title: shCTRL HDF rep2

city: Biella

first: Paola

last: Ostano

address: via Malta 3

institute: Fondazione Edo ed Elvo Tempia

data_processing:
Fastq files were subjected to quality control by means of FastQC.
Reads were trimmed using Trimmomatic (v0.22) and then mapped to the human hg19 reference genome using TopHat (v2.0.8b). Gene expression levels have been evaluated using the HTSeq package (release 0.5.4p1).
DeSeq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) were used to normalize count data, estimate biological variance and determine differential expression.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw reads counts

source_name: Dermal fibroblasts

extract_protocol:
Total RNA was extracted 7 days after shRNA infection using the directZol RNA miniprep kit (Zymo Research) with on-column DNase treatment.
RNA quality was verified on the Bioanalyzer (Agilent Technologies) with RNA integrity number (RIN) > 8.  For shUPF1 experiments, 500 ng of total RNA were depleted of Ribosomal RNA using Ribo-zero RNA removal kit (Illumina) and were used for library preparation using a Truseq kit (Illumina).  For shCSL experiments, 1 μg of total RNA was used for library preparation using a NEBNext Ultra DNA Library Preparation kit (New England Biolabs). A single read was done on the IlluminaHiSeq 2000 sequencer at the Genomic Technologies Facility (Lausanne University).

value: Dermal fibroblasts

tag: silencing

value: shRNA control

tag: cell strain

value: HDF


title: shCSL4 HDF rep2

status: Public on Sep 11 2019

type: SRA

country: Italy

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

value: shCSL


title: shCTRL HDF rep1


title: sh_UPF1_56 HDF2


title: shCTRL HDF1


title: shCSL5 HDF rep1


title: P1 [discovery]

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
Standard mRNA library.
Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation, and mRNA sequencing was performed on an Illumina HiSeq2000 sequencer.

data_processing:
The reads with good quality were firstly aligned to human reference databases including hg19 human genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering for reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mismatches for each transcript were then counted as expression level for corresponding transcript. The read counts were log2 transformed and normalized at an equal global median value in order to compare transcription level across samples, followed by quantile normalization.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include quantile-normalized counts.

source_name: whole blood

extract_protocol:
Total RNA was extracted from whole blood of kidney transplant recipients 3 months post-transplantation.
The library was generated standard TruSeq mRNA library generation kit (Illumina Inc).

value: Whole blood

tag: acr at 3m

value: No


title: P29 [discovery]


title: shCSL5 HDF rep2


title: sh_UPF1_57 HDF2


title: sh_UPF1_57 HDF1


title: shCTRL HDF2


title: HEB.hypoxia rep3

city: Chongqing

first: bao

last: liu

address: 30 Gaotanyan street

department: Institute of Medicine and Hygienic Equipment for High Altitude Region

country: China

institute: 3rd Military Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to reference gene using Bowtie2 (version 2.2.4)  and use BWA (version 0.7.10)  to reference genome hg19. Their alignment parameters change a little according different sequencing strategy：Bowtie2 parameters for PE reads: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --no-mixed --no-discordant -p 16 -k 200; BWA parameters for PE reads: -o 1 -e 63 -i 90 -L -k 2 -l 31 -t 4 -q 10  hg19 whole genome using  Bowtie2 version 2.2.4
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated.
Identify the differentially expressed genes of U87-MG versus HEB cells, U87-MG cells cultured in hypoxia versus normoxia and HEB cells cultured in hypoxia versus normoxia by using NOISeq (version 2.14.0) method.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Brain

extract_protocol:
Total RNA was extracted with TRIzol Reagentand quantified using a Nanodrop ND-1000 spectrophotometer.Illumina TruSeq RNA Sample Prep Kit v2 was used with 200ng of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEB cells and U87-MG cells were incubated in DMEM supplemented with 10% fetal bovine serum (FBS), 2mM L-glutamine, 100U/ml penicillin and 100μg/ml streptomycin for 24h at normoxia (21% O2) and followed by 24h at normoxic or hypoxic conditions (1% O2) in hypoxic chambers (Thermo scientific) separately.

tag: cell type

value: HEB cell line

tag: phenotype

value: control+hypoxia


title: sh_UPF1_56 HDF1


title: P24 [discovery]


title: HEB.hypoxia rep1


title: HEB.hypoxia rep2


title: HEB rep3

value: control


title: U87-MG.hypoxia rep3

value: U87-MG cell line

value: tumor+hypoxia


title: HEB rep1


title: HEB rep2


title: U87-MG.hypoxia rep2


title: shCSL4 HDF rep1


title: U87-MG.hypoxia rep1


title: U87-MG rep3

value: tumor


title: U87-MG rep2


title: U87-MG rep1


title: Pea3_Rep3

city: New york

first: Xin

state: New york

department: Ophthalmology

institute: Columbia University

data_processing:
We use RTA (Illumina) for base calling and bcl2fastq (version 1.8.4) for converting BCL to fastq format, coupled with adaptor trimming.
We map the reads to a reference genome (Human: NCBI/build37.2; Mouse: UCSC/mm9) using Tophat [1] (version 2.0.4) with 4 mismatches (--read-mismatches = 4) and 10 maximum multiple hits (--max-multihits = 10).
To tackle the mapping issue of reads that are from exon-exon junctions, Tophat infers novel exon-exon junctions ab initio, and combine them with junctions from known mRNA sequences (refgenes) as the reference annotation.
We estimate the relative abundance (aka expression level) of genes and splice isoforms using cufflinks [2] (version 2.0.2) with default settings.
We test for differentially expressed genes under various conditions using DEseq [3]. It is an R package based on a negative binomial distribution that models the number reads from RNA-seq experiments and test for differential expression.
Genome_build: Mouse: UCSC/mm9
Supplementary_files_format_and_content: Lens1-DEseq_KC001-KC003-KC005_KC007-KC009-KC011_DEG_list: diffrential gene analysis  through DE-seq
Supplementary_files_format_and_content: counts_table_normalized: FPKM values
Supplementary_files_format_and_content: count: raw counts

organism: Mus musculus

source_name: Lens transition zone

extract_protocol: After tissue harvest, RNA was extracted using Qiagen kit. Conversion to cDNA as well as amplification was performed by Clontech SMART-seq v4 Ultra low input RNA kit, as well as cDNA library construction was performed using Nextera XT DNA library preparation kit by core facility at Columbia university prior to RNA sequencing. After preparation of cDNA library, each sample was sequenced using Illumina platform.

treatment_protocol: Embryos were flash frozen in OCT

tag: age

tag: genotype

value: Le-Cre; Etv4-/-. Etv5fl/fl, Etv1 fl/fl

tag: strain

value: mixed background


title: Wildtype_Rep1

value: Le-Cre


title: Pea3_Rep1


title: Wildtype_Rep2


title: Pea3_Rep2


title: Wildtype_Rep3


title: Epyc saline Input2

first: Laura

last: Kus

address: 1230 York Avenue # 260

department: Heintz Laboratory

institute: The Rockefeller University

description:
Pooled 6 animals, Osmotic minipump model 2002, 11d saline
976_Epyc_saline_Input2_GCCAAT_L005

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to UCSC mm10 whole genome using STAR version 2.3.0e_r291, with default settings.
Quantification of aligned reads was done using htseq-count module, part of the ‘HTSeq’ framework, version 0.6.0, using default settings, with ‘union’ mode to handle reads overlapping more than one feature.
Differentially expressed genes were identified by performing a negative binomial test using DESeq2 (R-package version 1.4.5) with default settings.
Genome_build: mm10
Supplementary_files_format_and_content: Counts text

source_name: Interpeduncular nucleus

growth_protocol: All mice were maintained on a 12h light-dark cycle with ad lib access to food and water. Adult mice were used for all experiments (>8 weeks of age).

extract_protocol:
Brain regions of interest were microdissected, and homogenized immediately for IP using magnetic beads conjugated to anti-GFP. Total RNA was extracted from both the total homogenate (INPUT) and the IP fraction.
Ovation RNA-Seq System V2 kit (Nugen, Cat# 7102) was used with 10ug of RNA for MHb samples or 500pg of RNA for IPN samples for generation of SPIA cDNA. 1ug of SPIA cDNA was fragmented to 250bp before proceeding with library prepartion using the TruSeq DNA Nano LT Sample Prep Kit (Illumina, Cat# 20015964).

treatment_protocol: Animals were sacrificed by live decapitation, brains were rapidly removed and regions of interest dissected on ice. See sample details for specific drug treatments.

tag: background strain

tag: transgene(s)

value: Epyc-Cre (KR363)::Eef1a1-LSL.EGFPL10

tag: fraction

value: Input


title: Chat-TRAP-MHb-Nicotine

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water
1139_Chat_TRAP_MHb_Nicotine_CTTGTA_L005

source_name: Medial Habenula

value: ChAT-TRAP (DW167)

value: IP


title: Chat-TRAP-MHb-Sacchain_2

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin in drinking water
1140_Chat_TRAP_MHb_Saccharin_ACAGTG_L001


title: Amigo1-CRE_NP231 Rep4

description:
polysome bound mRNA
Pooled 5 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water
1919_Amigo1_CRE_NP231_Rep4_CGATGT_L002

value: Amigo1-Cre (NP231)::Eef1a1-LSL.EGFPL10


title: Chrna5 IP4

description:
polysome bound mRNA
Pooled 6 males, baseline
975_Chrna5_IP4_GTGAAA_L002

value: Chrna5-Cre (SN83)::Eef1a1-LSL.EGFPL10


title: Chat-TRAP-MHb-Sacchain

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin in drinking water
1138_Chat_TRAP_MHb_Saccharin_GCCAAT_L005


title: Chat-TRAP-MHb-Nicotine_2

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water
1141_Chat_TRAP_MHb_Nicotine_GTGAAA_L001


title: Epyc nictoine IP2

description:
polysome bound mRNA
Pooled 6 animals, Osmotic minipump model 2002, 11d nicotine, 24mg/kg/d, free base
979_Epyc_nicotine_IP2_GTGAAA_L006


title: Amigo1_Saline_Input1

description:
Pooled 5 animals, Osmotic minipump model 2002, 10d saline
882_Amigo1_Saline_Input1_GTGAAA_L005


title: Epyc_Nicotine_IP1

description:
polysome bound mRNA
Pooled 5 animals, Osmotic minipump model 2002, 10d nicotine, 24mg/kg/d, free base
887_Epyc_Nicotine_IP1_GTGAAA_L007


title: Epyc_Saline_IP1

description:
polysome bound mRNA
Pooled 6 animals, Osmotic minipump model 2002, 10d saline
886_Epyc_Saline_IP1_CGATGT_L007


title: Chrna5_IP2

description:
polysome bound mRNA
Pooled 8 animals, baseline
881_Chrna5_IP2_CAGATC_L005


title: Chrna5_Input2

description:
Pooled 8 animals, baseline
880_Chrna5_Input2_CGATGT_L005


title: Chrna5 Input4

description:
Pooled 6 males, baseline
973_Chrna5_Input4_ACAGTG_L002


title: Chrna5 Input3

description:
Pooled 6 animals, baseline
972_Chrna5_Input3_GCCAAT_L001


title: Amigo1_Saline_IP1

description:
polysome bound mRNA
Pooled 5 animals, Osmotic minipump model 2002, 10d saline
884_Amigo1_Saline_IP1_ACAGTG_L008


title: IP-MHb-Nicotine-Saline

description:
polysome bound mRNA
Pooled 3 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water, ip saline 3hr before tissue collection
829_Chat_IP-MHb-Nicotine-Saline_ACAGTG_L005


title: IP-MHb-Saccharin-Saline

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin in drinking water, ip saline 3hr before tissue collection
825_Chat_IP-MHb-Saccharin-Saline_CTTGTA_L008


title: Amigo1-CRE_NP231 Rep1

description:
polysome bound mRNA
Pooled 5 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water
1916_Amigo1_CRE_NP231_Rep1_TGACCA_L001


title: Amigo1-CRE_NP231 Rep3

description:
polysome bound mRNA
Pooled 7 animals, 6wk 0.2% saccharin + 500 mg/L nicotine tartrate in drinking water
1918_Amigo1_CRE_NP231_Rep3_CTTGTA_L001


title: IP1

description:
polysome bound mRNA
Pooled 6 animals, baseline
815_Chrna5_IP1_ATGTCA_L002


title: Input1

description:
Pooled 6 animals, baseline
814_Chrna5_Input1_GCCAAT_L002


title: IP3

description:
polysome bound mRNA
Pooled 7 animals, baseline
812_Epyc_IP3_CAGATC_L001


title: IP4_2

description:
polysome bound mRNA
Pooled 7 animals, baseline
813_Epyc_IP4_ACAGTG_L002


title: IP1_2

description:
Pooled 6 animals, baseline
767_Epyc_IP1_ACAGTG_L007


title: Input4

description:
Pooled 7 animals, baseline
811_Epyc_Input4_GTGAAA_L001


title: input2_2

description:
Pooled 7 animals, baseline
766_Epyc_input2_GCCAAT_L007


title: input1_2

description:
Pooled 6 animals, baseline
765_Epyc_Input1_GTGAAA_L006


title: input2

description:
Pooled 5 animals, baseline
759_Amigo1_input2_GCCAAT_L007


title: Saccharin_saline_IP2

description:
polysome bound mRNA
Pooled 4 animals, 6wk 0.2% saccharin in drinking water, ip saline 3hr before tissue collection
745_Chat_Saccharin_saline_IP2_GCCAAT_L008


title: IP1_3

description:
polysome bound mRNA
Pooled 5 animals, baseline
762_Amigo1_IP1_ACAGTG_L007


title: input1

description:
Pooled 5 animals, baseline
758_Amigo1_input1_GTGAAA_L006


title: input4

description:
Pooled 8 animals, baseline
760_Amigo1_input4_CGATGT_L006


title: IAF_05 Spleen wt Tregs

city: Neuherberg

first: Caspar

last: Ohnmacht

address: Ingolstaedter Landstrasse 1

department: Center of Allergy and Environment

country: Germany

institute: Helmholtz Center Munich

data_processing:
Basecalls were performed using Illumina bcl2fastq version 2.19.1.
Reads were aligned to the mouse genome assembly (mm10) using GSNAP (2018-03-11; parameters: --gunzip -A sam  --use-sarray=1 --input-buffer-size=500000 --output-buffer-size=500000 -B 5 -N 0 -n 1 -s EnsemblGene-81.ss.mm10.iit) with known splice sites from Ensembl (v81) as support.
Uniquely aligned fragments and gene annotations from Ensembl (v81) were used for featureCounts (v1.6.0; parameters: -a EnsemblGene-81.mm10.TR.gtf -s 0 -Q 1 -T 8) to obtain a table with read counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited counts table from featureCounts (bfx905.featureCounts.mm10.e81.txt.gz) with the following columns: Ensembl Gene ID, Chromosome, Gene Start, Gene End, Gene Length, then all sample counts; comments start with '#'

source_name: primary murine Foxp3pos Tregs

growth_protocol: Foxp3+ T cells were sort purified from adult RelB-dDC and littermate control animals backcrossed to faithful Foxp3 reporter line.

extract_protocol:
RNA was isolated using the RNeasy Micro Kit (Qiagen).
Complete cDNA was synthesized from 5 μl total RNA using the SmartScribe reverse transcriptase (Takara Bio) with a universally tailed poly-dT primer and a template switching oligo followed by amplification for 12 cycles with the Advantage 2 DNA Polymerase (Takara Bio). After ultrasonic shearing (Covaris LE220), amplified cDNA samples were subjected to standard Illumina fragment library preparation using the NEBnext Ultra DNA library preparation chemistry (New England Biolabs). In brief, cDNA fragments were end-repaired, A-tailed and ligated to indexed Illumina Truseq adapters. Resulting libraries were PCR-amplified for 15 cycles using universal primers, purified using XP beads (Beckman Coulter) and then quantified with the Fragment Analyzer.

treatment_protocol: primary sort-purified Foxp3pos T cells of adult mice

value: Spleen primary Tregs ctr


title: IAF_12 Thymus dDC Tregs

value: Thymus primary Tregs dDC


title: IAF_06 Spleen dDC Tregs

value: Spleen primary Tregs dDC


title: IAF_11 Thymus wt Tregs

value: Thymus primary Tregs ctr


title: IAF_03 Spleen wt Tregs


title: IAF_16 Thymus dDC Tregs


title: IAF_15 Thymus wt Tregs


title: c13 WT DEPL

city: Freising

first: Dietmar

last: Zehn

address: Weihenstephaner Berg 3

department: Division of Animal Physiology and Immunology

institute: Technical University of Munich

data_processing:
Fastq files (*_R1_001.fastq.gz) contain cell barcodes (pos: 1-7) and UMIs (pos: 8-17); Fastq files (*_R2_001.fastq.gz) contain biological reads (len: 49bp)
dropSeqPipe (v 0.32) was applied for the preprocessing
Sequence quality was assessed using fastqc
Cutadapt (v1.16) was used for trimming
Missing pairs were removed by bbmap (v38.22)
Sequence alignment was performed by STAR (v2.5.3a)
Dropseq_tools (v1.13) was applied for demultiplexing and file manipulation
Genome_build: Mus_musculus.GRCm38.91
Supplementary_files_format_and_content: Tab-delimited text files include raw UMI values for each cell

source_name: c13 WT DEPL

extract_protocol:
At day 40 post infection, splenocytes were enriched for CD45.1 + P14 T-cells using anti-CD45.1 biotin/ anti-biotin conjugated microbeads and magnetic MACS cell separation (Miltenyi Biotech, Bergisch-Gladbach, Germany). Single-cells were sorted on BD FACS Fusion (100 micron nozzle, standard operation settings, single-cell purity, index sorting). Individual cells meeting the gating strategy were sorted directly in lysis buffer into individual wells of a low-binding PCR plate. Immediately after sorting, each plate was spun down, snap-freezed on dry ice and stored at -80oC until use.
The single-cell libraries were generated using the previously described SCRB-seq protocol (doi: https://doi.org/10.1101/003236), with some modifications.  After RNA purification and reverse transcription, the generated single-cell cDNA was amplified for 22 cycles. The barcoded single-cell amplicons were purified with the use of (0.6x) Agencourt AMPure XP beads. 1 ng of the resulting amplified cDNA were used for library preparation with the Illumina Nextera XT DNA Library reagents (FC-131-1024, Illumina). After PCR amplification of the fragmented libraries, the samples were purified with (0.6x) Agencourt AMPure XP beads and eluted in 10 µl of molecular grade water. The quality of the resulting library was assessed with the use of Agilent High Sensitivity DNA Kit (5067-4626, Agilent). The library quantification was performed based on the Illumina recommendations (SY-930-1010, Illumina) with the use of KAPA SYBR FAST qPCR Master Mix (KK4600, Kapa Biosystems).

treatment_protocol: In vivo depletion of CD4 lymphocytes was achieved by intraperitoneal injection of 300 µg anti-mouse CD4 antibody (clone GK1.5; Bio X Cell, USA) diluted in PBS and injected on day -2, +1, and thereafter on each fifth day after infection.

tag: injection

value: wild-type LCMV c13

tag: depletion

value: in vivo depletion of CD4 lymphocytes

value: splenocytes were enriched for P14 T-cells


title: IAF_13 Thymus wt Tregs


title: IAF_20 PEC dDC Tregs

value: Peritoneal cavity primary Tregs dDC


title: IAF_04 Spleen dDC Tregs


title: IAF_02 Spleen dDC Tregs


title: IAF_19 PEC wt Tregs

value: Peritoneal cavity primary Tregs ctr


title: IAF_17 PEC wt Tregs


title: IP2

description:
polysome bound mRNA
Pooled 7 animals, baseline
768_Epyc_IP2_ATGTCA_L007


title: IAF_01 Spleen wt Tregs


title: IAF_18 PEC dDC Tregs


title: P213JAKO_mESC_RNA_replicate3

city: Copenhagen N

first: Jonas

middle: Westergaard

last: Hojfeldt

address: Ole Maaloes Vej 5

department: BRIC

country: Denmark

institute: University of Copenhagen

data_processing:
Allignment with STAR using Gencode vM21 annotation
Counts generated with Htseq
Genome_build: mm10
Supplementary_files_format_and_content: txt file with Htseq counts

source_name: Embryonic stem cells

growth_protocol: Cells grown on gelatin in 2i media

extract_protocol:
Total RNA from cells (Qiagen, RNeasy plus)
Illumina, Truseq RNA library kit v2

value: Pcl1-3 + Jarid2 + Aebp2 KO

tag: experiment type

value: RNA-Seq


title: IP4

description:
polysome bound mRNA
Pooled 8 animals, baseline
764_Amigo1_IP4_CAGATC_L006


title: P213JAEKO_mESC_RNA_replicate3

value: Pcl1-3 + Jarid2 + Aebp2 + Epop KO


title: c13 WT CTRL

source_name: c13 WT CTRL

value: control


title: JAKO_mESC_RNA_replicate3

value: Jarid2 + Aebp2 KO


title: P213JKO_mESC_RNA_replicate3

value: Pcl1-3 + Jarid2 KO


title: P213EKO_mESC_RNA_replicate3

value: Pcl1-3 + Epop KO


title: P213KO_mESC_RNA_replicate3

value: Pcl1-3  KO


title: Suz12KO_mESC_RNA_replicate3

value: Suz12 KO


title: P213JAEKO_mESC_RNA_replicate2


title: JAKO_mESC_RNA_replicate2


title: P213KO_mESC_RNA_replicate2


title: P213JKO_mESC_RNA_replicate2


title: P213JAKO_mESC_RNA_replicate1


title: WT_mESC_RNA_replicate2

value: WT


title: WT_mESC_RNA_replicate3


title: P213EKO_mESC_RNA_replicate2


title: P213JKO_mESC_RNA_replicate1


title: Suz12KO_mESC_RNA_replicate2


title: P213EKO_mESC_RNA_replicate1


title: P213KO_mESC_RNA_replicate1


title: JAKO_mESC_RNA_replicate1


title: P213JAKO_mESC_SUZ12_ChIP_replicate3

library_source: genomic

data_processing:
Trimmed with Trimmomatic: IlluminaClip; Crop to 73; SLIDINGWINDOW across 4 bases, average quality required 20
Mapped with Bowtie2 against mm10 using using (--sensitive) preset settings. Duplicates removed with rmdup.
Peak calling with Easeq software: Adaptive Local Thresholding (default settings)  with respective knocout samples as negative controls.
Genome_build: mm10
Supplementary_files_format_and_content: bed file containing ChIP-Seq peaks

molecule: genomic DNA

extract_protocol:
Immunoprecipitation of formaldehyde cross-linked and sonicated cell lysate.
NEBNext Ultra II protocol (NEB, E7645S)

tag: chip antibody

value: Suz12 (Cell Signaling, Rabbit mAb, D39F6)

value: ChIP-Seq


title: P213EJ_mESC_SUZ12_ChIP

value: Pcl1-3 + Epop + Jarid2 KO


title: WT_mESC_RNA_replicate1


title: P213EJ_mESC_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)


title: P213JAKO_mESC_H3K27me3_ChIP_replicate3


title: Pcl2KO_mESC_H3K27me3_ChIP_replicate2

value: Pcl2 KO


title: P213EA_mESC_SUZ12_ChIP

value: Pcl1-3 + Epop + Aebp2 KO


title: JAEKO_mESC_SUZ12_ChIP

value: Jarid2 + Aebp2 + Epop KO


title: P213EA_mESC_H3K27me3_ChIP


title: JAEKO_mESC_H3K27me3_ChIP


title: P213JAKO_mESC_RNA_replicate2

value: Pcl1-3 + Jarid2 + Aebp2 KO


title: P213JAKO_mESC_SUZ12_ChIP_replicate2


title: P213JAEKO_mESC_SUZ12_ChIP_replicate1


title: P213JAEKO_mESC_RNA_replicate1

value: RNA-Seq


title: P213JAKO_mESC_SUZ12_ChIP_replicate1


title: P213JKO_mESC_SUZ12_ChIP_replicate2


title: Suz12KO_mESC_RNA_replicate1


title: P213JKO_mESC_SUZ12_ChIP_replicate1


title: JAKO_mESC_SUZ12_ChIP_replicate2


title: P213EKO_mESC_SUZ12_ChIP_replicate2


title: P213EKO_mESC_SUZ12_ChIP_replicate1


title: P213JAKO_mESC_H3K27me3_ChIP_replicate1


title: P213JAEKO_mESC_H3K27me3_ChIP_replicate1

value: Pcl1-3 + Jarid2 + Aebp2 + Epop KO


title: P213JKO_mESC_H3K27me3_ChIP_replicate2


title: JAKO_mESC_SUZ12_ChIP_replicate1


title: JAKO_mESC_H3K27me3_ChIP_replicate1


title: P213JKO_mESC_H3K27me3_ChIP_replicate1


title: P213EKO_mESC_H3K27me3_ChIP_replicate2


title: Jarid2KO_mESC_JARID2_ChIP

value: Jarid2 (Cell Signaling, Rabbit mAb, D6M9X)

value: Jarid2 KO


title: P213EKO_mESC_H3K27me3_ChIP_replicate1


title: Suz12KO_mESC_JARID2_ChIP


title: P213JAEKO_mESC_SUZ12_ChIP_replicate2


title: Jarid2KO_mESC_PCL2_ChIP

value: Mtf2 (Proteintech, Rabbit pAb, #16208-1-AP)


title: FlagSUZ12_mESC_PCL2_ChIP

value: Suz12 KO + Flag-SUZ12


title: WT_mESC_JARID2_ChIP


title: Pcl1-3KO_mESC_JARID2_ChIP

value: Pcl1-3 KO


title: FlagC2_mESC_PCL2_ChIP

value: Suz12 KO + Flag-SUZ12-C2


title: Pcl1-3KO_mESC_PCL2_ChIP


title: P213JAEKO_mESC_H3K27me3_ChIP_replicate2


title: Suz12KO_mESC_PCL2_ChIP

value: Suz12 KO


title: P213JAKO_mESC_H3K27me3_ChIP_replicate2


title: WT_mESC_PCL2_ChIP

value: WT


title: JAKO_mESC_H3K27me3_ChIP_replicate2

value: Jarid2 + Aebp2 KO

value: ChIP-Seq


title: PostTAVR_D

city: Boulder

first: Kristi

last: Anseth

state: CO- COLORADO

address: 3415 Colorado Ave, 596 UCB

institute: University of Colorado - Boulder

description:
Post-TAVR serum treatment from human patient D
ProcessedDataFile.xlsx

data_processing:
Samples were sequenced on the NextSeq 500 (Illumina) using a high-output 75-cycle kit (single read, 1x75 bp).
Read quality, in fastq format, was evaluated using FastQC (V0.11.5)
Adapter sequences were removed from fastq files using Trimmomatic (V0.36)
Trimmed fastq read files were aligned to the sus scrofa genome (GCF_000003025.6_Sscrofa11.1_genomic.gff, obtained from NCBI) using the hierarchical indexing for spliced alignment of transcripts software known as HISAT2 (V2.1.0)
After converting aligned read sam files to bam files using Samtools (V1.3.1), transcript alignment was performed using the Rsubread and featureCounts
Counts were obtained using Rsubread (V1.30.9)
Genome_build: SusScrofa 11.1
Supplementary_files_format_and_content: The processed data file (ProcessedDataFile.xlsx) contains CPM values.

molecule: polyA RNA

organism: Sus scrofa

source_name: Aortic valve leaflets

growth_protocol: Male and female porcine VICs were isolated, seeded on PEG-norbornene hydrogels (elastic modulus ~5.8 kPa), and cultured in Media 199 (Life Technologies) supplemented with 1% human serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 48 hours.

extract_protocol:
mRNA was isolated using an RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA quality was assessed using an Agilent 2100 Bioanalyzer prior to library construction. RNA libraries were constructed using the mRNA KAPA Hyperprep kit (Kapa Biosystems).

treatment_protocol: Pre-TAVR and post-TAVR serum from 8 patients (4 male and 4 female) were tested in this experiment, resulting in 16 total samples.

value: Valvular Interstitial Cell

tag: passages

tag: animal age

value: 5-6 months


title: PostTAVR_F

description:
Post-TAVR serum treatment from human patient F
ProcessedDataFile.xlsx


title: FlagDeltaC2_mESC_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)

value: Suz12 KO + Flag-SUZ12-DeltaC2


title: PostTAVR_H

description:
Post-TAVR serum treatment from human patient H
ProcessedDataFile.xlsx


title: PostTAVR_G

description:
Post-TAVR serum treatment from human patient G
ProcessedDataFile.xlsx


title: PostTAVR_B

description:
Post-TAVR serum treatment from human patient B
ProcessedDataFile.xlsx


title: PostTAVR_C

description:
Post-TAVR serum treatment from human patient C
ProcessedDataFile.xlsx


title: FlagSUZ12_mESC_Flag_ChIP

value: Flag (Sigma, M2 affinity gel A2220)


title: PreTAVR_H

description:
Pre-TAVR serum treatment from human patient H
ProcessedDataFile.xlsx


title: PostTAVR_A

description:
Post-TAVR serum treatment from human patient A
ProcessedDataFile.xlsx


title: PreTAVR_G

description:
Pre-TAVR serum treatment from human patient G
ProcessedDataFile.xlsx


title: FlagDeltaC2_mESC_Flag_ChIP


title: WT_mESC_Flag_ChIP


title: PreTAVR_F

description:
Pre-TAVR serum treatment from human patient F
ProcessedDataFile.xlsx


title: PreTAVR_E

description:
Pre-TAVR serum treatment from human patient E
ProcessedDataFile.xlsx


title: Pcl2KO_mESC_SUZ12_ChIP

value: Suz12 (Cell Signaling, Rabbit mAb, D39F6)

value: Pcl2 KO


title: Pcl1-3KO_mESC_SUZ12_ChIP


title: PreTAVR_D

description:
Pre-TAVR serum treatment from human patient D
ProcessedDataFile.xlsx


title: Jarid2KO_mESC_SUZ12_ChIP


title: PostTAVR_E

description:
Post-TAVR serum treatment from human patient E
ProcessedDataFile.xlsx


title: PreTAVR_C

description:
Pre-TAVR serum treatment from human patient C
ProcessedDataFile.xlsx


title: PreTAVR_A

description:
Pre-TAVR serum treatment from human patient A
ProcessedDataFile.xlsx


title: Suz12KO_mESC_SUZ12_ChIP_replicate2


title: Aebp2KO_mESC_SUZ12_ChIP

value: Aebp2 KO


title: FlagSUZ12_mESC_H3K27me3_ChIP


title: FlagC2_mESC_Flag_ChIP


title: Suz12KO_mESC_SUZ12_ChIP_replicate1


title: WT_mESC_SUZ12_ChIP_replicate2


title: WT_mESC_SUZ12_ChIP_replicate1


title: Pcl2KO_mESC_H3K27me3_ChIP


title: mm10_J2_WT_Suz12

city: Dublin 2

first: Craig

last: Monger

state: Ireland

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

data_processing:
Align reads to reference genome (hg19) using bowite2 and the --very-sensitive-local parameter
Align reads to spike-in genome (mm9 or dm6) using bowtie2 and the --very-sensitive-local parameter
Convert sams to sorted bams using Samtools, and extract headers from both alignments for each of the 2 alignments (reference and spike-in)
Filter read ambiguosly aligned to both genomes using Picards FilterSamReads, mark duplicates using Picards MarkDuplicates and index the filtered, marked bam file with Samtools
The number of spike-in reads was used as a scale factor to generate normalised bigWigs using bamCoverage from the deeptools suite with a bin size of 10
Genome_build: hg19, mm9 & dm6
Supplementary_files_format_and_content: bigwig files of ChIP-Rx spike-in normalised tracks for each sample

organism:
Homo sapiens
Mus musculus

source_name: Embryonic stem cell and NT2 cell line

growth_protocol:
ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates.ChIPs for certain histone modification ChIP samples include a 17% spike in of Drosophila S2 chromatin that were cultured according to established protocols. ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human NT2 chroamtin that were cultured according to established protocols .
Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

extract_protocol:
Embryonic stem cells were washed once with PBS before crosslinking for 10 minutes with PBS containing 1% formaldehyde (Sigma). Crosslinking was quenched with 0.125M Glycine for 5 minutes before two PBS washes. The crosslinked cells were lysed in 6mL of SDS-Lysis buffer (100mM NaCl, 50mM Tris pH8.1, 5mM EDTA pH 8.0, 0.02% NaN3, 0.5% SDS, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF). Chromatin was pelleted by centrifugation at 1200rpm for 5 minutes at room temperature. The supernatant was then discarded, and the chromatin was resuspended in 3mL of ChIP buffer (2:1 dilution of SDS-Lysis buffer: Triton dilution buffer [100mM Tris pH 8.6, 100mM NaCl, 5mM EDTA pH 8.0, 0.02% NaN3, 5% Triton X-100, 2μg/mL Aprotonin, 1μg/mL Leupeptin, 1mM PMSF]). Chromatin was sheared to approximately 200bp-600bp fragments by sonication on a Branson Sfx150 Sonifier for a total of 4min at 50% amplitude. Sonicated chromatin was incubated overnight with antibody while rotating at 4°C. Following clarification, the chromatin was incubated for 3 hours with 50µL of protein A or G Dyna beads (ThermoFisher) beads. After incubation, the beads were washed three times in Mixed Micelle Buffer (150mM NaCl, 20mM Tris pH 8.1, 5mM EDTA pH 8.0, 5.2% Sucrose, 0.02% NaN3, 1% Triton X-100, 0.2% SDS), twice with Buffer 500 (0.1% Sodium Deoxycholate, 1mM EDTA pH 8.0, 50mM HEPES pH7.5, 1% Triton X-100, 0.02% NaN3), twice with LiCl detergent wash (0.5% Sodium Deoxycholate, 1mM EDTA pH 8.0, 250mM LiCl, 0.5% NP-40, 10mM Tris pH 8.0, 0.02% NaN3) and finally one wash with TE. Immunoprecipitated material was eluted from the beads with Elution buffer (0.1M NaHCO3, 1% SDS) while shaking for 1 hour at 65°C. The supernatant was retained and incubated overnight at 65°C while shaking to reverse the crosslinks. The eluted complexes were then subject to RNase (Thermo Fisher) and Proteinase K (Sigma) treatment prior to DNA clean up (Qiagen Qiaquick PCR Purification Kit). ChIP enrichments were analysed by qPCR using the SYBR Green I detection chemistry (M3003E NEB) on an Applied Biosystems Quant Studio 3 platform.
Following the ChIP experiment, the precipitated DNA was quantified using the Qubit dsDNA High Sensitivity Assay Kit (ThermoFisher Q32854). A Total of 2-10 ng of DNA from each ChIP-Rx experiment was used for library preparation using the NEBNext Ultra II DNA Library Kit for Illumina (E7645) and NEBNext Multiplex Oligos for Illumina (Set#1, NEB #7335). Following adaptor ligation, DNA was PCR amplified for 5-9 cycles, depending on amount of input DNA. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality of DNA libraries was analysed on a High Senstivity D1000 Screen Tape (Agilent). The resulting libraries were then used for cluster generation and sequencing using an Illumina NextSeq 500 (ID: NB501524), with 75bp read length.

value: Embryonic stem cell and NT2 cell line

value: Wild type

tag: antibody


title: Jarid2KO_mESC_H3K27me3_ChIP

value: Jarid2 KO


title: mm10_J2_KO_Suz12


title: mm10_J2_WT_Jarid2


title: mm10_J2_KO_Aebp2


title: mm10_J2_KO_Jarid2


title: Aebp2KO_mESC_H3K27me3_ChIP


title: EpopKO_mESC_SUZ12_ChIP

value: Epop KO


title: mm10_J2_WT_Pcl2


title: QKO_H2AK119ub1

growth_protocol:
ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates. ChIPs include a 10% spike in of human NT2 chromatin that were cultured according to established protocols.
Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

value: Pcl1-3/Jarid2 QKO


title: Suz12KO_mESC_H3K27me3_ChIP_replicate2

value: Suz12 KO


title: PreTAVR_B

description:
Pre-TAVR serum treatment from human patient B
ProcessedDataFile.xlsx


title: Suz12KO_mESC_H3K27me3_ChIP_replicate1


title: WT_mESC_H3K27me3_ChIP_replicate2

value: WT


title: QKO_H3K27me3


title: WT_H3K27me3

value: Wild type EV


title: WT_mESC_H3K27me3_ChIP_replicate1

value: ChIP-Seq


title: Pcl1-3KO_mESC_H3K27me3_ChIP_replicate1

value: Pcl1-3 KO


title: mm10_J2_WT_Aebp2


title: WT_H3K27me2


title: KO_EB_D8_rep1

first: Darren

middle: John

last: Fitzpatrick

description: ESCs that have been induced to differentiate by removal of LIF from culture media and growth on non-adherent plates

data_processing:
Raw sequencing reads were aligned to the reference transcriptome (mm10) using kallisto and counts per transcripts collapsed to counts per gene using tximport. Bigwigs were generated were generated by aligning to the mouse reference genome to where resulting bam files were converted to bigwig format and scaled to reads per billion.
Genome_build: mm10

source_name: Embryoid Body

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). For Embryoid body differentiation, 2-3x106 million ESCs were washed three times with PBS (Lonza) and seeded to non-adherent petri-dishes in ESC media without LIF. The media was changed every 2 days. RNA was harvested after 2, 4 and 8 days.

extract_protocol:
RNA was extracted using Rneasy Kit (Qiagen) according to manufacturers instructions.
RNA-Seq libraries were prepared using the NEBNext Ultra RNA Library Pep Kit for Illumina (E7770L), according to manufacturer’s instructions. Prior to starting library preparation, RNA concentrations were measured on a Qubit 3.0 and RIN scores calculated using an Agilent RNA ScreenTape (RIN >8.5). A total 1g of high quality RNA was used for library preparation. Following adaptor ligation, DNA was PCR amplified for 8 cycles. DNA purification was then performed using NEBNext Sample Purification Beads (E7767S). The quality of cDNA libraries was analysed on an Agilent High Sensitivity D1000 Screen Tape. The resulting libraries were then used for cluster generation and sequencing using an Illumina NextSeq 500 (ID: NB501524), with 75bp read length.

value: Embryoid Body

value: Pcl1-3 TKO


title: QKO_H3K27me2


title: WT_EB_D8_rep2


title: KO_EB_D8_rep2


title: QKO_H3K27me1


title: EpopKO_mESC_H3K27me3_ChIP

value: H3K27me3 (Cell Signaling, Rabbit mAb, C36B11)


title: WT_Aebp2


title: QKO_Cbx7


title: mm10_J2_KO_Pcl2


title: WT_EB_D8_rep1


title: WT_H3K27me1


title: KO_EB_D4_rep2


title: KO_EB_D4_rep1


title: QKO_Aebp2


title: TKO_Cbx7

value: Pcl1-3 TKO EV


title: WT_EB_D4_rep2


title: WT_EB_D4_rep1


title: WT_Cbx7


title: WT_EB_D2_rep2


title: KO_EB_D2_rep2


title: WT_H2AK119ub1


title: TKO_Rybp

value: RYBP


title: WT_EB_D2_rep1


title: KO_EB_D2_rep1


title: QKO_Rybp


title: WT_Rybp


title: TKO_Epop

value: EPOP


title: KO_ESC_2i_rep2

description: ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates

source_name: Embryonic Stem Cell

value: Embryonic Stem Cell


title: QKO_Epop

value: Embryonic stem cell and NT2 cell line


title: KO_ESC_2i_rep1


title: WT_ESC_2i_rep1

value: Wild type


title: WT_ESC_2i_rep2


title: WT_ESC_Ser_LIF_rep2


title: KO_ESC_Ser_LIF_rep2


title: KO_ESC_Ser_LIF_rep1


title: WT_Suz12


title: TKO_Suz12


title: QKO_Jarid2


title: WT_Epop


title: WT_ESC_Ser_LIF_rep1


title: KO INPUT (+NT2 Human)

description: ESCs that have been maintained in a pluripotent state through culturing with LIF on gelatinised plates.ChIPs for certain histone modification ChIP samples include a 1.67% spike in of Drosophila S2 chromatin that were cultured according to established protocols. ChIPs for PRC2 components and H2AK119ub1 include a 10% spike in of human NT2 chroamtin that were cultured according to established protocols .

data_processing:
Reads were alinged to the mouse reference genome (mm10) and the relevant spike-in genome (dm6 for S2 and hg38 for NT2) using bowtie2.
Bigwig files were generated at a resolution of 10bp using bamCoverage. Tracks were normalised using spike-in derived normalisation factors.
Genome_build: mm10

growth_protocol: Embryonic stem cells (ESCs) were grown on gelatinised culture dishes in GMEM (sigma) supplemented with 10% ES cell qualified FBS (Millipore), 100 U/mL penicillin (Gibco), 100 U/mL streptomycin (Gibco), 50µM β-mercaptoethanol (sigma), 1:100 Glutamax (Gibco), 1:100 non-essential amino acids (Gibco), 1mM sodium pyruvate (Gibco) and 1:500 homemade leukemia inhibitory factor (LIF). S2 cells were cultured in Schneider media supplemented with 10% Heat inactivated FBS

value: Input


title: WT_Jarid2


title: PH_WT_notreat_r3

city: Vienna

first: Jelle

last: Jacobs

address: Campus-Vienna-Biocenter 1

department: VBC

country: Austria

institute: Institute of molecular Pathology

data_processing:
RNA samples
Cleaning (fastq-mcf)
Mapping to the mm10 genome using STAR
Obtaining raw counts per gene using STAR and mm10 annotation
Library size normailsation and differential expression using R DESeq2
Genome_build: Mus_musculus.GRCm38.76
Supplementary_files_format_and_content: raw and processed counts matrix mm10

source_name: Liver-Hepatocytes

growth_protocol: Standard feed and housed in IVC cages

extract_protocol:
Hepatocytes were isolated using a percol gradient. The DNA was extracted from 0.5Mio cells using the Rneasy Mini Kit from QIAGEN. RNA concentration and purity were determined spectrophotometrically using the Nanodrop ND-1000 (Nanodrop Technologies) and RNA integrity was assessed using a Bioanalyser 2100 (agilent).
Per sample, an amount of 1 µg of total RNA was used as input. Using the Illumina TruSeq® Stranded mRNA Sample Prep Kit (protocol version Part 15031047 Rev. E, October 2013)

treatment_protocol: Tumor formation: 8 week old mice were hydrodynamically injected with  1ug of SB11, 20 ug of myc-NICD and 4ug of myr-ha-Akt. Tumors developed for 8 weeks and tissues were harvested . For injury, mice were treated with one IP injection of thioacetamide and livers were collected 24 and 48 hours after treatment.

tag: tissue

value: liver

value: hepatocytes

tag: treatment

value: Dissociation and percol gradient selection

value: Lats1tm1.1Jfm/RjoJ; Lats2tm1.1Jfm/RjoJ

value: 8 weeks


title: PH_WT_tumors_r2

tag: cell type


title: PH_WT_tumors_r3


title: PH_WT_tumors_r1


title: TKO_CBX7


title: WT INPUT (+NT2 Human


title: PH_WT_notreat_r1


title: L_TAA_control_r2

value: CD-1 IGS Mouse (Charles River)


title: PH_WT_notreat_r2


title: WT_SUZ12


title: TKO_AEBP2


title: WT_AEBP2


title: WT_CBX7


title: TKO_Jarid2


title: TKO_JARID2


title: WT_JARID2


title: L_TAA_48_r2


title: L_TAA_48_r1


title: L_TAA_24_r2


title: WT_EPOP


title: TKO_PCL2


title: L_TAA_24_r1


title: TKO_SUZ12


title: WT_PCL2


title: Repl-pSS11

city: Utrecht

first: Aridaman

last: Pandit

address: Heidelberglaan 100

country: Netherlands

institute: University Medical Center Utrecht

data_processing:
Reads were aligned using STAR aligner using the default parameters to the 65,217 annotated genes obtained from the GrCh38 (v79) built of the human genome.
The read counts per gene were quantified by the Python package HTSeq (2) using annotations from the GrCh38 (v79) built of the human genome
Genome_build: GrCh38 (v79)
Supplementary_files_format_and_content: read counts for discovery cohort
Supplementary_files_format_and_content: read counts for replication cohort
Supplementary_files_format_and_content: VST normalized data for discovery cohort
Supplementary_files_format_and_content: VST normalized data for replication cohort

source_name: Plasmacytoid dendritic cells

extract_protocol:
Plasmacytoid dendritic cells were isolated from peripheral blood mononuclear cells with MACS using the BDCA-4+ isolation kit (Miltenyi) according to manufacturer's instruction. Cells were lysed in RLTplus buffer (Qiagen) supplemented with beta-mercaptoethanol (1%). Total RNA was purified using AllPrep Universal Kit (Qiagen), according to the manufacturer’s instructions. RNA integrity was measured by capillary electrophoresis using a Bioanalyzer (Agilent), and the RNA 6000 Nano Kit (Agilent Technologies); all samples had RIN-score >7.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: group

value: pSS

tag: cohort

value: Replication

value: Plasmacytoid dendritic cells


title: Repl-pSS10


title: Repl-pSS9


title: Repl-pSS8


title: Repl-pSS6


title: Repl-pSS5


title: Repl-pSS7


title: U2OS cells, Clone4.G1S.R2

city: Leuven

first: Florian

last: Rambow

address: Herestraat 49 box 912

country: Belgium

institute: VIB

data_processing:
Sequencing was performed on a Nextseq500 platform (Illumina, SE75bp)
Reads were then mapped to the human genome (hg19) using STAR (2.4.1b) and quantified with Subread (1.4.6-p2)
Library size factor normalized using the DeSeq2 pipeline
Genome_build: hg19
Supplementary_files_format_and_content: CA_23samples_sfnorm_log2+1_30k.txt  (gene-level abundance measurements)

source_name: U2OS cells

extract_protocol:
Total RNA was extracted as described above using the NucleoSpin RNA kit (Machery Nagel, Cat. No. 740955)
About 500 pg of RNA per sample was reverse-transcribed and amplified using a modified SMARTseq2 protocol (Rambow et al. 2018).  Prior to generating sequencing libraries using the NexteraXT kit (Illumina, Cat. No. FC-131-10)

value: bone tissue

tag: cell line

value: Bone Osteosarcoma Epithelial Cell line U2OS

tag: cell cycle stage

tag: genotype

value: KO


title: U2OS cells, WT.1.G1S.R2

value: WT


title: U2OS cells, D7.G1S.R2


title: U2OS cells, WT.2.G1S.R1


title: U2OS cells, A10.G1S.R1


title: U2OS cells, D7.G1S.R1


title: U2OS cells, WT.2.G1S.R2


title: U2OS cells, B9.G1S.R2


title: U2OS cells, A10.G1S.R2


title: U2OS cells, Clone4.G1S.R1


title: L_TAA_control_r1

tag: age


title: Repl-pSS4


title: Repl-pSS3


title: U2OS cells, B9.G0.R2


title: TKO_EPOP

value: Pcl1-3 TKO

value: EPOP


title: Repl-pSS1


title: U2OS cells, Clone4.G0.R2


title: U2OS cells, Clone4.G0.R1


title: Repl-pSS2


title: QKO_Suz12

value: Embryonic stem cell and NT2 cell line

value: Pcl1-3/Jarid2 QKO


title: Repl-nSS11

value: nSS


title: U2OS cells, B9.G0.R1


title: U2OS cells, A10.G0.R2


title: Repl-nSS10


title: Repl-nSS9


title: U2OS cells, WT.2.G0.R2


title: U2OS cells, B9.G1S.R1


title: U2OS cells, D7.G0.R1


title: U2OS cells, A10.G0.R1


title: U2OS cells, WT.1.G0.R1


title: Repl-nSS7


title: Repl-nSS6


title: Repl-nSS2


title: Repl-nSS1


title: Repl-nSS4


title: Repl-nSS8


title: Repl-HC11

value: HC


title: Repl-nSS3


title: Repl-HC10


title: UC1

city: Niigata

first: Atsunori

last: Tsuchiya

state: %null%

address: 1-757, Asahimachi-dori, Chuo-ku, Niigata

country: Japan

institute: Niigata University

data_processing:
Sequenced reads were mapped to hg19 using BWA. Unmapped reads are then mapped to hg19 whole genome using HiSAT2 with the parameters set as default, to map the reads that covers at least a part of exon2 as well as exon1.
TSS clustering and tags per million reads (TPM) were calculated using CAGEr (Nucleic Acids Res. 2015 Apr 30;43(8)).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each sample

source_name: human UC-MSCs cultured without mouse serum

extract_protocol:
AD-MSCs and UC-MSCs were cultured for 2 weeks with medium changed twice weekly. Serum was obtained from mice who received DSS for 7 days. AD-MSCs and UC-MSCs were cultured with serum (final concentration: 10%) from DSS-induced colitis model mice and compared with AD-MSCs and UC-MSC treated with serum (final concentration, 10%) from normal mice. After 48 h, cells were harvested, and mRNA expression levels were analyzed.
First strand cDNAs were transcribed to the 5’ end of capped RNAs, attached to CAGE "bar code" tags.

value: Umbilical cord tissue


title: UCN2

source_name: human UC-MSCs cultured  with normal mouse serum


title: ADN1

source_name: human AD-MSCs cultured  with normal mouse serum

value: adipose tissue


title: UCI2

source_name: human UC-MSCs cultured with serum from mice with DSS-induced colitis.


title: AD2

source_name: human AD-MSCs cultured without mouse serum


title: U2OS cells, D7.G0.R2


title: Repl-HC6


title: Repl-HC9


title: Repl-HC8


title: Repl-HC5


title: ADI1

source_name: human AD-MSCs cultured with serum from mice with DSS-induced colitis.


title: Disc-pSS13

value: Discovery


title: Disc-pSS14


title: U2OS cells, WT.2.G0.R1


title: Repl-nSS5


title: Repl-HC4


title: Disc-pSS12


title: Repl-HC3


title: Repl-HC2


title: Disc-pSS9


title: Disc-pSS8


title: Disc-pSS11


title: Disc-pSS10


title: Disc-pSS7


title: Disc-pSS6


title: Disc-pSS4


title: FHSSRCAP_H2AZ2_rep3_CNCC_V5_ChIP

city: Stanford

first: Rachel

middle: S

last: Greenberg

state: CA

address: 265 Campus Drive

institute: Stanford University

data_processing:
ChIP-seq reads were trimmed with cutadapt and aligned with bowtie2 to hg19 reference genome.
ChIP peaks were called with macs2 callpeak using --broad setting with untagged line ChIP as control. Read counts over macs2 called peaks together with large set of random decoy sites was calculated with bedtools coverage and differential count analysis was performed with DESseq2 platform. Differential ChIP peak analysis between statistically robust peaks from previous steps was performed with DESeq2.
RNA-seq reads were aligned to hg19 reference genome with hisat2 and tabulated using featureCounts (subread package) against GENCODE 24 gene models, differential analysis from three wildtype biological replicates and four mutant biological replicates from two differentiations was performed with DESeq2. Unaccounted variation between replicates and batches were removed using SVA.
Genome_build: hg19

growth_protocol: Embryonic stem cell lines were differentiated into cranial neural crest cells as previously described (Rada-Iglesias et al. 2012; Prescott et al. 2015). hESCs were grown to confluence and colonies were detached from the plate with 2mg/ml collagenase (Invitrogen). The cells were then washed with PBS and manually dissociated into clusters of 100-200 cells by pipetting. The cells were then resuspended in NCC differentiation media and transferred into a petri dish. NCC differentiation media includes - 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 5 µg/ml bovine insulin (Sigma-Aldrich) and 1× Glutamax-I supplement (100× stock, Invitrogen). Neural spheres are cultured for 4 days with media changed daily and spheres separated from debris by gentle centrifugation. After 4 days, the neural spheres were allowed to sit for 3 days and attachment would begin to occur. After the neural rosettes began to attach to the plate, media was changed daily to provide necessary growth factors. Once neural crest cells were allowed to migrate out of the neural rosettes for ~4 days, neural crest cells were dissociated with accutase and passaged onto 7.5ug/ml Fibronectin coated plates, removing neurectoderm/sphere residue and selecting for the neural crest cells. These cells were moved into a new media Early Maintenance Media, which includes: 1:1 Neurobasal medium/D-MEM F-12 medium (Invitrogen), 0.5× B-27 supplement with Vitamin A (50× stock, Invitrogen), 0.5× N-2 supplement (100× stock, Invitrogen), 20 ng/ml bFGF (Peprotech), 20 ng/ml EGF (Sigma-Aldrich), 1 mg/ml bovine serum albumin, serum replacement grade (Gemini Bio-Products # 700-104P) and 1× Glutamax-I supplement (100× stock, Invitrogen). The cells could then be cultured on fibronectin plates, with passaging every ~3 days with accutase. After 2 additional passages, media was changed to BMP/ChIR media, which increased cell proliferation and decreased migration, and included the components from early maintenance media plus 3M ChIRON 99021 (Selleck, CHIR-99021) and 50pg/ml BMP2 (Peprotech). As previously described (Prescott et al. 2015)

extract_protocol: Approximately 7.5 million cells were fixed with 1% formaldehyde for 10 minutes, quenched with a final concentration of 0.125M glycine. Chromatin was sheared on a Covaris sonicator to approximately 500-2000bp fragments. Salt was added and chromatin was immunoprecipitated overnight at 4°C with 5ug antibody (histones) or 7.5ug antibody (transcription factors/other binding proteins). Protein G Dynabeads were used to select for antibody-bound chromatin in a 4-6 hour incubation. After washing the beads, the crosslinks were reversed and the DNA was purified by phenol-chloroform extraction. 10-30ng of DNA were used for library preparation with end repair, A-tailing, and adaptor ligation (New England Biosciences). The libraries were then size selected for a size of 220-500 bps. The libraries were then indexed using NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S) and 12-15 amplification cycles for ChIP-seq. Adaptors were depleted via size selection on a gel. Library quality and quantity was assessed by Bioanalyzer and multiplexed ten to twelve samples per lane for single-end, 75bp reads on next-gen sequencing on a NEXTseq platform. ChIP antibodies used include: V5 antibody (rabbit polyclonal, Abcam 15828). Total RNA was extracted from at least 1X106 CNCCs at passage 5 on fibronectin from two independent differentiations using Trizol reagent (Invitrogen). 10µg of total RNA underwent two rounds of polyA tail purification with Dynal oligo(dT) beads (Invitrogen) to purify the mRNA. The mRNA was then fragmented with 10X Fragmentation Buffer (Ambion) for exactly 5 minutes and the fragmented mRNA was purified. Then first strand cDNA synthesis was performed with Random Hexamer Primers (Invitrogen) and SuperScript II enzyme (Invitrogen). Next, second strand cDNA synthesis was performed with RNase H (Invitrogen) and DNA Pol I (Invitrogen), and cDNA was purified with a QIAquick column (Qiagen). 30ng of cDNA was used for library preparation, with end repair, A-tailing, and adaptor ligation (New England Biosciences). The double stranded cDNA was then prepared for sequencing using NEBNext Multiplex Oligos for Illumina kit (Cat# E7335S) and only 10-12 amplification cycles for RNA-seq. Adaptors were depleted via a size selection with magnetic beads (Agencourt XP). Library quality and quantity was assessed by Bioanalyzer and multiplexed four to six samples per lane for single-end, 75bp reads on next-gen sequencing on Illumina HiSeq 2500 or NEXTseq platform.

value: ES-derived cranial neural crest cells (CNCCs)

tag: cell line of origin

value: H9 ESCs (WA09)

tag: srcap crispr edit

value: FHS-R2444*-FLAG-HA C-terminal tag

tag: h2a.z crispr edit

value: H2A.Z.2 V5 N-terminal tag


title: FHSSRCAP_H2AZ2_rep4_CNCC_V5_ChIP


title: Disc-pSS5

value: pSS

value: Plasmacytoid dendritic cells


title: Disc-pSS3


title: FHSSRCAP_H2AZ2_rep1_CNCC_V5_ChIP


title: WTSRCAP_H2AZ2_rep2_CNCC_V5_ChIP

value: WT-SRCAP-FLAG-HA C-terminal tag


title: WTSRCAP_H2AZ2_rep3_CNCC_V5_ChIP


title: Disc-pSS1


title: Disc-pSS2


title: H9_rep3_CNCC_V5_ChIP

value: unedited


title: Disc-nSS9


title: FHSSRCAP_H2AZ2_rep2_CNCC_V5_ChIP


title: H9_rep4_CNCC_V5_ChIP


title: H9_rep2_CNCC_V5_ChIP


title: Disc-nSS8


title: H9_rep1_CNCC_V5_ChIP


title: Disc-nSS6


title: Disc-nSS7


title: Disc-nSS4


title: Disc-nSS5


title: pros-Gal4-m8-ChIP_1.fastq

city: St Lucia

first: Stefan

last: Thor

state: QLD

address: Otto Bldg (81) room 620

department: School of Biomedical Sciences

country: Australia

institute: University of Queensland

description: ChIP-seq

data_processing:
DNAstar Seqman NGN software (DNASTAR, Inc. version 12.2) was used for sequence assembly.
Genome_build: dm6
Supplementary_files_format_and_content: QSeq peak

organism: Drosophila melanogaster

source_name: Embryos

growth_protocol: Drosophila melanogaster embryos, at St9-16, grown at +26C.

extract_protocol:
Qiagen Blood and tissue DNA extraction kit. Two independent samples were analyzed for each genotype.
DNA sequencing was performed by (GeneWhiz, New Jersey, NJ, USA), on one lane of the HiSeq2500 with a 1x50bp or 1x100bp single-read sequencing configuration in rapid run mode (V4 chemistry).

treatment_protocol: DNA was extracted from embryos.

value: Embryos, Stage 9-16

tag: sample type

value: Flag


title: pros-Gal4-Su(H)-ChIP_2.fastq

description: ChIP-seq


title: WTSRCAP_H2AZ2_rep4_CNCC_V5_ChIP

tag: chip antibody


title: pros-gal4-m8-DamID_2.fastq

description: DamID-seq

value: DamID


title: Disc-nSS3


title: Disc-nSS2


title: WTSRCAP_V5-H2AZ2_rep1_CNCC_V5_ChIP


title: pros-Gal4-m8-DamID_1.fastq

description: DamID-seq


title: neuron_mRNA_L2427P_3

city: Daejeon

first: JangKeun

last: Kim

state: YuseongGu

address: South Korea, Daejeon, Yuseonggu, Guseongdong KAIST E7 7108, Biomedical Research Center

department: Biomedical Science and Engineering Interdisciplinary Program

country: South Korea

institute: KAIST

description: RNA-seq data of cortical neuron expressing  MTOR p.L2427P

data_processing:
Read processing using FASTX-Tool kit
rRNA and tRNA removal usign Bowtie ver 1.1.2
Read alignment to the mm10 using Tophat ver 2.1.1.
Read quantificatio using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: HT-seq quantified reads

source_name: Cortical neuron

growth_protocol: In utero electroporation at mouse cortex with MTOR mutation in E14. Electroporated tissues were surgically resected from E18. Electroporated cortical neurons were FACS sorted E18.

extract_protocol:
RNA was extract using Trizol
Libraries were prepared according to reference (Cho et al., Science 2015, Oct 2;350(6256):82-7. doi: 10.1126/science.aac7368). Libraries were prepared according to Illumina's instructions accompanying the TruSeq small RNA Kit (Cat#RS-200-0012). Briefly, Ribosome protected fragment (RPF) were purifed using a RNase I and Sephacryl S-400 column. mRNAs were heat fragmented. RPF and mRNAs were labeled with 32P using a T4 polynucleotide kinase. RPF and mRNAs were size selected usign Urea-PAGE. RPFs and mRNAs were end-repaired using antarctic phosphatase and T4 polynucleotide kinase. After purification, 3' adaptor and 5' adaptor ligated and purifed by UREA PAGE. After RT-PCR, libraries were sequenced using Hiseq 2000.

value: Cortical neuron sorted from brain

tag: strain

tag: developmental stage


title: neuron_mRNA_L2427P_2


title: pros-Gal4-m5-DamID_2.fastq

description: DamID-seq


title: neuron_mRNA_C1483Y_3

description: RNA-seq data of cortical neuron expressing  MTOR p.C1483Y


title: Disc-nSS1

value: nSS


title: Disc-HC7

value: HC


title: Disc-HC8


title: pros-Gal4-m5-DamID_1.fastq

description: DamID-seq


title: neuron_mRNA_L2427P_1


title: neuron_mRNA_WT_3

description: RNA-seq data of cortical neuron expressing WT MTOR

value: WT


title: Disc-HC6


title: neuron_mRNA_WT_2


title: neuron_mRNA_C1483Y_2


title: m8-DamID_1.fastq

description: DamID-seq


title: neuron_mRNA_WT_1


title: m8-DamID_2.fastq

description: DamID-seq


title: neuron_mRNA_C1483Y_1


title: m5-DamID_2.fastq

description: DamID-seq


title: m5-DamID_1.fastq

description: DamID-seq


title: Disc-HC5


title: Disc-HC4


title: U2OS cells, WT.1.G0.R2

value: bone tissue

value: Bone Osteosarcoma Epithelial Cell line U2OS


title: neuron_RPF_L2427P_1

description: Ribo-seq data of cortical neuron expressing  MTOR p.L2427P

data_processing:
Library strategy: Ribo-seq
Read processing using FASTX-Tool kit
rRNA and tRNA removal usign Bowtie ver 1.1.2
Read alignment to the mm10 using Tophat ver 2.1.1.
Read quantificatio using HTSeq
Genome_build: mm10
Supplementary_files_format_and_content: HT-seq quantified reads


title: neuron_RPF_C1483Y_3

description: Ribo-seq data of cortical neuron expressing  MTOR p.C1483Y


title: Disc-HC3

value: Discovery


title: neuron_RPF_C1483Y_1


title: neuron_RPF_C1483Y_2


title: WTSRCAP_line3_CNCCdiff1_RNA

value: ES-derived cranial neural crest cells (CNCCs)

value: H9 ESCs (WA09)


title: FHS_FH_line1_CNCCdiff1_RNA

value: FHS-R2444*-FLAG-HA C-terminal tag


title: Disc-HC2


title: neuron_RPF_WT_2

description: Ribo-seq data of cortical neuron expressing WT MTOR


title: pros-Gal4-Su(H)-ChIP_1.fastq

description: ChIP-seq


title: CFUE_RNA_3

city: New Haven

first: Vince

last: Schulz

state: CT

address: 333 Cedar St. LMP 4085

department: Department of Pediatrics

institute: Yale University

data_processing:
Illumina Casava 1.8.2 software was used for basecalling.
FASTQ format sequencing reads were aligned to the hg19 genome using TopHat Version 1.3.3 software with default parameters
Reads in every gene were counted using the Rsubread featureCounts function. Genes with less than 3 samples with >1 read counts/million (cpm)  were called not expressed and were not used in further analysis. The read count data was normalized using the TMM method. Differentially expressed genes were identified using the edgeR exact test.
Genome_build: hg19
Supplementary_files_format_and_content: Counts per gene and RPKM Reads per KB per Million Reads

source_name: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

extract_protocol:
Progenitor cells at each stage were sorted by a combination of cell surface markers for IL-3R, CD34 and CD36. Total RNAs were extracted by RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
Illumina TruSeq RNA Sample Prep Kit (Part # 15008136) was used with 1 ug of total RNA for the construction of sequencing libraries.  RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: Stage

value: CFUE

tag: surface markers to isolate cells by facs-based methods


title: mRNA_Torin1_1

description: RNA-seq data of NIH3T3 treated with 200 nM of Torin1

source_name: NIH3T3 cell line

growth_protocol: Cells were cultured with DMEM with 10% FBS and 1% p/s

treatment_protocol: Torin1 200 nM for 3 hr

value: fibroblast

tag: gneotype


title: H2AZ2_line3_CNCC_V5_ChIP

tag: cell type

value: H2A.Z.2 V5 N-terminal tag


title: mRNA_Torin1_3


title: mRNA_Torin1_2


title: WTSRCAP_line2_CNCCdiff1_RNA

value: WT-SRCAP-FLAG-HA C-terminal tag

value: unedited


title: CFUE_RNA_2

tag: tissue

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: mRNA_C1483Y_3

description: RNA-seq data of genome-edited (Mtor c.G4448A) NIH3T3 by CRISPR, which treated with vehicle (Park et al., Neuron 2018 Jul 11;99(1):83-97.e7. doi: 10.1016/j.neuron.2018.05.039. Epub 2018 Jun 21.)


title: mRNA_C1483Y_2


title: H2AZ2_line2_CNCC_V5_ChIP


title: neuron_RPF_L2427P_3


title: neuron_RPF_L2427P_2


title: CFUE_RNA_1


title: H2AZ2_line1_CNCC_V5_ChIP


title: mRNA_WT_2

description: RNA-seq data of NIH3T3 treated with vehicle


title: H2AZ1_line3_CNCC_V5_ChIP

value: H2A.Z.1 V5 N-terminal tag


title: neuron_RPF_WT_1

value: Cortical neuron sorted from brain


title: mRNA_C1483Y_1


title: neuron_RPF_WT_3


title: BFUE_RNA_2

value: BFUE


title: RPF_Torin1_3

description: Ribo-seq data of NIH3T3 treated with 200 nM of Torin1


title: H2AZ1_line2_CNCC_V5_ChIP


title: RPF_Torin1_1


title: RPF_Torin1_2


title: BFUE_RNA_1


title: H2AZ1_line1_CNCC_V5_ChIP


title: mRNA_WT_3


title: RPF_C1483Y_3

description: Ribo-seq data of genome-edited (Mtor c.G4448A) NIH3T3 by CRISPR, which treated with vehicle (Park et al., Neuron 2018 Jul 11;99(1):83-97.e7. doi: 10.1016/j.neuron.2018.05.039. Epub 2018 Jun 21.)


title: BFUE_RNA_3


title: H9_CNCC_V5_ChIP


title: HSPC_RNA_2

source_name: Human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

value: HSPC


title: RPF_C1483Y_2


title: RPF_C1483Y_1


title: HSPC_RNA_1

value: Human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: RPF_WT_1

description: Ribo-seq data of NIH3T3 treated with vehicle

value: WT


title: RPF_WT_2


title: mRNA_WT_1


title: RPF_WT_3


title: FHS_FH_line4_CNCCdiff2_RNA


title: Ortho_ATAC_2

data_processing:
Sequenced reads were trimmed using Trimmomatic version 0.32 and mapped to the human genome (hg19 GRCh37) using the Burrows-Wheeler Aligner version 0.7.9a mem alignment program. Reads mapping to the ENCODE project blacklist of repetitive regions and mitochondrial regions were removed (ENCODE Project Consortium, 2012). MACS2 program version 2.1.1.20160309 was used to identify peaks using parameters nomodel shift −100 extsize 200 with a q value of <0.05.
Bigwig files were created using bedtools genomeCoverageBed scaling per million read, followed by conversion to bigwig format using the UCSC bedGraphToBigWig program.
Genome_build: hg19
Supplementary_files_format_and_content: bigwig and narrowPeak

extract_protocol: Progenitor cells at each stage were sorted by a combination of cell surface markers for IL-3R, CD34 and CD36. Erythroblasts at each stage of terminal erythroid differentiation were sorted by a combination of cell surface markers for glycophorin A, band 3, and α4 integrin.  Cells were lysed in buffer (10mM Tris-HCl, 10mM NaCl 3mM MgCL2 and 0.1% IGEPAL) for 15 minutes at 4C, then centrifuged and re-suspended with transposase reaction mix (2x tagmented DNA buffer, transposase [Ilumina Nextera]), and nuclease-free water) and incubated for 30 min at 37 degrees.  DNA was purified using a MinElute column (Qiagen) and PCR amplified in KAPA HiFi 2x mix (Kapa Biosystems) with barcoding primers (Buenrostro et al., 2013) at 98C for 45 sec (45s) + 5 x at (98C for 15s + 63C for 30s + 72C for 30s) + 72C for 1 min. PCR products were cleaned with MinElute columns and size exclusion was performed with magJet NGS Cleanup and Size Selection kit (Thermo Fisher). Q-PCR library amplification test and PCR library amplification was performed as previously described(Buenrostro et al., 2015).

value: orthochromatic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin negative


title: FHS_FH_line3_CNCCdiff2_RNA

value: ES-derived cranial neural crest cells (CNCCs)


title: Heterozygous sample 2 [S-HET2]

city: Seoul

first: Kihoon

last: Han

address: 73, Inchon-ro, Seongbuk-gu

department: Neuroscience

institute: Korea University College of Medicine

data_processing:
Transcript abundance was estimated with Salmon(v0.9.1) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.3.6.0) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.19.11).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Heterozygous brain

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit  (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols (TruSeq Stranded mRNA Sample Preparation Guide)

tag: strain background

value: 10 to 12 week

value: Shank3 heterozygous

value: brain; striatum


title: Heterozygous sample 3 [S-HET3]


title: Knock-out sample 3 [S-KO3]

source_name: Knock-out brain

value: Shank3 knockout


title: FHS_FH_line2_CNCCdiff2_RNA

value: H9 ESCs (WA09)

value: FHS-R2444*-FLAG-HA C-terminal tag


title: Knock-out sample 2 [S-KO2]


title: HSPC_RNA_3


title: Knock-out sample 1 [S-KO1]


title: Poly_ATAC_2

value: polychromatic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin medium


title: Poly_ATAC_1

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: Disc-HC1

tag: group

value: HC

tag: cohort

value: Discovery

value: Plasmacytoid dendritic cells


title: Wild-type sample 2 [S-WT2]

source_name: Wild-type brain

tag: genotype


title: Wild-type sample 1 [S-WT1]

tag: age


title: WT_FH_line2_CNCCdiff2_RNA

tag: cell line of origin

value: WT-SRCAP-FLAG-HA C-terminal tag

value: unedited


title: LBaso_ATAC_2

value: late basophilic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin high


title: WT_FH_line1_CNCCdiff2_RNA

value: ES-derived cranial neural crest cells (CNCCs)

tag: srcap crispr edit


title: Heterozygous sample 1 [S-HET1]

value: 10 to 12 week


title: FHS_FH_line1_CNCCdiff2_RNA

tag: h2a.z crispr edit


title: Skin fibroblasts, h160066_siCF25

city: Suzhou

first: Hang

last: Ruan

state: Jiangsu

address: 199 Ren'ai Road

department: IBMS

institute: Soochow University

data_processing:
RNA-seq reads were mapping to human hg19 genome using hisat2 (version:2.2.0.5) with default parameters
The sorted BAM files were then converted to gtf format using stringtie (version: 1.3.3b)
Genome_build: hg19
Supplementary_files_format_and_content: gtf format

source_name: skin fibroblasts

growth_protocol: Normal Human skin fibroblasts were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplement with 10% fetal bovine serum (FBS) and antibiotics.

extract_protocol:
RNA was extracted with miRNeasy Mini Kit from Qiagen
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were transfected with 50 pmol/ml control or CFIm25 siRNA （sigma-Aldich） using RNAimax.

value: skin

value: fibroblasts

tag: replicate

tag: transfection

value: CFIm25 siRNA

value: CFIm25 knockdown


title: LBaso_ATAC_1


title: Skin fibroblasts, h160066_siCon

value: control siRNA

value: control


title: Skin fibroblasts, h110031_siCF25


title: FHS_FH_line4_CNCCdiff1_RNA

value: H9 ESCs (WA09)

value: FHS-R2444*-FLAG-HA C-terminal tag


title: Skin fibroblasts, h100155_siCon


title: FHS_FH_line3_CNCCdiff1_RNA


title: Skin fibroblasts, h100155_siCF25


title: Skin fibroblasts, h090094_siCon


title: WT_FH_line3_CNCCdiff2_RNA


title: Skin fibroblasts, h070337_siCon


title: FHS_FH_line2_CNCCdiff1_RNA


title: Wild-type sample 3 [S-WT3]

value: WT

value: brain; striatum


title: ProE_ATAC_2

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

value: proerythroblast

value: GPA low, Band3 negative and alpha 4 integrin high


title: WTSRCAP_line1_CNCCdiff1_RNA

value: WT-SRCAP-FLAG-HA C-terminal tag

value: unedited


title: Kasumi1-WT-input_rep11

city: Miami

first: Stephen

last: Nimer

state: FL

address: 1120 NW 14th ST

department: Sylvester Comprehensive Cancer Center

institute: University of Miami

data_processing:
Base calling using Illumina RTA 2.4.11
Trimmed fastq files with cutadapt v.1.15  --nextseq-trim=20  -u 2 -u -2 -m 18
Processed with Kundaje lab Aquas Pipeline (git commit SHA1: 5e0e6f119b70c6e7a0a2578d38847f30e200df95) with -peak_caller macs2 -species hg38
For histones, used naïve overlap for peak file.  For ETO peaks, used optimal replicate IDR < 0.05 for peaks.  For TAF1, used optimal pseudo-replicate IDR < 0.05.
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: .bw were gererated as fc singal over input from MACS2.

source_name: Kasumi-1 Cells

growth_protocol: 20% FBS in RPMI1 1640

extract_protocol:
SimpleChIP Enzymatic Chromatin IP kit (Cell Siganling Technology) was used for chromatin immunoprecipitation per manufacturers instructions.
Libraries were prepared using E7645S NEBNext(r) Ultra(tm) II DNA Library Prep Kit for Illumina® accoring to manufacturers instructions.

tag: cell line

value: Acute Myeloid Leukemia

tag: chip antibody


title: EBaso_ATAC_1

tag: Stage

value: early basophilic erythroblast

value: GPA positive, Band3 medium and alpha 4 integrin high


title: Kasumi1-shTAF1-2-ATAC_rep2

data_processing:
Base calling using Illumina RTA 2.4.11
Trimmed fastq files with cutadapt v.1.15
Processed with ENCODE atac-seq-pipeline (git commit SHA1:2b693abd4550943be1e8d9a686a1050c1acab92c) with cutadapt, bowtie2 and macs2
Genome_build: GRCh38.p3
Supplementary_files_format_and_content: .bw were gererated as fc singal over background from pooled aligned replicates using MACS2.

growth_protocol: Kasumi-1 cells grown in RPMI+20%FBS

extract_protocol:
following the protocol in Buenrostro et al  Curr Protoc Mol Biol 109, 21-29 (2015)
following the protocol in Buenrostro et al  Curr Protoc Mol Biol 109, 21-29 (2015)

treatment_protocol: infected with scrambled shRNA or TAF1 shRNAs

value: TAF1 shRNA


title: ProE_ATAC_1

tag: surface markers to isolate cells by facs-based methods


title: Skin fibroblasts, h110031_siCon

value: skin

value: fibroblasts


title: EBaso_ATAC_2


title: Kasumi1-WT-P300_rep11

description: processed data file: Kasumi1-WT-P300.filt.narrowPeak.gz

value: P300 (Santa Cruz sc-585)


title: Skin fibroblasts, h090094_siCF25

value: CFIm25 siRNA

value: CFIm25 knockdown


title: CFUE_ATAC_2

value: CFUE


title: Skin fibroblasts, h070337_siCF25


title: Kasumi1-shTAF1-1-ATAC_rep2


title: CFUE_ATAC_1


title: Kasumi1-scr-ATAC_rep2

value: scrambled shRNA


title: BFUE_ATAC_2

value: BFUE


title: BFUE_ATAC_1

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)


title: Kasumi1-shTAF1-1-ATAC_rep1


title: Kasumi1-scr-ATAC_rep1


title: Kasumi1-shTAF1-2-ATAC_rep1


title: HSPC_ATAC_1

value: Human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

value: HSPC


title: Kasumi1-shTAF1-AE_rep2

data_processing:
Base calling using Illumina BCL2fastq v2.19.0.316
Trimmed fastq files with cutadapt v.1.18  --a AGATCGGAAGAGCACACGTC -m 30
Aligned to human genome hg19 using bowtie2 2.2.6
AE peaks were called with MACS2 v2.1.1.20160309
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: bw were gererated with normalizing to 1 billion Wigsum.

tag: genotype/variation

value: AML1-ETO polyclonal antibody (Diagenode, C15310197)


title: HSPC_ATAC_2


title: Kasumi1-shControl-AE_rep2

tag: cell type

value: shControl-AE


title: Kasumi1-shTAF1-AE_rep1

value: Acute Myeloid Leukemia


title: Kasumi1-shControl-AE_rep1


title: SUPT1_NT_rep3

type: RNA

city: Milan

first: Matteo

last: Dugo

address: via Olgettina 60

department: Department of Medical Oncology

institute: IRCCS Ospedale San Raffaele

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Primary microarray data were collected using BeadStudio v3 software package. Raw data were log2-transformed and normalized using the robust spline normalization method, implemented in the lumi R/Bioconductor package.

label: Biotin

label_protocol: RNA was reverse transcribed, labeled with biotin and amplified overnight using the Illumina TotalPrep RNA Amplification Kit (Life Technologies).

growth_protocol: cells were grown in in a humidified chamber with 5% CO2 at 37°C, in RPMI 1640 medium supplemented with 10% FBS, 1% L-glutamine and 100 U/ml pen/strep.

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: cell were treated or not with CHOEP (cyclophosphamide monohydrate, doxorubicin hydrochloride, vincristine sulfate, prednisone and etoposide) for 24 hours.

tag: treatment

value: Untreated


title: HH_NT_rep3

value: HH


title: HH_NT_rep2


title: SUPT1_NT_rep1


title: HDMAR_NT_rep2

value: HDMAR


title: SUPT1_CHOEP_rep1

value: CHOEP


title: SUPT1_CHOEP_rep3


title: HDMAR_CHOEP_rep2


title: HDMAR_CHOEP_rep3


title: HDMAR_NT_rep1


title: SUPT1_NT_rep2


title: SUPT1_CHOEP_rep2


title: HDMAR_NT_rep3


title: HDMAR_CHOEP_rep1


title: HH_NT_rep1


title: HH_CHOEP_rep2


title: HH_CHOEP_rep3


title: KARPAS_NT_rep1

value: KARPAS


title: HH_CHOEP_rep1


title: MAT_DAP_DZA_Cy5

city: Beaucouze

first: Julia

last: Buitink

address: 42 rue Georges Morel

department: BAP

country: France

institute: INRAE

hyb_protocol: Hybridization was performed on a NimbleGen Hybridization System 4 (mix mode B) at 42° overnight. Slides were washed and dried prior to scanning.

scan_protocol: Slides were scanned at 532/635nm at 2 μm resolution and high sensitivity with a Roche_NimbleGen MS200. DEVA Software v1.2.1 was used to extract pair_data files from the scanned images.

data_processing: All statistical analyses on the gene expression data were performed using R language, version 2.5.1 (R Development Core Team, 2011) and LIMMA package (Smyth G.K., 2005) from the Bioconductor project. For the processing steps, data were normalized by the lowess method in LIMMA.

organism: Medicago truncatula

label_protocol: 400ng of total RNAs were amplified using the Ambion messageAmp II (Ambion, Austin TX) following manufacturer's instructions. 5µg of each aRNAs were retrotranscribed with 400U of Superscript II reverse_transcriptase (Invitrogen Corp., Carlsbad, CA) and labelled with 1.5mmol of Cyanine_3 (Cy3) or Cyanine_5 (Cy5) (Interchim, France), then purified with NucleoSpin Gel and PCR Clean_up column kits (Macherey_Nagel, GmbH & Co. KG, Germany). Purified labeled cDNA were quantified using NanoDrop ND_1000 (Nanodrop Technologies, DE, USA). Labelled samples (30 pmol) were combined and co_hybridized to the Medtr_v1 12x135K arrays.

growth_protocol: Five Medicago truncatula plants were grown at variable light and temperature conditions, under greenhouse environment (period March-June): from the stage of flowering to the end of seed maturation. Seeds were collected at different maturation stages, from 16 DAP to Abscission. Dry seeds (DS) was the last analysed stage of development, seeds were let at the same environmental conditions for one week after abscission

extract_protocol: For each data point of seed development and for each repetition, 50 seeds were collected and the total RNA was extracted with Macherey-Nagel's Nucleospin Plant II Kit according manufacturer's recommendations

treatment_protocol: Medicago truncatula seeds developed in greenhouse from 1 DAP to DS stage

tag: tissue

value: seeds

tag: genetic background

tag: developmental stage

value: mature

tag: phenotype

value: Wild-type

value: Seeds developed under greenhouse conditions 18-25°C, 16h light

value: dry mature

tag: harvest date


title: MAT_DAP_DZA_Cy3

tag: age


title: 36_DAP_DZA_Cy3

value: 36 days after pollination


title: ABS_DAP_DZA_Cy3

value: abscission

value: Abscission


title: KARPAS_CHOEP_rep3


title: ABS_DAP_DZA_Cy5


title: KARPAS_NT_rep2


title: KARPAS_NT_rep3


title: Ortho_ATAC_1

value: Cultured human umbilical cord derived CD34+ human hematopoietic stem and progenitor cells (HSPCs)

value: orthochromatic erythroblast

value: GPA positive, Band3 high and alpha 4 integrin negative


title: KARPAS_CHOEP_rep2


title: JURKAT_NT_rep2

value: JURKAT


title: JURKAT_NT_rep3

value: Untreated


title: JURKAT_NT_rep1


title: 36_DAP_DZA_Cy5


title: 28_DAP_DZA_Cy3

value: 28 days after pollination


title: JURKAT_CHOEP_rep2


title: JURKAT_CHOEP_rep3


title: MCF7-MKL1ΔN200_E2_rep4

city: Montevideo

first: Tamara

last: Fernandez-Calero

state: Montevideo

address: Mataojo 2020

department: Bioinfomatics Unit

country: Uruguay

institute: Institut Pasteur de Montevideo

description:
Gene expression after 4hr of E2
MCF7-MKL1ΔN200 cells, 10nM  E2, replicate 4

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing: Data analysis was performed using ‘R’ (R Foundation for Statistical Computing, Vienna, Austria), mainly through packages included in the Bioconductor suite. Probes were filtered considering saturation, signal above background and uniformity. Only those with no replicate flagged in at least one condition were taken into account for data analysis. Samples were normalized using 75-percentile shift normalization.

source_name: MCF7-MKL1ΔN200 cells, 10 nM E2

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Cells were routinely maintained in DMEM (Invitrogen) supplemented with 10% fetal calf serum (FCS) (Biowest) and antibiotics (Invitrogen) at 37ºC in 5% CO2.

extract_protocol: RNA was prepared using the RNAeasy column purification (Qiagen, Hilden, Germany), following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer (Nanodrop technology, Cambridge, UK) and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and the overall RNA integrity numbers (RIN) were between 9.8 and 10.

treatment_protocol: Before any experiments, MCF7 cells were grown in phenol red-free DMEM (Invitrogen) containing 2.5% charcoal-stripped FCS (Biowest) for at least 72 hours. In order to induce the expression of the constitutively active mutant of MKL1 (MKL1ΔN200), cells were treated the last 48 hours with 1 µg/mL tetracycline. 17β-estradiol (E2, Sigma-Aldrich) was used at a final concentration of 10 nM.

tag: subclone genotype

tag: agent


title: MCF7-MKL1ΔN200_EtOH_rep2

description:
Gene expression after 4hr of EtOH
MCF7-MKL1ΔN200 cells, EtOH, replicate 2

source_name: MCF7-MKL1ΔN200 cells, EtOH

value: EtOH


title: MCF7-MKL1ΔN200_EtOH_rep1

description:
Gene expression after 4hr of EtOH
MCF7-MKL1ΔN200 cells, EtOH, replicate 1


title: 28_DAP_DZA_Cy5


title: KARPAS_CHOEP_rep1

value: CHOEP


title: MCF7-MKL1ΔN200_EtOH_rep3

description:
Gene expression after 4hr of EtOH
MCF7-MKL1ΔN200 cells, EtOH, replicate 3


title: MCF7-MKL1ΔN200_E2_rep1

description:
Gene expression after 4hr of E2
MCF7-MKL1ΔN200 cells, 10 nM E2, replicate 1


title: MCF7-MKL1ΔN200_EtOH_rep4

description:
Gene expression after 4hr of EtOH
MCF7-MKL1ΔN200 cells, EtOH, replicate 4


title: MCF7-MKL1ΔN200_E2_rep3

description:
Gene expression after 4hr of E2
MCF7-MKL1ΔN200 cells, 10 nM E2, replicate 3


title: MCF7control_E2_rep4

description:
Gene expression after 4hr of E2
MCF7 control cells, 10nM  E2, replicate 4

source_name: MCF7 control cells, 10 nM E2

value: control


title: 24_DAP_DZA_Cy3

value: seeds

value: 24 days after pollination


title: 32_DAP_DZA_Cy5

value: 32 days after pollination

value: Wild-type


title: 32_DAP_DZA_Cy3

value: Seeds developed under greenhouse conditions 18-25°C, 16h light


title: MCF7-MKL1ΔN200_E2_rep2

description:
Gene expression after 4hr of E2
MCF7-MKL1ΔN200 cells, 10 nM E2, replicate 2


title: 24_DAP_DZA_Cy5


title: JURKAT_CHOEP_rep1


title: 20_DAP_DZA_Cy5

value: 20 days after pollination


title: MCF7control_E2_rep3

description:
Gene expression after 4hr of E2
MCF7 control cells, 10 nM E2, replicate 3


title: 20_DAP_DZA_Cy3


title: C032_36h

city: Pozuelo de Alarcón

first: Isabel

last: Díaz

state: Madrid

address: Campus Montegarcedo

department: Interacción de las Plantas con el Medio

country: Spain

institute: CBGP-INIA-UPM

data_processing:
Reads were mapped to the reference genome using HISAT.
Assembly and quantification of transcripts in each sample were performed using StringTie (Pertea et al., 2016)
Genome_build: AST_PRJEB5043_v1 (Chalhoub et al., 2014)
Supplementary_files_format_and_content: Excel file with columns specifying: t_name;gene_id;gene_name;chr;strand;start;end;num_exons;length;cov.C032_00h;cov.C032_02h;cov.C032_12h;cov.C032_36h;cov.C032_72h;cov.C033_00h;cov.C033_02h;cov.C033_12h;cov.C033_36h;cov.C033_72h;cov.C129_00h;cov.C129_02h;cov.C129_12h;cov.C129_36h;cov.C129_72h;TPM.C032_00h;TPM.C032_02h;TPM.C032_12h;TPM.C032_36h;TPM.C032_72h;TPM.C033_00h;TPM.C033_02h;TPM.C033_12h;TPM.C033_36h;TPM.C033_72h;TPM.C129_00h;TPM.C129_02h;TPM.C129_12h;TPM.C129_36h;TPM.C129_72h
Supplementary_files_format_and_content: excel file include coverage (cov.) and TPM values for each sample.

organism: Brassica napus

source_name: Seeds at 36 hai (hours after imbibition)

growth_protocol: 50-100 seeds sown in Jacobsen germination vessels ﬁlled with 50 ml distilled water and germinated in a growth chamber at a constant temperature of 20°C and with a relative humidity between 50 and 75% in the dark. For high-quality RNA extraction, three biological replicates (30 seeds each) were collected and pooled for each time point.

extract_protocol:
The total RNA was extracted using the Nucleospin miRNA kit (Mecherey-Nagel, Düren, Germany). The protocol dedicated to the isolation of total RNA was used.
cDNA libraries were constructed using the TruSeqnRNA Sample Prep Kit v2 (Illumina) and were sequenced on the Illumina HiSeq2000 platform at LGC Genomics (Berlin, Germany).

treatment_protocol: kinetics

tag: time

value: 36 hai (hours after imbibition)

tag: accession


title: C033_12h

source_name: Seeds at 12 hai (hours after imbibition)

value: 12 hai (hours after imbibition)


title: C033_02h

source_name: Seeds at 2 hai (hours after imbibition)

value: 2 hai (hours after imbibition)


title: C032_12h


title: C033_36h


title: C032_00h

source_name: Seeds at 0 hai (hours after imbibition)

value: 0 hai (hours after imbibition)


title: C033_72h

source_name: Seeds at 72 hai (hours after imbibition)

value: 72 hai (hours after imbibition)


title: C032_72h


title: C033_00h


title: C129_72h


title: P185 [validation]

city: New York

first: Weijia

last: Zhang

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

description: Total RNA was extracted from whole blood drawn from kidney transplant recipients at 3m post transplantation.

hyb_protocol: Hybridization was performed by following Affymetrix standard procedure.

scan_protocol: Affymetrix GeneChIP Scanner 3000 7G.

data_processing:
Gene-level intensity data were extracted and normalized by RMA stretch in Affymetrix Expression Console. Data were then log2 transformed.
Core exons were included in the analysis. Transcript assignments are based on NetAffx build 28 (hg18/NCBI36).

label: biotin

source_name: whole blood

label_protocol: ENCORE amplification and labeling kit (NuGen, San Carlos, CA) was applied to samples to generate biotin-labeled RNA fragments for hybridization to the chip.

growth_protocol: Not applicable.

extract_protocol: Total RNA was extracted from blood samples obtained at 3 month after transplantation using All prep kit (QIAGEN-ALLprep kit, Valencia, CA USA). RNA quality was assessed using Bioanalyzer 2100 (Agilent Technologies).

treatment_protocol: Not applicable.

value: Whole blood

tag: acr 3m

value: Yes


title: P186 [validation]


title: C032_02h


title: P183 [validation]


title: P184 [validation]


title: P181 [validation]


title: MCF7control_E2_rep2

description:
Gene expression after 4hr of E2
MCF7 control cells, 10 nM E2, replicate 2

tag: cell line


title: P182 [validation]


title: MCF7control_EtOH_rep3

description:
Gene expression after 4hr of EtOH
MCF7 control cells, EtOH, replicate 3

source_name: MCF7 control cells, EtOH


title: C129_36h


title: MCF7control_EtOH_rep1

description:
Gene expression after 4hr of EtOH
MCF7 control cells, EtOH, replicate 1


title: MCF7control_E2_rep1

description:
Gene expression after 4hr of E2
MCF7 control cells, 10 nM E2, replicate 1


title: C129_12h


title: P180 [validation]


title: 16_DAP_DZA_Cy3

value: 16 days after pollination


title: 16_DAP_DZA_Cy5


title: C129_00h


title: C129_02h


title: F11314: Specific immunity line 5

city: Münster

first: Joachim

last: Kurtz

address: Hüfferstraße 1

department: Evolution and Biodiversity

institute: University of Münster

data_processing:
The quality of the raw reads was first checked with FastQC, after which the first five base pairs were removed using Trimmomatic 0.36 to account for observed biases in sequence composition due to random hexamer priming.
After this filtering step, STAR v2.5.3 was used to map the reads to the Tribolium 5.2 reference genome downloaded from Beetlebase. The mapped reads were then converted from the .sam into the .bam format using
SAM tools v0.1.19 for downstream analyses. The .gff file used for mapping was then converted into a gtf reference file using the “gffread” function of cufflinks v2.2.1. To obtain total gene counts from the mapped reads,
the “htseq-count” function of HTSeq v0.7.2  was used to count by gene ID, after which the individual assemblies were merged into one count table files by means of a custom-made R pipeline.
Genome_build: Tribolium 5.2 reference genome

organism: Tribolium castaneum

source_name: 20 pooled larvae

extract_protocol:
Pooled larvae were immediately shock frozen in liquid nitrogen and stored at -80oC until further use. RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) according to the protocol of the manufacturer.
The libraries for Illumina sequencing were prepared using the TruSeq RNA sample V2 Kit (Illumina) following the manufacturer’s protocol. The libraries were then clustered on a cBot with the TruSeq PE Cluster Kit V4 (Illumina) with a final loading concentration of 10 pM according to the instructions of the manufacturer.

value: Whole body

tag: priming treatment

value: Naive control

tag: time point

value: 6h post priming


title: F11312: Specific immunity line 6


title: F11313: Unspecific immunity line 5

value: Heat-killed Btt


title: F11311: Untreated control line 1


title: F11316: Unspecific immunity line 1


title: P179 [validation]


title: F11315: Unspecific immunity line 2

value: Heat-killed Pf


title: F11308: Unspecific immunity line 4


title: F11307: Unspecific immunity line 2


title: F11309: Specific immunity line 6

value: Heat-killed Bt1


title: F11306: Untreated control line 2


title: F11310: Unspecific immunity line 1


title: F11304: Unspecific immunity line 6


title: F11303: Specific immunity line 1


title: P34 [validation]


title: F11305: Specific immunity line 3


title: F11302: Unspecific immunity line 1


title: P91 [validation]


title: P177 [validation]

value: No


title: F11301: Specific immunity line 4


title: P96 [validation]


title: P176 [validation]


title: P178 [validation]


title: F11300: Specific immunity line 4


title: P13 [validation]


title: P175 [validation]


title: F11299: Specific immunity line 4


title: F11295: Unspecific immunity line 6


title: F11298: Untreated control line 3


title: F11296: Specific immunity line 1


title: F11291: Unspecific immunity line 2


title: F11294: Specific immunity line 3


title: F11290: Untreated control line 1


title: F11293: Specific immunity line 6


title: F11292: Specific immunity line 1


title: P173 [validation]


title: F11289: Untreated control line 3


title: P174 [validation]


title: P169 [validation]


title: F11288: Specific immunity line 6


title: F11287: Specific immunity line 5


title: P170 [validation]


title: P172 [validation]


title: F11297: Specific immunity line 5


title: P171 [validation]


title: F11286: Specific immunity line 5


title: F11283: Unspecific immunity line 6


title: F11284: Unspecific immunity line 3


title: F11285: Specific immunity line 2


title: P167 [validation]


title: P168 [validation]


title: P166 [validation]


title: F11281: Unspecific immunity line 3


title: MCF7control_EtOH_rep4

description:
Gene expression after 4hr of EtOH
MCF7 control cells, EtOH, replicate 4

value: control

value: EtOH


title: F11282: Untreated control line 3


title: F11280: Unspecific immunity line 4


title: F11277: Unspecific immunity line 3


title: MCF7control_EtOH_rep2

description:
Gene expression after 4hr of EtOH
MCF7 control cells, EtOH, replicate 2


title: F11278: Specific immunity line 2


title: F11279: Unspecific immunity line 6


title: P163 [validation]


title: F11276: Specific immunity line 2


title: F11275: Untreated control line 1


title: P164 [validation]


title: P165 [validation]


title: F11272: Untreated control line 2


title: F11273: Unspecific immunity line 1


title: No UV control

city: Gothenburg

first: Martin

last: Boström

address: Medicinaregatan 9A

country: Sweden

institute: University of Gothenburg

description: untreated cells

data_processing:
Library strategy: CPD-seq
Pairwise alignment with Bowtie 2 version 2.3.1, default parameters
Duplicates were marked with Picard MarkDuplicates version 2.18.23, default parameters
Non-duplicate R1 reads belonging to proper pairs were imported into R and further processed with Bioconductor packages. The 2 bases upstream and on the opposite strand of each read on R1 were saved as CPDs.
CPDs outside the chromosome boundaries of chromosomes 1-22, X and Y were discarded
The DNA sequence of each CPD was obtained with the R Bioconductor package BSgenome's getSeq function and non-dipyrimidine "CPDs" were discarded.
CPDs within 100 bp of RepeatMasker satellite class repeats were discarded.
Genome_build: hg19
Supplementary_files_format_and_content: Bed. The files contain the positions of all CPDs detected by sequencing, with optical duplicates and non-dipyrimidine "CPDs" removed. Note that every detected CPD has its own row in the BED files, meaning multiple CPDs in one position will result in duplicate rows.

source_name: culture

growth_protocol: Cells were grown in DMEM + 10 % FCS + pen/strep

extract_protocol:
Genomic DNA was extracted with QIAgen DNA blood mini kit
CPDs were mapped with a modified CPD seq method (Mao et al 2016). Purified DNA 12 ug was sonicated to 400 bp and size selected with SPRI select beads (Life Technologies) and the purified product (approx. 4 ug) subjected to NEBNext end repair and NEBNext dA-tailing modules (NEB). ARC141/142 was then ligated to the sheared and repaired ends O/N with NEBNext Quick Ligation module. DNA was purified with CleanPCR beads and treated with Terminal Transferase (TdT, NEB) and dideoxy ATP (Roche) for 2h at 37 degrees. DNA was purified and incubated with 30 units T4 endonuclease V (NEB) at 37 degrees for 2 h, followed by purification and treatment with APE1 (NEB) at 37 degrees for 1.5 hr. DNA was purified and treated with rSAP (NEB) 37 degrees 1 hr followed by deactivation at 65 degrees for 15 minutes. DNA was purified, denatured at 95 degrees for 5 min, cooled on ice and ligated with the biotin-tagged “ARC double” overnight at 16 degrees with NEBNext quick ligation module. DNA fragments with the biotin tag were captured with Streptavidin Dynabeads (Invitrogen) and the DNA strand without the biotin label was released with 0.15 M NaOH.  This single stranded DNA was used as the template to synthesise double stranded products using ARC153. The now double stranded library was purified and amplified with ARC140 and either ARC78, ARC87 or ARC88 to add Illumina barcodes and indexes.

tag: cancer type

value: malignant melanoma

value: untreated


title: F11270: Unspecific immunity line 5


title: F11268: Untreated control line 3


title: F11267: Unspecific immunity line 4


title: UVB rep2

description: cells treated with 10000J/m2 UVB 310 nm


title: F11269: Specific immunity line 3


title: UVB rep1

description: cells treated with 10000J/m2 UVB 310 nm


title: F11266: Specific immunity line 4


title: F11271: Unspecific immunity line 4


title: P159 [validation]


title: P162 [validation]


title: P160 [validation]


title: P161 [validation]


title: F11264: Unspecific immunity line 5


title: Kasumi1-WT-P300_rep2

description: processed data file: Kasumi1-WT-P300.filt.narrowPeak.gz

tag: cell type

value: Acute Myeloid Leukemia

tag: chip antibody


title: F11265: Untreated control line 1

tag: tissue


title: F11274: Unspecific immunity line 2


title: P156 [validation]


title: P157 [validation]


title: F11261: Specific immunity line 2


title: F11263: Unspecific immunity line 3


title: P158 [validation]


title: F11262: Untreated control line 2


title: F11260: Specific immunity line 3


title: Kasumi1_TAF1i_rep1

description:
TAF1i_rep1
processed data file: RSEM.gene.counts.txt

data_processing:
Base calling using Illumina RTA 2.4.11.
Sequenced reads were hard clipped 1 bp at the 5' and 3 bps at the 3' read ends. Using Skewer v0.2.2, reads were then trimmed of adaptor sequences and low 3' base quality (q20), while read pairs with reads 18 or smaller were filtered out.
Reads mapped to GRCh38.p7 transcriptome using STAR v2.5.3 and RSEMv1.3.0 with default parameters.
Counts were estimated using RSEM gene.results.
Genome_build: Ensembl 87: GRCh38.p7
Supplementary_files_format_and_content: RSEM.gene.counts.txt: Tab-delimited text file contains aggregated normalized expected counts for all samples.

source_name: Kasumi-1, 3 days

growth_protocol: 20% FBS in RPMI 1640.

extract_protocol:
RNA was harvested using Qiagen RNeasy Plus Micro Kit (Cat#76034). NEBNext rRNA depletion Kit (E6310) and NEBNext Ultra directional RNA library prep Kit for Illumina (E7420) were used per manufacturer's instructions.
Libraries were prepared for sequencing using standard Illumina protocols.
Paired-end RNAseq for experiments A and C, and single-end RNAseq for Experiment B.

treatment_protocol: 20% FBS in RPMI 1640 for Lentivirus. Addition of DMSO or Bay-364 for Experiment C.

tag: virus

tag: shRNA

tag: experiment

value: C


title: P154 [validation]


title: F11259: Unspecific immunity line 5


title: P155 [validation]


title: F11258: Untreated control line 2


title: Kasumi1_DMSO_rep1

description:
DMSO_rep1
processed data file: RSEM.gene.counts.txt

value: DMSO

value: DMSO Control


title: F11257: Specific immunity line 1


title: Kasumi1_DMSO_rep2

description:
DMSO_rep2
processed data file: RSEM.gene.counts.txt


title: P153 [validation]

value: Whole blood


title: Kasumi1_AE_sh2_rep3

description:
shAE2-3
processed data file: RSEM.gene.counts.txt

source_name: Kasumi-1, 5 days

value: Lentiviral Constitutive

value: AE shRNA #2

value: B


title: Kasumi1_TAF1i_rep2

description:
TAF1i_rep2
processed data file: RSEM.gene.counts.txt