title: DLD1 siUHRF1-2

description:
DLD1 with UHRF1 siRNA2 plus mock
DLD1-siUHRF1-2

source_name: DLD1 with UHRF1 siRNA2 plus mock

value: UHRF1 siRNA2

value: UHRF1 depletion


title: H3K27ac_Pu-1_shRNA1_LSD1i

status: Public on May 21 2019

type: SRA

city: Melbourne

first: Mark

last: Dawson

state: VIC

address: 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

library_source: genomic

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak-calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed files of macs2 peaks

molecule: genomic DNA

organism: Mus musculus

source_name: MLL-AF9 I-BET resistant cells

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO), while MLL-AF9 I-BET sensitive cells were cultured with constant DMSO treatment (0.1%).

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: I-BET151 was used at a final concentration of 1000nM. LSD1i was used at a final concentration of 500nM.

tag: strain background

tag: tissue source

value: haematopoietic progenitors

tag: cell line

tag: cell phenotype

value: I-BET Resistant

tag: shRNA

value: Pu.1 shRNA1

tag: treatment

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: DLD1 siCONT plus TSA replicate1

type: RNA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

country: Japan

institute: Sapporo Medical University

description:
DLD1 with control siRNA plus TSA replicate1
DLD1-siCONT-TSA-1

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

molecule: total RNA

organism: Homo sapiens

source_name: DLD1 with control siRNA plus TSA

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: DLD1 cells were cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum.  The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was extracted using a TRIZOL reagent (Invitrogen).

treatment_protocol: DLD1 cells were transfected with a control siRNA (Thermo Fisher Scientific) or siRNAs targeting UHRF1 (Thermo Fisher Scientific) using using Lipofectamine RNAiMAX (Thermo Fisher Scientific) and incubated for 48 h. Cells were then treated with mock (ethanol) or 300 nM Trichostatin A (TSA) for additional 24 h.

tag: sirna

value: control

tag: genotype

tag: agent

value: Trichostatin A


title: H3K27ac_Scrambled_LSD1i

value: Pu.1 Scrambled


title: 1492

city: Beijing

first: Fan

last: Xiaolong

address: No.19,Waida Jie,Xinjie Kou, Haiding District

country: China

institute: Beijing Normal University

data_processing:
Raw sds files or eds files generated by 7900HT Fast Real-Time PCR System were imported to  Expression Suite Software v1.0.4 (Thermo Fisher Scientific).
The cycle threshold (CT ) for each gene was automatically determined by  Expression Suite Software v1.0.4 .
CT values  of the classifier genes were normalized against the geometric average CT values of ACTB，GAPDH and UBC.

label: FAM

source_name: Frozen glioma tissue

label_protocol: PCR assays were performed using a custom Taqman Low Density Array (TLDA, Life Technology). Two μl of cDNA template was diluted to 50 μl using RNAse-free water and subsequently mixed with 50 μl 2x TaqMan Universal PCR Master mix with UNG (Life Technology). This reaction mix was then loaded to each slot of the TLDA card. The card was centrifuged twice at 1500 rpm for 1 min to transfer 1 μl of the mix to each reaction cell, sealed and subsequently measured using ABI 7900HT fast real-time PCR system or ViiA™ 7 Flex Real-Time PCR system following the universal cycling conditions: 2 min at 50℃ for UNG incubation and 10 min at 95℃ for polymerase activation. Forty cycles (15 s at 95℃ for denaturation and 1 min at 60℃ for annealing and synthesis) were run for amplification.

extract_protocol: Total RNA was extracted from about 30mg frozen  tissue using AllPrep DNA/RNA Mini Kit (QIAGEN,Cat No./ID: 80204)

tag: gender

value: F

tag: age

tag: histology

value: GBM

tag: grade

tag: idh mutation

value: WT

tag: 1p19q co-deletion

value: non co-deletion

tag: em/pm class

value: EM


title: b6_lcmv_cd8_d07_r1_RNAseq

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

library_source: transcriptomic

data_processing:
Align ATAC-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ATAC-seq duplicates: Picard v1.141
Call ATAC-seq peaks: MACS2 v2.1.1
Align RNA-seq reads: STAR v2.5.0c
Remove RNA-seq duplicates: Picard v1.141
Count RNA-seq reads: GenomicAlignments v1.2.2
Align ChIP-seq reads: STAR v2.5.0c [disable splicing alignment]
Remove ChIP-seq duplicates: Picard v1.141
Call ChIP-seq peaks: MACS2 v2.1.1
Genome_build: GRCm38, CAST/EiJ and SPRET/EiJ
Supplementary_files_format_and_content: *_ATACseq.atlas.cnt: Peak abundance measurements.
Supplementary_files_format_and_content: *_RNAseq.gene.cnt, scRNAseq.cnt.csv: Gene abundance measurements.
Supplementary_files_format_and_content: *.pks.txt: ChIP-seq peaks.

source_name: BMC F1 Spleen B6 activated CD8 T cell

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit followed by KAPA Hyper Prep Kit.
Cells were collected in Trizol and RNA was extracted using RNeasy mini kit.

tag: strain

tag: tissue

value: Spleen

tag: cell type

value: Activated CD8 T cell

tag: time point


title: 1494

value: M


title: 1500


title: b6_spret_lcmv_cd8_d60_r3_RNAseq

source_name: B6/Spret F1 Spleen memory CD8 T cell

value: B6/Spret F1

value: Memory CD8 T cell


title: 1495

value: sGBM


title: b6_lcmv_cd8_nav_r1_RNAseq

source_name: BMC F1 Spleen B6 naïve CD8 T cell

value: Naive CD8 T cell


title: DLD1 siUHRF1-1

description:
DLD1 with UHRF1 siRNA1 plus mock
DLD1-siUHRF1-1

source_name: DLD1 with UHRF1 siRNA1 plus mock

tag: cell line

value: UHRF1 siRNA1

value: UHRF1 depletion

value: mock


title: KMMd11_rep1

city: Xuzhou

first: Hui

last: Liu

state: Jiangsu

address: #1 Daxue Road

institute: China University of Mining and Technology

data_processing:
Library strategy: CRISPR screen
CRISPR screen sequencing data processing was performed faithfully following the previously described protocol of Feng Zhang lab (Shalem et al., 2014).
After trimming of the adaptor sequences, the reads were mapped to the sgRNA library.
The summarized reads counting of each sgRNA for each sample is presented in the processed data file.
Genome_build: rn5
Supplementary_files_format_and_content: tab-delimited text files include reads count of each sgRNA for each CRISPR screening samples

organism: Rattus norvegicus

source_name: KMM cell

growth_protocol: Rat primary embryonic mesenchymal stem cells (MM), KSHV-transformed MM cells (KMM) were maintained in Dulbecco modified Eagle medium (DMEM) supplemented with 10% fetal bovine serum (FBS; Sigma-Aldrich), 4 mM L-glutamine, and 10 µg/ml penicillin and streptomycin.

extract_protocol:
Genomic DNA was extracted using QiAMP kit (Qiagen) and PCR was performed in two steps. First, the input genomic DNA was amplified by 30 cycles in order to achieve 300X coverage over the sgRNA library using the primers F1: TCG TCG GCA GCG TCA GAT GTG TAT AAG AGA CAG TAT CTT GTG GAA AGG ACG AAA and R1: GTC TCG TGG GCT CGG AGA TGT GTA TAA GAG ACA GTT ATT TTA ACT TGC TAT TTC TAG CTC. Then, to attach Illumina adaptors and barcode samples, a second PCR reaction was carried out by 6 cycles using 20ng purified PCR product and the primers F2: TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG, and R2:GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG.  Amplicons from the second PCR were gel-extracted, quantified, mixed and sequenced using HiSeq 2500 (Illumina).
Rat sgRNA library (Toolgen Rat genome RGEN library v1.0) was constructed by Toolgen (www.toolgen.com).
Amplified oligos in oligo library (Type:CTTGTGGAAAGGACGAAACACCG-X20-GTTTTAGAGCTAGAAATAGCAAGTTAAA) with ArrayF ( TAACTTGAAAGTATTTCGATTTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCG  ) and ArrayR (ACTTTTTCAAGTTGATAACGGACTAGCCTTATTTTAACTTGCTATTTCTAGCTCTAAAAC  ) were inserted into BsmB1-cut pLKO.1 Lentiviral plasmid.

treatment_protocol: We first generated MM and KMM cells stably expressing Cas9 by lentiviral transduction following by positive selection with blasticidin for 1 week. We then generated a library of sgRNAs targeting 19,840 genes of the rat genome, each with 3 independent sgRNAs. Cas9-expressing MM and KMM cells were transduced with the lentiviral sgRNA library via spinfection at a MOI of 0.3 and selected for 3 days with puromycin. The cultures were then switched to normal medium without any selection and cell samples were collected at day 1, 4, 11 and 21 after transduction, and subjected to DNA sequencing to determine the gain and loss sgRNAs over time.

tag: infection status

value: KSHV-infected

value: mesenchymal stem cell

tag: surviving days


title: 1497

value: F

value: AOA

value: MT

value: PM


title: DLD1 siCONT replicate2

description:
DLD1 with control siRNA plus mock replicate2
DLD1-siCONT-2

source_name: DLD1 with control siRNA plus mock

tag: sirna

value: control


title: KMMd11_rep3


title: KMMd21_rep1


title: b6_spret_lcmv_cd8_d60_r2_RNAseq

value: Spleen


title: KMMd4_rep3


title: H3K27ac_Pu-1_shRNA1_DMSO

tag: strain background

tag: tissue source

value: haematopoietic progenitors

tag: cell phenotype

value: I-BET Resistant

tag: shRNA

value: Pu.1 shRNA1

tag: treatment

value: DMSO

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: Scramble-shRNA LSD1i_ATAC

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak-calling was performed using MACS2 with the no lambda and no model method
Genome_build: mm10
Supplementary_files_format_and_content: bed files of macs2 peaks

extract_protocol:
50000 cells were lysed to isolate nuclei.
Isolated nuclei were then tagmented for 30mins at 37°C. Tagmented DNA was then amplified into the final ATACseq libraries using KAPA HotStart Ready Mix (2x) (KAPA Biosystems). Libraries were size selected from 150-700bps.

tag: condition

value: Scramble


title: KMMd4_rep2


title: b6_spret_lcmv_cd8_d60_r1_RNAseq

value: B6/Spret F1

value: Memory CD8 T cell


title: 1490

tag: gender

value: M

tag: age

tag: histology

value: sGBM

tag: grade

tag: idh mutation

tag: 1p19q co-deletion

value: non co-deletion


title: b6_spret_lcmv_cd8_d07_r3_RNAseq

source_name: B6/Spret F1 Spleen activated CD8 T cell

tag: strain

tag: tissue

tag: cell type

value: Activated CD8 T cell

tag: time point


title: KMMd4_rep1

tag: infection status

value: KSHV-infected

value: mesenchymal stem cell

tag: surviving days


title: 1491

value: GBM-O

value: MT

tag: em/pm class

value: PM


title: 1486

value: GBM

value: WT

value: EM


title: Pu1-shRNA2 DMSO_ATAC

value: haematopoietic progenitors

value: I-BET Resistant

tag: shRNA

value: Pu.1 shRNA2

value: DMSO


title: 1474

value: F

value: O

value: co-deletion


title: b6_spret_lcmv_cd8_d07_r2_RNAseq

value: B6/Spret F1

value: Spleen


title: KMMd1_rep2

value: KSHV-infected


title: KMMd1_rep3

value: mesenchymal stem cell


title: Pu1-shRNA1 LSD1i_ATAC

value: Pu.1 shRNA1

tag: treatment


title: b6_spret_lcmv_cd8_d07_r1_RNAseq

value: Activated CD8 T cell


title: 1394

value: M

value: rGBM

value: non co-deletion

value: PM


title: b6_spret_lcmv_cd8_nav_r3_RNAseq

source_name: B6/Spret F1 Spleen naïve CD8 T cell

value: Naive CD8 T cell


title: KMMd1_rep1


title: b6_spret_lcmv_cd8_nav_r2_RNAseq


title: 1459

value: AOA

value: WT

value: EM


title: Sensitive DMSO_ATAC

source_name: MLL-AF9 I-BET sensitive cells

value: haematopoietic progenitors

value: I-BET Sensitive

value: DMSO


title: Pu1-shRNA1 DMSO_ATAC

value: I-BET Resistant


title: MMd21_rep2

source_name: MM cell

value: Not infected


title: MMd21_rep3


title: 1384

value: F

value: GBM

value: MT

value: co-deletion


title: Scramble-shRNA DMSO_ATAC

value: Scramble


title: 1381

value: rGBM


title: Pu1-shRNA2 LSD1i_ATAC

value: Pu.1 shRNA2


title: 1378

value: M

value: PM


title: MMd21_rep1

value: mesenchymal stem cell


title: b6_spret_lcmv_cd8_d60_r3_ATACseq

extract_protocol:
Nextera
Qiagen MinElute reaction cleanup kit.

value: B6/Spret F1

value: Spleen

value: Memory CD8 T cell


title: Resistant LSD1i_ATAC

value: haematopoietic progenitors


title: 1371

value: WT

value: non co-deletion

value: EM


title: Resistant IBET_ATAC

value: I-BET Resistant

value: IBET


title: b6_spret_lcmv_cd8_d60_r2_ATACseq


title: Resistant DMSO IBET Rep 3 RNA-seq

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using tophat2 and bowtie2
Reads were assigned to genes using htseq-count. Differential expression was calculated using edgeR.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include CPM values for each Sample

molecule: polyA RNA

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
Libraries were prepared using QuantSeq 3’ mRNA-seq Library Prep kit (Lexigen)


title: Resistant DMSO IBET Rep 2 RNA-seq


title: b6_spret_lcmv_cd8_nav_r1_RNAseq

value: Naive CD8 T cell


title: b6_spret_lcmv_cd8_d60_r1_ATACseq


title: 1350

value: O

value: MT

value: co-deletion


title: b6_spret_lcmv_cd8_d07_r2_ATACseq

value: Activated CD8 T cell


title: b6_spret_lcmv_cd8_d07_r3_ATACseq


title: Resistant DMSO IBET Rep 1 RNA-seq


title: MMd11_rep1

value: Not infected


title: 1339

value: M

value: PM


title: MMd4_rep3

value: mesenchymal stem cell


title: MMd4_rep2


title: MMd11_rep2


title: MMd11_rep3


title: Resistant DMSO Rep 3 RNA-seq


title: 1336

value: OA


title: 1333

value: F

value: GBM


title: b6_spret_lcmv_cd8_d07_r1_ATACseq

value: B6/Spret F1

value: Spleen


title: MMd4_rep1


title: Resistant DMSO Rep 2 RNA-seq

value: haematopoietic progenitors


title: 1321

value: non co-deletion


title: MMd1_rep3


title: b6_spret_lcmv_cd8_nav_r3_ATACseq


title: Resistant DMSO Rep 1 RNA-seq

value: I-BET Resistant


title: b6_spret_lcmv_cd8_nav_r2_ATACseq

value: Naive CD8 T cell


title: Resistant LSD1i IBET Rep 3 RNA-seq


title: BM-MSCs_donor 2_transfected_hPL-medium_P12

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, purified, labeled, and hybridized to the array according to the manufacturer's instructions.

scan_protocol: The array was then washed using Affymetrix fluidic stations, and scanned using the Affymetrix GeneChip®Scanner GCS 3000 Genechip System.

data_processing: Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using Affymetrix CytoScanHD (version 3.2). Only CNVs >200 kb with a mean marker distance of <5kb were considered.

label: biotin

source_name: MSCs

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: MSCs were isolated from bone marrow after written consent using guidelines approved by the Ethic Committee on the Use of Human Subjects at the University of Aachen (permit number: EK300/13). Subsequently, MSCs were cultured in MSC-culture medium comprising 10% human platelet lysate (hPL).

extract_protocol: DNA was isolated using the NucleoSpin® Tissue Kit (MACHEREY-NAGEL, Düren, Germany). DNA quantity was assessed using a NanoDrop Spectrophotometer.

treatment_protocol: At passage 3, MSCs were transfected with pCXLE-based episomal plasmids (Addgene, Cambridge, MA, USA) carrying the OCT3/4, SOX2, KLF4, LIN28 and c-MYC genes, siRNA against P53, and the gene for the enhanced green fluorescent protein (EGFP), and with a pMSCV-based episomal plasmid carrying a puromycin resistance gene (Addgene). After tranfection, MSCs were selected by adding 1.5 µg/mL puromycin to the culture medium for three consecutive days. Cells were cultivated in hPL-medium and passaged every week and cell pellets of around 300,000 cells were collected and stored at -80°C for subsequent DNA extraction.

tag: donor

value: Donor 2

value: MSCs

value: Bone marrow

tag: passage


title: 1317

tag: gender

value: O

value: MT

value: co-deletion


title: MMd1_rep2

value: Not infected


title: 1318

value: M

tag: age

value: PM


title: b6_spret_lcmv_cd8_nav_r1_ATACseq


title: Resistant LSD1i Rep 3 RNA-seq

tag: condition


title: MMd1_rep1

value: mesenchymal stem cell


title: Resistant Rep 3 RNA-seq


title: 1312

tag: histology

value: GBM

tag: grade

value: WT


title: b6_cast_lcmv_cd8_d60_r3_RNAseq

source_name: B6/Cast F1 Spleen memory CD8 T cell

value: B6/Cast F1

value: Spleen

value: Memory CD8 T cell


title: Sensitive IBET Rep 3 RNA-seq

value: haematopoietic progenitors

value: I-BET Sensitive


title: b6_cast_lcmv_cd8_d60_r1_RNAseq


title: b6_cast_lcmv_cd8_d07_r4_RNAseq

source_name: B6/Cast F1 Spleen activated CD8 T cell

value: Activated CD8 T cell


title: DDX1_CLIP_2

first: Wen

address: Datun Road

institute: Institute of Biophysics, Chinese Academy of Sciences

data_processing:
After adaptor sequence removal, fastq files were aligned with Bowtie  to merged transcript sequences from the UCSC RefGene database. The parameter for the mapping program Bowtie was “-l22 -n2 -k11 -m10 -e200 –best –strata –sam –phred33-quals – 2”.
Piranha was then used to identify the DDX1 CLIP reads.
Genome_build: rn5
Supplementary_files_format_and_content: bigwig files: fwd means reads mapped to the forward strand and rev means reads mapped to the reversed strand in the reference rn5

source_name: INS-1 cells

growth_protocol: INS-1 cells were cultured with RPMI 1640 medium containing 10% fetal bovine serum (FBS), 1 mM sodium pyruvate, 50 μM 2-mercaptoethanol, 100 U/mL of penicillin, 100 ug/mL of streptomycin in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
INS-1 cells were irradiated with UV light (254 nm) to induce covalent RNA-protein cross-linking.Then the DDX1 and cross-linked RNAs were immunoprecipitated with anti-DDX1 antibody (Proteintech, 11357-1-AP), and digested with Mnase, labeled with 32P at 5’ terminal. The DDX1/RNA complex was excised from the SDS/PAGE gel visualization with a phosphorImager (fig). The cross-linked RNAs were recovered from the DDX1/RNA complex
The cross-linked RNAs were recovered from the DDX1/RNA complex, ligated to RNA adaptor, converted to cDNA, and sequenced on the Hiseq 2500 illumina platform.

tag: cell line


title: Resistant LSD1i IBET Rep 2 RNA-seq

source_name: MLL-AF9 I-BET resistant cells

value: I-BET Resistant

tag: strain


title: 1291

tag: idh mutation

tag: 1p19q co-deletion


title: Sensitive Rep 3 RNA-seq

tag: tissue


title: 1309


title: 1297

value: AOA

value: non co-deletion

value: EM


title: Resistant LSD1i Rep 2 RNA-seq


title: 1289

value: F

value: OA

value: MT

value: co-deletion


title: b6_cast_lcmv_cd8_d07_r2_RNAseq

tag: cell type

tag: time point


title: b6_cast_lcmv_cd8_d07_r3_RNAseq


title: Resistant Rep 2 RNA-seq


title: b6_cast_lcmv_cd8_d07_r1_RNAseq


title: Sensitive IBET Rep 2 RNA-seq


title: b6_cast_lcmv_cd8_d60_r2_RNAseq


title: DDX1_CLIP_1


title: 1283

value: M

value: sGBM

tag: em/pm class

value: EMlowPMlow


title: 1286

value: O

value: PM


title: b6_cast_lcmv_cd8_nav_r3_RNAseq

source_name: B6/Cast F1 Spleen naïve CD8 T cell

value: B6/Cast F1

value: Spleen

value: Naive CD8 T cell


title: 1280

source_name: Frozen glioma tissue

value: AA

value: WT


title: 1269


title: Sensitive Rep 2 RNA-seq

value: haematopoietic progenitors

value: I-BET Sensitive


title: Resistant LSD1i IBET Rep 1 RNA-seq

value: I-BET Resistant


title: b6_cast_lcmv_cd8_nav_r2_RNAseq


title: Group 4-II

city: wuhan

first: lifang

last: liu

address: HZAU

institute: HZAU

data_processing:
Raw data was checked and filtered with FastQC and fastp (Chen et al., 2018)
The clean data of each sample produced from DGE-seq was mapped to the reference transcriptome assembled before using Bowtie2 program (Langmead, Salzberg, 2012).
Gene expression levels were estimated using FPKM values (expected number of fragments per kilobase of transcript sequence per millions base pairs sequenced).
The read counts of each sample were imported into the R package NOISeq25 for the differential expression analysis.
The p value was adjusted using q value (false discovery rate), and q value < 0.05 and |log2 (foldchange)| > 1 were set as the threshold for significantly differential expression.
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Megalobrama amblycephala

source_name: blood

extract_protocol:
Blood samples were sampled from the caudal vein using heparinized syringes and placed in 2 mL centrifuge tubes. Total RNA was extracted using TRIzol reagent (Invitrogen, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: blood

tag: developmental stage

value: two-year-old sexually mature female individuals after 24 hour of successful spawning


title: Resistant LSD1i Rep 1 RNA-seq


title: b6_cast_lcmv_cd8_nav_r1_RNAseq


title: Group 4-I


title: 1251

value: F

value: GBM-O

value: non co-deletion


title: Group 3-II

value: two-year-old sexually mature female


title: Resistant Rep 1 RNA-seq


title: b6_cast_lcmv_cd8_d60_r4_ATACseq

value: Memory CD8 T cell


title: 1239

value: O

value: MT

value: co-deletion


title: Sensitive IBET Rep 1 RNA-seq


title: b6_cast_lcmv_cd8_d60_r3_ATACseq

value: B6/Cast F1

value: Spleen


title: 1235

value: PM


title: Group 3-I


title: 1233

value: M

value: OA


title: b6_cast_lcmv_cd8_d60_r2_ATACseq


title: Sensitive Rep 1 RNA-seq

value: haematopoietic progenitors

value: I-BET Sensitive


title: b6_cast_lcmv_cd8_d60_r1_ATACseq


title: b6_cast_lcmv_cd8_d07_r5_ATACseq

value: Activated CD8 T cell


title: H3K27ac HiChIP Resistant LSD1i

data_processing:
Library strategy: HiChIP
Illumina bcl2fastq v2 software was used for basecalling.
The Juicer HiC analysis pipeline was used to align reads, count the number of interactions between genomic bins and generate hic files. The files were visualized in Juicebox.
Genome_build: mm10
Supplementary_files_format_and_content: hic files containing the frequency of interactions between genomic bins.

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO).

extract_protocol:
5000000 cells were crosslinked with 1% formaldehyde for 10 mins, digested with Mbo1 and ligated to join close proximity fragments, as reported previously. Post ligation, nuclei were lysed using ChIP lysis buffer (1% SDS, 10mM EDTA, 50mM Tris-HCl pH 8) and sonicated using the Covaris S2 Ultrasonicator (Fill level:10, Duty Cycle:10%, Power: 70W, Burst:200, Time: 8mins-30 secs on, 30 secs off). Sonicated chromatin was then diluted 1:8 in ChIP dilution buffer (1% Triton-X, 0.1% Na-Doxycholate, 90mM NaCl, 10mM Tris-HCl pH 8) before being incubated with 5ug of H3K27ac antibody overnight at 4°C. Antibody-protein complexes were then incubated with Protein A Dynabeads (Thermo Fischer) for at least 2hrs before being washed twice with t low salt buffer (0.1% SDS, 1% Triton-X, 2mM EDTA, 150mM NaCl, 20mM Tris-HCl pH 8), once with high salt buffer (0.1% SDS, 1% Triton-X, 2mM EDTA, 500mM NaCl, 20mM Tris-HCl pH 8), once with LiCl wash buffer (1% Na-Doxycholate, 1% IGEPAL-CA630, 2mM EDTA, 250mM LiCl, 20mM Tris-HCl pH 8) and once with TE. Enriched complexes were then eluted with elution buffer (1% SDS, 0.1M NaHCO3) for 20mins at 30°C. Reverse crosslinking was performed overnight at 65°C with RNAse A and NaCl. The following day, purified DNA was isolated in TE with Minelute columns (Qiagen)
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

treatment_protocol: LSD1i was used at a final concentration of 500nM.

tag: treatment

tag: antibody

value: anti-H3K27ac (ab4729, Abcam)


title: Group 2-I

value: blood

value: two-year-old immature female individuals


title: b6_cast_lcmv_cd8_d07_r4_ATACseq


title: 1171

value: GBM

value: WT

value: non co-deletion

value: EM


title: Group 1-II

value: one-year-old immature female


title: H3K27ac HiChIP Resistant

value: I-BET


title: 1105

value: sGBM

value: MT

value: co-deletion


title: Group 2-II


title: 1072

value: M

value: PM


title: Sensitive Input for Click-seq

data_processing:
Library strategy: Click-seq
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak-calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed files of macs2 peaks

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then chem-precipitation was performed with pre-clicked JQ1 biotin conjugated beads
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

value: haematopoietic progenitors

value: DMSO


title: adjacent normal gastrointestinal tissue2

city: hefei

first: ning

last: jia

address: No.81 meishan road, shushan district

institute: Anhui medical university

description: Gene expression data from adjacent normal gastrointestinal tissue  lower than gastrointestinal stromal tumors

hyb_protocol: Each slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: adjacent normal gastrointestinal tissue

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: 3 gastrointestinal stromal tumors came from obvious lesions during operation as well as its corresponding gastric or intestinal tissues, which were 1-3 centimeter distant from tumor edge and contained no obvious cancer cells.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: The fresh samples were extremely quick intensive chilling in liquid nitrogen within 5 minutes of excision to avoid degradation. Then frozen specimens were storage at -80 °C refrigerator.

value: adjacent normal gastrointestinal tissue

value: male


title: Resistant Input for Click-seq

value: I-BET Resistant

value: IBET


title: BCBL1_h96_rep2

city: Nashville

first: Jeff

last: Rathmell

state: TN

address: 1211 Medical Center Drive

department: PMI

country: USA

institute: Vanderbilt University Medical Center

data_processing:
FastQC for reads QC and demultiplexed with cutadapt, then use STAR2.5.3 for mapping with parameters adopted from original RAMPAGE page.
Raw counts of 5’ signal of mate1 were pulled from bam files with STAR
Then the 5’ signal was subject to Paraclu for clustering
The clusters called from Paraclu were filtered by consistence between replicates and merged with 50bp distance.
The transcription initiation events from each merged clusters were counted by Rsubread, only uniquely mapped reads were counted
Genome_build: hg38
Supplementary_files_format_and_content: csv, counts of reads to each paraclu clusters

growth_protocol: ISLK.219 cells were kept in DMEM median with 10%FBS, TREx-BCBL1-RTA cells were kept with 10%FBS.

extract_protocol:
Trizol
RAMPAGE
ribosome-depleted total RNA

treatment_protocol: 1ug/ml doxycycline

value: PEL derived cell line

value: dox induced lytic activation

tag: time


title: b6_cast_lcmv_cd8_d07_r2_ATACseq

value: B6/Cast F1

value: Spleen

value: Activated CD8 T cell


title: adjacent normal gastrointestinal tissue3

tag: gender


title: Gastrointestinal stromal tumors (GISTs)  tissue3

value: Gastrointestinal stromal tumors

tag: age


title: Gastrointestinal stromal tumors (GISTs)  tissue1

value: female


title: adjacent normal gastrointestinal tissue1


title: BCBL1_h96_rep1


title: 1050

value: OA

value: MT


title: Sensitive DMSO Click-seq

tag: condition

value: I-BET Sensitive


title: b6_cast_lcmv_cd8_d07_r1_ATACseq


title: 1060

value: M

tag: histology

value: rGBM-O

value: non co-deletion

value: PM


title: Group 1-I

value: blood

value: one-year-old immature female


title: 1049

value: GBM

tag: grade

value: WT


title: b6_cast_lcmv_cd8_d07_r3_ATACseq


title: Gastrointestinal stromal tumors (GISTs)  tissue2

value: male


title: Resistant LSD1i Click-seq

value: haematopoietic progenitors

value: I-BET Resistant


title: BCBL1_h72_rep2

tag: cell line

value: PEL derived cell line

value: dox induced lytic activation


title: b6_cast_lcmv_cd8_nav_r4_ATACseq

tag: strain

value: B6/Cast F1

value: Spleen

value: Naive CD8 T cell


title: 1045

tag: idh mutation

value: EM


title: InputResistant_for_ChIP-seq

value: DMSO


title: BCBL1_h48_rep2


title: 1034

value: M

value: AA

tag: 1p19q co-deletion


title: b6_cast_lcmv_cd8_nav_r3_ATACseq

tag: tissue


title: BCBL1_h72_rep1

tag: cell type


title: b6_cast_lcmv_cd8_nav_r1_ATACseq


title: BCBL1_h24_rep2


title: Resistant IBET Click-seq

value: IBET


title: 1031

value: F

value: A

value: MT

value: non co-deletion

value: PM


title: InputSensitive_for_ChIP-seq

value: haematopoietic progenitors

value: I-BET Sensitive


title: BCBL1_h12_rep2

value: PEL derived cell line


title: WT817

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Base-calling
bcl2fastq v2.17.1.14
Adapter trimming, alignment, novel miRNA detection and read counting
Oasis 2 module 1 (sRNA detection)
https://oasis.dzne.de/
Differential expression analysis
Oasis 2 module 2 (DE analysis)
https://oasis.dzne.de/small_rna_de.php
Genome_build: mm10
Supplementary_files_format_and_content: Counts
DE_genes.xls and DE_genes_min5reads.xls, they both contain differential expression analysis of wild-type vs. knock-out samples generated with Oasis 2 module 2 (DE analysis) (Capece, Vincenzo, et al. "Oasis: online analysis of small RNA deep sequencing data." Bioinformatics 31.13
(2015): 2205-2207, https://oasis.dzne.de/small_rna_de.php), where DE_genes.xls contains the results for all small RNAs (sRNAs), and DE_genes_min5reads.xls contains the results for sRNAs with at least 5 raw reads on average in either condition (i.e. sRNAs with less than 5 reads on average in both conditions are filtered out). As for the contents of both files, those are as follows:

1) mature - accession ID of sRNA
2) structure - indication of the type of sRNA: micro (miRNA), novel micro, piwi-related (piRNA), ribosomal (rRNA), small nucleolar (snoRNA) or small nuclear (snRNA)
3) sRNA coordinates (4 columns containing chromosome name, start and stop positions and strand); entries of "multiple" indicate family of sRNAs associated with multiple genomic coordinates
4) Differential expression statistics, including log2FoldChange, adjusted p-value (padj), overall baseMean, base mean for wild-type samples only (baseMean_control) and for knock-out samples only (baseMean_treatment_files_1), log2 fold-change standard error (lfcSE), statistic score used by DESeq2 to calculate the p-values (stat), and the original pvalue
5) Normalised read counts for each sample (p404sWT817_Lize_S70_L008, p404sWT819_Lize_S72_L008, and p404sWT827_Lize_S73_L008 for the wild- type samples, and treatment_files_1_p404sKO818_Lize_S71_L008,
treatment_files_1_p404sKO820_Lize_S67_L008,
treatment_files_1_p404sKO832_Lize_S68_L008 and
treatment_files_1_p404sKO833_Lize_S69_L008 for the knock-out samples).

source_name: lateral ventricle and Choroid plexus from Mus musculus strain C57BL/6J

extract_protocol:
Phenol/Chloroform total RNA isolation.
TruSeq Illumina small-RNA sequencing (according to manufacture recommendations)

value: lateral ventricles and Choroid plexus

value: adult

tag: genotype/variation

value: Wild-type


title: MED1_SenDMSO_ChIP-seq

tag: chip antibody

value: anti-Med1/CRSP1/Trap220 (A300-793A, Bethyl Labs)


title: BCBL1_h48_rep1

value: dox induced lytic activation


title: 848

value: GBM

value: WT

tag: em/pm class

value: EM


title: b6_cast_lcmv_cd8_nav_r2_ATACseq

value: B6/Cast F1

value: Spleen

value: Naive CD8 T cell


title: 893

value: F

value: OA

value: MT


title: MED1_ResIBET_ChIP-seq

value: haematopoietic progenitors

value: I-BET Resistant

tag: treatment

value: IBET


title: KO833

value: lateral ventricles and Choroid plexus

tag: developmental stage

value: TAp73 Knock-out


title: WT827

value: adult

value: Wild-type


title: 822

value: M

value: sGBM

value: non co-deletion

value: PM


title: 807

value: A

value: WT

value: EMlowPMlow


title: 837

value: GBM-O

value: EM


title: 1024

value: GBM


title: BCBL1_h24_rep1

value: PEL derived cell line

value: dox induced lytic activation

tag: time


title: WT819


title: PUI1_ResIBET_ChIP-seq

value: haematopoietic progenitors

value: I-BET Resistant

value: anti-PU.1/SPI1 (sc325, Santa Cruz Biotechnology)

value: IBET


title: PUI1_SenDMSO_ChIP-seq

value: I-BET Sensitive

value: DMSO


title: KO832

value: lateral ventricles and Choroid plexus

value: adult

value: TAp73 Knock-out


title: KO820


title: BCBL1_h12_rep1


title: BCBL1_latency_rep1

value: control

value: latency


title: BM-MSCs_donor 2_transfected_hPL-medium_P4

tag: donor

value: Donor 2

value: MSCs

value: Bone marrow

tag: passage


title: H3K4me2_ResLSD1i_ChIP-seq

tag: condition

value: anti-H3K4me2 (ab32356, Abcam)


title: iSLK_h96_rep2

value: KSHV containing cell line


title: KO818


title: iSLK_h96_rep1

value: dox induced lytic activation


title: H3K4me2_ResIBET_ChIP-seq

value: haematopoietic progenitors


title: iSLK_h72_rep2


title: H3K4me2_SenDMSO_ChIP-seq


title: iSLK_h72_rep1


title: 5GB1C-JG15-N-BR2: LanA mutant, no lanthanum added, biological replicate 2

city: Seattle

first: Mitchell

middle: William

last: Pesesky

state: WA

address: 616 NE Northlake Place

institute: University of Washington

data_processing:
Alignment was performed using BWA version 0.7.12-r1044 using the BWA-MEM algorithm and default parameters.
The alignments were post-processed into sorted BAM files with SAMTools version 1.2-232-g87cdc4a.
Reads were attributed to open reading frames (ORFs) using the htseq-count tool from the ‘HTSeq’ framework version 0.6.1p1 in the ‘intersection-nonempty’ mode.
Differential abundance analysis was performed with DESeq2 1.2.10 using R 3.3.0.
Genome_build: CP035467
Supplementary_files_format_and_content: *.dat.txt files are two columns: locus tag and read count. At the bottom of the file five lines of summary read alignment statistics are given.

organism: Methylotuvimicrobium buryatense

source_name: exponential phase culture

growth_protocol: Starter cultures were grown to late logarithmic phase (OD600 ~ 0.8) and a 2% inoculum (v/v) was transferred into 50 mL NMS2 medium, under an atmosphere of 25% methane and 75% air.

extract_protocol:
Once samples reached OD600 ~ 0.6-0.7, 2.5 mL of a stop solution of 5% (v/v) phenol in ethanol was added to 22.5 mL of culture. Cells were pelleted for 15 min at 4°C, and resuspended in RNA extraction buffer (a 1:3 ratio of 5% cetrimonium brimide in 2.5 M NaCl to 0.1 M phosphate buffer at pH 5.8). An equal volume of phenol-chloroform-isoamyl alcohol (25:24:1 ratio) was added, and sodium dodecyl sulfate and N-lauroylsarcosine sodium salt were each added at 0.5% (v/v). Cells were lysed in a bead beater with 0.1-mm zirconia-silica beads (Biospec Products, Bartlesville, OK, USA) for 4 min, then centrifuged at 14,000 x g for 5 min. The aqueous fraction was then washed with chloroform-isoamyl alcohol (24:1 ratio), and the aqueous fraction from this wash was precipitated overnight with 150 mM sodium acetate (pH 5.5), 1.5 mM MgCl2, and 50% isopropanol at -80°C. Precipitated RNA was harvested at 14,000 x g for 30 min at 4°C, and treated with DNase I (Ambion, Foster City, CA, USA) before purification with the RNeasy minikit and on-column DNase (Qiagen, Hilden, Germany).
cDNA library preparation and RNA sequencing was performed by GENEWIZ using Illumina HiSeq 2x150 (pair ended) reads.

treatment_protocol: Wild-type and lanA- cells were growth in biological duplicate in either 0 µM or 30 µM lanthanum, for a total of 8 samples.

value: lanA mutant

value: exponential phase culture


title: 5GB1C-JG15-N-BR1 : LanA mutant, no lanthanum added, biological replicate 1


title: BCBL1_latency_rep2

value: PEL derived cell line


title: H3K4me1_ResLSD1i_ChIP-seq

extract_protocol:
Lysate were isolated from formaldehybe cross-linked cells and sonicated to release the chromatin, then immunoprecipitated with antibody
ThruPLEXTM-FD Prep Kit protocol (Rubicon Genomics)

value: I-BET Resistant

value: anti-H3K4me1 (ab8895, Abcam)


title: 5GB1C-JG15-La-BR2 : LanA mutant, lanthanum added, biological replicate 2


title: 766

tag: gender

value: M

tag: age

tag: histology

value: OA

value: MT

value: co-deletion

value: PM


title: H3K4me1_ResIBET_ChIP-seq

tag: strain

value: IBET


title: 5GB1C-JG15-La-BR1 : LanA mutant, lanthanum added, biological replicate 1


title: 757

value: A

tag: grade

tag: idh mutation

value: non co-deletion


title: iSLK_h48_rep2

tag: cell line


title: 804

value: F

value: GBM

value: WT

tag: 1p19q co-deletion


title: H3K4me1_SenDMSO_ChIP-seq

tag: tissue

value: haematopoietic progenitors

value: I-BET Sensitive

value: DMSO


title: iSLK_h48_rep1

tag: cell type

value: KSHV containing cell line

value: dox induced lytic activation


title: 5GB1C-5G-N-BR2 : Wild-type, no lanthanum added, biological replicate 2

tag: genotype/variation

value: Wild-type

value: exponential phase culture


title: iSLK_h24_rep2

tag: treatment


title: 791

value: M

value: AA

tag: em/pm class

value: EMlowPMlow


title: 5GB1C-5G-N-BR1 : Wild-type, no lanthanum added, biological replicate 1


title: H3K27ac_ResLSD1i_ChIP-seq

value: I-BET Resistant

tag: chip antibody

value: anti-H3K27ac (ab4729, Abcam)


title: 782

value: EM


title: H3K27ac_ResIBET_ChIP-seq

value: IBET


title: iSLK_h24_rep1

tag: time


title: 727

value: non co-deletion


title: 5GB1C-5G-La-BR2 : Wild-type, lanthanum added, biological replicate 2


title: 681

value: GBM

value: PM


title: 694

value: rA

value: MT


title: iSLK_h12_rep2


title: 678

value: rAA

value: WT


title: iSLK_h12_rep1

value: KSHV containing cell line

value: dox induced lytic activation


title: 676


title: BRD4_ResIBET_ChIP-seq

value: haematopoietic progenitors

value: anti-Brd4 (A301-985A100, Bethyl Labs)


title: 715

value: M

value: O


title: BRD4_ResLSD1i_ChIP-seq

value: I-BET Resistant


title: BRD4_SenDMSO_ChIP-seq

value: I-BET Sensitive

value: DMSO


title: 666

value: F

value: OA

value: co-deletion


title: CRISPR pool

data_processing:
Library strategy: CRISPR screen:
Illumina bcl2fastq v2 software was used for basecalling.
Reads containing the ampliifed sgRNA sequence were extracted by grep for the sequences present in the sgRNA vector
The sequences of the sgRNA and barcode were counted using the processAmplicons function in edgeR (biocondictor).
The sgRNA Rpa3_e1.1 was removed from further analysis as it was abberantly amplified.
sgRNA that show a signicantly change in representation were calculated using RSA (Konig Nat. Methods 2007)
Genome_build: mm10
Supplementary_files_format_and_content: counts table of sgRNA for each sample: CrisprCounts.txt
unique barcode for each sample: CRISPRbarcodes.txt
sequence of sgRNA in library: mouse epi_sgRNA.txt

extract_protocol:
Genomic DNA was extracted using QiAamp DNA mini kit (Qiagen).
PCR was conducted to maintain guide representation, using AmpliTaq Gold DNA Polymerase (Thermo Fisher). PCR products were pooled and sequenced

treatment_protocol: I-BET resistant cells were transduced with FUCas9Cherry and the sgRNA library. For the differentiation GR1 screen, transduced cells were sorted and allowed to grow in culture for 7 days. After 7 days, differentiated cells (GR1+) were isolated by flow cytometry. For the screen to identify proteins required for LSD1i mediated differentiation, transduced cells were sorted and allowed to grow in culture for 7 days. After 7 days, the cells were treated with LSD1i for another 7 days. The cells that didn’t respond to LSD1i (CD86-) were then isolated by flow cytometry.


title: 655

extract_protocol: Total RNA was extracted from about 30mg frozen  tissue using AllPrep DNA/RNA Mini Kit (QIAGEN,Cat No./ID: 80204)

value: PM


title: 624

value: rGBM

value: non co-deletion

value: EM


title: 5GB1C-5G-La-BR1 : Wild-type, lanthanum added, biological replicate 1

value: Wild-type

value: exponential phase culture


title: H3K27ac_SenDMSO_ChIP-seq

data_processing:
Illumina bcl2fastq v2 software was used for basecalling.
Reads were aligned to the mouse genome (GRCm38.78) using bwa mem
Duplicate reads and reads mapping to blacklist regions or the mitochondria were removed
Peak-calling was performed using MACS2
Genome_build: mm10
Supplementary_files_format_and_content: bed files of macs2 peaks

value: anti-H3K27ac (ab4729, Abcam)


title: Pooled single cell RNA-Seq

data_processing:
Reads from single-cell RNA-seq libraries were processed in R using the scPipe package to map reads to the transcriptome, demultiplex reads to individual cells and counts reads mapping to each gene.
Low quality cells and non-expressed genes were identified with the scater package and removed prior to analysis.
The cell counts were normalised using the scran package.
Genome_build: mm10
Supplementary_files_format_and_content: matrix of gene count for each cell
Genome_build: Barcode information for demultiplexing single cells

source_name: MLL-AF9 cells

extract_protocol:
Viable single cells from each treatment group were sorted based on GR1+/- phenotype on the BD FACSAria III, directly into pre-prepared 384 well plates that contained a mixture of oligo (dT) primer, dNTPs and ERCC spike ins, as outlined in the Cel-seq2 protocol.
A modified version of Cel-seq2 was used to generate single cell cDNA libraries. Briefly, the sorted cells were lysed and the primers annealed to the RNA at 65°C. Primers contained a 24bp polyT stretch, a 6bp unique molecular identifier (UMI), a cell-specific 8bp barcode, the 5′ Illumina adaptor and a T7 promoter. Reverse transcription, second strand synthesis and in vitro transcription were performed according to the Cel-seq2 protocol, with the exception of the cDNA cleanup step prior to IVT, whereby the volume of the Agencourt AMPure XP beads (A63880, Beckman Coulter) was 5% of the total volume of beads used in the original protocol. Following IVT, the amplified RNA was fragmented, cleaned up and reverse transcribed with a random hexamer primer containing the sequence complimentary to the 3’ Illumina adaptor. Fragments containing both adaptors were selected for by PCR using TruSeq Small RNA primers (Illumina).

treatment_protocol: MLL-AF9 drug naive parental cells were dosed with either 400nM I-BET151 or 0.1% DMSO (vehicle) for 4 days. MLL-AF9 I-BET resistant cell line was grown continuously in 1uM I-BET151. For drug withdrawal, MLL-AF9 I-BET resistant cell was removed from I-BET151 media 4 days prior to isolation.

value: haematopoietic progenitors


title: 605

data_processing:
Raw sds files or eds files generated by 7900HT Fast Real-Time PCR System were imported to  Expression Suite Software v1.0.4 (Thermo Fisher Scientific).
The cycle threshold (CT ) for each gene was automatically determined by  Expression Suite Software v1.0.4 .
CT values  of the classifier genes were normalized against the geometric average CT values of ACTB，GAPDH and UBC.

value: rAO

value: MT


title: BRD4_ResLSD1i_IBET_ChIP-seq

value: anti-Brd4 (A301-985A100, Bethyl Labs)


title: 603

value: M

value: rAA


title: iSLK_latency_rep1

value: KSHV containing cell line

value: control

value: latency


title: 565

value: AOA

value: WT

value: EMlowPMlow


title: HFD+HT_97

first: Juan

last: Feng

address: No.30, Shuangqing Road, Haidian District

department: School of Medicine

institute: Tsinghua University

description: After rats were fed with high-fat diet alone for 4 weeks, hawk tea extract (HT) were co-supplemented with HFD for further 11 weeks.

data_processing:
Raw image data files obtained from high throughput sequencing was delivered to Phred base calling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to rat whole genome using HISAT2 software.
Fragments Per Kilobase of exon per Million fragments (FPKM) were calculated using Stringtie-1.3.3b . 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: Rat reference genome (rn6) for read alignment
Supplementary_files_format_and_content: tab-delimited text files include raw and normalized counts or FPKM values for each Sample.

extract_protocol:
Livers were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: SD

value: Liver

tag: Sex

value: male

value: 6-8 weeks

tag: diet

value: high-fat


title: Highly developed thylakoid and chlorophyll containg cells 3

city: Rehovot

first: Gilgi

last: Friedlander

address: Hertzel st

country: Israel

institute: Weizmann Institute of Science

data_processing:
Reads were demultiplexed for the different samples
Reads were aligned to  the Solanum lycopersicum genome (Build 2.5) together with the Chloroplast sequence (NC_007898.3) using Bowtie2 (V 2.1.0) using local mode.
Reads with identical UMIs that are counted to a specific gene in the counting stage, are collapsed to a single read
Read counting to ITAG2.4  genes and to the Chloroplast annotations was done with HTseq-count (200 bp were added to the 3' end of each gene (not in the chloroplast genes due to short distances between genes) in order to ensure counting all reads per gene)
Differential expression analysis was performed with DESeq2 (1.4.0)
Genome_build: Solanum lycopersicum genome Build 2.5 & Chloroplast NC_007898.3
Supplementary_files_format_and_content: Excel file includes the DESeq2 normalized counts

organism: Solanum lycopersicum

source_name: Leaf Primordium (LP)

growth_protocol: 12-14 d old tomato (M82 SP+) seedlings were used as study material. Tomato seedlings were grown aseptically in magenta boxes at 200 mm m-2 s-1 light in long day conditions (11 h light, 13 h dark) at 21-23 0C, in half strength Nitch medium (Nitsch and Nitsch 1969).

extract_protocol:
Approximately 2 mm long SAM was dissected from seedlings was inserted into TissueTek@ OCT (Sakura Finetek) medium kept into 10x10x5 cm cryomoulds (Sakura Finetek) and freezed in Liq N2. Cryoblocks were cut in 10 um thick cryosections with cryostat (Leica CM3050 S.) 12-15 sections can be obtained from a single SAM. Sections were collected on 0.1mm Polyethylene Terephthalate (PET) or 1.0 mm Polyethylene Naphthalate (PEN) membrane slides. Different cell types were visualized based on their Chl fluorescence seen through DAPI filter (Ex 400; Em 460). Since the Chl flu is lost during ethanol fixation, flu images of some SAM section were taken and the adjacent sections were dissected based on these images. Sections were immediately fixed in 70%, dehydrated with 70%, 96% and 100%, 100%  ethanol, and dried in air for 2 min. LM was performed with a P.A.L.M.MicroBeam system mounted on AxioObserver microscope (Carl Zeiss). Cut areas were collected in 500ul adhesive caps containing 35 μl of RLT lysis buffer from RNeasy Micro RNA isolation kit (Qiagen), was put in cap. Cap was closed and put inverted for 30 min at room temp, then stored at -80 0C. RNA was isolated with Qiagen MicroRNA kit according to manufacturer’s instruction and quality was checked with Bioanalyzer 2100 (BA) with BA-PICO 6000 Chip (Agilent Technologies).
RT reaction was performed with indexed primers containing from 5' to 3' end is: T7 promoter, Illumina 5' adaptor, Unique barcode, UMI and polyT sequence, to do first strand cDNA synthesis for all the RNA samples separately. External RNA controls Consortium (ERCC) mRNA spike-ins (Ambion, Life Technologies) were added to the samples during initial step of first strand cDNA synthesis. Different indexes/barcodes were used for different samples. Second strand cDNA synthesis was also performed separately on each sample. After second strand cDNA synthesis, samples containing the different barcodes were pooled and further processing was performed with this single sample. One round RNA amplification was carried out with Ambion/Life Technology (Invitrogen) MessageAmp™ II aRNA Amplification Kit (AM1751) as described by the manufacturer using 1/10 of the reaction volume as per Hashimshony et al., 2012, to get amplified RNA (aRNA).  Sample volume of aRNA was adjusted to 16μl, either by adding water or drying down in a speedvac, depending on RNA concentration. Reaction was end repaired by treating with phosphatase at 37 °C  for 30 min and with PNK at 37 °C  for 60 min as described in supplementary methods of Hashimshony et al., 2012 , and cleaned on RNeasy spin column. 3’ adapter was ligated using T4 ligase at 28 °C  for (60 +15) min. Reaction was stopped, reverse transcribed and PCR amplified with following program 30 seconds at 98°C, 15 cycles of: 10 seconds at 98°C, 30 seconds at 60°C, 30 seconds at 72°C and 10 minutes at 72°C. PCR product was cleaned with AMPure XP Beads (Agencourt AMPure XP). Quality of library was checked on Bioanalyzer (BA).

value: M82 SP+


title: Kidney_IR_rep2

first: Ping

last: Jia

address: No. 180, Fenglin Road

department: Department of Nephrology

institute: Zhongshan Hospital, Fudan University

description: Gene expression in kidney 24h after renal ischemia reperfusion

hyb_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method (Arraystar Flash RNA Labeling Kit, Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000. 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned with using the Agilent DNA Microarray Scanner (part number G2505C).

scan_protocol: Slides were scanned immediately after washing on the Agilent Microarray Scanner (Agilent p/n G2565BA) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 3 out of 6 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: kidney, ischemia reperfusion,  24h

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from dissected kidney tissue was extracted using Trizol reagent (Invitrogen, Carlsbad, CA), followed by quantification. RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

value: kidney

tag: gender

tag: stress

value: IR


title: 551

tag: age

tag: histology

value: O

value: MT

value: co-deletion

value: PM


title: Kidney_sham_rep3

description: Gene expression in kidney 24h after sham operation

source_name: kidney, sham operation, 24h

value: control


title: Highly developed thylakoid and chlorophyll containg cells 2


title: Kidney_IR_rep3


title: HFD+HT_93

source_name: After rats were fed with high-fat diet alone for 4 weeks, hawk tea extract (HT) were co-supplemented with HFD for further 11 weeks.

tag: strain


title: Highly developed thylakoid and chlorophyll containg cells 1


title: Kidney_IR_rep1


title: 501

value: M

tag: grade

tag: idh mutation


title: HFD+HT_59


title: Ctl_poly_rep3

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

hyb_protocol: 1.5 µg of labeled fragments were hybridized to GeneChip Human Gene ST 2.0 arrays for 16 h at 45 °C with 60 rpm in an Affymetrix Hybridization oven 645.

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software Version 4.0.

data_processing: R/Bioconductor using Single-Channel Array Normalization (SCAN), (Picolo et al., Genomics 2012).

label: Biotin

source_name: HeLa Cell Line

label_protocol: The amplified cDNA was fragmented and labeled using the Affymetrix WT Terminal labeling and controls kit.

growth_protocol: Human HeLa cells were cultured at 37 °C/ 5 % CO2 and were maintained in Dulbecco modified Eagle’s medium (DMEM) supplemented with 10 % fetal calf serum (FCS, Sigma-Aldrich and PAA Laboratories).

extract_protocol: For polysome RNA profiling HeLa cells were infected with C. trachomatis or treated with stress inducers as described above. Shortly before harvesting, 50 µg/ml of cycloheximide was added for 5 min. Cells were lysed in lysis buffer containing 10 mM Tris-HCl (pH 7.5), 30 mM KCl, 10 mM MgCl2, 1 mM DTT, 0.5 % NP 40, 100 µg/ml CHX and 200 U/ml of RNAsin (Promega, #N2511) for 15 min on ice and disrupted by passage through a G26 syringe. Lysates were centrifuged at 4 °C for 30 min. Supernatants adjusted for protein content were layered on 7-45 % sucrose density gradients (10 mM Tris pH 7.5, 60 mM KCl, 10 mM MgCl2, 1 mM DTT, 7 or 50 % sucrose, 10 µg/ml CHX) and centrifuged at 260,000 x g for 2 h at 4 °C in a Beckman SW41Ti rotor. Fractions were collected by upward displacement through a Bio-Rad EM-1 UV monitor for continuous measurement of the absorbance at 254 nm. Polysomal RNA  as well as total RNA was isolated using the High Pure RNA Isolation Kit (Roche, #11828665001) and precipitated. Glycogen (300 µg/ml) was added as well as 1/10 the volume ammonium acetate (750 mM, Sigma, #A2706) and 2.5 volumes of 100 % ethanol. After incubation for 20 min at -20 °C, samples were washed with 75 % ethanol, dried and dissolved in water. Samples with an RNA integrity number (RIN) of greater than 8.5 were further processed with the Nugen Ovation Pico WTA V2 kit (NuGEN, #3302) according to the manufacturer’s protocol.

treatment_protocol: Chlamydia trachomatis biovar LGV L2/434/Bu was obtained from the American Type Culture Collection (ATCC), amplified in HeLa cells and stored in SPG medium (0.2 M sucrose, 8.6 mM Na2HPO4, 3.8 mM KH2PO4, and 5 mM glutamic acid, pH 7.4) at -80 °C. Host cells were seeded the day before infection. C. trachomatis was added directly to the 80 % confluent cells.

tag: cell line

value: HeLa

tag: replicate

value: uninfected control


title: Ctl_poly_rep2


title: Infection_poly_rep3

value: infected


title: Partially developed thylakoid and chlorophyll containg cells 3

source_name: Peripheral Zone (PZ) of SAM

tag: cell type


title: Kidney_sham_rep1

tag: tissue


title: Ctl_poly_rep1

tag: treatment


title: 495

value: GBM

value: WT

tag: 1p19q co-deletion

value: non co-deletion

tag: em/pm class

value: EM


title: Kidney_sham_rep2

value: male


title: Infection_poly_rep2


title: Partially developed thylakoid and chlorophyll containg cells 2

value: M82 SP+


title: Infection_poly_rep1


title: 490

value: F

value: AO


title: HFD_106

description: Rats were fed with high-fat diet for 15 weeks.

value: SD

value: Liver

value: 6-8 weeks

value: high-fat


title: Ctl_tot_rep3


title: ND_3

description: Rats were fed with normal diet for 15 weeks.

value: normal


title: Proplastid containg, no chlorophyll cells 3

source_name: Central Zone (CZ) of SAM


title: Partially developed thylakoid and chlorophyll containg cells 1


title: 458

value: M

value: rOA

value: MT

value: PM


title: HFD_16

source_name: Rats were fed with high-fat diet for 15 weeks.


title: Ctl_tot_rep2

value: HeLa

value: uninfected control


title: ND_1

source_name: Rats were fed with normal diet for 15 weeks.


title: 426

value: AA

value: WT

value: non co-deletion


title: 236

value: O

value: co-deletion


title: 241

value: OA

value: EMlowPMlow


title: hiHep_3D_RAS_16d_Rep2

status: Public on May 20 2019

first: Lulu

last: Sun

state: Shanghai

address: 320 Yueyang Road

institute: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences

data_processing:
Low quality reads were trimmed. The remained reads were aligned to the human genome (Ensemble GRCh38.84) using Tophat2
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized  by Cuffnorms
Genome_build: Ensemble GRCh38.84
Supplementary_files_format_and_content: Tab-delimited text files include counts for each sample

source_name: hiHep organoids which were infected with RAS and cultured for 16 days-Replicate2

growth_protocol: hiHep organoids consisted of hiHep cells. Organoids were formed by aggregating 5x105 hiHep cells in 24-well nonattachment plate. Lentiviruses of different oncogenes were transfected to hiHep organoids the time we seeded cells and the second infection was operated 4 days later. We changed half medium every day.hiHep cells were transdifferentiated from UCFs according to the published protocol(Huang, et al, Cell Stem Cell, 2014).

extract_protocol:
Total RNA of different groups of hiHep cells was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: hiHep hepatocyte-like cells

tag: mutation

value: hRASG12V overexpression

tag: culture time

value: 16 days


title: ProliHH organoid_RAS

description:
Sample_R18064072LR01-L527
Genes.counts-ProliHH organoids.txt

data_processing:
Low quality reads were trimmed. The remained reads were aligned to the human genome (Ensemble GRCh38.84) using Tophat2
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The counts expression profiles were normalized  by Cuffnorms
Genome_build: Ensemble GRCh38.84
Supplementary_files_format_and_content: Genes.counts-ProliHH organoids.txt: Counts for each sample (without running and mapping together with hiHep organoids)

source_name: ProliHH organoids which were transfected with RAS

growth_protocol: ProliHH organoids were cultured following the published protocol (Zhang et al, Cell Stem Cell, 2018).

extract_protocol:
Total RNA of different groups of ProliHH cells was extracted using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: ProliHH organoids were transfected with c-MYC and RAS oncogenes following the same protocol of transfection in hiHep organoids.

value: proliferating hepatocytes

value: Cultured primary hepatocytes

value: RAS over-expression


title: ProliHH organoid_c-MYC

description:
Sample_R18065338LR01-L577
Genes.counts-ProliHH organoids.txt

source_name: ProliHH organoids which were transfected with c-MYC

value: c-MYC over-expression


title: ProliHH organoid_Control

description:
Sample_R18064071LR01-L526
Genes.counts-ProliHH organoids.txt

source_name: ProliHH organoids which were transfected with GFP as a control


title: Proplastid containg, no chlorophyll cells 1

value: M82 SP+


title: hiHep_3D_RAS_16d_Rep1

source_name: hiHep organoids which were infected with RAS and cultured for 16 days-Replicate1


title: Ctl_tot_rep1

value: HeLa


title: Infection_tot_rep3

value: infected


title: Infection_tot_rep1


title: Proplastid containg, no chlorophyll cells 2


title: 446

source_name: Frozen glioma tissue

value: F

value: MT

value: PM


title: hiHep_3D_RAS_2d_Rep2

source_name: hiHep organoids which were infected with RAS and cultured for 2 days-Replicate2

value: 2 days


title: hiHep_3D_RAS_2d_Rep1

source_name: hiHep organoids which were infected with RAS and cultured for 2 days-Replicate1


title: hiHep_3D_c-MYC_Rep1

source_name: hiHep organoids which were infected with c-MYC-Replicate1

value: cMYC overexpression


title: ND_2

value: SD

value: Liver

tag: Sex

value: male

value: 6-8 weeks

tag: diet

value: normal


title: Infection_tot_rep2


title: hiHep_3D_GFP_Rep1

source_name: hiHep organoids which were infected with GFP-Replicate1

value: hiHep hepatocyte-like cells

value: 16 days


title: Uninjected 2

city: Bad Nauheim

first: Carsten

last: Kuenne

address: Ludwigstrasse 43

department: Bioinformatics

institute: Max Planck Institute for Heart and Lung Research

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC 0.11.8 (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 (GRCz11) using STAR 2.6.0c with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.6.0 from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.14.1 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 12.04.2018) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: danrer11 / GRCz11
Supplementary_files_format_and_content: The tab-delimited matrix with DESeq normalized counts.

organism: Danio rerio

source_name: Embryo

growth_protocol: Tg(hsp70l:loxP-STOP-loxP-npas4l-GGGGGLSRS-P2A-mCherry)bns298 injected with cre at the one-cell stage and uninjected  were grown in E3 medium at 28°C until tailbud stage.

extract_protocol:
For RNAseq, total RNA was isolated from zebrafish embryos at 6-somite stage using the miRNeasy micro Kit (Qiagen). For exclusion of genomic DNA contamination, the samples were treated by on-column DNase digestion (DNase-Free DNase Set, Qiagen). Total RNA and library integrity were verified with LabChip Gx Touch 24 (Perkin Elmer).
10ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - Pico Input Mammalian (Takara Clontech) following manufacturers protcol. Sequencing was performed on the NextSeq500 instrument (Illumina) using v2 chemistry, resulting in average of 30M reads per library with 1x75bp single end setup.

treatment_protocol: Fish embryos raised at 28 ̊C were subject to a 37 ̊C heat shock for 1 hr by replacing the egg water with pre-warmed (37 ̊C) egg water starting at different time points, and then keeping them in a 37 ̊C incubator.

tag: genotype


title: Npas4l-KO 2

data_processing:
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC (Andrews S. 2010, FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reaper version 13-100 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides (Davis et al., Kraken: A set of tools for quality control and analysis of high-throughput sequence data). Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.90) using STAR 2.4.0a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% (Dobin et al., STAR: ultrafast universal RNA-seq aligner).
The number of reads aligning to genes was counted with featureCounts 1.4.5-p1 tool from the Subread package (Liao et al., featureCounts: an efficient general purpose program for assigning sequence reads to genomic features). Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.62 (Love et al., Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2).
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (Activities at the Universal Protein Resource (UniProt)).
Genome_build: danRer10
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized counts.

growth_protocol: Wild-type AB embryos and npas4lbns297/bns297  were grown in E3 medium at 28°C until 6-somite stage.

value: npas4l bns297/bns297


title: Cre Injected 1

value: Tg(hsp70l:loxP-STOP-loxP-npas4l-GGGGGLSRS-P2A-mCherry)bns298 injected with Cre to induce recombinase


title: Uninjected 1


title: Cre Injected 2


title: Npas4l-KO 1


title: WT 2

value: wild type


title: hiHep_3D_RAS_6d_Rep2

source_name: hiHep organoids which were infected with RAS and cultured for 6 days-Replicate2

value: hRASG12V overexpression

value: 6 days


title: WT 1


title: Npas4l-HA [ChIP-Seq]

data_processing:
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.90) using STAR 2.5.3a with the parameters “--outFilterMismatchNoverLmax 0.2 --outFilterMatchNmin 20 --alignIntronMax 1 --outFilterMultimapNmax 1” (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.9.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
The Macs2 peak caller version 2.1.0 was employed for each sample with parameters “-q 0.0001” (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
Data was corrected for the background signal by subtracting coverage of the Input sample from coverage of the ChIP sample after application of a smoothing window of 100nt length using wiggletools (Zerbino DR et al., WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis).
DESeq2 1.14.1 was used to normalize the resulting matrix of peaks to compensate for differences in sequencing depth, library composition, and pull-down effectivity (Anders et al., Differential expression analysis for sequence count data).
Genome_build: danRer10
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized background-corrected peaks.

growth_protocol: Wild-type AB embryos were grown in E3 medium at 28°C until tailbud stage (n=3000).

extract_protocol:
Cells were lysed as described (Bogdanovic et al., 2013, Methods).  Chromatin was sonicated using a probe sonicator (SONOPULS, Bendelin) with a MS72 micro tip.  The sonication was performed with 20% amplitude with 12x3 cycles of 10 sec on, 50 sec off with 12 min on ice between each cycle.  After sonication, 120 μl of 10% Triton X-100 was added.  The size of sonicated chromatin was assessed by gel electrophoresis with fragment sizes between 100-300 bp.  ChIP was conducted as previously described (Bogdanovic et al., 2013, Methods), using Protein G Dynabeads (Invitrogen) and anti-HA antibody (Abcam, ab9110).  For the elution, we resuspended the beads in 100 μl of elution buffer (50mM Tris pH8.0, 10mM EDTA, and 1% SDS) at 65°C for 15 min and reversal of crosslinks was performed overnight at 65°C with shaking at 1000 rpm.  A total of 200 μl of TE buffer was added, and samples were incubated with RNaseA (final concentration 0.2 ug/mL) at 37°C for 2 h.  Then, proteinase K was added (final concentration 0.2 ug/mL) and samples were incubated at 55°C for 2h.  An equal amount (400 μl) of phenol:chloroform:isoamyl alcohol (25:24:1) was added and the aqueous phase extracted after centrifugation at 8,000 rpm for 5 min.  DNA was purified from the aqueous phase using the Qiagen MinElute PCR purification column according to manufacturer's protocol.
After reverse cross-linking and cleanup samples were quantified by HS DNA Qubit measurement (Thermo) and 10ng DNA form Input and ChIP samples were used as input for TruSeq ChIP Sample Prep protocol following manufacturers protocol until ligation of adapters and cleanup. Ligated products were not separated by gel but used directly to PCR amplification followed by double sided bead cleanup (0.85x + 0.75x). Insert size and Library integrity was tested on LabChip Gx Touch 24 (Perkin Elmer) and quantified by Qubit HS DNA assay. Libraries were sequenced on Nextseq500 with V2 chemistry resulting in a minimum of 25M reads.

treatment_protocol: Embryos were dechorionated with pronase (2mg/mL, Roche) and deyolked according to Link et al., 2006, BMC Dev. Biol.

tag: antibody

value: HA Antibody (ab9110 abcam)


title: Npas4l-KO [ATAC-Seq]

data_processing:
Trimmomatic version 0.36 was employed to trim reads after a quality drop below a mean of Q15 in a window of 5 nucleotides (Bolger et al., Trimmomatic: a flexible trimmer for Illumina sequence data). Only reads longer than 15 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer10 (GRCz10.90) using STAR 2.5.3a with the parameters “--outFilterMismatchNoverLmax 0.2 --outFilterMatchNmin 20 --alignIntronMax 1 --outFilterMultimapNmax 1” (Dobin et al., STAR: ultrafast universal RNA-seq aligner) retaining only unique alignments.
Reads were deduplicated using Picard 2.9.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format) to mitigate PCR artefacts leading to multiple copies of the same original fragment.
The Macs2 peak caller version 2.1.0 was employed for each sample with parameters “-q 0.0001” (Zhang et al., Model-based Analysis of ChIP-Seq).
Peaks overlapping ENCODE blacklisted regions (known misassemblies, satellite repeats) were excluded.
In order to be able to compare peaks in different samples to assess reproducibility, the resulting lists of significant peaks were overlapped and unified to represent identical regions. Reads were recounted after normalization for sequencing depth with bamCoverage 2.5.4 using bigWigAverageOverBed (UCSC Toolkit) (Fidel Ramírez  et al., deepTools: a flexible platform for exploring deep-sequencing data).
DESeq2 1.14.1 was used to normalize the resulting matrix of union peaks to compensate for differences in sequencing depth, library composition, and pull-down effectivity (Anders et al., Differential expression analysis for sequence count data).
Genome_build: danRer10
Supplementary_files_format_and_content: The tab-delimited matrix shows DESeq normalized unified peaks with mean count >25.

growth_protocol: Wild-type AB embryos were grown in E3 medium at 28°C until 1-somite stage (single embryos were used for the analysis).

extract_protocol:
We centrifuged the samples at 500g for 10 min at 4°C.  After removing the supernatant, we added 51 μl of cold PBS (one microliter was used for genotyping) and we centrifuged the samples again at 500g for 10 min at 4°C.  The supernatant was removed and 50 μl of cold lysis buffer, prepared as described (Doganli et al., 2016) was added.
Cell pellet was resuspended in 50µl PBS and mixed with 25µl TD-Buffer, 2.5µl Tn5 (Illumina Nextera DNA Sample Preparation Kit), 0.5µl 10% NP-40 and 22µl water. Cell/Tn5 mixture was incubated at 37°C for 30min with occasional snap mixing. Transposase treatment was followed by 30min incubation at 50°C together with 500mM EDTA pH8.0 for optimal recovery of digested DNA fragments. For neutralization of EDTA 100µl of 50mM MgCl2 was added followed by purification of the DNA fragments by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing was performed as described elsewhere (Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. (2013) Jason D Buenrostro, Paul G Giresi, Lisa C Zaba, Howard Y Chang & William J Greenleaf. Nature Methods. doi:10.1038/nmeth.2688). Libraries were mixed in equimolar ratios and sequenced on NextSeq500 platform using V2 chemistry with 2x38bp paired end mode.


title: Input [ChIP-Seq]


title: hiHep_3D_RAS_6d_Rep1

source_name: hiHep organoids which were infected with RAS and cultured for 6 days-Replicate1


title: MED1_ResLSD1_ChIP-seq

first: Mark

last: Dawson

address: 305 Grattan Street

institute: Peter MacCallum Cancer Centre

source_name: MLL-AF9 I-BET resistant cells

growth_protocol: Cell lines were grown in RPMI-1640 supplemented with mouse IL-3 (10ng/ml), 20% FCS, streptomycin (100ug/ml), penicillin (100 units/ml) and glutamax, under standard culture conditions (5% CO2, 37°C). MLL-AF9 I-BET resistant cells were cultured with constant I-BET treatment (1000nM, 0.1% DMSO), while MLL-AF9 I-BET sensitive cells were cultured with constant DMSO treatment (0.1%).

value: haematopoietic progenitors

tag: condition

value: I-BET Resistant

tag: chip antibody

value: anti-Med1/CRSP1/Trap220 (A300-793A, Bethyl Labs)


title: WT [ATAC-Seq]


title: hiHep_3D_GFP_Rep2

source_name: hiHep organoids which were infected with GFP-Replicate2


title: hiHep_3D_c-MYC_Rep2

source_name: hiHep organoids which were infected with c-MYC-Replicate2

value: cMYC overexpression


title: PUI1_ResLSD1i_ChIP-seq

tag: strain

value: anti-PU.1/SPI1 (sc325, Santa Cruz Biotechnology)


title: Atoh1_20

city: HOUSTON

first: Yichi

last: Niu

state: TX

address: ONE BAYLOR PALAZA

department: Molecular & human genetics

institute: Baylor college of medicine

data_processing:
The raw sequencing data was trimmed using skewer package.
The reads were mapped to the genome using STAR
A Python program using HT-seq package was written to analyze the barcode information
Genome_build: mm10
Supplementary_files_format_and_content: dat files include the read count and barcode count for exon-based analyses

extract_protocol:
Single cells were directly lysed in lysis buffer
custom Nextera library preparation

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

value: Outbred (ICR)

tag: genotype/variation

value: WT

tag: age

value: 4-6 weeks

tag: virus infection

value: Utricle supporting cells


title: Atoh1_18

tag: cell type


title: Atoh1_19


title: Atoh1_16


title: Atoh1_15


title: Atoh1_17


title: Atoh1_22


title: Atoh1_21


title: Atoh1_14


title: Atoh1_12


title: Atoh1_13


title: Atoh1_11


title: Atoh1_10


title: Atoh1_8


title: Atoh1_7


title: Atoh1_6


title: Atoh1_4


title: Atoh1_3


title: tdTomato_34

source_name: Ad-tdTomato_utricle supporting cells

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

value: Ad-tdTomato


title: Atoh1_5


title: Atoh1_1


title: tdTomato_31


title: tdTomato_33


title: tdTomato_32


title: tdTomato_30


title: tdTomato_28


title: tdTomato_29


title: tdTomato_27


title: tdTomato_26


title: tdTomato_24


title: tdTomato_23


title: tdTomato_25


title: tdTomato_20


title: tdTomato_21


title: tdTomato_22


title: Atoh1_9


title: tdTomato_19


title: tdTomato_18


title: tdTomato_17


title: tdTomato_15


title: tdTomato_14


title: tdTomato_13


title: Atoh1_2


title: tdTomato_16


title: iSLK_latency_rep2

data_processing:
FastQC for reads QC and demultiplexed with cutadapt, then use STAR2.5.3 for mapping with parameters adopted from original RAMPAGE page.
Raw counts of 5’ signal of mate1 were pulled from bam files with STAR
Then the 5’ signal was subject to Paraclu for clustering
The clusters called from Paraclu were filtered by consistence between replicates and merged with 50bp distance.
The transcription initiation events from each merged clusters were counted by Rsubread, only uniquely mapped reads were counted
Genome_build: hg38
Supplementary_files_format_and_content: csv, counts of reads to each paraclu clusters

extract_protocol:
Trizol
RAMPAGE
ribosome-depleted total RNA

tag: cell line

value: KSHV containing cell line

value: control

tag: time

value: latency


title: tdTomato_12


title: tdTomato_11


title: tdTomato_10


title: tdTomato_8


title: tdTomato_9


title: tdTomato_7


title: tdTomato_5


title: tdTomato_6


title: tdTomato_3


title: tdTomato_1


title: tdTomato_2


title: tdTomato_4


title: Ts_Replicate1_Bulk

city: Ithaca

first: Roman

last: Spektor

state: New York

address: 618 Tower Rd, Vet Research Tower, Room T2 007

institute: Cornell University

description:
Ts1 Bulk Single-end ATAC-seq
processed data files:
Pseudobulk vs Bulk_counts at peaks.txt

data_processing:
Each sequencing run contains 4 fastq files: Read 1 (37bp), Read2 (37bp), Index1 (16bp), Index 2 (16bp). Each SRR will contain data for the 4 files that can be recovered using the SRA toolkit with the using fastq-dump --split-file option.
Libraries were preprocessed and aligned as in Preissl et al [PMID: 29434377] with minor modifications. Briefly, read names were labeled with combined 32bp index reads. Pair-end reads were aligned to mm10 (or mm10 and hg19 for collision tests) using Bowtie2 in pair-end mode with parameters, -p 5 -t -X2000–no-mixed–no-discordant and reads < MAPQ 30 and flag=1804 were removed and deduplicated. Barcode arrangement and orientation is altered in our Nextseq500 run compared to the HiSeq run used in Preissl et al. Each 8bp Barcode was corrected within a 2bp edit distance to their nearest barcode and separated into individual cells based on their barcode combination after which PCR duplicates and mitochondrial were removed. Cells were filtered by a minimum of 20 % fraction of reads in peaks (FRiP) score and an 820 read per cell cutoff. Peaks were called using MACS2 [PMID: 18798982] with parameters, -g mm -p 0.05 --nomodel --shift 150 --keep-dup all.
Bigwig files were generated using Deeptools 3.0.2 2 bamCoverage --binSize 1 --normalizeUsing RPKM --ignoreForNormalization chrM using cell-clusters merged using from all samples and displayed using GViz
Data for Lane 1, 2 and 3 were all merged and processed together.
Nextera PCR barcodes Lane1: Ts1_Replicate1: I7_1 and I5_1, 2n1_Replicate2: I7_1 and I5_4, Ts2_Replicate1: I7_2 and I5_1
Nextera PCR barcodes Lane2: 2n1_Replicate2: I7_1 and I5_4, Ts2_Replicate2: I7_2 and I5_2, 2n2_Replicate1: I7_2 and I5_3
Nextera PCR barcodes Lane3: 2n1_Replicate1: I7_1 and I5_3, 2n2_Replicate2: I7_2 and I5_4, Ts1_Replicate2: I7_1 and I5_2
Nextera PCR barcodes Lane4: Collision: I7_2 and I5_1
Genome_build: mm10
Supplementary_files_format_and_content: All processed data files are on series record. Please see Instructions.txt for description of demultiplexing and analysis pipeline. Please see Description_of_processed_data_files.txt for processed data file content and descriptions.

source_name: Mouse Cortex

growth_protocol: B6EiC3Sn.BLiA-Ts(1716)65Dn/DnJ (Jackson #001924) mice were purchased from Jackson and crossed to B6EiC3Sn.BLiAF1/J (Jackson #003647) for maintenance. Mice used for sci-ATAC-seq were crossed to B6.Cg-Tg(Thy1-YFP)16Jrs/J (Jackson #003709).

extract_protocol:
Tissue was disaggregated using the Omni-ATAC-seq protocol [PMID: 28846090] with minor modifications. All steps were performed on ice or in a 4°C chilled centrifuge. Briefly, mice were sacrificed and cortices were rapidly dissected and transferred into a chilled 7 mL Dounce Homogenizer containing 2.5 mL HB (320 mM sucrose, 0.1 mM EDTA, 0.1 % NP40, 5 mM CaCl2, 3 mM Mg(Ac)2, 10 mM Tris pH 7.4, protease inhibitors (Pierce #88666), 0.016 mM PMSF). Tissue was homogenized using a Dounce Tissue Grinder set (Wheaton #357542) with 10 strokes using a loose pestle and filtered through a 100 µm nylon mesh (VWR #10199-658) followed by 20 strokes using a tight pestle and centrifuged for 1 minutes at 100g. 2 mL of supernatant was mixed with 2 mL 50 % iodixanol solution (50 % iodixanol in 1x homogenization buffer). 2 mL of a 29 % iodixanol solution (29 % iodixanol in 1x HB containing 480 mM sucrose) was layered under the 25 % iodixanol/tissue mixture. 2 mL of a 35 % iodixanol solution (35 % iodixanol in 1X homogenization containing 480 mM sucrose) was layered underneath the 29 % iodixanol solution. Nuclei were centrifuged for 20 minutes at 3,000g in a swing-bucket rotor. Nuclei at the 29 % and 35 % interface were transferred to a new tube and diluted 1:5 in ATAC-RSB (10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water) and centrifuged for 5 minutes at 500g. Nuclei were resuspended in 1X Tagmentation Buffer (10 mM Tris pH 7.4, 5 mM MgCl2, 10 % DMF, 33 % 1X PBS (without Ca++ and Mg++), 0.1 % Tween-20, 0.01 % Digitonin (ThermoFisher #BN2006) and counted using Trypan Blue on a hemocytometer.
Sci-ATAC-seq was performed using a protocol based on snATAC-seq [PMID: 29434377]. Nuclei were resuspended at 600,000 cells/mL in 1X Tagmentation Buffer. 8 µL of nuclei were aliquoted to each well of a 96-well plate (4,800 cells/well). 1 µL of each barcoded transposome at ~1.5 µM was added to each well and gently vortexed. Tagmentation was performed at 37°C for 1 hour, briefly vortexing once at 30 minutes. 10 µL of 40 µM EDTA was added each well, briefly vortexed, and incubated at 37°C for 15 minutes to inactivate the Tn5. 20 µL sort buffer (2 % BSA and 2 mM EDTA in PBS (without Ca++ and Mg++)) was added to each well. Nuclei from each well were pooled, filtered through a 35 µm mesh (Corning #352235) and Draq7 (Abcam #ab109202) was added to a final concentration of 3 µM (35-38 µL). 25 single nuclei were sorted into each well of a 96-well plate using a BD FACSAria Fusion and transferred to a -80°C freezer.
Frozen plates containing sorted nuclei were thawed on ice. 2 µL of 0.2 % SDS was added to each well and incubated for 7 minutes at 55°C. 2.5 µL of 10 % Triton X-100 was added to each well. 2 µL of 25 µM Primer i5 and 2 µL of 25µM Primer i7 was added to each well. PCR was performed for using Q5 DNA polymerase (NEB #M0491S) with 1X GC buffer (72°C 5min, 98°C 30sec, 15 cycles of: [98°C 10sec, 63°C 30sec, 72°C 30sec], 72°C 5min). In order to minimize batch effect, all PCRs were performed sequentially on a single machine. All wells were then pooled and diluted 5:1 (~24 mL) in Buffer PB (Qiagen #19066) with 1/20th volume of 3 M NaOAc pH 5.2 (~1.2 mL). This solution was run through MinElute columns (Qiagen #28004) using a QIAvac apparatus (Qiagen #19413) and washed once using 750 µL Buffer PE (Qiagen #19065). Samples were eluted twice using EB (10 mM Tris pH 8) warmed to 55°C. Samples were size selected using a 0.5X Ampure XP cleanup to remove large fragments followed by 3 consecutive 1.5X Ampure XP (Beckman Coulter # A63880) bead cleanup followed by a final 1.2X Ampure XP cleanup to completely remove all residual primers and resuspended in a final volume of 20 µL EB using the manufacturer’s recommended protocol.
Omni-ATAC-seq: Tagmentation was performed using the Omni-ATAC-seq protocol [PMID: 28846090] with modifications to inactivation and size selection. Briefly, 100,000 nuclei were tagmented in parallel to sci-ATAC-seq in 1X Tagmentation Buffer (10 mM Tris pH 7.4, 5 mM MgCl2, 10 % DMF, 33 % PBS (without Ca++ and Mg++), 0.1 % Tween-20, 0.01 % Digitonin) using 100 nM Tn5 Transposase for 30 minutes at 37°C. Tagmentation was inactivated with the addition of 5 volumes SDS Lysis Buffer (100mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA, 0.5 % SDS in DEPC H2O) and 100 µg Proteinase K (Invitrogen #25530049) for 30 minutes at 55°C followed by Isopropanol Precipitation using GlycoBlue (Invitrogen #AM9516) as a carrier. Samples were resuspended in EB and size selected using a 0.5X Ampure XP cleanup to remove large fragments followed by a 1.8X Ampure XP cleanup using the manufacturer’s recommended protocol. PCR was performed for using Q5 DNA polymerase (NEB #M0491S) with 1X GC buffer (72°C 5min, 98°C 30sec, 11 cycles of: [98°C 10sec, 63°C 30sec, 72°C 30sec], 72°C 5min) followed by a final 1.8X Ampure XP cleanup.

treatment_protocol: 2n or Ts mice

tag: tissue

value: cortex

value: 76 Days Old

tag: protocol

value: Omni-ATAC-seq


title: Ts_Replicate2_Bulk

description:
Ts2 Bulk Single-end ATAC-seq
processed data files:
Pseudobulk vs Bulk_counts at peaks.txt


title: 2n_Replicate1_Bulk

description:
2n1 Bulk Single-end ATAC-seq
processed data files:
Pseudobulk vs Bulk_counts at peaks.txt


title: 2n_Replicate2_Bulk

description:
2n2 Bulk Single-end ATAC-seq
processed data files:
Pseudobulk vs Bulk_counts at peaks.txt


title: 4BA-WT-3a

city: Paris

first: Nicolas

last: VENTECLEF

state: Ile de France

address: 15 rue de l’Ecole de Medecine

department: Physiology and Physiopathology

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
Illumina Bcl2fastq2 2.17 software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded. Reads were then aligned against the genome using STAR (version 2.4.0k)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, GRCm38.p4 GFF3 genome annotation version 81 from Ensembl database was used. All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq 1.8.3. Statistical treatments and differential analyses were also performed using DESeq 1.8.3
Genome_build: GRCm38.p4 Ensembl version 81
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …

source_name: Inguinal adipose tissue

extract_protocol:
RNA was extracted from tissues or purified cells using the RNeasy RNA Mini Kit (Qiagen). Complementary DNAs were synthesized using M-MLV Reverse Transcriptase kit (Promega). RT–qPCR was performed using the QuantStudio 3 Real-Time PCR Systems (ThermoFisher Scientific). 18S was used for normalization to quantify relative mRNA expression levels.  Illumina TruSeq stranded and purification of RNA kit was used with 30 ug of total RNA for the construction of sequencing libraries. Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Adipose tissue

value: 8 weeks


title: 4BA-WT-4a


title: Lane1_2n and Ts65Dn

description:
Lane1 Read1 and Read2 and Index R1 and Read 2
processed data files:
*genebodies.txt, *bw files, Cell-types pseudobulk_counts*, Merged_cells.narrowPeak, pseudobulk* files

value: 2n and Ts65Dn

value: sci-ATAC-seq


title: 4BA-WT-2a


title: 4BA-WT-1a


title: Lane3_2n and Ts65Dn

description:
Lane3 Read1 and Read2 and Index R1 and Read 2
processed data files:
*genebodies.txt, *bw files, Cell-types pseudobulk_counts*, Merged_cells.narrowPeak, pseudobulk* files


title: 4BA-KO-3a


title: 3BA-WT-3a


title: 4BA-KO-2a


title: 4BA-KO-1a


title: 3BA-WT-2a


title: 3BA-WT-1a


title: HFD_19

source_name: Rats were fed with high-fat diet for 15 weeks.

value: SD

value: Liver

value: male

value: 6-8 weeks

value: high-fat


title: 3BA-KO-4a


title: 3BA-KO-3a


title: 3BA-KO-2a


title: 2BA-WT-3a


title: 2BA-WT-2a


title: 3BA-KO-1a


title: 2BA-WT-1a


title: 2BA-KO-3a


title: 2BA-WT-4a


title: Lane2_2n and Ts65Dn

description:
Lane2 Read1 and Read2 and Index R1 and Read 2
processed data files:
*genebodies.txt, *bw files, Cell-types pseudobulk_counts*, Merged_cells.narrowPeak, pseudobulk* files


title: 4BA-KO-4a


title: 2BA-KO-2a


title: 2BA-KO-1a


title: 3BA-WT-4a


title: 1BA-KO-3a


title: 1BA-KO-2a


title: 1BA-WT-1a


title: 1BA-WT-3a


title: 1BA-KO-1a


title: 1BA-WT-2a


title: 1BA-WT-4a


title: 1BA-KO-4a


title: reads_AdipoKO3a

source_name: Intra abdominal adipocytes

value: Adipocytes

value: 19 weeks


title: reads_AdipoKO2a


title: reads_AdipoWT2a


title: reads_AdipoKO1a


title: reads_AdipoWT3a


title: reads_AdipoWT1a


title: reads_EpiKO3a

source_name: Intra abdominal adipose tissue


title: 2BA-KO-4a


title: reads_EpiKO1a


title: reads_EpiKO2a


title: reads_EpiWT3a


title: reads_EpiWT1a


title: reads_EpiWT2a


title: 4CD-KO-3a


title: 4CD-WT-3a


title: 4CD-WT-1a


title: 4CD-WT-2a


title: 4CD-KO-2a


title: 4CD-KO-1a


title: 3CD-WT-2a


title: 3CD-WT-3a


title: 3CD-WT-1a


title: 3CD-KO-3a


title: 3CD-KO-1a


title: 2CD-WT-3a


title: 2CD-WT-1a


title: 2CD-KO-3a


title: 1CD-WT-3a


title: 2CD-WT-2a


title: 2CD-KO-1a


title: 2CD-KO-2a


title: 1CD-WT-2a


title: 1CD-KO-3a


title: 1CD-KO-2a


title: 1CD-KO-1a


title: 1CD-WT-1a


title: 4HFD-WT-4a

value: 11 weeks


title: 4HFD-WT-2a


title: 4HFD-WT-3a


title: 4HFD-KO-4a


title: 4HFD-WT-1a


title: 4HFD-KO-3a


title: 3HFD-WT-2a


title: 4HFD-KO-2a


title: 4HFD-KO-1a


title: 3HFD-WT-4a


title: 3HFD-WT-1a


title: 3CD-KO-2a


title: 3HFD-KO-4a


title: 3HFD-KO-3a


title: 3HFD-KO-2a


title: 3HFD-KO-1a


title: 2HFD-WT-4a


title: 2HFD-WT-2a


title: 2HFD-WT-3a


title: 2HFD-KO-1a


title: 2HFD-KO-2a


title: 2HFD-WT-1a


title: 2HFD-KO-3a


title: 1HFD-WT-2a


title: 1HFD-KO-4a


title: 1HFD-WT-4a


title: 1HFD-WT-1a


title: 3HFD-WT-3a


title: 1HFD-WT-3a


title: 1HFD-KO-2a


title: 1HFD-KO-3a


title: 1HFD-KO-1a


title: HEK293T-N12-KO NAD-Capture 3

city: Piscataway

first: Ronald

middle: P.

last: Hart

state: NJ

address: 604 Allison Rd Rm B430

department: Cell Biology & Neuroscience

institute: Rutgers University

data_processing:
Illumina bcl2fastq2-v2.17.1.14 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and mapped to hg19 whole genome using TopHat v2.1.1 (with Bowtie 2.2.8.0) using default settings.
All samples were modeled using cuffdiff with options -p 6  --no-update-check and the UCSC hg19 genes.gtf file from the Illumina iGenomes site
Raw cuffdiff output files were loaded into the R package cummeRbund
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated by cuffdiff and output by cummeRbund
Genome_build: hg19
Supplementary_files_format_and_content: Gzipped, comma-separated-values (CSV) file containing isoform_ID row labels and sample replicate column labels.  The values are FPKM.

source_name: HEK293T-N12-KO NAD-Capture

growth_protocol: HEK293T cells were cultured under standard conditions with no modifications

extract_protocol:
Total RNA was isolated by TRIzol extraction, following the manufacturers recommended protocol
enrichment protocol: RiboMinus enrichment for non-ribosomal RNAs was performed as recommended by the kit manufacturer
NAD-Capture enrichment was performed using the NAD-RNA Capture protocol (Cahova et al., 2015) with minor modification.  NAD-Capture was carried out with 100µg total RNAs treated with 10µl 4-pentyn-1-ol (Sigma-Aldrich) and 1.5U Adenosine diphosphate-ribosylcyclase (ADPRC) in 100µl reaction containing 50mM HEPES, 5mM MgCl2 (pH 7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 37oC 60 minutes. The reaction minus ADPRC was used as background control. The reaction was stopped with phenol/chloroform extraction and RNAs were precipitated with ethanol. The precipitated RNAs were subjected to copper-catalyzed azide-alkyne cycloaddition (CuAAC) reaction by incubating with 250µM biotin-PEG3-azide, freshly mixed 1mM CuSO4, 0.5mM THPTA, 2mM Sodium Ascorbate in 100µl reaction with 50mM HEPES, 5mM MgCl2 (pH7) and 40U RNasin® Ribonuclease Inhibitor (Promega) at 30oC for 30 minutes. Following extraction with phenol/chloroform and RNA precipitation, the NAD clicked RNAs were captures by binding to 20µl streptavidin magnet beads at room temperature with gentle rocking for 1 hour in 100µl binding buffer (1M NaCl, 10mM HEPES (pH7) and 5mM EDTA). The beads were washed three time with wash buffer (8mM Urea, 50mM Tris-HCl (pH7.4), 0.25% Triton-X100) and three washes with nuclease free H2O.
RiboMinus-selected RNAs were reverse transcribed and converted to libraries using the Illumina TruSeq RNA Sample Preparation Kit v2.
For NAD-Capture RNAs, samples were reverse transcribed into cDNA and synthesized into dsDNA with the SMARTer® Universal Low Input RNA Kit for Sequencing (Clontech Laboratories, Inc.) following the manufacturer’s protocol.

treatment_protocol: No treatment

value: Nudt12-KO (N12-KO)

tag: enrichment

value: NAD-Capture


title: Lane4_2n and Ts65Dn

description:
Lane4 Read1 and Read2 and Index R1 and Read 2
processed data files:
barnyard.counts.txt

organism:
Homo sapiens
Mus musculus

source_name: A549 cells and Hepa1-6 cells

value: A549 cells and Hepa1-6 cells

value: passage9 and passage3


title: HEK293T-N12-KO NAD-Capture 1