title: BELINOSTAT 72hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Belinostat and collected at 72 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 72hpa. Samples were treated with Belinostat.

value: Belinostat


title: Gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

status: Public on Jan 31 2019

type: SRA

city: Utrecht

first: Helmuth

last: Gehart

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
sorted cells from small intestinal crypts (F03)
Extracted RNA from gate 2 (green-red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

library_source: transcriptomic

data_processing:
Paired end reads were aligned to the transcriptome using bwa. Paired end reads obtained by CEL-seq were aligned to the transcriptome using bwa (version 0.6.2-r126) with default parameters. The transcriptome contained all RefSeq gene models based on the mouse genome release mm10 downloaded from the UCSC genome browser and contained 31,109 isoforms derived from 23,480 gene loci. All isoforms of the same gene were merged to a single gene locus. The right mate of each read pair was mapped to the ensemble of all gene loci and to the set of 92 ERCC spike-ins in sense direction. Reads mapping to multiple loci were discarded. The left read contains the barcode information: the first eight bases correspond to the cell specific barcode followed by 4 bases representing the unique molecular identifier. The remainder of the left read contains a polyT stretch followed by few (<15 transcript derived bases). The left read was not used for quantification. CEL-Seq
Genome_build: mm10
Supplementary_files_format_and_content: coutc files contain raw counts (not normalized)

molecule: total RNA

organism: Mus musculus

source_name: murine small intestinal crypts

extract_protocol:
Cells were sorted into Trizol (Life Technologies) and total RNA was isolated according to the manufacturer's instructions, with the following alterations. RNA was precipitated overnight at -20 °C, with 2.5 ug GlycoBlue (Life Technologies).
RNA was processed using the previously described CEL-seq technique, with the indicated modifications. Libraries were sequenced on an Illumina NextSeq500 using 75bp paired end sequencing (Samples Neurog3ChronoBulk01-06) or on an Illumina Hiseq4000 using 150bp paired end sequencing (Samples Neurog3ChronoBulk09-16)

tag: genotype

value: Neurog3Chrono hom

tag: tissue

value: intestine

tag: sequencing

value: NextSeq500 75bp paired end

tag: strain

tag: barcode number

tag: barcode sequence

value: TGCATCGA


title: Input ChIP-seq

city: Iowa City

first: Long-Sheng

last: Song

state: Iowa

address: 285 Newton Road

department: Department of Internal Medicine

country: USA

institute: University of Iowa

library_source: genomic

data_processing:
For raw ChIP-seq and RNA-seq data analyses, the quality control was peformed by FastQC (version 0.11.3) and sequencing adaptors were trimmed by Cutadapt (version 1.8.1).
For ChIP-seq data analyses, processed sequencing reads were aligned to mouse genome (mm10) by Bowtie 2 (version 2.2.5) with the "--end-to--end" mode. MACS (version 1.4.2) with the default parameter was used to call peaks (p value < 10e-10). The Wig format file  (bin size = 10 bp) generated by MACS was normalized by RPM (reads per million) and then converted to bigWig format.
For RNA-seq data analyses, Kallisto (version 0.42.5) with the default parameter was used to quantify gene expression abundance.
Genome_build: mm10
Supplementary_files_format_and_content: For ChIP-seq processed data, the bigWig format files were derived from the output of MACS software and normalized by RPM (reads per million, bin size = 10bp). The RNA-seq processed data files were derived from the output of Kallisto with 5 columns splitted by Tab (transcript_id, length, effective_length, estimate_counts and transcrpt per million).

molecule: genomic DNA

source_name: Heart

growth_protocol: Cardiac specific JP2NT transgene was driven by a-MHC promoter in JP2NT-OE mice. Littermates that don't have the transgene were used as control. Heart samples for JP2NT and TBP ChIP-seq were harveste-d from 2 month old mice. Samples for MEF2C ChIP-seq were from 3 weeks old mice. Heart samples for RNA-seq were harvested from 12 weeks old mice.

extract_protocol:
For ChIP-seq, hearts were excised quickly, rinsed in PBS and snap frozen in liquid nitrogen. ChIP-seq experiments were performed by Active Motif Inc. The samples were crosslinked with PFA, homogenized and sonicated to fragment DNA. The DNA/protein complexes were pulled down by antibodies against  HA tag (Abcam, Catalog #ab9110), TBP (Abcam, Catalog #ab51841) or MEF2C (Santa Cruz, Catalog #sc-313). The crosslinking was reversed and DNA was purified and subjected to library construction. For RNA-seq, the left ventricle tissues were quickly harvested and washed in cold PBS and homogenized in trizol. Trizol manual was followed to extract RNA. Total RNA was treated with DNASE-I (New England Biolabs, Catalog #M0303S) to eliminate genomic DNA and then cleaned using RNA cleanup Kit (Qiagen, Catalog #74204).
For RNA-seq, Illumina TruSeq Stranded mRNA Library Prep Kit (catalog # 20020595) was used to prepare the sequencing library. For ChIP-seq, the sequencing library was prepared by Active Motif, Inc.

treatment_protocol: Transverse aortic banding (TAB) was performed on 9 weeks old male mice. 3 weeks after surgery, hearts were harvested for RNA-seq. Non-treated littermates (no surgery) were used as baseline and harvested on the same time point. For ChIP-seq, all mice were under baseline condition (no TAB surgery).

value: Heart


title: Gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

description:
sorted cells from small intestinal crypts (F03)
Extracted RNA from gate 3 (red) sorted cells of small intestinal crypts isolated from Neurog3Chrono animals, replicate 1

value: ACTGACGA


title: BELINOSTAT 72hr replicate 2

type: RNA

city: Lexington

first: Varun

middle: Bhamidipati

last: Dwaraka

state: Kentucky

address: 741 South Limestone St.

department: Spinal Cord and Brain Injury Research Center

institute: University of Kentucky

hyb_protocol: Microarray hybridization using an Ambystoma Affymetrix array (Huggins et al., 2012) was performed by the University of Kentucky Microarray Core Facility.

scan_protocol: Affymetrix Command Console was used according to manufacturer's instructions

data_processing: GeneChips were normalized using the affy R package (Gautier et al 2004) Affymetrix Expression Console software to accomplish robust multichip averaging (RMA) (Irizarry et al., 2003).

label: biotin

organism: Ambystoma mexicanum

label_protocol: Biotinylation was carried out according to the instructions in Affymetrix's 3'IVT Reagent Kit user's manual

growth_protocol: The use of pre-feeding stage axolotls does not require a protocol approved by the Institutional Animal Care and Use Committee (IACUC) at University of Kentucky, however embryos used in this study were treated according to the same ethical standards that apply to feeding axolotls. Rearing water (40% modified Holtfretter's solution) was changed three times per week.

extract_protocol: The tissue samples were maintained at 4 C in RNA later prior to RNA isolation using first the Trizol method and then a Qiagen minikit with on-the-column DNAse treatment of DNA.

treatment_protocol: Developmental stage 42 (Bordzilovskaya et al 1989) axolotl embryos were manually hatched by removing the egg jelly and membrane, anesthetized in 0.02% benzocaine, and administered tail amputations with a razor blade to remove 2 mm (~20% of the body length) of the distal tail tip. After amputation, animals were placed into microtiter plates containing rearing water (40% modified Holtfreter’s Solution) and 0.001% DMSO (controls) or rearing water with 10 um romidepsin or 10 um belinostat (treatements).

tag: time (hpa)

tag: treatment


title: BELINOSTAT 72hr replicate 1


title: ROMIDEPSIN 48hr replicate 2

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 48 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 48hpa. Samples were treated with Romidepsin.

value: Romidepsin


title: BELINOSTAT 72hr replicate 3


title: C57Bl6-JunKO_iBMDM_RNA_Veh_GJF_17-12-03-rep1

city: La Jolla

first: Jenhan

last: Tao

state: CA

address: 9500 Gilman Drive, Mail code 0651

department: Cellular and Molecular Medicine

institute: UC San Diego

data_processing:
Reads from each RNA-Seq sample were aligned to the mm10 genome using STAR.
Aligned read files were analyzed with HOMER (http://homer.ucsd.edu/homer/) to calculate RPKM from the exons of RefSeq genes (using the following command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -rpkm)
BigWig tracks were created using the HOMER makeBigWig.pl command
Genome_build: mm10
Supplementary_files_format_and_content: Processed files include a expression text file that contains expression values for each sample (RNA-Seq expression data, using the following HOMER command: analyzeRepeats.pl rna mm10 -count exons -condenseGenes -rpkm).  All genomic coordinates are relative to mm10 human assembly.

molecule: polyA RNA

source_name: mouse BRAF(V600E), Myc immortalized bone marrow (passage 3-8) cells

growth_protocol: TGEMs were grown for 3 days in 10%FBS, 1%Penicillin Streptomycin, DMEM

extract_protocol:
RNA isolation. RNA was isolated using TRIZOL-reagent (ambion cat# 15596018) and DIRECT-ZOL RNA mini-prep kit (cat# 11-330MB). Poly-A RNA isolation. Use 0.2 Total RNA as starting material for ideal mapping efficiency and minimal clonality.  Collect 10 μL oligo (dT) (NEB cat# S1419S) beads per RNA sample. Beads were washed twice with 1x DTBB (20mM Tris-HCl pH7.5, 1M LiCl, 2mM EDTA, 1% LDS, 0.1% Triton X-100). Beads were resuspended in 50uL of 2x DTBB.  50uL of beads were mixed with 50uL RNA and Heated to 65°C for 2 min. RNA-beads were then incubated for 10 min at RT while rotating. RNA-beads were then collected on a magnet and washed 1x each with RNA WB1 (10mM Tris-HCl pH7.5, 0.12 M LiCl, 1mM EDTA, 0.1% LDS, 0.1% Triton X-100)and WB3 (10mM Tris-HCl pH7.5, 0.5M LiCl, 1mM EDTA). Add 50uL Tris-HCl pH7.5 and heat to  80°C for 2 min to elute. Collect RNA and perform a second Oligo-dT bead collection. After washing the second collection, instead of eluting was 1X with 1X First strand buffer (250 mM Tris-HCl (pH 8.3), 375 mM KCl, 15 mM MgCl2 [ThermoFisher SSIII kit Cat# 18080093). Fragmentation. Then Add 10uL of 2X First strand buffer plus 10mM DTT and fragment DNA at 94°C for 9 min. Collect beads on magnet and transfer eluate containing fragmented mRNA to a new PCR strip.  Should recover 10 μL fragmented RNA. First strand synthesis. We mixed fragmented RNA with 0.5uL Random Primer (3 μg/μL) Life Tech #48190-011, 0.5uL oligo-dT (50uM from SSIII kit), 1uL dNTPs (10mM Life Tech, cat 18427088) and 0.5uL SUPERase-In (ThermoFisher Cat#AM2696) and heat 50°C for 1 min. Immediately place on ice. We then added 5.8uL ddH2O, 0.1 uL Actinomycin (2ug/uL Sigma cat#A1410), 1uL DTT (100mM Life Tech cat# P2325), 0.2uL of 1% Tween and 0.5 uL of Superscript III and incubate 25°C for 10 min, then 50°C for 50 min. Bead clean up. We added 36 μL of RNAClean XP (ampure XP) and mixed, incubating for 15 min on ice. The beads were then collected on a magnet and washed 2X with 75% ethanol. Beads were then air-dried for 10 min and elute with 10 μL nuclease free H2O. Second strand synthesis. 10uL of cDNA/RNA was mixed with 1.5uL 10X Blue Buffer (Enzymatics cat# B0110L), 1uL dUTP/dNTP mix (10mM Affymatrix cat# 77330), 0.1uL dUTP (100mM Affymatrix cat# 77206), 0.2uL RNase H (5U/uL Enzymatics cat# Y9220L), 1uL DNA polymerase I (10U/uL Enzymatics cat#P7050L), 0.15 uL 1% Tween-20 and 1.05uL nuclease free water. Reaction was incubated at 16°C for 2.5 hours. Bead clean up. DNA was purified by adding 1uL Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) per reaction in 28uL 20% PEG8000/2.5 M NaCl (13% final concentration) and incubating at RT for 10min. Beads were then collected on a magnet and washed 2X with 80% Ethanol. Beads were air-dried for 10min and eluted in 40uL of nuclease free water. DNA is ready for library prep.
dsDNA End Repair. We mixed 40uL of DNA from ChIP or RNA protocols with 2.9uL of H2O, 0.5uL 1% Tween-20, 5uL 10X T4 ligase buffer (Enzymatics cat# L6030-HC-L), 1uL dNTP mix (10 mM  Affymetrix 77119), 0.3 uL T4 DNA pol (Enzymatics P7080L), 0.3uL T4 PNK (Enzymatics Y9040L), 0.06uL Klenow (Enzymatics P7060L) and incubated for 30min at 20°C. 1uL of Seradyn “3 EDAC” SpeedBeads (Thermo 6515-2105-050250) in 93 μL 20% PEG8000/2.5 M NaCl (13% final) was added and incubated for 10 min. Bead clean-up. Beads were collected on a magnet and washed 2X with 80% ethanol. Beads were air-dried for 10 min and then eluted in 15uL ddH2O. dA-Tailing. DNA was mixed with 10.8uL ddH2O, 0.3uL 1% Tween-20, 3uL Blue Buffer (Enzymatics cat# B0110L), 0.6uL dATP (10mM Tech 10216-018), 0.3uL Klenow 3’- 5’ Exo (Enzymatics P7010-LC-L) and incubated for 30min at 37°C. 55.8uL 20% PEG8000/2.5 M NaCl (13% final) was added an incubated for 10 min. Then bead clean up was done. Beads were eluted in 14uL. Y-Shape Adapter Ligation. Sample was mixed with 0.5uL of a BIOO barcode adapter (BIOO Scientific cat# 514104), 15uL Rapid Ligation Buffer (Enzymatics cat@ L603-LC-L), 0.33uL 1% Tween-20 and 0.5uL T4 DNA ligase  HC (Enzymatics L6030-HC-L) and incubated for 15 min at RT.  7 μL of 20% PEG8000/2.5 M NaCl was added and incubated for 10min at RT. Bead clean up was performed and beads were eluted in 21uL. 10uL was then used for PCR amplification (14 cycles) with IGA and IGB primers (AATGATACGGCGACCACCGA, CAAGCAGAAGACGGCATACGA).

treatment_protocol: Veh (PBS) or KLA were added directly to the media

tag: Sex

value: male

value: Vehicle

value: C57Bl/6EiJ JunKO


title: ROMIDEPSIN 48hr replicate 4


title: ROMIDEPSIN 48hr replicate 3


title: C57Bl6-Atf3KO_iBMDM_RNA_Veh_GJF_18-02-18-rep2

value: mouse BRAF(V600E), Myc immortalized bone marrow (passage 3-8) cells

value: C57Bl/6EiJ Atf3KO


title: C57Bl6_iBMDM_RNA_zsGreen_GJF_17-12-03-rep1

value: C57Bl/6EiJ Scramble Control


title: C57Bl6-JunDKO_iBMDM_RNA_Veh_GJF_17-12-03-rep1

value: C57Bl/6EiJ JunDKO


title: C57Bl6-Atf3KO_iBMDM_RNA_Veh_GJF_17-12-03-rep1


title: ROMIDEPSIN 48hr replicate 1


title: untreated replicate 3

type: other

city: Houston

first: Yuan

last: Qi

state: TX

address: 1400 Pressler St

department: Bioinformatics & Computational Biology

institute: University of Texas M.D. Anderson Cancer Center

scan_protocol: After treatment, assay plates were imaged (IN-Cell Analyzer 6000, GE Healthcare Life Sciences) and cells were assessed for viability as determined after incubation with CellTiter-Blue® (Promega Corporation, Madison, WI) and quantification of fluorescence intensity (PHERAstar FS Plate Reader, BMG Labtech Inc., Cary, NC).

data_processing: the raw data were normalized using b-score normalization method, which used the median polished intensity divided by median absolute deviation(MAD).

label: resazurin

molecule: other

organism: Homo sapiens

source_name: TN-IBC cell line SUM149PT

growth_protocol: A reverse transfection method was performed in which 45 nM siRNA is initially allowed to complex in an assay plate with DharmaFECT-2 transfection reagent (0.07 µL, GE Dharmacon, Lafayette, CO) for 30 minutes, followed by addition of 30 µL of solution containing 750 cells/condition, after which the plates were incubated for 48 hours at 37°C in a 5% CO2 atmosphere.

treatment_protocol: After incubation, cells were treated with EPA (IC50: 50 µM) and incubated for an additional 72 hours at 37°C in a 5% CO2 atmosphere. OTP3 and TOX were identified as optimal negative and positive siRNA transfection controls, respectively.

value: untreated


title: C57Bl6-JunKO_iBMDM_RNA_Veh_GJF_17-12-03-rep2


title: C57Bl6_iBMDM_RNA_zsGreen_GJF_17-12-03-rep2


title: BELINOSTAT 48hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Belinostat and collected at 48 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 48hpa. Samples were treated with Belinostat.


title: untreated replicate 2

label_protocol: incubation with CellTiter-Blue® (Promega Corporation, Madison, WI) and quantification of fluorescence intensity (PHERAstar FS Plate Reader, BMG Labtech Inc., Cary, NC)


title: CONTROL 48hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected at 48 hours post amputation.

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails at 48hpa. Samples were untreated.

value: Control


title: CONTROL 48hr replicate 3


title: BELINOSTAT 48hr replicate 1

value: Belinostat


title: BELINOSTAT 48hr replicate 3


title: CONTROL 48hr replicate 2


title: D15_serum_GDF9_ctrl_0.1_C3 (bulk RNA-seq)

city: Warsaw

first: Marcin

last: Tabaka

address: Kasprzaka 44/52

country: Poland

institute: International Centre for Translational Eye Research

data_processing:
Reads were aligned to the UCSC mm10 transcriptome (using RNA-Seq genome-aligner  STAR), and a matrix of UMI counts was obtained using CELLRANGER from the 10X Genomics pipeline  (v2.0.0) with default parameters. Bulk RNAseq data were analyzed as follows: reads (83 bp) were aligned to the UCSC mm10 transcriptome, and a matrix of read counts was obtained using the QuantSeq processing pipeline (http://rpubs.com/chapmandu2/171024) with the reference genome sequence and gene annotations (GTF file) from the Cellranger 10X Genomics pipeline (v2.0.0) (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation).
Genome_build: mm10
Supplementary_files_format_and_content: expression_matrix_GDF9_bulk.csv.gz, h5

source_name: 2nd MEFs

growth_protocol: To determine the effect of GDF9 on reprogramming, we plated secondary MEFs at a concentration of 5,000 cells per well of a 24-well plate and added either recombinant mouse GDF9 (R&D Systems, 739-G9-010, lot SOZ0516121) daily from day 8 onward, or control (0.1% Bovine Serum Albumin in 4 mM HCl, R&D Systems, RB04). We initially tested different doses (0, 0.1 µg/ml, 0.5 µg/ml, and 1 µg/ml) and then confirmed results seen at the highest dose in multiple independent experiments. We used three distinct approaches to determine the proportion of pluripotent cell at day 15: (i) counting the number of Oct4-EGFP+ colonies using a fluorescence microscope, (ii) bulk RNAseq (Quantseq, Lexogen) and (iii) scRNAseq. For each assay, experiments were performed in biological triplicates (each assay using separate replicates).

extract_protocol:
We collected a total of ~50,000 cells. For all collections, selected wells were trypsinized for 5 mins followed by inactivation of trypsin by addition of MEF medium. Cells were subsequently spun down and washed with 1X PBS supplemented with 0.1% bovine serum albumin. The cells were then passed through a 40 micron filter to remove cell debris and large clumps.
Single-cell RNA-Seq libraries were generated from each time point using the 10X Genomics Chromium Controller Instrument (10X Genomics, Pleasanton, CA) and ChromiumTM Single Cell 3’ Reagent Kits v2  according to manufacturer’s instructions. Reverse transcription and sample indexing was performed using the C1000 Touch Thermal cycler with 96-Deep Well Reaction Module. Briefly, the suspended cells were loaded on a Chromium controller Single-Cell Instrument to first generate single-cell Gel Bead-In-Emulsions (GEMs). After breaking the GEMs, the barcoded cDNA was then purified and amplified. The amplified barcoded cDNA was fragmented, A-tailed and ligated with adaptors. Finally, PCR amplification was performed to enable sample indexing and enrichment of the 3’ RNA-Seq libraries. The final libraries were quantified using Thermo Fisher Qubit dsDNA HS Assay kit (Q32851) and the fragment size distribution of the libraries were determined using the Agilent 2100 BioAnalyzer High Sensitivity DNA kit (5067-4626). Pooled libraries were then sequenced using Illumina Sequencing By Synthesis (SBS) chemistry. Bulk RNA-seq libraries were generated from QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen). Libraries were made according to manufacturer's protocol and sequenced on illumina NextSeq 500.

tag: cell type

value: 2nd MEFs (OKSM)

tag: agent

value: control

tag: time

value: day 15


title: untreated replicate 1


title: ROMIDEPSIN 24hr replicate 3

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 24 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with Romidepsin.


title: treated replicate 3

value: EPA treatment


title: BELINOSTAT 48hr replicate 2


title: treated replicate 2


title: Elf1 AF RRBS

city: Seattle

first: David

last: Hawkins

state: WA

address: 1959 NE Pacific St, HSB K226

department: Division of Medical Genetics, Department of Genome Sciences

institute: University of Washington

data_processing:
Reads were aligned using Bismark v0.16.1
Methylation counts and levels were calculated using bismark_methylation_extractor and bismark2bedGraph
Genome_build: hg19
Supplementary_files_format_and_content: Methylation counts

source_name: Primed human embryonic stem cells

growth_protocol: As outlined in Sperber et al., 2015

extract_protocol:
DNA extracted using Qiagen All Prep Kit
genomic DNA was digested with MSPI; end repair, A-tail with Klenow exo- (NEB M0212S); gel size selection 150-350 bp; bisulfite conversion; PCR amplifcation with index primers

tag: developmental stage

value: primed

value: embryonic stem cell

tag: growth condition

value: Activin, FGF


title: Elf1 5iLA RRBS

source_name: Naïve human embryonic stem cells

value: naive


title: ROMIDEPSIN 24hr replicate 4

value: Romidepsin


title: treated replicate 1


title: CONTROL 24hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected at 24 hours post amputation.

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails at 24hpa. Samples were untreated.


title: ROMIDEPSIN 24hr replicate 1


title: CUP patient 61

city: Osaka-Sayama

first: Yoshihiko

last: Fujita

address: 377-2 Ohno-Higashi

country: Japan

institute: Kinki university School of Medicine

hyb_protocol: IVT products were magnetic-bead purified, frangmented, and hybridized onto Affymetrix U133 plus 2.0 GeneChip at 45° C for 16 h.

scan_protocol: Scanner in an Affymetrix GeneChip Scanner 3000 7G (Santa Clara, CA).

data_processing: Data extraction was done by the Affymetrix GCOS software v1.4.

source_name: metastatic lesion

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

extract_protocol: The mRNA extraction was done using the Isogen protocol

value: lymph node

tag: disease state

value: cancer of unknown primary


title: ROMIDEPSIN 24hr replicate 2


title: CONTROL 48hr replicate 1


title: Exp. Blastocyst 112415_03 SOLO

city: East Lansing

first: Uros

last: Midic

state: MI

address: 474 S. Shaw Lane

department: Animal Sciences

institute: Michigan State University

data_processing:
Illumina Real Time Analysis (RTA) v1.18.64 (SPIA libraries) & v2.7.6 (SoLo libraries)
Hisat2  to the Ensembl rhesus monkey genome (Mmul build v8.1.0, genome annotation relase-91)
Removing "ExAmp" duplicates with distance threshold 2500 using in-house developed Python code
DESeq2 comparisons between groups of libraries
Genome_build: Mmul 8.1.0 (Macaca Mulatta)
Supplementary_files_format_and_content: raw counts

organism: Macaca mulatta

source_name: Expanded Blastocyst

growth_protocol: Females were observed daily for signs of vaginal bleeding and the first day of menses was assigned cycle day 1. Beginning on cycle day 1–4 recombinant human FSH (r-hFSH: Organon, West Orange, NJ) was administered (37.5 IU) twice daily, intramuscularly for 7 days total. To obtain in vivo matured (VVM) oocytes, females were given recombinant hCG (1000 IU Ovidrel; Serono, Rockland, MA) on treatment day 8 in addition to the FSH treatment outlined above. COCs were removed at 28 – 30 h following hCG by ultrasound-guided aspiration. Oocytes were retrieved from aspirates. In vivo matured oocytes were rinsed and transferred into TL-PVA medium (37°C) under oil and inseminated according to standard procedure for IVF of rhesus macaque oocytes; this is Day 0 of embryo culture. Semen was collected from male macaques that had been trained for this procedure. Sperm were washed from seminal plasma and resuspended in TL-BSA medium. The next morning (Day 1), oocytes were transferred into 70 μl drops of chemically-defined, protein-free hamster embryo culture medium 9 (HECM-9) without or with relaxin (see below) under oil (37°C) and incubated at 37°C in a humidified atmosphere of 5% CO2, 10% O2 and 85% N2 for 48 hours. At approximately 60 hours post insemination non-cleaved oocytes were again assessed for developmental status. Non-cleaved oocytes exhibiting a polar body and all embryos were classified as having matured to metaphase II of meiosis (MII). Embryos were transferred into 70 μl drops of HECM-9 medium with 5% bovine calf serum (Gemini Bioproducts, West Sacramento, CA) with or without relaxin under mineral oil and incubated as described above. Embryos were transferred to fresh medium every other day until fixed on day 8 post insemination. Beginning on Day 5, embryos were observed with a Nikkon SMZ-2B microscope (Melville, NY) housed in a temperature-controlled isolette daily at 0700 and 1700 hrs for developmental stage.

extract_protocol:
All cumulus cells were removed by repeatedly pipetting oocytes with a narrow-gauge pipette that was just slightly larger than the oocytes while observing oocytes with a stereomicroscope. Using the PicoPureTM RNA Extraction kit, total RNA was isolated from each sample following the manufacturer protocol, including a DNAse digestion (RNase-Free DNase Set; Qiagen, Hilden, Germany) to remove any contaminating DNA.
SPIA libraries: 100 ng of each RNA sample was processed with the Ovation RNA-Seq System v2 using Ribo-SPIATM Technology (NuGen, San Carlos, CA).  After this initial processing, a Covaris-2 sonicator was used to mechanically fragment the cDNA to an average of 300 bp. This was then followed by a brief S1 nuclease digestion as previously described (Head et al., 2011).  After bead purification, the cDNA was processed through the Ovation Ultralow DR Multiplex Systems 1-16 (NuGen) for end repair, adaptor ligation and final library amplification.
SoLo libraries: cDNA libraries were produced with Nugen Ovation SoLo RNA-Seq(NuGEN, San Carlos, CA). After bead purification, the cDNA was processed: end repair, adaptor ligation and first round library amplification and purification. Then 20 ng of each library was used for the remainder of library preparation, which included use of InDA-C primers for rRNA depletion, as well as 2nd round library amplification and purification steps. SoLo Custom R1 primer was used instead of a standard Illumina R1 sequencing primer for the sequencing of the libraries.

value: embryo

value: Expanded Blastocyst

tag: library processing kit

value: SoLo


title: Exp. Blastocyst 111715_04 SOLO


title: C57Bl6-JunDKO_iBMDM_RNA_Veh_GJF_17-12-03-rep2

value: mouse BRAF(V600E), Myc immortalized bone marrow (passage 3-8) cells

value: male

value: Vehicle

value: C57Bl/6EiJ JunDKO


title: CONTROL 24hr replicate 3

value: Control


title: CONTROL 24hr replicate 2


title: CONTROL 24hr replicate 1


title: Exp. Blastocyst 111715_02 SOLO


title: Exp. Blastocyst 111715_01 SOLO


title: Exp. Blastocyst 111215_03 SOLO


title: Elf1 2iLIF RRBS

value: GSKi + MEKi (2i), Lif, IGF1, FGF


title: Exp. Blastocyst 111215_01 SOLO


title: Morula 022916_01 SOLO

source_name: Morula

value: Morula


title: Morula 022416_02 SOLO


title: Morula 021016_02 SOLO


title: Morula 021016_03 SOLO


title: 8-cell 112815_02 SOLO

source_name: 8-cell embryo

value: 8-cell embryo


title: 8-cell 020816_08 SOLO


title: BELINOSTAT 24hr replicate 3

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Belinostat and collected at 24 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 24hpa. Samples were treated with Belinostat.

value: Belinostat


title: BELINOSTAT 24hr replicate 4


title: BELINOSTAT 24hr replicate 2


title: 8-cell 020816_06 SOLO


title: 8-cell 020816_07 SOLO


title: BELINOSTAT 24hr replicate 1


title: 16HBE14o-

city: Kumamoto

first: Tsuyoshi

last: Shuto

state: Kumamoto

address: 5-1 Oe-honmachi, Chuo-Ku

department: Molecular Medicine

institute: Graduate School of Pharmaceutical Sciences, Kumamoto University

description: Gene expression data from normal 16HBE14o- cells.

hyb_protocol: Following fragmentation, 5.2 ug of ssDNA were hybridized for 16 hr at 45C on GeneChip HTA2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

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

data_processing:
The raw data were analyzed with Transcriptome Analysis Console 4.0 (TAC4.0) using Affymetrix default analysis settings and global scaling as shown below.
Array Type: HTA-2_0
Analysis Type: Expression (Gene + Exon)
Analysis Version: version 1
Summarization Method: Gene + Exon - SST-RMA
Pos vs. Neg AUC Threshold: 0.7
Genome Version: hg19 (Homo sapiens)
Annotation: HTA-2_0.na36.hg19.transcript.csv
Map File: HTA-2_0_MappingFile.r1.map
Probe group file: HTA-2_0.r3.pgf
Meta-probeset file: HTA-2_0.r3.Psrs.mps

source_name: Normal 16HBE14o- cells

label_protocol: Biotinylated ssDNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (Manual target preparation for GeneChip Whole Transcript (WT), Affymetrix).

growth_protocol: Grown in fibronectin/bovine serum albumin (BSA)-coated dishes from Invitrogen. MEM were supplemented with 10% fetal bovine serum, 100 U/mL of penicillin, and 100 mg/mL of streptomycin. Cells were cultured in a humidified incubator at 37°C with 5% CO2.

extract_protocol: RNA samples were extracted using RNeasy Mini Kit (QIAGEN, Valencia, CA).

tag: cell line

value: Normal bronchial epithelial cell line


title: WT-CFTR-CFBE41o-

description: Gene expression data from WT-CFTR-rescued CFBE41o- cells.

source_name: WT-CFTR-rescued CFBE41o- cells

value: CF bronchial epithelial cell line

value: WT-CFTR-rescue


title: CON

description: Gene expression data from negative control ASO-treated CF patients-derived CFBE41o- cells.

source_name: Negative control ASO-treated CF patients-derived CFBE41o- cells

treatment_protocol: Negative control and linc-SUMF1-2 ASO were treated to CFBE41o- cells for 48 h.

value: Control ASO


title: Tick_saliva_1A

city: Shanghai

first: Muhammad

middle: Irfan

last: Malik

state: China

address: 518 Ziyue Rd,

department: Shanghai Veterinary Research Institute

country: China

institute: Chinese Academy of Agricultural Sciences

data_processing:
Base-calling was performed using SOAPnuke software package
Data filtering: raw data contained different types of impurities. These included 5'-primer contaminants, no-insert tags, oversized insertion tags, low quality tags, poly A tags, small tags, and tags without a 3'-primer. All these contaminants were filtered according to the base quality value. We trimmed the adaptor sequence at the 3’-primer terminus, cleaned up 5’ adaptor contaminants formed by ligation, and collected the RNAs and analyzed their size distribution.
Alignment of clean reads were perofrmed using Bowtie2 software
sRNA and piRNA prediction was perforemed using miRDeep2 and Piano respectively.
sRNA expression level was calculated using Transcript Per Kilobase Million (TPM)
Genome_build: PRJNA16232
Supplementary_files_format_and_content: xlsx file include TPM value
column header Tick_saliva_1A in the file unknown.txt includes the read count of the novel identified miRNAs.

organism: Haemaphysalis longicornis

source_name: Saliva (Hypostome) from Semi-engorged fed adult tick

extract_protocol:
The collected saliva was put in trizol and total RNA was extracted according to the manufacturer’s protocol. Use Agilent 2100 Bioanalyzer（Agilent RNA 6000 Nano Kit）to test sample integrity and concentration, and NanoDrop to Inorganic ions or polycarbonate contamination.
Small RNA library was constructed according to the TruSeq Small RNA Sample Pre Kit (Illumina). Use the 200ng-1μg of RNA sample, then separate RNA segment of different size by PAGE gel,select 18-30nt（14-30 ssRNA Ladder Marker，TAKARA) stripe and recycle；

value: saliva

tag: feeding status

value: Semi-engorged fed

value: adult


title: CONTROL 12hr replicate 4

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, regenerating axolotl embryo tail tip tissue. Samples were untreated and collected at 12 hours post amputation.

source_name: 1.0mm distal tip of amputated, regenerating axolotl embryo tails at 12hpa. Samples were untreated.


title: ROMIDEPSIN 12hr replicate 3

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Romidepsin and collected at 12 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 12hpa. Samples were treated with Romidepsin.

value: Romidepsin


title: ROMIDEPSIN 12hr replicate 4


title: ROMIDEPSIN 12hr replicate 2


title: CFBE41o-

description: Gene expression data from CF patients-derived CFBE41o- cells.

source_name: CF patients-derived CFBE41o- cells


title: ROMIDEPSIN 12hr replicate 1


title: BELINOSTAT 12hr replicate 1

description: RAW microarray data quantified from 1.0 mm distal tip of heterogeneous, non-regenerating axolotl embryo tail tip tissue. Samples were treated with Belinostat and collected at 12 hours post amputation.

source_name: 1.0mm distal tip of amputated, non-regenerating axolotl embryo tails at 12hpa. Samples were treated with Belinostat.


title: CONTROL 12hr replicate 3


title: BELINOSTAT 12hr replicate 2


title: CONTROL 12hr replicate 2


title: 6874: D5_IFNg-IL10+

status: Public on Jan 30 2019

city: London

first: Esperanza

last: Perucha

address: Great Maze Pond

department: Inflammation Biology

country: United Kingdom

institute: King's College London

hyb_protocol: As per Affimetrix specifications

scan_protocol: As per Affimetrix specifications

data_processing: Raw data were summarised and normalised using Robust Multi-array Average (RMA)

source_name: Donor 5, sorted population IFNg-IL10+

label_protocol: As per Affimetrix specifications

growth_protocol: Cells were cultured in RPMI-1640 (containing 2mM L-glutamine + 0.1 g/l sodium bicarbonate) supplemented with 10mM Hepes, 100 U/ml Penicillin + 0.1 mg/ml Streptomycin and 10% fetal bovine serum

extract_protocol: Cell pellets for mRNA isolation were lysed in Trizol and RNA extracted by guanidium-isothescyanate phenol/chloroform extraction method following the manufacturer’s instructions

treatment_protocol: Cells were activated with plate bound CD3 (OKT3) and CD46 (TRA2.10) for 36h in the presence of IL2

tag: subject

value: Donor 5

tag: tissue

value: Peripheral blood CD4+ T cells


title: 6888: D9_IFNg+IL10-

source_name: Donor 9, sorted population IFNg+IL10-

value: Donor 9


title: 6876: D6_IFNg+IL10-

source_name: Donor 6, sorted population IFNg+IL10-

value: Donor 6


title: 6878: D6_IFNg-IL10+

source_name: Donor 6, sorted population IFNg-IL10+


title: 6887: D9_IFNg-IL10-

source_name: Donor 9, sorted population IFNg-IL10-


title: 6886: D8_IFNg-IL10+

source_name: Donor 8, sorted population IFNg-IL10+

value: Donor 8


title: 6889: D9_IFNg+IL10+

source_name: Donor 9, sorted population IFNg+IL10+


title: 6882: D7_IFNg-IL10+

source_name: Donor 7, sorted population IFNg-IL10+

value: Donor 7


title: 6879: D7_IFNg-IL10-

source_name: Donor 7, sorted population IFNg-IL10-


title: 6880: D7_IFNg+IL10-

source_name: Donor 7, sorted population IFNg+IL10-


title: linc-SUMF1-2 knockdown

description: Gene expression data from linc-SUMF1-2 ASO-treated CF patients-derived CFBE41o- cells.

source_name: Linc-SUMF1-2 ASO-treated CF patients-derived CFBE41o- cells

value: Linc-SUMF1-2 ASO


title: 6885: D8_IFNg+IL10+

source_name: Donor 8, sorted population IFNg+IL10+


title: 6883: D8_IFNg-IL10-

source_name: Donor 8, sorted population IFNg-IL10-


title: 6881: D7_IFNg+IL10+

source_name: Donor 7, sorted population IFNg+IL10+


title: 6877: D6_IFNg+IL10+

source_name: Donor 6, sorted population IFNg+IL10+


title: 6869: D4_IFNg+IL10+

source_name: Donor 4, sorted population IFNg+IL10+

value: Donor 4


title: 6875: D6_IFNg-IL10-

source_name: Donor 6, sorted population IFNg-IL10-


title: 6870: D4_IFNg-IL10+

source_name: Donor 4, sorted population IFNg-IL10+


title: 6884: D8_IFNg+IL10-

source_name: Donor 8, sorted population IFNg+IL10-


title: 6873: D5_IFNg+IL10+

source_name: Donor 5, sorted population IFNg+IL10+


title: 6890: D9_IFNg-IL10+

source_name: Donor 9, sorted population IFNg-IL10+


title: 6864: D3_IFNg+IL10-

source_name: Donor 3, sorted population IFNg+IL10-

value: Donor 3


title: 6871: D5_IFNg-IL10-

source_name: Donor 5, sorted population IFNg-IL10-


title: 6872: D5_IFNg+IL10-

source_name: Donor 5, sorted population IFNg+IL10-


title: 6867: D4_IFNg-IL10-

source_name: Donor 4, sorted population IFNg-IL10-


title: HCC1937_vector_DMSO

first: Baoyuan

last: Zhang

state: Shanghai

address: Ruijin er road

department: Ruijin hospital

institute: Shanghai jiaotong university

data_processing:
Illunima 2500 sequencer was used for raw data generation
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using tophat2.
FPKM values and expression data comparison were processed via cufflinks package.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each group ...

source_name: breast cancer cell

extract_protocol:
Cell culture medium was removed. Total RNA was extracted by Rneasy Plus Mini Kit and checked with Agilent bioanalyzer 2100 for RIN values. Then mRNA was isolated with NEBNext Poly(A) mRNA magnetic isolation module.
RNA library was prepared for sequencing using NEBNext Ultra Directional RNA Library Prep Kit for Illunima

value: Breast

tag: genotype

value: BRCA1 -/-

value: DMSO


title: HCC1937_wtBRCA1_DMSO

value: wild type


title: HCC1937_wtBRCA1_OTX-015

value: OTX-015 treated


title: HCC1937_vector_OTX-015


title: 6858: D2_IFNg-IL10+

source_name: Donor 2, sorted population IFNg-IL10+

value: Donor 2


title: 6866: D3_IFNg-IL10+

source_name: Donor 3, sorted population IFNg-IL10+


title: 6865: D3_IFNg+IL10+

source_name: Donor 3, sorted population IFNg+IL10+


title: 6868: D4_IFNg+IL10-

source_name: Donor 4, sorted population IFNg+IL10-


title: Tot_FH-Piwi_SL_GSS_Fly_rep3

city: Bethesda

first: Astrid

middle: Desiree

last: Haase

state: Maryland (MD)

address: 8 Center Drive, Bldg 8 1A04

department: NIDDK

institute: NIH

data_processing:
Trimming 5' (GTTCAGAGTTCTACAGTCCGACGATC) and 3' Adapters and barcode splitting (using cutadapt)
removal of strRNA by mapping (STAR) to strRNA sequences retrieved from UCSC (miRNA, rRNA, snRNA, snoRNA, tRNA)
Genome mapping to dm6 (igenome) using STAR
Genome_build: dm6
Supplementary_files_format_and_content: xlsx files: (1) mapping statistic (raw read counts), (2) Size ditribution (raw read counts), (3) Genomic annotation by category (raw read count)

organism: Drosophila melanogaster

source_name: Drosophila ovary

extract_protocol:
Please see small RNA library cloning protocol in manuscript for details.
In IP libraries, Flag tagged or endogenous protein was immunoprecipitated, and associated RNAs were extracted. In total RNA libraries, RNA was size selected before 5' and 3' ligation, RT-PCR, PCRs, and quality control.

value: ovary

tag: barcode

value: RPI27; 03-NNACAGAGTG


title: Tot_FH-Piwi_SL_GSS_Fly_rep2

value: RPI26; 03-NNACAGAGTG


title: Tot_FH-Piwi_SL_Ago3_Fly_rep3

value: RPI27; 04-NNGCGATATG


title: Tot_FH-Piwi_SL_GSS_Fly_rep1

value: RPI25; 03-NNACAGAGTG


title: Tot_FH-Piwi_SL_Ago3_Fly_rep1

value: RPI25; 04-NNGCGATATG


title: Tot_FH-Piwi_SL_Ago3_Fly_rep2

value: RPI26; 04-NNGCGATATG


title: 6857: D2_IFNg+IL10+

source_name: Donor 2, sorted population IFNg+IL10+

value: Peripheral blood CD4+ T cells


title: 6856: D2_IFNg+IL10-

source_name: Donor 2, sorted population IFNg+IL10-


title: Tot_FH-Piwi_SL_wt_Fly_rep3

value: RPI27; 47-NNTCTGTGTG


title: 6855: D2_IFNg-IL10-

source_name: Donor 2, sorted population IFNg-IL10-


title: 6854: D1_IFNg-IL10+

source_name: Donor 1, sorted population IFNg-IL10+

value: Donor 1


title: 6851: D1_IFNg-IL10-

source_name: Donor 1, sorted population IFNg-IL10-


title: 6863: D3_IFNg-IL10-

source_name: Donor 3, sorted population IFNg-IL10-

value: Donor 3


title: 6852: D1_IFNg+IL10-

source_name: Donor 1, sorted population IFNg+IL10-


title: 6853: D1_IFNg+IL10+

source_name: Donor 1, sorted population IFNg+IL10+


title: Tot_FH-Piwi_SL_wt_Fly_rep2

value: RPI26; 47-NNTCTGTGTG


title: Tot_FH-Piwi_SL_wt_Fly_rep1

value: RPI25; 47-NNTCTGTGTG


title: Tot_Piwi_SL_KO_Fly_rep3

value: RPI27; 01-NNTGACTGTG


title: Tot_Piwi_SL_wt_Fly_rep1

value: RPI25; 02-NNACACTCTG


title: Tot_Piwi_SL_wt_Fly_rep2

value: RPI26; 02-NNACACTCTG


title: Tot_Piwi_SL_KO_Fly_rep1

value: RPI25; 01-NNTGACTGTG


title: Tot_Piwi_SL_wt_Fly_rep3

value: ovary

value: RPI27; 02-NNACACTCTG


title: IP_FH-Piwi_SL_LD_Fly

value: NNTCTGTGTG


title: IP_FH-Piwi_SL_Ago3_Fly


title: IP_FH-Piwi_SL_LD_OSC_rep3

description: Experiments in OSC are done by transient transfection, where the mutant proteins are expressed from an episomal plasmid. The genetic background of the OSC cell line remains constant. The cell line was generated by Y. Niki et al., PNAS 2006, and is available from DGRC (Drosophila Genomics Resource Center) stock number 190.

source_name: Ovarian somatic sheath cell line

value: Ovarian somatic sheath cell line


title: IP_FH-Piwi_SL_GSS_Fly


title: IP_FH-Piwi_SL_wt_Fly


title: IP_FH-Piwi_SL_hAgo2PT_OSC


title: IP_FH-Piwi_SL_hAgo2wt_OSC


title: IP_FH-Piwi_SL_PiwiP4_OSC


title: IP_FH-Piwi_SL_dAt5_OSC


title: Tot_Piwi_SL_KO_Fly_rep2

value: RPI26; 01-NNTGACTGTG


title: IP_FH-Piwi_SL_GSS_OSC_rep3


title: IP_FH-Piwi_SL_wt_OSC_rep3


title: IP_FH-Piwi_SL_Aub_OSC


title: IP_FH-Piwi_SL_wt_OSC_rep5


title: IP_FH-Piwi_SL_wt_OSC_rep4


title: IP_FH-Piwi_SL_Ago3_OSC_rep3


title: IP_FH-Piwi_SL_wt_OSC_rep2


title: IP_FH-Piwi_SL_GSS_OSC_rep2


title: IP_FH-Piwi_SL_wt_OSC_rep1


title: IP_FH-Piwi_SL_LD_OSC_rep2


title: 21d_3

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

institute: Peking University

description: cell induced by TGF-beta for 21 days

data_processing:
Clean reads were aligned to human reference hg19 using Tophat (version 2.1.1)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: Cufflinks(cuffquant, cuffnorm version 2.2.1) were used  to aquire normalized expression matrix (FPKM) covering all the samples.

source_name: 21d, MCF10A cell line

extract_protocol:
Total RNA was isolated from the cell pellets with RNA extraction kit (Qiagen, Cat No. 74104)
All the RNA products were confirmed with high quality (RQN score = 10.0) using the Fragment AnalyzerTM platform (Advanced Analytical Technologies, Inc).

value: TGF-beta

value: 21 days


title: 12d_1

description: cell induced by TGF-beta for 12 days

source_name: 12d, MCF10A cell line

value: 12 days


title: 21d_2

description: cell induced by TGF-beta for 21 days


title: 21d_1

description: cell induced by TGF-beta for 21 days


title: IP_FH-Piwi_SL_LD_OSC_rep1


title: 12d_2

description: cell induced by TGF-beta for 12 days


title: 8d_1

description: cell induced by TGF-beta for 8 days

source_name: 8d, MCF10A cell line

value: 8 days


title: 8d_3

description: cell induced by TGF-beta for 8 days


title: 12d_3

description: cell induced by TGF-beta for 12 days


title: 8d_2

description: cell induced by TGF-beta for 8 days


title: 5d_3

description: cell induced by TGF-beta for 5 days

source_name: 5d, MCF10A cell line

value: 5 days


title: IP_FH-Piwi_SL_GSS_OSC_rep1


title: 3d_3

description: cell induced by TGF-beta for 3 days

source_name: 3d, MCF10A cell line

value: 3 days


title: 5d_1

description: cell induced by TGF-beta for 5 days


title: IP_FH-Piwi_SL_Ago3_OSC_rep1


title: IP_FH-Piwi_SL_Ago3_OSC_rep2


title: IP_FH-Piwi_SL_dAt1_OSC


title: 3d_2

description: cell induced by TGF-beta for 3 days


title: 3d_1

description: cell induced by TGF-beta for 3 days


title: 2d_3

description: cell induced by TGF-beta for 2 days

source_name: 2d, MCF10A cell line

value: 2 days


title: 12h_1

description: cell induced by TGF-beta for 12 hours

source_name: 12h, MCF10A cell line

value: 12 hours


title: 12h_2

description: cell induced by TGF-beta for 12 hours


title: 2d_1

description: cell induced by TGF-beta for 2 days


title: control_2

description: cell without inducing

source_name: control, MCF10A cell line

value: control


title: control_1

description: cell without inducing


title: macrophages_donor2_butyrate

city: Oxford

first: Fiona

last: Powrie

address: Roosevelt Drive

department: Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences

institute: University of Oxford

description: Single cells from donor 2 butyrate condition.

data_processing:
Reads were aligned using 10x Genomics Cell Ranger pipeline (version 2.0.2) and human reference sequences (version 1.2.0).
To circumvent known index-hopping issues with the HiSeq 4000 platform, cell barcodes common to more than one sample were removed from the aggregated count matrix.
UMI counts were randomly down-sampled so as to normalize the median number of per-cell counts between the samples.
Cells with > 20% mitochondrial reads or fewer than 500 genes were excluded from the analysis.
Genome_build: GRCh38-1.2.0

source_name: Monocyte-derived macrophages

growth_protocol: Peripheral blood mononuclear cells (PBMC) were obtained by ficoll gradient. Monocyte-derived macrophages were generated using adherence method selection and M-CSF differentiation.

extract_protocol:
Single-cell RNA-sequencing libraries were generated using the 10x Genomics Single Cell 3’ Solution (version 2) and subjected to Illumina sequencing (HiSeq 4000)
10x Genomics Chromium™ Single Cell 3' Reagent Kit (v2 Chemistry)

treatment_protocol: After 2 washes with PBS, adherent monocytes were differentiated into Mϕ over the period of 5 days in presence of 100 ng/ml M-CSF in RPMI supplemented with 10% fetal calf serum (FCS) (Sigma-Aldrich), 100 U/ml penicillin, 100 μg/ml streptomycin, 30 mM HEPES, and 0.05 mM β-mercaptoethanol.

value: Monocyte-derived macrophages

tag: donor

value: Donor 2

tag: condition

value: Butyrate


title: macrophages_donor2_control

description: Single cells from donor 2 control condition.

value: Control


title: macrophages_donor1_butyrate

description: Single cells from donor 1 butyrate condition.

value: Donor 1


title: macrophages_donor1_control

description: Single cells from donor 1 control condition.


title: Control3

city: Los Angeles

first: junjun

last: jing

address: 2250 Alcazar Street

institute: Center for Craniofacial Molecular Biology, University of Southern California

data_processing:
Basecalls performed using CASAVA (Version 1.8.2)
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using Tophat version 2.0.8 with default parameter settings
Gencode M3 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

source_name: incisor

growth_protocol: Mice were raised in animal facilities according to protocol.

extract_protocol:
Incisors of one-month-old Axin2-CreER;β-cateninfl/fl and β-cateninfl/fl mice were dissected out, and the cervical loops were cut with a fine blade. After removing the epithelial tissue, the mesenchymal tissue was collected for RNA isolation.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: incisor

tag: age

value: post natal day 1 month

value: beta-cateninfl/fl


title: Day50_+CHIR_differentiated lung_cells_bam_file

city: New York

first: Hans-Willem

last: Snoeck

state: NY

address: 650 W. 168th Street, BB816

department: Medicine

institute: Columbia University Medical Center

description: Read 1: 28, Index read 1 (i7): 8, Index read 2 (i5): 0, Read 2: 98

data_processing:
10x genomics' cellranger pipeline v2.0.0 was used to process the data.
Genome_build: GRCh38
Supplementary_files_format_and_content: Cloupe files containing read counts for visualization in the 10X Loop Browser. Tsv files containing the gene-barcode matrices.

source_name: RUES2 Human Embryonic Stem Cells

growth_protocol: ES cell–derived Lung Epithelial cells generated by directed differentiation of RUES 2 Embryonic Stem Cell line to first definitive endoderm,then anterior foregut endoderm followed by specification for the lung field according to established protocols (Huang, SX. et al. Nature Protocols (2015)).  Maturation of the lung progenitors was achieved after treatment with dexamethasone, c-AMP and IBMX in the presence or absence of CHIR9921.

extract_protocol:
Collagen I gels were digested with Colagenase type I. Cell clumps were collected and trypsinized with 0.05% Trypsin-EDTA until single cells.
Libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v2, 16 rxns PN-120237. The protocol was followed according to manufacturer's instructions.
We targeted 5000 cells/library, and used 12 cycles for cDNA Amplification and 12 cycles for the Sample Index PCR. Libraries were pooled and sequenced to a depth of ~350M reads on an Illumina HiSeq 4000.

tag: cell type

value: Lung progenitors


title: 5d_2

description: cell induced by TGF-beta for 5 days

tag: agent

value: TGF-beta


title: day4

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

description:
PBMCs isolated from a patient with AML 4 days after treatment with a combination of azacitidine and venetoclax.
processed data file: all_samples_raw_counts_matrix.txt
processed data file: cell_metadata.txt

data_processing:
Single-cell RNA sequencing data was initially processed by the Cell Ranger pipeline (v2.0.1) from 10x Genomics. The generated count matrices were then analyzed using the Seurat package (v2.2.1) in R . Read counts were normalized to library size, scaled by 10,000, log-transformed, and filtered based on the following criteria: cells with less than 250 genes detected or with a proportion of UMIs mapped to mitochondrial genes over 0.15 were excluded from analysis; genes detected in less than 5 cells were also excluded. Cell-to-cell variation in gene expression driven by the number of detected molecules and mitochondrial gene expression was regressed out using linear regression. Dimensionality reduction was performed with PCA followed by t-SNE projection and graph-based clustering using the first 15 principal components.
Genome_build: GRCh38
Supplementary_files_format_and_content: all_samples_raw_counts_matrix.txt: Count matrix with UMI counts per gene per cell in text format.
Supplementary_files_format_and_content: cell_metadata.txt: Cell annotation in text format.

source_name: PBMCs

extract_protocol:
Total mononuclear cells were isolated from specimens by standard Ficoll procedures.
10x Genomics 3' end library kit.

treatment_protocol: PBMCs isolated from a patient with AML at baseline, and at 2 and 4 days after treatment with a combination of azacitidine and venetoclax.

value: AML

value: PBMCs

tag: treatment

value: Azacitidine and venetoclax

tag: timepoint

value: Day 4


title: day0

description:
PBMCs isolated from a patient with AML at baseline.
processed data file: all_samples_raw_counts_matrix.txt
processed data file: cell_metadata.txt

value: Day 0


title: day2

description:
PBMCs isolated from a patient with AML 2 days after treatment with a combination of azacitidine and venetoclax.
processed data file: all_samples_raw_counts_matrix.txt
processed data file: cell_metadata.txt

value: Day 2


title: Axin2-betacko1


title: Axin2-betacko3


title: Control1


title: Control2


title: Axin2-betacko2


title: TAC2

data_processing:
Basecalls performed using CASAVA (Version 1.8.2)
Raw sequencing reads were first trimmed from both ends with Quality Score method (bases with quality score Phred less than 20 were trimmed from both ends, and trimmed reads shorter than 25 nt were excluded from downstream analyses)
Trimmed reads were then mapped to the mouse genome mm10 using Tophat version 2.0.8 with default parameter settings
Gencode M14 annotation was used to quantify the aligned reads to genes/transcripts using Partek E/M method.
read counts per gene/transcript in all samples were normalized using Upper Quartile normalization and analyzed for differential expression using Partek Gene Specific Analysis method (genes/transcripts with less than 10 reads in any sample among a data set were excluded).
Genome_build: mm10
Supplementary_files_format_and_content: .txt file with normalized gene counts

extract_protocol:
Incisors of one-month-old Gli1-CreER;tdT and Axin2-CreER;tdTmice were dissected out, and the cervical loops were cut with a fine blade. We performed laser capture microdissection  of the Axin2+ and Gli1+ cells using the Zeiss PALM Laser Capture Microdissection System
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 2d_2

description: cell induced by TGF-beta for 2 days

tag: time

value: 2 days


title: TAC3


title: 12h_3

description: cell induced by TGF-beta for 12 hours

value: 12 hours


title: control_3

description: cell without inducing

value: control


title: MSC3


title: TAC1


title: MSC1


title: MSC2


title: Day50_-CHIR_differentiated lung_cells_bam_file

treatment_protocol: ES cell–derived Lung Epithelial cells generated by directed differentiation of RUES 2 Embryonic Stem Cell line to first definitive endoderm,then anterior foregut endoderm followed by specification for the lung field according to established protocols (Huang, SX. et al. Nature Protocols (2015)).  Maturation of the lung progenitors was achieved after treatment with dexamethasone, c-AMP and IBMX in the presence or absence of CHIR9921.


title: KDM4E

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

department: UMR7216 "Epigenetics and Cell Fate"

country: France

institute: CNRS-Université Paris Diderot - Sorbonne Paris Cité

description: siRNA

hyb_protocol: Not applicable

scan_protocol: Not applicable

data_processing: RNA abundance was measured with Nanostring technology (Nanostring Flex nCounter analysis system). Raw count were normalized first with internal controls (Nanostring POS controls) and with three houseking gene (PGK1, TPB, TUBB2A) with R according nCounter Data expression analysis guide.

label: nanostring

label_protocol: The samples were not labeled

growth_protocol: IMR90 cells were grown in DMEM/10%FBS/PenStrep.

extract_protocol: Total RNA was collected by using Upzol and phenol-chloroform. Only samples with RIN>7.6 and 260nm/280nm ratio >1.8 were kept for Nanostring analysis.

treatment_protocol: siRNA pools were reverse transfected into 6-well plates and RNA was collected after 5 days

tag: sirna

value: 164 distinct siRNA pools


title: KDM5A

description: siRNA


title: KDM5C

description: siRNA


title: KDM6B

description: siRNA


title: KDM3B

description: siRNA


title: KDM5B

description: siRNA


title: PBRM1

description: siRNA


title: KDM4D

description: siRNA


title: KDM4C

description: siRNA


title: KMT2C

description: siRNA


title: KDM2B

description: siRNA


title: KDM4A

description: siRNA


title: DNMT1-2

description: CTRL+


title: 18_2.4 [Lung_6_0mM]

city: Jefferson

first: Aline

last: de Conti

state: Arkansas

address: 3900 NCTR Road

department: Biochmical Toxicology

institute: FDA-NCTR

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity > 9.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent GEx hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent-074809 SurePrint G3 Mouse GE v2 8x60K Microarray, Agilent, for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent).

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (Agilent Technologies G2600D SG14324425) using one color scan setting for G3 Microarray format 8x60k (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded. The raw data were normalized using ArrayTrack software (USFDA National Center for Toxicological Research, Jefferson, AR).

source_name: Mouse lung_Control

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.6 ug RNA using the Quick Amp Labeling Kit, one-color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was extracted from liver tissue using miRNeasy Mini kits (Qiagen, Valencia, CA) according to the manufacturer’s instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

tag: gender

value: Female

value: none (control)

value: liver


title: 19_1.1 [Liver_1_0mM]

source_name: Mouse liver_Control


title: 19_2.4 [Liver_4_0mM]


title: 19_1.4 [Liver_30_0.7mM]

source_name: Mouse liver_Acrylamide treated

value: 0.7mM Acrylamide


title: 18_1.4 [Lung_30_0.7mM]

source_name: Mouse lung_Acrylamide treated


title: 19_1.2 [Liver_27_0.7mM]


title: Ctrlneg-2

description: CTRL-

tag: cell line


title: 18_2.2 [Lung_4_0mM]


title: 18_1.2 [Lung_28_0.7mM]


title: 19_1.3 [Liver_3_0mM]


title: 18_2.3 [Lung_29_0.7mM]


title: KMT2E

description: siRNA


title: KMT2A

description: siRNA


title: KDM3A

description: siRNA


title: 19_2.3 [Liver_29_0.7mM]


title: 18_1.3 [Lung_5_0mM]


title: KDM2A

description: siRNA


title: KDM1A

description: siRNA


title: KDM1B

description: siRNA


title: HMGB3

description: siRNA


title: HDAC5

description: siRNA


title: HDAC8

description: siRNA


title: KAT6B

description: siRNA


title: INO80

description: siRNA


title: KAT2A

description: siRNA


title: HDAC3

description: siRNA


title: KAT6A

description: siRNA


title: KAT2B

description: siRNA


title: HDAC2

description: siRNA


title: HMGB1

description: siRNA


title: HDAC7

description: siRNA


title: ELP3

description: siRNA


title: HDAC11

description: siRNA


title: ARID1A

description: siRNA


title: DNMT1-4

description: CTRL+


title: EZH2

description: siRNA


title: Ctrlneg-1

description: CTRL-


title: EZH1

description: siRNA


title: ASF1A

description: siRNA


title: PLK4_ech_179

treatment_protocol: Infections with the indicated retroviruses were carried out in 6-well plates, and RNA was collected 4 days after infection.

value: infected with a collection of 192 genetically activated kinases (Addgene# 1000000012)

tag: kinase

value: activated kinase


title: PFKL_ech_177


title: NME7_ech_176


title: NTRK3_ech_173


title: MOBKL1A_ech_175


title: TNK2_ech_172


title: DGUOK_ech_174


title: CSNK1G1_ech_171


title: STK32B_ech_167


title: PBK_ech_166


title: MAP3K14_ech_170


title: CAMK4_ech_194


title: STK32C_ech_142


title: TIE1_ech_185


title: PLK3_ech_182


title: SRPK2_ech_186


title: PRKAR2A_ech_188


title: CAMK2D_ech_193


title: TSSK6_ech_191


title: CSNK1E_ech_192


title: RIOK1_ech_181


title: STK32A_ech_190


title: SPHK2_ech_141


title: ARN0203_ech_203

source_name: Agilent #750500

value: Human reference


title: STK4_ech_184


title: ITPKB_ech_139


title: MAPK12_ech_138


title: TESK1_ech_137


title: PAK4_ech_136


title: IHPK2_ech_140


title: DYRK4_ech_134


title: MVK_ech_135


title: MAST1_ech_131


title: ARN0202_ech_202


title: MAP2K6_ech_187


title: PIP5K1B_ech_165


title: YES1_ech_164


title: MAP3K8_ech_162


title: ITK_ech_158


title: EPHA4_ech_161


title: PCTK2_ech_155


title: ULK4_ech_157


title: HK3_ech_153


title: MAPKAP1_ech_156


title: BTK_ech_159


title: PRKAG2_ech_150


title: NADK_ech_133


title: PNKP_ech_149


title: PRKACG_ech_145


title: STK40_ech_146


title: SNF1LK_ech_152


title: HK1_ech_147


title: ARN0201_ech_201


title: TSSK1B_ech_130


title: CKB_ech_143


title: ITPK1_ech_144


title: AAK1_ech_129


title: MOBKL2A_ech_128


title: GK_ech_163


title: PFKM_ech_127


title: PLK2_ech_126


title: PIP5K2A_ech_154


title: NUAK2_ech_151


title: RPSK6A3_ech_160


title: PDIK1L_ech_132


title: FRK_ech_124


title: PIK3R5_ech_148


title: GRK5_ech_125


title: PI4K2B_ech_123


title: PIK4CA_ech_121


title: SYK_ech_107


title: STK33_ech_106


title: PRKCD_ech_120


title: PACSIN1_ech_104


title: CLK1_ech_105


title: PMVK_ech_103


title: HIPK1_ech_102


title: NEK3_ech_100


title: NEK11_ech_99


title: PIP5K3_ech_98


title: MAP2K7_ech_97


title: GRK6_ech_101


title: CSNK1A1L_ech_96


title: RPS6KA6_ech_117


title: PRKCI_ech_115


title: DLG5_ech_116


title: PDXK_ech_112


title: PIK3R3_ech_114


title: ADRBK2_ech_113


title: VRK3_ech_122


title: CERK_ech_111


title: RPS6KL1_ech_109


title: HK2_ech_110


title: ARN0200_ech_200


title: CAMK1G_ech_189


title: ADCK4_ech_183


title: ADRBK1_ech_108


title: MAPK6_ech_119


title: PKN1_ech_178


title: HCK_ech_118


title: CKMT2_ech_180


title: ADPGK_ech_169


title: CMPK_ech_168


title: FASTK_ech_70-2


title: PTK2_ech_4-2


title: PIK3CG_ech_3-2


title: PLAU_ech_81


title: ARN0197_ech_197


title: PCTK3_ech_82


title: OXSR1_ech_83


title: ARN0198_ech_198


title: AURKA_ech_80


title: PRKRA_ech_78


title: MAPK13_ech_79


title: AKT3_ech_2-2


title: MKNK1_ech_77


title: TYK2_ech_76


title: PKM2_ech_75


title: IMR90#2_ech_1-2

value: empty vector


title: LIMK1_ech_73


title: BLK_ech_74


title: AMHR2_ech_93


title: GK2_ech_94


title: MAP3K6_ech_84


title: ACVR1_ech_91


title: RIOK2_ech_88


title: PCK2_ech_89


title: STK3_ech_92


title: ADCK5_ech_95


title: FGR_ech_87


title: VRK2_ech_86


title: RPS6KB2_ech_85


title: LIMK2_ech_90


title: RIOK3_ech_57


title: GALK2_ech_58


title: MAPK14_ech_72


title: CDC2_ech_56


title: CALM2_ech_55


title: NEK6_ech_60


title: BMX_ech_52


title: PRKCZ_ech_54


title: TAOK3_ech_53


title: PCTK1_ech_50


title: DAK_ech_51


title: CSNK1G2_ech_49


title: PAPSS1_ech_48


title: IKBKE_ech_47


title: MAP2K5_ech_45


title: PIP5K1A_ech_59


title: CDK5_ech_46


title: CKM_ech_40


title: LCK_ech_42


title: MELK_ech_43


title: MATK_ech_44


title: CLK2_ech_66


title: STK38L_ech_41


title: PKN2_ech_39


title: PIK4CB_ech_38


title: RPS6KA5_ech_67


title: RPS6KA2_ech_68


title: RET_ech_69


title: TTK_ech_37


title: DGKG_ech_61


title: CDK2_ech_62


title: CDK7_ech_63


title: MPP1_ech_36


title: GCK_ech_65


title: RPS6KB1_ech_7


title: PRKAA1_ech_9


title: PIK3CB_ech_8


title: CDK4_ech_71


title: MAP3K7_ech_5


title: PDPK1_ech_11


title: FGFR1_ech_10


title: ILK_ech_6


title: AKT1_ech_4


title: PLK1_ech_3


title: CAMKV_ech_34


title: PIM1_ech_2


title: CKMT1A_ech_64


title: CLK3_ech_35


title: IMR90#1_ech_1


title: SW39#1_ech_12


title: CHEK1_ech_26


title: UCK2_ech_29


title: MAPK7_ech_27


title: DYRK2_ech_28


title: CKS2_ech_30


title: CDK9_ech_25


title: TK1_ech_32


title: PDK1_ech_23


title: CAMKK1_ech_22


title: STK17B_ech_33


title: SGK_ech_21


title: SW39#2_ech_24


title: PRKACB_ech_20


title: PTK2_ech_16


title: AXL_ech_17


title: TBK1_ech_18


title: PIK3CG_ech_15


title: AKT3_ech_14


title: CKS1B_ech_31


title: IMR90#2_ech_13


title: LMNB2

description: siRNA


title: MBD1

description: siRNA


title: HDAC6

description: siRNA


title: HDAC1

description: siRNA


title: EHMT2

description: siRNA


title: LMNA

description: siRNA


title: EED

description: siRNA


title: HDAC4

description: siRNA


title: DNMT3A

description: siRNA


title: PPM1D

description: siRNA


title: PRMT1

description: siRNA


title: RBBP4

description: siRNA


title: MBD6

description: siRNA


title: PRDM2

description: siRNA


title: HAT1

description: siRNA


title: MECP2

description: siRNA


title: MBD5

description: siRNA


title: MBD4

description: siRNA


title: CHD4

description: siRNA


title: CHD6

description: siRNA


title: CHD8

description: siRNA


title: CHD1

description: siRNA


title: DNMT3B

description: siRNA


title: PRMT5

description: siRNA


title: DNMT1

description: siRNA


title: CDYL2

description: siRNA


title: CBX7

description: siRNA


title: CDYL

description: siRNA


title: CTBP1

description: siRNA


title: CBX5

description: siRNA


title: CAMK2B_ech_19


title: CBX6

description: siRNA


title: C24NAHG3REP1

city: Acton

first: Ian

middle: K

last: Greaves

state: act

address: clunies ross street

country: Australia

institute: csiro

data_processing:
Libraries were mapped with STAR version 2.5.3 using the TAIR10 genome and the araport11 annotation.  Default settings were used apart from --alignTranscriptsPerReadNmax 500000 and --quantMode TranscriptomeSAM GeneCounts.
The R package DESEQ2 was used to standardize reads between samples and to determine differentially expressed genes using default settings.
Statistical significance was defined as ±1.2 fold change, p-value ≤ 0.01 and a false discovery rate ≤ 0.01 (FDR).
Genes were only considered expressed and analysed if one sample had an average normalized read fragment count ≥ 30
Genome_build: TAIR10 - araport11
Supplementary_files_format_and_content: NahG_processed_reads.txt contains output read counts for arabidopsis genes present in araport 11 annotation.

organism: Arabidopsis thaliana

source_name: rosette tissue

growth_protocol: Seeds were sterilized and stratified at 4°C for 3 days and then grown on Gamborg’s B-5 Basal Media.  At 14DAS plants were transferred into debco seed raising mix supplemented with 1g/L Osmocote Extract mini controlled release fertilizer.  Plants were grown under 16hr light/8hr dark at 21°C.

extract_protocol:
21 DAS rosette tissue was frozen in liquid nitrogen.  Tissue was ground in a mortar and pestle with the Qiagen RNAeasy plant minikit used to extract total RNA.  Total RNA was sent to AGRF for processing
illumina Tru-seq kit was used for library construction

tag: accession

value: rosette tissue

value: 21 days after sowing

tag: genotype/variation

value: NahG transgene


title: CBX3

description: siRNA


title: PHF8

description: siRNA


title: C24NAHG2REP2

tag: tissue


title: ZNF217

description: siRNA


title: C24NAHG2REP1


title: CBX1

description: siRNA


title: MBD3

description: siRNA


title: C24B_REP2

value: wildtype


title: MBD2

description: siRNA


title: ZHX1

description: siRNA


title: C24B_REP1


title: ZBTB38

description: CTRL+


title: CHD3

description: siRNA


title: C24 x Ler rep3

value: Hybrid


title: C24NAHG3REP2


title: C24 x Ler rep2


title: ZBTB33

description: CTRL+


title: YTHDC1

description: siRNA


title: C24 x Ler rep1


title: WTAP

description: siRNA


title: LERNAHGREP2


title: ZHX2

description: siRNA


title: LERNAHGREP3


title: UHRF1

description: siRNA


title: UHRF2

description: siRNA


title: LerREP2

value: widltype


title: ZBTB40

description: siRNA


title: ZBTB4

description: CTRL+


title: SMAD4

description: siRNA


title: C24REP2


title: TRIM33

description: siRNA


title: C24REP3


title: ZCCHC7

description: siRNA


title: LerREP3


title: SCAPER

description: siRNA


title: HOXA5

description: siRNA


title: RXRA

description: siRNA


title: C24REP1


title: ZNF416

description: siRNA


title: ZBTB17

description: siRNA


title: TET2

description: CTRL+


title: TET3

description: CTRL+


title: LERNAHGREP1


title: LerREP1


title: DLX5

description: siRNA


title: GFP-G3BP_SORB_TOT_3: sorbitol stress total RNA from GFP-G3BP expressing U-2 OS cells replicate 3

city: Boulder

first: Roy

middle: Robert

last: Parker

state: CO

address: 3415 Colorado Ave

department: Chemistry and Biochemistry

institute: University of Colorado at Boulder

data_processing:
Read quality was assessed using fastqc.
Reads were trimmed using Trimmomatic 0.32 in paired and (PE) mode.
Reads were aligned using Tophat (version 2.0.6) and Bowtie2 (version 2.0.2) and the following parameters:–b2 –fast –microexon-search.
Differential expression analysis was performed using Cuffdiff (version 2.2.1) with the default parameters (Trapnell et al., 2013)

source_name: GFP-G3BP U-2 OS cells

growth_protocol: All cells were maintained in DMEM with high glucose, 10% fetal bovine serum, and 1% penicillin/streptomycin at 37°C/5% CO2, were used in all experiments. For eac stress granule prep, cells were grown to 85% confluency in three 500 cm2 square TC-treated culture dishes.

extract_protocol:
RNA extraction was performed using Trizol LS
Libraries were prepared using the KAPA Hyperprep kit with RiboErase

treatment_protocol: All cells were stressed in 100 ml of media containing the designated concentration of stressing agent.

value: GFP-G3BP U-2 OS cells

tag: molecule subtype

value: total RNA

tag: treatment group

value: soritol stress

value: 2.5 hours .5 M sorbitol stress


title: ZNF695

description: siRNA

value: 164 distinct siRNA pools


title: GFP-G3BP_SORB_TOT_2: sorbitol stress total RNA from GFP-G3BP expressing U-2 OS cells replicate 2


title: CTBP2

description: siRNA


title: GFP-G3BP_SORB_SG_3: GFP purified sorbitol-stress SG cores from GFP-G3BP expressing U-2 OS cells replicate 3

value: GFP-G3BP purified RNA


title: YTHDF1

description: siRNA


title: TDG

description: siRNA


title: Ctrlneg-4

description: CTRL-


title: GFP-G3BP_SORB_SG_2: GFP purified sorbitol-stress SG cores from GFP-G3BP expressing U-2 OS cells replicate 2


title: GFP-G3BP_SORB_TOT_1: sorbitol stress total RNA from GFP-G3BP expressing U-2 OS cells replicate 1


title: YTHDF2

description: siRNA


title: ddG3BP1/2_U-2OS_unstressed_TOT_3: unstressed total RNA from ΔΔG3BP1/2 U-2OS cells

source_name: ΔΔG3BP1/2 U-2 OS cells

value: delta-delta-G3BP1/2 U-2 OS cells

value: unstressed

value: no stress


title: GFP-G3BP_SORB_SG_1: GFP purified sorbitol-stress SG cores from GFP-G3BP expressing U-2 OS cells replicate 1


title: MEIS1

description: siRNA


title: ddG3BP1/2_U-2OS_unstressed_TOT_2: unstressed total RNA from ΔΔG3BP1/2 U-2OS cells


title: ZBTB44

description: siRNA


title: ddG3BP1/2_U-2OS_unstressed_TOT_1: unstressed total RNA from ΔΔG3BP1/2 U-2OS cells


title: YTHDF3

description: siRNA


title: KLF5

description: siRNA


title: SETDB2

description: siRNA


title: MPHOSPH8

description: siRNA


title: SETDB1

description: siRNA


title: GFP-G3BP_U-2OS_unstressed_TOT_2: unstressed total RNA from GFP-G3BP exprssing U-2OS cells replicate 2


title: SETD8

description: siRNA


title: ZNF114

description: siRNA


title: GFP-G3BP_U-2OS_unstressed_TOT_1: unstressed total RNA from GFP-G3BP exprssing U-2OS cells replicate 1


title: PABPC1_ddG3BP1/2_SORB_TOT_3: sorbitol stress total RNA from ΔΔG3BP1/2 replicate 3

value: sorbitol stress


title: SETD2

description: siRNA


title: PABPC1_ddG3BP1/2_SORB_TOT_2: sorbitol stress total RNA from ΔΔG3BP1/2 replicate 2


title: SETD7

description: siRNA


title: PABPC1_ddG3BP1/2_SORB_SG_3: PABPC1 purified SG cores in ΔΔG3BP1/2  from sorbitol stress replicate3

value: PABPC1 purified RNA


title: PABPC1_SORB_TOT_2: sorbitol stress total RNA replicate2

source_name: parental U-2 OS cells

value: parental U-2 OS cells


title: PABPC1_ddG3BP1/2_SORB_SG_2: PABPC1 purified SG cores in ΔΔG3BP1/2  from sorbitol stress replicate2


title: SETD1A

description: siRNA


title: PABPC1_SORB_TOT_1: sorbitol stress total RNA replicate1


title: RNF2

description: siRNA


title: RING1

description: siRNA


title: zip-3 (gk3164) fed with P. aeruginosa, biological rep2

city: Worcester

first: Cole

last: Haynes

state: Massachusetts

address: 364 Plantation Street, 425

institute: U Mass Medical School

description:
counts.txt
S8
zip-3 pa14 2

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. Elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout --outFilterMultimapNmax 20  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --outFilterMismatchNmax 999  --outFilterMismatchNoverReadLmax 0.04  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  \)
featureCounts (subread-1.5.2) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: tab-delimited text file includes the raw count values from featureCounts for each sample

organism: Caenorhabditis elegans

source_name: zip-3 (gk3164) fed with P. aeruginosa

growth_protocol: Wildtype and zip-3(gk3164) worms were synchronized by bleaching, starved on empty NGM plates for 48h, transferred to E. coli or P. aeruginosa seeded NGM plates for 18h and then harvested.

extract_protocol:
Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols with standard Illumina P5 and P7 adapter sequence

treatment_protocol: Worms were fed with either E. coli or P. aeruginosa

value: whole organism

tag: genotype

tag: fed with

value: P. aeruginosa


title: PABPC1_SORB_SG_2: PABPC1 purified SG cores from sorbitol stress replicate2


title: RBBP7

description: siRNA


title: zip-3 (gk3164) fed with P. aeruginosa, biological rep3

description:
counts.txt
S12
zip-3 pa14 3

tag: age


title: REST

description: siRNA


title: TRIM28

description: siRNA


title: zip-3 (gk3164) fed with P. aeruginosa, biological rep1

description:
counts.txt
S4
zip-3 pa14 1


title: RCOR1

description: siRNA


title: zip-3 (gk3164) fed with E. coli, biological rep3

description:
counts.txt
S11
zip-3 op50 3

source_name: zip-3 (gk3164) fed with E. coli

value: E. coli


title: PABPC1_ARS_TOT_3: arenite stress total RNA replicate3

tag: cell type

value: arsenite stress

value: 1 hour .5 mM arsenite stress


title: zip-3 (gk3164) fed with E. coli, biological rep2

description:
counts.txt
S7
zip-3 op50 2


title: GFP-G3BP_U-2OS_unstressed_TOT_3: unstressed total RNA from GFP-G3BP exprssing U-2OS cells replicate 3

value: GFP-G3BP U-2 OS cells


title: PABPC1_ARS_TOT_2: arenite stress total RNA replicate2

value: total RNA


title: zip-3 (gk3164) fed with E. coli, biological rep1

description:
counts.txt
S3
zip-3 op50 1


title: wildtype fed with P. aeruginosa, biological rep3

description:
counts.txt
S10
wt pa14 3

source_name: wildtype fed with P. aeruginosa

value: wildtype


title: SUZ12

description: siRNA


title: TRIM24

description: siRNA


title: PABPC1_ARS_TOT_1: arenite stress total RNA replicate1


title: wildtype fed with P. aeruginosa, biological rep1

description:
counts.txt
S2
wt pa14 1


title: wildtype fed with P. aeruginosa, biological rep2

description:
counts.txt
S6
wt pa14 2


title: SETD1B

description: siRNA


title: PABPC1_ARS_SG_3: PABPC1 purified SG cores from arenite stress replicate3


title: wildtype fed with E. coli, biological rep3

description:
counts.txt
S9
wt op50 3

source_name: wildtype fed with E. coli


title: wildtype fed with E. coli, biological rep2

description:
counts.txt
S5
wt op50 2


title: PABPC1_ARS_SG_2: PABPC1 purified SG cores from arenite stress replicate2


title: wildtype fed with E. coli, biological rep1

description:
counts.txt
S1
wt op50 1


title: PABPC1_SORB_SG_1: PABPC1 purified SG cores from sorbitol stress replicate1

value: 2.5 hours .5 M sorbitol stress


title: SUV39H1

description: siRNA

value: 164 distinct siRNA pools


title: E14.5Lung Shh;Prmt5

first: jie

last: jiao

address: No. 1 West Beichen Road, Chaoyang District

institute: The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences (CAS)

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeqPE Cluster Kit v3-cBot-HS (Illumia)  according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Hiseq  platform and  125 bp/150 bp  paired - end reads were generated.
Index of the reference genome(mm10) was built using Bowtie v2.2.3  and paired - end  clean  reads  were  aligned  to  the  reference  genome  using  TopHat  v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped  to this gene.
Genome_build: mm10
Supplementary_files_format_and_content: Counts and FPKMs

source_name: mouse lung

extract_protocol:
Whole lung RNA was extracted as described for RT-PCR using TRIZOL.
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)

tag: strain

tag: developmental stage

value: embryo

value: lung

value: Prmt5 knockdown


title: SUV420H1

description: siRNA


title: PABPC1_ARS_SG_1: PABPC1 purified SG cores from arenite stress replicate1

tag: treatment


title: DNMT1-3

description: CTRL+


title: SMARCA5

description: siRNA


title: Ctrlneg-3

description: CTRL-


title: SMARCA4

description: siRNA


title: SUV420H2

description: siRNA


title: Sham-1

city: Birmingham

first: Junjie

last: Yang

state: AL

address: 1670 University Blvd

department: BME

institute: UAB

data_processing:
Basecalls performed using Illumina's bcl2fastq version 2.18.0.12
Raw sequence files were uploaded to Qiagen's GeneGlobe Data Analysis Center Primary QIAseq miRNA Quantification tool for alignment to the mouse genome.
Unique Molecular indexes (UMI) are counted for each microRNA and expression values are determined based on the UMI signature for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited Excel file containing raw UMIs and raw read counts for each microRNA

source_name: Plasma

extract_protocol:
Peripheral blood was collected from MI mice and sham mice and centrifuged to get plasma. And then RNA was harvested using miRNeasy Serum/Plasma Advanced Kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
microRNA libraries were prepared with the Qiagen microRNA kit for sequencing on the Illumina platforms

value: Plasma

tag: surgery

value: sham


title: E14.5Lung Control

value: control


title: Sham-2


title: SIRT1

description: siRNA

tag: sirna


title: MI-2

value: myocardial infarction


title: MI-1


title: SIN3A

description: siRNA


title: DICER1

description: siRNA


title: BRD7

description: siRNA


title: BRD4

description: siRNA


title: CAF1-TS1-Ctrl

city: Singapore

first: Gokce

last: OGUZ

address: 60 Biopolis St, GENOME, #02-01

department: Bioinformatics Consulting and Training Platform

country: Singapore

institute: Genome Institute of Singapore

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina GenomeStudio 2010, quantile normalization

source_name: Colon tumor tissue

label_protocol: Standard Illumina protocol. In brief, 500 ng total RNA was converted to single-stranded cDNA using a T7 Oligo(dT) primer, and subsequently converted to double-stranded DNA (dsDNA) template for transcription. The dsDNA was then amplified and labeled with biotin to generate biotinylated cRNA.

growth_protocol: The TS1 cells were maintained in cancer stem cell medium [serum-free DMEM/Ham’s F12, supplemented with B27, N2 (Invitrogen), 20 ng ml-1 epidermal growth factor (EGF) and 20 ng ml-1 basic-fibroblast growth factor (bFGF) (BD Biosciences), 0.5 µg ml-1 hydrocortisone (Sigma-Aldrich), and 4 µg ml-1 heparin (Stemcell Technologies)]. The CAF1 cells were maitained in DMEM medium (GIBCO) supplemented with 10% fetal bovine serum (FBS).

extract_protocol: Total RNA was isolated using Trizol (Invitrogen) and purified with the RNeasy Mini Kit (Qiagen).

treatment_protocol: The TS1 cells were transduced with RFP. Then TS1 or CAF1-TS1 co-culture were treated with or without TGFBR inhibitor (SD208) for 7 days. The RFP-TS1 cells were then FACS-sorted and subject to transcriptome analysis.

value: tumorspheres (TS) in coculture with cancer-associated fibroblast (CAF)

tag: disease state

value: colorectal cancer


title: CAF1-TS1-SD208


title: NF2

source_name: adjacent normal mucosa

growth_protocol: All the cells were maitained in DMEM medium (GIBCO) supplemented with 10% fetal bovine serum (FBS).

value: normal fibroblasts (NFs)


title: CAF1

value: cancer-associated fibroblasts (CAFs)


title: BRD3

description: siRNA

tag: cell line


title: NF4


title: TS1-SD208

value: tumorspheres (TS)


title: NF3


title: BPTF

description: siRNA


title: BRD1

description: siRNA


title: BRD2

description: siRNA


title: NF1


title: TS1-Ctrl


title: BRD8

description: siRNA


title: CAF4


title: BMI1

description: siRNA


title: ATRX

description: siRNA


title: ASH1L

description: siRNA


title: VTA_WT_ZT20_rep1

city: Lübeck

first: Henrik

last: Oster

address: Marie Curie Street

department: CBBM

country: Germany

institute: University of Lübeck

hyb_protocol: cDNAs were hybridized for 17 h at 45°C to GeneChip Mouse Gene 1.0 ST Arrays (Affymetrix)

scan_protocol: Arrays were washed and stained in the GeneChip Fluidics Station 450 (Affymetrix) and scanned on a GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Affymetrix Powertools and robust multi-array average (RMA) were used for background correction, quantile normalization and summarization of the raw intensity values. RMA, statistical analyses (Student’s t-test), calculation of the fold change of intensity values and graphical illustrations were performed using R software (version 2.13.1) along with the Bioconductor software package. Rhythmicity was assessed with CircWave (p < 0.05).
algorithm-name-0 = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
Q_probeset_summarize-Version = V916
affymetrix-algorithm-name = rma-bg,quant-norm.sketch=0.usepm=true.bioc=true,pm-only,med-polish
affymetrix-algorithm-version = 1.0

label_protocol: Biotin-labeled cDNA was synthesized using GeneChip Whole Transcript Sense Target Labeling Assay (Affymetrix)

growth_protocol: Animals were maintained under 12-h light: 12-h dark conditions at 21 °C and 50% humidity with food (standard chow) and water ad libitum

extract_protocol: RNeasy Mini Kit (Qiagen, Hilden Germany)

tag: gender

value: male

value: 10-12 weeks

tag: timepoint

value: brain; ventral tegmental area (VTA)


title: VTA_WT_ZT12_rep3


title: VTA_WT_ZT12_rep4


title: VTA_WT_ZT20_rep3


title: VTA_WT_ZT16_rep4


title: SMCHD1

description: siRNA


title: VTA_WT_ZT16_rep2


title: VTA_WT_ZT20_rep4


title: CAF3


title: VTA_WT_ZT20_rep2


title: SMARCD2

description: siRNA


title: VTA_WT_ZT12_rep2


title: VTA_WT_ZT16_rep3


title: SMARCC1

description: siRNA


title: SMARCB1

description: siRNA


title: VTA_WT_ZT12_rep1


title: VTA_WT_ZT16_rep1


title: SMARCD1

description: siRNA


title: VTA_WT_ZT8_rep4


title: AZI2

description: siRNA


title: SMARCC2

description: siRNA


title: SMARCA1

description: siRNA


title: SMARCA2

description: siRNA


title: SIRT7

description: siRNA


title: SIRT6

description: siRNA


title: SiO2d63_3 (3'SAGE-seq)

city: Chiba

first: Shigeyuki

last: Shichino

address: 2641, Yamasaki, Noda-shi

department: Department of Molecular regulation of Inflammatory and Immune Diseases

institute: Tokyo University of Science

data_processing:
Adapter trimming and quality filtering of sequencing data were performed by using Trimommatic-v0.36 and PRINSEQ-0.20.4. Filtered reads were mapped to Refseq mm10 by using Bowtie2-2.2.5. Reads that were not mapped to NlaIII sites were removed, and quantified tag numbers of each gene as the expression level of each gene.
Between-sample normalization was performed by using Microsoft R Open 3.3.3 and TCC package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw tag-count values for each sample

source_name: lung fibroblast

extract_protocol:
Murine lung fibroblasts were isolated at 0, 7, 14, and 63 days post-induction in both models. Lungs were cut into small pieces with a razor blade and digested enzymatically using 0.2% collagenase (Wako, Osaka, Japan), 0.96 mg/mL Dispase II (Roche, Basel, Switzerland), and 20 kU/mL DNase I (Sigma-Aldrich, St Louis, MO) for 60 min at 37°C. Erythrocytes and silica particles were removed by 70% Percoll (GE Healthcare, Buckinghamshire, UK) density separation. The single-cell suspensions were then depleted of lineage+ (CD31+, CD45+, EpCAM+, CD146+ and Ter119+) cells by negative selection with an AutoMACS cell separator (Miltenyi Biotech, Bergisch Gladbach, Germany). Propidium iodide− lineage− Col1a2GFP+ live fibroblasts were further purified by cell sorting using a FACS Aria II (BD).
PolyA RNAs were isolated and amplified from sorted fibroblasts according to the protocol described in (Huang H, Nucleic Actd Res, 2014) with some modifications. Briefly, 0.5 pmol of biotin-TEG-adapter-dT25 primers was bound to 20 μL of Dynabeads M270 streptavidin (Thermo Fisher Scientific). The washed beads (20 uL) were added to each cell lysis buffer containing 10,000 sorted fibroblasts and incubated for 30 min at room temperature with gentle rotation. Beads were washed once with wash buffer A [0.1% LiDS, 10 mM Tris-HCl (pH 7.5), 150 mM LiCl, and 1 mM EDTA] and three times with wash buffer B [10 mM Tris-HCl (pH 7.5), 150 mM LiCl, and 1 mM EDTA]. Beads were then suspended in 10 μL of RT mix 1 [1× SSIV buffer (Thermo Fisher Scientific), 2 mM dNTP, 2 M betaine (Sigma-Aldrich), 12 mM MgCl2, and 3.2 U/μL RNaseIn Plus (Promega)] and incubated for 90 s at 70ºC, 5 min at 35ºC, and immediately cooled on ice. RT mix 2 [10 μL; 1× SSIV buffer, 10 mM DTT (Thermo Fisher Scientific), 10 U/μL Superscript IV (Thermo Fisher Scientific), and 2 M betaine (Sigma-Aldrich)] was added, and reverse transcription was performed for 5 min at 35ºC and 15 min at 50ºC. Beads were washed once with cell lysis buffer, twice with B&W-T buffer [5 mM Tris-HCl (pH 7.5), 1 M NaCl, 0.5 mM EDTA, and 0.1% Tween-20], once with Tris-HCl (pH 8.0) and 20 μL of RNase H mix [1× first-strand buffer (Life Technologies, Carlsbad, CA, USA), 5 mM DTT, 0.6 U RNase H (Thermo Fisher Scientific)], and incubated for 20 min at 37ºC to digest reverse-transcribed mRNA. Beads were washed, 20 μL of TdT mix [50 mM Tris-HCl (pH 8.0), 100 mM KCl, 3 mM MgCl2, 1 mM CoCl2 (Roche), 0.65 mM dATP (Thermo Fisher Scientific), and 15.2 U/μL TdT (Roche)] was added on an ice-chilled aluminum rack, and polyA-tailing was performed for 3 min at 37ºC. The reaction was stopped by adding 5 μL of 0.5 M EDTA, and the enzyme was heat-inactivated by incubation for 10 min at 65ºC. Beads were washed, 20 μL of second-strand synthesis mix [1× KAPA Hifi ReadyMix (KAPA Biosystems, Wilmington, MA, USA) and 0.4 µM LNA anchored tagging primer] was added, and second-strand synthesis was performed according to the following program: 95ºC for 2 min, 98ºC for 20 s, 50ºC for 2 min, 72ºC for 7 min, and hold at 4ºC. Beads were washed, and 1/4 of the beads were used for the first round of whole-transcript amplification (WTA) in 25 μL of first-round WTA mix [1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.4 µM anchored tagging primer, and 0.4 µM 3′ WTA primer] using the following program: 95ºC for 3 min, five cycles of 98ºC for 20 s, 65ºC for 15 s, and 72ºC for 7 min, followed by 72ºC for 5 min and a hold at 4ºC. PCR products were purified twice with 0.6× AmPure XP beads (Beckman Coulter) and eluted with 23 μL of nuclease-free water. Second-round WTA mix [27 μL; 1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.614 µM 5′ WTA primer, and 0.614 µM Biotin-TEG-3′ WTA primer] was added, and the second round of WTA was performed using the following program: 95ºC for 3 min, nine cycles of 98ºC for 20 s, 65ºC for 15 s, and 72ºC for 7 min, followed by 72ºC for 5 min and a hold at 4ºC. PCR products were purified twice with 0.6× AmPure XP beads and eluted with 25 μL of Tris-HCl (pH 8.0). Amplified whole transcripts were quantified using a Nanodrop 1000 (Thermo Fisher Scientific), and size distribution was analyzed by agarose electrophoresis and SYBR Gold staining (Thermo Fisher Scientific).
3'SAGE-seq libraries were constructed according to the protocol described in (Matsumura H, Methods Mol Biol, 2012) with some modifications. Briefly, 150 ng of the whole-transcript library was restriction digested with NlaIII (New England Biolabs, Ipswich, MA, USA) for 2 h at 37ºC, and biotinylated 3′-tail transcripts were immobilized on Dynabead M-280 streptavidin beads (Thermo Fisher Scientific). Beads were washed, and 10 pmol of the CS1-EcoP15I-NlaIII adapter was ligated using a DNA ligation kit (Mighty Mix; Takara) for 30 min at 16ºC. Beads were washed three times with B&W-T buffer, once with 10 mM Tris-HCl (pH 8.0), suspended in 200 μL of EcoP15I digestion mix [1× NEBuffer 3.1, 1 mM ATP, and 0.2 U EcoP15I (New England Biolabs)], and digested for 16 h at 37ºC in a tightly sealed screw-cap tube with gentle rotation. Supernatant was purified using a Nucleospin Gel&PCR clean-up kit (Takara) and eluted twice with 12.5 μL of nuclease-free water. End-repair/polyA-tailing/ligation reactions were performed using NEBNext Ultra II modules (New England Biolabs) and 1.875 pmol of CS2-adapter according to manufacturer instructions. Reaction products were purified using a Qiagen MinElute Column (Qiagen, Hilden, Germany) and eluted with 13 μL of nuclease-free water. Barcoding mix [14.25 μL; 1× KAPA Hifi ReadyMix (KAPA Biosystems), 0.614 µM IonA-BC[N]-CS1-primer, and 0.614 µM Ion-trP1-CS2 primer] was added into 10.75 μL of elutant, and PCR enrichment was performed using the following program: 98ºC for 45 s, nine cycles of 98ºC for 15 s, 65ºC for 30 s, and 72ºC for 90 s, followed by 72ºC for 1 min and a hold at 4ºC. Reaction products were purified using double-size selection of AmPure XP beads (0.8× → 0.8×) and eluted with 10 μL of Tris-HCl (pH 8.0). The size distribution of each library was analyzed using an Agilent DNA high-sensitivity kit (Agilent Technologies, Santa Clara, CA, USA), and library concentration was quantified using a KAPA library quantification kit for Ion Torrent (KAPA Biosystems). Sequencing was performed by using Ion Hi-Q Chef Kit, Ion PI v3 Chip Kit and Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacture’s instructions except the input library concentration (100 pM) and cycle number (200).

treatment_protocol: Col1a2-GFP transgenic female mice were administered with a single dose of crystalline silica particles (400 mg/kg suspended in 50 μL of sterile saline solution; MIN-U-SIL5; mass-median-diameter [d50] Z: 1.4 μm; US Silica, Frederick, MD, USA) or bleomycin sulfate (2 mg/kg dissolved in 50 μL of sterile saline solution; Toronto Research Chemical, Toronto, ON, Canada) by oropharyngeal aspiration under deep anesthesia.

value: Col1a2-GFP Transgenic

value: lineage (CD45, CD31, EpCAM, CD146 and Ter119) negative, propidium iodide negative, Col1a2-GFP positive fibroblast

tag: time

value: day 63


title: SIRT3

description: siRNA

value: 164 distinct siRNA pools


title: VTA_WT_ZT4_rep2

tag: tissue


title: VTA_WT_ZT4_rep3


title: VTA_WT_ZT4_rep4


title: VTA_WT_ZT8_rep3


title: SCMH1

description: siRNA


title: SIRT2

description: siRNA


title: SiO2d63_1 (3'SAGE-seq)

value: lung


title: VTA_WT_ZT8_rep2


title: BLMd63_3 (3'SAGE-seq)

value: BLM


title: PHC2

description: siRNA


title: PCGF6

description: siRNA


title: PHC1

description: siRNA


title: BLMd63_2 (3'SAGE-seq)


title: VTA_WT_ZT8_rep1


title: SiO2d63_2 (3'SAGE-seq)


title: VTA_WT_ZT4_rep1


title: SiO2d14_3 (3'SAGE-seq)

value: day 14


title: PCGF5

description: siRNA


title: VTA_WT_ZT0_rep4


title: VTA_WT_ZT0_rep1


title: SiO2d14_2 (3'SAGE-seq)


title: PCGF3

description: siRNA


title: SiO2d14_1 (3'SAGE-seq)


title: VTA_WT_ZT0_rep3


title: PCGF2

description: siRNA


title: BLMd14_2 (3'SAGE-seq)


title: VTA_WT_ZT0_rep2


title: SiO2d7_3 (3'SAGE-seq)

value: day 7


title: BLMd14_1 (3'SAGE-seq)


title: atfs-1 (tm4919) fed with spg-7 RNAi, biological rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were aligned to the C. Elegans genome (WBcel235) using STAR (version 2.5.3a) with the following parameter (--outFilterType BySJout \  --outFilterMultimapNmax 20  \  --alignSJoverhangMin 8  \  --alignSJDBoverhangMin 1  \  --outFilterMismatchNmax 999  \  --outFilterMismatchNoverReadLmax 0.04  \  --alignIntronMin 20  \  --alignIntronMax 1000000  \  --alignMatesGapMax 1000000  \)
featureCounts (subread-1.5.2) was used to count the features after the alignment
Bioconductor packages edgeR (version 3.10.0 ) was used for differential gene expression analysis
Genome_build: WBcel235 (https://www.ncbi.nlm.nih.gov/assembly/GCF_000002985.6/)
Supplementary_files_format_and_content: tab-delimited text files include the raw count values from featureCounts for each sample

source_name: atfs-1 (tm4919) fed with spg-7 RNAi

growth_protocol: Wildtype, atfs-1(tm4919) and zip-3(gk3164) worms were synchronized by bleaching, raised to L4 on NGM plates seeded with control RNAi or spg-7 RNAi and then harvested.

extract_protocol:
Total RNA was isolated using the RNA STAT reagent (Tel-Test Inc) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Worms were fed with either control RNAi or spg-7 RNAi

value: whole organism


title: SiO2d7_1 (3'SAGE-seq)


title: BLMd63_1 (3'SAGE-seq)


title: BLMd14_3 (3'SAGE-seq)


title: atfs-1 (tm4919) fed with spg-7 RNAi, biological rep2


title: PCGF1

description: siRNA


title: BLMd7_3 (3'SAGE-seq)


title: atfs-1 (tm4919) fed with spg-7 RNAi, biological rep1


title: BLMd7_2 (3'SAGE-seq)


title: atfs-1 (tm4919) fed with control RNAi, biological rep2

source_name: atfs-1 (tm4919) fed with control RNAi


title: BLMd7_1 (3'SAGE-seq)


title: UT_3 (3'SAGE-seq)

value: untreated

value: control


title: SiO2d7_2 (3'SAGE-seq)


title: UT_2 (3'SAGE-seq)


title: atfs-1 (tm4919) fed with control RNAi, biological rep1


title: zip-3 (gk3164) fed with spg-7 RNAi, biological rep3

source_name: zip-3 (gk3164) fed with spg-7 RNAi


title: zip-3 (gk3164) fed with spg-7 RNAi, biological rep2


title: UT_1 (3'SAGE-seq)