title: WT 2

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
For scRNA-seq: Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA)
For scRNA-seq: Cells were partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, tagmentation and 5’ adaptor attachment.
For scRNA-seq: Libraries were sequenced on an Illumina NextSeq 500. Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics).
For total RNA-seq: Sequencing analysis was done using RNA-seq for Eukaryotes Analysis v3 by Banana Slug Genomics Center at University of California Santa Cruz
For total RNA-seq: Raw sequencing reads (paired-end reads) that were produced by Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC. Adapter sequences and primers were trimmed from the sequencing reads using Trimmomatic, then followed by removing the polyA tail, polyN, and read portions with quality score below 28 using PRINSEQ
For total RNA-seq: Trimmed reads were mapped to the reference genome (GRCm38/mm10) using (TopHat2) with NCBI RefSeq annotated genes as transcriptome index data. Read alignment coverage and summary statistics for visualization were computed using SAMtools, BEDtools, and UCSC Genome Browser utilities
For total RNA-seq: Using Cufflinks work flow, the sequencing reads aligned to RefSeq annotated genes were quanti fied using Cuffquant. Cuffnorm was then used to normalize the gene expression levels across the studied samples with FPKM computed for sample correlation assessment. Differential expression analysis between samples was performed using Cuffidff with the computed results from Cuffquant.
Genome_build: mm10

source_name: Murine small intestinal tissue

growth_protocol: For scRNA-seq: Crypts were isolated from approximately 10 cm of mouse small intestinal tissue. Crypts were plated in 24-well plates at a concentraton of 80 crypts per 20 µL Matrigel. Crypts were grown in DMEM/F12 media supplemented with 100 ng/mL R-spondin (Invitrogen), 50 ng/mL Noggin (Invitrogen), 1X penicillin/streptomycin (Invitrogen), 1X GlutaMAX (Invitrogen), 1X N2 (Invitrogen), 1X B27 (Invitrogen). 40 ng/mL EGF (Peprotech), 1µM N-acetylcysteine (Sigma), 20 µM Y-27632 (Tocris), and 5.6 µM CHIR 99021 (Tocris). Media was changed every 2 days.

extract_protocol:
For scRNA-seq: Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, an input of 10,000 cells was added to each channel of a chip with a recovery rate of 3000 cells. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, tagmentation and 5’ adaptor attachment. For total RNA-seq: Terminal ileum tissues were extracted and stored at -20°C in RNAlater. RNA from the terminal ileum of 6 weeks old Il22Ra1fl/fl;Defa6-cre+ and their littermate cre- mice was isolated using TRIZOL extraction methods as per manufacture instructions (Life Technologies).
For scRNA-seq: Libraries were sequenced on an Illumina NextSeq 500. Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics). For each cell, we quantified the number of genes for which at least one UMI was mapped and then excluded all cells with fewer than 1,000 detected genes. For total RNA-seq: Illumina compatible Total RNA cDNA libraries with RiboZero Gold depletion were generated following the TruSeq Stranded Total RNA Reference Guide (Illumina Document #1000000040499v00, TruSeq Stranded Total RNA Gold Illumina Kit #20020598).

treatment_protocol: For scRNA-seq: Cells were dissociated using TrypLE Express, washed with 1X PBS with 0.4% BSA and stored on ice until proceeding to single cell capture for RNA sequencing.

value: Terminal Ileum

tag: age

value: 6 weeks


title: HEK293T cells, A-800-MU82-0619-2

status: Public on Oct 14 2020

type: SRA

city: shanghai

first: Tian-Lin

last: Cheng

state: I am not in the U.S. or Canada

address: Dong An Road, No. 131

country: China

institute: Fudan University

description: all.counts.txt

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a)10% base quality <15 b) 13% base quality <20.
RNA sequencing data was aligned to the human reference genome (GRCh38) using STAR
Variants were called using the GATK best practices pipeline using Picard  and GATK 3.8
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contains counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: HEK293T cells

growth_protocol: HEK293T cells were cultured in DMEM (Gibco/Life Technologies) with 10%  FBS (Gibco/Life Technologies) at 37 °C in a 5% CO2 incubator (Thermo Scientific  Heraeus)

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293T cells were plated into 6-well plates  (Thermo Scientific) for transfection. About 20 h later, cells were transfected using  4 μL Lipofectamine 3000 (Thermo Scientific) with 3μg plasmid expressing specific  base editor and/or 1ug plasmid expressing specific sgRNA according to the manufacturer’s  manuals. After 48 h culture, positive cells were sorted using FACS for RNA purification.

tag: cell line

value: human embryonic kidney epithelial cell line HEK293T

tag: transfection

value: ABE-800-MU82, sgRNA-1


title: WT 3

country: USA

organism: Mus musculus

tag: genotype

tag: tissue


title: WT 1


title: HEK293T cells, CASN-175

description: all.counts.txt


title: HEK293T cells, A-800-MU82-0619-1

description: all.counts.txt


title: HEK293T cells, A-800-MU106-3

description: all.counts.txt


title: KO 3


title: KO 1


title: KO 2


title: HEK293T cells, A-800-MU106-1

description: all.counts.txt


title: HEK293T cells, A-800-MU106-2

description: all.counts.txt


title: HEK293T cells, A-800-MO-WT

description: all.counts.txt

value: ABE-800-TadAmowt, sgRNA-1


title: HEK293T cells, L8-286

description: all.counts.txt


title: HEK293T cells, A-800-Dua1

description: all.counts.txt

value: ABE-800-TadAWTMO, sgRNA-1


title: HEK293T cells, A-769-MU82-0619-1

description: all.counts.txt

value: ABE-769-MU82, sgRNA-1


title: HEK293T cells, A-769-MU106-3

description: all.counts.txt


title: atac_hpek_NVS-BET2_48h_3

status: Public on Oct 15 2020

city: Basel

first: Guglielmo

last: Roma

address: Fabrikstrasse 22

country: Switzerland

institute: Novartis Institutes for Biomedical Research

library_source: genomic

data_processing:
All paired-end ATAC-seq datasets were processed with the Encode pipeline ATAC v1.7.1 (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Reads were aligned using Bowtie2 (version 2.3.4.3) to homo sapiens genome version NCBI37/hg19. Alignments were performed using all default parameters.
We used the MACS2 peak finding algorithm (version 2.2.4) with default parameters to identify regions of enrichment over background.
Differential peaks were calculated using abs(log2FC) > 1 & p.value < 0.00001
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files are provided for visualization of results in the UCSC genome browser.

molecule: genomic DNA

source_name: keratinocytes

growth_protocol: Assay for Transposase-Accessible Chromatin (ATAC) was performed according to Omni-ATAC Supplementary Protocol 1 (Corces et al, Nature methods, 2017) using 3 × 10^5 HPEKs per treatment condition that were seeded in 6-well plates, washed once with 500 μl of PBS (on plate) and detached using Accutase (CELLnTEC).

extract_protocol:
Enriched nuclei were tagmented using Tn5 transposase (Illumina Tagment DNA Enzyme and Buffer Kit) at 37 °C for 30 min. Tagmented DNA was isolated using DNA Clean and Concentrator Kit  (Zymo).
ATAC-seq libraries were generated using NEBNext High Fidelity 2x PCR Mix (NEB) with IDT for Illumina Nextera DNA Unique Dual Indexes (UDI) using 10 cycles of amplification. Libraries were purified using Agencourt AMPure XP beads (Beckman Coulter) and their concentration was measured using Qubit dsDNA HS Assay Kit (Invitrogen). Library integrity and size distribution was checked by Agilent TapeStation.
ATAC libraries were sequenced dual-indexed paired-end (2 x 76) using a NovaSeq 6000 instrument (Illumina) according to manufacturer’s instructions.

treatment_protocol: HPEKs were treated in culture for 6h and 48h (6h+42h wash-out) with either 125nM NVS-BET1, 125nM NVS-BET2, or 0.0125% DMSO as control in triplicate per condition.

tag: cell type

value: keratinocytes

tag: treatment

tag: time

value: 48h (6h + 42h wash-out)


title: HEK293T cells, A-769-MU106-2

description: all.counts.txt


title: HEK293T cells, A-769-MU106-1

description: all.counts.txt


title: HEK293T cells, A-535-MU82-0619-2

description: all.counts.txt

value: ABE-535-MU82, sgRNA-1


title: HEK293T cells, A-535-MU82-0619-1

description: all.counts.txt


title: 24C_3

type: RNA

city: Kyoto

first: Akira

last: Hirasawa

state: Kyoto

address: 46-29 Yoshida Shimoadachi-cho, Sakyo-ku

department: Genomic Drug Discovery Science

country: Japan

institute: Kyoto University Graduate School of Pharmaceutical Sciences

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: The probe arrays were scanned with the GeneChip(R) Scanner.

data_processing: The data were analyzed with R software. The MAS 5.0 normalization were performed using the justMAS function in the simpleaffy package from Bioconductor.

label: biotin

label_protocol: The labeled cDNA were then hybridized on Affimetrix gene chip and stained.

growth_protocol: Human neuroblastoma SH-SY5Y cells were cultured in D-MEM/F-12 medium at 37 degree under 5 per CO2.

extract_protocol: cDNA labeling was performed according to the manufacturer’s instructions.

treatment_protocol: Total RNA was extracted byspin column method and transcribed to cDNA.

value: human neuroblastoma cells


title: HEK293T cells, A-535-MU106-2

description: all.counts.txt


title: HEK293T cells, A-800-M0

description: all.counts.txt

value: ABE-800-TadA-2m, sgRNA-1


title: HEK293T cells, A-800-8

description: all.counts.txt


title: HEK293T cells, A-769-MU82-0619-2

description: all.counts.txt


title: HEK293T cells, A-535-MU106-1

description: all.counts.txt


title: atac_hpek_DMSO_6h_1

value: DMSO


title: HEK293T cells, A-535-M0

description: all.counts.txt

value: ABE-535-TadA-2m, sgRNA-1


title: 24A_3

value: fibrillar Ab (24-h incubation)


title: 24C_2


title: 24C_1


title: 24A_1


title: 24A_2


title: 6C_2


title: No pyruvate morula treated with myc rep4

city: Los Angeles

first: Utpal

last: Banerjee

state: California

address: Charles E. Young Drive

institute: University of California, Los Angeles

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment using the STAR program 2.6.1d
Genome_build: mm10 Ensembl Transcripts release 97
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance for each sample

source_name: Preimplantation embryo

extract_protocol:
The RNA extraction was performed using the Smart-seq2 protocol as published with minor modification. Cells were lysed in 0.1% (vol/vol) Triton X-100 lysis containing 2.5µM of oligo-dT30VN primer, 2.5mM of dNTP mix and 1U/µl of RNase inhibitor. After 3 mins lysis at 72℃, the Smart-seq2 reverse transcription mixture was added for reverse transcription. cDNA was pre-amplified and AMPure XP beads were used for purification.
Smart-seq2 protocol

treatment_protocol: The standard growth media (KSOM) for embryo culture contains 0.2 mM glucose, 0.2 mM pyruvate and 5 mM L-lactate. In the "No pyruvate" and "No lactate" samples the embryo culture media had either pyruvate or lactate removed, respectively.  For "No pyruvate treated with myc" pyruvate was removed from the growth media and 20 nM of the myc inhibitor (KY-PYR-9) was included.

tag: strain

value: Preimplantation embryo

value: post -HCG 78 h

value: wild type


title: 6C_3


title: DU145_2_rep2

city: Huizhou

first: Chen

middle: Jia

last: hong

state: Guangdong

address: 41 erling North Road, Huicheng District, Huizhou City, Guangdong Province

department: Department of Urology

institute: Huizhou Municipal Central Hospital

data_processing:
Library strategy: DNA-Seq
Align the fastq files against the library’s sgRNAs sequences list using Bowtie2
Genome_build: The sgRNAs sequences as appear in Table S1 of Wang, T. et al. Identification and characterization of essential genes in the human genome. Science 350, 1096–1101 (2015).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: DU145 cells

growth_protocol: The human prostate cancer cells DU145 was purchased from American Type Culture Collection (ATCC, USA) and  cultured in the DMEM (HyClone, SH30022.01B) midium containing 10% fetal bovine serum (FBS, Gibco) and 100 U/mL of double antibody (penicillin and streptomycin， TBD, PS2004HY) in a humidified incubator with 5% CO2 at 37 ℃.

extract_protocol:
Polymerase chain reaction (PCR) was applied to identify the successful transfection of lentiCRISPRa vector in DU145 cells.
CRISPRa-F: TCTTGTGGAAAGGACGAAACACCG and CRISPRa-R: CTCCTTTCAAGACCTAGGATC were selected for PCR amplification region (209 bp) from lentiCRISPRa vector, followed by electrophoresis. The thermocycling parameters of PCR were 95℃ for 60 s, 35 cycles of (95℃for 10 s, 56℃ for 10 s, 72℃ for 30 s) and 72℃ for 1 min.
libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 22.5 μg of the human CRISPR/Cas9 SAM pooled library was transfected into 7.5×10^6 HEK293 T cells for 24 h. Viral supernatant was harvested, and DU145 cells were transduced at a calculated multiplicity of infection (MOI) of 0.4 followed by selection with hygromycin B (YEASEN, 60225ES03) and blasticidin (MDBio, D0120601) for 15 days. The DU145 cells were  treated three rounds with metformin (100 mM) for 24 h .

tag: tissue/cell type

value: prostate; derived from metastatic site:brain

value: treated with metformin


title: DU145_1_rep1


title: 6A_3

value: oligomeric Ab (6-h incubation)


title: 6C_1


title: No pyruvate morula treated with myc rep3


title: 6A_2


title: 6A_1


title: HEK293T cells, A-535-8

description: all.counts.txt

value: human embryonic kidney epithelial cell line HEK293T


title: No pyruvate morula treated with myc rep2


title: No pyruvate morula rep5


title: HEK293T cells, A-535-MU106-3

description: all.counts.txt


title: No pyruvate morula treated with myc rep1


title: No pyruvate morula rep4


title: HEK293T cells, A-1249-MU82-0619

description: all.counts.txt


title: HEK293T cells, A-1249-MU82

description: all.counts.txt


title: HEK293T cells, A-1249-MU106-3

description: all.counts.txt


title: No pyruvate morula rep2


title: HEK293T cells, A-1249-MU106-2

description: all.counts.txt


title: HEK293T cells, A-1249-MU106-1

description: all.counts.txt


title: HEK293T cells, A-315-8

description: all.counts.txt


title: HEK293T cells, A-1249-MO

description: all.counts.txt

value: ABE-1249-TadA-2m, sgRNA-1


title: HEK293T cells, A-1249-8

description: all.counts.txt


title: No pyruvate blastocyst rep2

value: post -HCG 114 h


title: No pyruvate blastocyst rep5


title: No pyruvate blastocyst rep4


title: No pyruvate blastocyst rep1


title: HEK293T cells, A-1029-MU82-0619-2

description: all.counts.txt


title: HEK293T cells, A-1029-MU82-0619-1

description: all.counts.txt


title: No pyruvate 2-cell latest rep3

value: post -HCG 55 h


title: HEK293T cells, A-1029-MU106-3

description: all.counts.txt


title: No pyruvate 2-cell latest rep2


title: No pyruvate morula rep3


title: No pyruvate 2-cell very late rep4

value: post -HCG 52 h


title: No pyruvate 2-cell latest rep1


title: HEK293T cells, A-1029-M0-142

description: all.counts.txt

value: ABE-1029-TadA-2m, sgRNA-1


title: NRK-52E,transcriptome 02

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

data_processing:
Sequenced reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a
Transcript abundances in TPM were caculated by  rsem 1.3.0
Genome_build: Ensembl Release 94
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

molecule: polyA RNA

organism: Rattus norvegicus

source_name: NRK-52E,transcriptome 02

growth_protocol: Cell lines were grown on transwell (see manuscript) to confluence before RNA isolation.

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Kidney Cells


title: No pyruvate morula rep1


title: HEK293T cells, A-1010-8

description: all.counts.txt


title: HEK293T cells, A-203-8

description: all.counts.txt


title: HEK293T cells, A-1029-MU106-1

description: all.counts.txt


title: No pyruvate blastocyst rep3


title: HEK293T cells, A-1249-BE-147

description: all.counts.txt


title: No pyruvate 2-cell very late rep2


title: NRK-52E,transcriptome 01

source_name: NRK-52E,transcriptome 01


title: HEK293T cells, A-113-8-181

description: all.counts.txt


title: SHR,transcriptome 03

source_name: SHR,transcriptome 03


title: No pyruvate 2-cell latest rep4


title: No pyruvate 2-cell very late rep1


title: METTL3KD-2

city: beijing

first: fuping

last: you

address: xueyuan street

institute: Peking University Health Science Center

data_processing:
Base calling was performed using  the software bcl2fastq (v2.17.1.14) to obtain pass filter data through preliminary quality analysis.
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1).
Gene expression was quantified as reads per kilobase of coding sequence per million reads (RPKM) algorithm.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes FPKM values for each Sample ...

source_name: Brain

extract_protocol:
At 3 dpi, brains were removed, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent and RNeasy Mini Kit (Qiagen). 1 μg total RNA with RIN value above 6.5 was used for following library preparation.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Each mouse was intravenously injected with HSV-1 at  5×10E6 PFU

value: Brain

value: 7 weeks

tag: infection


title: METTL3KD-1


title: SHR,transcriptome 02

source_name: SHR,transcriptome 02


title: HEK293T cells, A-1029-MU106-2

description: all.counts.txt


title: No pyruvate mid 2-cell rep3

value: post -HCG 42 h


title: NRK-52E,transcriptome 03

source_name: NRK-52E,transcriptome 03


title: SHR,transcriptome 01

source_name: SHR,transcriptome 01


title: No pyruvate 2-cell very late rep3


title: 01780012_non-cancerous tissue

city: Shanghai

first: Botai

last: Li

address: No. 25/Ln 2200 Xie-Tu Road

institute: Shanghai Jiao Tong University

hyb_protocol: One μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Axon GenePix 4000B microarray scanner(Molecular Devices, Inc.).

data_processing: Scanned images were then imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Quantile normalization and subsequent data processing were performed using the R software package. Differentially expressed circRNAs between two samples were identified through Fold Change and P value filtering.

source_name: 01780012,non-cancerous tissue

label_protocol: Sample labeling were performed according to the manufacturer’s protocol (Arraystar Inc.). Briefly, circRNA were treated with RNase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: Total RNAs were isolated from the paired tissues samples of three NSCLC patients by TRIzol reagent (Invitrogen) and purified by RNeasy Mini Kit (Qiagen).

treatment_protocol: Primary NSCLC cancer tissues and adjacent non-cancerous tissues were collected from patients who had undergone surgery at Shanghai Chest Hospital (Shanghai, China). None of the patients included in this study received any preoperative radiation or chemotherapy. Resected specimens were frozen in liquid nitrogen and then stored at -80 ℃ until use.

tag: gender

value: female

value: lung


title: WKY,transcriptome 03

source_name: WKY,transcriptome 03


title: No pyruvate mid 2-cell rep2

value: Preimplantation embryo


title: OK-WT,transcriptome 04

data_processing:
Sequenced reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a
Transcript abundances in TPM were caculated by  rsem 1.3.0
tab-delimited text files include TPM values for each sample
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

organism: Didelphis virginiana

source_name: OK-WT,transcriptome 04


title: 0143_non-cancerous tissue

source_name: 0143,non-cancerous tissue

value: male


title: WKY,transcriptome 02

source_name: WKY,transcriptome 02


title: OK-WT,transcriptome 03

source_name: OK-WT,transcriptome 03


title: No pyruvate late 2-cell rep5

value: post -HCG 48 h

value: wild type


title: No pyruvate mid 2-cell rep4


title: WKY,transcriptome 01

source_name: WKY,transcriptome 01


title: OK-WT,transcriptome 02

source_name: OK-WT,transcriptome 02


title: No pyruvate mid 2-cell rep1

source_name: Preimplantation embryo


title: 01780012_cancer tissue

source_name: 01780012,cancer tissue


title: No pyruvate late 2-cell rep4


title: 255_cancer tissue

source_name: 255,cancer tissue


title: OK-ATCC,transcriptome 03

source_name: OK-ATCC,transcriptome 03


title: OK-ATCC,transcriptome 02

source_name: OK-ATCC,transcriptome 02


title: 0143_cancer tissue

source_name: 0143,cancer tissue


title: 255_non-cancerous tissue

source_name: 255,non-cancerous tissue


title: No pyruvate late 2-cell rep3


title: No pyruvate late 2-cell rep2


title: OK-ATCC,transcriptome 01

source_name: OK-ATCC,transcriptome 01


title: GK1_12h

city: Farmington

first: Tingting

last: Geng

state: CT

address: 263 Farmington Avenue

department: Department of Immunology

institute: Uconn Health

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence unsing SOAPnuke v1.5.2 (https://github.com/BGI-flexlab/SOAPnuke)
Bowtie2 v2.2.5 and RSEM v1.2.12 were used to map sequencing read to mm9 genome and quantify reads.
DESeq2 v1.0.0 was applied to calculate the differential expression of genes.
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone-marrow-derived macrophage

growth_protocol: Bone marrows were isolated from the tibia and femur bones and then differentiated into macrophages (BMDMs) in conditioned RPMI1640 (20%FBS, 30% L929 –conditioned medium, antibiotics/antimycotics) in 10-cm Petri-dishes at 37 °C for 5 days. The attached BMDMs were cultured in tissue-culture treated plastic wares in regular RPMI1640 medium (10% FBS and 1% P/S) overnight before further treatment.

extract_protocol:
RNA was extracted using the QIAGEN RNeasy kit and quantitated using Agilent 2100 Bioanalyzer.
RNA libraries were prepared for sequencing using standard Illumina protocols
RNA-seq in BGISEG-500 using single-ended read and 50bp cycles.

treatment_protocol: 2x10e6 bone marrow-derived WT and Stinggt/gt macrophages were infected with CHIKV at a MOI of 5 for 12 hrs or mock-infected.

value: Bone-marrow-derived macrophage (BMDM)

value: CHIIKV MOI=5 12h

value: Stinggt/gt


title: WT-3

source_name: Brain

value: WT


title: WT-1


title: OKH,transcriptome 03

source_name: OKH,transcriptome 03


title: No pyruvate late 2-cell rep1


title: No lactate morula rep5

value: post -HCG 78 h


title: WT2_12h


title: No lactate morula rep4


title: WT3_12h


title: WT1_12h


title: OK-WT,transcriptome 01

source_name: OK-WT,transcriptome 01


title: No lactate morula rep2


title: OKH,transcriptome 01

source_name: OKH,transcriptome 01


title: GK3_0h

value: Mock


title: No lactate morula rep3


title: GK3_12h


title: GK1_0h


title: GK2_12h


title: B16JAK1KO + BO-112 B2

city: Stanford

first: Anusha

last: Kalbasi

state: CA

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

data_processing:
Reads were aligned to the mouse reference genome (mm9/GRCm38) using HISAT2 (v2.0.4)(44).
Gene expression was quantified using HTSeq-counts(v0.6.1)(45).
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: raw count data frame for every gene and sample

source_name: Tumor cells

extract_protocol:
Total RNA was extracted from cell lines using the AllPrep DNA/RNA Micro Kit (Qiagen).
RNA sequencing (RNAseq) libraries were prepared using the KAPA mRNA stranded library preparation kit, according to the manufacturer’s recommendations.
Libraries were pooled and sequenced on the Illumina HiSeq3000 platform (50bp reads).

tag: tumor

value: B16-JAK1KO tumor cell line

tag: in vitro treatment


title: GK2_0h


title: No lactate morula rep1


title: B16JAK1KO + BO-112 B1


title: B16JAK1KO + BO-112 B3


title: WT2_0h


title: B16JAK1KO + vehicle A3

value: vehicle


title: No lactate blastocyst rep3

value: post -HCG 114 h


title: WT1_0h


title: No lactate blastocyst rep4


title: B16JAK1KO + vehicle A2


title: WT3_0h


title: No lactate blastocyst rep1


title: B16JAK1KO + vehicle A1


title: OKH,transcriptome 02

source_name: OKH,transcriptome 02

value: Kidney Cells


title: Morula rep6


title: pmel T cells + BO-112 D4

description: single-end RNAseq

data_processing:
Reads were aligned to the mouse reference genome (mm9/GRCm38) using HISAT2 (v2.0.4)(44).
Gene expression was quantified using HTSeq-counts(v0.6.1)(45).
Genome_build: GRCm38 - mm10
Supplementary_files_format_and_content: raw count data frame

source_name: Tumor

extract_protocol:
Total RNA was extracted from tumors or cell lines using the AllPrep DNA/RNA Micro Kit (Qiagen).
RNA sequencing (RNAseq) libraries were prepared using the KAPA mRNA stranded library preparation kit, according to the manufacturer’s recommendations.
Libraries were pooled and sequenced on the Illumina HiSeq3000 platform (50bp reads).

value: pmel T cells


title: Morula rep5


title: pmel T cells + BO-112 D3

description: single-end RNAseq


title: pmel T cells + BO-112 D2

description: single-end RNAseq


title: genomic DNA from  PM256 IUGR chorionic villi

type: genomic

city: Vancouver

first: Wendy

last: Robinson

state: BC

address: 950 W 28th Ave

department: Medical Genetics

country: Canada

institute: University of British Columbia

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

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

data_processing:
R programming version 3.5.0.
matrix processed value definition: Average Beta

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted by standard salt method and purified using Qiagen DNeasy Kit according to standard instructions

tag: cohort label

tag: ethnicity

value: Caucasian

tag: aims coordinate1

tag: aims coordinate 2

tag: aims coordinate 3

tag: diagnosis

value: IUGR

tag: preeclamptic

value: FALSE

tag: gestational age

tag: fetal sex

value: M

tag: plate

tag: sentrix position

tag: sentrix id

tag: site a/b


title: pmel T cells + vehicle C4

description: single-end RNAseq

tag: strain

tag: cell type

tag: treatment


title: Morula rep2

tag: tissue

value: Preimplantation embryo

tag: age

tag: genotype


title: Morula rep3

value: wild type


title: No lactate blastocyst rep2


title: pmel T cells + vehicle C2

description: single-end RNAseq

tag: tumor


title: Morula rep1


title: genomic DNA from  PM343 CONTROL chorionic villi

tag: cohort label

tag: ethnicity

tag: aims coordinate1

tag: aims coordinate 2

value: CONTROL

value: F

value: A


title: genomic DNA from  PM329 CONTROL chorionic villi

tag: aims coordinate 3

tag: diagnosis

tag: preeclamptic

tag: gestational age


title: BL6 T cells + BO-112 B4

description: single-end RNAseq

value: BL6 T cells


title: Blastocyst rep3


title: mouse brain_AC infection 21 day_rep2

city: Guang zhou

first: Hongli

last: Zhou

address: 74 2nd Zhongshan Road, Guangzhou, China

institute: Sun Yat-Sen University

description: Gene expression profile of mouse brain with AC infection

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Mouse 44K custom high-definition whole-genome oligo array for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: mouse brain, 21 day, AC infection, replicate 2

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

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/n AM1556 ) following the manufacturer's instructions.

treatment_protocol: Four female BALB/c mice were randomly divided into two group (2 mice each group) named control group and Angiostrongylus cantonensis (AC) infection group. For AC infection group, mice were infected with 20 stage three larvae of AC intragastrically while the mice of control group were treated by saline with the same way. All mice were raised in the specic pathogen free (SPF) environment. At 21 days post-infection, all mice were sacrificed.

value: whole brain

tag: gender

value: Female

tag: infection

value: AC infection

tag: treatment time

value: 21 day


title: genomic DNA from  PM344_vc CONTROL chorionic villi

tag: fetal sex

tag: plate

tag: sentrix position

tag: sentrix id

tag: site a/b


title: BL6 T cells + BO-112 B3

description: single-end RNAseq

tag: strain

tag: tumor

tag: cell type

tag: treatment


title: pmel T cells + vehicle C1

description: single-end RNAseq

value: vehicle


title: Blastocyst rep2

source_name: Preimplantation embryo

tag: tissue

tag: age

value: post -HCG 114 h

tag: genotype


title: genomic DNA from  PM332_vc CONTROL chorionic villi

tag: cohort label

tag: ethnicity

tag: aims coordinate1

tag: aims coordinate 2

tag: aims coordinate 3

tag: diagnosis

tag: preeclamptic


title: mouse brain_control 21 day_rep1

description: Gene expression profile of mouse brain

source_name: mouse brain, 21 day, control, replicate 1

tag: gender

tag: infection

value: control

tag: treatment time


title: mouse brain_AC infection 21 day_rep1

source_name: mouse brain, 21 day, AC infection, replicate 1


title: BL6 T cells + BO-112 B1

description: single-end RNAseq

tag: strain


title: Blastocyst rep1


title: Morula rep4

value: post -HCG 78 h


title: D2_Ev3

city: Ithaca

first: David

middle: William

last: McKellar

state: NY

address: 237 Tower Rd

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using cellranger v3.1.0 pipeline
Ambient RNA content was removed using SoupX v1.4.5
Gene expression data was processed with Seurat v3.1.5
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 500)
Filtering by percent mitochondiral genes in included cells (maximum 30%), number of UMIs in included cells (minimum 1000)
Log-normalization of expression data
Cell annotations in metadata derived from shared nearest neighbor clustering
Genome_build: mm10
Supplementary_files_format_and_content: zipped, market exchange format (MEF) for raw, filtered, and scrubbed (SoupX) transcript count matrices; .csv files of single-cell metadata information
Supplementary_files_format_and_content: raw transcript counts for all cell barcodes (cellranger)
Supplementary_files_format_and_content: filtered transcript counts (cellranger)
Supplementary_files_format_and_content: counts after ambient RNA scrubbed (SoupX)

source_name: Tibialis anterior muscle

extract_protocol:
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v3 kit) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 7 months

tag: Sex

tag: injury

value: Notexin injury (Day 2)


title: D7_Ev3

value: Notexin injury (Day 7)


title: genomic DNA from  PM226 IUGR chorionic villi

value: IUGR

value: FALSE

tag: gestational age

tag: fetal sex

value: M

tag: plate

tag: sentrix position

tag: sentrix id

tag: site a/b


title: BL6 T cells + vehicle A4

description: single-end RNAseq

tag: tumor

tag: cell type

tag: treatment


title: Early 32-cell rep4

tag: tissue

value: Preimplantation embryo

tag: age

value: post -HCG 90 h

tag: genotype

value: wild type


title: RML961_WT3

city: Singapore

first: Jin Rong

last: Ow

state: Singapore

address: 61 Biopolis Drive

department: Institute of Molecular and Cell Biology

country: Singapore

institute: A*STAR

description:
sample name:
RML961

data_processing:
The gene and isoform expression levels from the RNASeq reads were quantified using the RSEM software version 1.2.31
The GTF file for the mm10 genome was used to prepare reference STAR genome index files
Fragments Per Kilobase of transcript per Million mapped (FPKM) were quantified using the "rsem-calculate-expression" function with "--star" as the sequence alignment program. Inputs were single-end read files.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited matrix file with FPKM values for every gene and every sample

source_name: 12 month old WT whole liver

growth_protocol: Mice were fed ad libitum with standard diet under 12 hour light/dark cycle in specific pathogen-free (SPF) conditions.

extract_protocol:
RNA was isolated by first homogenizing liver tissue or pelleted hepatocytes in TRIzol reagent, and upon phase separation step, aqueous portion was transferred to columns and extracted as per PureLink RNA Mini Kit, with rDNase treatment on column
Library was prepared using TruSeq Stranded mRNA Library Prep (Illumina) according to manufacturer's instructions. RNA-Seq, single-end, 75bp read length

treatment_protocol: Cdk1 Liv-/- mice were generated crossing Cdk1 flox/flox to Albumin-Cre mice.

value: Wild type

tag: sample type

value: Whole liver

value: 12 months


title: control_case_8

city: Brasília

first: Otavio

middle: T.

last: Nobrega

state: DF

address: RUA 3 SUL - EDIFICIO NETUNO - APTO 301, AGUAS CLARAS, 301, lote 08

department: Medicine Faculty

country: Brazil

institute: University of Brasilia

description: Individual without neuropathological lesions or neurological signs

hyb_protocol: 200 ng of labeled microRNA from each sample was hybridized to the array (Affymetrix® miRNA Array, version 4.1) in the hybridization instrument GeneTitan™ (Thermo Fisher Scientific), with the Array Strip Hybridization® kit as support. Hybridization settings were as recommended by the manufacturer.

scan_protocol: Scanned on an GeneTitan™ instrument using the Applied Biosystems™ GeneChip™ Command Console™ in standard mode (Thermo Fisher Scientific).

data_processing: Results analyzed for quality purposes using the Expression Console™ software, version 4.1 (Thermo Fisher Scientific), and then exported for processing in the Transcriptome Analysis Console™ software version 3.1 (Thermo Fisher Scientific) to allows statistical analyses.

label_protocol: direct labeling of the miRNAs, the FlashTag™ Biotin HSR Labeling Kit (Thermo Fisher Scientific), with biotinylation checked by an Enzyme Linked Oligosorbent Assay (ELOSA) used to detect binding of biotinyled samples to spike, control RNA oligos adsorbed to a Nunc® plate.

growth_protocol: All samples were obtained from the Human Brain Bank of the Brazilian Aging Brain Study Group (HBB-BABSG) of the University of São Paulo Medical School, in accordance with the standards of the local ethics committee.

extract_protocol: microRNA isolation was performed with the mirVana™ PARIS™ Kits (Life Technologies, Lithuania) following manufacturer’s instructions.

treatment_protocol: Brain samples were frozen at -80ºC.

tag: gender

value: female

value: Temporal Cortex (TC)


title: RML960_WT2

description:
sample name:
RML960


title: BL6 T cells + vehicle A1

description: single-end RNAseq

tag: strain

value: BL6 T cells

value: vehicle


title: BL6 T cells + vehicle A2

description: single-end RNAseq


title: mouse brain_control 21 day_rep2

description: Gene expression profile of mouse brain

source_name: mouse brain, 21 day, control, replicate 2

value: whole brain

value: Female

tag: infection

value: control

tag: treatment time

value: 21 day


title: Early 32-cell rep2


title: Early 32-cell rep3


title: Early 32-cell rep1


title: RML959_WT1

description:
sample name:
RML959


title: RML958_KO3

description:
sample name:
RML958

source_name: 12 month old Cdk1 Liv-/- whole liver

value: Cdk1 Liv-/-


title: Primary mPT,transcriptome 02

source_name: Primary mPT,transcriptome 02

value: Kidney Cells


title: AD_case_8

description: Braak stage V, CERAD moderate grade, CDR = 2, IQCODE > 3.41

source_name: Human Brain Bank of the Brazilian Aging Brain Study Group (HBB-BABSG) of the University of São Paulo Medical School


title: Blastocyst rep4

value: post -HCG 114 h


title: RML957_KO2

description:
sample name:
RML957


title: AD_case_7

description: Braak stage VI, CERAD severe grade, CDR = 3, IQCODE > 3.41


title: WT_4

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

data_processing:
Trimmed ChIP-seq reads (Trimmomatic v0.36) were aligned to the mm10 genome assembly using Bowtie2 (v2.2.9).
Peak-calling was done on concordantly aligned paired reads using MACS2 (2.1.1.20160309).
BigWig files were generated by converting BAM files to BEDGRAPH files using bedtools (v2.28.0) using arguments '-bg -pc' and converted to bigWig using UCSC's bedSort and bedGraphToBigWig (v4).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files are unscaled fragment pileups. BED file consists of peak regions used for differential binding analysis, with each range labeled with its associated peak identifier.

source_name: splenic B cells

extract_protocol:
10 million activated cells were crosslinked with 1% formaldehyde. Cells were lysed according to the protocol of truChIP Chromatin Shearing Kit with Formaldehyde (Covaris). Cell lysates were sonicated and precleared lysate was incubated with 2 g of anti-AID antibody at 4oC overnight. Immunocomplexes were recovered by incubation with Salmon Sperm DNA/Protein A Agarose Slurry, eluted, then de-crosslinked with NaCl and RNase A at 65oC for 4-6 hours, and treated with Tris pH 6.5, EDTA and proteinase K for 1 hour at 45oC. DNA was recovered by phenol-chloroform extraction and ethanol precipitation. See manuscript for more details.
Immunoprecipitated DNA was quantified by PicoGreen and the size was evaluated by Agilent BioAnalyzer. Illumina libraries were prepared using the KAPA HTP Library Preparation Kit (Kapa Biosystems KK8234) according to the manufacturer’s instructions with 0 (undetectable)-4.6 ng input DNA and 8-12 cycles of PCR. Barcoded libraries were run on the Hiseq 2500 in Rapid mode and the HiSeq 4000 in 50bp/50bp paired end runs, using the HiSeq Rapid SBS Kit v2 and HiSeq 3000/4000 SBS Kit, respectively (Illumina). An average of 35 million paired reads were generated per sample.

value: splenic B cells

value: WT

tag: replicate

tag: condition


title: Early 16-cell rep4

value: Preimplantation embryo

value: post -HCG 80 h

value: wild type


title: AD_case_6

description: Braak stage V, CERAD severe grade, CDR = 3, IQCODE > 3.41


title: AD_case_5

value: male


title: WT_3


title: control_case_7


title: Liver KO 3

description:
sample name:
RML888

source_name: P14 Cdk1 Liv-/- whole liver

value: Whole liver


title: WT_2


title: Early 16-cell rep3


title: RML956_KO1

description:
sample name:
RML956

value: 12 months


title: WT_1


title: Liver KO 2

description:
sample name:
RML887


title: Early 16-cell rep1


title: Early 16-cell rep2


title: Liver KO 1

description:
sample name:
RML886


title: control_case_6

value: female

value: Temporal Cortex (TC)


title: Primary mPT,transcriptome 01

source_name: Primary mPT,transcriptome 01


title: Late 8-cell rep2

value: post -HCG 74 h


title: Early 16-cell rep5


title: Liver WT 3

description:
sample name:
RML885

source_name: P14 WT whole liver

value: Wild type


title: AIDKO_3b

value: AIDKO


title: AIDKO_3a


title: Late 8-cell rep1


title: Liver WT 2

description:
sample name:
RML884


title: AIDKO_2


title: control_case_5


title: AD_case_3

description: Braak stage IV, CERAD moderate grade, CDR = 2, IQCODE > 3.41


title: AD_case_4


title: Liver WT 1

description:
sample name:
RML883


title: AD_case_2


title: Early 8-cell  rep2

value: post -HCG 66 h


title: AIDKO_1


title: control_case_4


title: Hepatocyte KO 3

description:
sample name:
RML882

source_name: P14 Cdk1 Liv-/- isolated hepatocytes

value: Cdk1 Liv-/-

value: Isolated hepatocytes


title: Early 8-cell  rep1


title: AD_case_1

description: Braak stage III, CERAD moderate grade, CDR = 3, IQCODE > 3.41


title: AIDG133V_4


title: Hepatocyte KO 2

description:
sample name:
RML881


title: Late 4-cell rep4

value: post -HCG 62 h


title: Hepatocyte KO 1

description:
sample name:
RML880


title: AIDG133V_3

value: splenic B cells


title: control_case_2


title: B3: dNKAP RNAi 3

city: Hangzhou

first: Wanzhong

last: Ge

state: Zhejiang

address: Yuhangtang Road 866

institute: Zhejiang University

data_processing:
Basic reads quality check was performed with FastQC
Reads were mapped to the Drosophila melanogaster reference genome assembly (version dm6.09, 2016) using Tophat2.0 and gene quantification was carried out using HTseq.
Differential expression analysis was performed using DEseq.

organism: Drosophila melanogaster

source_name: dNKAP knockdown wing discs

extract_protocol:
RNA extractions was performed using Trizol.
Libraries were prepared according to the Illumina protocol and sequenced on an Illumina NextSeq 500 platform

value: wing imaginal disc

tag: genotype/variaion

value: MS1096-Gal4>dNKAP RNAi


title: Late 4-cell rep3

value: Preimplantation embryo


title: AIDG133V_2


title: Early 8-cell  rep3

value: wild type


title: B2: dNKAP RNAi 2


title: AIDG133V_1


title: Hepatocyte WT 3

description:
sample name:
RML879

source_name: P14 WT isolated hepatocytes


title: Late 4-cell rep1


title: Late 4-cell rep2


title: control_case_3

value: male


title: Hepatocyte WT 2

description:
sample name:
RML878


title: B1: dNKAP RNAi 1


title: C57BL6/J,transcriptome 01

source_name: C57BL6/J,transcriptome 01

value: Kidney Cells


title: Hepatocyte WT 1

description:
sample name:
RML877


title: A3: Control 3

source_name: control wing imaginal discs


title: Primary small intestinal organoids

city: Stony Brook

first: Pawan

last: Kumar

address: 100 Nicolls Road

institute: Stony Brook University

data_processing:
For scRNA-seq: Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA)
For scRNA-seq: Cells were partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, tagmentation and 5’ adaptor attachment.
For scRNA-seq: Libraries were sequenced on an Illumina NextSeq 500. Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics).
For total RNA-seq: Sequencing analysis was done using RNA-seq for Eukaryotes Analysis v3 by Banana Slug Genomics Center at University of California Santa Cruz
For total RNA-seq: Raw sequencing reads (paired-end reads) that were produced by Illumina sequencer were quality checked for potential sequencing issues and contaminants using FastQC. Adapter sequences and primers were trimmed from the sequencing reads using Trimmomatic, then followed by removing the polyA tail, polyN, and read portions with quality score below 28 using PRINSEQ
For total RNA-seq: Trimmed reads were mapped to the reference genome (GRCm38/mm10) using (TopHat2) with NCBI RefSeq annotated genes as transcriptome index data. Read alignment coverage and summary statistics for visualization were computed using SAMtools, BEDtools, and UCSC Genome Browser utilities
For total RNA-seq: Using Cufflinks work flow, the sequencing reads aligned to RefSeq annotated genes were quanti fied using Cuffquant. Cuffnorm was then used to normalize the gene expression levels across the studied samples with FPKM computed for sample correlation assessment. Differential expression analysis between samples was performed using Cuffidff with the computed results from Cuffquant.
Genome_build: mm10

source_name: Small intestinal organoid

extract_protocol:
For scRNA-seq: Single cells were processed through the Chromium Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, an input of 10,000 cells was added to each channel of a chip with a recovery rate of 3000 cells. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, tagmentation and 5’ adaptor attachment. For total RNA-seq: Terminal ileum tissues were extracted and stored at -20°C in RNAlater. RNA from the terminal ileum of 6 weeks old Il22Ra1fl/fl;Defa6-cre+ and their littermate cre- mice was isolated using TRIZOL extraction methods as per manufacture instructions (Life Technologies).
For scRNA-seq: Libraries were sequenced on an Illumina NextSeq 500. Alignment to the mm10 mouse genome and unique molecular identifier (UMI) collapsing was performing using the Cellranger toolkit (version 1.3.1, 10X Genomics). For each cell, we quantified the number of genes for which at least one UMI was mapped and then excluded all cells with fewer than 1,000 detected genes. For total RNA-seq: Illumina compatible Total RNA cDNA libraries with RiboZero Gold depletion were generated following the TruSeq Stranded Total RNA Reference Guide (Illumina Document #1000000040499v00, TruSeq Stranded Total RNA Gold Illumina Kit #20020598).

value: Small intestine


title: Early 4-cell rep3

data_processing:
Illumina Casava1.7 software used for basecalling.
Alignment using the STAR program 2.6.1d
Genome_build: mm10 Ensembl Transcripts release 97
Supplementary_files_format_and_content: tab-delimited text files include normalized abundance for each sample

source_name: Preimplantation embryo

value: post -HCG 55 h


title: control_case_1

value: female

value: Temporal Cortex (TC)


title: A2: Control 2


title: Early 4-cell rep2


title: A1: Control 1


title: Negative_female_4

city: rehovot

first: Berta

last: Levavi-Sivan

state: Israel

address: Hertzel

department: Animal sciences

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
Libraries were subjected to next generation sequencing using Illumina® NextSeq® 500 system , with 76 bp single-end read sequencing
Raw reads (Fastq files) were inspected for quality issues with FastQC v0.11.4 and trimmed for quality and adaptor removal using Trim Galore default settings
End reads were mapped to O.niloticus (assembly O_niloticus_UMD_NMBU GCA_001858045.3), using STAR v 2.201
Uniquely mapped reads per gene were counted using HTSeq-count
Differential expression analysis was performed using DESeq2 R package. In the FACS sorted cells, each LH or FSH library was analyzed against the negative library
Genome_build: GCA_001858045.3
Supplementary_files_format_and_content: Tab-delimited text file matrix includes normalized read counts for each gene in each sample
Supplementary_files_format_and_content: Tab-delimited text file matrix includes fold change and FDR corrected p value according to DESeq analysis, for each gene in LH and FSH FACS fractions

organism: Oreochromis niloticus

source_name: FACS cells

growth_protocol: Nile tilapia (Oreochromis niloticus, Lake Manzala strain) were kept and bred in a recirculating water system at 26–28 °C and fed twice daily with commercial pellets (47% protein, 6% fat, Raanan Shivuk, Israel)

extract_protocol:
pituitaries were hravested and digested by trypsin into a single cell suspension, The cell suspensions were sorted in a FACSAriaIII sorter using a 488nm and 561nm lasers to excite the GFP and RFP labelled cells respectively, Total RNA was prepered using Trizol® Reagent (Invitrogen) ,
RNA libraries were prepared using the SMARTer® Stranded Total RNA-Seq Kit v2- Pico Input Mammalian (Takara Bio, USA)

treatment_protocol: pituitaries were surgicaly extracted and transferred into a modified HBS (HEPES Buffered Saline; 145mM NaCl, 5.4mM KCl, 1.8nM CaCl2, 1mM MgCl2, 20mM D-Glucose, 20mM HEPES)

tag: facs fraction

value: NEGATIVE

value: Female

tag: repeat


title: LH_female_4

value: LH

value: RFP positive


title: Early 4-cell rep1

extract_protocol:
The RNA extraction was performed using the Smart-seq2 protocol as published with minor modification. Cells were lysed in 0.1% (vol/vol) Triton X-100 lysis containing 2.5µM of oligo-dT30VN primer, 2.5mM of dNTP mix and 1U/µl of RNase inhibitor. After 3 mins lysis at 72℃, the Smart-seq2 reverse transcription mixture was added for reverse transcription. cDNA was pre-amplified and AMPure XP beads were used for purification.
Smart-seq2 protocol


title: APEX_RIP_2

city: Baltimore

first: Joseph

last: Tran

address: 3520 San Martin Drive

department: Embryology

institute: Carnegie Institution for Science

description: APEX NL RIP native

data_processing:
RNAseq data was aligned using Tophat v2.1.1 / Bowtie v2.3.2
RNAseq reads were counted using featurecounts from the Subread v1.5.2 package
RNAseq differential expression was calculated using the glmFit method in EdgeR v3.24.3 under R v3.5.2
DNA was aligned using bowtie v2.3.2
DNA reads were counted into 100kb windows using bedtools v2.26.0 coverage, and calculated as a log2(StrepD/input). Bigwigs were made with kentutils v3.62
Hidden Markov Model (HMM) was called using depmixS4 v1.4-0 in RStudio v0.98.953 (R v3.5.1)
HMM calls were intersected between replicates (e.g., G1 Rep1 and G1 rep2) to generate a consensus bed file for downstream analysis.
genome build: hg19
processed data files format and content: Original featureCounts output, bigwig files for cell cycle LADs, bedgraph files for the K562 APEXID LADs, bedgraph files for the cell cycle H3K9me3 ChIPseq, HMM calls in bed format for cell cycle LADs

growth_protocol: Cells were cultured at 37 degrees C with 5% carbon dioxide

extract_protocol:
RNA was isolated using Trizol reagent according to the manufacturer's protocol.
RNA libraries were generated with the Illumin TruSeq v2  with Ribodepletion.

treatment_protocol: Cells were transfected with the APEX2 lamin-b1 construct using Lipofectamine 2000 according to the manufacturer's protocol

tag: cell line

tag: Stage

value: Asynchronous

tag: material

value: APEXseq


title: Very late 2-cell rep3

first: Utpal

last: Banerjee

address: Charles E. Young Drive

value: post -HCG 52 h


title: C57BL6/J,transcriptome 02

data_processing:
Sequenced reads were mapped to Ensembl Release 94 genome using STAR-2.5.4a
Transcript abundances in TPM were caculated by  rsem 1.3.0
Genome_build: Ensembl Release 94
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each sample

source_name: C57BL6/J,transcriptome 02

extract_protocol:
RNAs were extracted using Zymo kit and cDNAs were sythesized using SMART-Seq V4 Ultra Low Input RNA Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: APEX_RIP_1

description: APEX NL RIP native


title: FSH_female_4

tag: cell type

value: FSH

value: GFP positive


title: APEX_PFA_RIP_2

description: APEX NL RIP PFA-fixed

value: APEXseq PFA


title: Very late 2-cell rep2

tag: tissue

value: Preimplantation embryo

value: wild type


title: OR03

city: Ness Ziona

first: Inbar

last: Cohen Gihon

address: Reuven 24

department: Biochemistry

institute: Israel Institute For Biological Research

data_processing:
RTA (Illumina) for base calling
bcl2fastq2 (version 2.20) for converting BCL to fastq format, coupled with adaptor trimming.
pseudoalignment to a kallisto index created from transcriptomes (Mouse: GRCm38) using kallisto (0.44.0).
Genome_build: Mouse: GRCm38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: total RNA extracted from mice lung

growth_protocol: Female CD-1 mice weighing 27-32 g were obtained from Charles River Laboratories Ltd. U.K. Prior to exposure, animals were habituated for 5 days. All mice were housed in filter-top cages in an enviromentally controled room and maintained at 21°C and 55% humidity. Lighting was set to mimic a 12/12 h dawn to dusk cycle. Animals had acess to food and water ad libitum.

extract_protocol:
Total RNA was extracted using the RNeasy kit (Qiagen) and residual DNA was digested using RNase-free DNase (Qiagen).
Library construction using Illumina TruSeq chemistry

treatment_protocol: Mice were anesthetized by an interperitoneal injection of ketamine (1.9 mg/mouse) and xylazine (0.19 mg/mouse), and were intranasally (50 µl/nostril) intoxicated with crude ricin.

tag: treatment

value: 48 hr post 1.7 ug/kg ricin

value: lung


title: C2

description: Cytosol fractionation-seq

value: Cytosol


title: OR04


title: OR02


title: APEX_PFA_RIP_1

description: APEX NL RIP PFA-fixed


title: Negative_female_3


title: OR01


title: Early 4-cell rep4

city: Los Angeles

institute: University of California, Los Angeles

tag: age

value: post -HCG 55 h

tag: genotype


title: Very late 2-cell rep1


title: Mid 2-cell rep3

value: post -HCG 42 h


title: LH_female_3

tag: gender


title: LH_female_2


title: FSH_female_3


title: C1

description: Cytosol fractionation-seq


title: Mid 2-cell rep4

tag: strain


title: Mid 2-cell rep2


title: FSH_female_2


title: Negative_female_1

value: NEGATIVE


title: Late 2-cell rep3

value: post -HCG 48 h


title: N1

description: Nuclear fractionation-seq

value: Nuclear


title: N2

description: Nuclear fractionation-seq


title: Mid 2-cell rep1


title: FSH_female_1

value: Female


title: Late 2-cell rep1


title: Late 2-cell rep2


title: HCT116_G2_H3K9me3_ChIP_1

description:
ChIPseq
HCT_G2_K9me3_100kb_window.bedgraph

extract_protocol:
DNA was isolated using Ampure XP beads according to the manufacturer's protocol.
DNA libraries were generated with the Rubicon Genomics ThruPlex kit

value: H3K9me3 ChIP


title: LH_female_1

value: LH

value: RFP positive


title: HCT116_G2_H3K9me3_input_1

value: H3K9me3 input


title: H12

city: Cambridge

first: Celine

last: Labouesse

address: Puddicombe Way

department: Cambridge Stem Cell Institute

country: United Kingdom

institute: University of Cambridge

description: countTable.txt

data_processing:
Read trimming: Trim Galore v 0.6.5 - Trimming of reads to remove adapter sequences
Read alignment: GSNAP version 2015-09-29 - Alignment of genome to genome build mm10
Read mapping: HTSeq - Genes were annotated using Ensembl release 81 and read counts were quantified using HTSeq
Count normalisation: R package DESeq2 - Used DESeq2 for normalisation of raw counts and subsequent analysis
Genome_build: mm10
Supplementary_files_format_and_content: countTable.txt: raw counts (output from mapping, prior to quality control and normalisation) in a tab-separated txt format -rows are Ensembl Gene Ids, columns are samples (given by well names)

source_name: mouse ES cell EZR_CA

growth_protocol: mES cells grown in 2i+LIF and exited in N2B27 for 24hr or 48hr, on gelatin-coated plates. The iEZR_CA and control parental line were seeded and samples collected in parallel.

extract_protocol:
RNA lysates were collected from cell cultures using RLT buffer. RNA was subsequently extracted from the lysates using RNEasy Kit (QIAGEN) including a genomic DNA digestion step.
NEBNext® Multiplex Oligos for Illumina

treatment_protocol: Doxycycline was added to the media of iEZR_CA overnight before the exit (~16hr) to induce constitutive expression of Ezrin

tag: medium

tag: exit timepoint


title: G9

description: countTable.txt


title: H9

description: countTable.txt


title: HCT116_S_H3K9me3_ChIP_1

description:
ChIPseq
HCT_S_K9me3_100kb_window.bedgraph

value: S

tag: replicate


title: Negative_female_2


title: LH_male_4

value: Male


title: G12

description: countTable.txt


title: Early 2-cell rep3

value: Preimplantation embryo

value: post -HCG 34 h


title: Early 2-cell rep2

value: wild type


title: Early 2-cell rep1


title: FSH_male_4

value: FSH

value: GFP positive


title: HCT116_S_H3K9me3_input_1


title: F12

description: countTable.txt


title: E12

description: countTable.txt


title: HCT116_G1_H3K9me3_ChIP_1

description:
ChIPseq
HCT_G1_K9me3_100kb_window.bedgraph


title: D12

description: countTable.txt


title: Negative_male_3


title: HCT116_G1_H3K9me3_input_1


title: Negative_male_4


title: LH_male_3


title: WT

city: Pittsburgh

first: Sayan

last: Ghosh

state: PA

address: 4401 Penn Avenue

department: Ophthalmology

institute: University of Pittsburgh

data_processing:
R package Seurat 3.1.0 was used to do an integrated analysis for performing clustering analysis after merging WT cells and Nuc1 cells together. Data was demultiplexed using CellRanger Software (version 3.1.0) from 10x Genomics, and paired end FASTQ files were generated. The reads were aligned to the reference genome using STAR aligner (version 2.7) and the alignment results were used to quantify the expression level of genes. Downstream analysis was done using Seurat (version 3.1.1). Data were pre-filtered to remove low quality cells, doublets, and potentially dead cells based on the percentage of mitochondrial genes, number of genes, and Unique Molecular Identifiers (UMI’s) expressed in each cell. The standard pipeline of normalization such as finding variable features, scaling, and dimensionality reduction by principal component analysis was followed. The integrated dataset of the WT and Nuc1 samples was then used for the UMAP clustering and differential gene expression analysis.
Supplementary_files_format_and_content: .mtx file (Genes.tsv, Barcodes.tsv,  Matrix.mtx )

source_name: Optic nerve

extract_protocol: Libraries were prepared using 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 with a cell target of 3000. WT had an input of 5092 cells with a viability of 90%, Nuc1 had an input of 5125 cells and a viability of 95%.

value: Postnatal day 7

value: WT


title: Nuc1

source_name: Optic Nerve


title: C12

description: countTable.txt


title: HCT116_G2_StrePD_2

description:
APEXID
G2APEXavgs.bw, HCT_G2_HMM_consensus.bed

value: APEXID StrePD


title: FSH_male_3


title: B12

description: countTable.txt


title: HCT116_G2_input_2

value: APEXID input


title: Negative_male_2

value: NEGATIVE


title: stl300 sibling

city: Saint Louis

first: Bo

last: Zhang

state: Missouri

address: 4515 McKinley Research Bldg 03212

department: Developmental Biology

institute: Washington University School of Medicine

data_processing:
Raw Reads were aligned to zebrafish genome GRCz10 using bwa (v 0.7.1) mem with default parameters and sorted by coordinate and bam compressed using samtools (1.6-8).
VCF files were generated from bam files using bcftools (v 1.9) commands mpileup, view, and call with options -q 20 and -Q 20 to filter low quality bases and alignments.
Genome_build: GRCz10
Supplementary_files_format_and_content: VCF formatted variants files

organism: Danio rerio

source_name: Whole Body

growth_protocol: Typical

extract_protocol:
Quiagen DNEasy kit
Nimblegene SEQCAP EZ CHOICE XL 24 RXN for whole exome sequencing (WES). NGS DNA library prep kit (WGS).
WGS for stl297. WES for stl300

value: Whole Body


title: A12

description: countTable.txt

source_name: mouse ES cell E14 wt

value: E14 wt


title: 30dpf-scospondin stl297 maternal zygotic mutant -Library 3

data_processing:
Raw reads were trimmed with cutadapt to remove low quality bases
Trimmed reads were aligned to danio rerio genome GRCz10 using STAR_2.5.4b with Ensembl v83 annotation
Aligned reads were quantified using featureCounts 1.6.3 from the subreads package
Genome_build: GRCz10
Supplementary_files_format_and_content: gene counts text file

extract_protocol:
Trizol isolation of RNA; Clean up on QIAGEN RNA column.
Takara Clontech SMARTer prep

value: WHOLE BODY

tag: iPSc source

tag: passage


title: stl300 mutant


title: HCT116_S_StrePD_2

description:
APEXID
SAPEXavgs.bw, HCT_S_HMM_consensus.bed


title: G11

description: countTable.txt


title: LH_male_2

value: LH

tag: facs fraction

value: RFP positive


title: 30dpf-scospondin stl297 maternal zygotic mutant -Library 2


title: HCT116_S_input_2

value: S


title: H11

description: countTable.txt


title: FSH_male_2

value: Male

tag: repeat


title: Negative_male_1


title: LH_male_1


title: HCT116_G1_input_2

description:
APEXID
G1APEXavgs.bw, HCT_G1_HMM_consensus.bed

tag: cell line


title: F11

description: countTable.txt


title: 30dpf-scospondin stl297 het -Library 3

source_name: 30dpf-scospondin stl297 het -Library 3


title: 30dpf-scospondin stl297 maternal zygotic mutant -Library 1


title: E11

description: countTable.txt


title: HCT116_G2_StrePD_1

tag: Stage


title: D11

description: countTable.txt


title: HCT116_G2_input_1

tag: material


title: 30dpf-scospondin stl297 het -Library 1

source_name: 30dpf-scospondin stl297 het -Library 1

tag: cell type


title: Articular Chondrocytes 12w WT

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

country: Germany

institute: University Medical Center Hamburg-Eppendorf

hyb_protocol: Following fragmentation, 5.5 ug of cDNA were hybridized for 16 h at 45 °C on Affymetrix Mouse Transcriptome Array 1.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: Microarrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: The data were analyzed with Transcriptome Analysis Console (TAC 4.0) using default analysis settings (version 2) and Gene + Exon - SST-RMA as summarization and normalization method.

source_name: hip joint articular cartilage

label_protocol: Proprietary labeled 2nd-cycle ss-cDNA was prepared from 100 ng total RNA using the mouse Clariom D kit according to the GeneChipTM WT PLUS Reagent Kit Manual Target Preparation for GeneChipTM Whole Transcript (WT) Expression Arrays user guide (version 23 January 2017) from ThermoFisher Scientific.

growth_protocol: All animals were kept at a 12h light /12h dark cycle and fed a standard diet and water ad libitum.

extract_protocol: Snap-frozen hip joint articular cartilage caps were crushed into a fine powder using mortar and pestel, and total RNA was extracted with PEQ Gold Total RNA Isolation Kit (VWR).

treatment_protocol: No specific treatment.

value: Wild-type

value: 12 weeks

tag: tissue

value: Hip joint articular cartilage


title: HCT116_S_StrePD_1


title: Articular Chondrocytes 12w MLIII

value: Gnptg-KO


title: FSH_male_1

value: FSH

value: GFP positive


title: 15dpf-scospondin stl297 maternal zygotic mutant -Library 3


title: HCT116_S_input_1


title: 15dpf-scospondin stl297 maternal zygotic mutant -Library 2


title: C11

description: countTable.txt


title: HCT116_G1_StrePD_1


title: 15dpf-scospondin stl297 maternal zygotic mutant -Library 1


title: HCT116_G1_input_1


title: 15dpf-scospondin stl297 het -Library 3

source_name: 15dpf-scospondin stl297 het -Library 3


title: A11

description: countTable.txt


title: HCT116_G1_StrePD_2


title: B11

description: countTable.txt


title: K562_input_2

description:
APEXID
K562_APEX_Rep2.bedgraph

value: Asynchronous


title: HK2,transcriptome 01

city: Bethesda

first: Lihe

last: Chen

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

source_name: HK2,transcriptome 01

value: Kidney Cells


title: 15dpf-scospondin stl297 het -Library 2

source_name: 15dpf-scospondin stl297 het -Library 2


title: 30dpf-scospondin stl297 het -Library 2

source_name: 30dpf-scospondin stl297 het -Library 2


title: K562_StrePD_2

description:
APEXID
K562_APEX_Rep2.bedgraph

value: APEXID input


title: 15dpf-scospondin stl297 het -Library 1

source_name: 15dpf-scospondin stl297 het -Library 1


title: K562_input_1

description:
APEXID
K562_APEX_Rep1.bedgraph

value: APEXID StrePD


title: HKC11,transcriptome 02

source_name: HKC11,transcriptome 02


title: K562_StrePD_1

description:
APEXID
K562_APEX_Rep1.bedgraph


title: 5dpf-scospondin stl297 maternal zygotic mutant -Library 3


title: HKC11,transcriptome 01

source_name: HKC11,transcriptome 01


title: Tumorperiphery_irradiatedbrain_3x5Gy_rep2

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

institute: University Heidelberg

description: grown in mouse5

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 6, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 20 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: We implanted 2.5x10^6 of U87 MG Luciferase-expressing glioblastoma cells into the caudate putamen of NSG mice which were then monitored via bioluminscence imaging and contrast enhanced micro-CT imaging. Following tumor detection, the treatment group received irradiation with 3x5 Gy of healthy brain tissue of hemisphere contralateral to tumor bearing hemisphere. All animals were monitored until extensive weight loss or neurological deficiencies

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

treatment_protocol: Animals were sacrifized via cervial dislocation, whole brains extracted and snap frozen, followed by Kryostat slicing, Acetone fixation, HE-staining and separation of tumor core and periphery via lasercapture-microdissection

tag: treatment

value: KontraRT - irradiated

tag: sample type

value: inv - invasive


title: 5dpf-scospondin stl297 maternal zygotic mutant -Library 2

value: WHOLE BODY


title: 5dpf-scospondin stl297 maternal zygotic mutant -Library 1


title: HKC8,transcriptome 02

source_name: HKC8,transcriptome 02


title: Tumorperiphery_irradiatedbrain_3x5Gy_rep3

description: grown in mouse4


title: HKC11,transcriptome 03

source_name: HKC11,transcriptome 03


title: Tumorperiphery_irradiatedbrain_3x5Gy_rep1

description: grown in mouse6


title: 5dpf-scospondin stl297 het -Library 2

source_name: 5dpf-scospondin stl297 het -Library 2


title: Tumorcore_irradiatedbrain_3x5Gy_rep1

description: grown in mouse6

value: prol - proliferative


title: CFKBRA-PNEX-DUAL-SMAD: BU3 NGPT Basal Cell Medium_2

city: Boston

first: Carlos

last: Villacorta-Martin

state: MA

address: 670 Albany St

institute: Center for Regenerative Medicine at Boston University

data_processing:
The sample was processed using the standard Cellranger v.3 pipeline
Reads were mapped to GRCh38
Downstream analysis and QC done on Seurat
Differential expression using MAST models
Genome_build: GRCh38
Supplementary_files_format_and_content: the processed files are the standard output from the cellranger count pipeline: count matrices compressed in the HDF5  format

source_name: iPSC derived

growth_protocol: This protocol is based on previously described approaches to derive airway organoid from hPSCs (Hawkins et al. 2017; McCauley et al. 2017) including a detailed step-by-step protocol prior to basal cell medium (McCauley et al. 2018).

extract_protocol:
single cells were captured for sequencing library prepration using a 10X Chromium
10X chromium chemistry

tag: sample name synonym

value: Day 46 BU3 NGPT Basal Cell Medium_2

value: iPSC-derived airway organoids

tag: culture media

value: PneumaCult-Ex-Plus media supplemented with SMAD inhibitors and Y-27632

tag: isolation method

value: Dispase followed by trypsin


title: 5dpf-scospondin stl297 het -Library 3

source_name: 5dpf-scospondin stl297 het -Library 3


title: CFKBRA-F210DCIY: BU3 NGPT FGF2+10+DCI+Y_2

value: Day 46 BU3 NGPT  FGF2+10+DCI+Y_2


title: CBRA-PNEX-DUAL-SMAD: BU3 NGPT Basal Cell Medium_1

value: Day 46 BU3 NGPT Basal Cell Medium_1


title: Tumorcore_irradiatedbrain_3x5Gy_rep2

description: grown in mouse5


title: Tumorcore_irradiatedbrain_3x5Gy_rep3

description: grown in mouse4


title: 5dpf-scospondin stl297 het -Library 1

source_name: 5dpf-scospondin stl297 het -Library 1


title: HPTC-05-CLA,transcriptome 01

source_name: HPTC-05-CLA,transcriptome 01


title: Tumorperiphery_nonirradiatedbrain_rep1

description: grown in mouse3

source_name: tumorperiphery control

value: Control


title: CBRA-F210DCIY: BU3 NGPT FGF2+10+DCI+Y_1

value: Day 46 BU3 NGPT in FGF2+10+DCI+Y_1


title: Tumorperiphery_nonirradiatedbrain_rep2

description: grown in mouse2


title: Tumorperiphery_nonirradiatedbrain_rep3

description: grown in mouse1


title: BU3NGPT-ALI: BU3 NGPT ALI

value: BU3 NGPT in ALI

value: iPSC-derived airway epithelium

value: PneumaCult-ALI

value: Trypsin


title: LLC-PK1,transcriptome 03

organism: Sus scrofa

source_name: LLC-PK1,transcriptome 03

value: Kidney Cells


title: DD001_Primary: Primary HBECs

source_name: Primary tissue

value: Adult trachea basal cells differentiation in ALI culture

value: BEGM


title: HKC8,transcriptome 01

source_name: HKC8,transcriptome 01


title: stl297 sibling

source_name: Whole Body

value: Whole Body


title: LLC-PK1,transcriptome 02

source_name: LLC-PK1,transcriptome 02


title: HPTC-05-LTR,transcriptome 02

source_name: HPTC-05-LTR,transcriptome 02


title: HPTC-05-CLA,transcriptome 02

source_name: HPTC-05-CLA,transcriptome 02


title: stl297 mutant


title: ALIDD001_Primary: Primary HBEC-derived ALI

value: Adult tracheal basal cells

value: UNC-ALI

value: Accutase


title: LLC-PK1,transcriptome 01

source_name: LLC-PK1,transcriptome 01


title: Tumorcore_nonirradiatedbrain_rep2

description: grown in mouse2

source_name: tumorcore control

value: prol - proliferative


title: BC-1 replicate 2

status: Public on Oct 13 2020

city: New York

first: JJ

last: Miranda

address: 3009 Broadway

institute: Barnard College, Columbia University

data_processing:
Reads were demultiplexed and aligned using Cell Ranger
Reads aligning to viral genomes were assigned to features using a heuristic algorithm implemented in python
Cells were filtered using R scripts
Data between samples was normalized with sctransform
Genome_build: hg38
Supplementary_files_format_and_content: Table with normalized gene counts for each sample

organism:
Homo sapiens
human gammaherpesvirus 4
Human gammaherpesvirus 8

source_name: BC-1 [KSHV+ EBV+ primary effusion lymphoma]

growth_protocol: Cells were maintained in RPMI 1640 medium with 25 mM HEPES and 2 g/liter NaHCO3 supplemented with 10% fetal bovine serum in 5% CO2 at 37°C

extract_protocol:
Gel bead in EMulsion microfluidic technology
Chromium Single Cell 3' Library & Gel Bead Kit v2


title: BC-1 replicate 1


title: HPTC-05-LTR,transcriptome 03

source_name: HPTC-05-LTR,transcriptome 03


title: nasal mucosa, normal rep2

city: Shanghai

first: Wei

last: Xian

address: 150 Jimo Road, Pudong New Area, Shanghai

institute: East Hospital Affiliated to Tongji University

description: Gene expression data from normal inferior turbinate mucosal tissue.

hyb_protocol: Following fragmentation, 500 ug of RNA were hybridized for 4 hr at 40°C on GeneChip Drosophila Genome Array. Next we washed and stained the GeneChips.

scan_protocol: GeneChips were scanned using the AffymetrixScanner 3000.

data_processing:
AffymetrixGeneChip Command Console (version4.0,Affymetrix) software was used to extract raw data. Next,Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for both gene and exon level analysis.Genesrping software (version 13.1; Agilent Technologies)was employed  to finish the basic analysis. Differentially expressedgeneswere then identified through fold changeas well as P value calculated with t-test. The threshold set for up- and down-regulatedgenes was a fold change>=2.0 and a P value<= 0.05. Afterwards, GO analysis and KEGG analysis were applied to determine the roles of these differentially expressed mRNAs played in these GO terms or pathways. Finally, Hierarchical Clustering was performed to display the distinguishable genes' expression pattern among samples.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
program-name = Expression Console
program-version = 1.4.1.46

source_name: mucosa of inferior turbinate, normal

label_protocol: Biotinylated aRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: Part of inferior turbinate mucosa was taken in the operation and stored in liquid nitrogen for total RNA extraction.

treatment_protocol: According to the diagnosis guidelines of allergic rhinitis, the samples were divided into AR group and non-AR group, and 3 samples were selected for microarray analysis in each group.

tag: sample group

value: non-AR; normal

value: inferior turbinate

value: epithelial cells of nasal mucosa


title: nasal mucosa, normal rep1


title: nasal mucosa, normal rep3


title: nasal mucosa, allergy rep1

description: Gene expression data from allergic inferior turbinate mucosal tissue.

source_name: mucosa of inferior turbinate, allergy

value: allergic rhinitis (AR)


title: 27-5A-AD-Input

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Alignment: ChIP-seq tags generated with the NextSeq 500 platform were demultiplexed with the bcl2fastq utility and aligned to the human reference genome (assembly  NCBI37/hg19)  using Bowtie v1.1.1 allowing up to two mismatches per sequencing tag (parameters -m 1 --best).
PCR deduplication: Aligned tags were filtered so that when N tags aligned to the same locus, only one representative tag was kept.
Tracks: Generation and visualization of ChIP-seq tracks was conducted as follows. BED files of each pooled study group dataset were converted into coverage maps using the BEDtools utility genomeCoverageBed. Resulting bedGraphs were scaled by using the RPM (reads per million) coefficient, a measure of the millions of tags sequenced per sample to correct for sequencing efficiency biases, and subsequently normalized by subtracting an Input coverage map. Finally, BigWig files were generated and uploaded on the UCSC (University of California Santa Cruz) Genome Browser.
Genome_build: hg19

source_name: lateral temporal lobe

growth_protocol: Frozen brain tissue samples from lateral temporal lobe (Brodmann area 21 or 20) were obtained from the Center of Neurodegenerative Disease Research (CNDR) biobank at the University of Pennsylvania in accordance with Institutional Review Board approved protocols. A neuropathological diagnosis of AD was established based on the presence of plaques and tangles using the CERAD scores and Braak stages, respectively.  All selected AD cases had high level of AD neuropathological changes (Braak=V/VI and CERAD=C). The Young and Old control brains had no or minimal neuritic amyloid plaques (CERAD=0) or neurofibrillary tangles (CERAD=0). None of the AD cases had other coincident neurodegenerative diseases. Control subjects had no deposits consistent with a frontotemporal lobar degeneration or Lewy body related pathology diagnosis. AD cases with severe neuronal loss were not included. The neuronal loss was originally assessed through semi-quantitative measurements by hematoxylin and eosin (H&E) staining by board-certified neuropathologists of the CNDR. The H&E scoring for neuronal loss ranges from 0-3 where 0 signifies no neuronal loss and 3 is severe neuronal loss. Only cases with neuronal loss of 1 or 2 (mild or moderate) were included.

extract_protocol:
Briefly, 200 mg brain tissue from each patient was minced on ice and nuclei were prepared by dounce homogenization in nuclei isolation buffer (50 mM Tris-HCl at pH 7.5, 25 mM KCl, 5 mM MgCl2, 0.25 M sucrose) with freshly added protease inhibitors and sodium butyrate, followed by ultracentrifugation on a 1.8 M sucrose cushion. Nuclei pellet was resuspended in 2 ml PBS and crosslinked in 1% formaldehyde for 10 min at room temperature. Crosslinking reactions were quenched with addition of glycine to 125 mM for 5 min followed by two washes in cold PBS. 2 x 106 nuclei were lysed in nuclei lysis buffer (10 mM Tris-HCl at pH 8.0, 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5% N-lauroylsarcosine) with freshly added protease inhibitors and sodium butyrate and chromatin was sheared using a Covaris S220 sonicator to ~250 bp size. Equal aliquots of sonicated chromatin were used per immunoprecipitation reaction with 5 ul H4K16ac antibody (Millipore, #07-329) preconjugated to Protein G Dynabeads (Life Technologies), and 10% of the amount was saved as input. ChIP reactions were incubated overnight at 4°C with rotation and washed three times in wash buffer.
Immunoprecipitated DNA was eluted from the washed beads, purified and used to construct sequencing libraries with 5 ng of DNA (ChIP or Input) using the NEBNext Ultra DNA library prep kit for Illumina (New England Biolabs, NEB). Libraries were multiplexed using NEBNext Multiplex Oligos for Illumina (dual index primers) and single-ended sequenced (75 bp) on the NextSeq 500 platform (Illumina) in accordance with the manufacturer’s protocol.

tag: study group

value: Aged, diseased

tag: age (years)

tag: antibody

value: lateral temporal lobe


title: 23-2A-AD-Input


title: 21-1A-AD-Input


title: 18-10A-Old-Input

value: Old


title: Patient 3 B55930T

first: xiaona

last: zhang

address: No.151 Libing Road

institute: Shanghai Biochip Corporation

description: Fifty five positive control probes and one negative control probe were designed following the instruction of Agilent’s design tool earray. Therefore, a total of 56 probe data were already eliminated from the whole 90795 probe data on the 085499_SBC human ceRNA microarray version 1.1.

hyb_protocol: Hybridizations to 085499_SBC human ceRNA microarray version 1.1. slides (Agilent Technologies, Inc., Santa Clara, CA) following the manufacturer's suggested protocols.

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

data_processing: Data were extracted with Feature Extraction software 12.1 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, using limma package in R software.

source_name: primary prostate cancer

label_protocol: 200ng total RNA was amplified and labeled by Low Input Quick Amp WT Labeling Kit (Cat.# 5190-2943, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

extract_protocol: Total RNA was isolated from tumor and corresponding adjacent normal prostate tissues using TRIzol Reagent (Life technologies, Carlsbad, CA, US), according to the manufacturer’s instructions. All samples were checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 4200 (Agilent technologies, Santa Clara, CA, US).

value: primary prostate cancer tumor tissue

tag: status after 5 years

value: Alive

tag: age

value: 73 years

tag: Sex

value: Male

value: IIC


title: HPTC-05-LTR,transcriptome 01

source_name: HPTC-05-LTR,transcriptome 01

value: Kidney Cells


title: 17-9A-Old-Input


title: 10-8A-Old-Input


title: 12-6A-Old-Input


title: Patient 2 B55903T

value: 44 years

value: IIIB


title: 9-16A-Young-Input

value: Young


title: nasal mucosa, allergy rep3


title: 8-15A-Young-Input


title: 14-7A-Old-Input


title: Patient 1 B50419T

value: 74 years


title: Tumorcore_nonirradiatedbrain_rep3

description: grown in mouse1

value: Control

value: prol - proliferative


title: nasal mucosa, allergy rep2

value: inferior turbinate

value: epithelial cells of nasal mucosa


title: 4-13A-Young-Input


title: 6-14A-Young-Input


title: 26-3A-AD-Input

value: Aged, diseased


title: 2-12A-Young-Input

value: lateral temporal lobe


title: 19-11A-Old-Input

value: Old


title: H3K27ac-MACROD5-shLUC_rep2

city: London

first: Marco

last: Trizzino

state: UK

address: Imperial College Road

department: Life Sciences

institute: Imperial College London

description: H3K27ac condition was performed in shLUC condition in differentiated macrophages (day 5 of GM-CSF treatment)

data_processing:
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters)
base calling: Bustard (Illumina pipeline 1.9, default parameters)
Quality Control FastQC
Adapter Trimming TRIM-GALORE
alignment (RNA-seq) STAR
alignment (ChIPseq, CUT&RUN, ATAC-seq) BWA
tag density files deepTools package was used to generate BigWiggle files
Genome_build: hg 19
Supplementary_files_format_and_content: strand specific bigWig, compatible with UCSC Genome Browser, were generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)

source_name: DIFFERENTIATING MACROPHAGES

growth_protocol: CD34 were cultured andf differentiated in IMDM, with heatinactivated FBS and  M-CSF. Primary Monocytes were cultured differentiated in IMDM with heat inactivated FBS and 25 ng/ul GM-CSF

extract_protocol: NEBNext ChIP-Seq ULTRAII DNA Sample Prep Kit (New England Biolabs, inc.)

treatment_protocol: M-CSF  14 days (monocyte diff); GM-CSF 5 days (macrophages)

value: DIFFERENTIATING MACROPHAGES

tag: chip antibody

value: ABCAM Rabbit polyclonal AB4729


title: ATAC-SEQ-MACRO-rep2

description: ATAC-seq was performed in  differentiating macrophages (day 4 of GM-CSF treatment)

extract_protocol: NextERA Illumina ATAC-seq kit


title: TL221_SHEP_CYC065_3

city: Houston

first: Tong

last: Liang

state: TX

address: One Baylor Plaza

institute: Baylor College of Medicine

description: RNA-seq in CYC065 SHEP rep3

data_processing:
Sequenced reads were aligned to HG19 referenece genome using HISAT
FPKM were caluclated by cufflinks
Genome_build: hg19
Supplementary_files_format_and_content: text file with fpkm

source_name: Neuroblastoma

growth_protocol:
10% FBS, DMEM
SH-EP-MYCN cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Direct-zol RNA Miniprep Kits (R2050; Zymo Scientific)
NEBNext® Ultra™ RNA Library Prep Kit for Illumina®

treatment_protocol: CYC065 drug treatment was performed by addition of 1uM CYC065 to growth media for 6hrs

tag: cell line

value: SHEP parental cells

value: Neuroblastoma

tag: exogenous myc genotype

value: 1uM CYC065 for 6HR

tag: barcode

value: GAGTGGAT


title: ATAC-SEQ-MONO-rep2

description: ATAC-seq was performed in primary monocytes

source_name: PERIPHERAL MONOCYTES

tag: cell type

value: PERIPHERAL MONOCYTES


title: TL220_SHEP_CYC065_2

description: RNA-seq in CYC065 SHEP rep2

tag: treatment

value: CGTACGTA


title: Patient 3 B55930P

tag: tissue

value: primary prostate cancer adjacent normal

value: Alive

value: 73 years

value: Male

tag: Stage

value: IIC


title: Tumorcore_nonirradiatedbrain_rep1

description: grown in mouse3

value: Control

tag: sample type

value: prol - proliferative


title: Patient 1 B50419P

value: 74 years


title: TL219_SHEP_CYC065_1

description: RNA-seq in CYC065 SHEP rep1

value: GTTTCGGA


title: TL218_SHEP_DMSO_3

description: RNA-seq in DMSO SHEP rep3

value: DMSO for 6HR

value: GTGGCCTT


title: TL217_SHEP_DMSO_2

description: RNA-seq in DMSO SHEP rep2

value: SHEP parental cells

value: GTGAAACG


title: TL216_SHEP_DMSO_1

description: RNA-seq in DMSO SHEP rep1

value: Neuroblastoma

value: GTCCGCAC


title: TL196_SHEP_MYCN_T58A_CYC065_2

description: RNA-seq in CYC065 SHEP_MYCN_T58A rep2

value: SHEP MYCN

value: 1uM CYC065 for 6HR


title: TL199_SHEP_MYCN_T58A_and_S62A_DMSO_2

description: RNA-seq in DMSO SHEP_MYCN_T58A_and_S62A rep2

value: MYCN T58A and S62A


title: TL200_SHEP_MYCN_T58A_and_S62A_DMSO_3

description: RNA-seq in DMSO SHEP_MYCN_T58A_and_S62A rep3

value: CGTACGTA


title: TL197_SHEP_MYCN_T58A_CYC065_3

description: RNA-seq in CYC065 SHEP_MYCN_T58A rep3


title: TL203_SHEP_MYCN_T58A_and_S62A_CYC065_3

description: RNA-seq in CYC065 SHEP_MYCN_T58A_and_S62A rep3

value: ATTCCTTT


title: TL202_SHEP_MYCN_T58A_and_S62A_CYC065_2

description: RNA-seq in CYC065 SHEP_MYCN_T58A_and_S62A rep2

value: ACTGATAT


title: TL201_SHEP_MYCN_T58A_and_S62A_CYC065_1

description: RNA-seq in CYC065 SHEP_MYCN_T58A_and_S62A rep1

value: GAGTGGAT


title: TL198_SHEP_MYCN_T58A_and_S62A_DMSO_1

description: RNA-seq in DMSO SHEP_MYCN_T58A_and_S62A rep1


title: TL193_SHEP_MYCN_T58A_DMSO_2

description: RNA-seq in DMSO SHEP_MYCN_T58A rep2

value: AGTTCCGT


title: TL191_SHEP_MYCN_S62A_CYC065_3

description: RNA-seq in CYC065 SHEP_MYCN_S62A rep3

value: CTTGTAAT


title: TL192_SHEP_MYCN_T58A_DMSO_1

description: RNA-seq in DMSO SHEP_MYCN_T58A rep1

value: AGTCAACA


title: H3K27ac-MACROD5-shEGR1_rep2

description: H3K27ac condition was performed in shEGR1 condition in differentiated macrophages (day 5 of GM-CSF treatment)

value: DIFFERENTIATING MACROPHAGES

value: ABCAM Rabbit polyclonal AB4729


title: EGR1_MACRO_D6_CHIP

description: EGR1 CHIP-seq was performed in differentiating macrophages (day 6 of GM-CSF treatment)

value: EGR1 BETHYL RABBIT POLICLONAL A303


title: TL190_SHEP_MYCN_S62A_CYC065_2

description: RNA-seq in CYC065 SHEP_MYCN_S62A rep2

value: GGCTACAT


title: TL195_SHEP_MYCN_T58A_CYC065_1

description: RNA-seq in CYC065 SHEP_MYCN_T58A rep1

value: CCGTCCGC


title: TL189_SHEP_MYCN_S62A_CYC065_1

description: RNA-seq in CYC065 SHEP_MYCN_S62A rep1

value: Neuroblastoma

value: TAGCTTAT


title: TL186_SHEP_MYCN_S62A_DMSO_1

description: RNA-seq in DMSO SHEP_MYCN_S62A rep1

value: SHEP MYCN

value: DMSO for 6HR

value: CAGATCAT


title: TL187_SHEP_MYCN_S62A_DMSO_2

description: RNA-seq in DMSO SHEP_MYCN_S62A rep2

value: ACTTGAAT


title: TL184_SHEP_MYCN_WT_CYC065_2

description: RNA-seq in CYC065 SHEP_MYCN_WT rep2

value: WT

value: 1uM CYC065 for 6HR

value: ACAGTGAT


title: TL183_SHEP_MYCN_WT_CYC065_1

description: RNA-seq in CYC065 SHEP_MYCN_WT rep1

value: TGACCAAT


title: TL181_SHEP_MYCN_WT_DMSO_2

description: RNA-seq in DMSO SHEP_MYCN_WT rep2

value: CGATGTAT


title: Patient 2 B55903P

value: primary prostate cancer adjacent normal

value: Alive

value: 44 years

value: Male

value: IIIB


title: TL180_SHEP_MYCN_WT_DMSO_1

description: RNA-seq in DMSO SHEP_MYCN_WT rep1

value: ATCACGAT


title: TL105_SHEP_MYCN_T58A_and_S62A_CYC065_WCE

first: Charles

middle: Yang

last: Lin

address: 1 Baylor Plaza

department: Molecular and Human Genetics

description: Input for SHEP_MYCN_T58A_and_S62A CYC065

data_processing:
Sequenced reads were aligned to HG19 referenece genome using BWA
Peaks were called using MACS2 with  p-val =1e-5 and background datasets as described in characteristic: input
Genome_build: hg19
Supplementary_files_format_and_content: Processed ChIP-Seq data files are in bedgraph format

source_name: SHEP MYCN neuroblastoma cell line

growth_protocol: SH-EP-MYCN cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared using Tn5 enzyme and amplified using 2x NEBNext HiFi master mix.

tag: input

tag: growth protocol

value: 10% FBS, DMEM

value: CGGCTATG


title: TL229_SHEP_CYC065_WCE

description: Input for SHEP CYC065

source_name: SHEP

value: AGCGATAG


title: TL54_SHEP_MYCN_T58A_CYC065_WCE

description: Input for SHEP_MYCN_T58A CYC065

value: ACTCGCTA


title: TL104_SHEP_MYCN_T58A_and_S62A_DMSO_WCE

description: Input for SHEP_MYCN_T58A_and_S62A DMSO

value: DMSO for 6HR

value: TAATGCGC


title: TL55_SHEP_MYCN_S62A_DMSO_WCE

description: Input for SHEP_MYCN_S62A DMSO

value: GGAGCTAC


title: TL228_SHEP_DMSO_WCE

description: Input for SHEP DMSO

value: TCTCGCGC


title: TL53_SHEP_MYCN_T58A_DMSO_WCE

description: Input for SHEP_MYCN_T58A DMSO

value: ATCTCAGG


title: TL48_SHEP_MYCN_S62A_CYC065_MYCN

description: Chromatin IP against MYCN in CYC065 SHEP_MYCN_S62A

value: 1uM CYC065 for 6HR

value: TGGGTTTC

value: MYCN sc791

tag: antibody maker

value: santa cruz

tag: antibody catalog number


title: TL51_SHEP_MYCN_WT_DMSO_WCE

description: Input for SHEP_MYCN_WT DMSO

value: CCACTCCT


title: TL47_SHEP_MYCN_S62A_DMSO_MYCN

description: Chromatin IP against MYCN in DMSO SHEP_MYCN_S62A

value: GTGTGGTG

tag: antibody


title: TL52_SHEP_MYCN_WT_CYC065_WCE

description: Input for SHEP_MYCN_WT CYC065

value: GCTCATGA


title: TL43_SHEP_MYCN_WT_DMSO_MYCN

description: Chromatin IP against MYCN in DMSO SHEP_MYCN_WT

value: TAAGGCGA


title: TL44_SHEP_MYCN_WT_CYC065_MYCN

description: Chromatin IP against MYCN in CYC065 SHEP_MYCN_WT

value: 10% FBS, DMEM

value: CGTACTAG


title: TL99_SHEP_MYCN_T58A_and_S62A_CYC065_MYCN

description: Chromatin IP against MYCN in CYC065 SHEP_MYCN_T58A_and_S62A

value: CGCTCATT


title: TL46_SHEP_MYCN_T58A_CYC065_MYCN

description: Chromatin IP against MYCN in CYC065 SHEP_MYCN_T58A

value: TCCTGAGC


title: TL188_SHEP_MYCN_S62A_DMSO_3

description: RNA-seq in DMSO SHEP_MYCN_S62A rep3

value: SHEP MYCN

value: Neuroblastoma

value: DMSO for 6HR

value: GATCAGAT


title: TL226_SHEP_CYC065_H3K27AC

description: Chromatin IP against H3K27ac in CYC065 SHEP

value: CGGCTATG

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6

value: cell signaling


title: TL98_SHEP_MYCN_T58A_and_S62A_DMSO_MYCN

description: Chromatin IP against MYCN in DMSO SHEP_MYCN_T58A_and_S62A

value: TCCGGAGA

value: MYCN sc791


title: TL160_SHEP_MYCN_T58A_and_S62A_CYC065_H3K27AC

description: Chromatin IP against H3K27ac in CYC065 SHEP_MYCN_T58A_and_S62A

value: 1uM CYC065 for 6HR

value: ATGCGCAG


title: TL225_SHEP_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO SHEP

value: TAATGCGC


title: TL182_SHEP_MYCN_WT_DMSO_3

description: RNA-seq in DMSO SHEP_MYCN_WT rep3

value: WT

value: TTAGGCAT


title: TL159_SHEP_MYCN_T58A_and_S62A_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO SHEP_MYCN_T58A_and_S62A

value: 10% FBS, DMEM

value: TACGCTGC


title: TL158_SHEP_MYCN_S62A_CYC065_H3K27AC

description: Chromatin IP against H3K27ac in CYC065 SHEP_MYCN_S62A

value: CGGAGCCT


title: TL156_SHEP_MYCN_T58A_CYC065_H3K27AC

description: Chromatin IP against H3K27ac in CYC065 SHEP_MYCN_T58A

value: GGAGCTAC


title: TL157_SHEP_MYCN_S62A_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO SHEP_MYCN_S62A

value: GCGTAGTA


title: TL56_SHEP_MYCN_S62A_CYC065_WCE

description: Input for SHEP_MYCN_S62A CYC065


title: TL154_SHEP_MYCN_WT_CYC065_H3K27AC

description: Chromatin IP against H3K27ac in CYC065 SHEP_MYCN_WT

value: ATCTCAGG


title: TL153_SHEP_MYCN_WT_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO SHEP_MYCN_WT

value: DMSO for 6HR

value: GCTCATGA


title: TL45_SHEP_MYCN_T58A_DMSO_MYCN

description: Chromatin IP against MYCN in DMSO SHEP_MYCN_T58A

value: AGGCAGAA

value: santa cruz


title: UGent11-60 Naive rep 3 lane 1

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

data_processing:
Reads were trimmed using cutadapt versin 1.11 to remove the “QuantSeq FWD” adaptor sequence
The reads were mapped against the Mus musculus GRCm38.p5 reference genome using CLC genomics workbench version 9.0.1 (CLC)
Only the reads that didn’t map against the GRCm38.p5 genome were subsequently mapped against the Homo sapiens hg19 GRCH37.74 genome using CLC
Count tables were generated by counting the reads that mapped against the genes defined by the Ensembl GRCh37.74 gene transfer format file (GTF) and exported from CLC
Genome_build: Mus musculus GRCm38.p5
Genome_build: Homo sapiens hg19 GRCh37.74
Supplementary_files_format_and_content: comma separated values files including Gene counts, Gene ID and other gene information

source_name: Human embryonic stem cells

growth_protocol: Primed hESC lines, UGent11-2 (female XX) and UGent11-60 (female XX) were cultured on mitomycin-C-treated (MEFs) and refreshed daily with primed medium.

extract_protocol:
Total RNA was extracted from biological triplicates of UGent11-2 and UGent11-60 hESC lines cultured in primed, Wnt-i and naive conditions, using the RNeasy mini kit (Qiagen), including a DNase digestion step
500 ng of RNA was used for library preparation using the QuantSeq 3' mRNA-Seq Library Prep Kits (Lexogen) following the manufacturer's protocol.

treatment_protocol: Primed hESCs were converted to Wnt-i hESCs by refreshing daily with Wnt-i medium (see above) for 5 consecutive passages; and to naive hESCs by refreshing daily with naive medium for 5 consecutive passages.

value: hESC

tag: passage

value: Naive


title: UGent11-60 Naive rep 2 lane 4


title: UGent11-60 Naive rep 3 lane 4


title: UGent11-60 Naive rep 3 lane 3


title: UGent11-60 Naive rep 2 lane 3


title: UGent11-60 Naive rep 3 lane 2


title: UGent11-60 Wnt-i rep 3 lane 1

value: Wnt-i


title: UGent11-60 Wnt-i rep 3 lane 4


title: UGent11-60 Naive rep 2 lane 2


title: UGent11-60 Naive rep 1 lane 2


title: UGent11-60 Wnt-i rep 2 lane 4


title: UGent11-60 Wnt-i rep 3 lane 3


title: UGent11-60 Wnt-i rep 2 lane 2


title: UGent11-60 Naive rep 1 lane 4


title: UGent11-60 Naive rep 1 lane 1


title: UGent11-60 Wnt-i rep 2 lane 3


title: UGent11-60 Wnt-i rep 1 lane 4


title: UGent11-60 Naive rep 1 lane 3


title: UGent11-60 Wnt-i rep 1 lane 3


title: UGent11-60 Wnt-i rep 3 lane 2


title: UGent11-60 Wnt-i rep 1 lane 2


title: UGent11-60 Wnt-i rep 2 lane 1


title: UGent11-60 Wnt-i rep 1 lane 1


title: TL155_SHEP_MYCN_T58A_DMSO_H3K27AC

description: Chromatin IP against H3K27ac in DMSO SHEP_MYCN_T58A

value: ACTCGCTA

value: Acetyl-Histone H3 (Lys27) (D5E4) XP® Rabbit mAb #8173 lot6

value: cell signaling


title: UGent11-60 Primed rep 3 lane 4

value: Primed


title: UGent11-60 Naive rep 2 lane 1


title: UGent11-60 Primed rep 3 lane 2


title: UGent11-60 Primed rep 2 lane 4


title: UGent11-60 Primed rep 2 lane 3


title: UGent11-60 Primed rep 2 lane 2


title: UGent11-60 Primed rep 3 lane 1


title: UGent11-60 Primed rep 2 lane 1


title: UGent11-60 Primed rep 1 lane 4


title: UGent11-2 Naive rep 3 lane 2