Mojosort Human CD3 T cell isolation kit (biolegend), followed by which fluorescence activated cell sorting was performed using a BD Influx high-speed sorter or a BD Aria IIu sorter to isolate populations of interest. RNA was isolated from cell pellets using the RNeasy Mini Kit (Qiagen), and RNA concentration and quality was assessed using an Agilent 2100 Bioanalyzer instrument (Agilent Technologies).
standard Truseq with poly-A pulldown

treatment_protocol: Tissue samples were maintained in cold saline and brought to the laboratory within 2-4hrs of organ procurement. Spleen, lung, and intestinal samples were processed using enzymatic and mechanical digestion resulting in high yields of live leukocytes, as described previously (Sathaliyawala et al., 2013; Thome et al., 2014). Lymphocytes were isolated from blood samples using centrifugation through lymphocyte separation medium (Corning) for recover of mononuclear cells.

value: Spleen

value: Spleen CD8+ CD45RA- CCR7- CD69+ T cells

tag: efflux status

value: Efflux(-)

value: Stimulated (anti CD3/28/2 beads for 12 hours)


title: si-ctrl_RRP6_DIS3

description: RNAi knockdown

value: si-ctrl RRP6 DIS3


title: si-ctrl_RRP40

description: RNAi knockdown

value: si-ctrl RRP40


title: si-PARN

description: RNAi knockdown

value: si-PARN


title: BD42


title: Donor A M1 RNA-Seq

description:
normCounts.csv
A_M1_count

value: M1-polarized macrophages


title: BD45

value: Efflux(+)


title: BD44

value: Unstimulated


title: BD37


title: BD36


title: BD43


title: Donor A M2 Enriched MBD-Seq

value: Donor A

value: M2-polarized macrophages


title: BD35


title: BD32


title: BD31


title: BD41


title: BD38


title: hADSC05 P(11)

city: Madrid

first: Fatima

last: Sanchez-Cabo

address: Melchor Fernandez Almagro

country: Spain

institute: CNIC

description: Expression of miRNAs from hADSC cell culture

hyb_protocol: 100 ng of Cy3 labelled RNA were hybridized for 20 hours at 55¼C in a hybridization oven  (G2545A, Agilent) set to 15 rpm in a final concentration of 1X GE Blocking Agent and 1X Hi-RPM Hybridization Buffer, according to manufacturer's instructions (miRNA Microarray System Protocol, Agilent Technologies)

scan_protocol: Arrays were scanned at 5μm resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for miRNA Microarray v1.0 (miRNA Microarray System Protocol, Agilent Technologies).

data_processing:
Images provided by the scanner were analyzed using Agilent´s software Feature Extraction version 9.5.3.1.
Processed Cy3 signal intensity data was normalized based on the VSN-invariant method (Huber 2002, Pradervand 2009)

source_name: hADSC (adult)

label_protocol: miRNA Microarray System Protocol (Agilent Technologies) was used to label RNA; 100 ng of total RNA were dephosphorylated and Cyanine 3-pCp molecule was ligated to the 3« end of each RNA molecule by using T4 RNA ligase.

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 2 mM glutamine, penicillin (100 U/ml)/streptomycin (1000 U/ml) (37ºC, 5% CO2); 3% Oxygen

extract_protocol: mirVana miRNA Isolation Kit (Applied Biosystems)

treatment_protocol: No specific treatment; compared samples were cultured for long and short passages.

tag: condition

value: Adult

tag: passage

value: Short


title: hADSC17 P(10)

source_name: hADSC (pediatric)

value: Pediatric


title: hADSC05 P(25)

value: Long


title: hADSC06 P(25)


title: hADSC16 P(30)


title: hADSC06 P(10)


title: hADSC32 P(6)


title: hADSC16 P(5)


title: Primate fetal hepatic response to maternal obesity [5304687013_D]

city: San Antonio

first: Sobha

last: Puppala

state: TX

department: Genetics

institute: Texas Biomedical Research Institute

description: Sample name: 5304687013_D

hyb_protocol: Standard Illumina hybridization protocol.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Gene expression data were processed and analyzed using GenomeStudio (Illumina) and GeneSifter (PerkinElmer). Gene array data were median normalized and log2 transformed (GeneSifter). Cluster analysis of gene expression was done using hierarchical clustering by adjusting expression values to a mean of zero and scale to standard deviation of one in Partek® Genomics Suite®. Supplementary Table 1 contains differentially expressed genes between MO and CON fetal livers at 0.9G.

label: Biotin

organism: Papio hamadryas

source_name: Baboon fetal liver, control

label_protocol: Complementary RNA (cRNA) was synthesized from total RNA using the Illumina Total Prep 96 RNA Amplification Kit.

extract_protocol: Total RNA was isolated from fetal livers using TRI Reagent (Ambion, USA) according to the manufacturer's instructions, followed by clean-up with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. RNA integrity and concentration were determined by an Agilent 2100 Bioanalyzer and UV-Vis Spectrophotometer (NanoDrop 2000).

value: control

tag: gender

value: male

tag: age

value: 165 days or 0.9 gestation

value: fetal liver


title: Primate fetal hepatic response to maternal obesity [5304687013_J]

description: Sample name: 5304687013_J

source_name: Baboon fetal liver, maternal obese

value: maternal obese

value: female


title: Primate fetal hepatic response to maternal obesity [5304687013_H]

description: Sample name: 5304687013_H


title: Primate fetal hepatic response to maternal obesity [5304687008_I]

description: Sample name: 5304687008_I


title: Primate fetal hepatic response to maternal obesity [5304687008_G]

description: Sample name: 5304687008_G


title: Primate fetal hepatic response to maternal obesity [5304687013_B]

description: Sample name: 5304687013_B


title: TXNDC9-KO rep2

city: Jiangyin

first: Dawei

last: Chen

address: No. 163, Shoushan Road

department: Jiangyin People's Hospital

institute: School of Medicine, Southeast University

data_processing:
Reads were mapping to human genome (hg38) using TopHat2 with a reference annotation from ensemble database. no-novel-juncs options were used to ignore de novo gene and transcript identification.
Gene expression profile of each samples as well as differentially expressed genes between wild-type and TXNDC9 knockout HepG2 cells were identified using the cuffdiff suite from cufflinks.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

growth_protocol: HepG2 cells were cultured in DMEM supplemented with 10%  FBS.

extract_protocol:
RNA was extracted from wild-type or TXNDC9 knockout HepG2 cells using TRIzol Reagent (ThermoFisher Scientific, USA) according to manufacturer’s protocol.  Sequencing were performed at the illumina Hiseq Xten platform.
Polyadenylated RNA was isolated from 5 g total RNA with the mRNA Capture Beads. RNA-seq library were constructed with VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (Vazyme Biotech Co, Nanjing, China) according to manufacturer’s protocol.

treatment_protocol: The CRISPR-Cas9 system were used for TXNDC9 knockout.

tag: genotype/variation

value: TXNDC9 knockout


title: Primate fetal hepatic response to maternal obesity [5304687013_F]

description: Sample name: 5304687013_F


title: Primate fetal hepatic response to maternal obesity [5304687013_L]

description: Sample name: 5304687013_L


title: Primate fetal hepatic response to maternal obesity [5304687008_E]

description: Sample name: 5304687008_E


title: Primate fetal hepatic response to maternal obesity [5304687013_A]

description: Sample name: 5304687013_A


title: Primate fetal hepatic response to maternal obesity [5304687008_K]

description: Sample name: 5304687008_K


title: WT rep2

value: Wild type


title: WT rep1


title: TXNDC9-KO rep1


title: Wildtype, beginning of day_2

city: Düsseldorf

first: Andreas

middle: PM

last: Weber

address: Universitätsstr. 1

department: Institute for Plant Biochemistry

country: Germany

institute: Heinrich-Heine-University

data_processing:
Illumina Casava-1.9software used for basecalling.
The software kallisto (v 0.43.0) was used for quantification with the Arabidopsis thaliana genome as a reference (TAIR10 cDNA). The resulting normalized counts (transcripts per million, tpm) were used for downstream analyses.
Kallisto was run with 30 bootstrapping replications. The resulting .h5 files were fed forward into differential gene expression analysis using sleuth (v 0.28.1).
Means and standard deviation of tpm of biological triplicates group were calculated.
Supplementary_files_format_and_content: Comma-separated table (.csv) file including Arabidopsis Gene Identifier (AGI) and TAIR10 description, raw estimated counts (kallisto), tpm (kallisto) for each sample and mean and standard deviation of tpm for biological triplicates, sleuth results of differential gene expression comparing each of the mutant lines against the wildtype at the respective time of sampling

organism: Arabidopsis thaliana

source_name: Leaf

extract_protocol:
Mature leaves were harvested and immediately frozen in liquid nitrogen. RNA was isolated from ground tissue using the Qiagen RNeasy plant mini kit. Residues of DNA were removed with DNase (New England Biolabs). RNA integrity, sequencing library and fragment size were analyzed on a 2100 Bioanalyzer (Agilent). Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina), and quantified with a Qubit 2.0 (Invitrogen).
Libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina). Samples were multiplexed with 12 libraries per lane and sequenced in paired-end mode (150 bp read length) on an Illumina HiSeq 3000 platform.

tag: genotype

value: Wildtype

tag: time of sampling

value: beginning of day


title: Wildtype, beginning of day_1


title: MCF-10A + pNG vector control rep3

first: Joan

middle: S.

last: Brugge

address: 240 Longwood Avenue

department: Department of Cell Biology

institute: Harvard Medical School

hyb_protocol: Following fragmentation, cRNAs were hybridized to the Affymetrix GeneChip Human Genome U133 Plus 2.0 Array.  GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneArray Chip Scanner, HP/Affymetrix Inc.

data_processing: Background correction and normalization was performed using the Robust Multichip Average method implemented in the rma function of R/BioConductor. Differential expression was assessed using the empirical Bayes method implemented in the limma package. The criteria for selecting differentially expressed genes was a false discovery rate (FDR)-corrected p-value of less than 0.05 and a fold change greater than 1.5.

source_name: MCF-10A human mammary epithelial cell line

label_protocol: Biotinylated cRNAs were prepared according to the Affymetrix standard labeling protocol.

extract_protocol: Total RNA was isolated according to manufacturer’s protocol with TRIzol-reagent (Invitrogen).

treatment_protocol: MCF-10A cells were retrovirally infected with Crb3 or vector control and puromycin selected.

value: vector control

tag: culture condition

value: Cells were cultured in normal MCF-10 growth media. RNA was harvested from proliferating monolayers at 70% confluence.


title: SP-2509 Drug resistant 6 months post washout R3

first: Cenny

last: Taslim

address: 700 Children's Drive

institute: Nationwide Children's Hospital

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to GRCh38.p9 whole genome using STAR-2.5.2b
Features were identified from the GFF file that came with the assembly from NCBI
Feature coverage counts were calculated using HTSeq
Differentially expressed features were calculated using DESeq2
Genome_build: GRCh38.p9
Supplementary_files_format_and_content: AllData_180202_RNAseq_Lessnick_Pishas_S_Results.xlsx contains the results from differential expression analysis

source_name: A673 cells (Ewing)

growth_protocol: A673 Ewing sarcoma cells were grown as described previously (Lessnick et al., 2002)

extract_protocol:
Cells were trypsinized, washed with PBS, pelleted, and flash-frozen. RNA was extracted using an RNeasy kit with on-column DNA digestion per kit instructions (Qiagen). 2.5 ug of total RNA was used for library prep.
Illumina ScriptSeq

treatment_protocol: Following generation of A673 SP-2509 drug resistant cells (chronic exposure for 7 months), drug was withdrawn with cell pellets collected 4 and 6 months after removal.

tag: sample type


title: Wildtype, end of night_2

value: end of night


title: SP-2509 Drug resistant 6 months post washout R1


title: Wildtype, end of night_1


title: tumor sample, 300 mg/kg_2

city: Tokyo

first: Hiroyuki

last: Seimiya

address: 3-8-31 Ariake, Koto-ku

department: Cancer Chemotherapy Center

country: Japan

institute: JFCR

description: Gene expression data from tumor sample after RK-287107 administration

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner GCS3000.

data_processing: The data were analyzed with GeneSpring GX12 using global scaling as normalization method.

source_name: Tumor sample from the xenograft mouse with 300 mg/kg of RK-287107 administration

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA using GeneChip 3' IVT PLUS Reagent Kit (Affymetrix).

growth_protocol: COLO-320DM cells were injected subcutaneously to NOD-SCID mice before administration.

extract_protocol: Tumor samples were collected in Allprotect Tissue Reagent (Qiagen) after 4 hours from the final administration. Samples were homogenized in a TissueLyser shaker (Qiagen) in RLT with b-mercaptoethanol with a ceramic bead. Total RNA extraction from tumor samples was performed using Rneasy Mini Kit (Qiagen) according to the manufacture's instructions.

treatment_protocol: RK-287107, a novel tankyrase inhibitor, was administered 5-days on/ 2-days off schedule to 2 weeks at dose of 300 mg/kg daily.

tag: tissue

value: Tumor, xenografted COLO-320DM cells

value: tankyrase inhibitor RK-287107


title: MCF-10A + pNG vector control rep2

city: Boston

growth_protocol: Cells were cultured in normal MCF-10 growth media.


title: MCF-10A + Crb3 rep2

value: retroviral overexpression of Crb3


title: tumor sample, 300 mg/kg_1


title: tumor sample, vehicle_2

description: Gene expression data from tumor sample after vehicle administration

source_name: Tumor sample from the xenograft mouse with vehicle administration

value: vehicle


title: MCF-10A + Crb3 rep1


title: SP-2509 Drug resistant 4 months post washout R1


title: MCF-10A + Crb3 rep3


title: MCF-10A + pNG vector control rep1


title: tumor sample, vehicle_1


title: Wildtype, end of night_3


title: A673 Parental DMSO R6 (dataset 2)

value: Parental A673


title: Wildtype, beginning of day_3


title: A673 SP-2509 Drug resistant DMSO R3

data_processing:
Illumina’s Bcl2fastq conversion software
Sequenced reads were mapped to GRCh38.p9 whole genome using STAR-2.5.2b
Features were identified from GFF that came with the assembly from NCBI
Feature coverage counts were calculated using HTSeq
Differentially expressed features were calculated using DESeq2
Genome_build: GRCh38.p9
Supplementary_files_format_and_content: AllData_170425_RNASeq_ScriptSeq_Lessnick_Results.xlsx contains results from differential expression analysis

source_name: A673 cells

treatment_protocol: A673 parental and SP-2509 Drug resistant cells were treated with DMSO and SP-2509 (2uM 48hrs)

value: DMSO


title: A673 SP-2509 Drug resistant SP-2509 R1


title: A673 SP-2509 Drug resistant DMSO R1


title: A673 SP-2509 Drug resistant SP-2509 R3


title: SP-2509 Drug resistant 6 months post washout R2


title: A673 Parental DMSO R1 (dataset 2)


title: A673 Parental SP-2509 R3


title: A673 SP-2509 Drug resistant DMSO R2


title: SP-2509 Drug resistant 4 months post washout R2


title: A673 SP-2509 Drug resistant SP-2509 R2


title: SP-2509 Drug resistant 4 months post washout R3


title: A673 Parental SP-2509 R2


title: A673 Parental SP-2509 R1


title: A673 Parental DMSO R6


title: A673 Parental DMSO R2


title: hBM_MSC_HOP_g10_AOC_D2

city: Oxford

first: Alison

middle: T

last: Merryweather-Clarke

address: Headington

country: United Kingdom

institute: University of Oxford

data_processing:
basecalling was performed with bclToFastq (Illumina) version 1.8.4
QC analysis with the fastQC package (http://www.bioinformatics. babraham. ac.uk/projects/fastqc)
reads were aligned using STAR
Non-uniquely mapped reads were discarded using SAMtools
Gene expression levels were quantified as read counts using the featureCounts function [63] from the Subread package [64] with default parameters.
The read counts were used for the identification of global differential gene expression between specified populations using the edgeR package
RPKM (reads per kilobase of transcript per million mapped reads) values were also generated using the edgeR package.
Genes were considered differentially expressed between populations if they had an adjusted p-value (FDR; false discovery rate) of less than 0.05 (high stringency) or 0.1 (relaxed stringency).
Genome_build: NCBI build37 (hg19) UCSC transcripts
Supplementary_files_format_and_content: RPKM

growth_protocol: Fresh human bone marrow aspirates (30 mls) from the iliac crest of healthy adult donors less than 40 years of age were purchased from Lonza, Slough, England. To avoid the loss of hBM MSCs on density (<1.077g/ml) gradients [25-27], red blood cells were lysed by adding 3 parts red cell lysis buffer (150mM ammonium chloride, 10mM potassium bicarbonate, 0.1mM EDTA) to 1 part bone marrow aspirate for 10 minutes at room temperature with gentle agitation. Samples were washed twice by centrifugation at 350g for 10 minutes in PBS (Lonza) prior to resuspension in mesenchymal stem cell growth media (MSCGM; Lonza). The cells were then passed through a 70µm cell strainer, counted using trypan blue to exclude dead cells and seeded directly onto tissue culture plastic flasks for expansion. Seeding densities varied depending on the assay. For standard bulk cell expansion, red blood cell depleted bone marrow cells were seeded at approximately 5x105/cm2 in MSCGM (Lonza) in tissue culture grade plastic dishes or flasks, the cells allowed to adhere for 48 hours before full replacement of the MSCGM (Lonza). The hBM MSCs were cultured in MSCGM (Lonza) with media changes every 3-4 days and passaged with trypsin/EDTA when approximately 90% confluent.

extract_protocol:
The hBM MSC clonal cultures cryopreserved at P1 were thawed and diluted in warm MSCGM (Lonza) before centrifugation at 300g and resuspended in FACS buffer. DAPI was added as a viability stain before flow cytometric sorting. One hundred single live cells (DAPI positive cells excluded) for each clonal culture being analysed were sorted into PCR tubes containing lysis buffer, oligo-dT primer and dNTP mix for generation of Smart-Seq2 cDNA libraries.
Smart-Seq2 cDNA libraries were then generated as described in Picelli S, OR Faridani, AK Bjorklund, G Winberg, S Sagasser and R Sandberg. (2014). Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9: 171-181

treatment_protocol: Bone marrow cells were seeded as a single cell suspension into 10cm diameter tissue culture plastic dishes at 1.25x104, 2.5x104 and 5x104 cells/cm2 in MSCGM (Lonza). The cells were cultured as described above for approximately 2 weeks, until large colonies formed. At this stage single colonies were picked using cloning cylinders, and the cells from these individual colonies transferred to individual wells of 12 well plates for further expansion. At 90% confluency the clonal cultures were passaged into T25 flasks. When the cultures reached 90% confluency (termed passage (P) 1), they were cryopreserved ready for hBM MSC cDNA library generation.

tag: donor id

tag: vascular support

value: Good

tag: cell type

value: bone marrow-derived mesenchymal stem/stromal cells (hBM MSCs)

tag: osteogenic potential

tag: chondrogenic potential

tag: adipogenic potential


title: hBM_MSC_LOP_p10_AOC_D2

value: Poor


title: hBM_MSC_LOP_g9_AOC_D2


title: hBM_MSC_LOP_p8_OC_D2


title: hBM_MSC_HOP_p4_OC_D2


title: hBM_MSC_HOP_g3_OC_D2


title: hBM_MSC_LOP_p3_OC_D2


title: hBM_MSC_LOP_p9_OC_D2


title: hBM_MSC_HOP_p2_AOC_D1


title: hBM_MSC_HOP_g1_O_D1


title: hBM_MSC_HOP_p1_AOC_D1


title: hBM_MSC_LOP_g6_OC_D1


title: hBM_MSC_LOP_p6_AOC_D1


title: hBM_MSC_LOP_g7_AOC_D1


title: Terminal_Bx_C1-3

first: Manoj

last: Bhasin

address: 99 Brookline Ave

institute: BIDMC

description: Abi/Enza Resistant_Bx

data_processing:
fastq
fastqc for quality control checks on fastq files.
trimmomatic and cutadapt used for trimming the adapters and poor quality reads.
Tophat2 alignment with hg19.
htseq-count for counting the reads.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.count.txt: Tab-delimited count files.

source_name: VCaP xenograft

growth_protocol: VCaP xenografts were grown up in intact male ICR SCID mice until tumors reached 500mm3. Tumors were biopsied, followed by castration of mice. When tumors relapsed following castration, tumors were biopsied again, then mice were placed on dual abiraterone plus enzalutamide therapy. When tumors relapsed on Abi/Enza therapy, they were harvested.

extract_protocol: Tumor biopsies were fixed in 10% formalin for 24hrs, then embedded in paraffin. For each tumor, five ribbons (10 microns in thickness) were cut into a microcentrifuge tube, then total RNA was extracted with the Qiagen RNeasy FFPE Kit.

treatment_protocol: Tumors were treated with sequential androgen deprivation, first by surgical castration, then upon tumor relapse by daily treatment with abiraterone and enzalutamide.

tag: tumor

value: VCaP xenograft

value: Abi/Enza resistant


title: hBM_MSC_HOP_g5_OC_D1


title: Terminal_Bx_C3-1

description: Abi/Enza Resistant_Bx

tag: condition


title: Pre_Bx_C1-4

value: Androgen sensitivity (Pre-Cx)


title: Post_Bx_C1-3

value: Castration resistance (CRPC)


title: Terminal_Bx_C2-17

description: Abi/Enza Resistant_Bx


title: A673 Parental DMSO R1

city: Columbus

tag: treatment


title: Post_Bx_C3-1


title: Pre_Bx_C3-1


title: hBM_MSC_LOP_p5_C_D1


title: Terminal_Bx_C1-4

description: Abi/Enza Resistant_Bx


title: D-458 Med -miR-NC

first: Yidong

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were normalised using quantile normalization with Illumina GenomeStudio version 1.9.0

source_name: scramble

label_protocol: Standard Ilumina BeadChip labeling protocol

extract_protocol: miRNeasy Mini kit (Qiagen), following manufacturer's protocol

treatment_protocol: Cells were transfected with either miR-NC or miR-584-5p using Lipofectamine® RNAiMAX reagent for 48 hours before harvesting and RNA extraction.

tag: cell line

value: Medulloblastoma cell line, D-458


title: Wheat root under Sp. NK, biological rep3

city: Hangzhou

first: Li

last: Ruan

address: Meiling South Road No. 9

institute: Tea Research Institute, Chinese Academy of Agricultural Science

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Wheat Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US).

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

organism: Triticum aestivum

source_name: Wheat root

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol:
3-week-old seedlings, which were first planted in normal K solutions, were transplanted to the above split-root system for 5 d
the day and night time were 16 h and 8 h, respectively; the day and night temperature were 25 ℃ and 18 ℃, respectively; the illumination intensity was 30000 lux in the day; the atmospheric humidity was 70%.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: (1) a homogeneous K-deprived condition (C. LK: both compartments had 0.005 mmol L-1 K2SO4), (2) a homogeneous K-replete condition (C. NK: both compartments had 1.0 mmol L-1 K2SO4), and (3) a heterogeneous split condition (Sp. LK/Sp. NK: one compartment had 0.005 mmol L-1 K2SO4, and the other had 1.0 mmol L-1 K2SO4).

value: root

tag: age

value: Sp NK (another compartment had normal K)


title: hmt1[delta], biological replicate 1

city: Sydney

first: Chi Nam Ignatius

last: Pang

state: NSW

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

country: Australia

institute: The University of New South Wales

hyb_protocol: Microarray analysis was performed in the Ramaciotti Centre for Genomics (University of New South Wales) using the Affymetrix GeneChip® Yeast Genome 2.0 Array.

data_processing: Microarray data was analysed using R/Bioconductor, the ‘.CEL’ data files imported using the affy package (1.52.0). Scripts from Gillespie et al. (2010,  BMC research notes 3: 81) was used to mask the S. pombe probes and to extract the data for the S. cerevisiae probes. The expression data was then normalized using the Robust Multi-array Average (RMA) function from the affy package. The quality of the normalized data were assessed using arrayQualityMetrics (v3.30.0).

organism: Saccharomyces cerevisiae

source_name: HMT1 knockout mutant

growth_protocol: Cells were maintained and selection performed according to previous methods described in Zhang L, Hamey JJ, Hart-Smith G, Erce MA, Wilkins MR (2014) Elongation factor methyltransferase 3--a novel eukaryotic lysine methyltransferase. Biochemical and Biophysical Research Communications 451: 229-34. Strains were grown in YEPD (2% D-glucose, 2 % bacteriological peptone, 1 % yeast extract), phosphate replete (MM-KH2PO4; 0.5% KH2PO4, 15 mM D-glucose, 10 mM MgSO4.7H2O, 13 mM glycine, 3 µM thiamine) or phosphate depleted (MM-KCl; 0.5% KCl, 15 mM D-glucose, 10 mM MgSO4.7H2O, 13 mM glycine, 3 µM thiamine) media as specified.

extract_protocol: Total RNA was extracted from four wild-type and three hmt1∆ biological replicates using the Qiagen RNeasy isolation kit following mechanical disruption with 0.5 mm glass beads.

treatment_protocol: Saccharomyces cerevisiae BY4741 haploid strain (Open Biosystems; MATa his3∆1 leu2∆0 met15∆0 ura3∆0) was used as the wild-type in all experiments in this study unless otherwise specified. HMT1-null yeast (Open Biosystems; hmt1∆:: KANMX4 in BY4741) was used for studies related to deletion of arginine methyltransferase Hmt1p unless otherwise specified.

tag: genotype/variation


title: hmt1[delta], biological replicate 2

scan_protocol: Microarray analysis was performed in the Ramaciotti Centre for Genomics (University of New South Wales) using the Affymetrix GeneChip® Yeast Genome 2.0 Array.


title: hmt1[delta], biological replicate 3

label_protocol: Microarray analysis was performed in the Ramaciotti Centre for Genomics (University of New South Wales) using the Affymetrix GeneChip® Yeast Genome 2.0 Array.


title: Wheat root under C. NK, biological rep1

tag: genotype

value: C NK (both compartments had normal K)


title: wild-type, biological replicate 1

source_name: Wild-type S. cerevisiae

value: wild type


title: D-458 Med -miR-584-5p

source_name: miR-584-5p mimic


title: D-425 Med -miR-584-5p

value: Medulloblastoma cell line, D-425


title: D-425 Med -miR-NC


title: wild-type, biological replicate 3


title: wild-type, biological replicate 4


title: Wheat root under C. NK, biological rep2


title: Wheat root under C. NK, biological rep3


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate6

city: Cefalù

first: Valentina

last: Bravatà

address: Contrada Pietrapollastra Pisciotto

country: Italy

institute: IBSBC CNR

description:
MDA-MB-231_9Gy_proton_rep6
Biological replicate 6 of 6

hyb_protocol: The microarrays (Agilent Whole Human Genome, 4x44k) were hybridazed according to an established protocol by Agilent Technologies (Santa Clara, CA, USA). Two-channel arrays were hybridized using Cy3 and Cy5 and quantified using Feature Extraction v9.5 software. The Agilent Whole Human Genome Array (4x44K) was used for competitive hybridization and the slides were washed, dried, and scanned in an Agilent microarray scanner (Agilent Technologies, Palo Alto, CA, USA).

scan_protocol: Images were scanned using Agilent scanner, G2505B (Agilent Technologies, Palo Alto, CA, USA).

data_processing: Agilent Data Processing Protocol Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software. FeatureExtractor_Version: 9.5.3.1. Protocol_Name: GE2-v5_95_Feb07.

label_protocol: 500 ng of total RNA was amplified according to the manufacturer’s instructions by double strand cDNA synthesis, followed by T7-based in vitro transcription. Untreated MCF10A epithelial breast cell line was used as a control for all samples. Amplified complementary RNA (cRNA) was labeled with cyanine 5 (Cy5)-conjugated dUTP, whereas cRNA from untreated MCF10A cells was labeled with cyanine 3 (Cy3)-conjugated dUTP.

growth_protocol: MCF10A epithelial breast cell line, MCF7 and MDA-MB-231 breast cancer cell lines were collected after 24 hours post treatments

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions

value: Human breast cancer MDA-MB-231 cell line

tag: original tissue

value: breast

value: 9Gy proton

tag: harvest time post treatment

value: 24 hours

value: not exposed to IR treatments


title: Wheat root under Sp. NK, biological rep1


title: Wheat root under Sp. LK, biological rep1

value: Sp LK (one compartment had low K)


title: Wheat root under Sp. NK, biological rep2


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate3

description:
MDA-MB-231_9Gy_proton_rep3
Biological replicate 3 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate5

description:
MDA-MB-231_9Gy_proton_rep5
Biological replicate 5 of 6


title: Wheat root under Sp. LK, biological rep3


title: wild-type, biological replicate 2


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate2

description:
MDA-MB-231_9Gy_proton_rep2
Biological replicate 2 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate4

description:
MDA-MB-231_9Gy_proton_rep4
Biological replicate 4 of 6


title: Wheat root under Sp. LK, biological rep2


title: Wheat root under C. LK, biological rep3

value: C LK (both compartments had low K)


title: Wheat root under C. LK, biological rep1


title: Wheat root under C. LK, biological rep2


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by proton beam-replicate1

description:
MDA-MB-231_9Gy_proton_rep1
Biological replicate 1 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate6

description:
MDA-MB-231_9Gy_electron_rep6
Biological replicate 6 of 6

value: 9Gy electron


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate2

description:
MCF7_9Gy_electron_rep2
Biological replicate 2 of 6

value: Human breast cancer MCF7 cell line


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate3

description:
MCF7_9Gy_electron_rep3
Biological replicate 3 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate4

description:
MCF7_9Gy_proton_rep4
Biological replicate 4 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate2

description:
MCF7_9Gy_proton_rep2
Biological replicate 2 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate1

description:
MDA-MB-231_9Gy_electron_rep1
Biological replicate 1 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate4

description:
MCF7_9Gy_electron_rep4
Biological replicate 4 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate7

description:
MCF10A_9Gy_electron_rep7
Biological replicate 7 of 7

value: Human non-tumorigenic breast epithelial MCF10A cell line


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate2

description:
MCF10A_9Gy_proton_rep2
Biological replicate 2 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate1

description:
MCF10A_9Gy_proton_rep1
Biological replicate 1 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate1

description:
MCF7_9Gy_electron_rep1
Biological replicate 1 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate4

description:
MDA-MB-231_9Gy_electron_rep4
Biological replicate 4 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate5

description:
MCF7_9Gy_electron_rep5
Biological replicate 5 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate5

description:
MCF7_9Gy_proton_rep5
Biological replicate 5 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate2

description:
MDA-MB-231_9Gy_electron_rep2
Biological replicate 2 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate4

description:
MCF10A_9Gy_proton_rep4
Biological replicate 4 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate3

description:
MDA-MB-231_9Gy_electron_rep3
Biological replicate 3 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate6

description:
MCF10A_9Gy_proton_rep6
Biological replicate 6 of 6


title: MDA-MB-231 cells treated with 9 Gy of IR dose delivered by electron beam-replicate5

description:
MDA-MB-231_9Gy_electron_rep5
Biological replicate 5 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate3

description:
MCF7_9Gy_proton_rep3
Biological replicate 3 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate1

description:
MCF7_9Gy_proton_rep1
Biological replicate 1 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate5

description:
MCF10A_9Gy_proton_rep5
Biological replicate 5 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by proton beam-replicate3

description:
MCF10A_9Gy_proton_rep3
Biological replicate 3 of 6


title: MCF7 cells treated with 9 Gy of IR dose delivered by electron beam-replicate6

description:
MCF7_9Gy_electron_rep6
Biological replicate 6 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate4

description:
MCF10A_9Gy_electron_rep4
Biological replicate 4 of 7


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate5

description:
MCF10A_9Gy_electron_rep5
Biological replicate 5 of 7


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate3

description:
MCF10A_9Gy_electron_rep3
Biological replicate 3 of 7


title: A673 Parental DMSO R2 (dataset 2)

tag: sample type

value: Parental A673


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate6

description:
MCF10A_9Gy_electron_rep6
Biological replicate 6 of 7


title: MCF7 cells treated with 9 Gy of IR dose delivered by proton beam-replicate6

description:
MCF7_9Gy_proton_rep6
Biological replicate 6 of 6


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate2

description:
MCF10A_9Gy_electron_rep2
Biological replicate 2 of 7


title: HSC-1_100nM everolimus_72h_rep1.

city: Daejeon

first: Seong-Lan

last: Yu

address: Gasuwon-dong

department: Myunggok Medical Research Institute

country: South Korea

institute: Konyang university

description: Gene expression data from HSC-1 cell treated with 100 nM everolimus for 72h

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Human 2.0 ST Array at 45°C for 16 h. Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned on a GCS3000 Scanner (Affymetrix)

data_processing: Signal values were computed using the Affymetrix® GeneChip™ Command Console software. The data was summarized and normalized with robust multi-average (RMA) method implemented in Affymetrix® Expression Console™ Software (EC).

source_name: HSC-1, 100nM everolimus, 72h

label_protocol: cDNA was synthesized using the GeneChip WT (Whole Transcript) Amplification kit as described by the manufacturer. The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: Each cells were cultured with Dulbecco’s Modified Eagle’s Medium (DMEM, Hyclone Laboratories, Logan, Utah) supplemented with 10 or 20 % fetal bovine serum (FBS, Hyclone Laboratories) and 1% penicillin/streptomycin (Hyclone Laboratories). The cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA from the cells was extracted using TRI reagent® (Ambion).

treatment_protocol: A431 and HSC-1 cells were treated with DMSO or 100 nM everolimus for 72 h.

tag: tissue of tumor

value: skin squamous cell carcinoma

value: 100nM everolimus, 72h


title: mouse spleen (+tumor cells injected) at T1

city: Seoul

first: Seung-yong

last: Seong

address: 28 Yongon-dong, Jongno-gu

department: Microbiology and Immunology

institute: Wide River Institute of Immunology, Seoul National University College of Medicine

description:
Sample name: T1
Gene expression data from mouse spleen

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45℃ on GeneChip Hybridization Oven 645. GeneChips were washed and stained with SAPE (Streptavidin Phycoerythrin) in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with AffymetrixExpressionConsole_1_4_1 (MAS5)

source_name: C57BL/6N mice (B6, Shizuoka, Japan) and C57BL/6-Il10tm1Cgn mice

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (GeneChip 3' IVT PLUS Reagent Kit Manual, Affymetrix).

growth_protocol: CD11b+Gr1hi cells were FACS-purified from the spleen of mice at 24h after LPS injection (L1 and L2), HY209 was infused intravenously into the group of mice at 30 min after LPS injection (LH1, LH2). CD11b+Gr1hi cells were FACS-purified from the spleen of EL4 tumor-bearing mice (T1, T2)

treatment_protocol: LPS i.p. ( L, LH group) at "0", HY209 i.v (LH group) at 30 min after LPS injection, EL4 tumor cells s.c. (T group)

tag: strain

value: C57BL/6N and C57BL/6-Il10tm1Cgn

tag: tissue

value: spleen

tag: cell markers

tag: gender

value: female


title: Huh7.5_miR-124 mimic

city: Ottawa

first: John

middle: Paul

last: Pezacki

address: 150 Louis-Pasteur Pvt

department: Chemistry and Biomolecular Sciences

institute: University of Ottawa

description:
Gene expression data from Huh7.5 cells transfected with miR-124 mimic
Ctrl1

hyb_protocol: 5.5 ug of cDNA were hybridized for 16 hr at 45C on Human Gene 2.0 ST microarrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450_0002.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed with the Affymetrix Expression Console using Affymetrix default analysis settings (RMA) and Affymetrix Transcriptome Analysis Console.

label_protocol: Biotinylated cDNA were prepared from 400 ng RNA using the Affymetrix WT Plus Kit.

growth_protocol: Huh7.5 cells were maintained in DMEM supplemented with 10% FBS, and 1X non essential amino acids

extract_protocol: 72 hours post-transfection, total RNA was isolated using Qiagen RNeasy Kit, as per manufacturer's protocol.

treatment_protocol: Huh7.5 cells were transfected with 100 nM control or miR-124-3p mimics (Ambion) using Lipofectamine RNAiMax, as per manufacturer's instructions.

value: Huh7.5 hepatoma cells

tag: transfection

value: miR-124 mimic


title: A-FABP+ biological rep1

city: Louisville

first: Bing

last: Li

state: Kentucky

address: 505 S Hancock St

institute: University of Louisville

description: Gene expression data from EO771 cells treated with 100ng/ml A-FABP

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45C to Mouse GeneArray 2.0 ST arrays according to the GeneChip 3' array Hybridization User Manual from Affymetrix

scan_protocol: GeneChips were scanned using GeneChip Scanner 3000 7G (Affymetrix) and the GeneChip Command Console 3.1 (Affymetrix)

data_processing: The CEL files were imported into Partek software Version 6.6 (Partek Inc) and normalized using Robust Multi-Array (RMA) normalization on a gene level, followed by a one-way ANOVA.

source_name: murine breast cancer cells treated with A-FABP

label_protocol: Biotinylated cRNA were prepared according to the standard protocol for Affymetrix 3' IWT Plus Reagent Kit

growth_protocol: EO771 cells were cultured with RPMI 1640 at 37°C in a humidified incubator in an atmosphere of 5% CO2. Before the treatment with A-FABP, cells were cultured for 24 hours with 70% confluence as a minimum.

extract_protocol: Directions for extraction and purifying total RNA from EO771 cells by the PureLink RNA Mini Kit are according to the manufacturer's instructions.

treatment_protocol: Always prepare mouse recombinant A-FABP immediatedly before use. Diltue the protein on a final concentration of 100ng/ml in culture medium.

value: EO771 cell line


title: mouse spleen (+tumor cells injected) at T2

description:
Sample name: T2
Gene expression data from mouse spleen


title: A-FABP- biological rep2

source_name: murine breast cancer cells control


title: C4-2 ABT rep 1

city: Philadelphia

first: Matthew

middle: J

last: Schiewer

state: Pennsylvania

department: Cancer Biology

institute: Sidney Kimmel Cancer Center at Jefferson

description: treated with 2.5uM veliparib

hyb_protocol: 5ug cDNA in 220ul hybridization cocktail was hybridized on the Affymetrix Human Gene 1.0 ST Array in a GeneChip Hybridization Oven 645. Target denaturation was performed at 99C for 2 minutes, 45C for 5min, followed by hybridization for 18h.

scan_protocol: Affymetrix Gene ChIP Scanner 3000 7G

data_processing: iterPLIER summarization, PM-GCBG correction, and quantile normalization were performed in Affymetrix Expression Console 1.1

source_name: C4-2 treated with 2.5uM veliparib

label_protocol: 5ug cDNA was fragmented and chemically labeled with biotin using the FL-Ovation cDNA biotin module (NuGen Technologies, Inc)

growth_protocol: LNCaP and C4-2 cells were cultured in steroid-deprived media for 72 hours

extract_protocol: Trizol RNA extraction, followed by cDNA amplification with the Ovation Pico WTA-system V2 RNA amplification system (NuGen Technologies, Inc)

treatment_protocol: Cells were treated as indicated and harvested 16 hours post-treatment

value: prostate cancer


title: MCF10A cells treated with 9 Gy of IR dose delivered by electron beam-replicate1

description:
MCF10A_9Gy_electron_rep1
Biological replicate 1 of 7

value: breast

value: 24 hours


title: C4-2 ABT rep 2

description: treated with 2.5uM veliparib


title: HSC-1_DMSO_72h_rep2.

description: Gene expression data from HSC-1 cell treated with DMSO

source_name: HSC-1, DMSO, 72h

value: DMSO 72h


title: mouse spleen (+LPS) at L1

description:
Sample name: L1
Gene expression data from mouse spleen


title: A-FABP- biological rep1


title: A-FABP+ biological rep2


title: LNCaP EtOH rep 2

description: treated with ethanol (vehicle)

source_name: LNCaP treated with ethanol (vehicle)

value: LNCaP


title: C4-2 DMSO rep 1

description: treated with DMSO (vehicle)

source_name: C4-2 treated with DMSO (vehicle)


title: HSC-1_100nM everolimus_72h_rep2.


title: Huh7.5_Ctrl mimic

description:
Gene expression data from Huh7.5 cells transfected with control mimic
miR-124-1

value: control mimic


title: LNCaP DHT rep 1

description: treated with 1nM DHT

source_name: LNCaP treated with 1nM DHT


title: LNCaP ABT-DHT rep 2

source_name: LNCaP treated with 2.5uM veliparib for 1 hour prior to treatment with 1nM DHT


title: HSC-1_DMSO_72h_rep3.


title: LNCaP DHT rep 2

description: treated with 1nM DHT


title: mouse spleen (+LPS/+HY209) at LH1

description:
Sample name: LH1
Gene expression data from mouse spleen


title: mouse spleen (+LPS/+HY209) at LH2

description:
Sample name: LH2
Gene expression data from mouse spleen


title: A431_100nM everolimus_72h_rep3.

description: Gene expression data from A431 cell treated with 100 nM everolimus for 72h

source_name: A431, 100nM everolimus, 72h


title: LNCaP ABT-DHT rep 1

description: treated with 2.5uM veliparib for 1 hour prior to treatment with 1nM DHT


title: HSC-1_DMSO_72h_rep1.


title: mouse spleen (+LPS) at L2

description:
Sample name: L2
Gene expression data from mouse spleen


title: HSC-1_100nM everolimus_72h_rep3.


title: C4-2 DMSO rep 2

description: treated with DMSO (vehicle)


title: LNCaP EtOH rep 1

description: treated with ethanol (vehicle)


title: mILC2_TL1A

city: New York

first: Gregory

last: Putzel

state: NY

address: 430 East 29th Street

department: Microbiology

institute: NYU Langone Health

data_processing:
Base calling and demultiplexing with CASAVA
Adapter trimming using FLEXBAR
Alignment to mm9 reference genome using STAR aligner
Read counts per gene computed using HTSeq
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text giving raw number of reads mapped to each gene (identified by RefSeq identifier) in each sample

source_name: Mouse ILC3s_TL1A stimulated

extract_protocol:
cDNAs were prepared using the SMARTer Ultra Low Input RNA Kit for Sequencing following the user manual (Clontech Laboratories).
Standard Illumina protocols

treatment_protocol: Cells were treated with either medium or with TL1A

tag: cell type

value: group 3 innate lymphoid cells (ILC3)


title: Xist[4658-5090] 90mM CMC A

city: West Haven

last: Simon

address: 600 West Campus Dr. MIC312

institute: Yale University Chemical Biology Instiute

description: Xist

data_processing:
FASTQ sequencing reads were trimmed with Cutadapt to remove Illumina adaptor sequences, and aligned using Bowtie2 local alignment to respective RNA target sequences.
Reverse transcription stops and mutations were identified, screened, and tallied using the previously published RTEventsCounter software (Sexton et al. 2017). Reverse transcription stop and mutation probabilities were calculated as the number of stops or mutations divided by the total number of read-through events plus stops, or the total number of observations for the nucleotide (depth). Only values from more than 100 read-throughs are eventually considered.
Human 7sk sequence was eventually brought to alignment with mouse 7sk sequence to facilitate comparison of EDC values by shifting nt 163-245 to +1 (164-246), with the original nt 247 value removed. None of these changes were in the studied stem-loop section.
Genome_build: Alignment to Mus musculus 7sk NR_030687.1, Homo sapiens 7sk NR_001445.2, or respective section intervals of Mus musculus Xist NR_001463.3 (nt 4701-5001 or 4658-5090).
Supplementary_files_format_and_content: The total tally and probability of modification-induced stop or mutation is indicated for each nucleotide in respective target RNA sequences in each experiment. The nucleotide number (1-based) in the aligned target sequence (nt), averaged alignment score (avgQual), the nucleotide identity (ref), depth, read-through (RT), and number of insertions and deletions are also included. The calculated probability values for each individual nucleotide is preceded with “iP”

source_name: Female MEF cells

growth_protocol: MEF cells were cultured in DMEM with 10% FBS (Thermo Fisher) and penicillin/streptomycin to 90% confluency in 15 cm plates.

extract_protocol:
After treatment, cells were lifted using Cell Scraper (Corning) and collected in PBS by centrifugation (3 min, 1000 rpm, 4 °C), and the supernatant was discarded. The RNA was extracted using TRIzol (Thermo Fisher) according to manufacturer’s instructions. The extracted RNA was treated with RQ1 DNase (1 h, 37 °C; Promega), and subsequently purified with phenol/chloroform extraction and ethanol precipitation.
Reverse transcription was carried out using either 2 μg (7SK) or 10 μg (Xist) of extracted RNA, and 1 pmol total of primers. The RNA/primer mix was brought up to 12 μL and incubated at 70 °C for 5 min, then 4 °C for 2 min for primer annealing. Next, 3 μL of 5X FS buffer was added for a 10 min incubation at 55 °C. Finally, 5 μL of reverse transcription mix (1 μL 5X FS buffer, 1 μL 10 mM dNTPs, 1 μL 100 mM DTT, 0.2 μL RNase OUT, 0.5 μL SuperScript III, 1.3 μL dH2O) was added and mixed before incubation at 55 °C for 45 min, followed by heat inactivation at 85 °C for 5 min. After reverse transcription, RNA was degraded by adding 0.4 μL of 5 M NaOH and incubating at 95 °C for 3 min, before neutralization with 0.4 μL of 10 M acetic acid and cooling on ice. The cDNA from reverse transcription was purified with AMPure XP beads by adding and mixing 1 volume of bead solution and 3 volumes of PEG solution (2.5 M NaCl, 20% PEG 8000) at room temperature. The mixture was let to incubate at room temperature for 15 min, before immobilizing the beads on a magnetic rack for 10 min. The beads were washed with fresh 80% ethanol twice before being dried for 10 min and eluted in 16 μL of dH2O. 3' adaptor ligation was carried out using T4 RNA Ligase I, followed by two rounds of PCR amplification, with Illumina indexes added in the second round.

treatment_protocol: Cells were washed with PBS and then incubated with respective reagent solutions. For CMC and EDC treatment, cells were incubated with 10 mL of respective concentrations of reagents (CMC: 10 mM, 30 mM, 90 mM; EDC: 100 mM, 300 mM, 1500 mM) in borate reaction buffer for 30 min at 25 °C. For glyoxal treatment, cells were incubated with 10 mL of 50 mM glyoxal solution in reaction buffer (50 mM HEPES pH 8.0, 50 mM KCl, 0.5 mM MgCl2) for 15 min at 25 °C (Mitchell et al. 2018). For DMS treatment, cells were incubated with 0.5% DMS in PBS (5 min, 25 °C) before removing DMS solution and quenching with three washes of wash buffer (50 mM Tris pH 7.5, 100 mM NaCl, 3 mM MgCl2, 40 mM β-mercaptoethanol). No-treatment control plates were incubated with PBS.

tag: rt-primer set

value: Xist[4658-5090] RT primer set

tag: probing treatment

value: 90mM CMC, 30 min


title: mILC1

source_name: Mouse ILC3s


title: mILC1_TL1A


title: mILC2


title: Xist[4658-5090] 300mM EDC B

description: Xist

value: 300mM EDC, 30 min


title: Xist[4658-5090] 90mM CMC B

description: Xist


title: Xist[4658-5090] 30mM CMC B

description: Xist

value: 30mM CMC, 30 min


title: Xist[4658-5090] 30mM CMC A

description: Xist


title: Xist[4658-5090] 300mM EDC A

description: Xist


title: Xist[4658-5090] 1500mM EDC A

description: Xist

value: 1500mM EDC, 30 min


title: Xist[4658-5090] untreated A

description: Xist

value: Untreated


title: 7SK (grp B) 30mM CMC B

value: 7SK primer set


title: 7SK (grp B) 90mM CMC B


title: 7SK (grp B) 90mM CMC A


title: 7SK (grp B) 1500mM EDC B


title: A431_100nM everolimus_72h_rep2.

value: skin squamous cell carcinoma

tag: treatment

value: 100nM everolimus, 72h


title: Embryo from heterozygous mutant (STAT3-K177K180R) mice 2

city: HangZhou City

last: Xu

state: ZheJiang Province

address: BinWen Street  358#

institute: ZJTCMU

description: Gene expression of embryo  from heterozygous  mutant (STAT3-K177K180R)mice

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 11 μl 10 × Blocking Agent and 2.2 μl of 25×Fragmentation Buffer, then heated at 60°C for 30 min, and finally 55 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 100 μl of hybridization solution was dispensed into the gasket slide and assembled to the gene expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.

source_name: Embryos (12 days)

label_protocol: total RNA from each sample was linearly amplified and labeled with Cy3-UTP.The Labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: The animal housing facility is a barrier housing facility, and it is maintained in accordance with the national standards (Laboratory Animal-Requirements of Environment and Housing Facilities, GB 14925–2001).

extract_protocol: Total RNA of tumor tissue were isolated using Trizol. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

treatment_protocol: Embryos (12 days) of STAT3mut/mut, STAT3mut/wt and STAT3wt/wt mice which come from the same womb were used for Agilent Mouse 4x44K Gene Expression Microarrays assay

value: Embryos

value: heterozygous mutant (STAT3-K177K180R)


title: A431_100nM everolimus_72h_rep1.

tag: cell line


title: Embryo from wild type mutant (STAT3-K177K180R) mice 2

description: Gene expression of embryo  from wild type  mutant (STAT3-K177K180R)mice

value: wild type mutant (STAT3-K177K180R)

tag: age


title: Embryo from homozygous mutant (STAT3-K177K180R) mice 2

description: Gene expression of embryo  from homozygous  mutant (STAT3-K177K180R)mice

value: homozygous mutant (STAT3-K177K180R)


title: 7SK (grp B) 30mM CMC A


title: Embryo from homozygous mutant (STAT3-K177K180R) mice 1


title: Embryo from wild type mutant (STAT3-K177K180R) mice 1


title: Xist[4658-5090] 1500mM EDC B

description: Xist


title: A431_DMSO_72h_rep1.

description: Gene expression data from A431 cell treated with DMSO

value: DMSO 72h


title: A431_DMSO_72h_rep3.


title: 7SK (grp B) 300mM EDC A


title: 7SK (grp B) 300mM EDC B


title: 7SK (grp B) untreated B


title: 7SK (grp B) glyoxal B

value: 50mM glyoxal, 15 min


title: 7SK (grp B) untreated A


title: A431_DMSO_72h_rep2.


title: 7SK (grp A) 100mM EDC A

value: 100mM EDC, 30 min


title: 7SK (grp A) 10mM CMC B

value: 10mM CMC, 30 min


title: Xist[4658-5090] untreated B

description: Xist

value: Xist[4658-5090] RT primer set


title: 7SK (grp A) untreated A


title: Embryo from heterozygous mutant (STAT3-K177K180R) mice 1


title: 7SK (grp A) 100mM EDC B


title: 7SK (grp A) untreated B


title: 7SK (grp A) 10mM CMC A


title: 7SK (grp A) DMS B

value: F1:129S1/CastEiJ x 129S9

value: 0.5% DMS, 5 min


title: 7SK (grp B) 1500mM EDC A


title: Xist[4701-5001]IVT 100mM EDC B

source_name: In vitro transcription

value: Xist[4701-5001] RT primer set

value: 100mM EDC, 20 min


title: Xist[4701-5001]IVT 100mM EDC A


title: Xist[4701-5001]IVT 10mM CMC B

value: 10mM CMC, 20 min


title: Xist[4701-5001]IVT untreated A

value: Untreated


title: Xist[4701-5001]IVT 10mM CMC A


title: Xist[4701-5001]IVT untreated B


title: micro-gravity R1_2

city: guangzhou

first: meiying

last: feng

address: College of Animal Science, South China Agricultural University, 483 Wushan Rd, Tianhe District, Guangzhou, Guangdong 510642, P.R. China.

institute: Zhaoqing University

data_processing:
The Smart-Seq2 method and the Qubit® RNA Assay Kit in a Qubit®3.0 fluorometer were used to prepare the single-cell cDNAs library .
The libraries were sequenced on the Illumina HiSeq 2500 platform using 150-bp paired-end sequencing. Sequencing reads were assessed with the FASTX tool kit (Patel and Jain, 2012) and were then subjected to standard QC criteria to remove short (<30 bp) and low-quality (quality score <20) reads.
We left genes/transcripts with FPKM greater than 10, which means that if there were only one exons, the length could be greater than 2000 bp, while if more than two exons were present, the length could be greater than 200 bp. The coding potential of the transcripts was then identified by CPC software; then, transcripts with coding potential were excluded, and the final lncRNAs were obtained.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

source_name: zygote

extract_protocol:
Zygotes were removed, flash frozen on dry ice, and collected on lysate buffer. Qubit® RNA Assay Kit in a Qubit®3.0 fluorometer was used with 20 ng of single-cell cDNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 7SK (grp B) glyoxal A

value: 7SK primer set


title: micro-gravity R1_3


title: micro-gravity R1_1


title: control 1_3


title: shCtl2_RA

first: Kristian

last: Laursen

address: 1300 York Ave.

department: Pharmacology

institute: Weill Cornell Medicine

description: Treatment: RA (1μM)

data_processing:
RNA integrity was determined using the Agilent 2100 BioAnalyzer, RIN ≥ 9.9
Dr. Tuo Zhang (Weill Cornell Medicine Genomics Core Facility) aligned the reads to the mouse mm9 reference genome using Tophat2
Gene expression values were measured in RPKM using cufflinks
Genome_build: mm9
Supplementary_files_format_and_content: Values are given in RPKM

source_name: J1 Embryonic Stem Cells

growth_protocol: Cells were grown on gelatin coated plates and grown in ES media with LIF

extract_protocol:
RNA was isolated using the Qiagen RNeasy Plus Kit
The cDNA libraries were generated using the Illumina TruSeq RNA Sample Preparation kit and sequenced with single-end 51 bps on HiSeq2500 sequencer.

treatment_protocol: Cells were treated with either Vehicle Control (EtOH) or 1μM Retinoic Acid (RA) for 48hrs

value: shRNA Scramble Control

value: J1 Embryonic Stem Cells


title: mouse retina progenitor cell

city: Shanghai

first: Qingjian

last: Ou

address: Siping Rd

department: Medical

institute: Tongji University

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 GRCm38.p3 whole genome using tophat-2.0.10 with parameters tophat -r 50 --library-type  fr-firststrand  -p 4
Fragments Per Kb per Million reads（FPKM）were calculated using a protocol from Trapnell C, et al., Nat Biotechnol,2010.
Genome_build: GRCm38.p3
Supplementary_files_format_and_content: text data files include FPKM values for each Sample.

source_name: Retina

growth_protocol: The mouse retina progenitor isolated from the mouse retina and cultured with condition medium for 24 passages.

extract_protocol:
Retina and cells were collected and RNA was extracted with Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: cultured retina progenitor cells

tag: sample name


title: control 1_2


title: control 1_1


title: 91173_Control

description: Treatment: Vehicle control (ETOH)

tag: genotype

value: shRNA CARM1 Knockdown


title: mouse retina tissue

value: retina tissue


title: J1_RA

description: Treatment: RA (1μM)

value: Wild-Type


title: 91173_RA

description: Treatment: RA (1μM)


title: shCtl2_Control

description: Treatment: Vehicle control (ETOH)


title: J1_Control

description: Treatment: Vehicle control (ETOH)


title: W7642_il1r1_rep2

first: Maxim

middle: N.

last: Artyomov

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

data_processing:
Second mate was used for sample demultiplexing.
Individual single-end fastqs were aligned to mm10 genome using STAR with following options --outFilterMultimapNmax 15 --outFilterMismatchNmax 6 --outReadsUnmapped Fastx --outSAMstrandField All.
Gene expression was obtained via ht-seq and DESeq2 for differential expression.
Gene expression was obtained using in-house scripts bassed on MACS and HTSeq (https://github.com/ctlab/quant3p).
Genome_build: mm10
Supplementary_files_format_and_content: counts.txt

source_name: Bone marrow-derived macrophages

growth_protocol: C57Bl/6 and Il1r1-/- mice were purchased from Jackson Laboratory (Stock No:  000664 and 003245).

extract_protocol:
mRNA was extracted from cell lysates using oligo-dT beads (Invitrogen).
cDNA synthesis was carrid out using custom oligo-dT primer with a barcode and adaptor-linker sequence (CCTACACGACGCTCTTCCGATCT-XXXXXXXX-T15). After first-strand synthesis, samples were pooled together based on Actb qPCR values and RNA-DNA hybrids were degraded with consecutive acid-alkali treatment. Subsequently, a second sequencing linker (AGATCGGAAGAGCACACGTCTG) was ligated with T4 ligase (NEB) followed by SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) clean-up. The mixture was enriched by PCR for 12 cycles and SPRI-beads (Agencourt AMPure XP, BeckmanCoulter) purified to yield final strand-specific RNA-seq libraries.

treatment_protocol: Bone marrow-derived macrophages (BMDMs) from WT and Il1r1–/– mice were derived in 7 days in GM-CSF supplemented complete DMEM.  Cells were infected with either Mtb HN878 or Mtb W_7642 (multiplicity of infection = 1) and RNA samples collected after 6 days.

tag: agent


title: W7642_wt_rep2

value: wt


title: W7642_il1r1_rep1


title: W7642_il1r1_rep3


title: W7642_wt_rep1


title: 7SK (grp A) DMS A

department: Molecular Biophysics & Biochemistry

value: F1:129S1/CastEiJ x 129S8


title: uninfected_wt_rep2

value: uninfected


title: HN878_il1r1_rep3

value: Mtb HN878


title: uninfected_wt_rep1


title: HN878_wt_rep2


title: HN878_wt_rep1


title: HN878_il1r1_rep1


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_2_2

city: Cambridge

first: Evangelia

last: Diamanti

address: Wellcome Trust / MRC Building, Hills Road

department: Haematology

institute: University of Cambridge

data_processing:
RNA-seq reads were aligned to mm10 using GSNAP (version 2015-09-29) with parameters (-B 5 -t 24 -n 1 -Q -N 1).
Reads in features were counted with htseq-count (HTSeq version 0.5.3p3) with the parameter (-s no).
Genome_build: mm10
Supplementary_files_format_and_content: HT-Seq counts(.txt)

source_name: Dissociated pancreatic organoid cells

extract_protocol:
Three-dimensional cultures of pancreatic ductal cells (organoids, Huch et al 2013) were infected with multiple vectors expressing GFP-Ngn3, LSS/Orange-Pdx1 and/or tdTomato-MafA. Organoids were dissociated to single cells and FACS sorted  (FACS Influx BD Biosciences). FACS sorting allows us to isolate cells that are expressing each of the transcription factors either individually or in each possible combination by sorting for the associated fluorescent reporter proteins. Pool of 50 cells were sorted by FACS directly into individual wells of a 96-well plate containing lysis buffer. RNA-Seq analysis was performed as described previously (Picelli et al., 2014). Pooled libraries were then run on the Illumina Hi-Seq 2500.
RNA libraries were prepared for sequencing using the Illumina Nextera XT DNA preparation kit

tag: expression

value: Dissociated pancreatic organoid cells

tag: days of transgene induction

value: 8 days

tag: passage


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_3

tag: strain


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_3_1

tag: tissue


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_2


title: 8d GFP-WTNgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_3


title: 8d tdTomato-MafA (from WTNgn3 culture) infected organoids_2_1

value: tdTomato-MafA (from WTNgn3 culture)


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_2


title: 8d tdTomato-MafA (from WTNgn3 culture) infected organoids_1_2


title: 8d tdTomato-MafA (from WTNgn3 culture) infected organoids_1_1


title: 8d GFP-6SANgn3 - LSSOrange-Pdx1 tdTomatoMafA infected organoids_1_1


title: 8d tdTomato-MafA (from 6SANgn3 culture) infected organoids_2_2

value: tdTomato-MafA (from 6SANgn3 culture)