title: AA7

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
CTL_AA7


title: hFXRBat2

status: Public on Apr 13 2020

type: RNA

city: Groningen

first: vincent

last: bloks

department: Pediatrics

country: Netherlands

institute: UMCG

description: SAMPLE 7

hyb_protocol: Hybridisation of 5.5ug labelled cDNA was done overnight for 17 hours, at 60 rpm, at 45C in a Hybridisation Oven 640 (Affymetrix). The protocol was conducted as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual.

scan_protocol: Washing and staining of the arrays was done on a Affymetrix 450 fluidics stations using the protocol FS450_0001, as described in the Affymetrix Whole Transcript (WT) Sense Target Labeling Assay Manual. Arrays where then scanned on an Affymetrix 3000 7G scanner, as described in the Genechip Expression Analysis Technical Manual.

data_processing: The data where normalized using VSN normalisation strategies using the MADMAX analysis pipeline pmid:21778530

label: Biotin

molecule: total RNA

organism: Mus musculus

label_protocol: The Affymetrix GeneChip WT Sense Target Labeling and Control Reagents kit (P/N 900652) was used for the preparation of labelled cDNA from 500ng of total RNA without rRNA reduction

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed a chow diet.

tag: strain background

tag: genotype/variation

value: adipose-specific human FXR overexpressors

tag: gender

value: male

tag: age

tag: diet

value: chow

tag: tissue

value: Brown Adipose Tissue (BAT)


title: HCC1954_siAP2C_rep1

type: SRA

city: St Louis

first: Tiandao

last: Li

state: MO

address: 4444 Forest Park Ave

country: USA

institute: Washington University

description: transient knockdown

library_source: transcriptomic

data_processing:
Sample processing was done by the University of Nebraska
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Cuffdiff was used for FPKM quantification and differential expression
Genome_build: Human Feb.2009 (GRCh37/hg19) (hg19)

organism: Homo sapiens

source_name: human breast carcinoma

growth_protocol: Cell lines HCC1954 and SKBR3 were purchased from the American Type Culture Collection (ATCC; Manassas, VA, USA) and propagated in the appropriate medium as recommended by manufacturer. Additionally, all media were supplemented with 10% FBS (LS26140079, Gibco, USA), 1% 100X Pen/Strep antibiotics (10378016, Gibco, USA), and 0.2% Plasmocin (Cat# ant-mpp, InvivoGen, USA). The cell lines were cultured in a standard humidified incubator at 37° C and 5% CO2 (16). The cells were not tested and authenticated by the authors. Only early passages of cell lines (less than 10) were used for experiments.

extract_protocol:
mRNA from cell lysates were obtained from cell lines using the Rneasy Mini Kit (Qiagen, Valencia, CA, USA). 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

treatment_protocol: Cells were transfected using small interfering RNA (siRNA) directed towards non-targeting #2 (NT Thermo Fisher Scientific ID:4390843), TFAP2C (TFS ID:10.7041) with lipofectamine RNAiMAX reagent (Cat# 13778150, Thermo Fisher Scientific, USA), accordingly a manufacturer’s instruction. After 72 to 96 hours of incubation, cell were immediately analyzed or used in consequent experiments. Cell clones of HCC1954 lines with stable knockdown of TFAP2C (Cat#TRCN0000019745, Sigma, USA) and negative control (Cat#SHC002, Sigma, USA) were generated using lentivirus-mediated shRNA cassette.

tag: passage

value: between 5 and 10

tag: cell line

tag: transfection reagent

value: Lipofectamine RNAi_Max

tag: sirna/shrna

value: TFAP2C siRNA ID:107041


title: AA5

city: Dallas

first: Genevieve

last: Konopka

state: TX

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: UT Southwestern Medical Center

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
D2CKO_AA5

data_processing:
Single cells were identified using UMI Tools
Reads corresponding to individual cells aligned to reference genome using STAR
R1 contains barcode (bp 1-16) and UMI (bp 17-26)
R2 contains the cDNA
Uniquely mapped reads were assigned to genes using featureCounts
UMI Tools was used to generate final raw count table
Raw counts were processed using Seurat for clustering and differentially expressed gene analysis
Genome_build: MM10/GRCm38p6
Supplementary_files_format_and_content: gzipped tab-delimited text file with rows as cells, columns as genes. Additional columns for meta data are also added prior to genes.

source_name: striatum

extract_protocol:
Mice (P9) were sacrificed by rapid decapitation and brains were quickly removed and placed in ACSF (126mM NaCl, 20mM NaHCO3, 20mM D-Glucose, 3mM KCl, 1.25mM NaH2PO4, 2mM of CaCl2 and MgCL2 freshly added) bubbled with 95%O2 and 5%CO2. Coronal slices at 500um were made using a VF-200 Compresstome in ACSF and transferred to a recovery chamber at room temperature in ACSF with 50uM AP5, 20uM DNQX, and 100nM TTX (ACSF+cb){Tasic:2016jp}. Striatal punches were taken from these slices and incubated in 1mg/ml of pronase in ACSF+cb for 5min. Punches were washed with ACSF+ 0.04% BSA twice and gently dissociated into single-cell suspension using polished Pasteur pipettes with 600um, 300um, and 150um opening diameters, sequentially. Cells were centrifuged and washed twice, filtered through Flowmi Tip 40uM strainers, and resuspended with ACSF+ 0.04% BSA. Cell viability was quantified using the trypan blue exclusion method and cell concentration was adjusted for targeted sequencing of 5,000 cells/sample using the 10X Genomics Single Cell 3’ Reagent Kits v2 protocol to prepare libraries (Zheng et al., 2017).  Libraries were sequenced using the McDermott Sequencing Core at UT Southwestern.
Followed 10X Genomics kit manufacturer guidelines

tag: strain

value: striatum

tag: Sex

value: M

value: post-natal day 9

tag: genotype

value: D2-Cre tg/+; Foxp1flox/flox


title: HCC1954_siNT_rep3

description: transient knockdown

value: Negative control siRNA#2


title: HCC1954_siAP2C_rep2

description: transient knockdown


title: AA3

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
DDCKO_AA3

value: D1-Cre tg/+; D2-Cre tg/+; Foxp1flox/flox


title: hFXRBat3

description: SAMPLE 8


title: hFXRBat1

description: SAMPLE 6


title: HCC1954_siNT_rep1

description: transient knockdown


title: WT ESC_Rep 2

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

country: France

institute: institut curie

data_processing:
Adapters were trimmed using Atropos v1.1.16.
The paired-end reads alignment was performed onto the Mouse reference genome (mm10) with STAR v2.7.0a reporting randomly one position, allowing 6% of mismatches (--outFilterMultimapNmax 5000 --outSAMmultNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.06).
Repeats annotation was downloaded from repeatmaskerull-length LTR copies, we used the same strategy as done previously using the perl tool “One code to find them all”.
Reconstructed transposons annotation and basic genes annotation from GENCODE v18 were merged and used as input for quantification with featureCounts v1.5.1. Differential expression analysis was performed using edgeR’s normalisation combined with voom transformation from limma R package. P-values were computed using limma and adjusted with the Benjamini-Hochberg correction. Genes and transposon families were declared as differentially expressed if FDR<5% and log2 Fold-change > 0.75
Genome_build: mm10
Supplementary_files_format_and_content: text file and Table count for gene and transposon family expression

molecule: polyA RNA

source_name: Embryonic Stem Cell

growth_protocol: ES Cells were either cultured in serum-free 'LIF +2i' medium

extract_protocol:
Total RNA was extracted using Trizol (Life Technologies), then DNase-treated and column purified (Qiagen RNeasy Kit).
RNA-seq libraries were prepared from 500ng of DNase-treated RNA with the TruSeq Stranded mRNA Library Prep Kit (Illumina). Sequencing was performed in 100pb paired-end reads using using Novaseq 6000.

tag: development stage

tag: medium

value: Wild-type


title: human CD34+ cells transduced with GFP-lentivirus (MOI50)

city: Bethesda

first: Mehdi

last: Pirooznia

state: MD

address: 12 SOUTH DR

institute: National Institutes of Health

data_processing:
Quality control of paired-end reads were assessed using FastQC tools.
Adapter sequences were trimmed using Trimmomatic
Reads were aligned to the human reference genome (GRCh38) using HISAT2
FeatureCounts was used for gene level abundance estimation using the GENCODE (v29)
Limma was used to process the read counts into log2 counts per million (log2CPM). The log2CPM values were normalized between samples using trimmed mean of M-values (TMM)
Genome_build: GRCh38
Supplementary_files_format_and_content: Count

extract_protocol:
RNA was extracted from differentiated cells using Qiagen Rneasy kit
The sequencing libraries were constructed from 100 ng – 1,000 ng of total RNA using Illumina’s TruSeq Stranded Total RNA kit with Ribo-Zero Globin

treatment_protocol: sHUDEP-2 and human CD34+ cells were transduced with either GFP or  βT87Q expressing lentiviral particules (MOI50) and differentiated towards red blood cells

tag: cell type

value: CD34+ derived human primary cells

value: transduced with GFP-lentivirus (MOI50)


title: WT ESC_Rep 1


title: AA4

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
CTL_AA4


title: AA2

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
DDCKO_AA2

value: F


title: Cardiomyocytes_stage2_p25

city: Cheongju-si

first: Kim

last: Jung-Hyun

address: 202, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu

department: Division of Intractable Diseases

country: South Korea

institute: Korea National Institute of Health

data_processing:
sequenced reads were aligned to human reference genome (GRCh38, hg38) using STAR 2.5.2b aligner with two-pass approach.
The read counts were normalized via regularized log transformation using the DESeq2 package.
Genome_build: GRCh38, hg38
Supplementary_files_format_and_content: comma-separated values file include normalized count values for each samples.

source_name: human induced pluripotent stem cell

extract_protocol:
RNA samples were prepared from collected cell pellets using an Rneasy plus mini kit (QIAGEN).
Illumina TruSeq Sample preparation kit (Illumina) was used to construct sequencing libraries.

value: iPSC-derived cardiomyocyte progenitor cells


title: HCC1954_siNT_rep2

description: transient knockdown


title: Non-transduced human CD34+ cells

value: Non-transduced human CD34+ cells


title: SKBR3_siAP2C_rep2

description: transient knockdown


title: sHUDEP-2 cells transduced with βT87Q-lentivirus (MOI50)

value: human erythroid cell line

value: transduced with <beta>T87Q-lentivirus (MOI50)


title: AA1

description:
10X single-cell
AAX_ALL_CLUST_RAW_COUNTS.txt.gz
CTL_AA1


title: SKBR3_siAP2C_rep1

description: transient knockdown

value: between 5 and 10


title: ControlBat4

description: SAMPLE 4

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed a chow diet during 6wks.

value: wild type (control)

value: male

value: chow

value: Brown Adipose Tissue (BAT)


title: SKBR3_siAP2C_rep3

description: transient knockdown

value: Lipofectamine RNAi_Max

value: TFAP2C siRNA ID:107041


title: ControlBat5

description: SAMPLE 5

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed a chow dieet


title: human CD34+ cells transduced with βT87Q-lentivirus (MOI50)


title: sHUDEP-2 cells transduced with GFP-lentivirus (MOI50)


title: ControlBat3

description: SAMPLE 3


title: ControlBat1

description: SAMPLE 1

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed an chow diet.


title: HC5

city: Copenhagen N

first: Thomas

last: Litman

state: Outside the US or Canada

address: Blegdamsvej 3C

department: ISIM

country: Denmark

institute: University of Copenhagen

hyb_protocol: The labeled samples were hybridized to HTA 2.0 GeneChip arrays (Affymetrix, Santa Clara, CA, USA), which were washed, stained with phycoerythrin-conjugated streptavidin (SAPE) and scanned to generate probe cell intensity (CEL) files.

scan_protocol: Scanned according to Affymetrix standard protocol.

data_processing: Probe intensities were preprocessed and converted to gene expression values using the GC-RMA (Robust Multichip Average) and quantile normalization algorithm of Bioconductor (https://www.bioconductor.org/), including ComBat batch effect correction, in R (https://www.r-project.org/).

label: biotin

source_name: healthy control skin

label_protocol: 100 ng total RNA was amplified and labeled using the WT Plus Expression Kit (Affymetrix)

extract_protocol: RNA was extracted from the snap frozen skin biopsies using RNeasy Mini Kit according to manufacturer’s recommendations (Qiagen)

tag: diagnosis

value: healthy control

value: Male

tag: scan date

tag: run


title: ControlBat2

description: SAMPLE 2

extract_protocol: Total RNA was prepared form WAT and BAT adipose tissue of 10wk old mice fed an chow diet during 6wks.

tag: strain background

tag: genotype/variation

tag: gender


title: Non-transduced sHUDEP-2 cells

value: Non-transduced


title: SKBR3_siNT_rep2

description: transient knockdown

value: Negative control siRNA#2


title: SKBR3_siNT_rep1

description: transient knockdown


title: DLD-1 Cell line treated by E-Coli-replicate 3

city: Shanghai

first: Haoyan

last: Chen

state: Shanghai

address: 145 Shandong Road

country: China

institute: Renji Hospital

data_processing:
Paired-end reads were filtered and trimmed using software Trimmomatic
Quality control before and after raw reads preprocessing was done using software FastQC
Count files of the aligned sequencing reads were generated by the  featurecount, using the GTF annotation file gencode.v22.gtf.file
Genome_build: hg38
Supplementary_files_format_and_content: Tab-separated matrices with read counts,

source_name: DLD1 cells

growth_protocol: DLD-1 cells were routinely cultured adherently in the six hole plate in the concertration of 5*107 per hole with 1640 medium

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested 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

treatment_protocol: DLD-1 Cells were co-cultured with ETBF or E-coli for different time 2h, 6h, 12h, 24h. Multiplicity of infection (MOI) was 500. The normal control samples were treated with the bacteria medium without ETBF.

value: human colorectal cancer cells


title: DLD-1 Cell line treated by E-Coli-replicate 2


title: P21USC_TRULI_d10_RNAseq_rep2

city: Los Angeles

first: Ksenia

last: Gnedeva

state: CA

address: 1501 San Pablo St

department: USC Caruso Department of Otolaryngology – Head and Neck Surgery

institute: USC

data_processing:
NOT PROVIDED; REQUESTED
Genome_build: GRCm38/mm10 genome

extract_protocol:
Supporting cells (Lfng-GFP+) were purified from P21 cultured utricles by FACS sorting. RNA was extracted using Quick RNA micro-kit (Zymo).
PolyA RNA were enriched and used for library with Illumina Trueseq RNA library kit

treatment_protocol: 5d 10 uM Lats1/2 inhibitor (TRULI) and 0.1% DMSO + no treatment 5d recovery

tag: tissue

value: Utricle/Vestibular sensory epithelium

value: Utricular supporting cells

tag: age

tag: culture condition


title: SAMPLE 6_MDA-MB-231 antimiR-138

city: Singapore

first: Prabha

last: Sampath

state: Singapore

address: 8A Biomedical Grove

department: Institute of Medical Biology

country: Singapore

institute: Institute of Medical Biology

description: Replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: The data was back ground substracted and normalized using  Illumina Inc. GenomeStudio version 1.9.0

source_name: MDA-MB-231 antimiR-138

label_protocol: Biotinylated cRNA were prepared with the Target Amp-Nano kit for Illumina arrays

growth_protocol: MDA-MB-231 cells were grown in complete medium containing DMEM and 10% FBS

extract_protocol: Total RNA, including miRNA, was isolated using Exiqon RNA Isolation Kit

treatment_protocol: MDA-MB-231 cells were transduced with 6 Transduction Units of scrambled or antimiR-138 control expressing lentivirus. Cells were harvested 72 hours post transduction.

tag: cell line

value: basal breast cancer cell line

tag: transduced with

tag: time point

value: Day 3 post transduction


title: SAMPLE 5_MDA-MB-231 antimiR-138

description: Replicate 2


title: HC6

tag: Sex

value: Female


title: HC4


title: P21USC_TRULI_d10_RNAseq_rep1

value: 5d 10 uM Lats1/2 inhibitor (TRULI) and 0.1% DMSO + no treatment 5d recovery


title: HC2


title: SAMPLE 3_MDA-MB-231 scamble control

description: Replicate 3

source_name: MDA-MB-231 scamble control

value: scamble control


title: SAMPLE 4_MDA-MB-231 antimiR-138

description: Replicate 1


title: Rif1null_WingDisc_RNA_Replicate3

city: Nashville

first: Jared

last: Nordman

state: Tennessee

address: 465 21st Ave South MRB III 4268

institute: Vanderbilt University

data_processing:
Reads from G1 and S samples were aligned to the dm6 reference genome (Release 6.04) using Bowtie 2 (v2.3.2) default parameters (Langmead et al. 2009).
Reads with a MAPQ score greater than 10 were retained using SAMtools (v1.9) (Li et al. 2009).
txtTools coverage (v2.26.0) was used to quantify the number of reads mapping to each 100kb window, with results normalized to read depth (Quinlan and Hall 2010).
Replication timing (RT) values were obtained by averaging the S/G1 ratio of reads per million (RPM) value from each S phase replicate for a particular window size. Profiles were generated by plotting the RT value at each window versus genomic location.
Quantile normalization was performed for comparisons between samples through the preprocess Core R package to equalize the dynamic range of RT values (Bolstad 2016).
The limma statistical package was used to identify 100kb windows with significantly altered RT values (lmFit, p value adjusted for multiple testing (p<0.01); absolute log2 fold change > 0.1) (Newville et al. 2014).
BEDTools intersect (v2.26.0) was used to determine overlap of 100kb windows with -f 0.5 and -u parameters (Quinlan and Hall 2010).
TopHat default parameters (v2.1.1) (Trapnell et al. 2012) were used to align single-end reads to the dm6 version of the Drosophila genome.
Transcriptomes were generated using Cufflinks (v2.2.1, see supplementary materials for parameters). We combined the Cufflinks generated transcriptome with transposons annotated by RepeatMasker (Smit et al. 2013-2015).
Differentially expressed transcripts were determined via edgeR statistical analysis (p value <0.01) (Robinson et al. 2010; McCarthy et al. 2012).
We assigned the RT log2 fold-change and associated limma-generated adjusted p-value determined at 10kb windows to individual transcripts; if a transcript overlapped multiple 10kb windows, we assigned the average RT log2 fold change and average adjusted p-value of all from all overlapping windows to that transcript.
Genome_build: dm6 (Release 6 plus ISO1 MT)
Supplementary_files_format_and_content: all_raw_avgRT_values.txt, bigWig files

organism: Drosophila melanogaster

source_name: female 3rd instar larval wing disc

extract_protocol:
Total RNA was isolated from 40 3rd instar wing imaginal discs. Wing imaginal discs were homogenized in Trizol (Invitrogen) and flash frozen in liquid nitrogen. RNA was isolated using the Direct-zol RNA miniprep kit (Zymo Research).
rRNA was depleted and libraries were prepared using the Ovation Drosophila RNA-Seq system (NuGEN).

value: Wing disc

tag: developmental stage

value: 3rd instar larvae


title: SKBR3_siNT_rep3

description: transient knockdown

tag: passage

value: between 5 and 10

tag: transfection reagent

tag: sirna/shrna


title: HC1

tag: diagnosis


title: SAMPLE 1_MDA-MB-231 scamble control

description: Replicate 1

tag: cell type


title: DLD-1 Cell line treated by E-Coli-replicate 1


title: SAMPLE 2_MDA-MB-231 scamble control

description: Replicate 2


title: HC3

tag: scan date

tag: run


title: Rif1null_WingDisc_RNA_Replicate2

tag: genotype/variation


title: Pt6-1m

source_name: CTCL lesional skin

value: MF (mycosis fungoides)


title: Normal Control-replicate 3


title: Yellow-white_WingDisc_RNA_Replicate3

value: Yellow-white


title: Normal Control-replicate 2


title: Yellow-white_WingDisc_RNA_Replicate2


title: P21USC_DMSO_d10_RNAseq_rep1

treatment_protocol: 5d 0.1% DMSO + no treatment 5d recovery

value: 5d 0.1% DMSO + no treatment 5d recovery


title: P21USC_TRULI_d5_RNAseq_rep3

treatment_protocol: 5d 10 uM Lats1/2 inhibitor (TRULI) and 0.1% DMSO


title: P21USC_DMSO_d10_RNAseq_rep2


title: Normal Control-replicate 4


title: Rif1null_WingDisc_RNA_Replicate1


title: Pt6-2m

value: Male


title: Normal Control-replicate 1


title: Yellow-white_WingDisc_RNA_Replicate1


title: P21USC_TRULI_d5_RNAseq_rep2

value: 5d 10 uM Lats1/2 inhibitor (TRULI) and 0.1% DMSO


title: Pt6-10d


title: Pt6-0d


title: Pt7-2m


title: DLD-1 Cell line treated by ETBF for 6 hours-replicate 3


title: DLD-1 Cell line treated by ETBF for 6 hours-replicate 1


title: DLD-1 Cell line treated by ETBF for 6 hours-replicate 2


title: P21USC_TRULI_d5_RNAseq_rep1


title: PP1_WingDisc_MS_Replicate1

description:
S phase DNA
processed data file: all_raw_avgRT_values.txt

library_source: genomic

molecule: genomic DNA

extract_protocol:
Tissue was disrupted by douncing and filtered over a 30 mM filter to collect follicle cell nuclei. DAPI-stained nuclei were sorted by 5-Laser FACS Aria III and G1 and S-phase populations were collected. Genomic DNA was fragmented by sonication and extracted by using a standard Phenol-Chloroform extraction protocol and precipitated with sodium acetate, glycogen, and isopropanol.
Libraries were prepared according to the protocol accompanying Rubicon Thruplex DNA-seq kit (R400427).

tag: phase

value: S phase


title: PP1_WingDisc_G1

tag: tissue


title: PP1_WingDisc_MS_Replicate2


title: P21USC_DMSO_d5_RNAseq_rep3

treatment_protocol: 5d 0.1% DMSO

tag: age

value: 5d 0.1% DMSO


title: P21USC_DMSO_d5_RNAseq_rep1

value: Utricle/Vestibular sensory epithelium

tag: culture condition


title: P21USC_DMSO_d5_RNAseq_rep2

value: Utricular supporting cells


title: DLD-1 Cell line treated by ETBF for 2 hours-replicate 3

value: human colorectal cancer cells


title: Pt7-10d


title: Pt7-0d


title: Pt2-2m

value: SS (Sezary syndrome)


title: Rif1null_WingDisc_MS_Replicate1

value: Female


title: DLD-1 Cell line treated by ETBF for 2 hours-replicate 2


title: LTsc1KO 287

city: Guangzhou

first: Ting

state: Guangdong

address: 253 Gongye Street

department: Department of Hepatobiliary Surgery II, Zhujiang Hospital

institute: Southern Medical University

data_processing:
lllumina Casava 1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm8
Supplementary_files_format_and_content: FPKM

extract_protocol:
Liver were removed, flash frozen on dry ice, and RNA was harvested using the RNeasy Plus Mini Kit (Qiagen, Valencia, CA, USA).
RNA libraries were prepared for sequencing using standard lllumina protocols

tag: strain background

value: 10 months

value: liver


title: WT 288

value: wild type


title: DLD-1 Cell line treated by ETBF for 24 hours-replicate 3


title: DLD-1 Cell line treated by ETBF for 2 hours-replicate 1


title: Rif1null_WingDisc_G1

description:
G1 phase DNA
processed data file: all_raw_avgRT_values.txt

value: Wing disc

value: 3rd instar larvae

value: G1 phase


title: DLD-1 Cell line treated by ETBF for 24 hours-replicate 2


title: Rif1null_WingDisc_MS_Replicate2


title: DLD-1 Cell line treated by ETBF for 12 hours-replicate 3


title: KPK_sgSlc33a1.3_BSO

city: Cambridge

first: A

last: Bhutkar

state: MA

address: 77 Massachusetts Avenue

institute: MIT

data_processing:
Illumina pipeline version 1.3+ used for basecalling and sequence read generation
Reads were mapped to the mouse transcriptome (UCSC annotation, genome build mm9) using rsem v1.2.12 and bowtie v1.0.1 with default options.
Genome_build: mm9
Supplementary_files_format_and_content: Microsoft Excel file includes estimated read counts (from rsem) per gene for each sample

source_name: Primary murine lung adenocarcinoma

growth_protocol: Autochthonous lung adenocarcinoma tumors were generated in genetically-engineered mice and isolated at signs of morbidity requiring euthanasia. Cell lines were established in vitro and transfected with control targeting or sgKeap1 targeting guides to establish KP and KPK cell lines.

extract_protocol:
Cell line total RNA was isolated using a Qiagen All prep kit per manufacturer's instruction. RNA quality and purity was assessed using an Agilent Bioanalyzer.
RNA libraries were prepared for sequencing with the Illumina Neoprep library preparation system per manufacturer's instructions.

treatment_protocol: All mice were housed in specific-pathogen free cages and given free access to food and water ad libitum. Lenti-pUSPmNG with respective sgRNA was used to infect cell lines in vitro. Cell lines were placed under vehicle or 50 uM BSO conditions post infection for 48 hours and harvested.

value: Primary murine lung adenocarcinoma

tag: genotype

value: KrasG12D/+; p53-/-; Keap1-/- ; sgSlc33a1 + 50 uM BSO

tag: treatment

value: infected with lenti-sgSlc33a1 treated with 50 uM BSO


title: KP_sgSlc33a1.3_BSO

value: KrasG12D/+; p53-/-; sgSlc33a1 + 50 uM BSO


title: Pt2-0d

tag: time point

tag: Sex

value: Male


title: Pt2-10d


title: Pt7-1m

value: MF (mycosis fungoides)


title: Pt2-1m


title: DLD-1 Cell line treated by ETBF for 24 hours-replicate 1

tag: passage


title: Yellow-white_WingDisc_G1

value: Yellow-white

tag: developmental stage


title: KP_sgSlc33a1.3

value: infected with lenti-sgSlc33a1 vehicle treated


title: Ishikawa

city: Brisbane

first: Tracy

last: O'Mara

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
HiChIP reads (fastq files) were aligned to the human reference genome (hg19) using HiC-Pro version 2.9.0 and default settings used to remove duplicate reads, assign reads to DpnII restriction fragments and filter for valid interactions.
Genome_build: hg19
Supplementary_files_format_and_content: allValidPairs output from the HiC-Pro pipeline. Aligned, filtered, and unique long-range contacts to call loops with.

source_name: Endometrial cancer cells

growth_protocol: Cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum (FBS) and antibiotics (100 IU/ml penicillin and 100 g/ml streptomycin)

extract_protocol:
Cell nuclei were extracted from fixed cell pellets and digested overnight with 375U of DpnII . After digestion, nuclei were resuspended in NEB buffer 2 (New England Biolabs) and restriction fragment overhangs were filled in with biotin-dATP using the DNA polymerase I, large Klenow fragment (incubated at 30oC for 2h). Proximity ligation was performed for 4 h at 16oC, then nuclei lysed and chromatin sheared for 9 min using the Covaris S220 Sonicator. For each sample, sheared chromatin was split into two tubes and incubated overnight with 4.6 mg of H3K27Ac antibody (Abcam, EP16602). The next day Protein A beads were used to capture H3K27Ac-associated chromatin which was eluted and purified with Zymo Research concentrator columns (columns were washed twice with 10 ml of water). The DNA concentration of the purified chromatin was to estimate the amount of TDE1 enzyme (Illumina) needed for tagmentation which was performed with biotin-labelled chromatin captured on streptavidin beads.
Sequencing libraries were then generated by PCR of tagmented samples using the Nextera DNA preparation kit (Illumina) as per the manufacturer’s instructions. Afterwards, size selection was performed using Ampure XP beads to capture 300-700 bp fragments. For each cell line, at least two independent sequencing libraries were pooled together to provide 25 ml of library at ≥10 nM for Illumina HiSeq4000

treatment_protocol: cells were stimulated with 10 nM estradiol for 3 h prior to fixation

tag: chip antibody

value: H3K27Ac (Abcam, EP16602)

value: endometrioid endometrial tumour


title: KPK_sgSlc33a1.3


title: KPK_sgChr4.1

value: KrasG12D/+; p53-/-; Keap1-/- ; sgChromosome4.1 (Ctrl)

value: infected with lenti-sgCtrl vehicle treated


title: Pt8-10d

tag: diagnosis

value: SS (Sezary syndrome)

value: Female


title: DLD-1 Cell line treated by ETBF for 12 hours-replicate 2

tag: cell type

value: human colorectal cancer cells


title: JHUEM-14

growth_protocol: Cells were cultured in DMEM/F12 medium with 10% FBS and antibiotics


title: KP_sgChr4.1

value: KrasG12D/+; p53-/-; sgChromosome4.1 (Ctrl)


title: E6E7hTERT

source_name: Normal immortalized endometrial cells

value: normal endometrium


title: Pt8-2m

tag: scan date


title: DLD-1 Cell line treated by ETBF for 12 hours-replicate 1


title: Pt1-2m

tag: run


title: ARK-1

value: serous endometrial tumour


title: METTL3-KO2

data_processing:
Sequence reads were mapped to the human genome (hg19) using TopHat v2.0.11 with the default options with a TopHat transcript index built from Ensembl_GRCh37.
Count files of the aligned sequencing reads were generated by the htseq-count script from the Python package HTSeq with union mode, using the GTF annotation file
Genome_build: hg19
Supplementary_files_format_and_content: count file

source_name: HCT116 cell line

growth_protocol: The human HCT116 colorectal cancer cells were cultured in McCoy's 5a Medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.

extract_protocol:
Total RNA of HCT116 cells with different treatment was harvested 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

treatment_protocol: We constructed METTL3 gene knock out cells by CRISPR/Cas9 system in HCT116 cells.

tag: genotype/variation

value: METTL3 knock out


title: Pt1-10d


title: Pt1-1m


title: METTL3-KO1


title: METTL3-KO3


title: CIRTS-3 YTHDF2 SMARCA4-rep3

city: Chicago

first: Bryan

middle: C

last: Dickinson

state: IL

department: Chemistry

institute: The University of Chicago

data_processing:
Reads were pseudoaligned to the hg38 transcriptome file downloaded from the UCSC database using kallisto.
Statistical analysis of the aligned reads was performed using the sleuth package in R.
Genome_build: hg38
Supplementary_files_format_and_content: tsv files containing aligned read counts in estimated counts and tpm

source_name: HEK-293T_CIRTS-3 YTHDF2 SMARCA4

extract_protocol:
RNA samples were extracted from HEK-293T cells using RNeasy Mini kit with the standard protocol; mRNA was enriched and sequenecing libraries were prepared.
Libraries were constructed using a commercial KAPA mRNA HyperPrep Kit.

tag: cell line

value: CIRTS-3 YTHDF2 SMARCA4


title: Pt8-1m


title: WT3

value: wild type


title: WT2


title: #4 H2B GFP 3 d OV

city: Lexington

first: Kevin

last: Murach

state: KY

address: 900 South Limestone CTW 445

department: Physical Therapy

institute: University of Kentucky

description:
zr2894_4
Overload.cg_unstranded.bw

data_processing:
Base calling with Illumina Software
Raw FASTQ files were adapter, filled-in nucleotides, and quality trimmed using TrimGalore
The effect of trimming and overall quality distribution was determined using FastQC
Alignment was performed using Bismark
Read totals were called using Bismark Methylation Extractor
Genome_build: mm10

source_name: plantaris muscle

extract_protocol:
Myonuclei and interstitial nuclei were collected via FACS, and DNA was isolated using the Qiagen QIAmp DNA Micro Kit
DNA was fragmented using MspI, ligated to pre-annealed adapters containing 5'-methyl-cytosine, bisulfite treated, then purified after preparative-scale PCR.

treatment_protocol: Sham and 3 days of synergist ablation overload

tag: tissue

value: plantaris muscle

tag: sample type

value: Purified myonuclei

tag: conditions

value: 3 d synergist ablation OV

tag: strain


title: #6 H2B GFP 3 d OV

description:
zr2894_6
Sham.cg_unstranded.bw

value: Sham


title: Pt8-0d


title: OV GFP- 3 d OV (Interstitial)

description:
zr2894_8
OV_GFP-.cg_unstranded.bw

value: Purified interstitial nuclei


title: Sham GFP- 3 d OV (Interstitial)

description:
zr2894_7
Sham_GFP-.cg_unstranded.bw


title: #3 H2B GFP 3 d OV

description:
zr2894_3
Overload.cg_unstranded.bw


title: CIRTS-3 YTHDF2 SMARCA4-rep1


title: #2 H2B GFP 3 d OV

description:
zr2894_2
Sham.cg_unstranded.bw


title: CIRTS-3 YTHDF2 NT-rep2

source_name: HEK-293T_CIRTS-3 YTHDF2 NT

value: CIRTS-3 YTHDF2 NT


title: CIRTS-3 YTHDF2 NT-rep3


title: #1 H2B GFP 3 d OV

description:
zr2894_1
Overload.cg_unstranded.bw


title: 46_925_8_15_17_Bx2

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to the Human Reference Genome Sequence and transcripts annotated with  Genome Reference Consortium Build 38 (GRCh38) using STAR software (v2·5·2b).
Unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.5.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: ectocervical biopsies

extract_protocol:
Snap frozen ectocervical biopsies were cut and placed into 350µl of RLT lysis buffer (QIAGEN) and 1% 2-mercaptogthanol (Sigma-Aldrich). The tissues were bead milled with a stainless-steel bead and Tissuelyser II (QIAGEN).
Total RNA was extracted using RNeasy Micro Kit with DNase digestion (QIAGEN). RNA quantity and quality were assessed using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis.
RNA quantity and quality were assessed using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis. 1ng of total RNA was used for mRNA amplifications using Clontech Smarter V4 chemistry (Takara Bio Inc).
Amplified mRNA was fragmented and barcodes appended using Illumina’s Nextera XT kits. Amplified libraries were validated using an Agilent 4200 Tapestation and quantified using a Qubit fluorimeter
Libraries were normalized, pooled and clustered on an Illumina HiSeq 3000/4000 flowcell using an Illumina cBOT. Libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read reactions with multiplexing to achieve approximately 20 million reads per sample.

tag: gender

value: female

value: ectocervical biopsies

tag: ID

tag: timepoint

value: Placebo


title: CIRTS-12 Nuclease SMARCA4-rep3

source_name: HEK-293T_CIRTS-12 Nuclease SMARCA4

value: CIRTS-12 Nuclease SMARCA4


title: 45_925_8_8_17_Bx2

tag: treatment


title: Pt5-1m

value: MF (mycosis fungoides)

tag: time point

tag: Sex

value: Male


title: Pt5-10d


title: Pt5-2m


title: HFD rep 3

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

department: Medicine

institute: UCSD

data_processing:
QC reads with FastQC
Align with STAR 2-pass
Analyze alternative splicing with JUM setting p<0.05
Analyze local splicing variants with MAJIQ setting p<0.05
Visualize MAJIQ results using VOILA
Genome_build: mm10
Supplementary_files_format_and_content: tsv or txt

source_name: liver

extract_protocol:
Mice were sacrificed and livers dissected. Hepatocytes were obtained as described in PMID: 25315009. Hepatocytes RNA was extracted and quantified using a NanoDrop 1000 (Thermo- Fisher, Waltham, MA) and assessed on a Tapestation (Agilent, Santa Clara, CA).
TruSeq Stranded mRNA libraries were prepared according to the manufacturer’s instructions (Illumina, San Diego, CA).
Each library was sequenced on the Illumina HISeq2000 platform using paired-end 100 cycles.

treatment_protocol: Male C57Bl/6 mice were fed normal chow (NC; 13.5% fat; LabDiet) until 8 weeks of age and then switched to either a high-fat diet (HFD; 60% fat; Research Diets, Inc.) or low fat diet (LFD, 10% kcal fat, Research diets)  for 12 weeks. The University of California San Diego Animal Care and Use Committee approved all procedures.

value: hepatocytes

value: liver

tag: diet

value: HFD

value: male


title: CIRTS-12 Nuclease SMARCA4-rep2


title: Pt5-0d

tag: diagnosis


title: CIRTS-12 Nuclease SMARCA4-rep1


title: Pt3-2m


title: WT1

value: wild type

tag: cell type

value: human colorectal cancer cells

tag: passage


title: HFD rep 2


title: Pt4-2m

tag: scan date

tag: run


title: Pt4-1m


title: 47_925_9_12_17_Bx1


title: CIRTS-3 YTHDF2 NT-rep1

tag: cell line

tag: genotype/variation


title: CIRTS-12 Nuclease NT-rep2

source_name: HEK-293T_CIRTS-12 Nuclease NT

value: CIRTS-12 Nuclease NT


title: LFD rep 2

tag: tissue

value: LFD


title: HFD rep 1


title: LFD rep 1


title: CIRTS-12 Nuclease NT-rep3


title: LFD rep 3


title: Pt4-10d


title: 41_922_8_30_17_Bx1

value: TDF


title: 43_924_8_18_17_Bx1


title: CIRTS-3 YTHDF2 SMARCA4-rep2

value: CIRTS-3 YTHDF2 SMARCA4


title: Pt3-1m


title: 44_924_9_14_17_Bx2


title: CIRTS-12 Nuclease NT-rep1


title: 40_922_6_8_17_Bx2


title: Input DNA rep4

city: Waltham

first: Ming

last: Tang

state: Massachusetts

address: 21 Hickory Drive, 1

department: Computational biology

institute: Immunitas Therapeutics

description: Input DNA

data_processing:
Basecalls performed using CASAVA version 1.7
ChIPseq reads were aligned to mm9 genome using bowtie1 with max 1 mismatch, duplicated reads were removed
peaks were called using MACS14 using pvalue cutoff of 1e-5, and was further filtered for downstream analysis using a more stringent cutoff of 1e-9
bigwig files were generated by deeptools bamCoverage normalized by RPKM
the pipeline used to process ChIPseq can be found at https://github.com/crazyhottommy/pyflow-ChIPseq
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contains the ChIPseq signal normalized by RPKM. Bed files contain the peaks called by MACS14

source_name: mouse lung tumor

extract_protocol:
Genome wide analysis of cromatin states in lung tumors induced by K-RasLSL-G12D and K-RasLSL-G12D;Mll4fl/fl  mice after Ad-CMV-Cre treatment.  Six histone modifications (H3K27Ac,H3K4me1, H3K79me2, H3K9me3, H3K4me3 and H3K27me3) were mapped by ChIP-seq. ChIP assays were performed as previously described (Terranova et al., 2018).Briefly, lung tumor tissue (3mg per antibody) were cut into 1mm pieces, homogenized using MACS dissociator using optimized conditions and cross-linked using 1% paraformaldehyde for 10 min at 37oC. Crosslinking was then stopped by adding 0.125M glycine for 5mins, and tissues were washed with PBS and stored at -80oC. Next day tissues were thawed on ice and lysed with ChIP harvest buffer (12 mM Tris-Cl, 0.1x PBS, 6 mM EDTA, 0.5% SDS) for 10min on ice. Sonication conditions were optimized for lung tumor tissues using bioruptor sonicator to achieve a shear length of 250- 500bp. Antibody-dynabead mixtures were incubated for 1hr at 4oC and tissue extracts were then incubated overnight with antibody-dynabead mixtures. After overnight incubation, immunecomplexes were washed in following order: 5 times with RIPA buffer, twice with RIPA-500 (RIPA with 500mM NaCl) and twice with LiCl wash buffer (10mM Tris-HCl pH8.0, 1mM EDTA pH8.0, 250mM LiCl, 0.5% NP-40, 0.1% DOC). For decrosslinking and elution, immunecomplexes were incubated overnight at 65oC in direct elution buffer (10mM Tris-Cl pH8.0, 5mM EDTA, 300mM NaCl, 0.5% SDS). Eluted DNA was then treated with Proteinase K (20mg/ml) and RNaseA and DNA cleaned up was done using SPRI beads (Beckman-Coulter). Library was prepared as described earlier (Terranova et al., 2018) using NEB adapters. Libraries were multiplexed together and sequencing was performed in Hiseq2000
Library was prepared as described earlier (Terranova et al., 2018) using NEB adapters

treatment_protocol: For fixation, 1% paraformaldehyde for 10 min at 37oC

value: lung

tag: chip antibody


title: Pt3-10d


title: H3K27me3_ChIPseq rep4


title: H3K4me3_ChIPseq rep4


title: 39_921_9_13_17_Bx2

value: female


title: HepG2_Zika-infected1

city: Boston

first: Francisco

middle: Javier

last: Quintana

address: 60 Fenwood Road

department: Neurology

institute: Brigham and Women's Hospital

data_processing:
DGE libraries were prepared by the Broad Technology Labs and sequenced by the Broad Genomics Platform.
Reads were first demulitplex using Picard (v.2.17.11) IlluminaBaseCallsToSam; with well indices CCGGCA (F4), CGCACC (F7), CGGACG (F10), CGTCCG (G1), GACGCC (G4), and GCCCAG (G7).
Reads were aligned using GRCh38 Human genome with STAR (v2.4.2a) with default parameters
Duplicate reads are marked with Picard UmiAwareMarkDuplicatesWithMateCigar to identify duplicate reads based on UMI sequence and alignment start site.
Gene are then quantified using RSEM v1.2.21 with paired-end option and accessed for quality using RNA-SeQC.
Genome_build: GRCh38
Supplementary_files_format_and_content: txt format with gene ID, symbol, and RPKM

source_name: HepG2 cells

growth_protocol: HepG2 cells were grown in Dulbecco's Modified Eagle's medium (DMEM, GIBCO) supplemented with 10 % fetal bovine serum, 100 IU/ml of penicillin and 100ug/ml of streptomycin.

extract_protocol:
Cells were trypsinized, washed and RNA was extracted using RNeasy kit (QIAGEN)
Libraries were prepared by the Broad Institute according to the 3' DGE protocol as described (Soumillon et al., bioRxiv 2014)

treatment_protocol: HepG2 cells were infected with Zika virus (Puerto Rico strain) at a multiplicity of infection (MOI) of 1 for 48 h

tag: agent

value: Zika

value: Liver hepatocellular carcinoma

tag: passages


title: Bmal1_KO_replicate 1

city: Santiago de Compostela

first: Miguel

last: Fidalgo

state: A Coruña

address: Barcelona Avenue s/n-Campus Vida

department: Physiology

country: Spain

institute: Universidade de Santiago de Compostela

data_processing:
Sequences reads were aligned to mouse genome (GRCm38, mm10) with TopHat2 (v2.1.1) and Bowtie2 (v.2.3.0), providing a GTF reference genome for mapping (-G)
Transcript assembly and diferential expression analysis was performed by cufflinks (v.2.2.1) following default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files including FPKM values for each sample.

source_name: Embryonic Stem Cells

extract_protocol:
Total RNA was extracted using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols. Briefly, rRNA was removed using Ribo-Zero kit. RNA was fragmented randomly by adding fragmentation buffer and cDNA was synthesized. Finally, sequencing adaptor ligation was performed and the double-stranded cDNA library was completed through size selection and PCR enrichment.

tag: initial cell type

value: Mouse Embryonic Stem Cells

tag: ko generation


title: HepG2_Zika-infected2


title: 38_921_7_11_17_Bx2

tag: gender

value: ectocervical biopsies

tag: ID

tag: timepoint

tag: treatment


title: Bmal1_WT_replicate 2

value: Wild type


title: Bmal1_KO_replicate 2


title: Bmal1_WT_replicate 1


title: HepG2_Mock-infected3

value: Mock

tag: Sex

value: Male


title: 42_924_7_20_17_Bx2

value: Placebo


title: H3K79me2_ChIPseq rep4


title: 37_920_9_7_17_Bx1


title: 35_920_6_21_17_Bx2


title: HepG2_Zika-infected3


title: H3K27ac_ChIPseq rep4


title: HepG2_Mock-infected1


title: HepG2_Mock-infected2


title: H3K9me3_ChIPseq rep4


title: Pt4-0d

extract_protocol: RNA was extracted from the snap frozen skin biopsies using RNeasy Mini Kit according to manufacturer’s recommendations (Qiagen)

tag: diagnosis

value: MF (mycosis fungoides)

tag: time point


title: 36_920_7_12_17_Bx1


title: 34_919_9_7_17_Bx1


title: ATAC_Treg_Tfam_KO_R2

city: Gainesville

first: Liang

last: Zhou

state: FL

address: 2015 SW 16th Ave

department: IDI

institute: University of Florida

data_processing:
[RNA-seq] The sequencing reads were mapped with HISAT2 (Kim D et al., 2015) to the Mus musculus genome (mm10 assembly) and filtered for uniquely mapped reads. Quantitated mRNA expression levels, FPKM and count aligned reads, were calculated based on exon regions using the cufflinks (Cole Trapnell et al., 2012) and HTSeq (Simon Anders et al., 2014) respectively. Significantly changed genes (max FPKM ≥ 1, fold change >1.5, q-value ≤ 0.05) were identified by DESeq2 (Michael Love et al., 2014) analysis.
[ATAC-seq] ATAC-Seq reads were mapped to the mouse genome (mm9) with bowtie2 (Langmead and Salzberg, 2012). The mapped reads were filtered using samtools (Li et al., 2009), keeping only the uniquely aligned reads, and bedgraph files (scaled to 10 million reads) were made with bedtools (Quinlan and Hall, 2010).
Genome_build: [RNA-seq]  mm10,  [ATAC-seq] mm9
Supplementary_files_format_and_content: [RNA-seq] Tab-delimited text file includes count values for each sample.  [ATAC-seq] bedgraph files for each sample

source_name: Spleen/Lymph Node Treg

extract_protocol:
[RNA-seq] Total RNA was extracted from about 1×10e6 sorted YFP+ Tregs pooled from spleen and lymph node of 2 to 3 Tfamfl/+Foxp3Yfp-Cre/+ or Tfamfl/flFoxp3Yfp-Cre/+ female littermate mice with RNAeasy Mini Kit (Qiagen), followed by DNase treatment (TURTBO DNA-freeTM Kit). [ATAC-seq] 5x10e4 sorted splenic Tregs were lysed in lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Pelleted nuclei were resuspended in transposition reaction mix with Tn5 transposase (Illumina) and incubated at 37°C for 30 min.
[RNA-seq] mRNA was purified with NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB) and RNA-seq libraries were generated using NEBNext Ultra II RNA library Prep Kit (NEB). [ATAC-seq] The DNA was purified with MinElute PCR Purification Kit (Qiagen) and was used as a template of PCR with 10 cycles of amplification. The library was cleaned up with 1.2x SPRIselect beads (Beckman Coulter) before sequencing.

value: Spleen and Lymph Node

tag: cell type

value: Treg

tag: strain

tag: genotype


title: ATAC_Treg_Tfam_KO_R1


title: ATAC_Treg_Tfam_Ctrl_R2


title: GFP-UVSSA_TIR

city: Jerusalem

first: Sheera

last: Adar

state: Israel

address: Botnar Building Room 001, Faculty of Medicine, Hebrew University, Ein Kerem

department: Department of Microbiology and Molecular Genetics

country: Israel

institute: Hebrew University of Jerusalem

description: Excised oligomer released in Nucleotide Excision Repair (XR-seq)

data_processing:
Library strategy: XR-seq
Base calling using Casava v1.8.2. Demultiplexing performed allowing 1 mismtach in the index
Flanking adapter sequences were removed from the reads using trimmomatic (Bolger et al. 2014).
Reads were aligned to the hg38 human genome using bowtie (Langmead et al. 2009) with the command options  -q --nomaqround --phred33-quals -m 4 -n 2 -e 70 -l 20 --best –S
PCR duplicates were removed using PicardCommandLine Mark Duplicates (http://broadinstitute.github.io/ picard/)
Per base read counts were calculated using bedtools genomecov and normalized per million mapped reads per chromosome and split to “plus” and “minus” strands. Read counts were calculated in 25nt windows to create repair signal maps in bigwig file format.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files of the data normalized to mapped read counts and separated by strands.

growth_protocol: Cell lines  were cultured at 37°C in an atmosphere of 5% CO2 in DMEM  supplemented with penicillin/streptomycin and 10% Fetal bovine serum

extract_protocol: XR-seq was performed as previously described (Hu. et al Genes and Dev. 2016, Adar S. et al PNAS 2016). Briefly, cells were harvested 3h after treatment with 20J/m2 UVC (254nm). Primary excision products were pulled down by TFIIH coimmunoprecipitation with anti-p62 and anti-p89 antibodies (Santa Cruz Biotechnology sc25329 and sc271500), and ligated to both 5′ and 3′ adaptors. Ligation products containing CPD were purified by immunoprecipitation with the anti-CPD antibody (Cosmo Bio NM-DND-001) and repaired in-vitro by Drosophila melanogaster CPD photolyase. Repaired DNA were PCR-amplified with Index primers and purified by 10% native polyacrylamide gels.

treatment_protocol: For UV irradiation cells were grown to ~70% confluence. Culture medium was removed, and then cells were placed under a 254 nm germicidal lamp for a total dose of 20J/m2 . Following irradiation, fresh culture medium was added to the cells, which were further incubated for the indicated time. Cells were washed with ice-cold PBS, harvested with a cell scraper in PBS and collected by centrifugation at 2500rpm for 4min.

value: osteosarcoma

tag: uv treatment

tag: time after irradiation


title: ATAC_Treg_Tfam_Ctrl_R1

tag: tissue


title: H3K4me1_ChIPseq rep4

tag: chip antibody


title: Input DNA rep3

description: Input DNA


title: 33_919_7_11_17_Bx1


title: GFP-UVSSA_CIR


title: RNA_Treg_Tfam_KO_R3


title: 32_919_6_15_17_Bx1


title: GFP-UVSSA_WT_CPD-Xrseq Rep2


title: 31_918_8_29_17_Bx2


title: 30_916_8_15_17_Bx2


title: H3K27me3_ChIPseq rep3


title: GFP-UVSSA_WT_CPD-Xrseq Rep1


title: H3K4me3_ChIPseq rep3


title: RNA_Treg_Tfam_Ctrl_R3


title: H3K27ac_ChIPseq rep3


title: 28_915_8_31_17_Bx1


title: H3K79me2_ChIPseq rep3


title: IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin , biological rep3

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

description: Transcriptome profile of IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin, biological rep3

data_processing:
Reads were aligned and assigned to Human Gencode release 19 transcripts and genes by using STAR 2.3.0 with Htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: IGROV-CP20 cells

growth_protocol: IGROV-CP20 cells were growth following standard culture conditions throughout the treatments with FDA compounds and cisplatin

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Mini Kit Cat No./ID: 74106 (250), Quiagen). RNA extract was precisely quantified and mixed at 50ng/5 µL
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp

treatment_protocol: IGROV-CP20 cells were incubated either with cisplatin for 24h or with Telmisartan, Tranilast or Amphotericin B for 24h followed by treatment with cisplatin for other 24h and then total RNA was extracted and transcriptomic analysis performed using QuantSeq 3’ mRNA sequencing

tag: cell line

value: IGROVF-CP20, human ovarian cancer cell line resistant to cisplatin


title: RNA_Treg_Tfam_Ctrl_R2


title: IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin , biological rep2

description: Transcriptome profile of IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin, biological rep2


title: 29_916_6_6_17_Bx1

value: TDF


title: IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin , biological rep1

description: Transcriptome profile of IGROV-CP20 cells treated with AMPHOTERICIN B and cisplatin, biological rep1


title: 27_915_6_7_17_Bx1


title: RNA_Treg_Tfam_Ctrl_R1


title: 26_914_8_24_17_Bx1


title: IGROV-CP20 cells treated with TRANILAST and cisplatin , biological rep3

description: Transcriptome profile of IGROV-CP20 cells treated with TRANILAST and cisplatin, biological rep3


title: H3K4me1_ChIPseq rep3


title: Input DNA rep2

description: Input DNA


title: WT uninfected_RNA-Seq_rep6

city: Bethesda

first: Stefano

last: Marenco

address: Building 10, Room 4N306

institute: National Institute of Mental Health

description:
sample name in processed data file:
WT_UnInf5

data_processing:
RTA 1.18.64 software used for basecalling.
The sequencing reads were trimmed using Trimmomatic (version 0.30), demultiplexing was done using Bcl2fastq 1.8.4, then mapped to hybrid genome of mm10 and LCMV using STAR version 2.5.2b with two-pass alignment option
The mapped reads in the genomic features were counted by RSEM (version 1.2.22)
Genome_build: hybrid genome (GENECODE Mouse (mm10) and Lymphocytic choriomeningitis virus (NC_004291.1))
Supplementary_files_format_and_content: tab-delimited text files include normalized read counts for each Sample.

source_name: NK cells

extract_protocol:
Lin-NK1.1+NKp46+ cells were sorted from spleens of naïve and B16F10 tumor-bearing mice. Total RNA was isolated from sorted cells using TRIzol (Ambion part of Life Technologies) following the manufacturer’s protocols. During RNA isolation, DNase treatment was additionally performed using the RNase-free DNase set (Qiagen). RNA quality was checked using an Agilent 2100 Expert bioanalyzer (Agilent Technologies). RNA quality was reported as a score from 1 to 10, and samples falling below the threshold of 8.0 were omitted from the study. cDNA library preparation involves the removal of ribosomal RNA (rRNA) using biotinylated, target-specific oligos combined with Ribo-Zero rRNA removal beads. The RNA is fragmented into small pieces and the cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. The resulting double-strand cDNA is used as the input to a standard Illumina library prep with end-repair, adapter ligation and PCR amplification being performed to give you a library that is ready to go to the sequencer. The final purified product is then quantitated by qPCR before cluster generation and sequencing. Paired-end sequencing (2 × 150 bp) of stranded total RNA libraries was performed on one HiSeq run with Illumina HiSeq3000/4000 chemistry pair end sequencing. The samples have 99 to 148 million pass filter reads with a base call quality of above 92% of bases with Q30 and above.
The HiSeq Real Time Analysis software (RTA 1.18) was used for processing image files, the Illumina bcl2fastq1.8.4 was used to demultiplex and convert binary base calls and qualities to fastq format. The sequencing reads were trimmed adapters and low-quality bases using Trimmomatic (version 0.30), the trimmed reads were mapped to mouse reference genome (GRCm38/mm10) and Gencode annotation M9 using STAR (version 2.5) with two-pass alignment option. RSEM (version 1.2.22) was used for transcript quantification.

value: spleen

value: natural killer (NK)

tag: cell markers

value: wildtype

tag: infected with

value: uninfected


title: WT uninfected_RNA-Seq_rep5

description:
sample name in processed data file:
WT_UnInf4_2x_B2


title: RNA_Treg_Tfam_KO_R1


title: IGROV-CP20 cells treated with TRANILAST and cisplatin , biological rep2

description: Transcriptome profile of IGROV-CP20 cells treated with TRANILAST and cisplatin, biological rep2


title: RNA_Treg_Tfam_KO_R2


title: Pt1-0d

city: Copenhagen N

first: Thomas

last: Litman

address: Blegdamsvej 3C

institute: University of Copenhagen

data_processing: Probe intensities were preprocessed and converted to gene expression values using the GC-RMA (Robust Multichip Average) and quantile normalization algorithm of Bioconductor (https://www.bioconductor.org/), including ComBat batch effect correction, in R (https://www.r-project.org/).

source_name: CTCL lesional skin

value: Female

tag: scan date

tag: run


title: H3K27me3_ChIPseq rep2

value: lung


title: H3K4me3_ChIPseq rep2


title: H3K9me3_ChIPseq rep3


title: 24_914_6_28_17_Bx1

tag: gender

value: female

value: ectocervical biopsies

tag: ID

tag: timepoint


title: 25_914_7_26_17_Bx1

tag: treatment


title: WT uninfected_RNA-Seq_rep4

description:
sample name in processed data file:
WT_UnInf4_B2


title: IGROV-CP20 cells treated with TRANILAST and cisplatin , biological rep1

description: Transcriptome profile of IGROV-CP20 cells treated with TRANILAST and cisplatin, biological rep1


title: IGROV-CP20 cells treated with TELMISARTAN and cisplatin , biological rep3

description: Transcriptome profile of IGROV-CP20 cells treated with TELMISARTAN and cisplatin, biological rep3


title: H3K79me2_ChIPseq rep2


title: 22_912_8_23_17_Bx1


title: 23_914_6_1_17_Bx1


title: Pt3-0d

tag: diagnosis

tag: time point

tag: Sex


title: IGROV-CP20 cells treated with TELMISARTAN and cisplatin , biological rep2

description: Transcriptome profile of IGROV-CP20 cells treated with TELMISARTAN and cisplatin, biological rep2

tag: cell type


title: 21_912_6_20_17_Bx2


title: IGROV-CP20 cells treated with TELMISARTAN and cisplatin , biological rep1

description: Transcriptome profile of IGROV-CP20 cells treated with TELMISARTAN and cisplatin, biological rep1


title: H3K9me3_ChIPseq rep2


title: H3K27ac_ChIPseq rep2


title: WT uninfected_RNA-Seq_rep1

description:
sample name in processed data file:
WT_UnInf2_B2

tag: genotype

value: Lymphocytic choriomeningitis virus


description: Transcriptome profile of IGROV-CP20 cells treated with cisplatin, biological rep3


title: H3K4me1_ChIPseq rep2


title: 20_908_7_24_17_Bx2


title: WT tumor bearing_RNA-Seq_rep4

description:
sample name in processed data file:
WT_TmBr_TBSp4_B2


description: Transcriptome profile of IGROV-CP20 cells treated with cisplatin, biological rep2


title: WT tumor bearing_RNA-Seq_rep3

description:
sample name in processed data file:
WT_TmBr_TBSp2_B2


title: 19_908_5_31_17_Bx1


description: Transcriptome profile of IGROV-CP20 cells treated with cisplatin, biological rep1


title: Input DNA rep1

description: Input DNA


title: H3K4me3_ChIPseq rep1


title: WT uninfected_RNA-Seq_rep3

description:
sample name in processed data file:
WT_UnInf2_2x


title: Cd47-/- uninfected_RNA-Seq_rep5

description:
sample name in processed data file:
KO_UnInf5


title: 18_908_5_1_17_Bx1


title: H3K27me3_ChIPseq rep1


title: 16_907_6_27_17_Bx2


title: H3K79me2_ChIPseq rep1


description: Transcriptome profile of IGROV-CP20 cells untreated, biological rep3


title: Cd47-/- uninfected_RNA-Seq_rep4

description:
sample name in processed data file:
KO_UnInf4


title: WT tumor bearing_RNA-Seq_rep1

description:
sample name in processed data file:
WT_TmBr_2


title: WT uninfected_RNA-Seq_rep2

description:
sample name in processed data file:
WT_UnInf2A


title: 17_907_7_25_17_Bx2


title: H3K9me3_ChIPseq rep1


title: L296

city: Milano

last: Percio

state: Milano

address: Via Amadeo 42

department: DRAST

institute: Fondazione IRCCS - Istituto Nazionale dei Tumori

data_processing:
Basecalls performed using bcl2fastq Conversion Software v2.18.0.12
Paired-end reads were trimmed for adaptor sequence, then mapped to a combined human-mouse reference genome (hg19+mm10) using STAR_2.5.3a with the parametes  --outFilterMultimapNmax 1 --outReadsUnmapped Fastx --outSAMtype BAM SortedByCoordinate. The partialy mapped sequences were aligned as single-end with the same procedure
Raw counts were computed with htseq-count (version 0.6.1p1) union mode using gene annotation from Ensembl GRCh37 release 72, then counts per million (CPM) were calculated with R Bioconductor package edgeR  adopting the function calcNormFactors
Genome_build: hg19+mm10
Supplementary_files_format_and_content: count

source_name: epithelioid sarcoma PDX

growth_protocol: From 6 to 8 week-old female SCID mice were implanted into the right flank with the PDX that grew from surgical specimen of INI1-deficient P-ES sample. Mice were randomized to receive different drugs when xenografts were approximately 150 mm3.

extract_protocol:
Total RNA was extracted from fresh frozen tumors grown in control (untreated) and in EPZ-011989-trated mice with RNeasy mini kit (Qiagen) according to manufacturer's instructions.
cDNA libraries were synthesized from 500 ng total RNA with TruSeq Stranded mRNA kit (Illumina) following manufacturers’ instructions.

treatment_protocol: EPZ-011989 was delivered orally twice a day for 28 consecutive days (500 mg/kg).

tag: agent


description: Transcriptome profile of IGROV-CP20 cells untreated, biological rep2


title: H3K27ac_ChIPseq rep1

tag: tissue


title: 14_904_6_15_17_Bx1


description: Transcriptome profile of IGROV-CP20 cells untreated, biological rep1


title: L295


title: H3K4me1_ChIPseq rep1

tag: chip antibody


title: L294

value: untreated


title: 13_904_5_9_17_Bx2


title: WT tumor bearing_RNA-Seq_rep2

state: MD

description:
sample name in processed data file:
WT_TmBr_3


title: 12_903_6_23_17_Bx1


title: Cd47-/- uninfected_RNA-Seq_rep1

description:
sample name in processed data file:
KO_UnInf1


title: Cd47-/- uninfected_RNA-Seq_rep2

description:
sample name in processed data file:
KO_UnInf2


title: K-Ras_RNAseq_rep2

data_processing:
Basecalls performed using CASAVA version 1.4
RNAseq reads were aligned using STAR
raw count for each gene was obtained by HTSeq-count
the pipeline used to process RNAseq data can be found at https://github.com/crazyhottommy/pyflow-RNAseq
Genome_build: mm9
Supplementary_files_format_and_content: HTSeq count txt file

extract_protocol:
Total RNA was prepared from CD45-depleted K-Ras and K-Ras Mll4-/- lung tumors using Trizol reagent (Life Technologies).Briefly, to isolate total RNA from lung tumor tissues, first tumor cells were enriched by depletion of CD-45 positive cells. The tumor tissues were dissected and cut into <1mm pieces. The tissues were then digested in Collagenase type 1 and DNAase1 for 45 min followed by 0.25% trypsin for 10 min. To remove RBC, the digested single cells suspension then treated with RBC lysis buffer for 2-3 min. CD45-positive cells were then depleted using MagniSort™ Mouse CD45 Depletion Kit (ThermoFisher Scientific). Total RNA was isolated using Trizol reagent (Life Technologies). RNA samples were sequenced using the Illumina HiSeq 2000.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: L293


title: 15_907_5_30_17_Bx1

value: Placebo


title: K-Ras_RNAseq_rep1


title: 11_903_5_25_17_Bx2


title: Cd47-/- tumor bearing_RNA-Seq_rep4

description:
sample name in processed data file:
KO_TmBr_TBSp4_B2


title: LEN+RUNXi3

city: Philadelphia

first: Luca

last: Busino

state: PA

address: 421 Curie Blvd, 705 BRB II/III

department: Cancer Biology

institute: Luca Busino

data_processing:
Illumina Nextseq500 reads were trimmed and clipped for quality control in …
Read quality was checked for each sample usign FastQC.
Alignment of reads were performed using STAR aligner.
Aligned reads were assembled using CUFFQUANT and normalized  using CUFFNORM
Differential expression analysis was performed using DESeq2 with DMSO samples for each cellline as the respective control
Genome_build: GRCh38

growth_protocol: OPM-1 cells were maintained in RPMI-1640 media  supplemented with 10% FBS , 1%Pen/Strep  and 1%L-Glutamine .  Cells were grown at 37°C in a 5% CO 2 incubator.

extract_protocol:
Total RNA was isolated using miRNeasy Kit (Invitrogen) following the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: OPM-1 cells were treated with DMSO, 0.1 μM lenalidomide (LEN), 1 μM RUNX inhibitor (AI-10-104), or combination for 48 hours.

value: multiple myeloma

tag: cell line


title: K-Ras Mll4-/- _RNAseq_rep2


title: LEN+RUNXi2


title: Cd47-/- uninfected_RNA-Seq_rep3

description:
sample name in processed data file:
KO_UnInf3

tag: cell markers


title: 9_903_4_20_17_Bx2


title: Cd47-/- tumor bearing_RNA-Seq_rep1

description:
sample name in processed data file:
KO_TmBr_3

tag: infected with


title: Cd47-/- tumor bearing_RNA-Seq_rep2

description:
sample name in processed data file:
KO_TmBr_4


title: LEN+RUNXi1


title: K-Ras Mll4-/- _RNAseq_rep1


title: 5_902_4_7_17_Bx2


title: TM402

city: New york

first: Valeria

last: Gerbino

state: Ny

address: 3227 Broadway

department: Zuckerman Mind Brain Behavior Institute

institute: Columbia University

description: RNA-Seq, Paired End

data_processing:
Adapter Sequences were trimmed with cutadapt (v1.9.1) (--minimum-length 18)
Alignment:RNA-seq samples were aligned with STAR (v2.5.3a)
Filtering: Unmapped reads and reads with a mapping quality below 30 were removed with Samtools (1.3.1).
bigWig files were generated with STAR.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Lumbar Spinal cord

extract_protocol:
Lumbar spinal cords were dissected from each mouse genotype in quadruplicate and RNA extracted using Trizol.
Libraries were prepared using the SMARTer Stranded Total RNA-Seq kit, according to the manufacturer's protocol.

value: TBK1 mut SOD_es

value: Lumbar Spinal cord


title: RUNXi3


title: 6_902_4_21_17_Bx2


title: RUNXi2


title: TM407

description: RNA-Seq, Paired End


title: TM409

description: RNA-Seq, Paired End


title: 7_902_5_19_17_Bx1


title: 10_903_4_27_17_Bx1


title: LEN3


title: LEN2


title: RUNXi1


title: TC557

description: RNA-Seq, Paired End

value: TBK1 WT SOD_es


title: DMSO3


title: Cd47-/- tumor bearing_RNA-Seq_rep3

description:
sample name in processed data file:
KO_TmBr_TBSp1_B2


title: TC556

description: RNA-Seq, Paired End


title: SV18207_008

city: Torrance

first: Robert

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

description:
cyclodextrin control
SV18207_008

data_processing:
Reads for each miR were quantitated using Oasis (v 2.0) by Norgen Biotek using standard methods for finding sequence reads, ignoring improper lengths.
Genome_build: miRbase version 21 microRNA Rat
Supplementary_files_format_and_content: The raw data are provided as FASTQ, and the processed data are provided as excel files showing the number of reads for each miR under the various treatments and cell types.

organism: Rattus norvegicus

source_name: pelvic floor muscle

growth_protocol: Cells were maintained in culture at 37 degrees C in the presence of 5% CO2  in either 6 well or 12 well plates.

extract_protocol:
Total RNA was extracted using the Norgen animal cell RNA extraction kit. Each well of the 6 or 12 well plate was aspirated, washed once with 1x phosphate buffered saline, and lysed using the Norgen lysing agent supplemented with mercaptoethanol. The lysates were further purified using the Norgen column binding and elution procedure using the Norgen reagents.
The total RNA samples were sent to Norgen Biotek where the libraries were constructed according to standard protocols using the Norgen Biotek small RNA Library Prep Kit (catalog 63600) .

treatment_protocol: Cells were exposed to serum from non-obese (LZ) or obese (OZ) strains for 4 days; alternatively they were exposed to cholesterol (linked to cyclodextrin) or palmitic acid for the same length of time.

tag: group

value: obese strain

value: cyclodextrin control


title: TM399

description: RNA-Seq, Paired End


title: 1_901_4_4_17_Bx1


title: e13.5 Aspn-/- fetal MSC, biological rep2

city: Baltimore

middle: M

last: Hughes

address: 1550 Orleans Street

institute: Johns Hopkins University School of Medicine

description: Gene expression data from passage 3 Aspn-/- fetal MSCs

hyb_protocol: affymetrix protocol

scan_protocol: Affymetrix GeneChip scanner 3000 with G7 upgrade (Affymetrix GeneChip Expression Analysis Technical Manual, Affymetrix, Santa Clara, CA).

data_processing: All bioinformatics analyses were performed in R. The dataset was normalized at a transcript level for core transcripts with the R/Bioconductor package oligo and annotated with the NetAffx Biological Annotations.  Artifacts from technical batches were removed with ComBat implemented in the R/Bioconductor package SVA.  Differential expression analyses were performed on ComBat adjusted data using the R/Bioconductor package LIMMA.  Genes with FDR adjusted p-values below 0.05 and absolute log fold change greater than or equal to two were called statistically significant.

source_name: e13.5 mouse embryos

label_protocol: affymetrix protocol

growth_protocol: Fetal MSCs were isolated by euthanizing C57BL/6J Aspn+/+ or Aspn-/- pregnant females at embryonic day 13.5 via isoflurane inhalation followed by cervical dislocation.  The uterine horns were dissected, and each embryo was separated from its placenta and embryonic sac.  The head and red organs were removed and discarded, while the remaining tissue was minced with a sterile razor, and digested with trypsin + DNAse I (1 mg/mL) for single cell isolation.  Fetal MSCs were cultured in DMEM supplemented with 10% FBS, GlutaMAX (1X), penicillin (100 U/mL), and streptomycin (100 µg/mL).  Fetal MSCs, expanded to passage 3, were cultured under normal growth conditions to 70-80% confluency prior to RNA isolation.

extract_protocol: RNA was isolated using the Qiagen RNeasy kit.

tag: developmental stage

value: e13.5 embryos

value: fetal MSCs

value: Aspn-/-

tag: background strain


title: 3_901_5_15_17_Bx2

tag: gender

tag: ID


title: e13.5 Aspn+/+ fetal MSC, biological rep2

description: Gene expression data from passage 3 Aspn+/+ fetal MSCs

value: Aspn+/+


title: e13.5 Aspn-/- fetal MSC, biological rep1


title: 8_902_6_16_17_Bx2

tag: timepoint

tag: treatment

value: TDF


title: SV18207_006

description:
cholesterol 50 mg/dl
SV18207_006

value: cholesterol 50 mg/dl


title: LEN1


title: e13.5 Aspn-/- fetal MSC, biological rep3


title: 2_901_4_17_17_Bx1

value: female


title: JMJ6-OE_GFP_ChIPSeq_Input rep2

city: Guangzhou

first: Li

last: Zhiwei

address: No.723,Xingke Road

institute: South China Botanical Garden, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to Tomato reference genome (version SL3.0) using the BWA program.
Peaks were called using MACS2 software with the following setting: MACS2 callpeak --nomodel -f BAMPE --keep-dup 1 -q 0.05 -B –SPMR --broad --broad-cutoff 0.05.
Genome_build: Tomato reference genome (version SL3.0)
Supplementary_files_format_and_content: bigwig files were generated using MACS2 software.

organism: Solanum lycopersicum

source_name: Ailsa-Craig background

growth_protocol: Wild-type tomato and transgenic lines in the Ailsa-Craig background were grown in a greenhouse at 23°C under 16 h light and 8 h dark condition.

extract_protocol:
Pericarp tissues were collected, immediately cross-linked in 1% formaldehyde for chromatin isolation and Lysates were clarified from sonicated nuclei and protein-DNA complexes were precipitated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: develpmental stage

value: At 37 days after anthesis (dpa)

value: Pericarp

value: transgenic line (JMJ6-OE)


title: SV18207_007

description:
cyclodextrin control
SV18207_007

tag: Sex


title: e13.5 Aspn+/+ fetal MSC, biological rep3


title: TC648

description: RNA-Seq, Paired End

value: TBK1 WT


title: SV18207_005

description:
cholesterol 100 mg/dl
SV18207_005

value: cholesterol 100 mg/dl


title: Screen II_late_+blast_rep2

city: paris

first: teissandier

last: aurelie

address: 26 rue d'Ulm

institute: institut curie

data_processing: The sequenced reads were mapped to the sgRNA library. Only reads that contained one sgRNA sequence without mismatch were counted. The MAGeCK test command line (version 0.5.8) was used to rank sgRNAs and genes with following parameters: --norm-method total --adjust-method fdr --remove-zero-threshold 10 --gene-lfc-method alphamean --remove-zero both.

source_name: Embryonic Stem Cell

growth_protocol: Mouse E14 ES cells were cultured in 'Serum + LIF' medium

extract_protocol: Library construction for Screen I was perfromed as in Joung, J., Konermann, S., Gootenberg, J. et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat Protoc 12, 828–863 (2017). https://doi.org/10.1038/nprot.2017.016. Library constructon for Screen II was performed as in  Wang T, Yu H, Hughes NW, Liu B, Kendirli A, Klein K, Chen WW, Lander ES, Sabatini DM. Cell. 2017 Feb 1. pii: S0092-8674(17)30061-2. doi: 10.1016/j.cell.2017.01.013.

treatment_protocol: Cells were infected with Lentiviral sgRNA library, selected with puromycin (2 days) and blasticidin S (5, 7 and 9 days).

tag: development stage

tag: medium

value: Serum+LIF

value: Wild-type


title: DMSO2

value: multiple myeloma


title: TC588

description: RNA-Seq, Paired End

tag: genotype

value: TBK1 WT SOD_es

value: Lumbar Spinal cord


title: JMJ6-OE_GFP_ChIPSeq_Input rep3

tag: tissue


title: TC539

description: RNA-Seq, Paired End


title: DMSO1


title: e13.5 Aspn+/+ fetal MSC, biological rep1

value: e13.5 embryos


title: JMJ6-OE_GFP_ChIPSeq_IP rep3

tag: chip antibody

value: GFP (ab290, Abcam)


title: JMJ6-OE_GFP_ChIPSeq_Input rep1


title: TC643

description: RNA-Seq, Paired End


title: TC637

description: RNA-Seq, Paired End


title: JMJ6-OE_GFP_ChIPSeq_IP rep2


title: Screen II_late_+blast_rep1


title: SV18207_004

description:
albumin control
SV18207_004

value: obese strain

tag: agent

value: albumin control


title: SV18207_003

description:
0.5 mM palmitate
SV18207_003

value: 0.5 mM palmitate


title: JMJ6-OE_H3K27me3_ChIPSeq_Input rep3


title: Screen II_late_-blast_rep2


title: Screen II_early_+blast_rep2


title: es3dd_smRNA_rep4

city: Shenzhen

first: Bosheng

last: Li

address: SUStech Huiyuan #1 406

department: MCDB

institute: SUSTC (current, may different with previous institution )

data_processing:
Sequence reads were filtered and then mapped to TAIR10 genome using Bowtie-1.2.2 with following parameters: -v  0  -a  -M  3  --best  --strata
22-nt small RNA read were selected using samtools v1.9
Tags Per Million (TPM) were calculated and differential 21- and 22-nt siRNA production genes were called out using DESeq2
Genome_build: TAIR10
Supplementary_files_format_and_content: Excel files include TPM values for each sample, the log2(FoldChange) value and the according p-value of pair-comparisons

organism: Arabidopsis thaliana

source_name: es3dd aerial part

growth_protocol: plants were grown on the MS medium for 6 days and then were transferred to the soil for another 14 days. Aerial parts of 20-day-old were collected for small RNA extraction.

extract_protocol:
miRNeasy mini kit(Qiagen)
NEBNext® Small RNA Library Prep Set for Illumina

treatment_protocol: No treatment

value: aerial part

tag: age

value: 20-day-old plant

value: ein5-1 ski2-3 dcl4-2 dcl2-1


title: JMJ6-OE_H3K27me3_ChIPSeq_Input rep2

value: At 37 days after anthesis (dpa)

value: Pericarp


title: Screen II_late_-blast_rep1


title: JMJ6-OE_GFP_ChIPSeq_IP rep1

value: transgenic line (JMJ6-OE)


title: SV18207_002

description:
1mM palmitate
SV18207_002

value: female

value: 1mM palmitate


title: Screen II_early_+blast_rep1

value: Serum+LIF

value: Wild-type


title: es3dd_smRNA_rep2


title: SV18207_001

description:
none
SV18207_001


title: SV18176_8

description:
none
SV18176_8


title: Screen II_early_-blast_rep2


title: es3dd_smRNA_rep1


title: TC651

description: RNA-Seq, Paired End

value: TBK1 WT


title: JMJ6-OE_H3K27me3_ChIPSeq_Input rep1


title: Screen II_early_-blast_rep1


title: SV18176_7

description:
none
SV18176_7

value: non-obese strain


title: SV18176_5

description:
5% LZ serum
SV18176_5

value: 5percent  LZ serum


title: Screen I_seq5_blast9D


title: es3dd_smRNA_rep3


title: JMJ6-OE_H3K27me3_ChIPSeq_IP rep3

value: H3K27me3 (07-449, Millipore)


title: JMJ6-OE_H3K27me3_ChIPSeq_IP rep2


title: es3_smRNA_rep3

source_name: es3 aerial part

value: ein5-1 ski2-3


title: Screen I_seq4_blast7D


title: SV18176_4

description:
5% OZ serum
SV18176_4

value: 5percent  OZ serum


title: Screen I_seq3_blast5D


title: JMJ6-OE_H3K27me3_ChIPSeq_IP rep1


title: WT_H3K27me3_ChIPSeq_Input rep3

value: wild type (WT)


title: es3_smRNA_rep2

value: aerial part


title: WT_H3K27me3_ChIPSeq_Input rep2


title: es3_smRNA_rep1

value: 20-day-old plant


title: SV18176_1

description:
none
SV18176_1

source_name: quadriceps muscle

value: male

value: non-diabetic


title: SV18176_6

description:
5% LZ serum
SV18176_6

value: obese strain


title: SV18176_2

description:
5% OZ serum
SV18176_2


title: Experiment 3

city: Madison

first: Sathish

last: Kumar

state: Wisconsin

address: 2015 Linden drive

department: School of Veterinary Medicine

institute: University of wisconsin Madison

description: Sprague Dawley rats

data_processing:
Image analysis and base calling was performed using Solexa pipeline V1.8 (Off-Line Base Caller software, version 1.8)
Reads (pass Solexa CHASTITY quality filter) were aligned to Rat reference genome (ENSEMBL build RNO6)  and Rat transcriptome (ENSEMBL build RNO6.0.98) using Hisat2 and transcript abundances for each sample was estimated with StringTie.
The gene expression level (FPKM value) and significant changes in gene expression was then calculated using R package Ballgown
rMATS was used to detecting alternative splicing events and plots.
Genome_build: Rat reference genome (ENSEMBL build RNO6) ) and Rat transcriptome (ENSEMBL build RNO6.0.98)
Supplementary_files_format_and_content: tab-delimited text matrix files with gene and transcript FPKM values along with fold change differences

source_name: Uterine artery

growth_protocol: Sprague-Dawley rats were purchased from Envigo laboratories and were maintained on 12 L/12 D cycles in a temperature-controlled room (23°C) and provided with food (Teklad global rodent diet # 2020X) and water ad libitum

extract_protocol:
Trizol extraction of total RNA form the uterien arteries were performed according to the manufacturer's instructions.
The rRNA depleted total RNA was reverse transcribed, fragmented, and 3’ end repaired, after adding a “dA” base to the 3’ end, the Illumina adapter was ligated to the double strand cDNA. The adpter ligated library was then amplified using Illumina’s proprietary amplification primers. Completed libraries were qualified on Agilent 2100 Bioanalyzer for concentration, fragment size distribution between 400~600 bp
paired end RNA- seq

treatment_protocol: Non pregnant (diestrus) and Timed Pregnant ( Gestational Day 20) were used in the study (3 per group)

tag: condition

value: Pregnant, Gestational Day 20

value: 10-12 weeks old

tag: diet

value: Tekla drodent diet # 2020X


title: SV18176_3

description:
5% OZ serum
SV18176_3

value: female

tag: group


title: Screen I_seq2_-blast

value: Serum+LIF

value: Wild-type


title: Screen I_seq1_+puro


title: P22 DSG Input Chd4 cKO

city: St. Louis

first: Jared

middle: V

last: Goodman

state: MO

address: 4523 Clayton Ave

institute: Washington University in St. Louis School of Medicine

data_processing: DNaseI-seq and ChIP-seq reads were aligned to mm10 using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012). Conversion of sam to bam files was performed using Samtools (v1.3) (Li et al., 2009). DNaseI-seq reads per kilobase per million (rpkm) was quantified using Deeptools (v2.4.2) bamCoverage with no extension (Ramírez et al., 2016). ChIP-seq rpkm was quantified using Deeptools bamCompare assuming a 300bp fragment size (-e 300) with reads centered (--centerReads) and input subtracted. Signal was then divided by the binsize to generate DNaseI- or ChIP-seq reads per million (rpm). To generate genomic tracks for viewing on the UCSC genome browser, DNaseI-seq biological replicates were concatenated using Samtools then quantified as described above (James Kent et al., 2002). ChIP-seq reads were concatenated using Samtools, then rpkm was quantified using Deeptools bamCoverage assuming a 300bp fragment size (-e 300) with reads centered (--centerReads). Signal was then divided by the binsize to generate DNaseI- or ChIP-seq rpm. DNaseI-seq peaks were called using MACS2 (v2.1.1.20160309) at a q-value of less than 0.01 (-q 0.01) without model building (--nomodel), an extension of 200bp (--extsize 200), and a shift of -100bp (--shift -100) (Zhang et al., 2008). Peaks from control and Chd4 cKO were then merged and called as significantly different using Diffbind (v2.6.6) running DESeq2 (v1.20.0) (Love et al., 2014; Ross-innes et al., 2012). Chd4 ChIP-seq peaks were called using MACS2 (v2.1.1.20160309) using the broad settings (--broad) at a q-value of less than 0.05 (-q 0.05 –-broad-cutoff 0.05) without model building (--nomodel) and an extension of 300bp (--extsize 300). DNaseI- and ChIP-seq signal at DHS was quantified as the average signal among biological replicates in the 1kb around the TSS or center of the DRE.

source_name: Cerebellum

extract_protocol: Protein-DNA complexes were isolated from sonicated lysates.

tag: developmental stage

tag: genotype/variation

value: Chd4 cKO

value: Cerebellum

value: none (input)


title: Experiment 1

description: Sprague Dawley rats


title: SV18088_7

description:
water soluble cholesterol
SV18088_7

value: early diabetes

value: water soluble cholesterol


title: es3_smRNA_rep4

state: Guangdong

value: ein5-1 ski2-3


title: WT_H3K27me3_ChIPSeq_Input rep1

value: At 37 days after anthesis (dpa)

value: Pericarp

value: wild type (WT)


title: Experiment 2

description: Sprague Dawley rats


title: P22 DSG Input Ctrl

value: control


title: WT_H3K27me3_ChIPSeq_IP rep2

value: H3K27me3 (07-449, Millipore)


title: Control 3

description: Sprague Dawley rats

value: Non pregnant, diestrus


title: Smc1 ChIP-seq Chd4 cKO2

data_processing:
DNaseI-seq and ChIP-seq reads were aligned to mm10 using Bowtie2 (v2.2.5) (Langmead and Salzberg, 2012). Conversion of sam to bam files was performed using Samtools (v1.3) (Li et al., 2009). DNaseI-seq reads per kilobase per million (rpkm) was quantified using Deeptools (v2.4.2) bamCoverage with no extension (Ramírez et al., 2016). ChIP-seq rpkm was quantified using Deeptools bamCompare assuming a 300bp fragment size (-e 300) with reads centered (--centerReads) and input subtracted. Signal was then divided by the binsize to generate DNaseI- or ChIP-seq reads per million (rpm). To generate genomic tracks for viewing on the UCSC genome browser, DNaseI-seq biological replicates were concatenated using Samtools then quantified as described above (James Kent et al., 2002). ChIP-seq reads were concatenated using Samtools, then rpkm was quantified using Deeptools bamCoverage assuming a 300bp fragment size (-e 300) with reads centered (--centerReads). Signal was then divided by the binsize to generate DNaseI- or ChIP-seq rpm. DNaseI-seq peaks were called using MACS2 (v2.1.1.20160309) at a q-value of less than 0.01 (-q 0.01) without model building (--nomodel), an extension of 200bp (--extsize 200), and a shift of -100bp (--shift -100) (Zhang et al., 2008). Peaks from control and Chd4 cKO were then merged and called as significantly different using Diffbind (v2.6.6) running DESeq2 (v1.20.0) (Love et al., 2014; Ross-innes et al., 2012). Chd4 ChIP-seq peaks were called using MACS2 (v2.1.1.20160309) using the broad settings (--broad) at a q-value of less than 0.05 (-q 0.05 –-broad-cutoff 0.05) without model building (--nomodel) and an extension of 300bp (--extsize 300). DNaseI- and ChIP-seq signal at DHS was quantified as the average signal among biological replicates in the 1kb around the TSS or center of the DRE.
Genome_build: mm10
Supplementary_files_format_and_content: Txt files represent the output from Diffbind. Bed files represent the MACS2-called DHS sites at or outside of transcription start sites. Bedpe files represent the Hi-C domains and loops called by Arrowhead and HiCCUPS, respectively. Hic files represent the binarized Hi-C matrices from individual replicates or the pooled sum of all replicates.

source_name: Smc1 ChIP-seq Chd4 cKO

value: Smc1 (Bethyl A300-055A)


title: SV18088_6

description:
cyclodextrin control
SV18088_6

value: male

value: cyclodextrin control


title: WT_H3K27me3_ChIPSeq_IP rep1


title: Control 2

description: Sprague Dawley rats

value: 10-12 weeks old

value: Tekla drodent diet # 2020X


title: SV18088_4

description:
albumin control
SV18088_4

value: albumin control


title: Smc1 ChIP-seq Chd4 cKO1

value: Chd4 cKO

value: Cerebellum


title: Control 1

description: Sprague Dawley rats


title: SV18088_3

description:
5% OZ serum
SV18088_3

value: early diabetes

value: 5percent  OZ serum


title: WS_12h_3

city: Wuhan

first: Zengdong

last: Tan

state: Hubei

address: shizishan street

institute: HZAU

data_processing:
The fastqc program is used to evaluate the quality of all original reads, and the trimmetric software filters them with default parameters to obtain clean data.
The clean reading of all samples was consistent with the reference genome of maize B73 (ref_gen4), which was downloaded from maizegdb (www.maizegdb. ORG) using hisat2 (v2.0.5) and default parameters.
The featurecount software in the rsubread package is used for quantification and standardization to obtain the read count and TPM (one million transcripts per thousand bases) value of each expressed gene, where TPMS represents the expression level of each transcripts.
Genome_build: Zea_mays.AGPv4.dna.toplevel.fa
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Zea mays

source_name: Root

extract_protocol:
Total RNA was extracted using TRIZOL reagent (Invitrogen, Gaithersburg, MD, USA) and purified with an RNeasy mini kit (QIAGEN) according to the manufacturer’s instructions. RNA integrity was detected by gel electrophoresis. High-quality RNA was used for library construction using the Illumina TruSeq Stranded RNA Kit (Illumina, San Diego, CA, USA) following the manufacturer’s recommendations.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cultivar

tag: waterlogging time

value: root


title: SV18088_8

description:
none
SV18088_8

value: late diabetes


title: Smc1 ChIP-seq Ctrl2

source_name: Smc1 ChIP-seq Ctrl


title: WS_12h_2


title: WT_H3K27me3_ChIPSeq_IP rep3

value: At 37 days after anthesis (dpa)

value: Pericarp


title: Smc1 ChIP-seq Ctrl1

value: control


title: dcl4dcl2_ABA_smRNA_rep3

source_name: dcl4-2  dcl2-1 seedlings on ABA medium

value: dcl4-2  dcl2-1

value: whole seedling

value: 14-day-old plant

tag: growth

value: grown on MS+1 μM ABA medium


title: dcl4dcl2_ABA_smRNA_rep2


title: WS_12h_1


title: SV18088_2

description:
5% LZ serum
SV18088_2

value: male

value: 5percent  LZ serum


title: SV18088_1

description:
none
SV18088_1


title: DNaseI-seq Chd4 cKO2

source_name: DNaseI-seq Chd4 cKO

extract_protocol: Nuclei were digested with DNaseI, then DNA under 500bp were selected.


title: HCT 116p53-/-RPL3 KO ACT D treated #3

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with Act D 5nM for 24h, biological rep6

data_processing:
Reads were aligned and assigned to Human ENSEMBLE transcripts and genes (hg38 reference) by using RSEM version 1.2.25 with standard parameters
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Colorectal Cancer stable cell line

growth_protocol: DMEM 10%FBS, splitting every 48-72h at confluency

extract_protocol:
RNA was quantified and mixed at 10ng/µl
For RNA-seq analysis, libraries were prepared according manufacturer’s instructions (TruSeq RNA Sample Preparation kit, Illumina) starting from 4 μg of total RNA
Libraries were sequenced by a paired-end chemistry on an NovaSeq6000 platform. Each library was loaded at a concentration of 8 pM, which was previously established as optimal. An average yield of ~4.5 Mb was obtained per sample. Quality control of library templates was performed using a High Sensitivity DNA Assay kit (Agilent Technologies) on a Bioanalyzer (Agilent Technologies). The Qubit quantification platform (Qubit 2.0 Fluorometer, Life Technologies) was used to normalise samples for the library preparation. Using multiplexing, up to 6 samples were combined into a single lane to yield sufficient coverage.

treatment_protocol: cells has been treated with Actinomycin D at concetration of 5nM for 24h and with Vehicle CTR

tag: cell line

tag: treatment

value: 5nM Act D for 24h


title: DNaseI-seq Chd4 cKO1


title: WS_10h_2


title: WS_10h_3


title: dcl4dcl2_ABA_smRNA_rep1


title: dcl4_ABA_smRNA_rep3

source_name: dcl4-2  seedlings on ABA medium


title: DNaseI-seq Ctrl 2

source_name: DNaseI-seq Ctrl


title: WS_10h_1


title: HCT 116p53-/-RPL3 KO ACT D treated #1

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with Act D 5nM for 24h, biological rep4


title: dcl4_ABA_smRNA_rep2


title: dcl4_ABA_smRNA_rep1


title: HCT 116p53-/-RPL3 KO ACT D treated #2

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with Act D 5nM for 24h, biological rep5


title: HCT 116p53-/-RPL3 KO vehicle CTR #3

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with vehicle CTR, biological rep3

value: vehicle CTR


title: 4_901_6_13_17_Bx1

city: Atlanta

first: Gregory

last: Tharp

address: 954 Gatewood Dr

institute: Yerkes National Primate Research Center

data_processing:
Reads were aligned to the Human Reference Genome Sequence and transcripts annotated with  Genome Reference Consortium Build 38 (GRCh38) using STAR software (v2·5·2b).
Unsorted bam files were sorted and indexed using samtools and converted to HTSeq-count format.
Estimates of gene-wise and isoform-wise expression levels for individual genes were performed using the R package DESeq2 with R version 3.5.0
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing normalized read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: ectocervical biopsies

extract_protocol:
Snap frozen ectocervical biopsies were cut and placed into 350µl of RLT lysis buffer (QIAGEN) and 1% 2-mercaptogthanol (Sigma-Aldrich). The tissues were bead milled with a stainless-steel bead and Tissuelyser II (QIAGEN).
Total RNA was extracted using RNeasy Micro Kit with DNase digestion (QIAGEN). RNA quantity and quality were assessed using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis.
RNA quantity and quality were assessed using Nanodrop 2000 Spectrophotometer and Agilent’s 4200 Bioanalyzer Capillary electrophoresis. 1ng of total RNA was used for mRNA amplifications using Clontech Smarter V4 chemistry (Takara Bio Inc).
Amplified mRNA was fragmented and barcodes appended using Illumina’s Nextera XT kits. Amplified libraries were validated using an Agilent 4200 Tapestation and quantified using a Qubit fluorimeter
Libraries were normalized, pooled and clustered on an Illumina HiSeq 3000/4000 flowcell using an Illumina cBOT. Libraries were sequenced on an Illumina HiSeq 3000 system in 101-base single-read reactions with multiplexing to achieve approximately 20 million reads per sample.

tag: gender

value: female

value: ectocervical biopsies

tag: ID

tag: timepoint

value: Placebo


title: HCT 116p53-/-RPL3 KO vehicle CTR #2

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with vehicle CTR, biological rep2

tag: genotype


title: WS_8h_1

tag: tissue


title: Col-0_ABA_smRNA_rep3

source_name: Col-0 seedlings on ABA medium


title: HCT 116p53-/-RPL3 KO vehicle CTR #1

description: Transcriptome profile of HCT 116p53-/-RPL3 KO treated with vehicle CTR, biological rep1


title: Col-0_ABA_smRNA_rep2


title: WS_6h_3


title: Col-0_ABA_smRNA_rep1


title: HCT 116p53-/- ACT D treated #3

description: Transcriptome profile of HCT 116p53-/- treated with 5nM Act D for 24h, biological rep3


title: GFP rep 1

city: La Jolla

first: Nick

last: Webster

address: 9500 Gilman Drive

institute: UCSD

data_processing:
QC reads with FastQC
Align with STAR 2-pass
Analyze alternative splicing with JUM setting p<0.05
Analyze local splicing variants with MAJIQ setting p<0.05
Visualize MAJIQ results using VOILA
Genome_build: mm10
Supplementary_files_format_and_content: tsv or txt

source_name: liver

growth_protocol: Srsf3 fklox/flox mice were sacrificed and livers dissected. Hepatocytes were obtained as described in PMID: 25315009 and cultured in vitro.

extract_protocol:
Hepatocyte RNA was extracted and quantified using a NanoDrop 1000 (Thermo- Fisher, Waltham, MA) and assessed on a Tapestation (Agilent, Santa Clara, CA).
TruSeq Stranded mRNA libraries were prepared according to the manufacturer’s instructions (Illumina, San Diego, CA).
Each library was sequenced on the Illumina HISeq2500 platform using paired-end 150 cycles.

treatment_protocol: Hepatocytes were infected with an adeno-associated virus expressing CRE recombinase or GFP for 48 h

tag: cell type

value: hepatocytes

tag: strain

value: liver


title: dcl4dcl2_MS_smRNA_rep3

source_name: dcl4-2  dcl2-1 seedlings on MS medium

tag: age

value: grown on MS medium


title: WS_6h_1

value: root


title: HCT 116p53-/- ACT D treated #2

description: Transcriptome profile of HCT 116p53-/- treated with 5nM Act D for 24h, biological rep2


title: dcl4dcl2_MS_smRNA_rep2


title: CRE rep 3


title: WS_6h_2


title: DNaseI-seq Ctrl 1

value: Cerebellum


title: WS_8h_3


title: GFP rep 4


title: WS_4h_3


title: WS_8h_2


title: HCT 116p53-/- vehicle CTR #3

description: Transcriptome profile of HCT 116p53-/- treated with vehicle CTR, biological rep3


title: dcl4dcl2_MS_smRNA_rep1


title: CRE rep 2


title: GFP rep 3


title: GFP rep 2


title: dcl4_MS_smRNA_rep3

source_name: dcl4-2  seedlings on MS medium


title: HCT 116p53-/- vehicle CTR #2

description: Transcriptome profile of HCT 116p53-/- treated with vehicle CTR, biological rep2


title: HCT 116p53-/- vehicle CTR #1

description: Transcriptome profile of HCT 116p53-/- treated with vehicle CTR, biological rep1


title: CRE rep 1


title: WS_4h_2


title: WS_4h_1


title: CRE rep 4


title: WS_2h_3


title: dcl4_MS_smRNA_rep2


title: Sal_7d3

city: Beltsville

first: Sunchung

last: Park

address: 10300 Baltimore ave, Bldg001

department: ARS-NEA

institute: USDA -ARS

data_processing:
Sequenced reads were trimmed for adaptor sequence, and those with N (based underterminded) > 10% or low quality bases (Qscore <=5) >50% were removed.
The filtered reads were mapped to lettuce (v8) whole genome using STAR v2.5.2  with default parameters; the resulting BAM files were used to count reads at the gene-level using featureCounts.
Counts per million (CPM) mapped reads for each of biological samples were calculated using edgeR based on raw counts of STAR.
Genome_build: version8; id 37106
Supplementary_files_format_and_content: A comma-delimited text file includes CPM values for each of all samples

organism: Lactuca sativa

source_name: aerial tissue

growth_protocol: Plants were grown on soil in pots in a growth chamber at 20°C under a 16-h photoperiod with a light intensity of 350-400 μmol m−2 sec−1.

extract_protocol:
Total RNA was isolated for each experimental replicate using Plant RNeasy kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: the 18-day-old plants were exposed to low temperature (4°C) for 4 h, 24 h, or 7 days at about 100 μmol m−2 sec−1 under a 16-h photoperiod.

value: Salinas

value: 18 days

value: aerial tissue

value: 4°C for 7 days


title: HCT 116p53-/- ACT D treated #1

institute: Tigem

description: Transcriptome profile of HCT 116p53-/- treated with 5nM Act D for 24h, biological rep1


title: Col-0_MS_smRNA_rep3

source_name: Col-0 seedlings on MS medium

value: whole seedling

value: 14-day-old plant