title: RNA-seq morula Eed/Xist matDKO rep2

first: Azusa

last: Inoue

address: Suehiro-cho 1-7-22, Tsurumi-ku

department: Center for Integrative Medical Sciences

data_processing:
Bases calling was performed with bcl2fastq software (version 2.17).
All reads after trimming by fastp (version 0.21.0) were mapped to the mouse reference genome (mm10) by STAR (version 2.7.6a) with default parameters "--runMode alignReads --alignEndsType EndToEnd --outSAMattributes NH NI NM MD --outSAMtype BAM Unsorted".
A mixed genetic background of C57BL/6 and 129S1/SvImJ mouse are produced as a oocyte donor. Then mating the chimeric C57BL/6 (129S1/SvImJ) mouse substrains with PWK/PhJ mouse substrains allow us to track the parental origin. For allele-specific analysis of RNA-seq in the C57BL/6 (129S1/SvImJ) x PWK F1 hybrid embryos, unique PWK SNPs (compared with C57BL/6J and 129S1/SvImJ ) were masked as "N" in the reference genome. SNPsplit was used to assign the SNP-containing reads to the maternal and paternal genomes.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene

source_name: Preimplantation embryo

extract_protocol:
To generate F1 hybrid embryos, 8-12-week-old females of Eed fl/fl, Zp3-Cre/Eed fl/fl, Eed/Xist fl/fl, Zp3-Cre/Eed/Xist fl/fl were injected with 0.2 ml of CARD HyperOva followed by 7.5 I.U. of hCG at a 48 h interval. Cumulus–oocyte complexes (COCs) were harvested 15-17 hrs after hCG injection and inseminated with activated spermatozoa in HTF medium supplemented with 10 mg/ml bovine serum albumin (BSA, Merck Millipore 12657). Sperms were obtained from the caudal epididymis of adult PWK/PhJ mice [RBRC00213 (RIKEN Bioresource Research Center) originated from 003715 (the Jackson Laboratory)]. Spermatozoa were capacitated by 1 h incubation in CARD FERTIUP (Kyudo Co., Ltd., Japan). At 6 hrs post-insemination (hpi), zygotes with two pronuclei were transferred to KSOM and cultured in a humidified atmosphere with 5% CO2/95% air at 37.8°C. At 79 hpi, morula embryos were treated with Acidic Tyrode’s solution to remove zona pellucida, washed in M2 media (Merck Millipore, MR-015-D), and then washed in 0.2% BSA/PBS. Five embryos per sample were pooled in Eed matKO and WT embryos, and 13 embryos per sample were pooled in Eed/Xist matDKO and WT embryos.
RNA-seq libraries were prepared and sequenced as described previously (Mei et al. 2021). Briefly, cDNA was prepared by SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (TAKARA, 634890) according to the manufacturer’s instructions. Two hundred picograms of cDNA were used for the library construction by using Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1024) according to the manufacturer’s instructions.

value: C57BL/6 (129S1/SvImJ) x PWK

tag: developmental stage

value: morula

value: Eed/Xist double maternal knockout

value: Preimplantation embryo


title: cyno late blastocyst 4-28

status: Public on Jun 30 2022

type: SRA

city: Los Angeles

first: Kevin

last: Huang

state: CA

address: Gonda BLDG Rm. 6554, P.O.Box 957088

department: Human Genetics

country: USA

institute: UCLA

library_source: transcriptomic

data_processing:
Raw reads from the Illumina HiSeq2000 were mapped to the cynomolgus genome (GCA_000364345.1 Macaca_fascicularis_5.0) using default parameters in BWA
Mapped transcripts reads were transformed using the reads per kilobase per million (RPKM) metric
Genes with low expression were filtered out, followed by quantile normalization.
Genome_build: GCA_000364345.1 (GenBank assembly accession)
Supplementary_files_format_and_content: monkey_processed_RPKM.txt: matrix listing normalized RPKM

molecule: polyA RNA

organism: Macaca fascicularis

source_name: late blastocyst

growth_protocol: Single blastomeres were isolated by removing the zona pellucida using acidic tyrode solution (Sigma, cat. no. T1788), then separated by gentle mouth pipetting in a calcium-free medium.

extract_protocol:
RNA was isolated from single cells or single morula embryos and amplified as previously described
Library construction was performed following Illumina manufacturer suggestions.

treatment_protocol: Single cells were washed twice with 1x PBS containing 0.1% BSA before placing in lysis buffer.

tag: sample type

value: late blastocyst


title: F-HDAC-4.E04

city: Yokohama

first: Andrew

middle: Tae-Jun

last: Kwon

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: IMS

country: Japan

institute: RIKEN

description: C1 CAGE

data_processing:
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of   alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set

molecule: total RNA

organism: Homo sapiens

source_name: Dermal fibroblasts, neonatal

growth_protocol: Cells were cultured in DMEM high glucose medium supplemented with 10% inactivated fetal bovine serum, 100 U/mL penicillin, 100 ug/mL streptomycin, and 1 mM sodium pyruvate.

extract_protocol:
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).

treatment_protocol: Three treatment groups were made, with 1) untreated, 2) 1 uM TSA for 6 hours, and 3) 1 mM VPA for 6 hours.

tag: treatment

value: Control


title: cyno early blastocyst 4-3

source_name: early blastocyst

value: early blastocyst


title: WT.C4

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

data_processing:
Raw sequencing reads (in a FASTQ format) were trimmed of residual adaptor sequences using Scythe software. Low quality bases at the beginning or the end of sequencing reads were removed using sickle then the quality of remaining reads was confirmed with FastQC.
Reads were aligned to the Mus musculus genome reference (GRCm39/mm39) using STAR and per transcript reads were counted with HTSeq.
Differentiall expression analyses was performed using edgeR package in the context of limma/voom workflow.
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes ENSEMBL id and raw read counts for each transcript, in each sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was isolated for approximately 25 mg of liver tissue using RNeasy Mini kit (Cat# 74106) from Qiagen (Valencia, CA, USA) . RNA was quantified using Qubit RNA BR Assay kit (Cat# Q10211,ThermoScientific, Waltham, MA) in a Qubit3.0 fluorometer.
Library preparation was done using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) as per the manufacturers instructions. The library preparation and sequencing were performed by the Clinical Genomics Core at the Oklahoma Medical Research Foundation

treatment_protocol: Wild type (WT), MLKL knockout (MLKL KO or Mlkl-/-)  and Ripk3 knockout (Ripk3KO or Ripk3-/-) at 2 months of age were fed with normal chow (control diet) , CD-LFD or CD-HFD  diet for 6 months.  Liver was dissected out, RNA isolated using Qiagen RNeasy mini kit. 500 ng of RNA was used for RNA sequencing.

tag: genotype

value: WT

tag: diet

value: control diet

tag: tissue

value: liver


title: WT.LFD3

value: CD-LFD


title: RNA-seq morula Eed/Xist CTR rep1

tag: strain

value: wild type


title: cyno late blastocyst 4-32


title: cyno early blastocyst 2-2


title: F-HDAC-4.E01

description: C1 CAGE


title: WT.C2


title: RNA-seq morula Eed matKO rep1

value: Eed maternal knockout


title: RNA-seq morula Eed/Xist matDKO rep1


title: cyno early blastocyst 3-2


title: F-HDAC-4.D01

description: C1 CAGE


title: cyno early blastocyst 3-3


title: F-HDAC-4.D05

description: C1 CAGE


title: F-HDAC-4.D08

description: C1 CAGE


title: F-HDAC-4.D10

description: C1 CAGE


title: cyno early blastocyst 2-1


title: F-HDAC-4.D06

description: C1 CAGE


title: WT SI Tissue Rep 8

city: Glasgow

first: Kathryn

last: Gilroy

address: Garscube

country: United Kingdom

institute: CRUK Scotland Institute

description:
WT.8
Tissue harvested 4 days after induction.

data_processing:
Raw sequence quality was assessed using FastQC version 0.11.8, then sequences were trimmed to remove adaptor sequences and low-quality base calls, defined as those with a Phred score of less than 20, using Trim Galore version 0.6.4.
Trimmed sequences were aligned to mouse genome build GRCm38.98 using HISAT2 version 2.1.0.
Raw counts per gene were determined using FeatureCounts version 1.6.4 with the following options: --primary -C -t exon -g gene_id.
Genome_build: GRCm38.98
Supplementary_files_format_and_content: Raw_counts_A.AK.WT_SI.csv: Matrix of raw counts.

source_name: Small Intestine

extract_protocol:
1cm of proximal intestine was collected and dissociated using Precyllis homogeniser in b-ME in RLT buffer. RNA was extracted using Qiagen RNA extraction kit following manufacturer's instructions.
Libraries for cluster generation and DNA sequencing were prepared following a previously described method (Fisher et al. 2011) using TruSeq RNA sample prep kit v2 (Illumina).
The libraries were run on Illumina Next Seq using the High Output 75 cycles kit (2x36 cycles, paired end reads, single index).

tag: genetic background

value: VilCreER

value: Small Intestine

tag: time point

value: 4 days after induction


title: WT SI Tissue Rep 7

description:
WT.7
Tissue harvested 4 days after induction.


title: WT SI Tissue Rep 6

description:
WT.6
Tissue harvested 4 days after induction.


title: RNA-seq morula Eed/Xist CTR rep2


title: cyno late blastocyst 4-29


title: F-HDAC-4.C10

description: C1 CAGE

value: TSA


title: F-HDAC-4.C08

description: C1 CAGE

value: VPA


title: cyno late blastocyst 4-20


title: cyno late blastocyst 4-30


title: RNA-seq morula Eed matKO rep2

value: C57BL/6 (129S1/SvImJ) x PWK

value: morula


title: F-HDAC-4.D04

description: C1 CAGE


title: cyno late blastocyst 4-25


title: cyno late blastocyst 4-26


title: F-HDAC-4.D02

description: C1 CAGE


title: F-HDAC-4.D03

description: C1 CAGE


title: cyno late blastocyst 4-24


title: RNA-seq morula Eed CTR rep1

value: Preimplantation embryo


title: F-HDAC-4.C11

description: C1 CAGE


title: cyno late blastocyst 4-23

value: late blastocyst


title: RNA-seq morula Eed CTR rep2


title: F-HDAC-4.C12

description: C1 CAGE

value: Control


title: F-HDAC-4.C09

description: C1 CAGE


title: cyno late blastocyst 4-22


title: WT SI Tissue Rep 5

description:
WT.5
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-21


title: cyno late blastocyst 4-27


title: WT SI Tissue Rep 4

description:
WT.4
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-19


title: WT SI Tissue Rep 3

description:
WT.3
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-18


title: F-HDAC-4.C05

description: C1 CAGE


title: cyno late blastocyst 4-15


title: F-HDAC-4.C04

description: C1 CAGE


title: F-HDAC-4.C07

description: C1 CAGE


title: Apc Kras flox SI Tissue Rep 5

description:
Apc.Kras.5
AK.5
Tissue harvested 3 days after induction.

value: VilCreER Apc fl/fl KRasG12D/+

value: 3 days after induction


title: F-HDAC-4.C03

description: C1 CAGE


title: Apc Kras flox SI Tissue Rep 6

description:
Apc.Kras.6
AK.6
Tissue harvested 3 days after induction.


title: cyno late blastocyst 4-16


title: WT SI Tissue Rep 1

description:
WT.1
Tissue harvested 4 days after induction.


title: F-HDAC-4.B12

description: C1 CAGE


title: Apc Kras flox SI Tissue Rep 4

description:
Apc.Kras.4
AK.4
Tissue harvested 3 days after induction.


title: cyno late blastocyst 4-14


title: cyno late blastocyst 4-17


title: Apc Kras flox SI Tissue Rep 3

description:
Apc.Kras.3
AK.3
Tissue harvested 3 days after induction.


title: F-HDAC-4.C06

description: C1 CAGE


title: F-HDAC-4.C02

description: C1 CAGE


title: F-HDAC-4.C01

description: C1 CAGE


title: cyno late blastocyst 4-13


title: WT SI Tissue Rep 2

description:
WT.2
Tissue harvested 4 days after induction.


title: Apc Kras flox SI Tissue Rep 2

description:
Apc.Kras.2
AK.2
Tissue harvested 3 days after induction.


title: Apc Kras flox SI Tissue Rep 1

description:
Apc.Kras.1
AK.1
Tissue harvested 3 days after induction.


title: cyno late blastocyst 4-10


title: F-HDAC-4.B11

description: C1 CAGE


title: cyno late blastocyst 4-12


title: cyno late blastocyst 4-8


title: cyno late blastocyst 4-9


title: Apc flox SI Tissue Rep 19

description:
Apc.19
A.19
Tissue harvested 4 days after induction.

value: VilCreER Apc fl/fl


title: Apc flox SI Tissue Rep 18

description:
Apc.18
A.18
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-11


title: F-HDAC-4.B06

description: C1 CAGE


title: F-HDAC-4.B07

description: C1 CAGE


title: F-HDAC-4.B08

description: C1 CAGE


title: Apc flox SI Tissue Rep 16

description:
Apc.16
A.16
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-6


title: cyno late blastocyst 4-7


title: F-HDAC-4.B03

description: C1 CAGE


title: Apc flox SI Tissue Rep 14

description:
Apc.14
A.14
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 15

description:
Apc.15
A.15
Tissue harvested 4 days after induction.


title: F-HDAC-4.B09

description: C1 CAGE


title: F-HDAC-4.B02

description: C1 CAGE


title: F-HDAC-4.B04

description: C1 CAGE


title: Apc flox SI Tissue Rep 13

description:
Apc.13
A.13
Tissue harvested 4 days after induction.


title: cyno late blastocyst 4-3


title: cyno late blastocyst 4-2


title: cyno late blastocyst 4-5


title: cyno late blastocyst 4-1


title: F-HDAC-4.B10

description: C1 CAGE


title: Apc flox SI Tissue Rep 11

description:
Apc.11
A.11
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 12

description:
Apc.12
A.12
Tissue harvested 4 days after induction.


title: cyno late blastocyst 3-13


title: cyno late blastocyst 4-4


title: Apc flox SI Tissue Rep 10

description:
Apc.10
A.10
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 17

description:
Apc.17
A.17
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 9

description:
Apc.9
A.9
Tissue harvested 4 days after induction.


title: F-HDAC-4.A11

description: C1 CAGE


title: F-HDAC-4.A12

description: C1 CAGE


title: Apc flox SI Tissue Rep 8

description:
Apc.8
A.8
Tissue harvested 4 days after induction.


title: F-HDAC-4.A10

description: C1 CAGE


title: cyno late blastocyst 3-11


title: F-HDAC-4.A09

description: C1 CAGE


title: F-HDAC-4.A08

description: C1 CAGE


title: Apc flox SI Tissue Rep 7

description:
Apc.7
A.7
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 5

description:
Apc.5
A.5
Tissue harvested 4 days after induction.


title: F-HDAC-4.B01

description: C1 CAGE


title: Apc flox SI Tissue Rep 6

description:
Apc.6
A.6
Tissue harvested 4 days after induction.


title: cyno late blastocyst 3-12


title: cyno late blastocyst 3-10


title: cyno late blastocyst 3-8


title: F-HDAC-4.A06

description: C1 CAGE


title: cyno late blastocyst 3-6


title: Apc flox SI Tissue Rep 3

description:
Apc.3
A.3
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 2

description:
Apc.2
A.2
Tissue harvested 4 days after induction.


title: Apc flox SI Tissue Rep 4

description:
Apc.4
A.4
Tissue harvested 4 days after induction.


title: cyno late blastocyst 3-5


title: F-HDAC-4.A04

description: C1 CAGE


title: cyno late blastocyst 3-4


title: F-HDAC-4.A03

description: C1 CAGE


title: F-HDAC-4.A05

description: C1 CAGE


title: Apc flox SI Tissue Rep 1

description:
Apc.1
A.1
Tissue harvested 4 days after induction.


title: F-HDAC-4.A02

description: C1 CAGE


title: cyno late blastocyst 3-2


title: cyno late blastocyst 3-3


title: MPP4_WT_r2

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Raw sequencing reads were mapped to the mm10 genome using STAR and the UCSC KnownGene reference transcriptome.
Reads mapping to exons were summarized for each unique ENTREZ gene using the GenomicRanges package in R/Bioconductor and normalized to reads per kilobase per million (RPKM).  Genes were filtered for detection based on being expressed at greater than or equal to 5 reads per million in all samples for at least one group.
Genome_build: mm10
Supplementary_files_format_and_content: rpkm normalized values for all detected genes

source_name: Multipotent Progenitor

extract_protocol:
Cells were FACS sorted directly into RLT+1%Bme using the indicated markers. Total RNA was purified using the Quick-RNA MicroPrep Kit (Zymo Research)
All purified RNA was used as input for the SMART-seq v4 cDNA synthesis kit (Takara). Final libraries were constructed using 400 pg of cDNA as input for the NexteraXT kit with the NexteraXT indexing primers (Illumina).

tag: sorting markers

value: Lin-Neg cKit+ Sca1+ FLK2+

value: Wild Type

tag: tissue source

value: Bone marrow

tag: age

value: 12 weeks

tag: Sex

value: male


title: cyno late blastocyst 3-7


title: F-HDAC-4.B05

description: C1 CAGE


title: F-HDAC-4.A01

description: C1 CAGE


title: F-HDAC-3.H10

description: C1 CAGE


title: MPP4_WT_r1

value: female


title: cyno late blastocyst 2-1


title: F-HDAC-4.A07

description: C1 CAGE


title: cyno early blastocyst 1-9

value: early blastocyst


title: F-HDAC-3.H08

description: C1 CAGE


title: F-HDAC-3.H11

description: C1 CAGE


title: cyno early blastocyst 1-7


title: MPP4_WT_r3

value: 10 weeks


title: MPP4_HOMO_r4

value: ETV6 mt/mt


title: cyno early blastocyst 1-8


title: F-HDAC-3.H09

description: C1 CAGE


title: MPP4_HOMO_r3


title: cyno late blastocyst 3-1


title: HSC_WT_r3

source_name: Hematopoietic Stem Cell

value: Lin-Neg cKit+ Sca1+ FLK2-neg CD150+ CD38-neg


title: HSC_WT_r2


title: MPP4_HOMO_r1


title: HSC_WT_r1


title: cyno early blastocyst 1-6


title: F-HDAC-3.H12

description: C1 CAGE


title: F-HDAC-3.H05

description: C1 CAGE


title: F-HDAC-3.H07

description: C1 CAGE


title: cyno early blastocyst 1-4


title: F-HDAC-3.H06

description: C1 CAGE

value: VPA


title: HSC_HOMO_r3


title: cyno early blastocyst 1-3


title: cyno early blastocyst 1-5


title: HSC_HOMO_r2


title: F-HDAC-3.H04

description: C1 CAGE

value: TSA


title: cyno early blastocyst 1-2


title: F-HDAC-3.H02

description: C1 CAGE


title: F-HDAC-3.H03

description: C1 CAGE


title: F-HDAC-3.H01

description: C1 CAGE


title: HSC_HOMO_r1


title: cyno early blastocyst 1-10


title: CLP_WT_r2

source_name: Common Lymphoid Progenitor

value: Lin-Neg IL7+Flk2+ cKit-low Sca1-low


title: cyno late blastocyst 1-1

value: late blastocyst


title: F-HDAC-3.G11

description: C1 CAGE


title: cyno late blastocyst 1-3


title: cyno late blastocyst 1-2


title: cyno 44-cell-1-4

source_name: morula

value: morula


title: CLP_HOMO_r3


title: CLP_WT_r1


title: HSC_HOMO_r4


title: F-HDAC-3.G09

description: C1 CAGE

value: Control


title: cyno early blastocyst 1-1


title: CLP_WT_r3


title: cyno 44-cell-1-3


title: F-HDAC-3.G12

description: C1 CAGE


title: F-HDAC-3.G10

description: C1 CAGE


title: MPP4_HOMO_r2


title: cyno 44-cell-1-2


title: F-HDAC-3.G08

description: C1 CAGE


title: cyno late blastocyst 3-9


title: F-HDAC-3.G07

description: C1 CAGE


title: F-HDAC-3.G06

description: C1 CAGE


title: CLP_HOMO_r2


title: CLP_HOMO_r1


title: F-HDAC-3.G04

description: C1 CAGE


title: cyno 30-cell-1-7


title: cyno 44-cell-1-1


title: cyno 30-cell-1-6


title: CLP_HOMO_r4


title: F-HDAC-3.G03

description: C1 CAGE


title: cyno 30-cell-1-5


title: cyno 30-cell-1-4


title: cyno 30-cell-1-2


title: cyno 30-cell-1-3


title: cyno 30-cell-1-1


title: F-HDAC-3.G02

description: C1 CAGE


title: F-HDAC-3.F10

description: C1 CAGE


title: F-HDAC-3.G01

description: C1 CAGE


title: F-HDAC-3.F12

description: C1 CAGE


title: cyno 16-cell-1-4

source_name: 16-cell blastomere

value: 16-cell blastomere


title: F-HDAC-3.F11

description: C1 CAGE


title: cyno 16-cell-1-5


title: F-HDAC-3.F08

description: C1 CAGE


title: cyno 16-cell-1-3


title: cyno 16-cell-1-7


title: F-HDAC-3.F07

description: C1 CAGE


title: Adipocyte_ko_1152

city: New York

first: Robert

last: Bauer

state: NY

department: Medicine

institute: Columbia University Irving Medical Center

data_processing:
Illumina Real-Time Analysis used for base calling.
bcl2fastq2 (version 2.17) was used to convert BCL to fast format, coupled with adaptor trimming.
Sequenced reads were mapped to mouse UCSC/mm10 reference genome using STAR (2.5.2b) and featureCounts(v1.5.0-pe).
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each sample

source_name: Adipocytes

extract_protocol:
Adipocytes were isolated from subcutaneous adipose tissue via collagenase digestion, and RNA was extracted using the Rneasy Lipid Tissue Minikit. Livers were homogenized in TRIzol, and RNA was chloroform extracted. RNA quality was assessed via BioAnalyzer (RIN: Adipose (>6), Liver (>9)).
Poly-A pull-down was used to enrich mRNAs from total RNA samples, and RNA libraries were prepared using the Illumina TruSeq RNA prep kit for sequencing using Illumina NextSeq 500 at Columbia Genome Center.

value: Adipocytes

value: adipocyte-specific Trib1 ko

tag: gender

value: post natal day 70


title: cyno 16-cell-2-5


title: F-HDAC-3.F02

description: C1 CAGE


title: Adipocyte_wt_1153

value: wild-type


title: cyno 16-cell-1-6


title: Adipocyte_ko_1151

value: male


title: cyno 16-cell-2-4


title: F-HDAC-3.F09

description: C1 CAGE


title: F-HDAC-3.F05

description: C1 CAGE


title: Adipocyte_ko_1139

value: post natal day 76


title: F-HDAC-3.G05

description: C1 CAGE


title: Adipocyte_wt_1138


title: cyno 16-cell-2-1


title: F-HDAC-3.F06

description: C1 CAGE


title: cyno 16-cell-2-3


title: F-HDAC-3.F01

description: C1 CAGE


title: F-HDAC-3.F03

description: C1 CAGE


title: Adipocyte_wt_1135


title: cyno 16-cell-1-2


title: cyno 12-cell-1-3

source_name: 12-cell blastomere

value: 12-cell blastomere


title: cyno 16-cell-2-2


title: cyno 12-cell-1-1


title: F-HDAC-3.F04

description: C1 CAGE


title: cyno 16-cell-1-1


title: cyno 12-cell-1-2


title: Adipocyte_wt_1136


title: Liver_wt_1153

source_name: Liver

value: Liver


title: Adipocyte_ko_1137


title: Liver_ko_1151


title: Liver_ko_1152


title: Liver_ko_1139


title: F-HDAC-3.E11

description: C1 CAGE


title: Liver_wt_1138


title: F-HDAC-3.E10

description: C1 CAGE


title: cyno 8-cell-2-1

source_name: 8-cell blastomere

value: 8-cell blastomere


title: F-HDAC-3.E06

description: C1 CAGE


title: cyno 8-cell-1-3


title: F-HDAC-3.E07

description: C1 CAGE


title: F-HDAC-3.E12

description: C1 CAGE


title: F-HDAC-3.E09

description: C1 CAGE


title: F-HDAC-3.E08

description: C1 CAGE


title: F-HDAC-3.E05

description: C1 CAGE


title: cyno 8-cell-2-4


title: Liver_ko_1137


title: F-HDAC-3.E02

description: C1 CAGE


title: cyno 8-cell-1-2


title: cyno 8-cell-1-1


title: cyno 8-cell-2-6


title: F-HDAC-3.E03

description: C1 CAGE


title: F-HDAC-3.E04

description: C1 CAGE


title: Liver_wt_1135


title: F-HDAC-3.E01

description: C1 CAGE


title: cyno 4-cell-2-2

source_name: 4-cell blastomere

value: 4-cell blastomere


title: cyno 4-cell-2-3


title: Liver_wt_1136


title: F-HDAC-3.D11

description: C1 CAGE


title: p31_vldlrKO_S4

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

country: Germany

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the mouse reference genome (Gencode, version M25) with RNA STAR Galaxy Version 2.7.5b (default parameters) using the Gencode main annotation file (Gencode, version M25).
Reads mapped to the mouse reference genome were counted using feature-Counts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation file.
The output of featureCounts was imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols were determined based on ENSEMBL release 101 (Mouse genes, download on 10/04/2020). Genes with 0 reads in all samples were removed from the analysis. Having confirmed distinct clustering of all 4 groups in t-distributed stochastic neighbor embedding (t-SNE) plots, differential gene expression was analyzed using the R package DESeq2 Version 1.22.2 (default parameters except using type = "iterate" in estimateSizeFactors). Transcripts with log2fold change (log2FC) > 1.5 or < -1.5 and Benjamini-Hochberg adjusted p-value < 0.05 were considered as differentially expressed genes (DEG). Gene enrichment analysis was performed using the R package cluster-Profiler 3.10.1 . Heatmaps and Venn diagrams were created using the R package ComplexHeatmap 1.20.0 and VennDiagram 1.6.20, respectively. Other data visualization was performed using the ggplot2 package.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts and statistics

source_name: p31 vldrlKO

extract_protocol: The sorting protocol is: CD45lowCD11b+Ly6C-Ly6G-Tom+

tag: cell type

value: retinal microglia

value: vldrlKO


title: cyno 4-cell-2-1


title: p31_vldlrKO_S5


title: cyno 4-cell-1-3


title: cyno 4-cell-1-2


title: cyno 4-cell-1-1


title: F-HDAC-3.D09

description: C1 CAGE

value: TSA


title: p31_control_S5

source_name: p31 control

value: control


title: F-HDAC-3.D07

description: C1 CAGE

value: VPA


title: p31_vldlrKO_S1


title: cyno 2-cell-2-2

source_name: 2-cell blastomere

value: 2-cell blastomere


title: F-HDAC-3.D08

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal


title: p31_control_S3


title: cyno 2-cell-1-2


title: cyno 2-cell-1-1


title: F-HDAC-3.D04

description: C1 CAGE


title: p17_vldlrKO_S5

source_name: p17 vldrlKO


title: F-HDAC-3.D10

description: C1 CAGE


title: Dissolved oxygen excess iron 63% rep3

city: Bethesda

first: Ashish

middle: K

last: Sharma

state: MD

address: 14 Service Rd West Building 14A Room 176 MS-5522

department: National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)

institute: National Institute of Health

data_processing:
bcl2fastq2 (Version 2.20)
Fastq Quality Score ASCII Qscore Offset 33
Partek Flow, Partek genomics suite version 7
Bowtie2 aligner
Transcripts per Million (TPM) normalization method
differential gene expression analysis using the analysis of variance (ANOVA) model
Assembly: ecoli_536
Supplementary files format and content: Excel file includes processed data with following information 1. Gene ID, 2.Transcript ID, 3. P-value, 4. FDR step up, 5. Ratio, 6. Fold change, 7. LSMean, 8. P-value, 9. FDR step up

organism: Escherichia coli

source_name: wt

extract_protocol:
Total RNA was isolated from the frozen cells in Trizol samples using the hot phenol method.
The ribosomal RNA was depleted from the purified total RNA by using the RiboMinus Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA, USA). The RNA-seq libraries were prepared using the NEBNext® Ultra™ RNA Library Prep Kit (NEB, Ipswich, MA, USA).

value: wt

value: Iron excess condition


title: Dissolved oxygen excess iron 63% rep1


title: p31_control_S1


title: p17_vldlrKO_S2


title: p31_control_S2


title: F-HDAC-3.D05

description: C1 CAGE

value: Control


title: cyno 2-cell-2-1


title: Dissolved oxygen excess iron 21% rep2


title: F-HDAC-3.C11

description: C1 CAGE


title: p31_vldlrKO_S3


title: F-HDAC-3.C12

description: C1 CAGE


title: F-HDAC-3.D03

description: C1 CAGE


title: p31_control_S4


title: F-HDAC-3.D12

description: C1 CAGE


title: p17_vldlrKO_S4


title: F-HDAC-3.D02

description: C1 CAGE


title: F-HDAC-3.C09

description: C1 CAGE


title: Dissolved oxygen excess iron 63% rep2


title: Dissolved oxygen excess iron 21% rep3


title: p31_vldlrKO_S2


title: p17_control_S7

source_name: p17 control


title: p17_vldlrKO_S3


title: Dissolved oxygen excess iron 6.3% rep2


title: F-HDAC-3.D06

description: C1 CAGE


title: F-HDAC-3.C06

description: C1 CAGE


title: p17_control_S3


title: p17_vldlrKO_S1


title: Dissolved oxygen excess iron 6.3% rep3


title: Dissolved oxygen excess iron 21% rep1


title: p17_control_S1


title: Dissolved oxygen excess iron 6.3% rep1


title: F-HDAC-3.C08

description: C1 CAGE


title: F-HDAC-3.C04

description: C1 CAGE


title: p17_control_S6


title: F-HDAC-3.C02

description: C1 CAGE


title: p17_control_S5


title: p17_control_S4


title: Dissolved oxygen limited iron 21% rep3

value: Limited Iron condition


title: F-HDAC-3.C10

description: C1 CAGE


title: F-HDAC-3.C07

description: C1 CAGE


title: Dissolved oxygen limited iron 6.3% rep3


title: Dissolved oxygen limited iron 63% rep2


title: F-HDAC-3.D01

description: C1 CAGE


title: Dissolved oxygen limited iron 63% rep3


title: Dissolved oxygen limited iron 63% rep1


title: Mouse_Control_S1

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human (hg38) or mouse (mm10) Galaxy built-in reference genome with RNA STAR Galaxy Version 2.6.0b-2 using Gencode annotation files (human: Gencode 31, release June 2019, https://www.gencodegenes.org/human/releases.html, mouse: Gencode M22, release June 2019, https://www.gencodegenes.org/mouse/releases.html).
Reads mapped to the human or mouse reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation files
The outputs of featureCounts were imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL database (human genes, GRCh38.p12, download on 08/31/2019, mouse genes GRCm38.p6, download on 08/25/2019). Ortholog genes were determined based on ENSEMBL one-to-one orthologs (download on 10/03/19). After principle component analysis, differential gene expression was analyzed using the R package DESeq2 1.22.2 with default parameters (Benjamini-Hochberg adjusted p-value). Transcripts with log2fold change (log2FC) > 0.5 or < -0.5 and adjusted p-value < 0.05 were considered as differentially expressed genes (DEG). Heatmaps were created with the R package ComplexHeatmap 1.20.0. Gene enrichment analysis and its visualization with dotplots and cnetplots was done using the R package clusterProfiler 3.10.1. Other data visualization was performed using the ggplot2 package.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: data.csv

source_name: Mouse Control

extract_protocol:
RNA isolation from FFPE specimens was carried out as previously described. Briefly, total RNA was extracted from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, California). Following DNAse I digestion using the Baseline-ZERO Kit (Epicentre, Madison, Wisconsin), the RNA concentration was quantified using the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, Carlsbad, California). RNA quality was determined via the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, Massachusetts).
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3’ RNA sequencing method, as previously described. We recently demonstrated that MACE allows sequencing of FFPE samples with high accuracy. Briefly, 20 barcoded libraries comprising unique molecule identifiers (six mouse CNV mem-branes, six mouse RPE-choroidal control samples, four human CNV membranes and four human RPE-choroidal control tissues) were sequenced on the NextSeq 500 (Illumina) with 1 × 75 bp. PCR bias was removed using unique molecular iden-tifier.

value: RPE/choroid control


title: Mouse_Control_S6


title: F-HDAC-3.B10

description: C1 CAGE


title: Dissolved oxygen limited iron 21% rep2


title: F-HDAC-3.B09

description: C1 CAGE


title: Mouse_CNV_S6

source_name: Mouse CNV

value: CNV


title: Mouse_Control_S5


title: Dissolved oxygen limited iron 21% rep1


title: F-HDAC-3.C05

description: C1 CAGE


title: FAPs, Bap1, cKO

city: Seoul

first: Kyusang

last: Yoo

address: 1 Gwanak-ro, Gwanak-gu

department: Biological Sciences Department

country: South Korea

institute: Seoul National University

data_processing:
Illumina HiSeq Control Software (HCS) HD 3.5.7.0 was used for the data acquistion on the sequencing instrument.
Basecalling was performed with the Illumina Real-Time Analysis (RTA) software 2.7.7., and Fastqc v.0.11.7 was used for QC by Phred scoring.
BCL to fastq file conversion was performed with bcl2fastq v2.20.0 by running mkfastq on CellRanger 3.1.0 with the default settings as parameters.
CellRanger(3.1.0) count was run to generate aligned and demultiplexed BAM files using mouse genome build mm10-3.0.0., and subsequent 10X format output was generated (matrix.mtx, features.tsv, barcode.tsv)
10X format output were loaded onto R 3.6.1, and Seurat package 3.2.1 was used for further clearing of the data and downstream analyses including dead cell removal, doublet cell gating out, normalization, filtering-out non-FAPs by gene expression, variable gene selection, cell cycle regression, PCA, UMAP clustering and DEG analyses.
Genome_build: mm10
Supplementary_files_format_and_content: csv files with genes as rows, columns as individual cells(barcodes) and values in raw counts

source_name: limb muscles

extract_protocol:
Limb muscles were removed from each genotype of mice and dissected and mechanically dissociated in Dulbecco’s modified Eagle’s medium (DMEM) containing 10% horse serum (Hyclone, Logan, UT, USA), collagenase II (800 units/mL; Worthington, Lakewood, NJ, USA), and dispase (1.1 units/mL; ThermoFisher Scientific, Waltham, MA, USA) at 37°C for 40 min. Digested suspensions were subsequently triturated by sterilized syringe with 20G1/2 needle (BD Biosciences, Franklin Lakes, NJ, USA) and washed with DMEM to harvest mononuclear cells. Mononuclear cells were stained with anti-CD45-APC, anti-CD31-APC, anti-Sca1-FITC, anti-Vcam1-biotin and streptavidin-PE/Cy7. To exclude dead cells, 7AAD (Sigma aldrich; St. Louis, MO, USA) was used prior to FACS sorting. 7AAD–Lin–Vcam–Sca1+ FAPs were isolated using a FACS Aria III cell sorter (BD Biosciences) with 4-way-purity precision. Isotype control density plots were used as a reference for positive gating.
Libraries for each genotype of FAPs were generated with the 10X Genomics Chromium Next GEM Single Cell 3p RNA library v3.1 kit, following the manufacturer’s instructions, and a total of 5,000 cells were targeted for recovery from each genotype of FAPs. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: limb muscle

value: Lin-Vcam1-Sca1+ fibro/adipogenic progenitors (FAPs)


title: F-HDAC-3.B12

description: C1 CAGE


title: Mouse_CNV_S5


title: Mouse_Control_S3


title: F-HDAC-3.C01

description: C1 CAGE


title: F-HDAC-3.B08

description: C1 CAGE


title: Dissolved oxygen limited iron 6.3% rep2


title: Mouse_Control_S2


title: F-HDAC-3.B06

description: C1 CAGE


title: Mouse_CNV_S3


title: EZH2 Wild-Type

city: LEXINGTON

first: Aria

last: Byrd

state: Kentucky

address: 2865 Middlesex Way

institute: University of Kentucky

data_processing:
Programming language - R version 4.0.0
Programming platform - Rstudio IDE version 1.4
Single cell RNA-seq data analysis using Seurat version 3.2; 1. Quality control on the gene count matrices of samples 2. Samples merging and feature selection 3. Dimension reduction and clustering 4. Cell type identification
Differential gene expression analysis using MAST version 1.16
Trajectory inference using Slingshot version 1.8
Supplementary_files_format_and_content: cloupe

source_name: Mouse Lung Organoid Cells

growth_protocol: Bronchioalveolar stem cells and alveolar type 2 cells were sorted from doxycycline-naïve, conditional Ezh2 knockout mice, then plated with neonatal mouse lung endothelial cells in air-liquid-interface Matrigel cultures. Cultures were passaged as needed, then those with sufficient cells were dispased, collected, trypsinized, sorted for GFP+ cells, and seeded at equal densities to grow for 4 weeks.  After 4 weeks, cultures were dispased, collected, trypsinized and re-sorted for GFP+ cells for scRNAseq analysis.

extract_protocol:
Single cells were captured using a 10x Genomics platform.
Library chemistry was the Single Cell 3' v3 and preparation was performed by the University of Kentucky College or Arts and Sciences Imaging Center

treatment_protocol: 100-200 ng/mL of Doxycyclin was added to the cultures approximately 5 days after plating.

value: Lung

value: At least 6 weeks old

tag: development stage

value: Adult

value: EZH2 Wild-Type


title: F-HDAC-3.B11

description: C1 CAGE


title: p17_control_S2

value: retinal microglia


title: F-HDAC-3.B05

description: C1 CAGE

value: TSA


title: Mouse_CNV_S1


title: Dissolved oxygen limited iron 6.3% rep1


title: flHSC-8

city: Guangzhou

first: Jinyong

last: Wang

state: GuangDong

address: 190 Kai Yuan Avenue, Science Park, Guangzhou, China

country: China

institute: Guangzhou Institutes of Biomedicine and Health (GIBH)

data_processing:
Bcl2fastq (verison 2.16.0.10) convert .bcl files into fastq files
Fastq files were aligned to mm10 genome.*.ht2 files to generate *.sam file by HISAT2 (version 2.1.0). And the used samtools (version 0.1.19) to convert and sort the sam file to bam file. StringTie (version 1.3.4) were used to calculated genes expression level in TPM.
Gene expression levels in TPM of different samples were normalized by Stringtie.
Genome_build: mm10

source_name: Bone Marrow

growth_protocol: Single cell from adult wild type HSC (BM HSC, Hoxb5LSL/+ mice, 8weeks old), fetal liver HSC (fl-HSC, Hoxb5LSL/+ mice, Day14.5, defined as CD45.2+Lin-Sca1+c-Kit+Mac1+CD150+), wild type MPP (WT-MPP, Hoxb5LSL/+ mice, 8 weeks old) and donor-derived CD48+Mac-1+ SK cells (Primary recipients, week 8th post-transplantation) were sorted by FACS.

extract_protocol: The qualified samples were used to prepare the sequencing library by the TruePrep DNA Library Prep Kit V2 (Vazyme)

treatment_protocol: The cDNA were generated by Discover-sc WTA Kit V2 (Vazyme)

value: fetal liver HSC


title: Mouse_Control_S4


title: flHSC-7


title: F-HDAC-3.A11

description: C1 CAGE


title: F-HDAC-3.A12

description: C1 CAGE


title: Mouse_CNV_S4


title: F-HDAC-3.B07

description: C1 CAGE


title: F-HDAC-3.C03

description: C1 CAGE


title: EZH2 Heterozygous

value: EZH2 Heterozygous


title: F-HDAC-3.A09

description: C1 CAGE


title: F-HDAC-3.B03

description: C1 CAGE


title: EZH2 Null

value: EZH2 Null


title: F-HDAC-3.A08

description: C1 CAGE


title: FAPs, Bap1, WT


title: Mouse_CNV_S2


title: flHSC-9


title: F-HDAC-3.B01

description: C1 CAGE

value: VPA


title: F-HDAC-3.A07

description: C1 CAGE


title: flHSC-52


title: F-HDAC-3.B04

description: C1 CAGE


title: F-HDAC-3.B02

description: C1 CAGE


title: flHSC-4


title: F-HDAC-3.A05

description: C1 CAGE


title: flHSC-6


title: flHSC-5


title: flHSC-56


title: flHSC-49


title: flHSC-54


title: F-HDAC-3.A03

description: C1 CAGE


title: flHSC-53


title: F-HDAC-3.A10

description: C1 CAGE


title: flHSC-51


title: F-HDAC-3.A06

description: C1 CAGE


title: flHSC-55


title: HSSY_SSX_input

city: Edinburgh

first: Nezha

middle: Suzanne

last: Benabdallah

state: Midlothian

address: Crewe Road South

department: Institute of Genetics and Cancer

institute: University of Edinburgh

library_source: genomic

data_processing:
Raw reads were trimmed for quality and Illumina adapter sequences using trim-galore
then aligned to the human genome assembly hg38 using Bowtie 2 (Langmead and Salzberg, 2012; Langmead et al., 2009) (with “--very-sensitive” option)
ChIP signals were normalised to their respective inputs using the pileup function from MACS2 (Feng et al., 2012; Zhang et al., 2008) using corresponding input for background normalization
To visualize ChIP-Seq tracks, normalized bigWig files were generated with ucsc-wigtobigwig tool
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: HS-SY-II

growth_protocol: DMEM, 10% fetal bovine serum and cultured at 37C at 5% CO2.

extract_protocol:
HS-SY-II cells were pre-fixed for 20 minutes with 1.5mM ethylene glycol bis(succinimidyl succinate) (EGS) (Thermo Scientific) and then fixed with 1% formaldehyde for 15min and the cross-linking reaction was stopped by adding 125mM of glycine. Cells were washed twice with cold PBS and lysed in swelling buffer (150mM NaCl, 1%v/v Nonidet P-40, 0.5% w/v deoxycholate, 0.1% w/v SDS, 50mM Tris pH8, 5mM EDTA) supplemented with protease inhibitors. Cell lysates were sonicated using Covaris E220 Sonicator to generate fragments less than 400 bp. Sonicated lysates were centrifuged and incubated overnight at 4°C with HA-tag Abcam 9110. Immunocomplexes were recovered by incubation with 30ul protein A/G magnetic beads (Thermofisher) for 2h at 4°C. Beads were sequentially washed twice with RIPA buffer and finally TE buffer
DNA fragments obtained after ChIP were quantified using Qubit dsDNA HS Assay Kit (Invitrogen). 5ng of DNA was used for libraries preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S), SPRIselect beads (Beckman Coulter, #B23317) and NEBNext Multiplex Oligos for Illumina (NEB, Set 1 #E7335S, Set 2 #E7500S). ChIP libraries were done following NEB’s guidelines (NEB, E7645S)

treatment_protocol: Cell were transduced with MSCV-HA-EGFP-PGK-Puro, MSCV-HA-EGFP-SSX-C-PGK-Puro or MSCV-HA-EGFP-SSX-C-DeltaRD-PGK-Puro was performed following puromycin selection and collected 6 days following transduction.

tag: cell line

value: HS-SY-II

value: Human synovial sarcoma cells

tag: chip antibody

value: retroviral insertion of HA-eGFP-SSX-C


title: HSSY_SSX_HA

value: HA-tag Abcam 9110


title: F-HDAC-3.A01

description: C1 CAGE


title: flHSC-50


title: flHSC-45


title: HSSY, eGFP, input

value: retroviral insertion of HA-eGFP


title: F-HDAC-2.H11

description: C1 CAGE


title: F-HDAC-3.A04

description: C1 CAGE

value: Control


title: HSSY_SSXDeltaRD_HA

value: retroviral insertion of HA-eGFP-SSX-C-DeltaRD


title: F-HDAC-3.A02

description: C1 CAGE


title: HSSY_SSXDeltaRD_input


title: Sample_06_tumor

city: Rozzano

first: Alberto

last: Termanini

state: MI

address: Via Manzoni, 113

country: Italy

institute: Istituto Clinico Humanitas

data_processing:
Raw blc files were converted into fastq files using the Cell Ranger pipeline suite of 10X Genomics (version 3.0.1).
The CellRanger analysis pipeline was used to generate a digital gene expression matrix starting from raw data.
Gene expression matrices were used as input for Seurat R package (R v3.6.1; Seurat v3.0.3)
Genome_build: Pre-build Human genome (version GRCh38) was used as genome reference and was provided as part of the CellRanger pipeline as a compatible transcriptome reference.
Supplementary_files_format_and_content: UMI counts per gene per cell

source_name: intrahepatic tissue

growth_protocol: not applicable

extract_protocol:
Tissue was collected in 5ml of RPMI media. Further disaggregation of tissue into a single-cell solution for sequencing was completed using the MACs tumor dissociation kit (Miltenyi Biotec) with the standard tough tumor protocol. Brieﬂy, the MACs tumor dissociation kit enzyme mix (300μl) was added to each sample. Next, samples were put into the gentleMACs Dissociator and ran through the tough tumor program. The cell suspension was then applied to a 70um cell strainer. Cells were pelleted, counted and frozen according to the slow freezing procedure in standard cryo-vials (1 ml cell suspension in the cryopreservation medium). Next, the cells were thawed, washed in PBS, stained with Live/dead Aqua Fluorescent Reactive Dye (Life Technologies) and anti-mouse CD45 antibody (30-F11, BD Biosciences) at 4°C for 20 minutes and sorted on a FACS Aria III (BD Biosciences) with a 100µm nozzle. Purity of live CD45+/CD45- cells was assessed after sorting, prior to downstream use.
CD45+/CD45- cells were resuspended in 1ml PBS plus 0.04% BSA and washed two times by centrifugation at 450 rcf for 7min. After the second wash cells were resuspended in 30 ul and counted with an automatic cell counter (Countess II, Thermo Fisher) to get a precise estimation of total number of cells recovered.   Afterwards CD45+/CD45- cells of each sample were loaded into one channel of the Single Cell Chip A using the Single Cell 3’ v2 single cell reagent kit (10X Genomics) for Gel bead Emulsion generation into the Chromium system. Following capture and lysis, cDNA was synthesized and amplified for 14 cycles following the manufacturer’s protocol (10X Genomics). 50 ng of the amplified cDNA were then used for each sample to construct Illumina sequencing libraries. Sequencing was performed on the NextSeq500 Illumina sequencing platform following 10x Genomics instruction for reads generation.

treatment_protocol: not applicable

value: CD45+ cells

value: intrahepatic tissue

tag: tissue type

value: tumoral tissue

tag: disease state

value: intrahepatic cholangiocarcinoma


title: flHSC-47


title: flHSC-48


title: F-HDAC-2.H12

description: C1 CAGE

tag: treatment


title: F-HDAC-2.H10

description: C1 CAGE


title: Sample_04_tumor


title: flHSC-41


title: Sample_02_tumor

value: CD45+/CD45- cells


title: Sample_03_tumor


title: flHSC-44


title: flHSC-43


title: Sample_01_tumor


title: Sample_05_tumor


title: F-HDAC-2.H09

description: C1 CAGE


title: flHSC-39


title: F-HDAC-2.H05

description: C1 CAGE


title: flHSC-3


title: F-HDAC-2.H08

description: C1 CAGE


title: Sample_04_healthy

value: Normal tissue adjcent to tumor


title: flHSC-46

value: fetal liver HSC


title: Sample_05_healthy


title: flHSC-36


title: flHSC-42


title: Sample_06_healthy


title: flHSC-38


title: HSSY, eGFP, HA

tag: genotype


title: flHSC-40


title: F-HDAC-2.H07

description: C1 CAGE


title: Sample_01_healthy

tag: tissue


title: F-HDAC-2.G12

description: C1 CAGE


title: F-HDAC-2.G11

description: C1 CAGE


title: F-HDAC-2.H02

description: C1 CAGE


title: F-HDAC-2.H03

description: C1 CAGE

value: TSA


title: flHSC-32

tag: strain


title: Sample_03_healthy


title: flHSC-37


title: F-HDAC-2.H01

description: C1 CAGE


title: F-HDAC-2.G08

description: C1 CAGE


title: Sample_02_MEOX

data_processing:
After demultiplexing with bcl2fastq v2.20 (Illumina, Inc.), quality control checks on raw sequencing data were performed with FastQC v0.11.8.
Adapters removal and dynamic trimming of low-quality bases were performed using Trimmomatic v0.39 (Bolger et al., 2014) with parameters “ILLUMINACLIP:TruSeq2-SE.fa:2:30:10, LEADING:30, MAXINFO:50:0.7, MINLEN:40”.
Single-end reads were aligned to the UCSC hg38 human genome using STAR v2.7.0f (Dobin et al., 2013) with parameters “--outSAMtype BAM SortedByCoordinate, --outFilterMultimapNmax 20, --outWigType wiggle, --outWigNorm RPM”.
Wiggle files were converted to bigWig files using wigToBigWig v2.8 from UCSC tools.
Genome_build: hg38
Supplementary_files_format_and_content: bigWig files RPM normalized

source_name: peripheral blood

growth_protocol: PBMCs were isolated from buffy coats from healthy donors via density-gradient separation and cryopreserved in FBS supplemented with 10% DMSO. T regulatory (Treg) cells were enriched using an EasySep Human CD4+CD127lowCD25+ Regulatory T cell Isolation kit.

extract_protocol:
RNA isolation of the FACS-purified GFP+ Treg cells was performed following the manufacturer’s protocol using the Quick-RNA Microprep kit (Zymo Research). RNA quality control was performed with the Agilent 2200 Tape Station system and only RNAs having a RIN >8 were used for library preparation.
Libraries for mRNA sequencing were prepared starting from 10 ng tot RNA for each sample by using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech-Takara)

treatment_protocol: Purified Treg cells were stimulated with dynabeads human T-ACT CD3/CD28 beads:cells ratio 1:2, in 96 U-bottomed wells plates and in the presence of IL-2 cytokine (50 ng/mL each). 24h and 48h after stimulation cells were infected with lentiviral particles harboring a custom human ORF for MEOX1 (Sigma-Aldrich, Mission TRC3) or empty backbone-vectors (CTRL), both expressing GFP (Sigma-Aldrich). Cells were cultured for additional 5 days and then stained with fluorochrome-conjugated monoclonal antibodies (CD3-BUV496, CD25-APCR700, CD4 BV570, CD8-BV786, CD127-PE-Cy5) from commercial vendors. Dead cells were excluded from all analyses using Zombie Aqua (BioLegend). GFP+ cells pregated as CD3+CD8-CD4+Aqua-CD25+CD127- were isolated with a FACSAria cell sorter (BD Biosciences).

value: Treg cells

value: peripheral blood

value: MEOX1 overexpression

value: healty donor


title: Sample_01_MEOX


title: F-HDAC-2.G06

description: C1 CAGE


title: flHSC-2


title: Sample_02_healthy


title: Sample_03_MEOX


title: flHSC-34


title: F-HDAC-2.H04

description: C1 CAGE


title: flHSC-29


title: flHSC-35


title: flHSC-28


title: flHSC-30


title: Sample_02_NHE

value: control


title: flHSC-31


title: flHSC-33


title: F-HDAC-2.G09

description: C1 CAGE

value: VPA


title: F-HDAC-2.G10

description: C1 CAGE


title: Sample_03_NHE


title: M22-

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

data_processing:
Base calling:  RTA-2.4.11
FASTQ generation:  bcl2fastq-2.9.1
RNA-Seq Alignment (BaseSpace Workflow) 1.1.0
Cufflinks Assembly & DE (BaseSpace Workflow) 2.1.0
Isis (Analysis Software) 2.6.25.18
STAR (Aligner) STAR_2.5.0b
Cufflinks 2.2.1
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited gene-level differential expression output from Cuffdiff

source_name: Huh7 cell clone containing G398S A1CF inducible expression construct without doxycycline

extract_protocol: Ilumina TruSeq Stranded Total RNA with Ribo-Zero Globin

value: Huh7 hepatoma cells


title: F-HDAC-2.G05

description: C1 CAGE

value: Control


title: F-HDAC-2.G07

description: C1 CAGE


title: M21-


title: F-HDAC-2.H06

description: C1 CAGE


title: flHSC-26


title: Sample_01_NHE


title: M2D3

source_name: Huh7 cell clone containing G398S A1CF inducible expression construct induced with doxycycline


title: flHSC-25


title: M23-


title: flHSC-24


title: F-HDAC-2.F12

description: C1 CAGE


title: F-HDAC-2.F10

description: C1 CAGE


title: FS72_WT-

source_name: Huh7 cell clone containing WT A1CF inducible expression construct without doxycycline


title: F-HDAC-2.G04

description: C1 CAGE


title: F-HDAC-2.G02

description: C1 CAGE


title: M2D1


title: flHSC-20


title: F-HDAC-2.F09

description: C1 CAGE


title: F-HDAC-2.F11

description: C1 CAGE


title: FS73_WT-


title: F-HDAC-2.G03

description: C1 CAGE


title: F-HDAC-2.F06

description: C1 CAGE


title: flHSC-1


title: flHSC-21


title: flHSC-27


title: F-HDAC-2.F07

description: C1 CAGE


title: flHSC-22


title: FS71_WT-D1

source_name: Huh7 cell clone containing WT A1CF inducible expression construct induced with doxycycline


title: FS71_WT-D3


title: F-HDAC-2.F04

description: C1 CAGE


title: FS71_WT-


title: T. denticola_infected_Biorep_6

city: Richmond

first: Daniel

last: Miller

state: Virginia

address: 1101 E. Marshall St. Sanger Hall 5-009

institute: Virginia Commonwealth University

data_processing:
Quality scores were tested by fastqc. None of the raw sequences was trimed because all of the samples have quality scores above 28.
Sequences were aligned to the transcript of homo sapiens by bowtie2 using GCF_000001405.39_GRCh38.p13_rna as the template.
The .sam files generated by bowtie2 were converted to .bam using samtools.
The .bam files were converted to a FPKM table using 'Rsamtools' package in R.
Assembly: GCF_000001405.39_GRCh38.p13_rna
Supplementary files format and content: matrix table with reads counts for each gene from all samples and a Tab-delimited file with FPKM

source_name: Gingival Keratinocyte

growth_protocol: HIGK cells used in this study were at passage 30, grown in Lifeline DermaLike K complete media

extract_protocol:
Total RNA was isolated from 6 biological replicates for both conditions using the Qiagen Rneasy Plus Mini kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HIGK cells were seeded on 6 well tissue culture plates to ~50-70% confluency. Cells were either left untreated or infected with an MOI of 100 of Treponema denticola ATCC 35405 for 6 hours. After infection, wells were washed and fresh media was applied and the cells were allowed to incubate for another 18 hours post-infection.

value: HPV 16-immortalized gingival keratinocytes (HIGK)

value: T. denticola ATCC 35405 Infected


title: T. denticola_infected_Biorep_5


title: flHSC-17


title: F-HDAC-2.F03

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal


title: flHSC-16


title: T. denticola_infected_Biorep_4


title: flHSC-19


title: F-HDAC-2.F08

description: C1 CAGE


title: flHSC-14


title: T. denticola_infected_Biorep_2


title: F-HDAC-2.F01

description: C1 CAGE


title: flHSC-13


title: F-HDAC-2.G01

description: C1 CAGE


title: F-HDAC-2.F05

description: C1 CAGE


title: T. denticola_infected_Biorep_3


title: F-HDAC-2.E11

description: C1 CAGE


title: Uninfected_Biorep_6

value: Uninfected


title: flHSC-23


title: M2D2


title: flHSC-11


title: F-HDAC-2.E09

description: C1 CAGE


title: flHSC-18


title: flHSC-10


title: BM-MPP-9

value: bone marrow MPP


title: F-HDAC-2.E07

description: C1 CAGE


title: BM-MPP-8


title: Uninfected_Biorep_2


title: F-HDAC-2.F02

description: C1 CAGE


title: F-HDAC-2.E12

description: C1 CAGE


title: Uninfected_Biorep_5


title: flHSC-15


title: T. denticola_infected_Biorep_1


title: BM-MPP-5


title: flHSC-12


title: F-HDAC-2.E03

description: C1 CAGE


title: F-HDAC-2.E10

description: C1 CAGE


title: BM-MPP-42


title: F-HDAC-2.E02

description: C1 CAGE


title: SAS input DNA

city: Chiba

first: Tomoaki

last: Saito

address: 1-8-1 Inohana, Chuo-ku

department: Oral Science

institute: Chiba University

data_processing:
Sequences: Standard Illumina software base-calling and quality-control filtering was applied
Sequences (75 nt reads, single end) were aligned to the mouse genome (mm10) using the BWA algorithm (v0.7.12, default parameters).
Aligns were extended in silico at their 3’-ends to a length of 200 bp, which is the average genomic fragment length in the size-selected library, and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWIG files.
Peak locations were determined using the MACS algorithm (v2.1.0) with a cutoff of pvalue = 1E-7.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations
Assembly: mm10
Supplementary files format and content: BW = signal map in bigWIG format (UCSC)
Supplementary files format and content: BED = standard BED file containing MACS peaks

source_name: OSCC

growth_protocol: All of the cells were grown and maintained in Dulbecco's modified Eagle medium/DMEM (Sigma) supplemented with 10% fetal bovine serum and 50 units/mL penicillin and streptomycin at 37 °C, 5% CO2 in humidified atmosphere.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine.  Lysates were sonicated with a microtip sonicator to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4 C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
Illumina sequencing libraries were prepared from the ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on NextSeq 500.

treatment_protocol: To establish cetuximab-resistant cells, the parental cell lines (HSC-3-P and SAS-P) were exposed to varying concentrations of cetuximab (10, 20, 50, and 100 μg/mL for 24 hr) as described previously (https://doi.org/10.1038/s41598-019-48717-w).

value: none (input)

value: Oral squamous cell carcinoma (OSCC)


title: HSC-3 input DNA


title: BM-MPP-41


title: FS71_WT-D2


title: F-HDAC-2.E06

description: C1 CAGE

data_processing:
Remove low quality and rDNA reads
Map to the human genome (hg38) using BWA version 0.5.9 (r16) with default parameters, except: : (1) maximum long deletion (-d) = 10 for bwa_aln and (2) maximum number of   alignments (-n) = 100 for bwa_samse
Convert mapped reads to CAGE Transcription Start Sites (CTSS) and read in using CAGEfightR package in R (4.0.3). For C1 CAGE, keep only those that are expressed in at least 3 samples. Merge reads within 20bp of one another.
Map processed reads to GENCODE v31 annotation to the nearest 1kbp up/100 bp down, and remove those overlapping known axons
Annotate enhancers using our custom enhancer set, and quantify raw expression counts by summing the overlapping reads
Assembly: hg38
Supplementary files format and content: *_CTSS.tar.gz: CAGE CTSS files (CAGE_Transcription Start Sites in BED format)
Supplementary files format and content: *_annotations.tar.gz: sample and CAGE tag cluster annotation tables
Supplementary files format and content: *_expression_tables.tar.gz: raw and normalized expression tables for CAGE tag clusters
Supplementary files format and content: gold_enhancers.bed.gz: BED file of the curated gold enhancer set

extract_protocol:
Single cell RNA extraction and cDNA amplification were performed according to the C1 CAGE procedure deposited in Fluidigm’s Script Hub (https://www.fluidigm.com/c1openapp/scripthub/script/2015-07/c1-cage-1436761405138-3). For bulk CAGE, total RNA was extracted using RNeasy Mini Kit.
For C1 CAGE, the library was constructed following the same C1 CAGE procedure outlined in the above link. For bulk CAGE, libraries were constructed using the published nAnT-iCAGE protocol.
The prepared libraries were sequenced on Illumina HiSeq 2500 (50 nt single read).


title: F-HDAC-2.E05

description: C1 CAGE


title: Uninfected_Biorep_1


title: F-HDAC-2.E01

description: C1 CAGE


title: HSC-3 cetuximab resistant-H3K27ac

value: Active Motif, cat# 39133, Lot 16119013


title: BM-MPP-7


title: F-HDAC-2.E08

description: C1 CAGE


title: BM-MPP-6


title: BM-MPP-3


title: BM-MPP-4


title: F-HDAC-2.E04

description: C1 CAGE


title: HSC-3 control-H3K27ac


title: SAS cetuximab resistant-H3K27ac


title: BM-MPP-39


title: Uninfected_Biorep_4


title: SAS control-H3K27ac


title: BM-MPP-38


title: HSC-3 cetuximab resistant-BRD4

value: Active Motif, cat# 91301, Lot 21019002


title: BM-MPP-40


title: F-HDAC-2.D10

description: C1 CAGE


title: F-HDAC-2.D11

description: C1 CAGE


title: HSC-3 control-BRD4


title: SAS cetuximab resistant-BRD4


title: SAS control-BRD4


title: F-HDAC-2.D07

description: C1 CAGE


title: F-HDAC-2.D09

description: C1 CAGE


title: BM-MPP-33


title: F-HDAC-2.D05

description: C1 CAGE

value: TSA


title: F-HDAC-2.D04

description: C1 CAGE


title: F-HDAC-2.D12

description: C1 CAGE


title: F-HDAC-2.D03

description: C1 CAGE


title: SRSF5 siRNA (No.1) transfetction

city: Tokushima

first: Daigo

last: Sumi

state: Not US or Canada

address: 180, Yamashiro-cho

department: Faculty of Pharmaceutical Sciences

institute: Tokushima Bunri University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: HaCaT cells

growth_protocol: HaCaT cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: The siRNA was transfected into HaCaT cells to a final concentration of 10 nM. RNAiMAX (ThermoFisher)  reagent was used for transfection.

value: HaCaT cells

value: immortalized keratinocyte

value: SRSF5 knockdown


title: BM-MPP-37


title: F-HDAC-2.D06

description: C1 CAGE


title: BM-MPP-35


title: BM-MPP-31


title: INPUTn2

city: Sao Paulo

first: Barbara

last: Passaia

address: Prof Lineu Prestes Avenue

country: Brazil

institute: University of Sao Paulo

data_processing:
Quality check with FastQC (v.0.11.7).
Filtering low sequencing quality with FASTP (v 0.20.0).
Reads mapped using bwa (v. 0.7.13).
Duplications filtering with Samtools (v.1.8).
Mapping quality with Qualimap (v.2.2.1).
Exclusion of reads mapped to mitochondria and that are considered as noise by blacklist performed by ENCODE.
Peak calling with MACS2 (v2.1.1) using the AQUAS pipeline (https://github.com/NHLBI-BCB/TF_chipseq_pipeline). p-value 0.01.
Assignment of closest genes with BEDTools.
IDR <0.05
Genome_build: GRCh38 Homo sapiens (release 99) from Ensembl database
Supplementary_files_format_and_content: BigWig Replicate 1 – Sample-rep3.merged.rmdup.sort.2M.tagAlign_x_INPUTn1_S3.merged (joined samples: TCF21n3, NCITCF21A and NCITCF21B).
Supplementary_files_format_and_content: BigWig Replicate 2 - TCF21n2_S1.merged.fastq.rmdup.sort.2M.tagAlign_x_INPUTn1_S3.merged.
Supplementary_files_format_and_content: Peak file: Table-peak-annotated-IDR0.05.xlsx: Output of IDR < 5% overlap of Replicate1 and Replicate2.

source_name: Carcinoma adrenocortical

growth_protocol: Cells were cultured in RPMI medium with 2% fetal bovine serum (FBS) and 1% insulin-transferrin-selenium.

extract_protocol:
Chromatin immunoprecipitation was performed with 100 µl of fragmented chromatin, protein G magnetic beads, and 5 µg of anti-TCF21 antibody ChIP Grade (ab32981, Abcam, Cambridge, UK) using the ChIP-IT Express kit (Active Motif, Carlsbad, CA, USA) following the manufacturer’s instructions. Chromatin was fragmented by sonication with 6 pulses of 10 sec each at 25% amplitude using a VCX130PB ultrasonic processor (Sonics & Materials, Newtown, Connecticut, USA).
Libraries were prepared using the TruSeq® ChIP Sample Preparation kit (Illumina, San Diego, CA, USA), starting with 7 ng of enriched ChIP DNA and selecting 250 bp fragments on average.

treatment_protocol: Approximately 9.0x10^6 cells were plated for 24 h before transfection with plasmid pCMVMycPOD1 and maintained for 48 h after transfection.

value: carcinoma adrenocortical cells

tag: vector overexpression


title: INPUTn1


title: BM-MPP-30


title: NCITCF21B

description: Sample-rep3.merged.rmdup.sort.2M.tagAlign_x_INPUTn1_S3.merged.fastq.rmdup.sort.500K_pooled.tagAlign.fc.signal.bw

value: anti-TCF21 antibody (ab32981)


title: F-HDAC-2.D02

city: Yokohama

first: Andrew

last: Kwon

institute: RIKEN

description: C1 CAGE


title: control siRNA transfetction

value: WT


title: F-HDAC-2.D08

description: C1 CAGE


title: BM-MPP-32


title: BM-MPP-28


title: NCITCF21A


title: F-HDAC-2.C12

description: C1 CAGE

value: VPA


title: BM-MPP-29


title: F-HDAC-2.D01

description: C1 CAGE


title: BM-MPP-2


title: BM-MPP-34


title: F-HDAC-2.C10

description: C1 CAGE


title: BM-MPP-27


title: F-HDAC-2.C11

description: C1 CAGE

value: Control


title: SRSF5 siRNA (No.2) transfetction


title: BM-MPP-25


title: F-HDAC-2.C08

description: C1 CAGE


title: NCIinput


title: F-HDAC-2.C09

description: C1 CAGE


title: BM-MPP-26


title: WM983B cell line in ACM media, PD901 treated, replicate3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.PD901.3

data_processing:
RNA-Seq data analysis was done with rsem (ver. 1.2.3) and hg38 genome with ensemble transcriptome information
DESeq2 was used for differentail expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: AMACM_RNAseq_counts.txt contains the raw counts for each gene

source_name: cell line WM983B

extract_protocol:
Total RNA was isolated from cells using the Qiagen RNeasy® Mini Kit (Qiagen: 74106) according to the manufacturer’s protocol.
RNA quantity was determined using the Qubit 2.0 Fluorometer (ThermoFisher Scientific, Waltham, MA) and the quality was validated using the TapeStation RNA ScreenTape (Agilent, Santa Clara, CA). 500ng of DNAse I treated, total RNA was used to prepare library for Illumina Sequencing using the Quant-Seq 3’mRNA-Seq Library Preparation Kit (Lexogen, Vienna, Austria)

tag: medium

value: ACM

tag: replicate


title: BM-MPP-24


title: WM983B cell line in ACM media, PD901 treated, replicate1

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.PD901.1


title: WM983B cell line in ACM media, PD901 treated, replicate2

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.PD901.2


title: F-HDAC-2.C07

address: 1-7-22 Suehiro-cho, Tsurumi-ku

description: C1 CAGE


title: F-HDAC-2.C06

description: C1 CAGE


title: WM983B cell line in AM media, PD901 treated, replicate3

description:
AMACM_RNAseq_counts.txt
WM983B.AM.PD901.3

value: AM


title: TCF21n3


title: WM983B cell line in AM media, PD901 treated, replicate2

description:
AMACM_RNAseq_counts.txt
WM983B.AM.PD901.2


title: BM-MPP-23


title: BM-MPP-22


title: BM-MPP-21


title: TCF21n2

description: TCF21n2_S1.merged.fastq.rmdup.sort.2M.tagAlign_x_INPUTn1_S3.merged.fastq.rmdup.sort.500K_pooled.tagAlign.fc.signal.bw


title: F-HDAC-2.C03

description: C1 CAGE


title: WM983B cell line in AM media, PD901 treated, replicate1

description:
AMACM_RNAseq_counts.txt
WM983B.AM.PD901.1


title: F-HDAC-2.C04

description: C1 CAGE


title: F-HDAC-2.C05

description: C1 CAGE


title: WM983B cell line in ACM media, untreated, replicate3

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.unt.3

value: untreated


title: BM-MPP-20

value: bone marrow MPP


title: WM983B cell line in ACM media, untreated, replicate1

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.unt.1


title: F-HDAC-2.C01

description: C1 CAGE


title: BM-MPP-1


title: BM-MPP-19


title: WM983B cell line in ACM media, untreated, replicate2

description:
AMACM_RNAseq_counts.txt
WM983B.ACM.unt.2


title: WM983B cell line in AM media, untreated, replicate3

description:
AMACM_RNAseq_counts.txt
WM983B.AM.unt.3


title: F-HDAC-2.B12

description: C1 CAGE


title: WM983B cell line in AM media, untreated, replicate1

description:
AMACM_RNAseq_counts.txt
WM983B.AM.unt.1


title: BM-MPP-17


title: WM983B cell line in AM media, untreated, replicate2

description:
AMACM_RNAseq_counts.txt
WM983B.AM.unt.2


title: BM-MPP-18


title: F-HDAC-2.B10

description: C1 CAGE


title: F-HDAC-2.B11

description: C1 CAGE


title: BM-MPP-16


title: BM-MPP-15


title: BM-MPP-14


title: F-HDAC-2.B09

description: C1 CAGE


title: WM4265-3 cell line in ACM media, PD901 treated, replicate2

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.PD901.2

source_name: cell line WM4265-3


title: F-HDAC-2.C02

description: C1 CAGE


title: WM4265-3 cell line in ACM media, PD901 treated, replicate1

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.PD901.1


title: BM-MPP-12


title: BM-MPP-11


title: F-HDAC-2.B07

description: C1 CAGE


title: F-HDAC-2.B05

description: C1 CAGE


title: WM4265-3 cell line in ACM media, PD901 treated, replicate3

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.PD901.3


title: BM-MPP-13


title: F-HDAC-2.B08

description: C1 CAGE


title: WM4265-3 cell line in AM media, PD901 treated, replicate1

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.PD901.1


title: BM-MPP-10


title: BM-HSC-5

value: bone marrow HSC


title: WM4265-3 cell line in ACM media, untreated, replicate1

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.unt.1


title: BM-HSC-4


title: WM4265-3 cell line in ACM media, untreated, replicate2

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.unt.2


title: F-HDAC-2.B03

description: C1 CAGE


title: BM-HSC-6


title: WM4265-3 cell line in AM media, untreated, replicate3

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.unt.3


title: F-HDAC-2.B01

description: C1 CAGE


title: BM-HSC-8


title: F-HDAC-2.A10

description: C1 CAGE


title: WM4265-3 cell line in AM media, PD901 treated, replicate2

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.PD901.2


title: F-HDAC-2.A12

description: C1 CAGE


title: F-HDAC-2.A11

description: C1 CAGE


title: F-HDAC-2.B04

description: C1 CAGE


title: WM4265-3 cell line in ACM media, untreated, replicate3

description:
AMACM_RNAseq_counts.txt
WM4265-3.ACM.unt.3


title: H3K27Ac ChIP in HEK293T transduced with GFP_replicate 2

city: Charlestown

first: Keith

last: Joung

state: MA

institute: MGH

data_processing:
ChIP-seq reads were aligned to human reference genome hg19 using Burrows-Wheeler Alignment (BWA) tool (PMC2705234). Genome-wide coverage was calculated after extending to 200 bases(approximate fragment size) and averaged over 25 bp windows using igvtools (https://doi.org/10.1093/bib/bbs017). Coverage was then normalized and scaled using RSeqC (http://rseqc.sourceforge.net/#normalize-bigwig-py)
Genome_build: hg19
Supplementary_files_format_and_content: ChIP-seq: bigwig files for visualization on igv

extract_protocol:
For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250
ChIP-seq: Sequencing libraries were prepared with 1-5 ng of ChIP DNA samples and input sample using the Ovation Ultralow System V2 kit (Nugen). Libraries were sequenced with single-end (SE) 50-75 cycles on an Illumina Nextseq 500 Illumina genome analyzer

tag: antibody

value: H3K27Ac antibody (Active motif, cat#39133, lot#16119013)

value: transduced with GFP


title: F-HDAC-2.A09

description: C1 CAGE


title: BM-HSC-38


title: WM4265-3 cell line in AM media, PD901 treated, replicate3

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.PD901.3


title: F-HDAC-2.B02

description: C1 CAGE


title: BM-HSC-37


title: BM-HSC-40


title: F-HDAC-2.B06

description: C1 CAGE


title: BM-HSC-36


title: BM-HSC-3


title: H3K9me3 ChIP in HEK293T transduced with GFP_replicate 2

value: H3K9me3 antibody (Abcam, cat# ab8898, lot# GR257151-1 )


title: BM-HSC-39


title: WM4265-3 cell line in AM media, untreated, replicate1

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.unt.1


title: F-HDAC-2.A04

description: C1 CAGE

value: TSA


title: HA ChIP in HEK293T transduced with KRAB-ZFA7_replicate 2

value: transduced with KRAB-ZFA7


title: H3K9me3 ChIP in HEK293T transduced with KRAB-ZFA7_replicate 2


title: HA ChIP in HEK293T transduced with GFP_replicate 2

source_name: HA ChIP in HEK293T transduced with GFP


title: F-HDAC-2.A06

description: C1 CAGE


title: F-HDAC-2.A08

description: C1 CAGE


title: WM4265-3 cell line in AM media, untreated, replicate2

description:
AMACM_RNAseq_counts.txt
WM4265-3.AM.unt.2


title: H3K27Ac ChIP in A673 transduced with KRAB-ZFA7_replicate 2


title: H3K27Ac ChIP in HEK293T transduced with KRAB-ZFA7_replicate 2


title: BM-HSC-31


title: BM-HSC-33


title: BM-HSC-30


title: BM-HSC-32


title: BM-HSC-34


title: F-HDAC-2.A01

description: C1 CAGE


title: F-HDAC-2.A03

description: C1 CAGE


title: F-HDAC-1.H11

description: C1 CAGE


title: FLI1 ChIP in A673 transduced with KRAB-ZFA7_replicate 2

value: FLI1 antibody (Abcam, cat# ab15289, lot# GR3229309-6)


title: F-HDAC-2.A02

description: C1 CAGE


title: F-HDAC-1.H10

description: C1 CAGE


title: BM-HSC-28


title: BM-HSC-29


title: FLI1 ChIP in A673 transduced with GFP_replicate 2

source_name: FLI1 ChIP in A673 transduced with GFP


title: F-HDAC-1.H08

description: C1 CAGE


title: F-HDAC-2.A07

description: C1 CAGE


title: F-HDAC-1.H12

description: C1 CAGE


title: F-HDAC-2.A05

description: C1 CAGE


title: HA ChIP in A673 transduced with GFP_replicate 2

source_name: HA ChIP in A673 transduced with GFP


title: F-HDAC-1.H06

description: C1 CAGE


title: RNA-seq of SKNMC transduced with KRAB-ZFA7_replicate 1

description: native cells

data_processing:
RNA-seq reads were aligned to hg19 using STAR(doi: 10.1093/bioinformatics/bts635) and PCR duplicates were removed using Picard tools(http://broadinstitute.github.io/picard/). Reads aligning to ribosomal RNA were then filtered out of the alignment. Genomic coverage from filtered alignments were calculated by normalizing to sequencing depth using bedtools(https://doi.org/10.1093/bioinformatics/btq033). FPKMs were calculated using Cufflinks(https://doi.org/10.1038/nbt.1621)
ChIP-seq reads were aligned to human reference genome hg19 using Burrows-Wheeler Alignment (BWA) tool (PMC2705234). Genome-wide coverage was calculated after extending to 200 bases(approximate fragment size) and averaged over 25 bp windows using igvtools (https://doi.org/10.1093/bib/bbs017). Coverage was then normalized and scaled using RSeqC (http://rseqc.sourceforge.net/#normalize-bigwig-py)
Genome_build: hg19
Supplementary_files_format_and_content: RNA-seq: Tab-delimited text files that include FPKM values for each gene
ChIP-seq: bigwig files for visualization on igv

extract_protocol:
For ChIP-seq, chromatin from 1% formaldehyde-fixed cells were fragmented to 200-500 bps by sonication for 5-6 mins using the Branson sonifer SFX250
RNA-seq:Single-end libraries were prepared using the Illumina TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) and TruSeq RNA Single Indexes, pooled, and sequenced using an NextSeq500.
ChIP-seq: Sequencing libraries were prepared with 3 ng of each H3K27Ac ChIP DNA and input sample using SMARTer ThruPLEX DNA-seq kit (Takara, Cat# R400675). Libraries were sequenced with single-end (SE) 75 cycles on an Illumina Nextseq 500 system

treatment_protocol: For RNA-seq, total RNA was extracted from native cells using the NucleoSpin RNA Plus Kit (Clontech, cat# 740984.250)

value: SKNMC


title: HA ChIP in A673 transduced with KRAB-ZFA7_replicate 2


title: F-HDAC-1.H05

description: C1 CAGE


title: BM-HSC-35

source_name: Bone Marrow


title: BM-HSC-23


title: H3K27Ac ChIP in A673 transduced with GFP_replicate 2


title: BM-HSC-22


title: F-HDAC-1.H09

description: C1 CAGE


title: H3K9me3 ChIP in A673 transduced with GFP_replicate 2


title: RNA-seq of MSC transduced with GFP_replicate 2

description: native cells

source_name: RNA-seq of MSC transduced with GFP

value: MSC


title: RNA-seq of SKNMC transduced with GFP_replicate 1

description: native cells

source_name: RNA-seq of SKNMC transduced with GFP


title: BM-HSC-26


title: BM-HSC-27


title: BM-HSC-1


title: F-HDAC-1.H01

description: C1 CAGE


title: BM-HSC-24


title: RNA-seq of SKNMC transduced with GFP_replicate 2

description: native cells


title: BM-HSC-21


title: BM-HSC-20


title: RNA-seq of SKNMC transduced with KRAB-ZFA7_replicate 2

description: native cells


title: F-HDAC-1.H03

description: C1 CAGE


title: BM-HSC-19


title: F-HDAC-1.G12

description: C1 CAGE


title: F-HDAC-1.H02

description: C1 CAGE


title: BM-HSC-18


title: F-HDAC-1.H07

description: C1 CAGE


title: F-HDAC-1.G10

description: C1 CAGE


title: HA ChIP in HEK293T transduced with GFP_replicate 1

description: native cells


title: BM-HSC-15


title: BM-HSC-14


title: H3K9me3 ChIP in HEK293T transduced with KRAB-ZFA7_replicate 1

description: native cells


title: RNA-seq of MSC transduced with GFP_replicate 1

description: native cells


title: BM-HSC-25


title: F-HDAC-1.G11

description: C1 CAGE


title: Input of A673 transduced with KRAB-ZFA7

description: native cells

source_name: Input of A673 transduced with KRAB-ZFA7


title: BM-HSC-11


title: F-HDAC-1.G04

description: C1 CAGE


title: H3K9me3 ChIP in A673 transduced with KRAB-ZFA7_replicate 2


title: F-HDAC-1.H04

description: C1 CAGE


title: H3K27Ac ChIP in HEK293T transduced with GFP_replicate 1

description: native cells


title: Input of HEK293T transduced with GFP

description: native cells

source_name: Input of HEK293T transduced with GFP


title: H3K27Ac ChIP in HEK293T transduced with KRAB-ZFA7_replicate 1

description: native cells


title: H3K9me3 ChIP in HEK293T transduced with GFP_replicate 1

description: native cells


title: BM-HSC-17


title: Input of HEK293T transduced with KRAB-ZFA7

description: native cells


title: BM-HSC-16


title: F-HDAC-1.G08

description: C1 CAGE


title: BM-HSC-13


title: FLI1 ChIP in A673 transduced with KRAB-ZFA7_replicate 1

description: native cells


title: HA ChIP in HEK293T transduced with KRAB-ZFA7_replicate 1

description: native cells


title: H3K27Ac ChIP in A673 transduced with KRAB-ZFA7_replicate 1

description: native cells


title: F-HDAC-1.G09

description: C1 CAGE


title: F-HDAC-1.G05

description: C1 CAGE


title: F-HDAC-1.G03

description: C1 CAGE


title: F-HDAC-1.G02

description: C1 CAGE


title: BM-HSC-10


title: CD48+Mac1+SK-7


title: F-HDAC-1.G07

description: C1 CAGE


title: F-HDAC-1.F12

description: C1 CAGE


title: CD48+Mac1+SK-6


title: CD48+Mac1+SK-8


title: F-HDAC-1.G01

description: C1 CAGE


title: H3K9me3 ChIP in A673 transduced with KRAB-ZFA7_replicate 1

description: native cells


title: F-HDAC-1.F11

description: C1 CAGE


title: CD48+Mac1+SK-9


title: Input of A673 transduced with GFP

description: native cells

source_name: Input of A673 transduced with GFP


title: F-HDAC-1.G06

description: C1 CAGE


title: CD48+Mac1+SK-5


title: HA ChIP in A673 transduced with KRAB-ZFA7_replicate 1

description: native cells


title: H3K27Ac ChIP in A673 transduced with GFP_replicate 1

description: native cells


title: FLI1 ChIP in A673 transduced with GFP_replicate 1

description: native cells


title: CD48+Mac1+SK-4


title: CD48+Mac1+SK-48


title: H3K9me3 ChIP in A673 transduced with GFP_replicate 1

description: native cells


title: F-HDAC-1.F09

description: C1 CAGE


title: F-HDAC-1.F10

description: C1 CAGE


title: HA ChIP in A673 transduced with GFP_replicate 1

description: native cells


title: CD48+Mac1+SK-47


title: CD48+Mac1+SK-45


title: CD48+Mac1+SK-44


title: F-HDAC-1.F06

description: C1 CAGE


title: F-HDAC-1.F08

description: C1 CAGE


title: FLI1 ChIP in SKNMC transduced with KRAB-ZFA7_replicate 1

description: native cells


title: F-HDAC-1.F04

description: C1 CAGE


title: F-HDAC-1.F05

description: C1 CAGE


title: FLI1 ChIP in SKNMC transduced with KRAB-ZFA7_replicate 2

description: native cells


title: H3K27Ac ChIP in SKNMC transduced with KRAB-ZFA7_replicate 2

description: native cells

value: H3K27Ac antibody (Active motif, cat#, lot#10918010)


title: H3K27Ac ChIP in SKNMC transduced with KRAB-ZFA7_replicate 1

description: native cells


title: F-HDAC-1.F07

description: C1 CAGE


title: CD48+Mac1+SK-43


title: CD48+Mac1+SK-42


title: CD48+Mac1+SK-41


title: CD48+Mac1+SK-40


title: H3K9me3 ChIP in SKNMC transduced with KRAB-ZFA7_replicate 1

description: native cells


title: H3K9me3 ChIP in SKNMC transduced with KRAB-ZFA7_replicate 2

description: native cells


title: F-HDAC-1.F03

description: C1 CAGE


title: F-HDAC-1.F01

description: C1 CAGE


title: CD48+Mac1+SK-3


title: HA ChIP in SKNMC transduced with KRAB-ZFA7_replicate 2

description: native cells


title: F-HDAC-1.E12

description: C1 CAGE


title: Input of SKNMC transduced with KRAB-ZFA7

description: native cells


title: CD48+Mac1+SK-39


title: HA ChIP in SKNMC transduced with KRAB-ZFA7_replicate 1

description: native cells


title: CD48+Mac1+SK-46


title: F-HDAC-1.F02

description: C1 CAGE


title: CD48+Mac1+SK-37


title: F-HDAC-1.E09

description: C1 CAGE


title: Input of SKNMC transduced with GFP

description: native cells

source_name: Input of SKNMC transduced with GFP


title: CD48+Mac1+SK-35


title: CD48+Mac1+SK-36


title: FLI1 ChIP in SKNMC transduced with GFP_replicate 1

description: native cells

source_name: FLI1 ChIP in SKNMC transduced with GFP


title: F-HDAC-1.E10

description: C1 CAGE

source_name: Dermal fibroblasts, neonatal


title: F-HDAC-1.E11

description: C1 CAGE


title: CD48+Mac1+SK-34


title: F-HDAC-1.E07

description: C1 CAGE


title: CD48+Mac1+SK-38


title: H3K9me3 ChIP in SKNMC transduced with GFP_replicate 2

description: native cells


title: F-HDAC-1.E06

description: C1 CAGE


title: CD48+Mac1+SK-33


title: FLI1 ChIP in SKNMC transduced with GFP_replicate 2

description: native cells


title: H3K27Ac ChIP in SKNMC transduced with GFP_replicate 2

description: native cells


title: Input of MSC transduced with GFP

description: native cells

source_name: Input of MSC transduced with GFP


title: H3K9me3 ChIP in SKNMC transduced with GFP_replicate 1

description: native cells


title: F-HDAC-1.E08

description: C1 CAGE


title: CD48+Mac1+SK-32


title: CD48+Mac1+SK-27


title: CD48+Mac1+SK-28


title: H3K27Ac ChIP in SKNMC transduced with GFP_replicate 1

description: native cells


title: F-HDAC-1.D11

description: C1 CAGE


title: F-HDAC-1.D09

description: C1 CAGE


title: CD48+Mac1+SK-26


title: CD48+Mac1+SK-25


title: H3K27Ac ChIP in MSC transduced with EWS-FLI1_replicate2

description: native cells

value: transduced with EWS-FLI1


title: F-HDAC-1.E04

description: C1 CAGE


title: CD48+Mac1+SK-29


title: F-HDAC-1.E03

description: C1 CAGE

value: VPA


title: CD48+Mac1+SK-24


title: HA ChIP in SKNMC transduced with GFP_replicate 2

description: native cells

source_name: HA ChIP in SKNMC transduced with GFP


title: F-HDAC-1.E05

description: C1 CAGE

value: Control


title: CD48+Mac1+SK-30


title: F-HDAC-1.E02

description: C1 CAGE


title: F-HDAC-1.E01

description: C1 CAGE


title: F-HDAC-1.D12

description: C1 CAGE


title: F-HDAC-1.D05

description: C1 CAGE


title: H3K27Ac ChIP in MSC transduced with EWS-FLI1_replicate1

description: native cells


title: HA ChIP in MSC transduced with GFP_replicate 1

description: native cells

source_name: HA ChIP in MSC transduced with GFP


title: H3K27Ac ChIP in MSC transduced with GFP_replicate 2

description: native cells

source_name: H3K27Ac ChIP in MSC transduced with GFP


title: F-HDAC-1.D04

description: C1 CAGE


title: CD48+Mac1+SK-21


title: F-HDAC-1.D07

description: C1 CAGE


title: H3K27Ac ChIP in MSC transduced with GFP_replicate 1

description: native cells


title: HA ChIP in SKNMC transduced with GFP_replicate 1

description: native cells


title: HA ChIP in MSC transduced with EWS-FLI1_replicate2

description: native cells

source_name: HA ChIP in MSC transduced with EWS-FLI1


title: F-HDAC-1.D08

description: C1 CAGE


title: H3K27Ac ChIP in MSC transduced with EWS-ZFA7_replicate2

description: native cells

value: transduced with EWS-ZFA7


title: CD48+Mac1+SK-31


title: F-HDAC-1.D10

description: C1 CAGE


title: CD48+Mac1+SK-22


title: HA ChIP in MSC transduced with EWS-ZFA7_replicate2

description: native cells

source_name: HA ChIP in MSC transduced with EWS-ZFA7


title: HA ChIP in MSC transduced with GFP_replicate 2

description: native cells


title: CD48+Mac1+SK-18


title: CD48+Mac1+SK-23


title: CD48+Mac1+SK-1


title: F-HDAC-1.D03

description: C1 CAGE


title: HA ChIP in MSC transduced with EWS-FLI1_replicate1

description: native cells


title: CD48+Mac1+SK-17


title: Human_Control_S4

source_name: Human Control

value: RPE/choroid control


title: CD48+Mac1+SK-16


title: Human_Control_S3


title: H3K27Ac ChIP in MSC transduced with EWS-ZFA7_replicate1

description: native cells


title: CD48+Mac1+SK-15


title: F-HDAC-1.C11

description: C1 CAGE


title: F-HDAC-1.C12

description: C1 CAGE


title: F-HDAC-1.C10

description: C1 CAGE


title: F-HDAC-1.C09

description: C1 CAGE


title: Human_CNV_S4

source_name: Human CNV

value: CNV


title: CD48+Mac1+SK-13

source_name: Bone Marrow


title: F-HDAC-1.D02

description: C1 CAGE


title: CD48+Mac1+SK-11


title: F-HDAC-1.D01

description: C1 CAGE


title: CD48+Mac1+SK-20


title: CD48+Mac1+SK-10


title: CD48+Mac1+SK-14


title: 293T_PRMT4-inhibitor_2ribosome

city: ShangHai

first: Zefeng

address: 320 YueYang Road

department: CAG-MPG Partner Institution for Computational Biology

institute: Chinese Academy of Sciences

description: ribosome bound mRNA

data_processing:
Library strategy: Polysome-Seq
Illumina Casava1.7 software used for basecalling
the adaptors and low-quality bases of paired-end 150bp reads were trimmed using Cutadapt (v1.18)
The trimmed reads with length < 20 nt were excluded, and the remaining reads were mapped to the human genome (GRCh37 with annotation of GENCODE v27lift37) using STAR (v2.5.3a)
Genes expression levels (FPKM) were estimated by RSEM, and the relative fold changes were calculated.
The Hierarchical clustering of log2 fold changes was carried out using Cluster 3.0 with centered correlation and average linkage parameter
Genome_build: GRCh37
Supplementary_files_format_and_content: FPKM values for each Sample

source_name: HEK293T cell line

extract_protocol:
DMSO or Inhibitor-treated HEK293T cells were lysed in polysome lysis buffer. The lysates were loaded onto 10-50% sucrose gradients and ultra-centrifuged. Fractions were collected using a Brandel Density Gradient Fractionation System.
mRNAs from indicated fractions of polysome profiling samples were extracted with TriZol reagent.
RNA-seq libraries were prepared by NEBNext®EUltra™ II Directional RNA Library Prep Kit for Illumina (NEB)

value: treated with PRMT4 inhibitor

tag: polysome fraction

value: bound with two ribosomes


title: LCL

first: Jingxiao

state: Guangdong Province

address: Dongfengdong Road 651

institute: Sun Yet san university

data_processing:
Illumina Bcl2FastQ software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.13 with parameters -p 8 --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2 -G hg19
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include Counts and RPKMs for each Sample

source_name: B cell

extract_protocol:
Total RNA from TW03-EV and TW03-Gal-9 cells were isolated using TRIzol reagent, and dissolved in RNase-free water.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: subject status

value: healthy donor

value: peripheral blood

value: mature lymphocytoblast cell line (LCLs)


title: AKATA

source_name: B cell lymphoma cell

value: AKATA

value: B cell lymphoma

value: EBV positive B cell lymphoma cell line


title: F-HDAC-1.C04

description: C1 CAGE


title: HA ChIP in MSC transduced with EWS-ZFA7_replicate1

description: native cells


title: Uninfected_Biorep_3

source_name: Gingival Keratinocyte

value: HPV 16-immortalized gingival keratinocytes (HIGK)

value: Uninfected


title: F-HDAC-1.C06

description: C1 CAGE


title: 293T_PRMT4-inhibitor_1ribosome

description: ribosome bound mRNA

value: bound with one ribosome (monosome)


title: Human_Control_S1

first: Clemens

institute: Uniklinik Freiburg

data_processing:
Quality control FastQC Galaxy Version 0.72
Reads were mapped to the human (hg38) or mouse (mm10) Galaxy built-in reference genome with RNA STAR Galaxy Version 2.6.0b-2 using Gencode annotation files (human: Gencode 31, release June 2019, https://www.gencodegenes.org/human/releases.html, mouse: Gencode M22, release June 2019, https://www.gencodegenes.org/mouse/releases.html).
Reads mapped to the human or mouse reference genome were counted using featureCounts Galaxy Version 1.6.4 (default parameters) using the aforementioned annotation files
The outputs of featureCounts were imported to RStudio (Version 1.2.1335, R Version 3.5.3). Gene symbols and gene types were determined based on ENSEMBL database (human genes, GRCh38.p12, download on 08/31/2019, mouse genes GRCm38.p6, download on 08/25/2019). Ortholog genes were determined based on ENSEMBL one-to-one orthologs (download on 10/03/19). After principle component analysis, differential gene expression was analyzed using the R package DESeq2 1.22.2 with default parameters (Benjamini-Hochberg adjusted p-value). Transcripts with log2fold change (log2FC) > 0.5 or < -0.5 and adjusted p-value < 0.05 were considered as differentially expressed genes (DEG). Heatmaps were created with the R package ComplexHeatmap 1.20.0. Gene enrichment analysis and its visualization with dotplots and cnetplots was done using the R package clusterProfiler 3.10.1. Other data visualization was performed using the ggplot2 package.
Genome_build: hg38 and mm10
Supplementary_files_format_and_content: data.csv

extract_protocol:
RNA isolation from FFPE specimens was carried out as previously described. Briefly, total RNA was extracted from FFPE samples using the Quick-RNA FFPE Kit (Zymo Research, Irvine, California). Following DNAse I digestion using the Baseline-ZERO Kit (Epicentre, Madison, Wisconsin), the RNA concentration was quantified using the Qubit RNA HS Assay Kit on a Qubit Fluorometer (Life Technologies, Carlsbad, California). RNA quality was determined via the RNA Pico Sensitivity Assay on a LabChip GXII Touch (PerkinElmer, Waltham, Massachusetts).
RNA sequencing was performed using massive analysis of cDNA ends (MACE), a 3’ RNA sequencing method, as previously described. We recently demonstrated that MACE allows sequencing of FFPE samples with high accuracy. Briefly, 20 barcoded libraries comprising unique molecule identifiers (six mouse CNV mem-branes, six mouse RPE-choroidal control samples, four human CNV membranes and four human RPE-choroidal control tissues) were sequenced on the NextSeq 500 (Illumina) with 1 × 75 bp. PCR bias was removed using unique molecular iden-tifier.


title: Human_Control_S2


title: F-HDAC-1.D06

description: C1 CAGE


title: LCLd14

value: primary B cells

value: EBV infected B cells for 14 days


title: F-HDAC-1.C05

description: C1 CAGE

value: Control


title: Human_CNV_S1


title: F-HDAC-1.C07

description: C1 CAGE


title: F-HDAC-1.C08

description: C1 CAGE


title: CD48+Mac1+SK-19


title: CD48+Mac1+SK-12


title: LCLd0


title: F-HDAC-1.B10

description: C1 CAGE

value: TSA


title: F-HDAC-1.B11

description: C1 CAGE


title: F-HDAC-1.B08

description: C1 CAGE


title: Human_CNV_S3


title: 293T_DMSO_3ribosome

description: ribosome bound mRNA

value: treated with DMSO

value: bound with three or more ribosomes


title: 293T_DMSO_2ribosome

description: ribosome bound mRNA


title: 293T_PRMT4-inhibitor_3ribosome

description: ribosome bound mRNA

value: treated with PRMT4 inhibitor


title: LCLd21

value: EBV infected B cells for 21 days


title: F-HDAC-1.B06

description: C1 CAGE


title: LCLd3

value: healthy donor

value: EBV infected B cells for 3 days


title: F-HDAC-1.C01

description: C1 CAGE


title: LCLd7

value: peripheral blood

value: EBV infected B cells for 7 days


title: 293T_PRMT4-inhibitor_input

description: ribosome bound mRNA

value: total input


title: F-HDAC-1.B12

description: C1 CAGE


title: F-HDAC-1.C02

description: C1 CAGE


title: F-HDAC-1.B04

description: C1 CAGE

value: VPA


title: 293T_PRMT1-inhibitor_1ribosome

description: ribosome bound mRNA

value: treated with PRMT1 inhibitor


title: 293T_PRMT1-inhibitor_3ribosome

description: ribosome bound mRNA


title: 293T_PRMT1-inhibitor_2ribosome

description: ribosome bound mRNA

value: bound with two ribosomes


title: F-HDAC-1.C03

description: C1 CAGE


title: F-HDAC-1.B03

description: C1 CAGE


title: F-HDAC-1.B09

description: C1 CAGE


title: 293T_DMSO_1ribosome

description: ribosome bound mRNA

value: bound with one ribosome (monosome)


title: 293T_DMSO_input

description: ribosome bound mRNA


title: Human_CNV_S2

value: CNV


title: WT, rep2, sRNA-seq

city: Riverside

first: Xuemei

last: Chen

state: CALIFORNIA

address: 900 University AVe

institute: University of California

data_processing:
Raw reads were subjected to adapter trimming using cutadapt. Reads without an adapter or shorter than 18-nt after trimming were discarded from further processing.
Trimmed reads were aligned to the Arabidopsis genome using ShortStack v3.8 with parameters (--mismatches 0 --mmap u --bowtie_m 1000 --ranmax 50).
Mapped reads were separated by size and normalization was performed by calculating the RPM (Reads per million).
The miRNAs are annotated based on Araport11.
Assembly: TAIR 10
Supplementary files format and content: CSV file containing normalized read counts for all the annotated miRNAs.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: 16 hr light and 8 hr dark on 1/2 MS medium

extract_protocol:
14-day-old seedlings were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent.
Small RNA library construction using NEBNext Multiplex Small RNA Library Prep Set for Illumina (E7300).

value: seedling

value: Wild type


title: 293T_PRMT1-inhibitor_input

description: ribosome bound mRNA


title: F-HDAC-1.A10

description: C1 CAGE

value: TSA


title: U937_72h_untreated_2

type: genomic

city: Heidelberg

first: Benedikt

last: Brors

address: Im Neuenheimer Feld 280

department: Div. Applied Bioinformatics

institute: German Cancer Research Center (DKFZ)

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

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

data_processing: DNA methylation data  quality control and analysis were were performed using the Bioconductor package RnBeads (version 1.10.8). Sites that overlapped with SNPs and cross-reactive probes were filtered.  Furthermore, probes giving unreliable measurements, determined by the Greedycut algorithm, were excluded from analysis. The data were subjected to background subtraction using the methylumi package (method enmix.oob) and beta-mixture quantile normalization (BMIQ).

label: cy3, cy5

source_name: U-937 cells; untreated; harvested after 72 hours

label_protocol: Standard Illumina Protocol

extract_protocol: Cells were harvested after 72 and 120 hours of treatment. Genomic DNA was extracted using the DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany) for cell culture according to the manufacturer's protocol. Frozen cell pellets were thawed carefully and dissolved in PBS. Treatment with Proteinase K led to digestion of contaminating protein. By adding ethanol DNA was precipitated. After centrifugation the DNA was eluted in Tris-EDTA containing buffer.

treatment_protocol: U-937 cells were treated in triplicates with daily pulses of 200 nM DAC for three consecutive days. After 48 hours, simultaneously to the third DAC dose, 1 µM ATRA was administered.

value: U-937; human AML cell line


title: U937_72h_untreated_1


title: F-HDAC-1.B05

description: C1 CAGE


title: F-HDAC-1.B07

description: C1 CAGE

value: Control


title: WT, rep3, sRNA-seq


title: aar2-1, rep1, sRNA-seq


title: F-HDAC-1.A12

description: C1 CAGE


title: F-HDAC-1.B02

description: C1 CAGE


title: F-HDAC-1.A11

description: C1 CAGE


title: aar2-1, rep2, sRNA-seq


title: F-HDAC-1.B01

description: C1 CAGE


title: U937_72h_untreated_3


title: aar2-2, rep3, RNA-seq

data_processing:
Reads were mapped to the Arabidopsis genome Araport11 using STAT v2.6(47) with default settings. Mapped reads were counted using featureCounts v1.64(48) and differential expressed gene were analyzed using the R package DESeq2.
Assembly: TAIR 10
Supplementary files format and content: CSV file containing normalized read counts for all detected genes

extract_protocol:
14-day-old seedlings were ground to a fine powder in liquid nitrogen and subjected to RNA extraction using TRI Reagent.
RNA library construction using NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (NEB# E7770)
mRNAseq


title: aar2-1, rep3, RNA-seq


title: aar2-2, rep2, RNA-seq


title: WT, rep1, sRNA-seq


title: F-HDAC-1.A08

description: C1 CAGE


title: F-HDAC-1.A07

description: C1 CAGE


title: aar2-1, rep1, RNA-seq


title: F-HDAC-1.A09

description: C1 CAGE


title: aar2-1, rep3, sRNA-seq


title: F-HDAC-1.A06

description: C1 CAGE


title: U937_72h_DAC_3

source_name: U-937 cells; treated with DAC after 0, 24 und 48 hours; harvested after 72 hours


title: U937_72h_DAC_2