title: cbfs treated with 3 h, rep 2 [cbf3_2]

source_name: cbfs treated with 3 h

value: under 4 degree for 3h


title: P5-2-Ampli-FFPE

status: Public on May 07 2019

type: SRA

city: Edinburgh

first: Carlos

last: Martinez-Perez

address: Western General Hospital, Crewe Road South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

description:
Sample 2
Patient 5 early on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.

library_source: transcriptomic

data_processing:
Samples were analysed in an Ion Proton instrument.
Data were generated using the AmpliSeq RNA plugin in the Torrent Suite Software and normalised using RPM (reads assigned per million mapped reads) method.
Probes were mapped to Ensembl gene annotations using BioMart.
Data were log2 transformed and quantile normalised using R/Bioconductor software and packages.
Genome_build: Human genome version GRCh38.77
Supplementary_files_format_and_content: The processed data files contain expression data for each sample mapped to Ensemble gene IDS.

molecule: total RNA

organism: Homo sapiens

source_name: breast cancer

extract_protocol:
RNA was extracted from 2x20µm FFPE tissue sections using the RNeasy FFPE kit.
All samples were processed and libraries constructed following the manufacturer's guidelines in the Edinburgh Clinical Research Facility.

tag: tissue

value: breast cancer

tag: time point

value: early on-treatment biopsy


title: P9-1-Ampli-FFPE

description:
Sample 3
Patient 9 pre-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.

value: pre-treatment biopsy


title: P2-2-Ampli-FFPE

description:
Sample 1
Patient 2 early on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.


title: P10-2-Ampli-FFPE

description:
Sample 7
Patient 10 early on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.


title: P9-2-Ampli-FFPE

description:
Sample 4
Patient 9 early on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.


title: P9-3-Ampli-FFPE

description:
Sample 5
Patient 9 late on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.

value: late on-treatment biopsy


title: P10-3-Ampli-FFPE

description:
Sample 8
Patient 10 late on-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.


title: P10-1-Ampli-FFPE

description:
Sample 6
Patient 10 pre-treatment biopsy sequenced using Ion AmpliSeq technology from FFPE.


title: WT treated with 24 h, rep 2 [Col24_2]

city: Beijing

first: Yuxin

last: Jia

address: No. 2 Yuanmingyuan west road, Haidian district

department: Biology

country: China

institute: China Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Arabidopsis TAIR10 genome using TOPHAT v.2.1.0
CUFFLINKS v.2.2.1 was used to assemble the new transcripts
HTSEQ v.0.6.0 was used to calculate the raw read counts for each gene.
Gene expression normalization among samples was performed by using DESEQ2.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Arabidopsis thaliana

source_name: WT treated with 24 h

growth_protocol: The plants were grown on 1/2 MS mediam under long day condition at 22 degree  for 14 d

extract_protocol:
The total RNA extraction was performed following the protocol of Tiangen RNAprep pure Plant Kit
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 14-day-old plants were treated with 4 degree for indicated time: 0, 3 and 24 h

tag: genotype/variation

value: WT

tag: developmental stage

value: seedling

tag: treatment

value: under 4 degree for 24h


title: WT treated with 24 h, rep 1 [Col24_1]


title: WT treated with 3 h, rep 2 [Col3_2]

source_name: WT treated with 3 h


title: WT treated with 3 h, rep 1 [Col3_1]


title: WT treated with 0 h, rep 1 [Col0_1]

source_name: WT treated with 0 h

value: under 4 degree for 0h


title: WT treated with 0 h, rep 2 [Col0_2]


title: C-GAL3-6 KO-2

type: RNA

city: Quebec

first: Dimcho

last: Bachvarov

state: Quebec

address: 9, rue McMahon

country: Canada

institute: CHU-Q, Centre de recherche-HDQ

description: Gene expression comparison of GALNT3/6 knockout clone (GAL3/6 KO-2) vs control (C) A2780s clone

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers.

scan_protocol: Scanned on an Agilent G2565AA scanner.

data_processing: Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.

source_name: control (mock-transfected) A2780s clone

label_protocol: Fluorescently labeled cRNA targets were generated from 0.5 µg of total RNA in each reaction using the Fluorescent Linear Amplification Kit (Agilent) and 10.0 mM Cyanine 3- or 5-labeled CTP (PerkinElmer, Boston, MA), following the user’s manual. Labeled cRNAs were purified using the RNeasy Mini Kit (Qiagen) and applied to the Agilent Whole Human Genome microarrays, containing ~ 44,000 genes.

growth_protocol: A2780s cells were maintained in Roswell Park Memorial Institute (RPMI) 1640 (HyClone Europe Ltd, Cramlington, UK) supplemented with 10% heat-inactivated fetal calf serum, 2 mM l-glutamine, 1 mM sodium pyruvate, 100 units/ml penicillin and 100 μg/ml streptomycin (all reagents were from HyClone Europe). Cells were grown as adherent cells in a humidified atmosphere at 37°C in 5% CO2.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions. The quality of all RNA samples was examined by capillary electrophoresis using the Agilent 2100 Bioanalyzer.

treatment_protocol: A CRISPR-Cas9 targeting the GALNT3 gene was used for the generation of the GALNT3 Knockout clones (GAL3 KO-1 and GAL3 KO-2), additionally GALNT3 and GALNT6 double knockout clones were generated with the use of shRNA targeting GALNT6 (x, x) in the GALNT3 Knokcout CRISPR clones (GAL3/6 KO-1 and GAL3/6 KO-2).

tag: cell line

value: ovarian adenocarcinoma cell line

source_name: CRISPR-Cas9 GALNT3 knockout and GALNT6 shRNA knckdown A2780s clone GAL3/6 KO-2


title: C-GAL3-6 KO-1

description: Gene expression comparison of GALNT3/6 knockout clone (GAL3/6 KO-1) vs control (C) A2780s clone

source_name: CRISPR-Cas9 GALNT3 knockout and GALNT6 shRNA knckdown A2780s clone GAL3/6 KO-1


title: C-GAL3 KO-1

description: Gene expression comparison of GALNT3 knockout clone (GAL3 KO-1) vs control (C) A2780s clone

source_name: CRISPR-Cas9 GALNT3 knockout A2780s clone GAL3 KO-1


title: 293TAdar2OE_STRBPOE_1

city: Stanford

first: Jin

middle: Billy

last: Li

state: CA

address: 300 Pasteur Dr, Alway M341

department: Genetics

country: USA

institute: Stanford University

description: rRNA-depleted RNA

data_processing:
Paired-end, 76-base-pair reads were trimmed using Trim Galore 0.4.5 to remove adapter sequences.
Reads were mapped to the Hg19 genome using STAR 2.4.2a with the parameters (--outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverReadLmax 0.1   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000  --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1 --twopassMode Basic.
To call editing levels, samtools (v1.4) mpileup function was used to extract base calls from uniquely mapped reads at known editing sites. Editing levels were detemined as the number of G reads out of all A and G reads at a site.
To determine gene expression levels, RSEM 1.2.21 was used to count the number of reads mapping to each gene. RSEM calculated expected counts were rounded down to the nearest integer and used as input to DESeq2 v1.20.0
Genome_build: hg19
Supplementary_files_format_and_content: For RNA editing analysis: A and G counts and editing levels at known editing sites. Tab-delimited filtes are formatted as: chromosome,position,gene,strand,annotation1,annotation2,coverage,editedreads,editlevel
Supplementary_files_format_and_content: For expression analysis: genes.results output files from RSEM. Tab-delimited files are formatted as: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM, posterior_mean_count, posterior_standard_deviation_of_count, pme_TPM, pme_FPKM, TPM_ci_lower_bound, TPM_ci_upper_bound, FPKM_ci_lower_bound, FPKM_ci_upper_bound.

source_name: H239T Adar2 overexpression cells

growth_protocol: 293T and 293TAdar2OE cells were cultured in DMEM supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Total RNA was extracted from cells using Qiagen Micro or Mini RNeasy kit (Qiagen cat:74004 or 74104) using RNAdvanced Tissue Kit (Beckman Coulter) followed by TURBO DNase treatment (Thermo Fisher).
rRNA was depleted from total RNA following RNase H-based protocols adopted from (Adiconis et al., 2013; Morlan et al., 2012). We mixed approximately 250 ng of RNA with 61.54 pmoles of pooled DNA oligos designed antisense to rRNA (gift from J. Salzman lab at Stanford) in a 5ul reaction with 1 ul of 5X RNase H(-)Mg buffer (500 mM Tris-HCl pH 7.4, 1 M NaCl) and 0.25 ul 1mM EDTA. We annealed rRNA antisense oligos to total RNA samples for 2 minutes at 95°C, slowly reduced the temperature to 45°C and then added 5 ul of RNase H mix (1.7 ul water, 1 ul 5X RNase H(-)Mg buffer, 0.2 ul 1 M MgCl2, 0.1ul RiboLock RNase Inhibitor (40 U/µL) (ThermoFisher EO038), 2 ul of Hybridase Thermostable RNase H (Epicenter, Madison, WI: Lucigen H39500) to make 10 ul total and incubated for 30 minutes at 45°C. rRNA-depleted RNA was then purified using 2.2X reaction volume of Agencourt RNAClean XP beads (Beckman Coulter: A63987), treated with TURBO DNase (Invitrogen: AM1907), and then purified with RNAClean XP beads again. rRNA-depleted RNA was used as input to the KAPA HyperPrep RNA-seq Kit (Kapa Biosystems: KK8540). All libraries were sequenced with 76 base-pair paired-end reads using an Illumina NextSeq (Illumina, San Diego, CA).

treatment_protocol: All transient transfection constructs were generated by subcloning the cDNA of interest into the pCDNA 3.1-3xFLAG (GFP, ADAR1, ADAR2, ILF2, ILF3, STRBP).  All transient transfections were performed with Lipofectamine 2000 according to manufacturer’s protocol.

tag: genotype

value: H293TAdar2OE; STRBP_OE

tag: replicate

value: 48 hours after transfection


title: 293TAdar2OE_ILF2OE_2

description: rRNA-depleted RNA

value: H293TAdar2OE; ILF2_OE


title: 293TAdar2OE_STRBPOE_2

description: rRNA-depleted RNA


title: C-GAL3 KO-2

description: Gene expression comparison of GALNT3 knockout clone (GAL3 KO-2) vs control (C) A2780s clone

source_name: CRISPR-Cas9 GALNT3 knockout A2780s clone GAL3 KO-2


title: siERK1n2_12 [WGC100709R]

city: new haven

first: Nicolas

last: Ricard

state: CT

address: 300 george street

department: internal medicine

institute: yale university

data_processing:
Bases were called in real-time on the Illumina HiSeq X
Paired-end reads were aligned to hg38 (GRCh38) using STAR 2.5.1b aligner with a custom-built index in two-pass mode.  The first pass parameters were: --twopassMode Basic --outFilterType BySJout --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 --outFilterMultimapNmax 20 --outFilterMatchNminOverLread 0.66 --outFilterIntronMotifs None --outSJfilterReads All --outSAMstrandField intronMotif --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 0 --chimScoreDropMax 20 --chimScoreSeparation 10 --chimScoreJunctionNonGTAG -1 --quantMode TranscriptomeSAM. The second pass genome index was created from the first pass SJ.out.tab file with an --sjdbOverhang 149.  The second pass alignment was run against the new index, with the same initial alignment parameters.
Expression quantification was performed using RSEM v1.2.28 with GENCODE release 24 annotation using the following parameters: --bam --no-bam-output --estimate-rspd --append-names --paired-end --forward-prob 0.5
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file including RSEM counts for each sample

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) were purchased from Lonza and cultivated in EBM-2 MV medium (Lonza)

extract_protocol:
RNA extractions were done using RNeasy mini kit (Qiagen) with DNAse digestion (Qiagen).
Paired-end sequencing library was prepared using Illumina Truseq v1 library prep kit.

treatment_protocol: siRNAs were purchased from Qiagen: siRNA MAPK1_10 and MAPK3_6, and siSCR  #1027281.  siRNA transfetions were done in OptiMem medium (ThermoFisher) with the lipofectamine RNAimax transfection agent (ThermoFisher).

tag: cell type

value: Human umbilical vein endothelial cells (HUVEC)


title: 293TAdar2OE_ILF2OE_1

description: rRNA-depleted RNA


title: 293TAdar2OE_ILF3OE_2

description: rRNA-depleted RNA

value: H293TAdar2OE; ILF3_OE


title: cbfs treated with 0 h, rep 2 [cbf0_2]

source_name: cbfs treated with 0 h

value: cbfs-1 mutant


title: cbfs treated with 0 h, rep 1 [cbf0_1]


title: cbfs treated with 3 h, rep 1 [cbf3_1]


title: 293T_STRBPOE_2

description: rRNA-depleted RNA

source_name: H239T cells

value: H293T; STRBP_OE


title: 293TAdar2OE_GFPOE_2

description: rRNA-depleted RNA

value: H293TAdar2OE; GFP_OE


title: 293TAdar2OE_GFPOE_1

description: rRNA-depleted RNA


title: 293T_STRBPOE_1

description: rRNA-depleted RNA


title: 293T_ILF2OE_2

description: rRNA-depleted RNA

value: H293T; ILF2_OE


title: 293T_ILF3OE_1

description: rRNA-depleted RNA

value: H293T; ILF3_OE


title: 293TAdar2OE_ILF3OE_1

description: rRNA-depleted RNA


title: 293T_GFPOE_2

description: rRNA-depleted RNA

value: H293T; GFP_OE


title: 293T_ILF2OE_1

description: rRNA-depleted RNA


title: 293T_GFPOE_1

description: rRNA-depleted RNA


title: H293TAdar2OE_ILF3RBDOE_Rep1

data_processing:
Paired-end, 76-base-pair reads were trimmed using Trim Galore 0.4.5 to remove adapter sequences.
Reads were mapped to the Hg19 genome using STAR 2.4.2a with the parameters (--outFilterMultimapNmax 20   --outFilterMismatchNmax 999   --outFilterMismatchNoverReadLmax 0.1   --alignIntronMin 20   --alignIntronMax 1000000   --alignMatesGapMax 1000000  --alignSJoverhangMin 8   --alignSJDBoverhangMin 1 --sjdbScore 1 --twopassMode Basic.
To call editing levels, samtools (v1.4) mpileup function was used to extract base calls from uniquely mapped reads at known editing sites. Editing levels were detemined as the number of G reads out of all A and G reads at a site.
Genome_build: hg19
Supplementary_files_format_and_content: For RNA editing analysis: A and G counts and editing levels at known editing sites. Tab-delimited filtes are formatted as: chromosome,position,gene,strand,annotation1,annotation2,coverage,editedreads,editlevel

extract_protocol:
RNA was extracted Total RNA was extracted from cells using Qiagen Micro or Mini RNeasy kit (Qiagen cat:74004 or 74104).using RNAdvanced Tissue Kit (Beckman Coulter) followed by TURBO DNase treatment (Thermo Fisher).
The mmPCR–seq was performed as described in (Zhang et al 2014 ). Briefly, total RNA is extracted from cells using a Qiagen Micro or Mini RNeasy kit (Qiagen cat:74004 or 74104) and reverse transcribed using iScript Advanced reverse transcriptase (Bio-Rad). The cDNAs were purified using Ampure XP Beads (Beckman Coulter), with an elution volume of 10 ul. 250 ng of cDNA was used in a preamplification reaction and amplified cDNA was purified using Ampure XP beads and eluted in 10 ul.  50 ng of pre-amplified cDNA was loaded into each well of an Access Array microfluidic chip (Fluidigm). The PCR reactions were performed on the Access Array System (Fluidigm) using KAPA2G 5X Fast Multiplex PCR Mix (Kapa Biosystems). Barcodes were added in a second round of PCR using Phusion DNA polymerase (NEB cat: M0531S). Samples were sequenced with 76 base-pair paired-end reads using an Illumina NextSeq (Illumina, San Diego, CA).
mmPCR-seq

treatment_protocol: All transient transfection constructs were generated by subcloning the cDNA of interest into the pCDNA 3.1-3xFLAG (GFP, ADAR1, ADAR2, ILF2, ILF3, ILF3dsRBD, STRBP).  All transient transfections were performed with Lipofectamine 2000 according to manufacturer’s protocol.

value: H293TAdar2OE; ILF3 dsRBD mutant_OE

tag: biological replicate

tag: technical replicate


title: 293T_ILF3OE_2

description: rRNA-depleted RNA


title: H293TAdar2OE_GFPOE_Rep4


title: H293T_ILF3RBDOE_Rep1

value: H293T; ILF3 dsRBD mutant_OE


title: H293TAdar2OE_GFPOE_Rep3


title: H293T_ILF3RBDOE_Rep2


title: H293TAdar2OE_STRBPOE_Rep2T1


title: H293TAdar2OE_STRBPOE_Rep2T2


title: H293TAdar2OE_ILF3OE_Rep2T2


title: H293TAdar2OE_STRBPOE_Rep1T2


title: H293TAdar2OE_ILF3OE_Rep2T1


title: H293T_GFPOE_Rep3


title: H293TAdar2OE_ILF3OE_Rep1T2


title: H293TAdar2OE_STRBPOE_Rep1T1


title: H293TAdar2OE_ILF3RBDOE_Rep2


title: H293TAdar2OE_ILF2OE_Rep2T1


title: H293TAdar2OE_ILF3OE_Rep1T1


title: H293TAdar2OE_ILF2OE_Rep2T2


title: H293TAdar2OE_GFPOE_Rep1T2


title: H293TAdar2OE_GFPOE_Rep2T2


title: H293T_ILF3OE_Rep2T1


title: H293TAdar2OE_GFPOE_Rep1T1


title: H293TAdar2OE_GFPOE_Rep2T1


title: H293T_STRBPOE_Rep2T1


title: H293T_ILF2OE_Rep2T2


title: H293T_ILF2OE_Rep2T1


title: H293T_STRBPOE_Rep2T2


title: H293T_ILF3OE_Rep2T2


title: H293T_ILF3OE_Rep1T2


title: H293TAdar2OE_ILF2OE_Rep1T1


title: H293T_STRBPOE_Rep1T1


title: H293T_STRBPOE_Rep1T2


title: H293TAdar2OE_ILF2OE_Rep1T2


title: H293T_GFPOE_Rep1T2


title: H293T_ILF3OE_Rep1T1


title: H293T_ILF2OE_Rep1T2


title: H293T_GFPOE_Rep2T2


title: H293T_GFPOE_Rep4


title: H3K27me3_Sox9_2

city: Durham

first: Sara

middle: A.

last: Garcia-Moreno

state: North Carolina

address: Nanaline Bldg. Research Drive

institute: Duke University

library_source: genomic

data_processing:
Files were trimmed for quality using trim_galore with a stringency setting of 5
Reads were aligned to the mm9 genome with bowtie using the parameters -m 1 and --best
Unmapped reads were eliminated with samtools view using -F 4 settings
HOMER was used for calling peaks with the findPeaks function and settings “--style histone”, with a size of 5000 for H3K27me3 and 1000 for H3K4me3. The setting “-C 0” was used in MNase ChIP to  disable fold enrichment limit of expected unique tag positions. H3K27me3 and H3K4me3 were used as treament (-t) and H3 as control (-c)
bigwig files were created from .bdg files using BedGraphToBigWig for visualization on the UCSC genome browser. For optimal visualization, ChIP-seq replicates were concatenated to increase number of reads.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain tracks for visualization on the UCSC genome browser of concatenated replicates. bed files contain coordinates of called peaks.

molecule: genomic DNA

organism: Mus musculus

extract_protocol:
Embryonic gonads were micro-dissected at according stage, removed from the mesonephros and incubated in 0.05% trypsin for 5 minutes at 37C. Gonads were then mechanically dissasociated in PBS/3% BSA and passed through a filter cap to obtain a single cell suspension. Fluorescently-labeled cells were collected by Fluorescence Activated Cell Sorting (FACS).  For ChIP-seq, 30K-100K cells were collected per replicate.
ChIP-seq libraries were prepared with no modifications according to Van Galen et al., 2016.

tag: strain background

value: C57BL/6 x CD1

tag: embryonic stage

tag: Sex

value: male

value: FACS-sorted Sertoli cells

tag: chip antibody

value: H3K27me3 CST 9733S

tag: chip protocol

value: Van Galen et al, 2016


title: H3_Sox9_1

value: H3 Active Motif 39763


title: H3K4me3_Sox9_1

value: H3K4me3 Active Motif 39159


title: H3K27me3_TESm_2

value: TESM-CFP

value: female

value: FACS-sorted granulosa cells


title: H3K27me3_Sox9_1


title: H3K4me3_Sox9_2


title: H293T_ILF2OE_Rep1T1

value: 48 hours after transfection


title: H3_Sox9_2


title: H3K4me3_TESm_1


title: H3_TESm_2


title: H3K4me3_TESm_2


title: H293T_GFPOE_Rep1T1


title: H3K27me3_TESm_1


title: H293T_GFPOE_Rep2T1


title: H3K4me3_SF1_M_2

value: FACS-sorted gonadal progenitor cells


title: H3_SF1_M_1


title: H3K4me3_SF1_F_2


title: H3K27me3_SF1_F_2


title: H3_TESm_1


title: H3_SF1_F_1


title: H3K4me3_SF1_M_1


title: H3_SF1_F_2


title: H3K27me3_SF1_M_1


title: H3K4me3_SF1_F_1


title: r26_x267_3D_nuc_R1

city: Chapel Hill

first: Mauro

last: Calabrese

address: 120 Mason Farm Road

department: Pharmacology

institute: University of North Carolina at Chapel Hill

description: Nuclear RNA, ribo-depleted

data_processing:
RNA sequence reads were aligned to genomic sequence using Star (version 2.5.4b) (Dobin A et al. Bioinformatics 2013) with default parameters. All mm9 genome annotations were obtained from the UCSC genome browser (Casper J et al. Nucleic Acids Research 2018). For allele-specific analysis in Rosa26-RMCE cells, variant sequence data were obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/), and CAST/EiJ pseudogenome creation and allele-specific read retention was performed as in (Calabrese et al. G3 2015; Calabrese et al. Cell 2012).
Only reads with a mapping quality of greater than or equal to 30 were used.
Reads were assigned to genes using FeatureCounts (Liao et al. Bioinformatics 2014)
Genome_build: mm9
Supplementary_files_format_and_content: For pSM33 samples, *_fc files are the output from featureCounts after aligning reads to the mm9 genome. Files are tab separated and include columns: Gene ID, Chr, Start, End, Strand, Length, Reads.
Supplementary_files_format_and_content: For Rosa26-RMCE samples, *_fc_hygro files are the output from featureCounts after aligning reads to custom genome based on mm9 and including a 'chrR' chromosome with the pCargo insertion sequence and annotations. Files are tab separated and include columns: Gene ID, Chr, Start, End, Strand, Length, Reads.
Supplementary_files_format_and_content: For Rosa26-RMCE samples, *_allelic_ase files are the output from a custom script assigning SNP-overlapping reads to the B6 or Cast genomes as in (Calabrese et al. G3 2015; Calabrese et al. Cell 2012). Files are tab separated and include columns: Gene ID, Chr, Strand, Start, Stop, B6 reads, Cast reads.

source_name: Rosa26-RMCE Xist-2kb+6,7

growth_protocol: E14 and pSM33 ESCs were grown on gelatin coated dishes at 37°C in a humidified incubator at 5% CO2.  Medium was changed daily and consisted of DMEM high glucose plus sodium pyruvate, 15% ESC qualified fetal bovine serum, 0.1 mM non-essential amino acids, 100 U/mL penicillin-streptomycin, 2 mM L-glutamine, 0.1mM 2-mercaptoethanol, and 1:500 LIF conditioned media produced from Lif-1Cα (COS) cells (kind gift of N. Hathaway). ESCs were split at an approximate ratio of 1:6 every 48hr. Rosa26-RMCE cells were grown on gamma-irradiated mouse embryonic fibroblast (MEF) feeder cells plated at approximately 1.5x10^6 cells per 10cm plate. Prior to harvesting of RNA for sequencing, Rosa26-RMCE cells were passaged twice off of MEF feeder cells with a 40-minute pre-plate each passage and grown in 70% MEF-conditioned medium supplemented as above.

extract_protocol:
All steps were performed at 4°C. Cells were washed twice with 1mL cold PBS, scraped in 1mL PBS, centrifuged at 1500xrcf for 5min, and resuspended in 250µL low salt solution (10mM KCl, 1.5mM MgCl2, 20mM Tris-HCl pH 7.5) supplemented with 1mM PMSF, 1mM DTT, and 1:100 protease inhibitor cocktail (PIC; Sigma P8340). Triton X-100 was added to a final concentration of 0.1% and cells were rotated for 10min, then centrifuged for 5min at 1500xrcf. 200µL of supernatant was added to 1mL Trizol (Invitrogen; cytosolic fraction). The remaining supernatant was discarded and the nuclear pellet was washed by rotating for 2min in low salt solution without Triton X-100 and centrifuged at 1300rpm for 10min. Nuclear pellets, which at this stage contained both soluble nuclear and chromatin-bound fractions, were resuspended in 1mL Trizol. Isolation of RNA from Trizol was performed according to manufacturer protocol.
RNA-seq libraries were prepared using the RNA HyperPrep Kit with RiboErase (Kapa Biosciences) and sequenced on an Illumina NextSeq 500 machine using a 75-cycle high output NextSeq kit (Illumina).

treatment_protocol:
Cells were treated with 1µg/mL doxycycline (Sigma) for 3 days prior to fractionation and RNA harvest
Cells were plated on 6-well or 12-well plates at an approximate density of 4x10^5 or 2x10^5 cells per well, respectively. Cells were induced with doxycycline at 1µg/mL (Rosa26-RMCE cells) or 2µg/mL (pSM33 cells) for 3hr to 3d.

value: embryonic stem cell

value: Xist-2kb+6,7 cargo inserted at Rosa26

tag: gender

tag: strain

value: C57BL/6 x CAST/EiJ

tag: induction

value: 3 days 1ug/mL doxycycline

tag: subcellular fraction

value: Nucleus


title: r26_x267_3D_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

value: Cytoplasm


title: r26_x267_3D_nuc_R2

description: Nuclear RNA, ribo-depleted

value: male


title: r26_x5_3D_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

source_name: Rosa26-RMCE Xist-5.5kb

value: Xist-5.5kb cargo inserted at Rosa26


title: SB2

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

data_processing:
FASTQ files were created with the Illumina supplied scripts in the BCL2FASTQ software (v2.17)
Illumina adapters trimmed with Trim Galore! v0.4.3
FASTQs aligned to the mm10 reference genome with STAR v2.5.0a using default parameters
--quantMode GeneCounts option in STAR used to count genes against the GENCODE M16 GTF annotation file
Genome_build: mm10
Supplementary_files_format_and_content: Processed files are one tab delimited text file per sample indicating the raw counts for each gene in the GENCODE M16 GTF file with --quantMode GeneCounts option in STAR. A read is counted if it overlaps (1bp or more) with only one gene. STAR outputs read counts per gene into ReadsPerGene.out.tab file with 4 columns which correspond to different strandedness options: column 1: gene ID, column 2: counts for unstranded RNA-seq, column 3: counts for the 1st read strand aligned with RNA, column 4: counts for the 2nd read strand aligned with RNA. The TruSeq RNA libraries are 2nd stranded so column 4 is the most appropriate for gene expression analysis, though other counts may be useful for other analyses.

source_name: Adult neural precursor

growth_protocol: Olfactory basal cells were isolated from adult olfactory epithelium on the basis of c-KIT expression (as described in Goldstein et al., 2016, Development). Cells were maintained as adherent cultures on gelatin-coated tissue culture plastic. Medium consisted of NeuroCult Basal Medium (Stemcell Tech #05700), supplemented with NeuroCult Proliferation Supplement (Stemcell Tech #05701), EGF, FGF2, Heparin, and Pen/Strep.

extract_protocol: Total RNA was collected following manufacturer's instructions using the Quick RNA MiniPrep Kit (Zymo #R1054)

treatment_protocol: Cells were treated with an Activin/TGF-beta pathway inhibitor: SB431542 or RepSox. Cells grown in medium containing SB431542 also contained BMP4, following our published protocol for culturing olfactory basal cells (Goldstein et al., 2016, Development). Cells were treated with RepSox overnight and maintained in normal growth medium described above in "Growth Protocol".

tag: tissue source

value: Adult olfactory epithelium

tag: small molecule inhibitor treatment


title: r26_x267_3D_cyt_R1

description: Cytoplasmic RNA, ribo-depleted

tag: cell line


title: SB3


title: r26_x5_3D_nuc_R2

description: Nuclear RNA, ribo-depleted

tag: genotype


title: SB1


title: r26_x5_3D_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: r26_x5_3D_nuc_R1

description: Nuclear RNA, ribo-depleted


title: H3K27me3_SF1_M_2

value: C57BL/6 x CD1

tag: genotype/variation

value: H3K27me3 CST 9733S

value: Van Galen et al, 2016


title: H3K27me3_SF1_F_1

tag: cell type


title: H3_SF1_M_2

value: H3 Active Motif 39763


title: RS2

value: RepSox


title: RS3


title: RS1


title: uHC rep2

city: Houston

first: Hsin-i

last: Jen

state: TX

address: One baylor plaza

department: Developmental biology

institute: Baylor college of medicine

description: Isolated utricles were dissociated with the papain dissociation system. GFP positive cells were FAC sorted directly into lysis buffer for downstream processing.

data_processing:
Illumina software used for basecalling.
RNA-seq datasets were uploaded to the Galaxy web platform for data analysis.
Sequenced reads were trimmed for adaptor sequence, paired-end reads were mapped to the mouse reference genome (mm10) using HISAT2.
Read counts were calculated through HTseq-count and differentially expressed genes were identified using the DESeq2 package
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

source_name: Utricle hair cells

extract_protocol:
RNA extraction was performed using a SMART-seq v4 Ultra Low input RNA kit. The extracted and amplified cDNA was measured with Agilent Bioanalyzer and DNA
Libraries prepared with the Nextera XT DNA Library preparation kit.

tag: age

value: 4-6 weeks

tag: virus infection

value: Outbred (ICR)

value: Ai3; Atoh1-CreERT2 (Gt(ROSA)26Sortm3(CAG-EYFP)Hze/J; Tg(Atoh1-cre/Esr1*)14Fsh)


title: uSC rep1

description: Isolated utricles were dissociated with the papain dissociation system. Dissociated cells were stained with anti-CD326 conjugated with Allophycocyanin (APC). GFP negative and APC postive cells were FAC sorted directly into lysis buffer for downstream processing.

source_name: Utricle supporting cells


title: tdTomato rep1

description: Isolated utricle were treated with 0.1mM gentamicin for 24 hours, follow by adenovirus Ad-tdTomato for 24 hours. The viral infected utricle is then being cultured for additional 9 days.Isolated utricles were dissociated with the papain dissociation system. Dissociated tdTomato positive cells were FAC sorted directly into lysis buffer for downstream processing.

value: Ad-tdTomato

value: WT


title: uSC rep2


title: tdTomato rep2


title: YAP5SA_MGC_10X_run2

city: Cambridge

first: Matthew

middle: C

last: Hill

state: MA

address: 75 Aimes Street

institute: Broad Institute of MIT and Harvard

data_processing:
The scRNA data was analyzed as previously described with minor modifications (Xiao et. al. 2018 Dev Cell, and Li et. al. 2018 Development ). Briefly, raw sequencing data were handled using the 10X Genomics Cell Ranger software (www.10xgenomics.com). Fastq files were mapped to the mm10 genome, and gene counts were quantified using Cellranger count function. Subsequently, expression matrices from each experiment were merged and then were imported into Seurat (version 2.3.4) where log normalization was performed. We corrected for batch effects by regressing out the number of molecules per cell and the batch identity with the Seurat implementation of regression (ScaleData function). Next, we performed a principle components analysis (PCA), and significant principle components (PCs) were used as input for graph-based clustering. We used tSNE for 2-dimensional visualization of the multi-dimensional data set. Differential expression of the individual clusters was achieved by using the Wilcoxon rank sum test (FindMarkers, default). To avoid over-clustering, we merged clusters that were not transcriptionally distinct into a single cluster. Clusters composed of doublets (2 different cell types within a single droplet) were removed from the data set. And clusters that were not MGCs were also removed, including rod cells, cone cells, and astrocytes.
Supplementary_files_format_and_content: Digital gene expression (dge) files for the raw merged data, and processed and scaled data were exported directly from Seurat as csv files.

molecule: polyA RNA

source_name: Retina

extract_protocol:
FACS sorted TdTomato+ cells were counted and diluted in 1X PBS with 0.04 % BSA before being loaded onto the 10X Genomics Chromium instrument.
The scRNA-seq libraries were generated using the 10X Chromium Single Cell 3’ v2 reagent kit according to the manufacturer’s instructions and were sequenced on an Illumina Nextseq500.

tag: tissue

value: Retina

tag: injury

value: N-methyl-D-aspartate (NMDA)

value: FACS sorted tdTomato+ Muller Glia Cells


title: Atoh1 rep1

description: Isolated utricle were treated with 0.1mM gentamicin for 24 hours, follow by adenovirus Ad-tdTomato-Atoh1 for 24 hours. The viral infected utricle is then being cultured for additional 9 days.Isolated utricles were dissociated with the papain dissociation system. Dissociated tdTomato positive cells were FAC sorted directly into lysis buffer for downstream processing.


title: tdTomato rep3


title: YAP5SA_MGC_10X_run3


title: Atoh1 rep2


title: uHC rep1


title: YAP5SA_MGC_10X_run1


title: r26_xfl_3D_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

molecule: cytoplasmic RNA

source_name: Rosa26-RMCE Xist-full length

value: embryonic stem cell

value: Xist-full length cargo inserted at Rosa26

value: C57BL/6 x CAST/EiJ

value: 3 days 1µg/mL doxycycline

value: Cytoplasm


title: r26_xfl_3D_nuc_R2

description: Nuclear RNA, ribo-depleted

molecule: nuclear RNA

value: male

value: Nucleus


title: r26_xfl_3D_nuc_R1

description: Nuclear RNA, ribo-depleted


title: r26_xfl_3D_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: psm33_24h_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

source_name: pSM33 24h dox

treatment_protocol:
Cells were treated with 2µg/mL doxycycline (Sigma) for 24 hours prior to fractionation and RNA harvest
Cells were plated on 6-well or 12-well plates at an approximate density of 4x10^5 or 2x10^5 cells per well, respectively. Cells were induced with doxycycline at 1µg/mL (Rosa26-RMCE cells) or 2µg/mL (pSM33 cells) for 3hr to 3d.

value: Inducible promoter driving Xist at endogenous locus

value: C57BL/6 x 129SV-Jae

value: 24 hours 2µg/mL doxycycline


title: psm33_5h_nuc_R1

description: Nuclear RNA, ribo-depleted

source_name: pSM33 5h dox

treatment_protocol:
Cells were treated with 2µg/mL doxycycline (Sigma) for 5 hours prior to fractionation and RNA harvest
Cells were plated on 6-well or 12-well plates at an approximate density of 4x10^5 or 2x10^5 cells per well, respectively. Cells were induced with doxycycline at 1µg/mL (Rosa26-RMCE cells) or 2µg/mL (pSM33 cells) for 3hr to 3d.

value: 5 hours 2µg/mL doxycycline


title: psm33_0h_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

source_name: pSM33 0h dox

treatment_protocol:
Cells were not treated with doxycycline prior to fractionation and RNA harvest
Cells were plated on 6-well or 12-well plates at an approximate density of 4x10^5 or 2x10^5 cells per well, respectively. Cells were induced with doxycycline at 1µg/mL (Rosa26-RMCE cells) or 2µg/mL (pSM33 cells) for 3hr to 3d.


title: psm33_3h_nuc_R1

description: Nuclear RNA, ribo-depleted

source_name: pSM33 3h dox

treatment_protocol:
Cells were treated with 2µg/mL doxycycline (Sigma) for 3 hours prior to fractionation and RNA harvest
Cells were plated on 6-well or 12-well plates at an approximate density of 4x10^5 or 2x10^5 cells per well, respectively. Cells were induced with doxycycline at 1µg/mL (Rosa26-RMCE cells) or 2µg/mL (pSM33 cells) for 3hr to 3d.

value: 3 hours 2µg/mL doxycycline


title: psm33_0h_nuc_R2

description: Nuclear RNA, ribo-depleted


title: psm33_3h_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: psm33_24h_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: uSC rep3

value: 4-6 weeks

value: Outbred (ICR)


title: psm33_24h_nuc_R1

description: Nuclear RNA, ribo-depleted


title: psm33_0h_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: r26_x2kb_3D_nuc_R3

description: Nuclear RNA, ribo-depleted

source_name: Rosa26-RMCE Xist-2kb

value: Xist-2kb cargo inserted at Rosa26


title: r26_x2kb_3D_nuc_R2

description: Nuclear RNA, ribo-depleted


title: r26_empty_3D_nuc_R3

description: Nuclear RNA, ribo-depleted

source_name: Rosa26-RMCE empty

value: empty cargo inserted at Rosa26


title: r26_x2kb_3D_cyt_R3

description: Cytoplasmic RNA, ribo-depleted


title: r26_empty_3D_cyt_R3

description: Cytoplasmic RNA, ribo-depleted


title: psm33_0h_nuc_R1

description: Nuclear RNA, ribo-depleted


title: psm33_5h_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: r26_empty_3D_nuc_R2

description: Nuclear RNA, ribo-depleted


title: r26_x2kb_3D_nuc_R1

description: Nuclear RNA, ribo-depleted


title: r26_empty_3D_nuc_R1

description: Nuclear RNA, ribo-depleted


title: r26_x2kb_3D_cyt_R1

description: Cytoplasmic RNA, ribo-depleted


title: psm33_24h_nuc_R2

description: Nuclear RNA, ribo-depleted


title: r26_empty_3D_cyt_R2

description: Cytoplasmic RNA, ribo-depleted


title: uuo-day14-1 (miRNA-Seq)

city: Boston

first: Lorena

last: Pantano

address: 655 Huntington Ave

department: Biostatistics

institute: Harvard Chan School of Public Health

description: for small RNA seq

data_processing:
All samples were processed using a small RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org/en/latest/).
Quality control of the raw reads was performed as above for the RNA-seq data using FastQC and atropos.
Trimmed reads were aligned to miRBase v2124 to the specific species with seqbuster 25. In addition, the trimmed reads were aligned to the Mus musculus genome (version mm10) using STAR16,25.
The aligned reads were analyzed with seqcluster26 to characterize the whole small RNA transcriptome and classify reads into rRNA, miRNA, repeats, genes, tRNAs and others from the UCSCannotation 27.
Data were loaded into R using the bcbioSmallRna R package (https://github.com/lpantano/bcbioSmallRna) and isomiRs Bioconductor package 29,30 to get normalized expression values
Genome_build: mm10
Supplementary_files_format_and_content: normalized expression values

source_name: uuo-day14, kidney

growth_protocol: Male BALC/c mice were obtained from Charles River Laboratories (USA). All experimental protocols concerning the use of laboratory animals were performed according to the NIH guidelines for the care and use of laboratory animals, and approved by the Institutional Animal Care and Use Committees (IACUC) of Harvard Medical School. Mice were housed in groups of three on a 12-h light/dark cycle with access to food and water ad libitum. At the age of 8-10 weeks they entered the experiment.

extract_protocol:
Total RNA was isolated using Qiagen’s miRNeasy Mini Kit. Quality and quantity of the RNA was assessed photometrically and with the Bioanalyzer (Agilent).
1 µg total RNA were transcribed utilizing Illumina‘s TruSeq Small RNA Library Prep Kit. Libraries were pooled and sequenced on Illumina’s NextSeq500 as single end, 75 bp reads.

treatment_protocol: Unilateral ureter obstruction (UUO) model: Before surgery, mice were anaesthetized with an intraperitoneal injection of sodium pentobarbital (50 mg/kg of body weight), the left kidney was exposed via a flank incision and 3.0 silk suture thread was used to tie off the ureter at the lower pole. Before the obstruction and 3, 7, and 14 days later, mice were sacrificed, kidneys were removed and immediately snap frozen in liquid nitrogen.

value: BALC/c

tag: Sex

tag: treatment

value: unilateral ureter obstruction

tag: time

value: 14 days

value: kidney


title: uuo-day14-4 (miRNA-Seq)

description: for small RNA seq


title: uuo-day14-2 (miRNA-Seq)

description: for small RNA seq


title: uuo-day7-3 (miRNA-Seq)

description: for small RNA seq

source_name: uuo-day7, kidney

value: 7 days


title: uuo-day7-2 (miRNA-Seq)

description: for small RNA seq


title: uuo-day14-3 (miRNA-Seq)

description: for small RNA seq


title: uuo-day3-3 (miRNA-Seq)

description: for small RNA seq

source_name: uuo-day3, kidney

value: 3 days


title: uuo-day3-4 (miRNA-Seq)

description: for small RNA seq

value: male


title: uuo-day3-2 (miRNA-Seq)

description: for small RNA seq


title: uuo-day7-4 (miRNA-Seq)

description: for small RNA seq


title: r26_empty_3D_cyt_R1

description: Cytoplasmic RNA, ribo-depleted

value: embryonic stem cell

tag: gender

value: C57BL/6 x CAST/EiJ

value: 3 days 1µg/mL doxycycline

value: Cytoplasm


title: uuo-day3-1 (miRNA-Seq)

description: for small RNA seq

tag: strain


title: r26_x2kb_3D_cyt_R2

description: Cytoplasmic RNA, ribo-depleted

tag: induction


title: normal-3 (miRNA-Seq)

description: for small RNA seq

source_name: normal, kidney

value: no treatment

value: control


title: normal-2 (miRNA-Seq)

description: for small RNA seq


title: uuo-day14-4 (RNA-Seq)

description: for mRNA seq

data_processing:
All samples were processed using an RNA-seq pipeline implemented in the bcbio-nextgen project (https://bcbio-nextgen.readthedocs.org).
Raw reads were examined for quality issues using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) to ensure library generation and sequencing were suitable for further analysis. Adapter sequences, other contaminant sequences (such as polyA tails and low quality sequences with PHRED quality scores less than five) were trimmed from reads using atropos15.
Trimmed reads were aligned to UCSC build mm10 of the Mus musculus genome, augmented with transcript information from Ensembl release GRCm38.84 using STAR 16. Alignments were checked for evenness of coverage, rRNA content, genomic context of alignments (for example, alignments in known transcripts and introns), complexity and other quality checks using a combination of FastQC, Qualimap17,  MultiQC18 and custom code within the bcbio-nextgen pipeline. Counts of reads aligning to known genes were generated by featureCounts19.
In parallel, Transcripts Per Million (TPM) measurements per isoform were generated by quasialignment using Salmon 20. Differential expression at the gene level was called with DESeq219–21, preferring to use counts per gene estimated from the Salmon quasialignments by tximport 19–22
The DEGreport Bioconductor package was used for QC and clustering analysis (10.18129/B9.bioc.DEGreport).
Genome_build: mm10
Supplementary_files_format_and_content: TPMs

extract_protocol:
Total RNA was isolated using Qiagen’s RNeasy Mini Kit. Quality and quantity of the RNA was assessed photometrically and with the Bioanalyzer (Agilent).
330 ng total RNA were transcribed utilizing Illumina‘s TruSeq Stranded mRNA Library Prep Kit. Libraries were pooled and sequenced on Illumina’s NextSeq500 as single end, 75 bp reads.

value: BALB/c


title: uuo-day14-3 (RNA-Seq)

description: for mRNA seq


title: uuo-day7-3 (RNA-Seq)

description: for mRNA seq


title: uuo-day7-4 (RNA-Seq)

description: for mRNA seq


title: uuo-day7-2 (RNA-Seq)

description: for mRNA seq


title: uuo-day14-1 (RNA-Seq)

description: for mRNA seq


title: uuo-day3-4 (RNA-Seq)

description: for mRNA seq


title: uuo-day3-2 (RNA-Seq)

description: for mRNA seq


title: uuo-day7-1 (RNA-Seq)

description: for mRNA seq


title: uuo-day3-3 (RNA-Seq)

description: for mRNA seq


title: uuo-day3-1 (RNA-Seq)

description: for mRNA seq


title: uuo-day7-1 (miRNA-Seq)

description: for small RNA seq


title: normal-3 (RNA-Seq)

description: for mRNA seq


title: normal-1 (RNA-Seq)

description: for mRNA seq


title: OT1_H9

city: New York

first: Hanseul

last: Yang

state: NY

address: 1230 York Avenue

institute: Rockefeller University

data_processing:
Alignment: Sequence reads were obtained and mapped to the mouse genome (mm10) using the Bowtie2 program (version 2.2.9).
The expression values of each gene were quantified as transcript per million (TPM) using RSEM (v1.2.30)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: Mouse skin squamous cell carcinoma

extract_protocol:
Mouse skin squamous cell carcinoma cells including tumor initiating cells before and after adoptive cell transfer (ACT)-based immunotherapy were FACS-purified, collected into 96 well plates containing lysis buffer and stored in -80oC
Single cells were lysed by incubating at 72oC for 3 min. Revers transcritpion reaction and whole transcriptome amplification were perforemd according to Smart-seq2 protocol with a few modifications (Yang et al., Cell, 2017). The amplified cDNA libraries were purified by Ampure XP beads (Beckman Coulter), and tagmentation reaction was perforemd by Illumina Nextera XT DNA Library Prep Kit. The libraries were pooled and sequecned on Illumina Nextseq 500 with mid-output 75cycles paired-end mode.

value: Mixed

value: skin squamous cell carcinoma

tag: sorting markers

value: After ACT immunotherapy


title: normal-1 (miRNA-Seq)

description: for small RNA seq

value: BALC/c


title: OT1_H5


title: OT1_H6


title: OT1_H7


title: OT1_H12


title: OT1_H3


title: OT1_H11


title: OT1_H4


title: OT1_H10


title: OT1_G7


title: normal-2 (RNA-Seq)

description: for mRNA seq


title: OT1_G6


title: OT1_H2


title: uuo-day14-2 (RNA-Seq)

description: for mRNA seq

value: unilateral ureter obstruction


title: OT1_G4


title: OT1_G3


title: OT1_G1


title: OT1_G12


title: OT1_G11


title: OT1_F6


title: OT1_F4


title: OT1_F7


title: OT1_F5


title: OT1_G10


title: OT1_F3


title: OT1_H1


title: OT1_F12


title: OT1_F11


title: OT1_E6


title: OT1_E7


title: OT1_F2


title: OT1_E5


title: OT1_F1


title: OT1_E4


title: OT1_E1


title: OT1_E12


title: OT1_E11


title: OT1_E3


title: OT1_E2


title: OT1_E10


title: OT1_G5


title: OT1_G2


title: OT1_D6


title: OT1_D3


title: OT1_D12


title: OT1_D1


title: OT1_D2


title: OT1_D11


title: OT1_D4


title: OT1_D10


title: OT1_E9


title: OT1_C9


title: OT1_F10


title: OT1_C7


title: OT1_C4


title: OT1_C5


title: OT1_C3


title: OT1_C6


title: OT1_C2


title: OT1_C12


title: OT1_D9


title: OT1_C10


title: OT1_C1


title: OT1_B5


title: OT1_B6


title: OT1_D7


title: OT1_B2


title: OT1_D5


title: OT1_B4


title: OT1_B3


title: OT1_B7


title: OT1_B12


title: OT1_B10


title: OT1_B11


title: OT1_B1


title: OT1_A1


title: OT1_A2


title: OT1_A3


title: OT1_A4


title: OT1_A7


title: OT1_A12


title: OT1_C11


title: TN_H5

value: Before ACT immunotherapy


title: OT1_A11


title: TN_H4


title: TN_H6


title: OT1_A10


title: TN_H9


title: TN_H2


title: TN_H1


title: TN_H12


title: TN_G5


title: TN_H10


title: TN_G6


title: TN_H11


title: TN_G7


title: OT1_A6


title: OT1_A5


title: TN_G2


title: TN_G1


title: TN_G3


title: TN_G12


title: TN_G10


title: TN_G11


title: TN_H7


title: TN_F9


title: TN_F5


title: TN_F6


title: TN_H3


title: TN_F4


title: TN_F3


title: TN_F11


title: TN_F1


title: TN_F2


title: TN_E7


title: TN_F12


title: TN_E6


title: TN_E5


title: TN_G4


title: TN_E4


title: TN_E12


title: TN_E1


title: TN_E3


title: TN_E2


title: TN_E11


title: TN_D7


title: TN_D4


title: TN_E10


title: TN_D6


title: TN_F7


title: TN_D2


title: TN_D5


title: TN_D1


title: TN_D3


title: TN_D10


title: TN_D11


title: TN_D12


title: TN_C9


title: TN_F10


title: TN_C7


title: TN_C12


title: TN_C10


title: TN_C3


title: TN_C1


title: TN_C4


title: TN_B7


title: TN_C11


title: TN_B6


title: TN_B4


title: TN_B5


title: TN_C2


title: TN_B2


title: TN_B11


title: TN_B1


title: TN_B12


title: TN_B3


title: TN_A9


title: TN_B10


title: TN_A7


title: TN_A6


title: TN_C6


title: TN_A3


title: TN_A1


title: TN_A4


title: TN_A5


title: TN_A12


title: TN_A2


title: TN_C5


title: TN_A11


title: TN_A10


title: OT_D_H6


title: OT_D_H5


title: OT_D_H8


title: OT_D_H4


title: OT_D_H7


title: OT_D_H9


title: OT_D_H3


title: OT_D_H12


title: OT_D_H2


title: OT_D_H11


title: OT_D_H1


title: OT_D_H10


title: OT_D_G8


title: OT_D_G6


title: OT_D_G9


title: OT_D_G7


title: OT_D_G5


title: OT_D_G4


title: OT_D_G1


title: OT_D_G2


title: OT_D_G10


title: OT_D_G12


title: OT_D_G3


title: OT_D_F9


title: OT_D_F8


title: OT_D_G11


title: OT_D_F7


title: OT_D_F5


title: OT_D_F6


title: OT_D_F4


title: OT_D_F2


title: OT_D_F10


title: OT_D_F3


title: OT_D_F12


title: OT_D_F11


title: OT_D_E9


title: OT_D_E7


title: OT_D_E8


title: OT_D_E5


title: OT_D_E4


title: OT_D_E1


title: OT_D_E11


title: OT_D_F1


title: OT_D_E10


title: OT_D_D6


title: OT_D_D4


title: OT_D_D5


title: OT_D_D1


title: OT_D_D3


title: OT_D_D11


title: OT_D_D2


title: OT_D_D10


title: OT_D_D7


title: OT_D_E2


title: OT_D_D12


title: OT_D_C9


title: OT_D_E6


title: OT_D_C6


title: OT_D_C5


title: OT_D_E3


title: OT_D_C3


title: OT_D_C2


title: OT_D_C12


title: OT_D_C1


title: OT_D_C11


title: OT_D_C8


title: OT_D_D8


title: OT_D_B9


title: OT_D_C10


title: OT_D_C4


title: OT_D_B8


title: OT_D_B6


title: OT_D_B5


title: OT_D_B1


title: OT_D_B2


title: OT_D_B3


title: OT_D_B7


title: OT_D_B11


title: OT_D_B12


title: OT_D_B4


title: OT_D_A9


title: OT_D_C7


title: OT_D_A7


title: OT_D_B10


title: OT_D_A6


title: OT_D_A8


title: OT_D_A3


title: OT_D_A5


title: OT_D_A4


title: OT_D_A1


title: OT_D_A12


title: OT_D_A2


title: OT_C_H8


title: OT_D_A11


title: OT_C_H7


title: OT_C_H6


title: OT_C_H4


title: OT_C_H3


title: OT_C_H11


title: OT_C_H12


title: OT_C_H2


title: OT_C_G6


title: OT_C_H10


title: OT_C_H1


title: OT_C_G7


title: OT_C_G2


title: OT_C_G5


title: OT_C_G3


title: OT_C_G4


title: OT_C_G11


title: OT_C_G12


title: OT_C_F7


title: OT_C_F4


title: OT_D_A10


title: OT_C_F6


title: OT_C_F2


title: OT_C_F5


title: OT_C_F1


title: OT_C_F3


title: OT_C_H5


title: OT_C_F11


title: OT_C_F10


title: OT_C_E6


title: OT_C_E5


title: OT_C_E2


title: OT_C_G10


title: OT_C_E1


title: OT_C_E3


title: OT_C_E12


title: OT_C_F12


title: OT_C_E4


title: OT_C_C9


title: OT_C_D4


title: OT_C_D12


title: OT_C_E11


title: OT_C_D1


title: OT_C_C7


title: OT_C_D7


title: OT_C_D3


title: OT_C_E10


title: OT_C_D6


title: OT_C_D11


title: OT_C_D5


title: OT_C_E7


title: OT_C_D2


title: OT_C_C5


title: OT_C_D10


title: OT_C_C12


title: OT_C_C2


title: OT_C_C3


title: OT_C_C4


title: OT_C_C1


title: OT_C_B7


title: OT_C_G1


title: OT_C_B1


title: OT_C_B5


title: OT_C_B11


title: OT_C_A5


title: OT_C_B10


title: OT_C_A3


title: OT_C_A7


title: OT_C_B4


title: OT_C_B6


title: OT_C_C11


title: OT_C_A9


title: OT_C_A4


title: OT_C_B3


title: OT_C_B12


title: OT_C_B2


title: OT_C_C10


title: OT_C_A1


title: OT_C_A12


title: OT_B_H8


title: OT_C_A11


title: OT_B_H9


title: OT_B_H7


title: OT_B_H6


title: OT_C_A6


title: OT_C_A2


title: OT_B_H5


title: OT_B_H4


title: OT_B_H10


title: OT_B_H3


title: OT_B_G7


title: OT_B_G8


title: OT_B_H12


title: OT_B_G3


title: OT_B_G4


title: OT_B_G6


title: OT_B_G9


title: OT_B_G2


title: OT_B_G1


title: OT_C_A10


title: OT_B_G5


title: OT_B_G11


title: OT_D_E12


title: OT_B_F9


title: OT_B_F8


title: OT_B_G10


title: OT_B_F6


title: OT_B_F5


title: OT_B_H2


title: OT_B_H1


title: OT_B_H11


title: OT_B_G12


title: OT_B_F2


title: OT_B_F1


title: OT_B_E9


title: OT_B_F12


title: OT_B_E7


title: OT_B_E6


title: OT_B_F11


title: OT_B_E8


title: OT_B_F10


title: OT_B_E5


title: OT_B_E4


title: OT_B_E3


title: OT_B_F3


title: OT_B_E1


title: OT_B_E10


title: OT_B_F7


title: OT_B_D9


title: OT_B_E12


title: OT_B_D8


title: OT_B_D7


title: OT_B_D6


title: OT_B_D5


title: OT_B_F4


title: OT_B_D4


title: OT_B_D11


title: OT_B_D1


title: OT_B_D10


title: OT_B_C8


title: OT_B_E2


title: OT_B_D12


title: OT_B_D3


title: OT_B_C6


title: OT_B_D2


title: OT_C_H9


title: OT_B_C7


title: OT_B_C5


title: OT_B_C9


title: OT_B_C10


title: OT_B_C11


title: OT_B_B6


title: OT_B_C1


title: OT_B_C3


title: OT_B_C12


title: OT_B_E11


title: OT_B_B3


title: OT_B_B4


title: OT_B_B7


title: OT_B_B5


title: OT_B_C4


title: OT_B_B12


title: OT_B_B1


title: OT_B_B10


title: OT_B_B2


title: OT_C_C6


title: OT_B_C2


title: OT_B_B11


title: OT_B_A8


title: OT_B_A4


title: OT_B_A6


title: OT_B_A7


title: OT_B_A12


title: OT_B_A2


title: OT_B_A5


title: OT_B_A3


title: OT_B_B9


title: OT_B_A10


title: OT_B_A11


title: OT_A_H7


title: OT_A_H9


title: OT_A_H2


title: OT_A_H3


title: OT_A_H5


title: OT_B_A9


title: OT_A_H6


title: OT_A_H4


title: OT_A_H1


title: OT_A_H12


title: OT_A_G9


title: OT_A_H11


title: OT_B_A1


title: OT_A_G7


title: OT_A_G4


title: OT_A_G6


title: OT_A_G3


title: OT_A_G2


title: OT_A_G5


title: OT_A_H10


title: OT_A_G1


title: OT_A_G10


title: OT_A_G11


title: OT_A_F9


title: OT_A_F7


title: OT_A_F6


title: OT_A_F5


title: OT_D_D9


title: OT_A_F4


title: OT_A_F2


title: OT_A_G12


title: OT_A_F1


title: OT_A_F12


title: OT_A_F3


title: OT_A_F11


title: OT_A_E9


title: OT_A_E7


title: OT_A_E5


title: OT_A_E3


title: OT_A_E4


title: OT_A_E2


title: OT_A_E6


title: OT_A_E10


title: OT_A_E12


title: OT_A_E1


title: OT_B_B8


title: OT_A_D9


title: OT_A_F10


title: OT_A_D8


title: OT_A_E11


title: OT_A_D7


title: OT_A_D3


title: OT_A_D2


title: OT_A_D6


title: OT_A_D4


title: OT_A_D5


title: OT_A_D12


title: OT_A_D1


title: OT_A_D10


title: OT_A_C7


title: OT_A_C8


title: OT_A_D11


title: OT_A_C6


title: OT_A_C9


title: OT_A_C5


title: OT_A_C4


title: OT_A_C3


title: OT_A_C1


title: OT_A_C12


title: OT_A_C10


title: OT_A_B6


title: OT_A_B4


title: OT_A_B3


title: OT_A_B5


title: OT_A_B2


title: OT_A_B7


title: OT_A_B1


title: OT_A_B12


title: OT_A_B11


title: OT_A_B10


title: OT_A_A6


title: OT_A_A5


title: OT_A_A9


title: OT_A_A4


title: OT_A_A7


title: OT_A_A12


title: OT_A_C2


title: OT_A_A10


title: OT_A_A1


title: OT_A_A2


title: OT_A_C11


title: OT_A_A11


title: OT_A_A3


title: OT2_H6


title: OT2_H7


title: OT2_H9


title: OT_A_B9


title: OT2_H3


title: OT2_H1


title: OT2_H2


title: OT2_H12


title: OT2_H10


title: OT2_H11


title: OT2_H8


title: OT2_H4


title: OT2_G9


title: OT2_G8


title: OT2_G7


title: OT2_G6


title: OT2_G5


title: OT2_G4


title: OT2_G12


title: OT2_G1


title: OT2_G3


title: OT2_G2


title: OT2_H5


title: OT2_F9


title: OT2_F8


title: OT2_G11


title: OT2_G10


title: OT2_F1


title: OT2_F2


title: OT2_F4


title: OT2_F6


title: OT2_F7


title: OT2_F11


title: OT2_E6


title: OT2_E9


title: OT2_E8


title: OT2_F12


title: OT2_F3


title: OT2_F5


title: OT2_E7


title: OT2_F10


title: OT2_E5


title: OT2_E2


title: OT2_E12


title: OT2_E11


title: OT2_D8


title: OT2_D9


title: OT2_D7


title: OT2_D6


title: OT2_D3


title: OT2_D5


title: OT2_D4


title: OT2_D2


title: OT2_E4


title: OT2_D11


title: OT2_D10


title: OT2_C7


title: OT2_C9


title: OT2_C8


title: OT2_E3


title: OT2_C4


title: OT2_C12


title: OT2_D1


title: OT2_C2


title: OT2_E1


title: OT2_D12


title: OT2_C5


title: OT2_C6


title: OT2_C3


title: OT2_C1


title: OT2_C10


title: OT2_E10


title: OT2_B8


title: OT2_B7


title: OT2_B6


title: OT2_B4


title: OT2_B5


title: OT2_B2


title: OT2_B3


title: OT2_B1


title: OT2_B12


title: OT2_C11


title: OT2_B11


title: OT2_A9


title: OT2_B10


title: OT2_A8


title: OT2_A5


title: OT2_A4


title: OT2_A12


title: OT2_A11


title: DN_H9


title: OT2_A7


title: OT2_A1


title: OT2_A2


title: OT2_A6


title: OT2_B9


title: OT2_A10


title: DN_H8


title: DN_H6


title: DN_H7


title: DN_H5


title: DN_H4


title: DN_H3


title: DN_H1


title: DN_H12


title: DN_H11


title: OT2_A3


title: DN_G9


title: DN_G8


title: DN_G6


title: DN_H10


title: DN_G7


title: DN_G5


title: DN_G3


title: DN_G2


title: DN_G4


title: DN_G1


title: DN_G12


title: DN_G11


title: DN_H2


title: DN_G10


title: DN_F9


title: SARC16

first: Hui

last: Yao

address: 1515 Holcombe Blvd.

department: Bioinformatics and Computational Biology

institute: MD Anderson Cancer Center

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Limma package was used to process the IDAT files. Genes that were absent (dection p value>0.05) in more than 50% of the samples were removed. The rest of the genes were background corrected, log-transformed, and normalized to have the same median expression value per sample.

source_name: Sarcomatoid (SARC)

label_protocol: biotinylated primers were used in the conversion of RNA to cDNA

extract_protocol: RNA was isolated using the MasterPure Complete DNA and RNA Purification Kit (Epicenter Biotechnologies, Madison, WI, USA)

value: Sarcomatoid (SARC)


title: DN_F8


title: SARC24


title: SARC17


title: SARC23


title: SARC13


title: SARC18


title: SARC25


title: SARC21


title: SARC20


title: SARC28


title: SARC26


title: SARC19


title: DN_F6


title: DN_F5


title: SARC27


title: DN_F4


title: SARC22


title: SARC15


title: SARC12


title: DN_F3


title: SARC11


title: SARC10


title: DN_F7


title: SARC14


title: SARC09


title: SARC08


title: DN_F11


title: DN_F12


title: DN_F2


title: DN_F10


title: SARC06


title: DN_E8


title: DN_E9


title: DN_E7


title: DN_E6


title: DN_E5


title: DN_E4


title: DN_E3


title: SARC07


title: SARC05


title: DN_F1


title: SARC01


title: UC82

source_name: Urolthelial carcinoma (UC)

value: Urolthelial carcinoma (UC)


title: UC84


title: UC81


title: SARC03


title: SARC04


title: DN_E2


title: DN_E1


title: DN_E11


title: DN_E10


title: DN_D9


title: DN_D7


title: UC79


title: DN_D6


title: SARC02


title: DN_E12


title: UC83


title: UC76


title: UC75


title: DN_D5


title: DN_D4


title: DN_D3


title: DN_D1


title: DN_D8


title: DN_D2


title: DN_D12


title: UC78


title: UC80


title: UC77


title: UC71


title: UC73


title: UC72


title: DN_D11


title: UC70


title: DN_D10


title: UC74


title: UC68


title: UC69


title: UC63


title: UC66


title: UC65


title: DN_C9


title: DN_C8


title: DN_C7


title: UC62


title: DN_C5


title: DN_C4


title: DN_C3


title: DN_C2


title: DN_C12


title: UC67


title: UC64


title: DN_C6


title: DN_C11


title: UC61


title: DN_B9


title: UC58


title: UC55


title: DN_C10


title: DN_B8


title: DN_B7


title: UC56


title: UC60


title: DN_B6


title: UC54


title: DN_C1


title: DN_B5


title: UC59


title: UC52


title: UC53


title: DN_B4


title: DN_B3


title: UC51


title: DN_B1


title: UC57


title: DN_B2


title: DN_B12


title: DN_B11


title: UC50


title: UC49


title: DN_A9


title: DN_A8


title: DN_A7


title: UC47


title: DN_A6


title: UC44


title: UC48


title: UC46


title: DN_A5


title: DN_A4


title: DN_A2


title: UC39


title: UC45


title: UC43


title: DN_A12


title: DN_A1


title: UC42


title: UC38


title: UC40


title: UC37


title: DN_A10


title: UC34


title: UC32


title: CSC2_F9


title: UC30


title: UC36


title: UC41


title: CSC2_F7


title: UC35


title: UC29


title: CSC2_F6


title: CSC2_F3


title: CSC2_F5


title: UC28


title: UC31


title: CSC2_F2


title: UC27


title: CSC2_F12


title: UC25


title: CSC2_F11


title: UC33


title: CSC2_F10


title: UC26


title: UC20


title: UC22


title: CSC2_E8


title: UC18


title: UC21


title: CSC2_E7


title: CSC2_E6


title: UC23


title: UC19


title: UC24


title: CSC2_E4


title: CSC2_E3


title: UC17


title: UC15


title: CSC2_E2


title: CSC2_E5


title: CSC2_E12


title: UC16


title: CSC2_E11


title: UC13


title: UC12


title: DN_A11


title: UC11


title: UC09


title: UC08


title: UC10


title: CSC2_E1


title: UC06


title: CSC2_D9


title: UC05


title: UC07


title: exp214Hi50k-3

city: Pleasanton

first: Maeve

last: Ohuallachain

state: CALIFORNIA

address: 4300 Hacienda Drive

institute: ROCHE SEQUENCING SOLUTIONS INC

data_processing:
FLASH-1.2.11 was used to merge the paired end reads.
seqtk-v1.2 was used to convert merged fastq file to fasta format.
The reads were then parsed to identify cell-id and marker-id based on the white-list info in the associated qdata folder, deduplicated based on cell-id and marker-ids and finally chimeric reads were filtered out.
Expression counts were then used to remove putative debris and doublets cells based on the criteria listed in Singlet_settings.txt in the corresponding qdata folder.
Expression counts matrix was then normalized by scaling the counts by row-means and multiplying by a factor of 10.
Genome_build: A github repository for the software used to process the raw-fastqs is available at the following location: https://github.com/bioinform/QBC_Single_Cell_Analysis_NGS
Supplementary_files_format_and_content: Tab separated text files containing jittered expression counts (both normalized and un-normalized) for different markers for each individual cell
The *tar.gz contains various files containing white-list information for cell-barcode ids, anchor-sequence info, marker-sequence info and settings information for removal of cell-debris and cell-doublets. The files in this folder is used to process the raw fastqs for each of the experiment.

source_name: primary spleen cells

growth_protocol: Spleen cells were obtained from C57/Blk6 mice, between 6-8 weeks of age. 16% formaldehyde solution (Thermo Scientific, 28908) was added directly to cells to a final concentration of 1.6% and incubated for 10 min at room temperature to fix the cells. Cells to be analyzed for only protein expression were stored in 1X PBS with 10% DMSO at -80°C until antibody staining.

extract_protocol:
QIAquick Gel Extraction Kit (Qiagen, 28704).
PCR with Illumina dual index primers
Single cell barcoding by split-pool synthesis via ligation

value: primary spleen cells

tag: molecule type

value: various proteins


title: UC03


title: UC04


title: UC14


title: UC01


title: CSC2_D8


title: CSC2_D7


title: UC02


title: CSC2_E9


title: CSC2_D5


title: CSC2_E10


title: DN_B10


title: CSC2_D4


title: EE35_cy3_8b

city: San Diego

first: Goran

last: Bozinovic

address: 3370 Dale Street

institute: Boz Institute

hyb_protocol: Labeled aRNA samples (2 pmol dye/µl) were hybridized to slides in 10 µl of hybridization buffer [50% formamide buffer, 5x SSPE, 1% sodium dodecyl sulfate, 0.2 mg/ml bovine serum albumin, 1 mg/ml denatured salmon sperm DNA (Sigma), and 1 mg/ml RNase free poly(A) RNA (Sigma)] for 44 hours at 42° C.  Slides were prepared for hybridization by blocking in 5% ethanolamine, 100 mM Tris pH 7.8, and 0.1% SDS added just before use for 30 minutes at room temperature, washed for one hour in 4x SSC, 0.1% SDS at 50° C, and then boiled for 2 minutes in distilled water to denature the cDNAs.

scan_protocol: Arrays were scanned using  a ScanArray Express 4000 (Perkin Elmer).  Resulting 16 bit Tiff Images were quantified using ImaGene® (Biodiscovery, Inc.) spotfinding software.

data_processing: Log2 measures of gene expression were normalized using a linear mixed model in SAS (JMP v6.0.0 with a microarray platform beta-version in SAS v9.1.3) to remove the effects of dye (fixed effect) and array (random effect) following a joint regional and spatial Lowess transformation in MAANOVA Version 0.98.8 for R to account for both intensity and spatial bias (47). The model was of the form yij = µ  + Ai + Dj + (AxD)ij + eij, where, yij is the signal from the ith array with dye j, µ is the sample mean, Ai and Dj are the overall variation in arrays  and dyes (Cy3 and Cy5), (AxD)ij is the array x dye interaction and eij is the stochastic error (48, 49).  Residuals from above model were used for a gene-by-gene analyses using stage, treatment, population, population x treatment, stage x treatment, population x stage, stage x treatment x population and dye as fixed effects.  The model was rijkngm = µ  + Ai + Dj + Tk + Pn + Sm + (TxP)nk + (TxS)km + (SxP)mn + (SxTxP)mkn + eijknm where Tk is the kth treatment (sediment extract), Pn is the nth population, Sm is the mth stage (TxP)nk is treatment by population interaction, (TxS)km is the treatment by stage interaction, (SxP)mn is the stage by population interaction, and (SxTxP)mkn is the stage by treatment by population interaction.Because we were interested in treatment and population effects more than stage effects, we also analyzed the data by stage.  Here the model was rijkn = µ  + Ai + Dj + Tk + Pn + (TxP)nk + eijkn where Tk is the kth treatment (polluted or reference sediment extract), Pn is the nth population, and (TxP)nk is treatment by population interaction.For all mixed model analyses, we used a nominal p-value cut-off for significant genes of p < 0.01.  Using this p-value reveals more genes that may be differentially expressed but risks identifying genes that may be false positives.    Hierarchical clustering used JmpGenomics, Cluster 3.0 for Mac OS X, and Java TreeView version 1.0.8

organism: Fundulus heteroclitus

label_protocol: RNA for hybridization was prepared by one round of amplification (aRNA) using Ambion’s Amino Allyl MessageAmp aRNA Kit to form copy template RNA by T7 amplification.  Amino-allyl UTP was incorporated into targets during T7 transcription, and resulting amino-allyl aRNA was coupled to Cy3 and Cy5 dyes (GE Healthcare, Piscataway, NJ, USA).

growth_protocol: Adult Fundulus were captured from the Elizabeth River, VA (polluted Superfund site; N 36° 10.551’; W 75° 56.533”)  and Magotha, VA (clean, reference site; N 36° 48.473’; W 76° 17.654’) by minnow traps in April 2007 and transported under controlled temperature and aeration condition to the NCSU Aquatic Laboratory.  Fish were acclimated to common conditions of 20° C and 15 ppt salinity in 40-gal flow-through re-circulating aquatic system tanks for 4 months prior to laboratory spawning.  Effluent from the tanks was passed through an activated charcoal filter system and 20% water was changed weekly.  Tanks were maintained, and fish were fed (brine shrimp flake, blood meal flake, and Spirulina flake - FOD, Aquatic Biosystems) daily and monitored for heath.  Fish were maintained under a pseudo-summer cycle (8 h dark / 16 h light). Eggs were stripped from 10 females and fertilized by sperm collected from 10 males from each population, resulting in 10 sensitive (C = clean) and 10 resistant (P = polluted) family sets, each with multiple embryo offspring. Fertilized embryos were maintained in Petri dishes with 15 ppt filtered seawater in a 25°C environmental chamber under light during the initial two stages of development.  Fertilization success was confirmed using a stereo microscope.  Embryos that successfully reached 2-cell stage within a predetermined time (25) were used in the sediment extract exposure experiment.  All experiments were performed according to approved protocols (Institutional Animal Care and Use Committees, North Carolina State University and Duke University).

extract_protocol: Pools of ten frozen embryos collected at four developmental stages (21, 25, 31, 35; Armstrong and Childs, 1965) were used for RNA isolation, labeling, and microarray hybridization.  Embryo RNA was extracted using a Trizol buffer (Invitrogen, Carlsbad, CA, USA) followed by purification using the Qiagen RNeasy Mini Kit (Qiagen Inc., Valencia, CA, USA.

treatment_protocol: Sediment extracts were thawed to room temperature and 20 ml aliquots were transferred to 50 ml glass scintillation vials pre-rinsed with DI-water. 10 embryos were placed into each vial.  Developing sensitive and resistant embryos exposed to clean and contaminated sediment extracts were maintained in an environmental chamber (818 Low Temperature Illuminated Incubator, Precision Scientific, USA) at 25°C and 16 h light / 8 h dark cycle.  Embryo condition and development were monitored daily by examining representative stages using a dissecting stereo microscope (Nikon SME1500, Japan), and time to stage, % normal versus abnormal development, and % mortality were noted.  Unfertilized eggs, malformed and/or dead embryos were removed from the population, and times and stages of arrest and abnormal development were recorded accordingly.  Criteria for time-to-stage was based on >80% success rate of reference embryos cultured in the vials with 15 ppt filtered seawater as well as established developmental timelines (42, 43).  Once the normally developing embryos reached one of four developmental stages (21, 25, 31, or 35), images of embryos were recorded using a Micropublisher 5.0 RTV Camera (QImaging) fitted on the stereo microscope, and embryos were either preserved in neutral buffer-formalin for histopathological analysis (stage 31 only) or placed in pre-chilled 1.5 ml eppendorf tubes and snap-frozen at -80°C for chemical and microarray analyses (stages 21, 25, 31, and 35).  In addition, heart rates were recorded at stages 31 and 35.

tag: population

value: Elizabeth River, VA

value: Whole embryo

tag: Stage


title: CSC2_D3


title: CSC2_D2


title: ME21_cy5_8b

value: Magotha Bay, VA


title: EM31_cy3_13d


title: CSC2_D11


title: CSC2_D1


title: CSC2_D12


title: CSC2_D6


title: MM25_cy5_13c


title: CSC2_C9


title: CSC2_C8


title: CSC2_D10


title: CSC2_C7


title: MM25_cy3_18d


title: CSC2_F8


title: CSC2_C6


title: CSC2_C5


title: ME25_cy3_13c


title: EE35_cy5_13d


title: EE21_cy3_13a


title: ME25_cy5_13a


title: EM31_cy5_18d


title: EE21_cy5_12c


title: EM35_cy5_11c


title: EM35_cy3_12c


title: CSC2_C4


title: CSC2_C2


title: CSC2_C3


title: CSC2_F1


title: CSC2_C12


title: CSC2_C1


title: MM31_cy5_10d


title: MM31_cy3_11c


title: ME31_cy3_10d


title: CSC2_C11


title: ME31_cy5_14b


title: CSC2_C10


title: CSC2_B9


title: CSC2_B8


title: CSC2_B7


title: CSC2_B6


title: CSC2_B5


title: EM21_cy3_15a


title: EE25_cy5_15a


title: DN_A3


title: EE25_cy3_14b


title: EE31_cy5_14c


title: CSC2_B3


title: CSC2_B4


title: CSC2_B1


title: EM25_cy3_14c


title: ME35_cy5_10b


title: EE31_cy3_10b


title: EM25_cy5_12d


title: MM35_cy5_8a


title: EM21_cy5_21d


title: ME35_cy3_8a


title: CSC2_B12


title: MM21_cy3_12d


title: CSC2_B10


title: CSC2_B11


title: EM35_cy3_10c


title: CSC2_B2


title: MM35_cy5_10c


title: MM35_cy3_21c


title: ME21_cy5_21c


title: MM21_cy5_18a


title: ME21_cy3_18a


title: CSC2_A9


title: CSC2_A8


title: CSC2_F4


title: CSC2_A5


title: CSC2_A6


title: CSC2_A3


title: EM35_cy5_11b


title: CSC2_A1


title: EE35_cy5_13b


title: CSC2_A2


title: EM31_cy3_12b


title: CSC2_A12


title: CSC2_A11


title: MM31_cy5_12b


title: MM31_cy3_8d


title: CSC2_A7


title: ME35_cy5_8d


title: MM35_cy3_21d


title: EM31_cy5_8c


title: CSC2_A10


title: CSC1_H7


title: EE31_cy3_8c


title: EE35_Cy3_11b


title: CSC2_A4


title: CSC1_H6


title: CSC1_H5


title: ME35_cy3_13b


title: CSC1_H4


title: CSC1_H3


title: CSC1_H2


title: EE31_cy5_15d


title: CSC1_H1


title: MM25_Cy5_18b


title: CSC1_H12


title: ME31_cy3_15d


title: ME31_cy5_15b


title: MM25_Cy3_15b


title: EE25_Cy3_10a


title: EM25_cy3_18b


title: CSC1_H11


title: EM25_Cy5_10a


title: CSC1_G9


title: CSC1_H10


title: EE25_Cy5_18c


title: CSC1_G6


title: CSC1_G5


title: CSC1_G4


title: EM21_Cy3_14a


title: ME25_Cy5_14d


title: CSC1_G3


title: MM21_Cy3_14d


title: RNA-seq_ILC3a_1

city: St. Louis

first: Marco

last: Colonna

state: MO

address: 660 S. Euclid Ave.

institute: Washington University in St. Louis

description:
gene_counts.txt
sample name in processed data file:
sample.1

data_processing:
RNA seq counts were determined using STAR
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited files include raw counts for each sample

source_name: tonsil

extract_protocol:
Briefly, tissue was mechanically disrupted, passed through 0.0059 inches opening sieve, and filtered extensively through 70μm cell strainers. CD56+ cells were enriched via positive selection with CD56 microbeads (Myltenyi), according to manufacturer’s recommendations. RNAs from the sorted ILC subsets were prepared by using RNeasy Plus Micro kit (Qiagen), following manufacturer instructions.
cDNA was amplified with SMARTer Universal Low Input RNA Kit (Clontech). RNA libraries were prepared for sequencing using standard Illumina protocols

value: tonsil

tag: batch

tag: celltype

tag: markers


title: MM21_Cy5_14a


title: CSC1_G2

tag: age

tag: cell type


title: CSC1_G1


title: CSC1_G12


title: EM21_Cy5_15c

tag: tissue


title: CSC1_G11


title: CSC1_G10


title: RNA-seq_ILC1b_1

description:
gene_counts.txt
sample name in processed data file:
sample.3


title: EE21_Cy3_15c


title: RNA-seq_ILC1a_1

description:
gene_counts.txt
sample name in processed data file:
sample.4


title: CSC1_F9


title: ME25_Cy3_18c


title: RNA-seq_ILC3b_2

description:
gene_counts.txt
sample name in processed data file:
sample.6


title: RNA-seq_ILC1b_2

description:
gene_counts.txt
sample name in processed data file:
sample.7


title: CSC1_G7


title: ME21_Cy3_11a


title: CSC1_F6


title: RNA-seq_ILC3a_3

description:
gene_counts.txt
sample name in processed data file:
sample.9


title: RNA-seq_ILC1a_2

description:
gene_counts.txt
sample name in processed data file:
sample.8


title: CSC1_F3


title: CSC1_F4


title: CSC1_F2


title: RNA-seq_ILC3b_3

description:
gene_counts.txt
sample name in processed data file:
sample.10


title: RNA-seq_ILC1a_3

description:
gene_counts.txt
sample name in processed data file:
sample.12


title: EE21_Cy5_11a


title: RNA-seq_ILC1b_3

description:
gene_counts.txt
sample name in processed data file:
sample.11


title: RNA-seq_ILC3b_1

description:
gene_counts.txt
sample name in processed data file:
sample.2


title: CSC1_F1


title: CSC1_F7


title: RNA-seq_ILC3a_2

description:
gene_counts.txt
sample name in processed data file:
sample.5


title: CSC1_F12


title: CSC1_F11


title: CSC1_E9


title: CSC1_F10


title: d24_GFP_pos_Cherry_pos_H3K27ac_input

city: Vancouver

first: Martin

last: Hirst

state: British Columbia

address: 2125 East Mall

department: Microbiology and Immunology

institute: University of British Columbia

data_processing:
H3K27me3 and H3K27ac ChIP-seq read sequences were aligned to NCBI Build 37 (hg19) human reference genome using BWA-backtrack v0.5.7 and default parameters.
Peak enrichment was computed using MACS v2.1.1 (https://github.com/taoliu/MACS) with a false discovery rate (FDR) value cutoff of 0.1 for H3K27me3 (in “-- broad” option for H3K27me3) and FDR cutoff of 0.01 for H3K27ac. Input sample was used as control background.
Paired-end reads were trimmed from the 3’ end based on quality score (end min quality level (Phred) = 20) using Partek Flow software (version 6.0.17.0503; Partek Inc, St Louis, MO). Samples were then aligned to human genome reference assembly GRCh37/hg19 using STAR 2.5.2b (Dobin, Bioinformatics 2014:  30, 923-930) in Partek Flow software. All further analysis steps were done in RStudio 0.99.903 (R version 3.3.1). Raw gene expression counts were calculated using featureCounts in Rsubread v1.24.2 with GRCh37 Ensemble release 75 as annotation (Liao, Bioinformatics 2014: 30, 923-930). Genes with summated counts of 1 or less across all included samples were filtered out. mRNA expression values were then derived after normalization with rlog function in DESeq2 v1.18.1, which log2 transforms and normalizes the data for library size, as well as minimizes the effect of low-expression genes (Love, Genome Biology 2014: 15, 550).
Genome_build: hg19
Supplementary_files_format_and_content: Bed files generated using MACS v2.1.1 (https://github.com/taoliu/MACS)

source_name: NOTCH1ΔE/LMO2/TAL1/BMI1-transduced CB-derived T-cell progenitors

growth_protocol: Transduced cord blood cells were plated on top of confluent monolayers of OP9-DL1 cells in αMEM media supplemented with 20% FBS (Invitrogen) plus 10 ng/mL SCF, 5 ng/mL FLT3L, and 3 ng/mL IL-7 (Peprotech).

extract_protocol:
Live sorted cells were lysed in non-ionic detergents and protease inhibitor cocktail. Cells were digested  by Micrococcal nuclease (MNase) at room temperature for 5 minutes and 0.25mM EDTA was used to stop the reaction. H3K27me3 antibody was incubated with anti-IgA magnetic beads for 2 hours. Digested chromatin was incubated with magnetic beads alone for 1.5 hours. Digested chromatin was separated from beads and incubated with antibody-bead complex overnight in IP buffer. IPs were washed twice and eluted for 1.5 hours. Histones were digested by Protease for 30min and DNA fragments were purified using Sera Mag magnetic beads in 30% PEG. The PCR program included an initial denaturation step at 98C for 30 sec, followed by 8 cycles at 98C for 15 sec, 65C for 30 sec, and 72C for 30 sec, and ending with a final step at 72C for 5 min.
We performed native chromatin immunoprecipitation (ChIP) as described previously (Cell Reports, Lorzadeh et al., 2016). Libraries were constructed using an Agilent Bravo automated liquid handling platform. Illumina sequencing libraries were generated by end repair, 3’ A-addition, and Illumina sequencing adaptor ligation.

treatment_protocol: CD34+ cord blood cells were transduced with lentiviral constructs encoding activated NOTCH1 (NOTCH1ΔE-GFP), LMO2, TAL1, and BMI1 (LMO2/TAL1/BMI1-Cherry).

value: CB-derived T progenitor cells

tag: transduced oncogenes

value: NOTCH1ΔE, LMO2, TAL1, and BMI1

tag: culture conditions

value: 24 days on OP9-DL1 feeders

tag: sorted cell phenotype

value: hCD45+ GFP+ Cherry+

tag: experimental trial number

tag: chip antibody


title: d24_GFP_neg_Cherry_neg_H3K27ac_input

source_name: Non-transduced CB-derived T-cell progenitors

value: hCD45+ GFP- Cherry-


title: d47_GFP_pos_Cherry_pos_H3K27me3_input

value: 47 days on OP9-DL1 feeders


title: d14_GFP_neg_Cherry_neg_H3K27ac_input

value: 14 days on OP9-DL1 feeders


title: CSC1_E7

tag: Sex

value: Mixed

tag: strain

value: skin squamous cell carcinoma

tag: treatment


title: CSC1_E6

tag: sorting markers

value: Before ACT immunotherapy


title: CSC1_F5


title: CSC1_E5


title: d14_GFP_pos_Cherry_pos_H3K27me3_input


title: CSC1_E2


title: CSC1_E3


title: CSC1_E12


title: CB-derived T progenitor cells, d24_GFP_neg_Cherry_neg_H3K27ac

value: anti-H3K27ac (Hiroshi Kimura, Kimura et al. 2008 PMID:18227620)


title: d14_GFP_pos_Cherry_pos_H3K27ac_input


title: CB-derived T progenitor cells, d24_GFP_pos_Cherry_pos_H3K27ac


title: CSC1_E1


title: CSC1_E11


title: MNK3-Tbet-IKZF3_IKZF3_2

description: Cut and Run-seq

data_processing:
Library strategy: Cut and Run-seq
Cut and Run-seq reads were aligned ot the mm9 genome assemply using NovaAlign with the following options:-r None -l 30 -e 100 -i 230 140
duplicates were removed using Picard markDuplicates
RPKM normalized Bigwigs for visulazation were created using bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: processed data is in bigwig format

extract_protocol:
Cut and Run extracts were prepared as in published protocol (Skene, Henikoff, Henikoff - 2018, Nature Protocols). using 2 ug of antibody, 2 M cells per C&R. Briefly, MNK3 cells were permeabalized with 0.02% of DMSO-dissolved digitonin, bound to conA-beads, incubated with antibody, protein-A Mnase (a gift from Heinkoff), and finally chromatin was digested with ice-cold EDTA for 25 minutes. Antibodies were as follows: H3K27ac (abcam ab4729), IKZF3 (Biolegend 371002) and rabbit-anti-mouse IgG (invitrogen 31188). Antibody or pa-MN incubation, as well as washes, were done at room temperature for 5 minutes without rotation.
Nextera DNA Library Preparation Kit, Illuminia

tag: transfected with

tag: chip target

tag: replicate number


title: MNK3-Tbet-IKZF3_IKZF3

description: Cut and Run-seq


title: CSC1_E10


title: CB-derived T progenitor cells, d14_GFP_pos_Cherry_pos_H3K27ac


title: d47_GFP_neg_Cherry_neg_H3K27me3_input


title: MNK3-Control_IKZF3

description: Cut and Run-seq

value: Control


title: CB-derived T progenitor cells, d14_GFP_neg_Cherry_neg_H3K27ac


title: MNK3-Tbet_IKZF3

description: Cut and Run-seq

value: pTbet


title: MNK3-Tbet-IKZF3_H3K27ac

description: Cut and Run-seq


title: CB-derived T progenitor cells, d47_GFP_pos_Cherry_pos_H3K27me3

value: anti-H3K27me3 (Diagenode:Catalogue# pAb-069-050, lot# A1811-001P)


title: d24_GFP_neg_Cherry_neg_H3K27me3_input


title: CSC1_E4


title: MNK3-Tbet_H3K27ac

description: Cut and Run-seq


title: MNK3-Control_H3K27ac

description: Cut and Run-seq


title: d14_GFP_neg_Cherry_neg_H3K27me3_input


title: CB-derived T progenitor cells, d47_GFP_neg_Cherry_neg_H3K27me3


title: CB-derived T progenitor cells, d24_GFP_pos_Cherry_pos_H3K27me3


title: CSC1_D5


title: CB-derived T progenitor cells, d24_GFP_neg_Cherry_neg_H3K27me3


title: CSC1_D4


title: CB-derived T progenitor cells, d14_GFP_pos_Cherry_pos_H3K27me3


title: CSC1_D2


title: CSC1_D7


title: KDhTS2_RNA

city: Fukuoka

first: Takashi

last: Ishiuchi

address: 3-1-1 Maidashi, Higashi-ku

department: Medical Institute of Bioregulation

country: Japan

institute: Kyushu University

description:
processed data file: hTS_FPKM.txt
KD2_FPKM

data_processing:
For RNA-seq, reads were aligned using TopHat (v2.1.1) with the option ‘--segment-length 34 --library-type fr-secondstrand’, and the Cufflinks program (v2.2.1) with the option ‘-u --library-type fr-secondstrand’ was used to calculate the fragments per kilobase of exon per million mapped fragments (fpkm) value.
For H3K4 ChIP-seq, reads were aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1’after removing adaptor sequences and low quality reads by TrimGalore. The enrichment of H3K4me3 was analyzed through the normalization with input samples.
ATAC-seq reads were aligned  aligned to the mouse genome (mm9) using Bowtie2 (v2.2.9) with the option ‘-N 1 -L 25’.
Genome_build: mm9, hg38
Supplementary_files_format_and_content: Text files include FPKM values for each sample. BigWig files include the information of genomic distributions of ChIP or ATAC reads.

source_name: TS cells

growth_protocol: Mouse TS cells were cultured in RPMI medium containing 70% feeder-consitioned medium, FGF4, heparin and Activin A (Peprotech). Human TS cells were cultured as described previously (Okae et al, Cell Stem Cell, 2018).

extract_protocol:
Total RNA was extracted with RNeasy Mini kit (QIAGEN). For ChIP-seq, chromatin was sonicated with Covaris S2. ATAC-seq was carried out with a standard protocol.
150 ng of total RNA from each sample was used for library preparation. mRNA was purified with NEBnext poly(A) mRNA magnetic isolation module (NEB), and sequence libraries were prepared with NEBnext Ultra II Directional RNA library prep kit (NEB) following the manufacturer’s protocol. ChIPmentation was carried out for H3K4me3 ChIP-seq library construction with 7 min incubation with a Tn5 tagmentation enzyme solution (Schmidl et al., 2015). ATAC-seq was carried out as described previously (Buenrostro et al., 2013).

value: trophoblast stem (TS) cells

value: ZNF281 siRNA

tag: genotype/variation

value: Zfp281 knockdown


title: CB-derived T progenitor cells, d14_GFP_neg_Cherry_neg_H3K27me3

value: CB-derived T progenitor cells


title: CSC1_D12


title: CSC1_D6


title: KDhTS1_RNA

description:
processed data file: hTS_FPKM.txt
KD1_FPKM


title: d24_GFP_pos_Cherry_pos_H3K27me3_input

value: NOTCH1ΔE, LMO2, TAL1, and BMI1


title: CSC1_D1


title: CONThTS1_RNA

description:
processed data file: hTS_FPKM.txt
CONT1_FPKM

value: Control siRNA


title: CSC1_D10


title: CSC1_C9


title: CONThTS2_RNA

description:
processed data file: hTS_FPKM.txt
CONT2_FPKM


title: 1551_E: Stim-TRIP On.E

city: Goettingen

first: Ronald

last: Kühnlein

state: Lower Saxony

address: Am Fassberg 11

department: Department of Molecular Developmental Biology

country: Germany

institute: Max Planck Institute for Biophysical Chemistry

description: OligoDT enriched cDNA library

data_processing:
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to  dmel-all-gene-r6.06.fasta.gz whole genome using CLC
Raw reads counting was done with CLC
Gene differential analysis was done with DESeq2.
Genome_build: dmel-all-gene-r6.06.fasta.gz
Supplementary_files_format_and_content: csv file

organism: Drosophila melanogaster

source_name: Stim-TRIP On.E

extract_protocol:
Abdominal fat body tissues were dissected flash frozen in liquid nitrogen, and total RNA was isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-Seq, around 30 million sequencing depth for each sample's library

tag: genotype

value: ts-FB-Gal4>UAS-Stim dsRNA RNAi

value: fat body tissue of adult male flies

value: day 10-11 after Stim-TRIP On


title: 1551_F: Stim-TRIP Off.F

description: OligoDT enriched cDNA library

source_name: Stim-TRIP Off.F

tag: age

value: day 10-11 after Stim-TRIP Off


title: CSC1_D11

value: Mixed

tag: cell type


title: 1551_D: Stim-TRIP Off.D

description: OligoDT enriched cDNA library

source_name: Stim-TRIP Off.D

tag: tissue


title: CSC1_D3

value: skin squamous cell carcinoma


title: CSC1_C7

value: Before ACT immunotherapy


title: 1551_C: Stim-TRIP On.C

description: OligoDT enriched cDNA library

source_name: Stim-TRIP On.C


title: CSC1_C5


title: 1551_B: Stim-TRIP Off.B

description: OligoDT enriched cDNA library

source_name: Stim-TRIP Off.B


title: CSC1_C4


title: CSC1_C3


title: CSC1_C6


title: 1551_A: Stim-TRIP On.A

description: OligoDT enriched cDNA library

source_name: Stim-TRIP On.A


title: Per14 year 1

type: genomic

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

description:
Per14
CpG methylation
Sample27

hyb_protocol: Bisulphite converted DNA hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Illumina scaner

data_processing: Raw intensity data files (idat files) for both mouse and human samples were processed using the R package Minfi.

label: Cy3, Cy5

source_name: buffy coat

label_protocol: Illumina

extract_protocol: DNA provided by Health ABC biorepository; standard DNA extraction protocol

tag: year (visit year when sample was collected)

tag: baseline age

tag: self reported race

value: Caucasian

tag: self sex

value: Male


title: Per20 year 6

description:
Per20
CpG methylation
Sample37

value: Female


title: Per16 year 6

description:
Per16
CpG methylation
Sample31


title: Per18 year 1

description:
Per18
CpG methylation
Sample33

value: African American


title: Per15 year 1

description:
Per15
CpG methylation
Sample28


title: CSC1_C2


title: Per13 year 6

description:
Per13
CpG methylation
Sample26


title: Per18 year 6

description:
Per18
CpG methylation
Sample34


title: Per12 year 1

description:
Per12
CpG methylation
Sample23


title: Per19 year 6

description:
Per19
CpG methylation
Sample35


title: Per16 year 1

description:
Per16
CpG methylation
Sample30


title: CSC1_C1


title: Per20 year 1

description:
Per20
CpG methylation
Sample36


title: Per7 year 2

description:
Per7
CpG methylation
Sample14


title: CSC1_C12


title: Per12 year 6

description:
Per12
CpG methylation
Sample24


title: Per17 year 1

description:
Per17
CpG methylation
Sample32


title: Per9 year 1

description:
Per9
CpG methylation
Sample17


title: D3

city: Fuzhou

first: Fei

last: He

address: No.1 Xuefubei Road

institute: Fujian Medical University

hyb_protocol: Total RNAs were hybridized using mRNA + lncRNA Human Gene Expression Microarray V4.0 (4×180K format, CapitalBio Corp, Beijing, China)

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: lung adjacent non-tumor tissues

label_protocol: The purity and concentration of RNA was determined by Nano Drop ND-1000 spectrophotometer according to OD260/280 reading.

extract_protocol: Tumor samples were microdissected to ensure the purity of the tumor. From the same patient, adjacent normal tissue samples were collected from resected, located approximately 3.5-5 cm away from the tumor site.

treatment_protocol: Samples were fresh frozen and were shipped on ice for subsequent RNA extraction

value: lung adjacent non-tumor


title: Per10 year 1

description:
Per10
CpG methylation
Sample19


title: D4


title: Per10 year 6

description:
Per10
CpG methylation
Sample20


title: CSC1_C11


title: Per11 year 1

description:
Per11
CpG methylation
Sample21


title: D2


title: D1


title: CSC1_C10


title: Per15 year 6

description:
Per15
CpG methylation
Sample29


title: Per13 year 1

description:
Per13
CpG methylation
Sample25


title: Per9 year 6

description:
Per9
CpG methylation
Sample18


title: Per7 year 1

description:
Per7
CpG methylation
Sample13


title: CSC1_B9


title: C4

source_name: lung adenocarcinoma tissues

value: lung adenocarcinoma


title: C3


title: CSC1_B7

source_name: Mouse skin squamous cell carcinoma


title: CSC1_B6


title: Per8 year 6

description:
Per8
CpG methylation
Sample16


title: Per5 year 6

description:
Per5
CpG methylation
Sample10


title: C2


title: Per6 year 1

description:
Per6
CpG methylation
Sample11


title: B4


title: CSC1_B4


title: Col0-2

first: Paul

middle: William

last: Denny

state: Durham

address: Lower Mountjoy

department: Biosciences

institute: Durham University

data_processing:
Fastq files were aligned to Arabidopsis genome (Arabidopsis Araport 2017) using  STAR
BAM files resulting from the alignments were summarized to genes using the HTSeq package
Expression data was normalized using the DESeq package from bioconductor in R
Differentially expressed genes (³2-fold and £5% false discovery rate) were identified using the DESeq package
Genome_build: Arabidopsis thaliana genome (Arabidopsis Araport 2017)
Supplementary_files_format_and_content: Tab-delimited text files include log2 counts per million (CPM) values for each sample

source_name: seedlings

growth_protocol: Arabidopsis thaliana plants were grown on 0.8% Murashige and Skoog (MS) agar for 10 days. Plants were grown at 20°C under 16h day/8 h night photoperiod.

extract_protocol:
RNA was isolated using the ReliaPrep™ RNA Tissue Miniprep System (Promega) and processed as per manufacturer’s instructions.
Libraries were prepared using the Illumina Truseq stranded mRNA sample preparation kit, according to the manufacturer’s instructions.

treatment_protocol: Seedling were untreated

value: seedlings

tag: developmental stage

value: 10 day old seedlings

tag: background strain

value: Wildtype

value: untreated


title: Col0-3


title: Col0-1


title: B3


title: C1


title: CSC1_B3

tag: Sex

tag: strain


title: At3++_5-3

value: AtIPCS3 over expressing line

tag: treatment


title: At3++_5-1


title: Per5 year 1

description:
Per5
CpG methylation
Sample9


title: At3++_5-2


title: CSC1_B2

tag: sorting markers


title: CSC1_B5


title: At3+_4-3


title: B2


title: At3+_4-2


title: Per4 year 1

description:
Per4
CpG methylation
Sample7


title: CSC1_B1


title: B1


title: Per3 year 6

description:
Per3
CpG methylation
Sample6


title: ΔmgrA rep2

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

description:
mgrA_vs_LAC.csv
5_mgrA2_CTTGTA_L007_R1_001

data_processing:
Paired-end reads mapped using CLC Genomics Workbench version 12 (Qiagen).
Reads Per Kilobase of transcript per Million mapped reads (RPKM) were calculated using CLC Genomics Workbench version 12 (Qiagen).
Genome_build: CP000255.1
Supplementary_files_format_and_content: csv file containing total raw counts, RPKM values, TPM values, and CPM values for each replicate.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: cultures

growth_protocol: S. aureus cultures were grown with shaking at 37 °C to an OD600 of 1.5 in tryptic soy broth.

extract_protocol:
1 h lysis step with lysostaphin followed by RNA purification using Qiagen RNeasy Mini Kit.
rRNA depleted using Ribo-Zero rRNA Removal kit for Gram positive bacteria (Illumina) and libraries prepared using TruSeq Stranded mRNA Library Prep Kit (Illumina).

treatment_protocol: 2 min treatment with RNAprotect (Qiagen).


title: At2++_9-3

value: AtIPCS2 over expressing line


title: CSC1_B12


title: ΔmgrA rep1

description:
mgrA_vs_LAC.csv
4_mgrA1_CAGATC_L007_R1_001


title: Per4 year 6

description:
Per4
CpG methylation
Sample8


title: Per2 year 1

description:
Per2
CpG methylation
Sample3


title: CSC1_B10


title: Per2 year 6

description:
Per2
CpG methylation
Sample4


title: WT rep3

description:
mgrA_vs_LAC.csv
3_LAC3_GCCAAT_L007_R1_001

value: wildtype


title: At2++_9-1


title: A2


title: ΔmgrA rep3

description:
mgrA_vs_LAC.csv
6_mgrA3_GTGAAA_L007_R1_001


title: Input_rep3

city: Los Angeles

first: Suhn

middle: K

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

data_processing:
Short sequence reads (SR50) were aligned to the hg19 genome assembly using BWA and data was preprocessed using the ENCODE3 ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/). ChIP-seq peaks were called using MACS2 from each replicate first and then reproducible peaks were selected using the naïve overlap tool, as suggested in the ENCODE3 ChIP-seq standards document (https://www.encodeproject.org/pages/pipelines/) and previously described.
Genome_build: GRCh37

growth_protocol: HCT116 cells (ATCC #CCL-247) were maintained in McCoy's 5A medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
HCT116 cells were transfected with D3A-dCas9/D3L and either KRAB-dCas9 or Ezh2-dCas9 and three gRNAs targeting the HER2 promoter. Control cells were transfected with dCas9 and the same three gRNAs. For transient repression timepoints, cells were cross-linked 5 days after transfection and growth in puromycin-containing media. For persistent repression timepoints, cells were sorted as described above and dCas9 control cells were cross-linked 24 days after transfection. Cross-linking was carried out in 1% formaldehyde for 10 min at room temperature and was stopped with 0.125 M glycine. Cross-linked cells were lysed with ChIP lysis buffer (5 mM PIPES pH8, 85 mM KCl, 1% Igepal) with a protease inhibitor (PI) cocktail (Roche). Nuclei were collected by centrifugation at 2,000 rpm. for 5 min at 4 °C and lysed in nuclei lysis buffer (50 mM Tris pH8, 10 mM EDTA, 1% SDS) supplemented with PI cocktail. Chromatin was fragmented using the Bioruptor 2000 (Diagenode) and diluted with 5 vol RIPA buffer (50 mM Tris pH 7.6, 150 mM NaCl, 1 mM EDTA pH8, 1% Igepal, 0.25% Deoxycholic acid). ChIP enrichment was performed by incubation with 3 µg H3K9me3 antibody (Diagenode C15410056), 2 µg H3K27me3 antibody (MP07–449), 2 µg H3K27ac antibody (Active Motif #39133) or 2 µg normal rabbit IgG (Abcam ab46540) for 16 h at 4°C. Immune complexes were bound to 20 µl magnetic protein A/G beads (ThermoFisher) for 2 hours at 4°C. Beads were washed 2x with RIPA and 3x with ChIP wash buffer (100 mM Tris pH8, 500 mM LiCl, 1% Deoxycholic acid). The final wash was performed in ChIP wash buffer with 150 mM NaCl. Cross-links were then reversed by heating beads in 100 µl ChIP elution buffer (50 mM NaHCO3, 1% SDS) overnight at 65°C and DNA was purified using the QIAquick PCR Purification Kit (Qiagen).
Each entire ChIP sample was used to prepare Illumina sequencing libraries using the KAPA Hyper Prep Kit (Roche) and NEXTflex DNA barcodes (BIOO Scientific). Illumina sequencing libraries were pooled and sequenced using the HiSeq 4000 platform (Illumina) at the UC Davis DNA Technologies Sequencing Core.

treatment_protocol: Cells of 60-70% confluency were transfected using Lipofectamine 3000 (Life Technologies) following the manufacturer’s instructions. Transfections were performed in 12-well plates using 625 ng individual or combinations of dCas9 expression vector, 500 ng of equimolar pooled gRNA expression vectors. All experiments were cotransfected with 125 ng of puromycin-resistant plasmid pBABE-puro to select for transfected cells. Transfection medium was replaced 24 hours post-transfection with growth medium containing 3 µg /mL puromycin to enrich for transfected cells. After 72 hours of puromycin selection, HER2 negative cell population was collected by flow cytometry and cells were maintained in standard growth media for a total of 24 day and cross-linked for ChIP assays.

tag: disease state

value: colorectal carcinoma

tag: antibody


title: Per1 year 1

description:
Per1
CpG methylation
Sample1


title: WT rep2

description:
mgrA_vs_LAC.csv
2_LAC2_ACAGTG_L007_R1_001


title: Input_rep2


title: Per1 year 6

description:
Per1
CpG methylation
Sample2


title: Input_rep1


title: WT rep1

description:
mgrA_vs_LAC.csv
1_LAC1_CGATGT_L007_R1_001


title: KRAB_17d_rep2

description: 17 days post transfection

hyb_protocol: standard Illumina protocol

scan_protocol: standard Illumina protocol

data_processing: Samples were normalized (background corrected) using the ‘noob’ function in the minfi software program in R computing language. For each probe, methylated (M) and unmethylated (U) signal intensities were recorded as well as the beta value (M/(M+U)).

label_protocol: Genomic DNA was bisulfite converted and EPIC DNA methylation array data were processed in the USC Molecular Genomics Core

extract_protocol: HCT116 cells were transfected with D3A-dCas9/D3L and either KRAB-dCas9 or Ezh2-dCas9 and three gRNAs targeting the HER2 promoter. Each replicate (n = 2) was performed as an entirely separate transfection experiment. Transfected cells were sorted by flow cytometry as described above and genomic DNA was extracted. Control cells were transfected with three HER2 gRNAs and dCas9 (no effector domain). Genomic DNA from sorted and control cells was isolated 17 and 24 days after transfection using the Quick-gDNA MiniPrep kit (ZYMO). The Infinium Human MethylationEPIC BeadChip (Illumina) was used to analyze global DNA methylation.

tag: cell line

tag: transfection

value: KRAB-dCas9+D3A-dCas9+D3L + HER2 gRNAs 1,2+3


title: KRAB_17d_rep1

description: 17 days post transfection


title: CSC1_A6

value: Mixed

tag: age

value: skin squamous cell carcinoma


title: A4