title: xRescue rep2 (dataset2)

data_processing:
50 bp paired-end reads were mapped to the reference genome (X. tropicalis v9.1 available from Xenbase) using STAR (version 2.7.1a). Gene models (XENTR_9.1_Xenbase) were provided as a gtf file, which was created from gff3 format using Cufflinks gffread (version 2.2.1). Reads were counted for each gene in the same STAR run by the --quantMode GeneCounts.
Genome_build: Xenopus tropicalis v9.1, http://ftp.xenbase.org/pub/Genomics/JGI/Xentr9.1/XENTR_9.1_Xenbase.gff3
Supplementary_files_format_and_content: Tab-separated text file: read counts per gene

tag: mrna injection

value: Xenopus Phf8 mRNA


title: xRescue rep1 (dataset2)

status: Public on Sep 01 2021

type: SRA

city: Munich

first: Tamas

last: Schauer

address: Feodor-Lynen-Straße 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Zentrum München

library_source: transcriptomic

molecule: total RNA

organism: Xenopus tropicalis

extract_protocol:
RNA extraction was performed usingTRIzol (Ambion) and phenol/chloroform extraction. RNA clean-up and DNA digestion were performed with RNeasy Mini-Kit (Qiagen).  RNA quality was checked with an Agilent Bioanalyzer 2100 using Agilent RNA 6000 Pico Kit. rRNA was depleted using Ribo-Zero Gold rRNA Removal Kit (Human/Mouse/Rat) (Illumina). rRNA depleted RNa was cleaned up using RNA Clean & ConcentratorTM-5 (Zymo Research).
Library preparation was performed using NEBNext UltraTM Directional RNA Library Prep Kit for Illumina (New England Biolabs) with NEBNext Multiplex Oligos for Illumina primer sets 1 and 2. DNA purification and size selection was performed using Agencourt AMPure XP (Beckman Coulter). Quality and size of the libraries were verified on the Agilent Bioanalyzer using Agilent DNA 1000 Kit.

tag: morpholino treatment

value: Suv4-20H1/2 morpholino

tag: genotype

value: Suv4-20H1/2 knockdown

tag: developmental stage

tag: tissue

value: animal caps


title: NRG1

type: RNA

city: Changchun

first: Yong

last: Liu

address: 71 Xinmin Avenue, Chaoyang District

country: China

institute: The First Hospital of Jilin University

description: circulating Tfh cells from CHB patients with PEG-IFN-α treatment

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit in Hybridization Oven 645 and Fluidics Station 450 followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000

data_processing: Command Console Software 4.0 with default settings. Raw data were normalized by RMA algorithm, Gene Spring Software11.0  11.0

label: biotin

organism: Homo sapiens

source_name: peripheral blood

label_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100

growth_protocol: Peripheral blood was collected and Tfh cells were sorted

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The  sorted Tfh cells were added with Trizol reagent and frozen at -80 degrees.

tag: disease state

value: chronic hepatitis B

tag: patient treatment

value: 48-week PEG-IFN-α treatment

tag: response to treatment

value: non-response

tag: cell type

value: circulating Tfh cells


title: NRG4


title: NRG2


title: embryo2-limb-8

city: Shanghai

first: Tengjiao

last: Zhang

state: Shanghai

address: 1239 Siping Road

department: School of life science and technology

institute: Tongji University

data_processing:
Raw reads were demultiplexed, filtered and mapped to the human reference genome (GRCh38) using Cell Ranger 3.0.2 with default settings. The filtered feature-barcode matrices generated by Cell Ranger were used for further analysis.
To exclude low-quality cells and doublets, cells with fewer than 1000 genes or over 60000 UMIs were discarded. The expression matrix was normalized into UMIs per 10000 by size factors.
Iterative clustering was performed to identify cell types. First, we partitioned cells into main clusters with Seurat (r=0.5, PCs=20) using only transcription factors in highly variable genes (HVGs). Second, for each main cluster, we performed one or two rounds of clustering with HVGs of the particular cluster.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix table with raw gene counts; csv files with gene and cell annotations.

molecule: polyA RNA

growth_protocol: Aborted embryos from donations were washed with PBS, transferred into cold Hibernate-E medium (Gibco) and immediately transported to the laboratory. Embryos with good quality were staged based on anatomical characters.

extract_protocol:
Samples were incubated at 37°C for 10 minutes and were pipetted up and down thoroughly and gently every 3 minutes. To quench the dissociation, we added 300μl FBS into each tube and centrifuge cells at 300xg for 5 min at 4°C. Cells were then resuspended in 500μl cold PBS, filtered through a 35μm strainer. Single cells were subsequently washed twice with cold PBS, centrifuged at 300xg for 5 min at 4°C and resuspended in cold PBS.
To generate sequencing libraries, a suspension of 10,000 single cells per sample was processed following the 10x Genomics protocol using Single Cell 3’ Reagent Kits v2 (10x Genomics).

treatment_protocol: We dissected each embryo on ice into four main sections, i.e., head, trunk, viscera and limb. After the dissection, each sample was placed into separate tubes, washed twice with cold PBS, cut into pieces and suspended in 300μl Hibernate-E medium with 0.05mg/ml Liberase TM (Roche).

value: embryo limb

tag: gender

value: Female

tag: Stage

value: Carnegie Stages 13


title: NRG3


title: ICRG1

value: incomplete response


title: iPSC34_WT2

city: Leuven

first: Kian

middle: Peng

last: Koh

state: Select...

address: Herestraat 49, O&N IV - box 804

country: Belgium

institute: KULeuven

description:
sequencing_2nd batch
biological replicate_2
countMatrix_by_FeatureCounts_2.count

data_processing:
Illumina Casava2.18 software used for basecalling and demultiplexing
Index-trimmed single-end 75bp reads were aligned to the mouse reference genome (mm10) by using Hisat2 (v2.1.0)
Gene-level read count matrix was summarized from mapped reads by using featureCounts (v1.5.3; http://bioinf.wehi.edu.au/featureCounts/)
Count matrix was imported into the R Bioconductor DESeq2 package (v1.18.1) for differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: text file provide count information

organism: Mus musculus

source_name: wild-type iPSC clonal line

growth_protocol: 1x105 to 3x106 cells in each reprogramming intermediate fraction ( mCherry+ and mCherry+/GFP+) were sorted from three independent lines as biological replicates. iPSC samples were passaged 6-7 times on feeders in KSR media, then feeder-depleted and harvested for RNA.

extract_protocol:
RNA was purified using TRIzol (Cat.#15596026,Invitrogen) and RNeasy mini kit (Cat#74004, Qiagen).
300 ng of RNA was used for library preparation using the KAPA stranded mRNA-seq kit (Cat#07692193001, Roche) according to the manufacturer’s instructions (V5.17). KAPA single-indexed adapters (Cat#08005699001, Roche) were added to the A-tailed cDNA for library amplification with 14 cycles of PCR. The final library was purified by using Agencourt AMPure XP beads (Cat#A63881, Beckman Coulter) to size select fragments of 200-300 bp.
stranded RNA-seq

tag: strain

value: Terminal iPSC clonal line at passage 6-7

value: wt/wt;GFP/wt

value: male


title: iPSC34_WT3

description:
sequencing_2nd batch
biological replicate_3
countMatrix_by_FeatureCounts_2.count


title: embryo2-limb-6


title: ICRG2


title: CRG1

value: complete response


title: Suv4-20H1/2 rep2 (dataset1)


title: xPhf8 rep2 (dataset2)

value: no

value: control


title: Suv4-20H1/2 rep1 (dataset1)

value: Suv4-20H1/2 morpholino


title: iPSC34_WT1

description:
sequencing_2nd batch
biological replicate_1
countMatrix_by_FeatureCounts_2.count


title: iPSC34_KO9

source_name: TET1 KO iPSC clonal line

value: mut/mut;GFP/wt


title: embryo2-limb-5


title: embryo2-limb-4


title: xPhf8 rep1 (dataset2)

value: Xenopus Phf8 mRNA

value: animal caps


title: iPSC34_KO8


title: CoMo rep2 (dataset1)

value: control morpholino (CoMo)


title: CoMo rep1 (dataset1)


title: embryo2-limb-3


title: NRPC7-GFP-IP-2(ChIP-seq)

city: Beijing

first: QIANWEN

last: SUN

address: Zhongguancun Street

department: School of life sciences

institute: Tsinghua University

library_source: genomic

data_processing:
Illumina Casava software used for basecalling.
Reads were aligned to the TAIR10 genome using bwa version 0.7.12.
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Genome_build: TAIR10
Supplementary_files_format_and_content: bigwig files were generated with bamCoverage from deepTools include peacks for each Sample

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: NRPC7-GFP in nrpc7-1

extract_protocol: For ChIP-seq: Chromatin immunoprecipitation (ChIP) assays (Liu et al., 2017) were performed using 12-day-old Arabidopsis culture in growth chamber under LD conditions.

tag: background

value: Columbia

value: seedlings

value: NRPC7-GFP in nrpc7-1


title: embryo2-limb-7

value: embryo limb

value: Female


title: embryo2-limb-2

value: Carnegie Stages 13


title: embryo2-limb-1


title: 73E8_d8Ch

source_name: Day 8 totalx2 mCherry+/GFP-

value: B6- Tet1tm1.1Koh x B6;129S4-Pou5f1tm2Jae/J

value: Stage I reprogramming intermediate

value: Tg(mCherry)/wt; Tg(GFP)/wt


title: iPSC34_KO7

value: Terminal iPSC clonal line at passage 6-7

value: male


title: 73E8_d12Ch

source_name: Day 12 totalx2 mCherry+/GFP-


title: NRPC7-GFP-IP-1(ChIP-seq)


title: 73E8_d12ChGFP

source_name: Day 12 totalx2 mCherry+/GFP+

value: Stage III reprogramming intermediate


title: embryo2-viscera-8

value: embryo viscera


title: NRPC7-GFP-Input(ChIP-seq)


title: nrpb2-3-2(RNA-seq)

extract_protocol:
For RNA-seq: RNA isolation from plant samples was performed using TRI Reagent according to the manufacturer’s instructions (Ambion). to prepare RNA-seq library in a strand-specific manner. The RNA-seq libraries were sequenced on an IlluminaHiSeq X Ten system.
For RNA-seq: NEB Next Ultra Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq library in a strand-specific manner.


title: embryo2-viscera-6


title: PBL-3_blood

type: genomic

city: Dublin

first: Antoinette

last: Perry

address: Science West, University College Dublin, Belfield, Dublin, Ireland

country: Ireland

institute: University College Dublin

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450K Beadchip using standard Illumina protocol

scan_protocol: samples were scanned using na Illumina BeadArrayTM reader

data_processing: .idat files were quality filtered and converted to beta values using the minfi R package. Normalization method = FunNorm

label: Cy5 and Cy3

source_name: blood

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted Qiagen DNA FFPE Tissue Kit according to standard instructions

value: blood


title: PBL-2_blood


title: embryo2-viscera-5


title: nrpb2-3-1(RNA-seq)


title: embryo2-viscera-7


title: 73E8_d10Ch

source_name: Day 10 totalx2 mCherry+/GFP-


title: 73E7_d8Ch


title: nrpc7-1-2(RNA-seq)


title: embryo2-viscera-4


title: Col-0-2(RNA-seq)

source_name: Wild type

value: Wild type


title: nrpc7-1-1(RNA-seq)


title: PCM11_metastatic prostate cancer tissue

source_name: prostate tissue

value: prostate tissue

tag: tissue preparation

value: FFPE

value: metastatic prostate cancer tissue


title: 73E7_d12


title: PBL-1_blood


title: embryo2-viscera-3


title: 73E8_d10ChGFP

source_name: Day 10 totalx2 mCherry+/GFP+

value: Stage II reprogramming intermediate


title: 73E7_d12ChGFP


title: Col-0-1(RNA-seq)

value: Columbia

value: seedlings


title: embryo2-viscera-2

value: Female


title: 73E7_d10Ch


title: nrpc7-1-2(ssDRIP-seq)

extract_protocol:
For ssDRIP-seq: Nuclei were isolated from Arabidopsis plants, followed by SDS/proteinase K treatment at 37°C overnight. Genome DNA was extracted by the phenol-chloroform method and precipitated with isopropanol. DNA fragmentation was performed overnight using endonucleases (MboI, MseI, NlaIII, DdeI); the negative control was treated with RNase H (New England Biolabs) overnight. DRIP was performed as described in Xu et al., 2017 and Sun et al., 2013. Briefly, 3.5 ug of DNA was bound with 10 ug of S9.6 antibody in 1 X binding buffer (10 mM NaPO4 pH 7, 140 mM NaCl, 0.05% Triton X-100) overnight at 4˚C. 50 ul Protein G sepharose beads were added for 4 hours. Bound beads were washed 4 times in binding buffer and elution was performed in elution buffer (50 mM Tris pH 8, 10 mM EDTA, Proteinase K) for 45 min at 55˚C. DNA was purified and sonoicated to 150 bp fragments .
For ssDRIP-seq and ChIP-seq: The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.


title: nrpc7-1-1(ssDRIP-seq)


title: embryo2-trunk-7

value: embryo trunk

value: Carnegie Stages 13


title: PCM07_metastatic prostate cancer tissue


title: Col-0-2(ssDRIP-seq)


title: 73E6_d12Ch

value: B6- Tet1tm1.1Koh x B6;129S4-Pou5f1tm2Jae/J

value: Stage I reprogramming intermediate


title: embryo2-viscera-1


title: Col-0-1(ssDRIP-seq)


title: 73E7_d10ChGFP

value: Tg(mCherry)/wt; Tg(GFP)/wt


title: embryo2-trunk-6


title: 73E6_d12ChGFP

value: male


title: PCM04_metastatic prostate cancer tissue


title: PCA09_agressive prostate cancer tissue

value: agressive prostate cancer tissue


title: embryo2-trunk-5


title: embryo2-trunk-8


title: 73E6_d10Ch


title: PCM05_metastatic prostate cancer tissue


title: dental pulp stem cell 3

city: Tsukuba

first: Aiki

last: Marushima

state: Ibaraki

address: 1-1-1, Tennodai

department: Department of Neurosurgery

country: Japan

institute: University of Tsukuba

hyb_protocol: Following labeling, 5.2 ug of cDNA were hybridized for 16 hr at 45 degree C on Clariom S Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

scan_protocol: GeneChips were scanned using GeneChip Scanner 7G system.

data_processing: The data analysis were used Transcriptome Analysis Console Ver.4.0. Normalization was performed using the Signal Space Transformation-Robust multiple-array average normalization method (SST-RMA), Expression Analysis was perfoermed using ebayes ANOVA.

source_name: dental pulp

label_protocol: The fragmented 5.2 μg of single-stranded cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the DNA Labeling Reagent that is covalently linked to biotin. (GeneChip WT PLUS Reagent Kit USER GUIDE revB, ThermoFisher Scientific)

value: cultured cell


title: PCM03_metastatic prostate cancer tissue


title: embryo2-trunk-4


title: embryo2-trunk-3


title: 65E5_iPSC4

description:
sequencing_1st batch
biological replicate_3
countMatrix_by_FeatureCounts_1.count

source_name: naivex2 iPSC clonal line

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J

value: Terminal iPSC clonal line at passage 6-7


title: 73E6_d10ChGFP


title: PCA08_agressive prostate cancer tissue

value: prostate tissue


title: PCA10_agressive prostate cancer tissue

value: FFPE


title: PCM01_metastatic prostate cancer tissue

value: metastatic prostate cancer tissue


title: embryo2-trunk-2


title: embryo2-trunk-1


title: dental pulp stem cell 2


title: 65E5_d14Ch

source_name: Day 14 naivex2 mCherry+/GFP-

value: Stage III reprogramming intermediate


title: 65E5_d14ChGFP

source_name: Day 14 naivex2 mCherry+/GFP+

value: Stage V reprogramming intermediate


title: dental pulp stem cell 1


title: PCA02_agressive prostate cancer tissue


title: neural cell 3


title: PCA06_agressive prostate cancer tissue


title: neural cell 2


title: PCA05_agressive prostate cancer tissue


title: 65E5_d12ChGFP

source_name: Day 12 naivex2 mCherry+/GFP+

value: Stage IV reprogramming intermediate


title: hRescue rep3 (dataset3)

data_processing:
50 bp single reads were mapped to the reference genome (X. tropicalis v9.1 available from Xenbase) using STAR (version 2.7.1a). Gene models (XENTR_9.1_Xenbase) were provided as a gtf file, which was created from gff3 format using Cufflinks gffread (version 2.2.1). Reads were counted for each gene in the same STAR run by the --quantMode GeneCounts.
Genome_build: Xenopus tropicalis v9.1, http://ftp.xenbase.org/pub/Genomics/JGI/Xentr9.1/XENTR_9.1_Xenbase.gff3
Supplementary_files_format_and_content: Tab-separated text file: read counts per gene

extract_protocol:
RNA extraction was performed usingTRIzol (Ambion) and phenol/chloroform extraction. RNA clean-up and DNA digestion were performed with RNeasy Mini-Kit (Qiagen).  RNA integrity quality was analysed using an Agilent 2100 Bioanalyzer. Ribosomal RNA was removed using NEBNext rRNA Depletion Kit (Human/Mouse/Rat).
Total stranded RNA sequencing libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina according to the manufacturer's instructions

value: Suv4-20H1/2 morpholino

value: Suv4-20H1/2 knockdown

value: human Phf8 mRNA

value: animal caps


title: PCA03_agressive prostate cancer tissue


title: embryo1-tail_viscera-4

source_name: embryo1-lower trunk and viscera

value: embryo lower trunk and viscera

value: Male

value: Carnegie Stages 12


title: 65E5_d12Ch

source_name: Day 12 naivex2 mCherry+/GFP-

value: Tg(mCherry)/wt; Tg(GFP)/wt

value: male


title: embryo1-tail_viscera-2


title: neural cell 1

value: cultured cell


title: embryo1-tail_viscera-3


title: hRescue rep1 (dataset3)


title: embryo1-tail_viscera-1


title: 65E5_d10Ch

source_name: Day 10 naivex2 mCherry+/GFP-

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J


title: 73E6_d8Ch

value: B6- Tet1tm1.1Koh x B6;129S4-Pou5f1tm2Jae/J

value: Stage I reprogramming intermediate


title: 65E5_d0MEF

source_name: Day 0 mouse embryonic fibroblasts

value: Parental mouse embryonic fibroblast


title: embryo1-head_trunk-4

source_name: embryo1-head and upper trunk

value: embryo head and upper trunk


title: PCI10_indolent prostate cancer tissue

value: prostate tissue

value: FFPE

value: indolent prostate cancer tissue


title: PCI06.1_indolent prostate cancer tissue


title: 65E4_d14Ch

description:
sequencing_1st batch
biological replicate_2
countMatrix_by_FeatureCounts_1.count

value: Stage III reprogramming intermediate


title: embryo1-head_trunk-3


title: PCA01_agressive prostate cancer tissue

value: agressive prostate cancer tissue


title: 65E4_iPSC2

value: Terminal iPSC clonal line at passage 6-7


title: PCI06.2_indolent prostate cancer tissue


title: hPhf8 rep3 (dataset3)

value: no

value: control

value: human Phf8 mRNA

value: animal caps


title: LacZ rep3 (dataset3)

value: LacZ mRNA


title: PCI13_indolent prostate cancer tissue


title: embryo1-head_trunk-1

value: Male

value: Carnegie Stages 12


title: PCI04_indolent prostate cancer tissue


title: 65E4_d14ChGFP

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J

value: Stage V reprogramming intermediate

value: Tg(mCherry)/wt; Tg(GFP)/wt

value: male


title: embryo1-head_trunk-2

value: embryo head and upper trunk


title: 65E4_d12Ch


title: LacZ rep2 (dataset3)


title: V_C_D5_3

first: Fei

last: Liang

address: 1678 Dong Fang Road

department: Shanghai Children's Medical Center

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
clean data were mapped to human reference genome hg19 by STAR_2.5.0a
HTSeq count was used for FPKM estimation
Differential expressed genes were identified by DESeq2
Genome_build: hg19
Supplementary_files_format_and_content: .txt file including fpkm

source_name: cardiac progenitor cells

growth_protocol: Undifferentiated H1 hESC lines were maintained in a feeder-free culture system. Briefly, we precoated the well plates with Matrigel (354277, BD Biosciences), and then seeded and cultured cells with TeSR™-E8™ medium (05840,Stemcell). When cells reached 80% confluence, they were passaged routinely with Accutase (07920, Stemcell).

extract_protocol:
Total RNA was extracted from D0, D2, , D3, D5 and D10 cells using Trizol reagent (15596018,Thermo Fisher Scientific). Reverse transcription was accomplished with Reverse Transcription Kit (RR037A,Takara) according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For cardiomyocyte differentiation, cells were induced using a chemically defined medium consisting of three components (CDM3): the basal medium RPMI 1640 (C14065500, Gibco), L-ascorbic acid 2-phosphate (213µg/ml,113170-55-1,Sigma) and Oryza sativa-derived recombinant human albumin (500µg/m,HY100M1,Healthgen Biotechnology Corp). In brief, single cell suspensions were prepared using Accutase and were seeded in 12-well Matrigel-coated plate at a density of 4×105 cells/well. When cells reached 80%-90% confluence (Day 0), cells were fed daily by 2ml CDM3 basal medium supplemented with CHIR99021 (6μM, 72052, Stem cell). 48 hours later (Day 2), medium was replaced with 2ml CDM3 supplemented with Wnt-C59 (2μM, 1248913, Peprotech Biogems). After 96 houres(day 4) , the medium was replaced with CDM3 basal medium (every other day) without any medium change until the appearance of cell beating.

value: ES-derived cardiac progenitor cells

tag: passages


title: LacZ rep1 (dataset3)


title: CoMo rep3 (dataset3)

value: control morpholino (CoMo)


title: PCI05_indolent prostate cancer tissue

value: prostate tissue

value: FFPE

value: indolent prostate cancer tissue


title: V_C_D5_2


title: 65E4_d12ChGFP

value: Stage IV reprogramming intermediate


title: 65E4_d0MEF

value: Parental mouse embryonic fibroblast


title: hPhf8 rep2 (dataset3)

value: no

value: control

value: human Phf8 mRNA


title: V_C_D5_1


title: hRescue rep2 (dataset3)

value: Suv4-20H1/2 morpholino

value: Suv4-20H1/2 knockdown

value: animal caps


title: 65E4_d10Ch

value: B6; 129S4-Tg(Tet1-mCherry)B37Koh x B6;CBA-Tg(Pou5f1-EGFP)2Mnn/J

value: Stage III reprogramming intermediate


title: CoMo rep2 (dataset3)


title: 34_11_D5_1


title: PCI01_indolent prostate cancer tissue


title: hPhf8 rep1 (dataset3)


title: HGPIN08_indolent prostate cancer tissue


title: CoMo rep1 (dataset3)


title: 33_8_D5_2


title: PCI02_indolent prostate cancer tissue


title: 33_1_D5_3


title: 65E1_iPSC3

description:
sequencing_1st batch
biological replicate_1
countMatrix_by_FeatureCounts_1.count

value: Terminal iPSC clonal line at passage 6-7

value: Tg(mCherry)/wt; Tg(GFP)/wt

value: male


title: low IMF2(L2)

city: Jinzhong

first: wufeng

last: li

state: Shanxi provence

address: 1 Mingxian South Road, Taigu District

department: college of Life Sciences

institute: Shanxi Agricultural University

data_processing:
Illumina Casava1.8 software used for basecalling.
Align the clean reads after quality control to the reference genome. Use HISAT2 to compare Clean Reads with a reference genome to obtain position information on the reference genome or gene, and unique sequence feature information of the sequenced sample
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: peak text files

organism: Equus asinus

source_name: Low Intramuscular Fat Content

extract_protocol:
The longissimus dorsi muscle samples were collected within 30 minutes after slaughter and stored in liquid nitrogen rapidly. The total RNA of longissimus dorsi was extracted by Trizol reagent. After total RNA library construction and quality inspection, sequencing was performed on the Illumina HiSeq2000 platform.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: breed

value: Guangling donkey

tag: age

value: 24 months

value: Longissimus dorsi muscle


title: low IMF3(L3)


title: 65E1_d14ChGFP

value: Stage V reprogramming intermediate


title: T3_D11_DT

city: Gaithersburg

first: Yinong

last: Sebastian

address: One MedImmune Way

country: USA

institute: Medimmune

description: processed data file: T3D11_gene_count.txt

data_processing:
Basecalls performed using cellranger mkfastq (v3.0.2)
Reads were aligned to GRCh38 reference and transcripts were quantified using cellranger count (v3.0.2)
Genome_build: GRCh38
Supplementary_files_format_and_content: Counts provided in a log2 scale

source_name: NSCLC tumor

extract_protocol:
Cells were diluted to 1000 cells per μL in phosphate-buffered saline plus 0.04% bovine serum albumin. Cells were loaded and Gel Bead-in-Emulsion were generated with the Chromium Controller (10X Genomics), followed by reverse transcription, cleanup, and cDNA amplification according to the manufacturer’s protocol.
Libraries were prepared for sequencing using 10X Genomics protocols.

value: NSCLC tumor

tag: sample type

value: needle biopsy

tag: treatment

value: Durva+Treme


title: 65E1_d12ChGFP

value: Stage IV reprogramming intermediate

tag: genotype


title: 65E1_d14Ch


title: T3_D11_Durva

value: Durva


title: high IMF3(H3)

source_name: High Intramuscular Fat Content


title: 65E1_d10Ch


title: 65E1_d12Ch


title: T3_D0

description: processed data file: T1T3D0_gene_count.txt


title: high IMF2(H2)


title: T3_D11_IsoCtrl


title: low IMF1(L1)


title: high IMF1(H1)


title: HGPIN07_high grade prostatic intra-epithelial neoplasia tissue

value: prostate tissue

value: FFPE


title: 65E1_d0MEF

value: Parental mouse embryonic fibroblast


title: T1_D7_DT

description: processed data file: T1D7_gene_count.txt


title: T1_D7_Durva


title: T1_D7_IsoCtrl


title: M5BBz_1

city: Philadelphia

first: Lexus

last: Johnson

state: Pennsylvania

address: 421 Curie Blvd, 532

department: Radiation Oncology

institute: University of Pennsylvania

description: 3' Poly-A mRNA

data_processing:
Orginal intensity file (.bcl) was transferred to fastq with tool cellranger mkfastq (bcl2fastq2 wrapper), which was subsequently subjected to cellranger count function for alignment.
Genome_build: hg19
Supplementary_files_format_and_content: .mtx

source_name: Human CAR-T Cells

growth_protocol: ASPC-1 tumors were implanted in flanks of NSG mice

extract_protocol:
Live cells were FACS sorted. 10X 3' v3.1 RNA processing/isolation kit used
Protocol for 10X 3' v3.1 kit utilized

treatment_protocol: Mice were treated i.v. (tail vein) with CAR-T cells of indicated genotype on day 25 post-tumor implantation

value: Mixed human tumor and CAR-T cells

value: NSG

value: Healthy donor M5BBz CAR-T cells


title: M5BBz_7SL_2

description: 3' Poly-A mRNA

value: Healthy donor M5BBz-7SL CAR-T cells


title: M5BBz_2

description: 3' Poly-A mRNA


title: T1_D0


title: M5BBz_7SL_1

description: 3' Poly-A mRNA


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-0h-Rep2

status: Public on Aug 31 2021

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

description: ChIP-seq yeast Pol II

data_processing:
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

organism: Saccharomyces cerevisiae

growth_protocol: Human DLD-1 cells that constitutively express OsTIR1 were cultured at 37°C in DMEM (Sigma #D6429) supplemented with 10% FBS (Sigma #F2442), 1% Pen-Strep (Gibco #15140-122) in CO2 incubators. Yeast cells were grown in YPAD medium

extract_protocol:
For ChIP-seq in human DLD1 cells, 20-50 million cells were crosslinked with 1% paraformaldehyde (Electron Microscopy Sciences) in PBS for 10 min at r.t. Spike-in mouse embryonic fibroblast fixed cells were added to samples as described previously (Orlando et al., 2014). Chromatin was sonicated with the Covaris E220 for 4 min with 10% duty cycle, 140 peak intensity power, 200 cycles per burst. Immunoprecipitations were carried out with antibodies and Dynabeads Protein G (Invitrogen). For ChIP-seq in yeast cells, cells were fixed with 2.2% formaldehyde for 15 min. PRO-seq sample preparation was performed according to the previously described qPRO-seq protocol (Judd et al., 2020). ~5 million DLD-1 nuclei mixed with spike-in Drosophila S2 nuclei were used for nuclear run-on assay. For pulse-chase nascdnt RNA labeling with TT-seq, cells were treated with 250 nM NVP-2 for 1 h, followed by nascent RNA labeling with 500 µM 4-thiouridin (Sigma # T4509) for 15 min.
For ChIP-seq, DNA libraries were prepared by the HTP Library Preparation Kit for Illimina (KAPA). For PRO-seq, adapter sequences previously described (Mahat et al., 2016) were used. PRO-seq libraries were prepared according to the previously described qPRO-seq protocol (Judd et al., 2020). TT-seq library was prepared as described previously (Schwalb et al., 2016; Rosencrance wt al., 2020).

treatment_protocol: To induce degradation of AID-tagged proteins, 500 µM auxin was added to culture. To induce anchor-away depletion, exponentially growing yeast cultures were treated with 1.0 ug/mL Rapamycin.

tag: cell line

value: SPT5-FRB CDC48-FRB RPL13A-2xFKBP12

tag: antibody

value: RPB1 CTD (BioLegend # 664912)

tag: molecule subtype

value: genomic DNA


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-3h-Rep2

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-1h-Rep2

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-1h-Rep2

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-0h-Rep2

description: ChIP-seq yeast Pol II


title: HGPIN06_high grade prostatic intra-epithelial neoplasia tissue

source_name: prostate tissue

tag: tissue

tag: disease state


title: ChIP-seq-E-yPol2-Parental-Rapamycin-1h-Rep2

description: ChIP-seq yeast Pol II


title: HGPIN05_high grade prostatic intra-epithelial neoplasia tissue


title: PIA05_proliferative inflammatory atrophy tissue


title: PIA09_proliferative inflammatory atrophy tissue


title: ChIP-seq-E-yPol2-Parental-Rapamycin-3h-Rep2

description: ChIP-seq yeast Pol II


title: PIA02_proliferative inflammatory atrophy tissue


title: PIA01_proliferative inflammatory atrophy tissue


title: ChIP-seq-E-yPol2-Parental-Rapamycin-0h-Rep2

description: ChIP-seq yeast Pol II


title: HGPIN02_high grade prostatic intra-epithelial neoplasia tissue


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-3h-Rep1

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-0h-Rep1

description: ChIP-seq yeast Pol II


title: PIA03_proliferative inflammatory atrophy tissue


title: PIA07_proliferative inflammatory atrophy tissue


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-1h-Rep1

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-3h-Rep1

description: ChIP-seq yeast Pol II

value: SPT5-FRB RPL13A-2xFKBP12


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-1h-Rep1

description: ChIP-seq yeast Pol II


title: THP-1 cell line, RCB3686

first: Fumio

last: Kasai

address: Koyadai 3-1-1

institute: RIKEN

hyb_protocol: As per manufacturer (Affymetrix)

scan_protocol: As per manufacturer (Affymetrix)

data_processing: The data analyses can be performed using a Transcriptome Analysis Console (TAC) 4.0.2.15 (Thermo Fisher Scientific). RMA processed data.

label_protocol: As per manufacturer (Affymetrix)

growth_protocol: Cell lines were grown according to standard conditions.

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen 80204).

value: acute monocytic leukemia

value: THP-1 cell line, RCB3686


title: ChIP-seq-E-yPol2-Parental-Rapamycin-1h-Rep1

description: ChIP-seq yeast Pol II


title: ChIP-seq-E-yPol2-SPT5FRB-Rapamycin-0h-Rep1

description: ChIP-seq yeast Pol II


title: THP-1 cell line, RCB1189

value: THP-1 cell line, RCB1189


title: ChIP-seq-E-yPol2-SPT5FRBCDC48FRB-Rapamycin-3h-Rep2

description: ChIP-seq yeast Pol II


title: B11_benign prostate tissue

value: benign prostate tissue


title: ChIP-seq-E-yPol2-Parental-Rapamycin-3h-Rep1

description: ChIP-seq yeast Pol II


title: THP-1 cell line, JCRB0112.1

value: THP-1 cell line, JCRB0112.1


title: THP-1 cell line, JCRB0112

value: THP-1 cell line, JCRB0112


title: B10_benign prostate tissue

value: prostate tissue


title: ChIP-seq-E-yPol2-Parental-Rapamycin-0h-Rep1

description: ChIP-seq yeast Pol II


title: AV-3

city: Anseong

first: Dong Hwan

last: Kim

state: Gyeonggi

address: 4726 Seodong-daero, Daedeok-myeon

department: Department of Plant science and Technology

country: South Korea

institute: Chung-Ang University

description: replicate 3

data_processing:
Quality of the RNA-seq reads were evaluated using the FastQC software
The raw reads were trimmed and quality-filtered before alignment, and those with more than 90 % threshold (Q>30) were used for mapping. Radish reference genome was obtained from NODAI radish genome database and were used for mapping using the TopHat2 software with default parameters
Aligned reads were converted to digital counts using HTseq-count and were analyzed using edgeR.
Differentially expressed genes (DEGs) were identified based on a 0.05 p-value and a cutoff of two-fold difference in expression.
Genome_build: Radish reference genome was obtained from Nodai radish genome database
Supplementary_files_format_and_content: tab-delimited text files with raw gene counts for individual samples

organism: Raphanus sativus

source_name: radish

growth_protocol: 4 weeks old radish (Raphanus sativus cv. Taebaek) plants were grown in greenhouse prior to vernalization treatment

extract_protocol:
Total RNA was extracted from whole seedling samples using RNeasy Mini Kit (Qiagen, Germany) and treated with DNase I (New England Biolabs, USA) to remove genomic DNA contamination.
RNA-seq libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina Inc., USA) according to the manufacturer’s instructions. Libraries were then sequenced on NovaSeq 6000 system (Macrogen Inc., South Korea)

treatment_protocol: NV: non-vernalized 4 weeks old seedling; V: 4-week cold treated; AV; 4-week cold treated and then further grown in warm temperature for 2 weeks

tag: tissues

value: leaf and roots

tag: cultivar

value: Taebaek

value: AV


title: B12_benign prostate tissue

value: FFPE


title: AV-2

description: replicate 2


title: V-3

description: replicate 3

value: V


title: AV-1

description: replicate 1


title: B05_benign prostate tissue


title: V-2

description: replicate 2


title: B03_benign prostate tissue


title: V-1

description: replicate 1


title: B04_benign prostate tissue


title: HGPIN01_high grade prostatic intra-epithelial neoplasia tissue


title: B06_benign prostate tissue


title: CL 6 AS3MT 1.5

city: Abu Dhabi

first: Kirsten

last: Sadler Edepli

state: Abu Dhabi

department: Biology

country: United Arab Emirates

institute: New York University Abu Dhabi

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and low-quality sequence, -p 4 -e 100 -y -a -m 10 --best --strata
Trimmed read were mapped to GRCz10 whole genome using hisat2 with default parameters
Accepted bam files were used for counting read numbers of each gene with HTSeq, -a 10 -s no
Test of differential expression of each transposonis was implemented by DESeq2 in Bioconductor
Genome_build: GRCz10
Supplementary_files_format_and_content: .txt Reads count of genes and repeats

organism: Danio rerio

source_name: Liver

growth_protocol: Zebrafish larvae were kept in petri dish at a density of 60 larvae/plate in a 10:14 light/dark cycle.

extract_protocol:
12  embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions.
total RNA, stored at -80 until use
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol
PolyA RNA-seq library

treatment_protocol: 0 , 1 and 1.5mM iAs exposure from 4-5dpf in  10ml , 20 fish in a 6-well plate

tag: pool

value: 5 dpf

value: 1.5 mM iAs

value: Liver

tag: rna qbit concentration


title: NV-1

description: replicate 1

value: NV


title: CL 5 AS3MT 1.5


title: CL 6 AS3MT 1.0

value: 1.0 mM iAs


title: B08_benign prostate tissue


title: NV-2

description: replicate 2


title: B02_benign prostate tissue


title: CL 2 AS3MT 1.5


title: CL 4 AS3MT 1.5


title: CL 6 AS3MT 0

value: 0 mM iAs


title: CL 1 AS3MT 1.5


title: PIA10_proliferative inflammatory atrophy tissue


title: CL 2 AS3MT 0


title: CL 4 AS3MT 0


title: CL 1 AS3MT 0

value: 19 ng/ul


title: mCherry Week1

city: Memphis

first: Tian

last: Mi

state: TN

address: 262 Danny Thomas Pl MS351

department: Immunology

institute: St. Jude Children's Research Hospital

data_processing:
Basecalling was performed using Illumina Casava 1.7
Sequencing reads were aligned to the hg19 reference genome using the BSMAP v.2.74 software
CpG methylation levels were determined by methratio.py script from BSMAP
Genome_build: hg19
Supplementary_files_format_and_content: txt files with columns of chr, loc, cov, meth

source_name: CD8+ T Cells

extract_protocol:
DNA was extracted from the sorted cells by using a DNA-extraction kit (Qiagen) and then bisulfite treated using an EZ DNA methylation kit (Zymo Research).
Bisulfite-modified DNA sequencing libraries were generated using the EpiGenome kit (Epicentre) according to the manufacturer’s instructions. Bisulfite-modified DNA libraries were sequenced using Illumina HiSeq 4000 and NovaSeq 6000 systems

tag: stimulation

tag: cell type

value: CD8+ T Cells


title: TET2 KO Week1


title: mCherry Week2


title: Naïve + TCR + IL12 - rep3

value: anti-CD3/CD28 + IL-12


title: Naïve + TCR + IL12 - rep1


title: Naïve + TCR + IL12 - rep2


title: Naïve + TCR - rep1


title: Naïve T Cells - rep2


title: Naïve + TCR - rep2


title: SK-N-BE2-Input

city: wuhan

first: song

last: zemin

address: no.185 the road of eastlake

institute: wuhan university

description: Input

data_processing:
ChIP-seq reads were aligned to the human genome (UCSC hg38) with Bowtie version 1.1.2, allowing only uniquely mapping reads with up to two mismatches within the 150 bp reads . The resulting reads were extended to 200 bp toward the interior of the sequenced fragments and normalized to the total reads used for aligning (reads per million, r.p.m.). The aligned human BAM files were normalized to the total aligned reads and converted to bigwig files for visualization in the UCSC Genome Browser. Peaks were called using MACS2 (model-based analysis of ChIP-Seq) version 2.1.2 with default parameters and were annotated with ChIPseeker. Heatmap and metagene plots were made for the indicated windows around the transcription start site (TSS) using the average coverage (r.p.m.). For ChIP-Rx experiments, sonicated human chromatin was spiked-in with 10%-30% mouse chromatin to quantitatively normalize across experiments. ChIP signals were normalized by the normalization factors as previous reported.
Genome_build: hg38
Supplementary_files_format_and_content: Library normalized bigWig files were provided for all samples

growth_protocol: SK-N-BE2 cell line was  grown in complete RPMI-1640 (Hyclone) supplemented with 10% FBS and 1% penicillin/streptomycin and cultured at 37℃ under 5% CO2.

extract_protocol:
1x10^7 cells were fixed with 1% paraformaldehyde in PBS for 10 minutes and then quenched with 0.125 M glycine for 5 minutes at room temperature. Fixed cells were sequentially lysed with 10 mL lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100 and 1× protease inhibitors) and 10 mL lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and 1× protease inhibitors). The cells were then resuspended in 300 ml lysis buffer 3 (10 mM Tris-HCl, pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine and 1× protease inhibitors), and were sheared using the Diagenode Bruptor Plus with the high-power mode for 25 cycles (sonication cycle: 30 seconds ON, 30 seconds OFF). After sonication, 1% Triton X-100 was added to the chromatin and centrifuged at 20,000 g for 10 minutes to remove the insoluble debris. The chromatin was immunoprecipitated with 10 mg individual antibodies and 15 ml pre-blocked Protein A/G beads (Smart-Lifesciences). The beads were washed three times with 1 mL lysis buffer 3, and three times with wash buffer (50 mM HEPES-KOH, pH 7.5, 300 mM LiCl, 1 mM EDTA, 1.0% NP-40 and 0.7% Na-Deoxycholate). The immunoprecipitated DNA was eluted with 200 ml elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1.0% SDS and 200 mg/mL proteinase K) at 55°C for overnight, and purified by phenol-chloroform extraction and ethanol precipitation.
Library preparation was done using the NEBNext ultra II DNA library prep kit for Illumina, followed by sequencing on a NovaSeq 6000.

treatment_protocol: no treatment

value: cancer cell

value: neuroblastoma

value: MYCN-amplification

value: Ctrl

tag: chip antibody


title: SK-N-BE-2-Ctrl-Pol_II

description: ChIP-seq Pol_II (Rpb1 NTD (D8L4Y) Rabbit mAb, from CST)


title: SK-N-BE-2-EZH2-shRNA-Pol_II

value: Pol_II (Rpb1 NTD (D8L4Y) Rabbit mAb, from CST)


title: SK-N-BE-2-Ctrl-MYCN

description: ChIP-seq MYCN (N-Myc (D1V2A) Rabbit mAb, from CST)


title: Sample A

city: Guangzhou

first: XInwei

last: Lin

address: No. 135, Xingang Xi Road, Guangzhou, 510275, P. R. China

department: Stomatology

institute: Sun Yat-sen University

description: one sample from patients with common chronic apical periodontitis

data_processing:
Raw sequencing reads were demultiplexed by bcl2fastq software to convert them into 150-bp paired-end reads and stored in the FASTQ format.
Genome_build: GRCh38 human reference genome
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: inflammatory periapical tissue from patients with common chronic apical periodontitis

extract_protocol:
Once the inflammatory periapical tissue of the three teeth was carefully scraped off, the collected samples were immediately placed in an ice-cold preservation solution and then transported to the laboratory to maintain viability.
Using the manufacturer's protocol (10x Single Cell 3' Reagent Kits v2 manual, USA) (10X Genomics, 2016), the prepared cell suspensions were loaded onto barcoded scRNA-seq. In brief, the generation of gel beads in emulsions (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were performed.

tag: gender

value: Female

tag: tooth position

value: Maxillary posterior teeth at right

tag: chief complaint

value: Demand for restoration of residual root


title: ChIP-seq-G-CUL3-SPT5AID7-shCUL3-2-Vehicle-90m

description: ChIP-seq CUL3

value: Colorectal adenocarcinoma

value: SPT5-AID7 AtAFB2

tag: treatment

value: genomic DNA


title: Sample B

tag: age

value: Male

value: Mandible posterior teeth at right

value: Felt intermittent pain and uncomfortable more than six months


title: TET2 KO Week2


title: ChIP-seq-G-CUL3-SPT5AID7-shCUL3-2-Auxin-90m

description: ChIP-seq CUL3

tag: cell line

tag: genotype


title: ChIP-seq-G-CUL3-SPT5AID7-shCUL3-1-Vehicle-90m

description: ChIP-seq CUL3

tag: antibody

tag: molecule subtype


title: Sample C

description: one sample from patients with with a typical periapical granuloma

source_name: inflammatory periapical tissue from patients with a typical periapical granuloma

value: Mandible posterior teeth at left


title: B01_benign prostate tissue

tag: tissue

value: prostate tissue

tag: tissue preparation

value: FFPE

tag: disease state

value: benign prostate tissue


title: ChIP-seq-F-CUL3-SPT5AID-Auxin-90m

description: ChIP-seq CUL3

value: SPT5-AID OsTIR1


title: SK-N-BE-2-EZH2-shRNA-MYCN

value: cancer cell

value: neuroblastoma

value: MYCN-amplification

value: MYCN (N-Myc (D1V2A) Rabbit mAb, from CST)


title: ChIP-seq-G-CUL3-SPT5AID7-shNT-Auxin-90m

description: ChIP-seq CUL3


title: Naïve + TCR - rep3

value: CD8+ T Cells


title: Naïve T Cells - rep1


title: ChIP-seq-F-CUL3-SPT5AID-Vehicle-90m

description: ChIP-seq CUL3


title: ChIP-seq-G-CUL3-SPT5AID7-shNT-Vehicle-90m

description: ChIP-seq CUL3


title: NV-3

description: replicate 3

tag: tissues

value: leaf and roots

tag: cultivar

value: Taebaek

value: NV


title: ChIP-seq-G-CUL3-SPT5AID7-shCUL3-1-Auxin-90m

description: ChIP-seq CUL3

value: Colorectal adenocarcinoma

value: SPT5-AID7 AtAFB2

value: genomic DNA


title: TT-seq-SPT5AID-VCPiAuxin-NVP2-60m-Rep2

description: Pulse-chase nascent RNA labeling

data_processing:
Library strategy: TT-seq
For ChIP-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to a concatenated genome comprised of human hg38 and mouse mm10 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. The aligned reads with MAPQ ≥ 30 were extended to 150 bp and read counts were normalized to total reads aligned to spike-in genome. Metaplots of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
For PRO-seq, low-quality bases and adapters from 3’ ends of reads were removed using cutadapt 1.14 (Martin, 2011) requiring a read length of 16–36 bp. Reads derived from ribosomal RNA were filtered out by mapping reads on human and fly ribosomal DNA. The remaining reads were aligned using bowtie 2.2.6 with --very-sensitive option (Langmead and Salzberg, 2012), to a concatenated genome comprised of human hg38 and fly dm6 assemblies. The 5’ ends of aligned reads with MAPQ ≥ 30 were taken by bedtools genomecov 2.25 (Quinlan and Hall, 2010) with -strand and -5 options, and strands of the 5’ ends of reads were then swapped. Read counts were normalized to total reads aligned to the spike-in genome. Heatmaps and metaplots of PRO-seq signal were generated by deepTools 3.1.1 (Ramírez et al., 2016).
For TT-seq, single-end raw reads trimmed by Trimmomatic 0.33 (Bolger et al., 2014) were aligned to human genome hg38 assemblies, using bowtie 2.2.6 (Langmead and Salzberg, 2012) with --sensitive option. Heatmaps of ChIP-seq signals were generated using deepTools 3.1.1 (Ramírez et al., 2016).
Genome_build: hg38, mm10, dm6
Supplementary_files_format_and_content: bigWig files with normalized read counts were provided for all samples.

molecule: nuclear RNA

value: nuclear RNA


title: TT-seq-SPT5AID-Auxin-NVP2-60m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-VCPiAuxin-NVP2-30m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-VCPiAuxin-NVP2-0m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-Vehicle-NVP2-30m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-VCPiAuxin-NVP2-60m-Rep1

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-Auxin-NVP2-30m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-Vehicle-NVP2-0m-Rep2

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-Auxin-NVP2-60m-Rep1

description: Pulse-chase nascent RNA labeling


title: TT-seq-SPT5AID-Auxin-NVP2-0m-Rep2

description: Pulse-chase nascent RNA labeling


title: Wild-type (Rubinstein-Taybi cohort) replicate 2

city: Baltimore

first: Teresa

middle: Romeo

last: Luperchio

state: MD

address: 733 N Broadway

department: Department of Genetic Medicine

institute: Johns Hopkins School of Medicine

data_processing:
Reads were mapped to the mm10 mouse assembly.
Duplicates were removed with the MarkDuplicates function from Picard, and mitochondrial reads were removed with samtools
Samples from the same genotype were merged, and peaks were called on these merged meta-samples using MACS2. For wild-type mice two meta samples were created, one for the wild-type mice of the Kabuki cohorts, and one for the wild-type mice of the Rubinstein-Taybi cohort.
The peaks from each meta-sample were unionized to yield a final set of genomic intervals. The number reads from each sample that map onto each of these intervals were counted using the featureCounts function from the Rsubread package.
Genome_build: mm10
Supplementary_files_format_and_content: The processed data files are matrices (in csv format), with rows corresponding to the genomic intervals obtained after unionizing the peaks called from the individual meta-samples (each interval has its unique coordinates), and columns to samples (each sample name contains information about genotype). The entries in the matrices are counts, as obtained using the featureCounts function from the Rsubread R package. One matrix (atac_peaks_by_samples_matrix_Kabuki_cohort.csv) contains samples from Kabuki type 1/2 mutants and wild-type littermates, and the other matrix (atac_peaks_by_samples_matrix_Rub_Taybi_cohort.csv) contains samples from Rubinstein-Taybi mutants and wild-type littermates.

source_name: CD19+ B cells

extract_protocol:
Peripheral blood was obtained from facial vein bleed and CD19+ cells were isolated by positive selection using magnetic microbeads (Miltenyi 130-052-201) per manufacturer protocols and placed on ice. 5k cells were used per reaction, resuspended in 1xPBS and quickly spun to remove residual EDTA from isolation steps.
Samples were resuspended in tagmentation reaction mix for 30 min (2.5uL TD1, 1X TD Buffer, Illumina Nextera DNA, FC-121-1030; .25uL 1% digitonin, Promega G9441; 1xPBS; ) gently shaking (300rpm on Eppendorf thermomixer) at 37’. We purified reactions using Zymo DNA Clean and Concentrator-5 kit (Zymo D4013) following manufacturer protocols and eluted with 10.5uL water to recover 10uL. Each reaction was then amplified and indexed per standard ATAC-seq protocol, total sample amplification cycles range from 6-10 cycles. After indexing and amplification, we purified samples using Select-A-Size purification columns (Zymo D4080) with a cutoff of 150bp to remove adapter dimers to allow for efficient sequencing on patterned flow cells, checked library size on BioAnalyzer using DNA High Sensitivity reagents (Agilent 5067-4626) and determined concentration using Qubit dsDNA HS Assay Kit (ThermoFisher Q32851).

tag: strain

value: CD19+ B cells from peripheral blood

tag: age (approximate)

value: 85 days

value: Wild-type (Rubinstein-Taybi cohort)

value: Wild-type


title: Wild-type (Rubinstein-Taybi cohort) replicate 6

tag: cell type


title: TT-seq-SPT5AID-Vehicle-NVP2-60m-Rep1

description: Pulse-chase nascent RNA labeling

value: SPT5-AID OsTIR1


title: Wild-type (Rubinstein-Taybi cohort) replicate 3


title: Wild-type (Kabuki cohorts) replicate 4

value: 74 days

value: Wild-type (Kabuki cohorts)


title: Wild-type (Rubinstein-Taybi cohort) replicate 4


title: Wild-type (Rubinstein-Taybi cohort) replicate 5


title: TT-seq-SPT5AID-Vehicle-NVP2-60m-Rep2

description: Pulse-chase nascent RNA labeling


title: Wild-type (Kabuki cohorts) replicate 5

value: 82 days


title: Wild-type (Kabuki cohorts) replicate 12


title: Wild-type (Kabuki cohorts) replicate 11

value: 72 days


title: Wild-type (Rubinstein-Taybi cohort) replicate 1


title: Wild-type (Kabuki cohorts) replicate 10

value: 97 days


title: Wild-type (Kabuki cohorts) replicate 8


title: Wild-type (Kabuki cohorts) replicate 9


title: Wild-type (Kabuki cohorts) replicate 6

value: 98 days


title: Wild-type (Kabuki cohorts) replicate 7


title: Wild-type (Kabuki cohorts) replicate 2

value: 84 days


title: Wild-type (Rubinstein-Taybi cohort) replicate 7


title: Wild-type (Kabuki cohorts) replicate 3


title: Wild-type (Kabuki cohorts) replicate 1


title: Rubinstein-Taybi syndrome type 1 replicate 5

value: Rubinstein-Taybi syndrome type 1

value: Crebbp+/-


title: Rubinstein-Taybi syndrome type 1 replicate 4


title: Rubinstein-Taybi syndrome type 1 replicate 3


title: Rubinstein-Taybi syndrome type 1 replicate 2


title: Kabuki syndrome type 2 replicate 1

value: Kabuki syndrome type 2


title: Kabuki syndrome type 2 replicate 4


title: Kabuki syndrome type 2 replicate 5


title: Kabuki syndrome type 2 replicate 3


title: Rubinstein-Taybi syndrome type 1 replicate 1


title: Kabuki syndrome type 1 replicate 5

value: Kabuki syndrome type 1


title: rotator cuff tear without shoulder stiffness 3

first: Yaying

last: Sun

state: Please Select

address: 12# Middle Wulumuqi Road, Jing'an District

institute: Huashan Hospital, Fudan University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Genome_build: GRCh38
Supplementary_files_format_and_content: txt files with identified miRNA ID, arm, accession number, read accounts, etc.

source_name: circulating exosomes

extract_protocol:
Total RNA was extracted from exosome pellet using the TRIzol reagent (Invitrogen/Life Technologies) following the manufacturer’s protocol. RNA concentration was quantitated using the NanoDrop ND-100 Spectrophotometer (NanoDrop Technologies, Wilmington, DE).  Small RNA libraries were constructed using New England Biolabs (NEB) NEBNext Multiplex Small RNA Library Prep Set for Illumina sequencers and the NEB standard protocol. Individual libraries were constructed using 1µg of total RNA isolated from each sample.
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: blood

tag: disease

value: rotator cuff tear

tag: combined condition

value: no

tag: molecule

value: microRNA


title: rotator cuff tear with shoulder stiffness 3

value: shoulder stiffness


title: rotator cuff tear without shoulder stiffness 2


title: rotator cuff tear without shoulder stiffness 1


title: Kabuki syndrome type 1 replicate 4

value: CD19+ B cells from peripheral blood


title: Kabuki syndrome type 2 replicate 2


title: rotator cuff tear with shoulder stiffness 2


title: Kabuki syndrome type 1 replicate 7


title: Kabuki syndrome type 1 replicate 6


title: rotator cuff tear with shoulder stiffness 1


title: Kabuki syndrome type 1 replicate 3


title: Kabuki syndrome type 1 replicate 2


title: T47DRBplus-Ever-a2

city: Buffalo

first: Ram

middle: Mohan

last: Nambiar

state: NY

address: 665 Elm Street

institute: Roswell Park

data_processing:
The adaptors of the sample files were removed using Trimmomatic in Single End (SE) or Paired end(PE) mode and. Trimmomatic also removes leading and trailing low quality bases (below quality 3),reads who’s average quality score per base falls below 15 for 4 base wide sliding window and those reads who’s length is below 20.
After the Fastq files are preprocessed, they were aligned to the Human genome(hg38) using tophat2 with default parametrs(i.e read-mismatch=2,read-gap-length=2) for each samples to create a bam file
Finally, the corresponding bam files are collected and sorted using samtools sort and the number of reads for each genes in each samples are computed using HTSeq.
Genome_build: hg38

source_name: T47D-WT cells treated with Everolimus (500 nM)

growth_protocol: MCF7-Wt and RB-del cells were grown in DMEM medium supplemented with 10%FBS. T47D cells were cultured in RPMI medium supplemented with 10% FBS. All cells were maintained in 5% CO2

extract_protocol:
RNA was extracted using the Rneasy Quiagen kit according to the manufacturerer's protocol.
RNA libraries for sequencing using standard Illumina protocols

treatment_protocol: MCF7-WT and RB-del cells were treated with palbociclib (250 nM), everolimus (500 nM) as single agents and in combination up to 48 H. T47D-WT cells were treated with everolimus for 48 H. MCF7-WT and RB-del were treated with MK1775 (200 nM) in combination with Alisertib (200 nM) up to 48 H.

value: Human cell line

tag: rb genotype

value: RB positive

tag: treatment

value: Everolimus


title: CL 5 AS3MT 0

tag: pool

tag: age

value: 5 dpf

value: 0 mM iAs

value: Liver

tag: rna qbit concentration


title: T47DRBplus-Ever-b2

tag: cell line


title: T47DRBplus-Control-b2

source_name: T47D-WTcells treated with DMSO

tag: tissue

value: Control


title: Kabuki syndrome type 1 replicate 1

value: 98 days

tag: genotype

value: Wild-type


title: T47DRBplus-Control-a2


title: MCF7RBplus-PDplusEver-b

source_name: MCF7-WT cells treated with palbociclib (250 nM) and Everolimus (500 nM)

value: Palbociclib+Everolimus


title: THP-1 cell line, JCRB0112

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

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing: The data analyses can be carried out using the Chromosome Analysis Suite software, ChAS 4.2 (Thermo Fisher Scientific).

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA Mini Kit (Qiagen 80204).

tag: disease state

value: acute monocytic leukemia


title: MCF7RBplus-MKAlisertib-b

source_name: MCF7-WT cells treated with MK1775 (200 nM) and Alisertib (200 nM)

value: MK Alicertib


title: MCF7RBPlus-Ever-a2

source_name: MCF7-WT cells treated with Everolimus (500 nM)


title: MCF7RBplus-PD-a5

source_name: MCF7-WT cells treated with palbociclib (250 nM)

value: Palbociclib


title: MCF7RBplus-Ever-b2


title: MCF7RBplus-Control-b2

source_name: MCF7-WTcells treated with DMSO


title: MCF7RBplus-Control-a2


title: MCF7RBplus-PD-b5


title: MCF7RBplus-Control-c3


title: MCF7RBdel-PDplusEver-b

source_name: MCF7-RB-del cells treated with palbociclib (250 nM) and Everolimus (500 nM)

value: RB deleted


title: MCF7RBplus-MKAlisertib-c


title: MCF7RBdel-PDplusEver-a


title: MCF7RBdel-PD-b5

source_name: MCF7-RB-del cells treated with palbociclib (250 nM)


title: MCF7RBplus-PDplusEver-a


title: MCF7RBdel-MKAlisertib-c

source_name: MCF7-RB-del cells treated with MK1775 (200 nM) and Alisertib (200 nM)


title: MCF7RBdel-PD-a5


title: MCF7RBdel-Control-c3

source_name: MCF7-RB-del cells treated with DMSO


title: MCF7RBdel-Control-b2


title: pros-RNAi E(z)-RNAi neuroblast tumors

city: Marseille

first: Cédric

last: Maurange

address: Parc Scientifique de Luminy

department: Developmental Biology Institute of Marseille (IBDM)

country: France

institute: CNRS

data_processing:
Single-cell mRNA seq data were analyzed using the 10x Genomics suite Cell Ranger 2.0.1 with default settings for de-multiplexing, aligning reads to the Drosophila genome (10X Genomics pre-built dm6 reference genome) with STAR and counting unique molecular identifiers (UMIs) to build transcriptomic profiles of individual cells. This first level of analysis generates quality metrics (Q30, number of reads by sample…), FASTQ files and filtered genes matrices. Cell Ranger pre-processing retained 5796 cells with a median number of 1806 genes/cell for the control condition (Genovese, Clement, et al., 2019), 2977 cells with a median number of 1959 genes/cell for the E(z)RNAi condition, 2410 cells with a median number of 700 genes/cell for the trxRNAi condition and 3942 cells with a median number of 1190 genes/cells for the E(z)RNAi, trxRNAi condition. Filtered gene matrices generated via Cell Ranger 2.0.1
Genome_build: dm6 reference genome

organism: Drosophila melanogaster

source_name: neuroblast tumors induced by RNAi mediated inactivation of prospero (pros) and Enhancer of Zeste (E(z)) using poxn-GAL4

growth_protocol: Fly stocks were raised at 18°C on standard food (8 % cornmeal, 8 % yeast and 1 % agar).  Crosses were performed at 29°C and the progeny were maintained at 29°C to maximize RNAi-mediated knockdown efficiency

extract_protocol:
Adult flies were killed in 70% ethanol and washed once in PBS. VNCs were dissected in PBS, collected in a RNase-free Protein LoBinding tube filled with ice-cold PBS, and incubated in a freshly prepared dissociation solution containing 0,4% bovine serum albumin (BSA), 1 mg/mL collagenase I and papain (Sigma Aldrich) in PBS for 75 min at 29°C with low agitation. Tissues were then disrupted manually by pipetting up and down with a 200 µL tip. Dissociated cells were pelleted for 20 min at 300 g at 4°C to remove the dissociation solution and resuspended in ice-cold PBS + 0,4% BSA. The cell suspension was filtered through a 30 µm mesh Pre-Separation Filter (Miltenyi) to remove debris and transferred in new RNase-free Protein LoBinding tube for FACS sorting. Forty thousand GFP+ tNBs cells were isolated using a FACSAriaII machine (BD) with an 85 μm nozzle, at 45 psi low pressure and according to viability, cell size and GFP intensity. In the next 30 min, sorted-cells were encapsidated using the Chromium Single Cell Controller (10X Genomics) for single-cell RNA-seq.
Single cells were processed using the Single cell 3’ Library, Gel beads and multiplex kit (10X Genomics, Pleasanton) as per the manufacter’s protocol. Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) with the Chromium Single Cell Controller (10X genomics, Pleasanton), where all generated cDNA share a common 10x Barcode. Libraries were generated and sequenced from the cDNA and the10x Barcodes are used to associate individual reads back to the individual partitions. Analysis using molecular indexing information provides an absolute digital measurement of gene expression levels. Sequencing was performed using a NextSeq 500 Illumina device (1sample) containing transcript lengh of 57 bp.

tag: developmental stage

value: adult 5-7 days-old

value: poxn-GAL4, uas-dicer2, UAS-GFP, UAS-prospero-RNAi, UAS-E(z)-RNAi,

tag: fly stock used

value: uas-prosRNAi (Bloomington # 26745), UAS-E(z)-RNAi (VDRC KK107072)


title: pros-RNAi trx-RNAi neuroblast tumors

source_name: neuroblast tumors induced by RNAi mediated inactivation of prospero (pros) and trithorax (trx) using poxn-GAL4

value: poxn-GAL4, uas-dicer2, UAS-GFP, UAS-prospero-RNAi,  UAS-trx-RNAi

value: uas-prosRNAi (Bloomington # 26745), UAS-trx-RNAi(VDRC KK 108122)


title: MCF7RBdel-Ever-a2

source_name: MCF7-RB-del cells treated with Everolimus (500 nM)

value: Human cell line

value: Everolimus


title: MCF7RBdel-Ever-b2


title: THP-1 cell line, RCB1189


title: Brain tumour stem cells LGALS1 CRISPR KO rep3

city: Ottawa

first: Arezu

last: Jahani-Asl

state: Ontario

address: 451 Smyth Road

department: Department of Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

data_processing:
RNA-seq reads were mapped to the human genome assembly (hg38) using HISAT2.
The number of aligned reads per gene was obtained with HTSeq and gene annotations were retrieved from GENCODE
Genes with an average read counts smaller than 10 were filtered out. Differential expression analysis was performed with DESeq2, p-values were corrected by independent hypothesis weighting (Ignatiadis et al., 2016; Love et al., 2014)
Genome_build: hg38
Supplementary_files_format_and_content: sample_*_s_no.tab files contain the read counts per gene. DESeq2_results_LFC_for_all_genes_LGALS1_KO.csv contains LFC

source_name: Brain tumour stem cells

growth_protocol: BTSCs were recovered from cryopreservation in 10% dimethyl sulfoxide and cultured in Nunc ultra-low attachment flasks as maintained in neurospheres in serum free NeuroCult NS-A medium (Stemcell Technologies, #05750) supplemented with 100 U/mL penicillin, 100 µg/mL streptomycin (Sigma Aldrich, #P4333), heparin (2 μg/mL, Stemcell Technologies, #07980), human EGF (20 ng/mL, Miltenyi Biotec, #130-093-825), and human FGF (10 ng/mL, Miltenyi Biotec, #130-093-838). BTSCs were passaged up to 7 times and all cell lines were tested negative for mycoplasma.

extract_protocol:
Total RNAs were isolated from cells using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.
Libraries for poly(A)+ RNA were prepared according to the Illumina protocol. Libraries were sequenced on Illumina GAIIX Genome Analyzer or on HI-SEQ 2000 platforms

treatment_protocol: Untreated

tag: age of donor/age of host

value: 52 years old male

tag: tissue/cell type

value: patient-derived brain tumour stem cells

tag: genotype/variation

value: LGALS1 KO


title: Brain tumour stem cells control rep2

value: Control


title: THP-1 cell line, RCB3686


title: pros-RNAi trx-RNAi E(z)-RNAi neuroblast tumors

source_name: neuroblast tumors induced by RNAi mediated inactivation of prospero (pros), trithorax (trx) and Enhancer of Zeste (E(z)) using poxn-GAL4

value: adult 1-5 days-old

value: poxn-GAL4, uas-dicer2, UAS-GFP, UAS-prospero-RNAi, UAS-E(z)-RNAi, UAS-trx-RNAi

value: uas-prosRNAi (Bloomington # 26745), UAS-E(z)-RNAi (VDRC KK107072); UAS-trx-RNAi(VDRC KK 108122)


title: THP-1 cell line, JCRB0112.1

value: acute monocytic leukemia


title: Brain tumour stem cells control rep1


title: Brain tumour stem cells LGALS1 CRISPR KO rep2


title: Brain tumour stem cells LGALS1 CRISPR KO rep1


title: Brain tumour stem cells control rep3


title: Liver, CL 6 CAAX 1

source_name: Liver

extract_protocol:
12 embryo livers were pooled per sample and extracted with Trizol as per manufacturer's instructions.
total RNA, stored at -80 until use
RNA-seq libraries were prepared according to Illumina TruSeq RNA sample preparation version 2 protocol
PolyA RNA-seq library

treatment_protocol: 0 , 1 and 1.5mM iAs exposure from 4-5dpf in 10ml , 20 fish in a 6-well plate

value: 5 dpf

value: 1 mM iAs

value: Liver


title: MCF7RBdel-MKAlisertib-b

value: RB deleted

value: MK Alicertib


title: bone marrow cells, T1D

city: Hangzhou

first: Linlin

last: Wang

state: Zhejiang

address: Yuhangtang Road No.866

department: Department of Basic Medicine Sciences

institute: Zhejiang University

description: single-cell RNA-sequencing

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: bone marrow

extract_protocol:
The femur and tibia were dissected. After removing the muscle and periosteum on the outer surfaces of the femur and tibia, the bones were cut into approximately 1 mm long fragments and digested with 1 mg/ml collagenase I/dispase II (Roche, 46793022). After incubating for 40 min at 37°C, the cell suspension was filtered through a 40-μm cell strainer (Corning, 431751) to obtain a single cell suspension and centrifuged at 1500 × g for 5 min. To remove the red blood cells, cells were resuspended in 1x RBC lysis buffer (BioLegend, 420301) on ice for 5 min. The solution was then centrifuged at 500 × g for 5 min and resuspended in PBS. The sample was stained with trypan blue (Sigma), and cell survival was evaluated microscopically.
Single cell suspension was loaded onto a microfluidic chip and single cell RNA-seq libraries were constructed according to the manufacturer’s instructions (Singleron GEXSCOPE Single Cell RNAseq Library Kit, Singleron Biotechnologies).
scRNA_seq

value: bone marrow

tag: strain

tag: tissue source

value: femurs and tibias

value: streptozotocin

tag: phenotype

value: high blood sugar

value: Type 1 diabetes (T1D)


title: Liver, CL 4 CAAX 1.5

value: 1.5 mM iAs


title: Liver, CL 2 CAAX 1.5


title: Liver, CL 6 CAAX 1.5


title: Liver, CL 5 CAAX 1.5


title: Liver, CL 1 CAAX 1.5


title: pros-RNAi neuroblast tumors

source_name: neuroblast tumors induced by RNAi mediated inactivation of prospero (pros) using poxn-GAL4

value: adult 5-7 days-old

value: poxn-GAL4, uas-dicer2, UAS-GFP, UAS-prospero-RNAi

value: uas-prosRNAi (Bloomington # 26745)


title: MUC5307_6881_IP_HEP_Frozen_IP_fasted

status: Public on Aug 30 2021

city: Odense M

first: Anne

last: Loft

address: Campusvej 55

department: Biochemistry & Molecular Biology

country: Denmark

institute: University of Southern Denmark

description: IP'ed nuclei from HEP-INTACT mice (prepared from frozen liver tissue)

data_processing:
The STAR aligner (v 2.4.2a) (Dobin et al., 2013) with modified parameter settings (--twopassMode=Basic) was used for split-read alignment against the mouse genome assembly mm10 and UCSC knownGene annotation.
Quantification of the number of mapped reads of each gene was performed using iRNA-seq (v 1.1) specifying the "-count gene" option (Madsen et al., 2015)
Differential expression was determined using DESeq2 (v 1.24.0) (Love et al., 2014)
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files containing unnormalized counts (output from iRNA-seq)
Supplementary_files_format_and_content: Tab-delimited text with log2FC and differential gene expression analyses (output from DESeq2)

source_name: Hepatocyte Nuclei

extract_protocol:
Whole liver nuclei as well as bead-bound and supernatant nuclei prepared from INTACT mice were directly resuspended in Trizol. RNA purification was performed using EconoSpin columns (Epoch) with on-column DNase digestion (Qiagen).
Total RNA (50-100ng) was prepared for sequencing using VAHTS Stranded mRNA-seq Library Kit for Illumina (Vazyme NR602) following manufacturer’s recommendations, except that no selection for poly-adenylated RNA was used.
Prepared PCR products were purified and size-selected on AMPure XP beads (Beckman A63881), and library quality was assessed on the Agilent Bioanalyzer 2100 system. RNA libraries were sequenced as 50 bp paired-end runs on a HiSeq 4000 platform (Illumina, San Diego, USA).

value: Hepatocyte Nuclei

tag: feeding state


title: MUC5308_6911_IP_HEP_Frozen_IP_fasted


title: MUC5309_6912_IP_HEP_Frozen_IP_fasted


title: MUC6499_6854_IP_HEP_Frozen_IP_fed


title: MUC5306_6839_IP_HEP_Frozen_IP_fed


title: MUC5305_6853_IP_HEP_Frozen_IP_fed


title: bone marrow cells, normal

description: single-cell RNA-sequencing

tag: treatment

value: sodium citrate solution

value: normal blood sugar

value: control


title: MUC5300_6854_FT_HEP_Fresh_Sup_fed

description: Supernatent nuclei from HEP-INTACT mice (prepared from fresh liver tissue)

source_name: Non_Hepatocyte Nuclei

value: Non_Hepatocyte Nuclei


title: MUC5298_6912_IP_HEP_Fresh_IP_fasted

description: IP'ed nuclei from HEP-INTACT mice (prepared from fresh liver tissue)


title: MUC5297_6911_IP_HEP_Fresh_IP_fasted


title: MUC5301_6839_FT_HEP_Fresh_Sup_fed


title: MUC5303_6911_FT_HEP_Fresh_Sup_fasted


title: MUC5302_6881_FT_HEP_Fresh_Sup_fasted


title: MUC5304_6912_FT_HEP_Fresh_Sup_fasted


title: Miglustat

city: Nagoya

first: Kazunori

last: Hamamura

address: 1-100 Kusumoto-cho, Chikusa-ku

department: Pharmacology

institute: Aichi Gakuin University, School of Dentistry

description: Gene expression after treatment of miglustat

hyb_protocol: 0.6 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a Agilent fragmentation buffer and was hybridized at 65°C for 17 hr using Gene Expression Hybridization Kit.

scan_protocol: Microarray slides were scanned at 3 μm resolution using an Agilent SureScan (G4900DA).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.1.1.1(Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: MC3T3-E1 cells treated with miglustat

label_protocol: Agilent one-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling protocol

extract_protocol: An RNeasy Plus mini kit (Qiagen, Germantown, MD, USA) was used for extraction of total RNA.

treatment_protocol: Four groups for MC3T3-E1 cells were Control, Miglustat, D-PDMP, and D-PPMP.  The concentrations of Miglustat, D-PDMP, and D-PPMP were 50 microM, 10 microM, and 1.0 microM, respectively.  Four days after treatment of their inhibitors of GCS, the cells were plated at 2.5 x 105 cells into 60 mm dishes, and cultured for 24 h.  The cells were harvested for microarray analysis.

tag: cells

value: osteoblasts

value: Miglustat


title: D-PPMP

description: Gene expression after treatment of D-PPMP

source_name: MC3T3-E1 cells treated with D-PPMP

value: D-PPMP


title: MUC5293_6853_IP_HEP_Fresh_IP_fed


title: MUC5296_6881_IP_HEP_Fresh_IP_fasted


title: MUC5299_6853_FT_HEP_Fresh_Sup_fed


title: MUC5324_6839_fed_Frozen

data_processing:
Sequence tags from ATAC-seq libraries were aligned to the mm10 using the BWA aligner (version 0.7.5a-r405) (Li and Durbin, 2009).
Post-alignment processing of reads was performed with Samtools (0.1.19-44428cd) (Li et al., 2009) by removing duplicate reads and filtering for high quality reads using Samtools view using the following settings ”-b -h -f 1 -F 4 -F 8 -F 256 -F 2048 -q 30”. Furthermore, only reads with a fragment length<100bp was used corresponding to the reads located in nucleosome-free regions.
ATAC seq peaks were identified, annotated and tags in peaks were counted using HOMER (Heinz et al., 2010). Tag directories from conditions with technical duplicates were combined into one before further analyses. Peaks were called in each library with HOMER findPeaks using the following settings: ‘peaks’, ‘-fragLength 70’, ‘-style factor’, ‘-minDist 140’, ‘-size 70’.
For all peak files, overlapping peaks were merged and collected in one master peak file. Tags were then counted in a 200bp window around the peak centers for each individual library in the resulting master peak file.
Differential accessible sites (fed vs fasted) were determined using DESeq2 using default parameters.
Bedgraph files for individual libraries were generated using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Bedgraph files for each condition were generated by merging the individual tag directories of one condition into one and using HOMER makeUCSCfile specifying ‘-fragLength 70’ and ‘-fsize 20e’
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text with norm counts and log2FC (fed vs fasted) (output from DESeq2)
Supplementary_files_format_and_content: Bedgraph files for individual libraries
Supplementary_files_format_and_content: Bedgraph files (merged) - one from each condition

extract_protocol:
Approximately 25,000 bead-bound nuclei from INTACT reactions were transposed in a 50 μL volume of 1X TTBL buffer and 3.5 μL TTE Mix V50 (from TruePrep™ DNA Library Prep Kit V2 for Illumina, Vazyme TD501) for 30 minutes at 37°C. Fragmented genomic DNA was recovered using Buffer ERC coupled with MinElute spin column purification (Qiagen). Samples originating from MAC INTACT mice were run in technical duplicates.
Transposed genomic DNA was amplified by 12 cycles of quantitative PCR. Amplified DNA was purified and size-selected on AMPure XP beads (Beckman A63881), analyzed on an Agilent Bioanalyzer, and sequenced (paired-end) on an Illumina HiSeq 4000 platform.


title: MUC5327_6912_fasted_Frozen


title: MUC5294_6854_IP_HEP_Fresh_IP_fed


title: MUC5326_6911_fasted_Frozen


title: MUC5325_6881_fasted_Frozen


title: MUC5323_6854_fed_Frozen


title: Control

description: control

source_name: MC3T3-E1 cells

value: Control


title: D-PDMP

description: Gene expression after treatment of D-PDMP

source_name: MC3T3-E1 cells treated with D-PDMP

value: D-PDMP


title: MUC5322_6853_fed_Frozen


title: MUC5320_6911_fasted_Fresh


title: MUC5295_6839_IP_HEP_Fresh_IP_fed


title: MUC5319_6881_fasted_Fresh


title: N80-H3K27ac

status: Public on Aug 26 2021

city: Wuhan City

first: Qinglan

last: Li

state: Hubei Province

address: Room 5005, Life Science College, Wuhan University

institute: Wuhan University

data_processing:
All ChIP-seq raw fastq data was cleaned by removing adaptor sequence.
Cleaned reads were aligned to mouse reference genome (hg19) using Bowtie2 (-q --phred33 --end-to-end --sensitive -k 1 -p 5 --fr --no-mixed --no-discordant -X 1000)
Peaks calling was finished by MACS2 (v 2.1.1) with the parameters --nomodel --keep-dup all -p 1E-10 --broad --broad-cutoff 1E-10 --extsize 147.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files were generated from bam files; Scores represent the RPM value.

source_name: Native tissue from colorectal cancer patient

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
ChIP-seq libraries were constructed by VATHS Universal DNA Library Prep Kit for Illumina (Vazyme ND606).

value: tumor

tag: chip antibody

value: H3K27ac (abcam, ab4729)

value: colorectal cancer


title: N78-H3K27ac


title: N76-H3K27ac


title: MUC5317_6854_fed_Fresh


title: N75-H3K27ac


title: N79-H3K27ac


title: N77-H3K27ac


title: N74-H3K27ac


title: N69-H3K27ac


title: N68-H3K27ac


title: N70-H3K27ac


title: N67-H3K27ac


title: N62-H3K27ac


title: N61-H3K27ac


title: N65-H3K27ac


title: N60-H3K27ac


title: MUC5318_6839_fed_Fresh


title: N64-H3K27ac


title: N58-H3K27ac


title: N63-H3K27ac


title: N59-H3K27ac


title: N57-H3K27ac


title: N56-H3K27ac


title: MCF7RBdel-Control-a2

value: Human cell line

tag: rb genotype

value: RB deleted


title: N55-H3K27ac


title: N73-H3K27ac


title: N72-H3K27ac


title: N54-H3K27ac


title: N53-H3K27ac


title: N66-H3K27ac


title: N50-H3K27ac


title: N51-H3K27ac


title: N48-H3K27ac


title: N49-H3K27ac


title: N41-H3K27ac


title: N47-H3K27ac


title: N44-H3K27ac


title: N45-H3K27ac


title: N43-H3K27ac


title: N40-H3K27ac


title: N39-H3K27ac


title: N37-H3K27ac


title: N42-H3K27ac


title: N38-H3K27ac


title: N35-H3K27ac


title: N36-H3K27ac


title: MUC5316_6853_fed_Fresh


title: N34-H3K27ac


title: N32-H3K27ac


title: N33-H3K27ac


title: N31-H3K27ac


title: T80-H3K27ac

source_name: Tumor from colorectal cancer patient


title: N52-H3K27ac


title: T79-H3K27ac


title: T77-H3K27ac


title: T78-H3K27ac


title: T74-H3K27ac


title: T73-H3K27ac


title: N46-H3K27ac


title: T76-H3K27ac


title: T69-H3K27ac


title: T61-H3K27ac


title: T65-H3K27ac


title: T75-H3K27ac


title: T59-H3K27ac


title: T70-H3K27ac


title: T56-H3K27ac


title: T51-H3K27ac


title: T68-H3K27ac


title: T67-H3K27ac


title: T63-H3K27ac


title: T71-H3K27ac


title: T66-H3K27ac


title: T60-H3K27ac


title: T64-H3K27ac


title: N30-H3K27ac


title: T62-H3K27ac


title: T58-H3K27ac


title: T57-H3K27ac


title: T55-H3K27ac


title: T43-H3K27ac


title: T54-H3K27ac


title: T44-H3K27ac


title: T39-H3K27ac


title: T37-H3K27ac


title: T53-H3K27ac


title: T38-H3K27ac


title: T52-H3K27ac


title: T72-H3K27ac


title: T48-H3K27ac


title: T50-H3K27ac


title: T35-H3K27ac


title: MUC5321_6912_fasted_Fresh


title: T49-H3K27ac


title: T31-H3K27ac


title: T45-H3K27ac


title: T42-H3K27ac


title: T47-H3K27ac


title: N29-H3K27ac

value: Colorectal cancer

value: Native tissue


title: T41-H3K27ac


title: T30-H3K27ac


title: T46-H3K27ac


title: N24-H3K27ac


title: T40-H3K27ac


title: N27-H3K27ac


title: T36-H3K27ac


title: T34-H3K27ac


title: N28-H3K27ac


title: N16-H3K27ac


title: N19-H3K27ac


title: T33-H3K27ac


title: N26-H3K27ac


title: N22-H3K27ac


title: N5-H3K27ac


title: N23-H3K27ac


title: T32-H3K27ac


title: N3-H3K27ac


title: N6-H3K27ac


title: N9-H3K27ac


title: N10-H3K27ac


title: T28-H3K27ac

value: Tumor


title: N17-H3K27ac


title: N21-H3K27ac


title: N1-H3K27ac


title: N2-H3K27ac


title: N4-H3K27ac


title: T27-H3K27ac


title: T29-H3K27ac


title: T24-H3K27ac


title: T23-H3K27ac


title: N7-H3K27ac


title: N20-H3K27ac


title: T22-H3K27ac


title: T20-H3K27ac


title: T21-H3K27ac


title: N18-H3K27ac


title: T17-H3K27ac


title: T10-H3K27ac


title: T8-H3K27ac


title: N8-H3K27ac


title: T19-H3K27ac


title: T18-H3K27ac


title: T16-H3K27ac


title: T5-H3K27ac


title: T4-H3K27ac


title: T7-H3K27ac


title: T26-H3K27ac


title: 237

status: Public on Aug 24 2021

city: New York

first: Darwin

last: D'Souza

address: 1470 Madison Avenue

department: ImmunoBio

institute: Human Immune Monitoring Center

description: lamina propria cells of noninflamed colonic mucosa

data_processing:
Cell Ranger 3 for demultiplexing, alignment and cell counting
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw and filtered cell x genes matrix

source_name: Colon lamina propria

growth_protocol: Cells freshly extracted from colonic biopsies collected during colonoscopy as follow : During the colonoscopy procedure, 8 to 12 biopsies from inflamed and/or noninflamed parts of the colon of each patient were collected with forceps directly in RPMI, on wet ice. Biopsies were processed fresh within 2 hours of collection. They were first transferred in 10 ml HBSS (free of calcium and magnesium) containing EDTA (0.5M, pH 8, Invitrogen) and Hepes (1M, Lonza) and incubated for 20 minutes at 37°C. The biopsies were then vortexed, washed with HBSS and transferred in a digestion media (10 ml of RPMI containing 0.005 mg of collagenase IV (Sigma-Aldrich) and DNAse I (Sigma-Aldrich). After an incubation of 40 minutes at 37°C in a rotating incubator (215 rpm), biopsies were physically disrupted by pipetting up and down 10 times through a 25-gauge needle, filtered through a 100-µm and a 40- µm cell strainer and washed with RPMI twice

extract_protocol: none provided by the submitter

value: Colon

tag: status

value: non inflamed

tag: disease

value: Healthy control


title: 219

tag: tissue


title: 206


title: 204

description: lamina propria cells of inflamed colonic mucosa

value: Ulcerative colitis


title: T2-H3K27ac


title: T1-H3K27ac


title: 238

value: Inflamed


title: 221


title: T9-H3K27ac


title: SC_spt4del_R1_rep1

status: Public on Aug 20 2021

city: Daejeon

first: Youngseo

last: Cheon

address: 291 Daehak-ro, Yuseong-gu

institute: Korea Advanced Institute of Science and Technology

description:
Detecting active RNA polymerase
SC_spt4d_Norm_plus.bw
SC_spt4d_Norm_minus.bw

data_processing:
Sequence alignment and data processing were performed based on the publicly available alignment pipelines on GitHub used in the previous study (Booth et al., 2018; only Read 1 (R1) was used for analysis) with minor modifications.
Raw sequencing reads were processed using FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) in the following orders: Adaptor sequences (5’-TGGAATTCTCGGGTGCCAAGG-3’) were removed, reads length was trimmed to a maximum length of 36 bp and, for PRO-seq, reads were then reverse-complemented.
The reads mapped to rRNA sequences were depleted using SortMeRNA (Kopylova et al., 2012)
The reads that were not mapped to rRNA sequences were uniquely aligned to a genome using Bowtie allowing for two mismatches (Langmead et al., 2009).
The processed reads of yeast samples that were generated with the spike-in approach were mapped to a combined genome consisting of S. cerevisiae (sacCer3) and S. pombe (SpombeASMv2) and unique reads from each genome were parsed for downstream analysis. The processed reads of mESCs were mapped to the M. musculus mm10 genome.
Genome_build: S. cereivisae (sacCer3), S. pombe (SpombeASMv2) and M. musculus (mm10)
Supplementary_files_format_and_content: The coverage of the aligned reads was generated using genomecov function of BEDtools (Quinlan and Hall, 2010). Only the most 3’ nucleotide of each read was calculated for PRO-seq and only the most 5’ nucleotide of each read was calculated for PRO-cap. For the spike-in control, the recorded coverage in the bedGraph file was normalized to the relative number of uniquely mapped spike-in counts, and these normalized reads were counted in reads per million mapped reads (RPM) considering the sequencing depth of experimental reads. For mESCs data, which was generated without the spike-in control, the reads were presented in RPM. BedGraph files were converted to BigWig files by bedGraphToBigWig (Kent et al., 2010) and the downstream analysis was processed based on the publicly available custom R scripts on GitHub, as previously reported (Booth et al., 2018).

source_name: S. cerevisiae

growth_protocol: All cells were grown to mid-log phase at 30°C in yeast peptone dextrose (YPD).

extract_protocol:
Nuclear run-on reactions and RNA extractions were performed based on the published protocol (Mahat et al., 2016) with minor modifications according to the previous study (Booth et al., 2018; Hou et al., 2019).
Library was generated followed by the published PRO-seq or PRO-cap protocol (Mahat et al., 2016) from RNA fragmentation by base hydrolysis to full-scale PCR amplification with few differences of reagent. DNA libraries of ~100bp to 350bp were selected by agarose gel extraction (Zymo Research, D4007) according to the manufacturer’s protocol.

tag: experiment

value: PRO-seq

tag: genotype


title: SC_spt4del_R1_rep2


title: SC_arp5del_R1_rep2

description:
Detecting active RNA polymerase
SC_arp5d_Norm_plus.bw
SC_arp5d_Norm_minus.bw


title: T6-H3K27ac


title: SC_arp5del_R1_rep1


title: SC_htz1del_R1_rep1

description:
Detecting active RNA polymerase
SC_htz1d_Norm_plus.bw
SC_htz1d_Norm_minus.bw


title: SC_wt_R1_rep1

description:
Detecting active RNA polymerase
SC_wt_Norm_plus.bw
SC_wt_Norm_minus.bw


title: PRO-cap_SC_Ino80p-AID_KD_R1_rep2

description:
Detecting transcription start sites
PRO-cap_SC_Ino80p-AID_KD_Norm_plus.bw
PRO-cap_SC_Ino80p-AID_KD_Norm_minus.bw

treatment_protocol: Ino80p-AID cells with ethanol were grown to mid-log phase at 30°C in yeast peptone dextrose (YPD). Ethanol was washed from the media and cells with Auxin were incubated for 3 hours to conditional depletion. Auxin was washed from the media and cells without auxin were incubated for 3 hours more.

value: PRO-cap

value: Auxin treatment with 3 hrs


title: SC_htz1del_R1_rep2


title: PRO-cap_SC_Ino80p-AID_KD_R1_rep1


title: PRO-cap_SC_Ino80p-AID_Ctrl_R1_rep2

description:
Detecting transcription start sites
PRO-cap_SC_Ino80p-AID_Ctrl_Norm_plus.bw
PRO-cap_SC_Ino80p-AID_Ctrl_Norm_minus.bw

value: Auxin treatment for 0 hr (mock treatment with EtOH)


title: T3-H3K27ac


title: SC_Ino80p-AID_Rescue_R1_rep2

description:
Detecting active RNA polymerase
SC_Ino80p-AID_Rescue_Norm_plus.bw
SC_Ino80p-AID_Rescue_Norm_minus.bw

value: Auxin withdrawl for 3 hrs


title: PRO-cap_SC_Ino80p-AID_Ctrl_R1_rep1


title: SC_Ino80p-AID_KD_R1_rep2

description:
Detecting active RNA polymerase
SC_Ino80p-AID_KD_Norm_plus.bw
SC_Ino80p-AID_KD_Norm_minus.bw

value: Auxin treatment for 3 hrs


title: SC_Ino80p-AID_KD_R1_rep1


title: 200


title: SC_Ino80p-AID_Ctrl_R1_rep2

description:
Detecting active RNA polymerase
SC_Ino80p-AID_Ctrl_Norm_plus.bw
SC_Ino80p-AID_Ctrl_Norm_minus.bw


title: MM_E14Tg2a_siINO80_R1_rep2

description:
Detecting active RNA polymerase
MM_E14Tg2a_siINO80_RPM_plus.bw
MM_E14Tg2a_siINO80_RPM_minus.bw

growth_protocol: E14Tg2a mESCs were maintained under feeder-free conditions at 37°C with 5% CO2 in humidified air.

treatment_protocol: The siRNAs against EGFP (5’-GUUCAGCGUGUCCGGCGAG-3’) and INO80 (5’-GGCUUAUCUGUAAAGGCACAAUUGA-3’) were synthesized and annealed by Bioneer. mESCs were seeded to plates, incubated for 24 hr, and transfected with the indicated siRNAs (final concentration, 50 nM) using DharmaFECT I (Dharmacon, T-2001-03) according to the manufacturer’s protocol. The culture medium was replaced at 24 hr of transfection, and cells were harvested at 48 hr of transfection.

value: siINO80 transfection


title: 198


title: MM_E14Tg2a_siINO80_R1_rep1


title: SP_wt_R1

description:
Detecting active RNA polymerase
SP_wt_RPM_plus.bw
SP_wt_RPM_minus.bw

organism: Schizosaccharomyces pombe

source_name: Schizosaccharomyces pombe

growth_protocol: Cells were grown to mid-log phase at 30°C in yeast extract with supplements (YES).

extract_protocol:
Nuclear run-on reactions and RNA extractions were performed based on the published protocol (Mahat et al., 2016) with minor modifications according to the previous study (Booth et al., 2018; Hou et al., 2019).
Library was generated followed by the published PRO-seq protocol (Mahat et al., 2016) from RNA fragmentation by base hydrolysis to full-scale PCR amplification with few differences of reagent. DNA libraries of ~100bp to 350bp were selected by agarose gel extraction (Zymo Research, D4007) according to the manufacturer’s protocol.


title: SC_wt_R1_rep2


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_NOsrm_24hr_S_6.1.1

status: Public on Jul 30 2021

city: Bethesda

first: Kathleen

middle: Shaindel Metz

last: Reed

address: 41 Medlars Dr, B507

department: Genetics and Molecular Biology

institute: National Cancer Institute, NIH

data_processing:
Libraries were sequenced as paired-end 75bp reads on an Illumina NextSeq 500, to an average depth of approximately 55-70 M reads per sample.
Low-quality reads and adapters were trimed using Trim Galore! (v 0.4.3; parameters: --paired)
Trimed reads were mapped to the hg19 transcriptome and quantified using Salmon (v 0.8.2; mapping mode, parameters: -l A)
Gene-level quantifications were summarized from each sample using tximport (v 1.2.0; default settings)
Differential analysis was conducted in R (v 3.5.1) with DESeq2 (v 1.22.2) using a design adjusting for replicate variability when calulating differences between groups (design: LRT, full=~ replicate + condition, reduced = ~ replicate, lfcShrink (apeglm), LFC threshold = 1, FDR-adjusted p-value threshold = 0.01)
Genome_build: hg19
Supplementary_files_format_and_content: ADAB_RNA_<CellType>_<Genotype>_<AbetaType>_<AbetaConc>_<OtherTreatments>_<Serum>_<Time>_S_quant.sf (Salmon output: transcript-level quantification, a tab-delimited file listing transcript name, length, effective length, TPM, and estimated number of reads mapped); ADAB_geneCounts.tsv (combined gene-level quantification listing ENSEMBL and HGNC gene identifiers, and raw counts from quant.sf "numReads" column for each sample); ADAB_Fig3_DESeqDesigns.xlsx (an excel file containing coldata objects and contrasts used in DESeq2 for each experiment, used to generate the bargraph in Figure 3).

source_name: THP-1 monocyte cell line

growth_protocol: Different cell types were grown under different conditions, as described in the "characteristics: growth conditions" in the SAMPLES section. iPSC-derived HPCs, iPSC-derived microglia, PBMCs and THP-1 cells were all differentiated prior to treatment. Other cell lines were cultured in the media listed.

extract_protocol:
RNA was extracted using a Qiagen RNeasy kit. RIN were checked with Tapestation RNA HS tape and confirmed to be in range of 8.5-10
Libraries were prepared using the KAPA RNA HyperPrep with RiboErase kit using 500 ng of isolated RNA as input.. Ribosomal RNA was removed using the NEBNext rRNA Depletion Kit.

treatment_protocol: Each sample was treated by substituting the growth media with fresh media containing the treatment, incubating for 24 or 4 hours, and then extracting RNA. For some treatments, this media contained 10% FBS, while others were serum-free. The amount of FBS in the treatment media is detailed in the "characteristics: serum in treatment" column in the SAMPLES section. Treatments included: PBS (control); a combination of 10 ng/mL LPS and 20 ng/mL IFN-gamma; oligmerized A-beta (oA[beta]) from two separate methods (A and B, from Tseng et al. 2017 and Abud 2017, respectively); and fibrilized A-beta (fAβ) from both methods. Fibrilized A-beta from Method A could be incubated for 5 or 7 days, and both forms are used. Details on length, concentration, and type of treatment are listed in the "characteristics: treatment" column of the SAMPLES section. Samples were collected from many different experiments across different days, as described in the "characteristics: experiment number" column. For each treatment, two replicates were conducted, as listed under the "characteristics: technical replicate" column.

tag: growth conditions

value: RPMI, 10% FBS, 1% pen/strep; differentiated to macrophages with PMA for Z hr

value: 24hr 10 ng/mL LPS, 20 ng/mL IFN-gamma

tag: serum in treatment media

tag: experiment number

tag: technical replicate


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_6.2.1

value: 24hr PBS


title: P20 mouse cochlea 2

status: Public on Aug 05 2021

city: Shanghai

last: Xue

address: Zhizaoju Road 639

department: Otolaryngology

institute: Shanghai Jiaotong University School of Medicine

data_processing:
10x Genomics pipeline Cell Ranger v2.1.0 was used for demultiplexing, barcode processing, and UMI counting.
The cellranger mkfastq pipeline was used to demultiplex Illumina raw files into FASTQ files.
The cellranger pipeline was then used to filter the Cell barcodes and UMIs, concatenate into one matrix, and normalize them to the same sequencing depth.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell.

source_name: cochlea

extract_protocol:
5~8 wild type C57 mice at postnatal day 20 were purchased from Jackson Laboratory (Bar Harbor, Maine), euthanized and cochleae harvested. Single cells disassociated by trypsin digestion were used for SCRNA seq.
Single-cell libraries were sequenced on the Illumina HiSeq platform

tag: strain

value: cochlea

tag: age

value: post natal day 20


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_NOsrm_24hr_S_6.2.1


title: P20 mouse cochlea 1


title: MM_E14Tg2a_siEGFP_R1_rep2

description:
Detecting active RNA polymerase
MM_E14Tg2a_siEGFP_RPM_plus.bw
MM_E14Tg2a_siEGFP_RPM_minus.bw

value: wt

value: siEGFP transfection


title: ADAB_RNA_THP1_WT_OL30_01uM_NONE_HIsrm_24hr_S_5.2.1

value: RPMI, 10% FBS, 1% pen/strep; differentiated to macrophages with 24hr of 25 uM PMA, then 72hr of rest

value: 24hr 1 uM oA[beta] (Method A:Abud, 2017)

value: 10% FBS


title: ADAB_RNA_iMGL_FE_NOAB_NONE_NONE_NOsrm_24hr_S_2.2.1

source_name: iPSC-derived microglia

value: Differentiated from iPSC-derived HPCs using STEMdiff microglia Differentiation/Maturation Kits; treated/collected in Microglia Maturation Media


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_6.1.1


title: ADAB_RNA_iMGL_FE_NOAB_NONE_LPIF_NOsrm_24hr_S_2.2.1


title: ADAB_RNA_iMGL_FE_NOAB_NONE_LPIF_NOsrm_24hr_S_2.1.1


title: SC_Ino80p-AID_Rescue_R1_rep1

value: PRO-seq


title: ADAB_RNA_iMGL_FE_NOAB_NONE_NONE_NOsrm_24hr_S_2.1.1


title: ADAB_RNA_THP1_WT_OL30_01uM_NONE_HIsrm_24hr_S_5.1.1


title: MM_E14Tg2a_siEGFP_R1_rep1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_24hr_S_5.2.1


title: ADAB_RNA_THP1_WT_FBR7_01uM_NONE_HIsrm_24hr_S_5.2.1

value: 24hr 1 uM 7-day fAβ (Method A:Abud, 2017)


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_HIsrm_24hr_S_5.2.1


title: ADAB_RNA_THP1_WT_FBR5_01uM_NONE_HIsrm_24hr_S_5.2.1

value: 24hr 1 uM 5-day fAβ (Method A:Abud, 2017)


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_HIsrm_24hr_S_5.1.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_24hr_S_5.1.1


title: ADAB_RNA_THP1_WT_FBR5_01uM_NONE_HIsrm_24hr_S_5.1.1


title: ADAB_RNA_THP1_WT_FBR7_01uM_NONE_HIsrm_24hr_S_5.1.1


title: 202

value: Colon

value: Inflamed

value: Ulcerative colitis


title: SC_Ino80p-AID_Ctrl_R1_rep1

value: Auxin treatment for 0 hr (mock treatment with EtOH)


title: ADAB_RNA_THP1_WT_FIBR_01uM_NONE_HIsrm_24hr_S_4.2.1

value: 24hr 1 uM fAβ (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_24hr_S_4.2.1

value: 24hr PBS


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_HIsrm_24hr_S_4.2.1

value: 24hr 1 uM oA[beta] (Method B:Tseng et al. 2017)


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_HIsrm_24hr_S_4.1.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_HIsrm_24hr_S_4.1.1


title: ADAB_RNA_THP1_WT_FIBR_01uM_NONE_HIsrm_24hr_S_4.1.1


title: ADAB_RNA_THP1_WT_OLGO_01uM_NONE_NOsrm_24hr_S_3.2.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_NONE_NOsrm_24hr_S_3.2.1


title: ADAB_RNA_THP1_WT_OLGO_01uM_LPIF_NOsrm_24hr_S_3.2.1

value: 24hr 1 uM oA[beta] (Method B:Tseng et al. 2017), 10 ng/mL LPS, 20 ng/mL IFN-gamma


title: ADAB_RNA_THP1_WT_OLGO_01uM_LPIF_NOsrm_24hr_S_3.1.1


title: ADAB_RNA_THP1_WT_NOAB_NONE_LPIF_NOsrm_24hr_S_3.1.1

value: 24hr 10 ng/mL LPS, 20 ng/mL IFN-gamma