title: Visible light 3

city: Wuhan

first: Pier-Luc

last: Tremblay

state: Hubei

address: 122 Luoshi Road

department: School of Chemistry, Chemical Engineering and Life Science

institute: Wuhan University of Technology

data_processing:
Quality-scored basecalling was performed with the Illumina HiSeq Control software
Sequenced reads were mapped on the reference C. autoethanogenum DSM 10061 genome with Bowtie 2
Transcripts per million (TPM) were calculated with RSEM
FDR-adjusted p-values were calculated with DeSeq2
Assembly: NZ_CP012395.1
Supplementary files format and content: Tab-delimited text file including gene locus, gene name, annotation, fold change, Log2 fold change, p-value, adjusted p-value, TPM for each replicate, TPM mean

organism: Clostridium autoethanogenum

growth_protocol: C. autoethanogenum wild type was grown autotrophically under an H2:CO:CO2 (35:50:15) atmosphere (1.7 atm) in 10 ml Tanner modified medium at 37 ℃ and an initial pH of 5.8. C. autoethanogenum was either grown in the dark or under white visible light at an intensity of 4200 lux and sampled for total RNA extraction after 48 hours

extract_protocol:
Total RNA was extracted from C. autoethanogenum with the TRIzol reagent from ThermoFisher Scientific
The RNA sequencing library were prepared with the Illumina TruSeq RNA sample preparation Kit

value: Bacteria

value: Visible light 4200 lux


title: HiC_S2_MES4_KD_rep1

status: Public on Jul 01 2023

type: SRA

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

library_source: genomic

data_processing:
alignment: Juicer version 1.6; BWA 0.7.17-r1188; openjdk version 1.8.0_302
Assembly: genome_version : dm6-r6.32
Supplementary files format and content: HiC contact matrix (.hic format)

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: S2 (Schneider 2)

growth_protocol: Schneider 2 (S2) Drosophila cells were cultured in Schneider Drosophila medium complemented with 10% heat-inactivated FBS and 1% pen-strep

extract_protocol:
ARIMA HiC Kit
KAPA hyperprep

treatment_protocol: S2 cells were treated for RNAi-mediated depletion, T7-driven synthesis (Fermentas TranscriptAid™ T7 High Yield Transcription Kit) of double-stranded RNAs (dsRNA) specific for Mes4/NSD, Hypb/dSET2 or luc were used. 400 µg of dsRNA were added to 36 millions cells in 10 mL media without FBS following for 2h at 25°C before adding FBS. Depletion was optimized for incubation of 4 days and cells were then harvested.

tag: cell line

value: S2 (Schneider 2)

tag: cell type

value: Late embryonic derived S2 cells

tag: treatment

value: Mes4 KD


title: defined_end_hepg2 biol rep 1-5

city: Seattle

first: Sebastian

middle: Martin

last: Castillo Hair

state: Washington

address: West Stevens Way NE

department: Electrical and Computer Engineering

country: USA

institute: University of Washington

description: Polysome profiling of the defined-end N50 5'UTR library in HepG2

library_source: transcriptomic

data_processing:
bcl2fastq
Custom scripts were used to filter reads where the 3' end matched the expected constant sequence right after the variable 5'UTR region
Starcode was used to collapse UMIs
A custom script was used to calcualte MRLs for each sequence in the library.
Supplementary files format and content: Columns "UTR" or "utr" contain the variable 5'UTR sequence. Columns 0-13 contain the number of UMIs in each polysome fraction, and column "total" contains their sum for each sequence. Columns r0-r13 contain the normalized read count in each polysome fraction, and r_total" contains their sum. Column "rl" contains the calculated MRL.

molecule: total RNA

organism: Homo sapiens

growth_protocol: HEK293T cells were cultured on ECM-coated plates in Dubelco's DMEM media supplemented with FBS (5%), penicillin (.05%), and streptomycin (.05%). HepG2 cells were cultured in EMEM + 10% FBS in a T-75 flask. T cells were grown in T cell growth medium (TCGM) at 37C, 5% CO2.

extract_protocol:
Cells were lysed in the presence of cycloheximide to halt translating ribosomes so that polysome profiling could be run with the lysate. Lysis and RNA isolation for HEK293T and HepG2 were performed as described in Sample, Wang et al. 2019. For T cells, cycloheximide was first added dropwise to the media to a final concentration of 100 ug/mL and incubated for 5 additional minutes. Cells were then spined down at 1500 rpm for 5 min and the supernatant was discarded. 300 uL of cold lysis buffer (Sample, Wang et al. 2019) was used to resuspend the cells, and the mixture was incubated on ice for 10 minutes. Cells were then triturated by passing the mixture through a 25-gauge needle ten times. The mixture was spined down at 16,000 rpm for 5 min at 4C and the supernatant was transferred to another tube. 1.5 uL of 1U/uL DNAse was added, the mixture was set on ice for 30 minutes, and stored at -80C. Polysome profiling was performed as in Sample, Wang et al. 2019.
Sequencing libraries for the defined-end reporters were constructed for each extracted polysome fraction as in Sample, Wang, et al. 2019. For the random-end reporter libraries, sequencing library preparation comprised reverse transcription, template switching, and qPCR amplification, all of which were performed separately for each polysome fraction. For reverse transcription, we first mixed 10.5 uL of purified RNA with 2 uL of 2 uM RT primer (AGGGACATCGTAGAGAGTCGTACTTANNNNNNNNNNAGATGAACTTCAGGGTCAGC, where Ns comprise the UMI) and 2uL of 10mM dNTP mixture (NEB), incubated the mixture at 65C for 5 minutes, and placed on ice for at least one minute. Then, we added 4 uL Maxima RT buffer, 0.5 uL Superase-In RNAse inhibitor (Thermo Fisher), and 1 uL Maxima RT RNaseH minus Enzyme (Thermo Fisher), incubated at 50C for 15 min, then 85C for 10 min, and transferred back to ice. Next, we added 1 uL RNase (from bovine pancreas, DNase free, Roche) and 1 uL RNase H (NEB) and incubated at 37C for 15 minutes. Finally, the product was cleaned with KAPA beads (Roche) with a 3x ratio of beads to DNA volume, and resuspended in 25 uL dH2O. For template switching, we added 8 uL Maxima RT buffer, 6 uL 50% PEG-8000, 0.5 uL Superase-In, 1 uL Maxima RT RNaseH minus enzyme, and 0.5 uL of 10 uM template switching oligo (AAGCAGTGGTATCAACGCAGAGTACATrGrGrG). This mixture was incubated at 42C for 30 minutes, then 85C for 10 minutes. Next, 1uL RNase (Roche) and 1uL RNase H (NEB) were added and the mixture was incubated at 37C for 15 minutes. Finally, the product was cleaned with 3x KAPA beads and resuspended in 20 uL dH2O.  qPCR amplification was performed using the KAPA HiFi master mix (Roche) with forward primers AATGATACGGCGACCACCGAGATCTACAC[8nt-long index barcode]AGCGTGACAGGGACATCGTAGAGAGTCGTACTTA and reverse primers CAAGCAGAAGACGGCATACGAGAT[8nt-long index barcode]AAGCAGTGGTATCAACGCAGA, where the barcodes were specific to each polysome fraction. qPCR reactions were stopped before reaching saturation and purified via gel extractions.

treatment_protocol: HEK293T growth and transfection was performed as described in Sample, Wang et al. 2019. HepG2 cells were seeded at 200,000 cells/mL into a T-75 flask and allowed to expand for 3 days. 1ug library mRNA was transfected into one million cells using the Lonza 4D nucleofector. Cell lysis was performed 8 hours later. T cells were enriched from peripheral blood mononuclear cells (PBMCs) isolated via Ficoll-Paque gradient centrifugation from healthy donors. Activation was performed with anti CD3/CD28 antibodies in the presence of IL-2. 1 ug library mRNA was transfected into one million cells with the Lonza 4D Nucleofector, following the manufacturer’s protocol. Transfected cells were plated in T cell growth medium (TCGM) at 1 million cells/mL and incubated at 37C, 5% CO2. Cell lysis was performed 12 hours later.


title: Visible light 2

country: China

tag: genotype

value: WT

tag: time


title: TBPW_1.1j

type: RNA

city: Oxford

first: David

last: Church

address: Roosevelt Drive

country: United Kingdom

institute: University of Oxford

hyb_protocol: Affymetrix protocols

scan_protocol: Affymetrix protocols

data_processing: robust multi array (RMA) averaged using R Oligo package

label: biotin

organism: Mus musculus

source_name: PR-Cre

label_protocol: Affymetrix protocols

growth_protocol: Mice were housed under standard conditions

extract_protocol: Qiagen Rneasy blood and tissue as per manufacturer protocol

treatment_protocol: Untreated

tag: tissue

value: uterus at 8 weeks age

value: PR-Cre


title: HiC_S2_luc_KD_rep1


title: T727_00h_rep1

city: Nankang, Taipei

first: Hung-Che

last: Lin

address: 128 Academia Road, Section 2

country: Taiwan

institute: Academia sinica

data_processing:
Adapter trimming and quality filtering of pair-end raw reads with Fastp version 0.14.1 (fastp  -l 100 -f 0 -F 0 -t 10 -T 10 -i R1.fastq.gz -I R2.fastq.gz)
Mapping and quantification of reads against a reference transcriptome of A. oligospora TWF154 was done with Salmon v0.9.1 (salmon quant -i Ao_TWF154_Salmon_Index -l A --numBootstraps 200 -1 R1_filtered.fastq.gz -2 R2_filtered.fastq.gz
Transcript abundance estimates from Salmon were converted to a Sleuth-compatible format using the Wasabi package version 0.2
Likelihood ratio and Wald tests were performed to establish overall and differential expression for each transcript using the Sleuth program
Supplementary files format and content: Spreedsheet table with all the betas, normalized TPMs, and statistics from LTR tests merged toegher.

organism: Orbilia oligospora

growth_protocol: Fungal mycelium were plated on low nutritent medium (LNM) agar plates for 5 days at 25 °C

extract_protocol:
Total RNA was extracted from lyophilized samples via a Trizol-chloroform based protocol
Library preparation for total RNA samples (Genomic Core Facility, Institute of Molecular Biology, Academia Sinica) were carried out using the Illumina TruSeq stranded mRNA library preparation kit.

treatment_protocol: Approximately 2500 to 3000 C. elegans N2 strain at L4 larval stage were placed on each fungal plate, and hyphal collections were taken at 2, 4, 10, 24, and 48 hours after exposure, with worms being washed for 2 and 4 hours prior to collection for the 2 and 4 hpe samples, respectively. The fungal mycelium was immediately collected with a cell scraper, frozen in liquid nitrogen, and lyophilized.

tag: strain


title: Visible light 1


title: Dark 3

value: Dark


title: Dark 1


title: K56_Che

city: Seodaemun-gu, Seoul

first: Dongeun

last: Yong

address: 50-1 Yonsei-ro

country: South Korea

institute: Yonsei University College of Medicine

data_processing:
Preprocessing with bcl2fastq2 (v2.20.0.422)
Quality control with cutadapt (v1.18) and fastqc (v0.11.7)
Aligment with HISAT2 (v2.1.0)
Transcriptome assembly with Stringtie (v2.0.6)
Identification of DEG with LPEseq
Assembly: Reference genome (K. pneumoniae HS11286 strain)
Supplementary files format and content: tab-delimited text files with count values for each sample

organism: Klebsiella pneumoniae

source_name: Gram-negative bacteria

extract_protocol:
RNA was extracted with the RNeasy MiniKit (Qiagen) and a RNase-free DNase set and processed according to the guidelines from the manufacturer's handbook.
Library was prepared with a Truseq Stranded Total RNA Library prep kit as per manufacturer's protocols.

value: Gram-negative bacteria

value: Clinically isolated K56

value: Chemical #3 treated for 14hr 50min


title: defined_end_hepg2 biol rep 1-1


title: K56_Co_Che

value: Colistin and Chemical #3 treated for 14hr 50 min


title: defined_end_hepg2 biol rep 1-2


title: K56

value: untreated


title: K56_Co

value: Colistin treated for 14hr 50min


title: O-092:T4

status: Public on Jun 27 2023

city: Kawasaki-City

first: Yoshiyuki

last: Watanabe

state: Kanagawa

address: 3-13-1 Nakajima, Kawasaki-ku

department: Dept. of Internal Medicine

country: Japan

institute: Kawasaki Rinko General Hospital

data_processing:
Bclfiles were converted to fastqfiles using bcl2fastq2(v2.17.1.14) (Illumina).
We then processed fastqfiles into adigital expression matrix, as in our previous study [10].
During this process, we trimmed read2 length to 63nucleotides using the FASTX-Toolkit (version 0.0.14)(https://github.com/agordon/fastx_toolkit/blob/master/reconf).
Assembly: hg38

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood by centrifugation at 1,800 g for 15 min at room temperature, using the BD Vacutainer CPT Cell Preparation Tube. QIAzol Lysis Reagent was added to the isolated PBMCs, and total RNA was extracted according to the manufacturer's instructions.
The total RNA was used to prepare a next-generation sequencing library using Quartz-Seq2 (Sasagawa et al. (2018)) modified for bulk RNA-seq.

value: day 360

tag: infection

value: Severe acute respiratory syndrome coronavirus 2

value: Blood

value: PBMC


title: O-071:T4


title: WT_18M

status: Public on Jun 29 2023

city: MARSEILLE CEDEX 09

first: Christelle

last: Cayrou

address: 27 Boulevard Lei Roure

institute: CRCM

data_processing:
Raw sequences are demultiplexed and reads are mapped onto the mm10 reference genome using the v2.3 Cell Ranger pipeline (10X Genomics) to generate a count matrix for each sample.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with filtered gene counts for every gene and every sample

source_name: Lung

extract_protocol:
Mouse trachea is injected with 1,5 ml dispase 50 U/ml followed by 0,5 ml agarose 1%. Lung is resected and minced in 3 ml DPBS 1x CaCl2+ and MgCl2. Collagenase/dispase 100 mg/ml is added to the chopped tissue and placed on a rotator at 37 °C for 30 min. Enzymatic activity is inhibited by adding 5 ml of DPBS containing 10% FBS and 1mM EDTA. Cell suspension is filtered through 100 μm nylon cell strainer, treated by DNase I and filtered again through a 40 μm nylon cell strainer. Red blood cells are removed by red blood cell lysis treatment for 90s at room temperature. Finally, lung cells are centrifuged at 150g, 4 °C for 6 min, resuspended in DPBS 1x containing 0,02% BSA and counted.
Single-cell 3’-RNA-Seq samples were prepared using single cell V2 reagent kit and loaded in the Chromium controller according to standard manufacturer protocol (10x Genomics)

tag: genotype/variation

value: wild type (+/+)

tag: age

value: 18 month-old

value: Lung


title: p21mTert_18M

value: p21 mTert (+/mTert)

value: 20 month-old


title: O-054:T4


title: O-113:T4


title: defined_end_hepg2 biol rep 1-4


title: O-035:T4


title: O-018:T4


title: O-001:T4


title: U138-MG GBM cell line

type: genomic

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

description: status quo genomic copy number characterisation

hyb_protocol: Hybridisation and washing of slides was carried out according to Agilent's protocol for gene expression microarrays.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).

data_processing: Raw intensities were imported into R using the Biocinductor package Agi4x44PreProcess. Data were quality filtered using default parameters followed by quantile normalization.

source_name: Human glioblastoma cell line

label_protocol: Labelling of samples was carried out according to Agilent's protocol (low input).

growth_protocol: The human GBM cell lines A172, LN18, LN229, T98G, U87-MG, U138-MG and U251-MG were analyzed in this study. A172, LN18, LN229, U87-MG and T98G were obtained from the American type culture collection (ATCC, Manassas, Virginia, USA), U138-MG and U251-MG from the cell line repository CLS (Eppelheim, Germany). The cells were cultivated at 37°C and 7,5% CO2 in DMEM Glutamax (ThermoFisher, Waltham, MA, USA) supplemented with 10% FCS and 1% penicillin/streptomycin and kept at low passage numbers (<10).

extract_protocol: Total RNA was extracted from cell line pellets using the Qiagen Allprep kit.


title: Dark 2

value: Bacteria

value: WT


title: F-006:T4


title: LN229 GBM cell line


title: defined_end_hepg2 biol rep 1-3


title: U251-MG GBM cell line


title: T98G GBM cell line


title: U87-MG GBM cell line


title: LN18 GBM cell line


title: E-003:T4


title: O-133:T3

value: day 180


title: A172 GBM cell line


title: O-133:T4


title: O-113:T3


title: O-071:T3


title: O-092:T3


title: O-018:T3


title: E-008:T3


title: B-006:T3


title: O-112:T4


title: O-091:T4


title: O-054:T3


title: p21Het_18M

value: p21 heterozygotes (+/-)

value: 19 month-old


title: O-036:T3


title: O-053:T4


title: O-034:T4


title: E-002:T4


title: M-004:T4


title: O-112:T3


title: O-070:T4


title: O-017:T4


title: O-070:T3


title: O-132:T3


title: E-007:T3


title: O-091:T3


title: F-006:T3


title: B-005:T3


title: O-002:T3


title: O-017:T3


title: F-007:T3


title: O-089:T4


title: O-109:T4


title: O-130:T4


title: O-132:T4


title: O-069:T4


title: O-052:T4


title: M-003:T4


title: O-033:T4


title: F-004:T4


title: O-129:T3


title: B-006:T4


title: O-109:T3


title: F-005:T4


title: O-089:T3


title: O-016:T4


title: O-035:T3


title: M-004:T3


title: O-052:T3


title: O-016:T3


title: O-034:T3


title: O-107:T4


title: F-005:T3


title: B-004:T3


title: O-032:T4


title: O-015:T4


title: O-068:T4


title: O-087:T4


title: E-006:T3


title: B-004:T4


title: O-051:T4


title: O-150:T3


title: M-002:T4


title: F-003:T4


title: O-127:T3


title: O-107:T3


title: O-087:T3


title: O-051:T3


title: O-033:T3


title: O-015:T3


title: F-004:T3


title: M-003:T3


title: B-003:T3


title: O-129:T4


title: O-150:T4


title: E-005:T3


title: O-086:T4


title: O-031:T4


title: O-067:T4


title: F-002:T4


title: M-001:T4


title: O-149:T3


title: O-106:T3


title: O-126:T3


title: O-106:T4


title: B-002:T4


title: O-050:T3


title: O-068:T3


title: O-086:T3


title: O-067:T3


title: O-014:T4


title: F-003:T3


title: B-002:T3


title: E-004:T3


title: O-149:T4


title: O-126:T4


title: O-105:T4


title: O-085:T4


title: O-127:T4


title: O-066:T4


title: O-050:T4


title: O-030:T4


title: J-008:T4


title: F-001:T4


title: B-001:T4


title: O-148:T3


title: O-032:T3


title: O-105:T3


title: O-125:T3


title: O-014:T3


title: O-049:T3


title: O-085:T3


title: O-031:T3


title: O-013:T4


title: M-001:T3


title: O-013:T3


title: B-001:T3


title: F-002:T3


title: E-003:T3


title: M-002:T3


title: O-148:T4


title: O-084:T4


title: O-012:T4


title: O-065:T4


title: O-048:T4


title: O-147:T3


title: E-017:T4


title: O-066:T3


title: A-010:T4


title: O-084:T3


title: O-104:T3


title: J-007:T4


title: O-065:T3


title: O-048:T3


title: O-030:T3


title: J-008:T3


title: O-104:T4


title: F-001:T3


title: A-010:T3


title: E-002:T3


title: O-147:T4


title: O-082:T4


title: O-125:T4


title: O-064:T4


title: O-124:T4


title: O-027:T4


title: J-006:T4


title: O-011:T4


title: O-029:T4


title: O-047:T4


title: E-016:T4


title: A-009:T4


title: O-064:T3


title: O-012:T3


title: O-029:T3


title: O-047:T3


title: O-102:T3


title: O-123:T3


title: E-018:T3


title: J-007:T3


title: O-145:T4


title: A-009:T3


title: O-081:T4


title: E-001:T3


title: O-102:T4


title: O-122:T4


title: E-015:T4


title: O-062:T4


title: O-101:T4


title: O-101:T3


title: O-026:T4


title: A-008:T4


title: O-081:T3


title: O-043:T4


title: O-144:T3


title: O-062:T3


title: O-145:T3


title: O-046:T3


title: O-027:T3


title: O-122:T3


title: O-011:T3


title: O-010:T3


title: J-006:T3


title: D-004:T3


title: E-017:T3


title: A-008:T3


title: O-144:T4


title: O-121:T4


title: J-005:T4


title: O-080:T4


title: O-099:T4


title: O-042:T4


title: A-007:T4


title: J-004:T4


title: O-025:T4


title: O-143:T3


title: E-014:T4


title: O-099:T3


title: O-121:T3


title: O-080:T3


title: E-016:T3


title: O-026:T3


title: D-003:T3


title: A-007:T3


title: O-009:T3


title: J-005:T3


title: O-142:T4


title: O-061:T3


title: O-120:T4


title: O-079:T4


title: O-098:T4


title: O-041:T4


title: O-060:T4


title: O-024:T4


title: O-008:T4


title: J-003:T4


title: A-006:T4


title: O-098:T3


title: O-120:T3


title: E-013:T4


title: O-061:T4


title: O-079:T3


title: O-042:T3


title: O-060:T3


title: O-025:T3


title: J-004:T3


title: A-006:T3


title: E-015:T3


title: D-002:T3


title: O-097:T4


title: O-078:T4


title: O-118:T4


title: O-007:T4


title: O-059:T4


title: O-023:T4


title: O-141:T4


title: O-040:T4


title: A-005:T4


title: E-012:T4


title: O-141:T3


title: O-059:T3


title: O-118:T3


title: O-097:T3


title: O-041:T3


title: J-002:T4


title: O-007:T3


title: J-003:T3


title: O-024:T3


title: E-014:T3


title: D-001:T3


title: O-008:T3


title: A-005:T3


title: O-139:T4


title: O-096:T4


title: O-117:T4


title: O-077:T4


title: O-039:T4


title: O-058:T4


title: O-006:T4


title: O-117:T3


title: J-001:T4


title: O-139:T3


title: O-096:T3


title: A-004:T4


title: E-011:T4


title: O-077:T3


title: O-040:T3


title: O-023:T3


title: O-058:T3


title: J-002:T3


title: C-005:T3


title: O-006:T3


title: E-013:T3


title: A-004:T3


title: O-095:T4


title: O-136:T4


title: O-116:T4


title: O-076:T4


title: O-057:T4


title: O-038:T4


title: O-005:T4


title: O-021:T4


title: O-022:T4


title: F-009:T4


title: E-008:T4


title: A-003:T4


title: O-095:T3


title: O-039:T3


title: O-076:T3


title: O-116:T3


title: J-001:T3


title: E-012:T3


title: O-005:T3


title: C-004:T3


title: A-003:T3


title: O-094:T4


title: O-135:T4


title: O-075:T4


title: O-037:T4


title: F-008:T4


title: O-004:T4


title: E-005:T4


title: A-002:T4


title: O-115:T3


title: O-135:T3


title: O-094:T3


title: O-136:T3


title: O-075:T3


title: O-020:T3


title: O-021:T3


title: O-038:T3


title: F-009:T3


title: O-004:T3


title: C-002:T3


title: A-002:T3


title: E-011:T3


title: O-114:T4


title: O-093:T4


title: O-073:T4


title: O-055:T4


title: O-056:T4


title: O-020:T4


title: F-007:T4


title: E-004:T4


title: A-001:T4


title: O-003:T4


title: O-019:T4


title: O-056:T3


title: O-036:T4


title: O-073:T3


title: O-114:T3


title: O-093:T3


title: O-037:T3


title: O-134:T4


title: O-019:T3


title: C-001:T3


title: E-009:T3


title: F-008:T3


title: A-001:T3


title: O-133:T2

value: day 22


title: O-003:T3


title: O-096:T2


title: O-079:T2


title: O-029:T2


title: O-062:T2


title: O-013:T2


title: J-005:T2


title: O-134:T3


title: O-055:T3


title: F-007:T2


title: O-046:T1

value: day 0


title: O-079:T1


title: B-006:T2


title: O-096:T1


title: O-062:T1


title: O-013:T1


title: O-133:T1


title: J-005:T1


title: F-007:T1


title: O-150:T2


title: O-114:T2


title: O-115:T2


title: O-095:T2


title: B-006:T1


title: O-149:T2


title: O-078:T2


title: O-061:T2


title: O-132:T2


title: O-045:T2


title: J-004:T2


title: O-046:T2


title: F-006:T2


title: O-028:T2


title: O-149:T1


title: O-132:T1


title: O-114:T1


title: O-095:T1


title: O-012:T1


title: B-005:T2


title: O-045:T1


title: F-006:T1


title: O-078:T1


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title: O-061:T1


title: O-148:T2


title: O-115:T1


title: O-131:T2


title: O-113:T2


title: O-094:T2


title: O-077:T2


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title: O-011:T2


title: J-003:T2


title: O-043:T2


title: O-027:T2


title: B-004:T2


title: O-148:T1


title: O-113:T1


title: O-060:T1


title: O-027:T1


title: O-043:T1


title: O-077:T1


title: O-011:T1


title: O-094:T1


title: B-005:T1


title: F-005:T1


title: O-147:T2


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title: O-130:T2


title: B-004:T1


title: O-093:T2


title: O-059:T2


title: O-010:T2


title: F-005:T2


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title: O-076:T2


title: O-026:T2


title: O-147:T1


title: O-093:T1


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title: O-076:T1


title: O-059:T1


title: O-131:T1


title: O-130:T1


title: O-042:T1


title: J-003:T1


title: E-007:T2


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title: J-002:T1


title: B-003:T1


title: O-010:T1


title: O-111:T2


title: O-025:T2


title: O-092:T2


title: O-041:T2


title: J-001:T2


title: O-042:T2


title: O-058:T2


title: O-112:T1


title: E-007:T1


title: O-111:T1


title: B-002:T2


title: O-092:T1


title: O-075:T1


title: O-058:T1


title: O-129:T1


title: O-041:T1


title: O-009:T1


title: J-001:T1


title: B-002:T1


title: F-003:T1


title: O-129:T2


title: O-127:T2


title: O-109:T2


title: O-073:T2


title: O-057:T2


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title: O-075:T2


title: O-024:T2


title: O-091:T2


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title: B-001:T2


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title: E-005:T1


title: O-144:T2


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title: O-008:T1


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title: O-073:T1


title: O-126:T2


title: O-056:T2


title: O-145:T2


title: E-004:T2


title: A-010:T2


title: O-144:T1


title: O-127:T1


title: O-145:T1


title: O-107:T1


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title: O-039:T1


title: O-126:T1


title: O-023:T1


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title: O-038:T1


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title: E-006:T1


title: O-006:T1


title: O-142:T2


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title: O-124:T2


title: O-105:T2


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title: O-142:T1


title: O-105:T1


title: O-054:T1


title: O-087:T1


title: O-124:T1


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title: O-037:T1


title: O-021:T1


title: O-141:T2


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title: O-020:T2


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title: D-002:T2


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title: O-004:T1


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title: O-047:T2


title: E23_KO_Unstim_Total_BioRep_4

city: Rehovot

first: Ivo

last: Spiegel

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

data_processing:
Basecall and quality scoring was performed by the RTA software, version 2.11.3.0
Sequenced reads were trimmed for adaptor sequence using Cutadapt v1.18 and mapped to the mm10 genome using STAR version 2.5.3a.
Reads in genes (intronic and exonic together) were counted using Homer v4.9.1.
Assembly: mm10
Supplementary files format and content: .csv files include raw read counts for every gene in the sample

molecule: nuclear RNA

source_name: Mouse Visual Cortex

growth_protocol: Animals were standard housed until p55-60

extract_protocol:
A nuclear suspension was prepared from frozen visual cortices and subsequently nuclei were FACS sorted directly into a lysis buffer.
Libraries were prepared based on Meso-Seq protocol. Briefly, 50-100 nuclei were collected by FACS directly into 2.03 µl lysis buffer (0.2% Triton X-100 in ddW) supplemented with dNTPs (2mM each), SMART-dT30VN primers (1mM), ERCC (1:1.25x107), and RNAse inhibitor. RT was performed directly on isolated nuclei, followed by PCR-amplification (17 cycles). RNA is cleaned using Agencourt Ampure XP beads (Beckman Coulter) and cDNA libraries were generated using Nextera XT (Illumina).

treatment_protocol: At P55-60 animals were injected with one of the above AAVs in the visual cortex and were put in dark housing 3 days later for 10-12 days. Visual cortices were harvested in the dark or after 1hr of re-exposure to light and the tissue was stored in -80C

value: Mouse Visual Cortex

tag: Sex

value: female

value: Igf1-E23 fl/fl  x VIP flp/wt

value: 10-12 days dark housed

tag: aav injection

value: Total nuclei


title: O-031:T2

value: Severe acute respiratory syndrome coronavirus 2

value: Blood

value: PBMC


title: E23_KO_Unstim_VIP_BioRep_3

value: male

value: VIP nuclei


title: E23_KO_Unstim_Total_BioRep_2


title: E23_KO_Unstim_VIP_BioRep_2


title: E23_KO_Unstim_Total_BioRep_3


title: E23_KO_Unstim_VIP_BioRep_1


title: E23_KO_Stim_VIP_BioRep_4

value: 10-12 days dark housed + 1 hr light stimulation


title: E23_KO_Unstim_Total_BioRep_1


title: O-134:T2


title: E23_KO_Stim_VIP_BioRep_3


title: No_aav_VIP__BioRep_2

value: m

value: INTACT wt/ki x VIP Cre wt/ki

value: 10 days dark housed

value: VIP


title: E23_KO_Stim_Total_BioRep_3


title: E23_KO_Stim_Total_BioRep_4


title: No_aav_All_nuclei__BioRep_3


title: No_aav_VIP__BioRep_1


title: No_aav_All_nuclei__BioRep_1


title: No_aav_All_nuclei__BioRep_2


title: Kir21_Mutant_VIP_Trans_BioRep_9

tag: transduced

value: Transduced (i.e. infected)


title: E23_KO_Unstim_VIP_BioRep_4


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_9

value: Non Transduced (i.e. non infected)


title: Kir21_Mutant_Neurons_Trans_BioRep_9

value: Mouse Visual Cortex

value: Neurons


title: E23_KO_Stim_VIP_BioRep_1

value: female

value: Igf1-E23 fl/fl  x VIP flp/wt


title: E23_KO_Stim_VIP_BioRep_2


title: Kir21_Mutant_VIP_Non_Trans_BioRep_9


title: E23_KO_Stim_Total_BioRep_1

value: Total nuclei


title: Kir21_Mutant_VIP_Trans_BioRep_8


title: E23_KO_Stim_Total_BioRep_2


title: Kir21_Mutant_VIP_Non_Trans_BioRep_8


title: Kir21_Mutant_Neurons_Trans_BioRep_8


title: No_aav_VIP__BioRep_3


title: Kir21_Mutant_VIP_Non_Trans_BioRep_7


title: E23_Ctrl_Unstim_Total_BioRep_4

value: 10-12 days dark housed


title: E23_Ctrl_Unstim_VIP_BioRep_4


title: Kir21_Mutant_Neurons_Trans_BioRep_7


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_8


title: E23_Ctrl_Unstim_VIP_BioRep_2


title: E23_Ctrl_Unstim_Total_BioRep_3


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_7


title: Kir21_Mutant_VIP_Non_Trans_BioRep_6

value: f


title: E23_Ctrl_Unstim_Total_BioRep_2


title: E23_Ctrl_Unstim_VIP_BioRep_1


title: E23_Ctrl_Stim_VIP_BioRep_4


title: H3K27Ac, ab4729, MGE, Unstimulated, BioRep 1

description: 50bp reads

data_processing:
Demultiplexed raw fastq files were obtained from BGI China
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Cutadapt v1.18, discarding reads left with < 36 bp.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.3.3 with default settings.
Broad peaks were called uing MACS3 v3.0.0a7 with the significance cut-off q-value <=0.05.
Assembly: bigWig files were generated from BAM files using bamCoverage from  deepTools v3.4.3 with a binsize of 3 and smoothing 20. Score represents the raw read coverage of DNA fragments at a given genomic coordinate. broadPeak files were generated using MACS3 v3.0.0a7 with the significance cut-off q-value <=0.05.
Supplementary files format and content: mm10
Supplementary files format and content: bigWig, broadPeak

source_name: E16 mouse embryos

growth_protocol: Neurobasal, 2% B27 (Invitrogen), 1mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Forty million cortical neurons were fixed with 1% formaldehyde for 10 minutes at RT followed by quenching and nuclei isolation. The chromatin was then sonicated using Misonix 3000 (Misonix) to obtain fragments of 200 bp to 2 kb and incubated with the H3K27Ac antibody (Abcam, #ab4729) for immunoprecipitation.
Purified immunoprecipitated DNA was sent to BGI China for library construction and sequencing.

treatment_protocol: Neurons at DIV6 were silenced with 1µM TTX and 100µM D-AP5 overnight. At DIV7 neurons were either stimulated for 2hrs with 55mM KCl or left untreated.

value: E16 mouse embryos

value: Primary cortical neurons

value: Unstimulated

tag: chip antibody

value: H3K27Ac (Abcam, #ab4729)


title: H3K27Ac, ab4729, MGE, Unstimulated, BioRep 2

description: 50bp reads


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_6


title: E23_Ctrl_Stim_Total_BioRep_4

value: 10-12 days dark housed + 1 hr light stimulation


title: Kir21_Mutant_VIP_Trans_BioRep_5

value: INTACT wt/ki x VIP Cre wt/ki


title: E23_Ctrl_Unstim_Total_BioRep_1


title: E23_Ctrl_Stim_VIP_BioRep_3

value: male

value: VIP nuclei


title: Kir21_Mutant_VIP_Non_Trans_BioRep_5

value: 10 days dark housed

value: VIP


title: Kir21_Mutant_Neurons_Trans_BioRep_5

value: Mouse Visual Cortex

value: Transduced (i.e. infected)


title: Kir21_Mutant_VIP_Trans_BioRep_7

value: m


title: E23_Ctrl_Stim_Total_BioRep_3

value: Igf1-E23 fl/fl  x VIP flp/wt


title: H3K27Ac, ab4729, MGE, KCl, BioRep 2

description: 50bp reads

value: 2hr KCl stimulation


title: H3K27Ac, ab4729, MGE, KCl, BioRep 1

description: 50bp reads


title: E23_Ctrl_Stim_VIP_BioRep_2


title: E23_Ctrl_Unstim_VIP_BioRep_3

value: 10-12 days dark housed


title: H3K27Ac, ab4729, E14CTX, Unstimulated, BioRep 2

description: 50bp reads


title: Kir21_Mutant_VIP_Trans_BioRep_6

value: f


title: Kir21_Mutant_VIP_Trans_BioRep_4


title: A-001:T1

value: day 0

value: Severe acute respiratory syndrome coronavirus 2

value: Blood

value: PBMC


title: Kir21_Mutant_Neurons_Trans_BioRep_6

value: Neurons


title: Kir21_Mutant_VIP_Non_Trans_BioRep_4

value: INTACT wt/ki x VIP Cre wt/ki

value: Non Transduced (i.e. non infected)


title: H3K27Ac, ab4729, E14CTX, Unstimulated, BioRep 1

description: 50bp reads

value: E16 mouse embryos

value: Primary cortical neurons

value: Unstimulated

value: H3K27Ac (Abcam, #ab4729)


title: H3K27Ac, ab4729, E14CTX, KCl, BioRep 2

description: 50bp reads


title: E23_Ctrl_Stim_Total_BioRep_2

value: Mouse Visual Cortex

value: male

value: 10-12 days dark housed + 1 hr light stimulation

value: Total nuclei


title: E23_Ctrl_Stim_VIP_BioRep_1

value: female

value: Igf1-E23 fl/fl  x VIP flp/wt

value: VIP nuclei


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_4

value: f

value: 10 days dark housed


title: H3K27Ac, ab4729, E14CTX, KCl, BioRep 1

description: 50bp reads

value: 2hr KCl stimulation


title: E123_KO_Unstim_Total_BioRep_3

value: Igf1-E123 fl/fl  x VIP flp/wt

value: 10-12 days dark housed


title: E123_KO_Unstim_VIP_BioRep_3


title: E123_KO_Unstim_VIP_BioRep_2


title: Kir21_Mutant_VIP_Trans_BioRep_3

value: INTACT wt/ki x VIP Cre wt/ki

value: Transduced (i.e. infected)

value: VIP


title: Kir21_Mutant_VIP_Non_Trans_BioRep_3

value: Non Transduced (i.e. non infected)


title: E123_KO_Unstim_Total_BioRep_2


title: Kir21_Mutant_Neurons_Trans_BioRep_3

value: Neurons


title: E123_KO_Unstim_VIP_BioRep_1

value: Mouse Visual Cortex


title: E123_KO_Unstim_Total_BioRep_1


title: Kir21_Mutant_VIP_Trans_BioRep_2

value: m


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_3


title: Kir21_Mutant_Neurons_Trans_BioRep_2


title: E123_KO_Stim_VIP_BioRep_4

value: 10-12 days dark housed + 1 hr light stimulation


title: Kir21_Mutant_VIP_Non_Trans_BioRep_2


title: E123_KO_Stim_Total_BioRep_4

value: Total nuclei


title: Kir21_Mutant_Neurons_Trans_BioRep_4


title: E123_KO_Stim_VIP_BioRep_3

value: female


title: E123_KO_Stim_Total_BioRep_3


title: Kir21_Mutant_VIP_Trans_BioRep_1


title: E23_Ctrl_Stim_Total_BioRep_1

value: Igf1-E23 fl/fl  x VIP flp/wt


title: Kir21_Mutant_VIP_Non_Trans_BioRep_1


title: E123_KO_Stim_VIP_BioRep_2

value: male

value: VIP nuclei


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_1

value: 10 days dark housed


title: E123_KO_Stim_Total_BioRep_2


title: E123_KO_Stim_VIP_BioRep_1


title: Kir21_VIP_Trans_BioRep_10


title: E123_KO_Stim_Total_BioRep_1


title: Kir21_VIP_Non_Trans_BioRep_10


title: Kir21_All_nuclei_Non_Trans_BioRep_10


title: E123_Ctrl_Unstim_Total_BioRep_4


title: Kir21_VIP_Trans_BioRep_9


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_2


title: E123_Ctrl_Unstim_Total_BioRep_3


title: E123_Ctrl_Unstim_VIP_BioRep_2


title: Kir21_All_nuclei_Non_Trans_BioRep_9


title: E123_Ctrl_Unstim_Total_BioRep_2


title: Kir21_VIP_Trans_BioRep_8


title: E123_Ctrl_Unstim_Total_BioRep_1


title: Kir21_Neurons_Trans_BioRep_8

value: f


title: E123_Ctrl_Unstim_VIP_BioRep_1

value: Igf1-E123 fl/fl  x VIP flp/wt


title: Kir21_VIP_Non_Trans_BioRep_8


title: Kir21_All_nuclei_Non_Trans_BioRep_8


title: Kir21_VIP_Non_Trans_BioRep_7


title: E123_Ctrl_Stim_Total_BioRep_3


title: E123_Ctrl_Stim_VIP_BioRep_3


title: E123_Ctrl_Stim_Total_BioRep_4


title: Kir21_Neurons_Trans_BioRep_10


title: Kir21_VIP_Trans_BioRep_7


title: E123_Ctrl_Stim_VIP_BioRep_2


title: E123_Ctrl_Unstim_VIP_BioRep_4

value: 10-12 days dark housed


title: E123_Ctrl_Unstim_VIP_BioRep_3


title: Kir21_VIP_Trans_BioRep_6

value: INTACT wt/ki x VIP Cre wt/ki


title: E123_Ctrl_Stim_Total_BioRep_2


title: Kir21_Neurons_Trans_BioRep_9

value: Transduced (i.e. infected)


title: Kir21_All_nuclei_Non_Trans_BioRep_7


title: Kir21_VIP_Non_Trans_BioRep_6

value: VIP


title: Kir21_VIP_Non_Trans_BioRep_9

value: Non Transduced (i.e. non infected)


title: E1_KO_Unstim_VIP_BioRep_5

value: Igf1-E1 fl/fl  x VIP flp/wt


title: E123_Ctrl_Stim_Total_BioRep_1

value: Mouse Visual Cortex


title: Kir21_All_nuclei_Non_Trans_BioRep_6


title: E123_Ctrl_Stim_VIP_BioRep_4


title: E1_KO_Unstim_Total_BioRep_5


title: Kir21_Neurons_Trans_BioRep_6

value: Neurons


title: Kir21_Mutant_All_nuclei_Non_Trans_BioRep_5


title: E1_KO_Unstim_VIP_BioRep_4


title: E1_KO_Unstim_Total_BioRep_4


title: Kir21_VIP_Trans_BioRep_5


title: E1_KO_Unstim_VIP_BioRep_3


title: Kir21_All_nuclei_Non_Trans_BioRep_5


title: Kir21_Neurons_Trans_BioRep_7


title: Kir21_Neurons_Trans_BioRep_5


title: Kir21_VIP_Trans_BioRep_4

value: m


title: Kir21_Neurons_Trans_BioRep_4


title: E1_KO_Unstim_VIP_BioRep_2


title: E1_KO_Unstim_Total_BioRep_2

value: Total nuclei


title: E123_Ctrl_Stim_VIP_BioRep_1

value: 10-12 days dark housed + 1 hr light stimulation


title: Kir21_VIP_Non_Trans_BioRep_4


title: E1_KO_Unstim_VIP_BioRep_1


title: Kir21_VIP_Non_Trans_BioRep_5


title: Kir21_Neurons_Trans_BioRep_3


title: Kir21_All_nuclei_Non_Trans_BioRep_4


title: E1_KO_Unstim_Total_BioRep_1


title: E1_KO_Stim_VIP_BioRep_4


title: E1_KO_Stim_Total_BioRep_4


title: Kir21_VIP_Non_Trans_BioRep_3


title: Kir21_All_nuclei_Non_Trans_BioRep_3


title: E1_KO_Stim_VIP_BioRep_3

value: female


title: E1_KO_Stim_Total_BioRep_3


title: Kir21_VIP_Trans_BioRep_2


title: Kir21_VIP_Non_Trans_BioRep_2


title: E1_KO_Stim_Total_BioRep_2


title: E1_KO_Stim_VIP_BioRep_2


title: E1_KO_Stim_VIP_BioRep_1


title: Kir21_VIP_Trans_BioRep_1


title: Kir21_VIP_Trans_BioRep_3


title: E1_KO_Unstim_Total_BioRep_3

value: male


title: E1_KO_Stim_Total_BioRep_1


title: Kir21_All_nuclei_Non_Trans_BioRep_2


title: E1_Ctrl_Unstim_Total_BioRep_2


title: Kir21_VIP_Non_Trans_BioRep_1


title: E1_Ctrl_Unstim_VIP_BioRep_2

value: VIP nuclei


title: E1_Ctrl_Stim_VIP_BioRep_5


title: E1_Ctrl_Unstim_VIP_BioRep_1


title: E1_Ctrl_Stim_VIP_BioRep_4


title: E1_Ctrl_Unstim_Total_BioRep_3


title: Kir21_All_nuclei_Non_Trans_BioRep_1

value: 10 days dark housed


title: E1_Ctrl_Unstim_Total_BioRep_1


title: E1_Ctrl_Unstim_VIP_BioRep_3


title: E1_Ctrl_Stim_Total_BioRep_4


title: E1_Ctrl_Stim_Total_BioRep_5


title: E1_Ctrl_Stim_Total_BioRep_3


title: E1_Ctrl_Stim_VIP_BioRep_2


title: E1_Ctrl_Stim_VIP_BioRep_3


title: E1_Ctrl_Stim_VIP_BioRep_1


title: E1_Ctrl_Stim_Total_BioRep_1


title: 69-CR-TT

status: Public on Jun 23 2023

city: Duarte

first: Yanhong

last: Shi

address: 1500 E Duarte Road

institute: City of Hope

data_processing:
Illumina bcl2fastq v2.18.0.12 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using STAR 2.6.0.a with default parameters
The HTSeq software (v.0.6.0) was applied to generate the count matrix, with default parameters. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using EdgeR 3.28.1.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: iPSC-derived astrocytes

growth_protocol: Astrocytes were cultured on astrocytes medium containing 1X N2, 1X B27, EGF, FGF. For final maturation of astrocytes, CNTF was supplemented to medium containing 1X N2, 1X B27, 1X NEAA and 1X Glutamax, for 1 week.

extract_protocol: Total RNA was extracted from cultured cells using Trizol

value: iPSC-derived astrocytes


title: 18-CT


title: 69-CR-CC


title: 18-CC


title: Patient12 meningioma

status: Public on Jun 22 2023

city: Los Angeles

first: Michelle

middle: Ariana

last: Wedemeyer

state: California

address: 1200 N State St, Suite 3300

department: Neurosurgery

institute: University of Southern California

description:
meningioma
12M

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:
Copy number variant detection: Raw IDAT files were imported with the R Bioconductor package minfi and the preprocessIllumina normalization function was used to generate a GenomicRatioSet object for input into conumee.  The 12 dura samples were used as controls.  To generate ratios for meningioma-specific detail lists, the list of oncogenes included with the conumee package was appended to include genes previously identified as mutated in meningiomas, components of the BAF (SWI/SNF) complex, and chromosomal regions that have been associated with aggressive behavior in meningiomas.  A ratio cutoff of +/-0.25 to call amplifications (>0.25) or deletions (<0.25). Additionally, tumor/dura ratios generated for the loci included in the detail list were used with a cutoff of +/-0.25 to call loci as amplified (>+0.25), neutral (-0.25 to +0.25), or deleted (<-0.25) using custom scripts written in R.  Methylation Analysis: Raw red/green IDAT files were imported into R using the package minfi to obtain beta-values and M-values after functional normalization.  Mapping to the hg38 genome build and general masking filtering criteria of Zhou et al., Nucleic Acids Research 2017 were used for all downstream analysis. To determine the fraction of methylated probes in the promoter region of each gene, probes mapping within +/-2kb of transcription start sites (TSS) of all genes in the the GENCODE v29 primary assembly were identified. and called as methylated or hemi-methylated (β value >=0.3) or unmethylated (β value <0.3).  The percentage of methylated probes in each promoter region was calculated as (#methylated probes)/(total #probes)*100.
Normalized beta-values (functional normalization)

label: Cy5 and Cy3

source_name: meningioma

label_protocol: Purified DNA underwent bisulfite conversion using Zymo EZ DNA Methylation kit (Cat No.: D5001) then labeled using standard Illumina protocol.

extract_protocol: Tumor/dura samples were obtained at the time of surgery.  DNA was extracted using Qiagen DNeasy Blood & Tissue Kit (Cat No./ID: 69506).

value: FEMALE

tag: who grade

value: I

tag: reoperation

value: Unknown

tag: progression


title: Patient11 dura

description:
dura
11D

source_name: dura

value: dura

value: No


title: Patient11 meningioma

description:
meningioma
11M


title: Patient12 dura

description:
dura
12D


title: Patient10 meningioma

description:
meningioma
10M


title: Patient9 meningioma

description:
meningioma
9M

value: MALE


title: Patient9 dura

description:
dura
9D


title: Patient10 dura

description:
dura
10D


title: Patient8 meningioma

description:
meningioma
8M


title: Patient8 dura

description:
dura
8D


title: Patient7 meningioma

description:
meningioma
7M

value: II

value: Yes


title: Patient7 dura

description:
dura
7D


title: Patient4 meningioma

description:
meningioma
4M


title: Patient5 dura

description:
dura
5D


title: Patient6 meningioma

description:
meningioma
6M


title: Patient3 meningioma

description:
meningioma
3M


title: Patient5 meningioma

description:
meningioma
5M


title: Patient6 dura

description:
dura
6D


title: Patient4 dura

description:
dura
4D


title: Patient3 dura

description:
dura
3D


title: E1_Ctrl_Stim_Total_BioRep_2

value: Mouse Visual Cortex

value: Igf1-E1 fl/fl  x VIP flp/wt


title: Patient2 dura

description:
dura
2D


title: Patient1 meningioma

description:
meningioma
1M


title: Patient2 meningioma

description:
meningioma
2M


title: Patient1 dura

description:
dura
1D


title: sos2-2_salt_rep1

status: Public on Jun 21 2023

city: Beijing

first: Jingrui

last: Li

address: Yuanmingyuan West Road No.2

institute: China Agricultural Universtiy

data_processing:
Kallisto_0.46.2 was used for quantification. TPM values were calculated for each transcript of genes.
Differential expression analysis of genes was performed by Sleuth_0.30.0
Assembly: Tair10
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Arabidopsis thaliana

source_name: root tip

growth_protocol: The sterilized seeds of wild-type and sos2-2 were sown on 1/2 MS medium containing 1% sucrose and 1% agar. Seeds were kept at 4 ℃ for 2 days and then transferred into a growth chamber under constant illumination at 22 ℃ for 5-6 days.

extract_protocol:
RNA was extracted by using TRIzol reagent (Invitrogen).
RNA-seq libraries were constructed by using Illumina RNAseq kit (RS-122-2201).

treatment_protocol: Six-day-old seedlings of the wild type and sos2-2 mutant were treated in liquid 1/2 MS medium containing 100 mM NaCl for 12 hours.

value: root tip

value: sos2-2 mutant

value: 100 mM NaCl treatment


title: sos2-2_salt_rep3


title: sos2-2_salt_rep2


title: WT_salt_rep3

value: WT


title: Rep E12.5e1 TEPC, scRNAseq SmartSeq2

city: Edinburgh

first: Catherine

middle: Clare

last: Blackburn

address: IRR North, 5 Little France Drive

department: School of Biological Sciences

institute: University of Edinburgh

library_source: transcriptomic single cell

data_processing:
Preprocessing of the FASTQ files was performed using the BD: Precise Whole Transcriptome Assay Analysis Pipeline v2.0. This pipeline performs all required steps to demultiplex, align, and quantitate sequencing reads from BD™ Precise Whole Transcriptome Assay. After performing a quality control assessment using FastQC, the pipeline filters and demultiplexes sequencing reads based on the sequence of the 8 base sample barcode. It aligns reads from each sample to the transcriptome using STAR, with feature counting by the union rules of HTSeq-count. The initial quantification is performed by counting the unique molecular indices (MI) mapped to each feature. Lastly, the pipeline uses two error correction algorithms to remove MI errors. In brief, MI errors that are derived from sequencing base calls and PCR substitution errors are identified and adjusted to a single MI barcode using Recursive Substitution Error Correction™ (RSEC). Subsequently, MI errors that are derived from library preparation steps or sequencing base deletion errors are adjusted using Distribution-Based Error Correction™ (DBEC).
Assembly: GRCm38.p5
Supplementary files format and content: 7Bridges PDF Summary Report =  Provides an overview of each sequenced library.
Supplementary files format and content: 7Bridges DBEC Molecular Index Mapping report =  Reports the number of unique molecular indices seen associated with each individual transcript per well.
Supplementary files format and content: 7Bridges DBEC Read Mapping report =  Reports the number of reads that mapped to a given transcript in each of 96 wells.
Supplementary files format and content: 7Bridges Sample Barcodes (Sample Index) report =  Summarizes the number of reads that have been assigned to each well.
Supplementary files format and content: 7Bridges Raw Molecular index counts =  Reports the raw counts for each unique molecular index detected for each gene in each well.
Supplementary files format and content: 7Bridges Raw read counts =  Reports raw read counts for each gene in each well.
Supplementary files format and content: 7Bridges FastQC Reports =  Provides metrics to assess overall quality of the input sequencing reads.
Supplementary files format and content: 7Bridges RSEC Molecular Index Counts =  Reports RSEC adjusted MI counts for each gene in each well.
Supplementary files format and content: 7Bridges Status Report =  Reports sequencing depth metrics according to gene and well. The summary is in the MI_Detection column in the DBEC Molecular Index Mapping report.

molecule: polyA RNA

source_name: thymus

extract_protocol:
Individual EPCAM+PLET1+ cells from E10.5 or E12.5 primordia were sorted into 96-well BD Precise WTA Single Cell Encoding Plates. The plates were sealed and stored at -80oC until library preparation.  Four plates (376 cells) were collected per timepoint.
Reverse transcription was performed in the presence of ERCC RNA control. The 96 samples from each plate were then pooled and purified with Agencourt® AMPure® XP magnetic beads (clean-up step). Second strand synthesis was carried out and the resulting products cleaned up. Following adaptor ligation and clean-up, ligation products were PCR amplified for 18 cycles overnight, and all subsequent steps were performed in a separate post-amplification area.  The amplified products were cleaned up and quantified using Qubit dsDNA HS Assay. 50ng of the products then underwent random primer extension and 12 cycles of further amplification. The amplified libraries were cleaned up and quantified with Qubit assay. The libraries were stored at -80oC until sequencing. The libraries were sequenced on Illumina MiSeq at the Wellcome Centre for Human Genetics in Oxford within 6 months of preparation.

value: thymus

value: thymic epithelial progenitors

value: wild type

tag: developmental stage

value: E12.5 primordia


title: Rep E12.5d TEPC, scRNAseq SmartSeq2

tag: cell type


title: E12.5e TEPC, scRNAseq SmartSeq2


title: Rep E12.5a TEPC, scRNAseq SmartSeq2


title: Rep E12.5c TEPC, scRNAseq SmartSeq2


title: WT_salt_rep1

tag: treatment


title: E12.5c TEPC, scRNAseq SmartSeq2

tag: genotype


title: E10.5c TEPC, scRNAseq SmartSeq2

value: E10.5 primordia


title: Si-LIPG-3

status: Public on Jun 17 2023

city: chengdu

first: Yinggui

last: Wang

state: sichuan

address: 2-31, Jingwenyuan, South District, Airport Campus, Southwest University for Nationalities, Chengdu, Sichuan

institute: Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization Key Laboratory of Sichuan Province

data_processing:
fastp
Sequence readswere trimmed for adaptor sequnce/low-quality sequence using fastp
Trimmed sequnence reads wrere mapped to ARS1 using hisat2 samtools
The transcript was assembled using htseq-count.
Assembly: ARS1
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Capra hircus

source_name: goat intramuscular preadipocyte

growth_protocol: Goat intramuscular precursor adipocytes were cultured using DMEM medium (containing 10% fetal bovine serum, 1% double antibody) at 37°C and 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel.
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp.

treatment_protocol: The negative control groups was treated with negative control interfering RNA (NC) and the experimental groups treated cells with interfering RNA that silences LIPG (si-LIPG).

value: goat intramuscular preadipocyte

value: LIPG Knock down

value: Adipose differentiation


title: E10.5b TEPC, scRNAseq SmartSeq2


title: Si-LIPG-2


title: E12.5b TEPC, scRNAseq SmartSeq2


title: E10.5a TEPC, scRNAseq SmartSeq2


title: E12.5d TEPC, scRNAseq SmartSeq2


title: E10.5d TEPC, scRNAseq SmartSeq2


title: Si-LIPG-1


title: WT_salt_rep2


title: NC-1


title: E12.5a TEPC, scRNAseq SmartSeq2


title: NC-2


title: mouse tibia treated with Titanium particles and I-OG, rep3

city: Erlangen

first: Xi

last: Chen

address: Universitätsstraße 42-44, 91054 Erlangen

department: Department of Internal Medicine 3 - Rheumatology and Immunology

institute: Friedrich-Alexander University Erlangen-Nuremberg (FAU) and Universitätsklinikum Erlangen

data_processing:
Quantification of Gene Abundance.The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Principal component analysis (PCA) was performed with R package gmodels (http://www.r- project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Gene Ontology (GO) is an international standardized gene functional classification system which offers a dynamic-updated controlled vocabulary and a strictly defined concept to comprehensively describe properties of genes and their products in any organism. GO has three ontologies: molecular function, cellular component and biological process. The basic unit of GO is GO-term. Each GO-term belongs to a type of ontology.
Protein-Protein interaction network was identified using String v10[15], which determined genes as nodes and interaction as lines in a network. The network file was visualized using Cytoscape (v3.7.1)[16] software to present a core and hub gene biological interact.
Assembly: Filtering of Clean Reads.Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp [1] (version 0.18.0). The parameters were as follows:1) removing reads containing adapters;2) removing reads containing more than 10% of unknown nucleotides (N);3) removing low quality reads containing more than 50% of low quality bases.
Supplementary files format and content: all.genes.expression.annot.xls

source_name: tibia

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads.
Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina(NEB #7530,New England Biolabs, Ipswich, MA, USA).The purified double-stranded cDNA fragments were end repaired, A base added, and ligated to Illumina sequencing adapters.The ligation reaction was purified with the AMPure XP Beads(1.0X).Ligated fragments were subjected to size selection by agarose gel electrophoresis and polymerase chain reaction (PCR) amplified.The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

value: tibia

value: Titanium particles and I-OG


title: mouse tibia treated with Titanium particles and I-OG, rep1


title: Rep E10.5a TEPC, scRNAseq SmartSeq2


title: mouse tibia treated with Titanium particles and I-OG, rep2


title: mouse tibia treated with Titanium particles, rep1

value: treated with Titanium particles


title: Rep E10.5d2 TEPC, scRNAseq SmartSeq2


title: Rep E10.5c TEPC, scRNAseq SmartSeq2


title: Rep E10.5b TEPC, scRNAseq SmartSeq2


title: mouse tibia without treatment, rep3

value: without treatment


title: Rep E10.5d1 TEPC, scRNAseq SmartSeq2


title: RNA_RhM22_Post Kleptose_CD8M

status: Public on Jun 12 2023

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID

description: 9-16_RhM22_Post Kleptose_CD8M

data_processing:
RNA-seq samples were sequenced as 101bp paired-end libraries on a Novaseq S4. All samples had over 120 million reads.
Reads were trimmed using Cutadapt (v1.18) and aligned to the Mmul_10/RheMac10 reference genome and Gencode (Ensembl release 108) using STAR (v2.7.6a) in 2-pass basic mode. Expression levels were quantified with RSEM (v1.3.3) before being converted into FPKM values.
Assembly: RheMac10
Supplementary files format and content: Kleptose.RawCountFile_rsemgenes.txt: tab-delimited raw counts for each sample
Supplementary files format and content: Kleptose.FPKM.all_samples.txt: tab-delimited FPKM values for each sample

organism: Macaca mulatta

source_name: peripheral blood

extract_protocol:
RNA was extracted from pelleted cells resuspended in Buffer RLT Plus (Qiagen) with 1% BME. RNA was extracted using RNeasy Micro kit (Qiagen).
SMART-Seq® v4 Ultra® Low Input RNA was used for mRNA library preparation.

treatment_protocol: 2-hydroxypropyl-beta-cyclodextrin-treated animals received 15% (w/w) KleptoseTM HBP parenteral grade (Roquette #346111109D) subcutaneously at 1 ml/kg/day for up to 120 days.

value: peripheral blood

value: CD8+ memory T cell


title: mouse tibia treated with Titanium particles, rep2


title: mouse tibia without treatment, rep1


title: NC-3


title: RNA_RhM22_Post Kleptose_CD4M

description: 9-14_RhM22_Post Kleptose_CD4M

value: CD4+ memory T cell


title: RNA_RhM22_Pre Kleptose_CD8M

description: 9-12_RhM22_Pre Kleptose_CD8M


title: RNA_RhM22_Post Kleptose_CD4N

description: 9-13_RhM22_Post Kleptose_CD4N

value: CD4+ naive T cell


title: RNA_RhM22_Post Kleptose_CD8N

description: 9-15_RhM22_Post Kleptose_CD8N

value: CD8+ naive T cell


title: RNA_RhDBCb_Post Kleptose_CD4M

description: 9-6_RhDBCb_Post Kleptose_CD4M


title: RNA_RhM22_Pre Kleptose_CD4N

description: 9-9_RhM22_Pre Kleptose_CD4N


title: RNA_RhM22_Pre Kleptose_CD4M

description: 9-10_RhM22_Pre Kleptose_CD4M


title: RNA_RhDBCb_Post Kleptose_CD8M

description: 9-8_RhDBCb_Post Kleptose_CD8M


title: RNA_RhDBCb_Post Kleptose_CD4N

description: 9-5_RhDBCb_Post Kleptose_CD4N


title: RNA_RhDBCb_Pre Kleptose_CD8M

description: 9-4_RhDBCb_Pre Kleptose_CD8M


title: RNA_RhDBCb_Pre Kleptose_CD4N

description: 9-1_RhDBCb_Pre Kleptose_CD4N


title: RNA_RhDBCb_Pre Kleptose_CD4M

description: 9-2_RhDBCb_Pre Kleptose_CD4M


title: RhM22_Post Kleptose_CD8N

data_processing:
ATAC-seq samples were sequenced as 151bp paired-end libraries on a Novaseq S4. All samples had over 60 million reads.
Samples were trimmed for adapters using Cutadapt v 1.18 before alignment. The trimmed reads were aligned to the RheMac10 reference using Bowtie2 v2.3.4.1 with flag -k 10.
The peaks were called using Genrich v0.6 with the following flags -j -y -r -v -d 150 -m 5 -e chrM,chrY.
Genrich-produced bedgraphs were normalized by library size (reads per million sequenced reads, RPM) for visualization.
Assembly: RheMac10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
10,000 sorted cells from each population were pelleted and resuspended in 2x Tagmentation Buffer (Illumina), 0.02% Digitonin, and 0.1% Tween-20, with Tagment DNA TDE1 Enzyme (Illumina) and incubating at 37°C for one hour.  The mix was then incubated with proteinase K for 30 minutes at 40°C.
High molecular weight DNA was removed with a 0.7x selection ratio of Agencourt AMPureXP beads (Beckman Coulter) and low molecular weight DNA was isolated from the remainder with a 1.2x selection ratio. Library amplification was performed with KAPA HiFi HotStart ReadyMix (KAPA) and i5 and i7 indexing primers (Nextera DNA CD Indexes) for 11-15 total cycles depending on the sample concentration reached after 5 cycles (KAPA Library Quantification kit). Library DNA was purified with a 1x selection ratio of AMPureXP beads. The final library was verified by High Sensitivity DNA Bioanalyzer (Agilent).


title: mouse tibia treated with Titanium particles, rep3


title: RhM22_Post Kleptose_CD4M


title: mouse tibia without treatment, rep2


title: RhM22_Pre Kleptose_CD8N


title: RhDBCb_Post Kleptose_CD8N


title: RhM22_Post Kleptose_CD4N


title: RhM22_Pre Kleptose_CD4M


title: RhDBCb_Post Kleptose_CD4N


title: RhDBCb_Post Kleptose_CD4M


title: RhDBCb_Post Kleptose_CD8M


title: RNA_RhM22_Pre Kleptose_CD8N

description: 9-11_RhM22_Pre Kleptose_CD8N


title: RhDBCb_Pre Kleptose_CD8M


title: RNA_RhDBCb_Pre Kleptose_CD8N

description: 9-3_RhDBCb_Pre Kleptose_CD8N


title: FM10 WM3623 melanoma cells, Split B, treatment with therapy drug 10 nM trametinib

status: Public on Jun 03 2023

city: Chicago

first: Yogesh

last: Goyal

state: IL

address: 303 E Superior St

institute: Northwestern University

description:
sequencing single-cell libraries
FM10_WM3623_Trametenib_SplitB

data_processing:
We adapted the cellranger v3.0.2 by 10X Genomics to map and align the reads from NextSeq sequencing run(s). Briefly, we downloaded the bcl counts and usedcellranger mkfastqto demultiplex raw base call files into library-specific FASTQ files. We aligned the FASTQ files to the hg19 human reference genome and extracted gene expression count matrices usingcellranger count, while also filtering and correcting cell identifiers and unique molecular identifiers (UMI) with default settings.
We then performed the downstream single-cell expression analysis in Seurat v3. Within each experimental sample, we removed genes that were present in less than three cells, as well as cells with less than or equal to 200 genes. We also filtered for mitochondrial gene fraction which was dependent on the cell type. For non-identically treated samples, we integrated them using scanorama, which may work better to integrate non-similar datasets and avoid over-clustering.
For each experiment, we used these integrated datasets to generate data dimensionality reductions by principal component analysis (PCA) and Uniform Manifold Approximation and Projection (UMAP), using 50 principal components for UMAP generation.
Assembly: hg19
Supplementary files format and content: *.matrix.mtx: Sparse gene expression matrix; rows are features/genes, columns are 10x barcodes (what we call "cellID")
Supplementary files format and content: *.barcodes.tsv: Barcodes
Supplementary files format and content: *.features.tsv: Features/genes

source_name: skin-derived

extract_protocol:
RNA was extracted as per the manufacter's protocol using a 10x Genomics v3 kit. We generated gel beads-in-emulsion (GEMs) using the 10X Chromium system and a Chromium Next GEM Single Cell 3' Reagent Kit v3.1 as per the manufecturer's protocol, aiming for 10,000 cells for recovery.
We used the 10X Genomics single-cell RNA-seq kit v3 to sequence cells. We resuspended the cells (targeting ~10,000 cells for recovery/ sample) in PBS and followed the protocol for the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 as per manufacturer directions (10X Genomics, Pleasanton, CA). Briefly, we generated gel beads-in-emulsion (GEMs) using the 10X Chromium system, and subsequently extracted and amplified (11 cycles) barcoded cDNA as per post-GEM RT-cleanup instructions. We then used a fraction of this amplified cDNA (25%) and proceeded with fragmentation, end-repair, poly A-tailing, adapter ligation, and 10X sample indexing per the manufacturer’s protocol.
We quantified libraries using the High Sensitivity dsDNA kit (Thermo Fisher Q32854) on Qubit 2.0 Fluorometer (Thermo Fisher Q32866) and Bioanalyzer 2100 (Agilent G2939BA) analysis prior to sequencing on a NextSeq 500 machine (Illumina) using 28 cycles for read 1, 55 cycles for read 2, and 8 cycles for i7 index. A subset of FateMap sequencing runs (NRAS melanoma samples and Metronomic therapy experiments), we used NextSeq 2000 (Illumina) using 26 cycles for read 1, 124 cycles for read 2, and 8 cycles for i7 index.

value: skin-derived

tag: cell line

value: Human melanoma cells

value: NRAS - Q61L

value: FM10 Split B, treatment with therapy drug 10 nM trametinib


title: GSC456 cells, DMSO-1

status: Public on Jun 10 2023

city: Wuhan

first: Wei

address: 13 Hangkong Road

institute: Huazhong University of Science and Technology Tongji Medical College

data_processing:
The raw reads were quality-controlled and trimmed using Fastp (v0.20.1) with default parameters.
The resulting Clean RNA-seq reads were aligned to the human reference genome (GRCh38) using Hisat2 (v2.2.1), sorted and indexed using Samtools (v1.14).
The number of reads (raw_counts) per gene was determined using featureCounts (v2.0.1)
Assembly: Homo sapiens
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

growth_protocol: GSCs were cultured in DMEM/F12 media supplemented with B27, 20 ng/ml EGF, and 20 ng/ml basic fibroblast growth factor. Cells were incubated at 37 °C in a humidified 5% (v:v) CO2 incubator.

extract_protocol:
Total RNA was isolated using the Trizol Reagent.
Three micrograms of RNA were used as input material for the RNA sample preparations. Sequencing libraries were generated according to the following steps. Firstly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in fragmentation buffer. First strand strand was synthesized by random hexamers, and the second cDNA strand was synthesized by adding buffer, dNTPs, RNase H and DNA polymerase I. Double stranded cDNA was repaired and A was added to the 3 'end. Hieff NGS® DNA Selection Beads were used for purification and fragment Selection. After purification and fragment selection, the products were amplified and enriched by PCR. Qubit was used for quantitative .  The target region library of the duplex was denatured, cycled, and digested to yield a single-stranded circular DNA. Single-stranded circular DNA is amplified by a rolling circle amplification (RCA), known as DNA nano balls (DNB). After library construction, Qubit was used for quantitative.

value: GBM stem cell

value: DMSO; control

tag: time

value: 12 hours


title: RhM22_Post Kleptose_CD8M

tag: tissue


title: RhDBCb_Pre Kleptose_CD8N


title: FM10 WM3623 melanoma cells, Split A, treatment with therapy drug 10 nM trametinib

description:
sequencing single-cell libraries
FM10_WM3623_Trametenib_SplitA

value: FM10 Split A, treatment with therapy drug 10 nM trametinib


title: RhDBCb_Pre Kleptose_CD4M


title: FM09 WM3451 melanoma cells, Split A, treatment with therapy drug 25 nM trametinib

description:
sequencing single-cell libraries
FM09_WM3451_Trametenib_SplitA

value: FM09 Split A, treatment with therapy drug 25 nM trametinib


title: Rep E12.5e2 TEPC, scRNAseq SmartSeq2

value: thymus

value: thymic epithelial progenitors

value: wild type

value: E12.5 primordia


title: FM09 WM3451 melanoma cells, Split B, treatment with therapy drug 25 nM trametinib

description:
sequencing single-cell libraries
FM09_WM3451_Trametenib_SplitB

value: FM09 Split B, treatment with therapy drug 25 nM trametinib


title: FM08 Split B, Primary melanocytes, no treatment

description:
sequencing single-cell libraries
FM08_PrimaryMelanocytes_SplitB

value: Human primary melanocytes

value: WT

value: FM08 Split B, No treatment, just cells expanded for a few generations


title: FM08 Split A, Primary melanocytes, no treatment

description:
sequencing single-cell libraries
FM08_PrimaryMelanocytes_SplitA

value: skin-derived

value: FM08 Split A, No treatment, just cells expanded for a few generations


title: FM07 WM989 A6-G3 melanoma cells, Split A, treatment with therapy drug 1uM vemurafenib -- continuously

description:
sequencing single-cell libraries
FM07_WM989_ContinuousDose_SplitA

value: Human melanoma cells

value: BRAF - V600E

value: FM07 Split A, treatment with therapy drug 1uM PLX (vemurafenib) -- continuously


title: RhDBCb_Pre Kleptose_CD4N

value: peripheral blood

value: CD4+ naive T cell


title: FM06 WM989 A6-G3 melanoma cells, Split B, Naïve

description:
sequencing single-cell libraries
FM06_Naive_SplitB

value: FM06 Split B, No treatment, just cells expanded for a few generations


title: FM07 WM989 A6-G3 melanoma cells, Split B, treatment with therapy drug 1uM PLX vemurafenib -- discontinuously in cycles

description:
sequencing single-cell libraries
FM07_WM989_DiscontinuousDose_SplitB

value: FM07 Split B, treatment with therapy drug 1uM PLX (vemurafenib) -- discontinuously in cycles


title: RhM22_Pre Kleptose_CD4N


title: RhM22_Pre Kleptose_CD8M

value: CD8+ memory T cell


title: FM06 WM989 A6-G3 melanoma cells, Split A, Naïve

description:
sequencing single-cell libraries
FM06_Naive_SplitA

value: FM06 Split A, No treatment, just cells expanded for a few generations


title: FM05 Split A1, treatment with therapy drug 250nM vemurafenib

description:
sequencing single-cell libraries
FM05_WM983B_250nMPLX_SplitA1

value: FM05 Split A1, treatment with therapy drug 250nM PLX (vemurafenib)


title: FM02 WM989 A6-G3 melanoma cells, Split D, treatment with combination therapy drug 5nM Trametenib and 100nM vemurafenib

description:
sequencing single-cell libraries
FM02_WM989_100nMPLX5nMTrametenib_SplitD

value: FM02 Split D, treatment with combination therapy drug 5nM Trametenib and 100nM PLX (vemurafenib)


title: FM04 MDA-MB-231-D4, Split B1, treatment with chemotherapy drug 1nM paclitaxel

description:
sequencing single-cell libraries
FM04_MDAMB231_BC18_SplitB1

source_name: breast; mammary gland

value: breast; mammary gland

value: Human breast adenocarcinoma

value: triple-negative (does not express HER2, estrogen, or progesterone)

value: FM04 Split B1, treatment with chemotherapy drug 1nM paclitaxel


title: FM03 WM989 A6-G3 melanoma cells, Split A, DMSO pre-treated, then treatment with therapy drug 1uM vemurafenib

description:
sequencing single-cell libraries
FM03_WM989_DMSO1uMPLX_SplitA

value: skin-derived

value: FM03 Split A, DMSO pre-treated, then treatment with therapy drug 1uM PLX (vemurafenib)


title: FM02 WM989 A6-G3 melanoma cells, Split B, treatment with therapy drug 100nM vemurafenib

description:
sequencing single-cell libraries
FM02_WM989_100nMPLX_SplitB

value: Human melanoma cells

value: FM02 Split B, treatment with therapy drug 100nM PLX (vemurafenib)


title: FM02 WM989 A6-G3 melanoma cells, Split C, treatment with therapy drug 5nM trametenib

description:
sequencing single-cell libraries
FM02_WM989_5nMTrametenib_SplitC

value: BRAF - V600E

value: FM02 Split C, treatment with therapy drug 5nM Trametenib


title: FM02 WM989 A6-G3 melanoma cells, Split A, treatment with therapy drug 1uM vemurafenib

description:
sequencing single-cell libraries
FM02_WM989_1uMPLX_SplitA

value: FM02 Split A, treatment with therapy drug 1uM PLX (vemurafenib)


title: FM04 MDA-MB-231-D4, Split B2, treatment with chemotherapy drug 1nM paclitaxel

description:
sequencing single-cell libraries
FM04_MDAMB231_BC18_SplitB2

value: FM04 Split B2, treatment with chemotherapy drug 1nM paclitaxel


title: FM01 WM989 A6-G3 melanoma cells, Split A, 1uM vemurafenib

description:
sequencing single-cell libraries
FM01_WM989_1uMPLX_SplitA

value: FM01 Split A, treatment with therapy drug 1uM PLX (vemurafenib)


title: FM01 WM989 A6-G3 melanoma cells, Split B, 1uM vemurafenib

description:
sequencing single-cell libraries
FM01_WM989_1uMPLX_SplitB

value: FM01 Split B, treatment with therapy drug 1uM PLX (vemurafenib)


title: 1-2-6dpi | 017 | Full ROI

status: Public on May 02 2023

city: Farmington

first: Carolyn

last: Paisie

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

description: Human_NGS_Whole_Transcriptome_Atlas_RNA_1

data_processing:
Human_NGS_Whole_Transcriptome_Atlas
QC with FASTQC and processed by the GeoMx NGS DnD Pipeline
Calculating counts according to NanoString, MAN-10133_03

source_name: primary human broncho-alveolar epithelia

growth_protocol: Pneumacult-Ex Plus Medium containing the ROCK inhibitor Y-27632 until confluence (8-10 days). ALI differentiation in Pneumacult-ALI Medium (STEMCELL) containing the ROCK inhibitor Y-27632 (5-7 days). Pneumacult-ALI Medium (STEMCELL) without ROCK inhibitor Y-27632 (~28 days) and removal of the media at apical side (air-lift).

treatment_protocol: Primary lung-organoid derived ALI was washed three times with PBS. Viruses were diluted in 1X PBS for a final concentration of 105PFU per ALI for SARS-CoV-2 infections and spread out on apical side. Control (Mock-infected, media without virus) and SARS-CoV-2 (USA/WA1-2020, Wuhan-like)

tag: donor

tag: timepoint

tag: virus

value: wuhan-like virus

tag: batch


title: 1-2-6dpi | 016 | Full ROI

value: primary human broncho-alveolar epithelia


title: foxo gain-of-function, replicate 2, scRNAseq

status: Public on Jun 01 2023

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description:
10x Genomics
foxo2

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) using parameter --force-cell=10000.
The counts matrices were then analyzed in Seurat, filtering out cells with nCount <100 and nUMI<100 from downstream analysis
Batch correction was performed using the Harmony algorithm before creating a UMAP and performing clustering analysis.
Assembly: BDGP6.32
Supplementary files format and content: 2023-02-21_normalized_count_Pedro_thorax_10K.csv (normalized count matrix)
Supplementary files format and content: 2023-02-21_metadata_Pedro_thorax_10K_final.csv (cell annotation)

source_name: thorax

growth_protocol: Crosses were kept at 18°C to avoid expression of REPTOR or FoxO during development. Adult males were collected every 48-72 hours and incubated 3-4 days at 18°C before being shifted to 29°C to induce expression of REPTOR or FoxO

extract_protocol:
After 4 days at at 29°C, around 30 thoraces per genotype were dissected making sure the guts were completely removed, snap frozen and stored at -80°C. Single nuclei extractions were prepared according to Fly Cell Atlas protocol with few modifications (Li et al., 2022). Thoraces were homogenized in 1 ml of homogenization buffer (Li et al., 2022) using 1ml dounce (Wheaton 357538). After filtering the extract with a cell strainer (40 µm) and a 40 µm Flowmi (BelArt, H13680-0040), nuclei were collected via centrifugation for 10 minutes at 1000g at 4 ºC, and then re-suspended in 800 ul PBS/BSA buffer (1xPBS/0.5%BSA with RNase inhibitor). Nuclei solutions were filtered again using 40 µm Flowmi (BelArt, H13680-0040) and stained with DRAQ7™ Dye (Invitrogen, D15106). Single nuclei were sorted using a Sony SH800Z Cell Sorter.  Around 400k nuclei were collected, centrifuged for 1000g for 10 minutes at 4 ºC, ressuspended at 800-1000 cells/µl in PBS/BSA buffer, and then processed for snRNA-seq 10x genomics following the manufacturer instructions.
Libraries were generated according to 10X genomics Next GEM Single Cell 3’ Library and Gel Bead Kit v3.1
10x snRNA-seq

treatment_protocol: Male flies were incubated for 4 days at 29°C

value: thorax

tag: Sex

value: male

value: tub-Gal80ts/UAS-FoxO[ACT]; dMef2-GAL4/+


title: foxo gain-of-function, replicate 1, scRNAseq

description:
10x Genomics
foxo1


title: wildtype, replicate 1, scRNAseq

description:
10x Genomics
wt1

value: tub-Gal80ts/+ ; dMef2-GAL4/+


title: wildtype, replicate 2, scRNAseq

description:
10x Genomics
wt2


title: 1-2-6dpi | 014 | Full ROI


title: 1-2-6dpi | 018 | Full ROI

description: Human_NGS_Whole_Transcriptome_Atlas_RNA_2


title: FM03 WM989 A6-G3 melanoma cells, Split B, DOT1Li pre-treated, then treatment with therapy drug 1uM vemurafenib

description:
sequencing single-cell libraries
FM03_WM989_DOT1Li1uMPLX_SplitB

value: FM03 Split B, DOT1Li pre-treated, then treatment with therapy drug 1uM PLX (vemurafenib)


title: reptor gain-of-function, replicate 1, scRNAseq

description:
10x Genomics
reptor1


title: 1-2-6dpi | 010 | Full ROI


title: reptor gain-of-function, replicate 2, scRNAseq

description:
10x Genomics
reptor2


title: 1-2-6dpi | 015 | Full ROI


title: 1-2-6dpi | 012 | Full ROI


title: FM05 Split A2, treatment with therapy drug 250nM vemurafenib

description:
sequencing single-cell libraries
FM05_WM983B_250nMPLX_SplitA2

value: skin-derived

value: FM05 Split A2, treatment with therapy drug 250nM PLX (vemurafenib)


title: 1-2-6dpi | 009 | Full ROI


title: 1-2-6dpi | 008 | Full ROI


title: 1-2-6dpi | 007 | Full ROI


title: 1-2-6dpi | 006 | Full ROI


title: 1-2-6dpi | 005 | Full ROI


title: 1-2-6dpi | 004 | Full ROI


title: 1-2-6dpi | 003 | Full ROI


title: 1-2-6dpi | 002 | Full ROI


title: 1-2-6dpi | 001 | Full ROI


title: 4dpi | 018 | Full ROI


title: 1-2-6dpi | 013 | Full ROI


title: 4dpi | 017 | Full ROI


title: 1-2-6dpi | 011 | Full ROI


title: 4dpi | 016 | Full ROI


title: 4dpi | 011 | Full ROI


title: 4dpi | 015 | Full ROI


title: 4dpi | 010 | Full ROI


title: 4dpi | 005 | Full ROI


title: 4dpi | 004 | Full ROI


title: 4dpi | 003 | Full ROI


title: 4dpi | 006 | Full ROI


title: 4dpi | 012 | Full ROI


title: 4dpi | 014 | Full ROI


title: 4dpi | 009 | Full ROI


title: 4dpi | 001 | Full ROI


title: Mock2 | 006 | Full ROI

value: Mock


title: Mock2 | 005 | Full ROI


title: 4dpi | 007 | Full ROI


title: 4dpi | 013 | Full ROI


title: 4dpi | 002 | Full ROI


title: Mock2 | 003 | Full ROI


title: Mock2 | 002 | Full ROI


title: Mock2 | 004 | Full ROI


title: Mock2 | 001 | Full ROI


title: Mock1 | 005 | Full ROI


title: Mock1 | 006 | Full ROI


title: Mock1 | 004 | Full ROI


title: Mock1 | 001 | Full ROI


title: Mock1 | 002 | Full ROI


title: 5dpi | 018 | Full ROI


title: 5dpi | 017 | Full ROI


title: 5dpi | 016 | Full ROI


title: 5dpi | 014 | Full ROI


title: 5dpi | 012 | Full ROI


title: 5dpi | 013 | Full ROI


title: 5dpi | 010 | Full ROI


title: 5dpi | 011 | Full ROI


title: 5dpi | 005 | Full ROI


title: 5dpi | 001 | Full ROI


title: 5dpi | 004 | Full ROI


title: Mock1 | 003 | Full ROI


title: 5dpi | 003 | Full ROI


title: 3dp1 | 008 | Full ROI


title: 3dp1 | 010 | Full ROI


title: 5dpi | 006 | Full ROI


title: 3dp1 | 012 | Full ROI


title: 5dpi | 008 | Full ROI


title: 5dpi | 009 | Full ROI


title: 5dpi | 002 | Full ROI


title: 3dp1 | 011 | Full ROI


title: 3dp1 | 005 | Full ROI


title: 4dpi | 008 | Full ROI


title: 3dp1 | 009 | Full ROI


title: 3dp1 | 004 | Full ROI


title: 06 dpi, strain omicron, batch 12, donor 18224 [20-omicron-6dpi-18224]

data_processing:
QC with FASTQC and MultiQC
Trimming with bbduk on quality (20) and min length (11bp) and rRNA removal
Mapping to SARS-CoV2 (different depending on the strain) genome and hg38 with bowtie
Calculating counts with RSEM
Deifferential Expression analysis with DESEQ2, batch correction with svaseq
Assembly: hg38/SARS-CoV2 genomes
Supplementary files format and content: tab-delimited text files include counts, TPMs and FPKMs produced by RSEM

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep kits (zymo research) following the manufacturer’s protocols
cDNA libraries were prepared with polyA mRNA selection and Kapa Stranded mRNA-Seq Library Prep kit (Kapa Biosystems) according to the manufacturer’s instructions. Paired-end sequencing (2 × 150 bp) of stranded total RNA libraries was performed in Illumina Novaseq.

treatment_protocol:
Primary lung-organoid derived ALI was washed three times with PBS. Viruses were diluted in 1X PBS for a final concentration of 10^5PFU per ALI for SARS-CoV-2 infections and spread out on apical side.
Control (Mock-infected, media without virus) and SARS-CoV-2 (USA/WA1-2020, Wuhan-like), Beta (B.1.351), Delta (B.1.617.2) and Omicron (B.1.1.529, BA.1) variants

value: omicron


title: 5dpi | 015 | Full ROI


title: 3dp1 | 003 | Full ROI


title: 3dp1 | 001 | Full ROI


title: 5dpi | 007 | Full ROI


title: 06 dpi, strain omicron, batch 12, donor 7049 [20-omicron-6dpi-07049]


title: 05 dpi, strain omicron, batch 12, donor 18224 [20-omicron-5dpi-18224]


title: 05 dpi, strain omicron, batch 12, donor 7049 [20-omicron-5dpi-07049]


title: 3dp1 | 007 | Full ROI


title: 04 dpi, strain omicron, batch 12, donor 18224 [20-omicron-4dpi-18224]


title: 3dp1 | 006 | Full ROI


title: 03 dpi, strain omicron, batch 12, donor 18224 [20-omicron-3dpi-18224]


title: 02 dpi, strain omicron, batch 12, donor 18224 [20-omicron-2dpi-18224]


title: 02 dpi, strain omicron, batch 12, donor 7049 [20-omicron-2dpi-07049]


title: 03 dpi, strain omicron, batch 12, donor 7049 [20-omicron-3dpi-07049]


title: 01 dpi, strain omicron, batch 12, donor 18224 [20-omicron-1dpi-18224]


title: 05 dpi, mock, batch 12, donor 7049 [20-mock-5dpi-07049]

value: mock


title: 05 dpi, mock, batch 12, donor 18224 [20-mock-5dpi-18224]


title: 06 dpi, mock, batch 12, donor 7049 [20-mock-6dpi-07049]


title: 06 dpi, mock, batch 12, donor 18224 [20-mock-6dpi-18224]


title: 04 dpi, mock, batch 12, donor 7049 [20-mock-4dpi-07049]


title: 02 dpi, mock, batch 12, donor 7049 [20-mock-2dpi-07049]


title: 03 dpi, mock, batch 12, donor 7049 [20-mock-3dpi-07049]


title: 03 dpi, mock, batch 12, donor 18224 [20-mock-3dpi-18224]


title: 02 dpi, mock, batch 12, donor 18224 [20-mock-2dpi-18224]


title: 3dp1 | 002 | Full ROI


title: 01 dpi, mock, batch 12, donor 18224 [20-mock-1dpi-18224]


title: 00 dpi, mock, batch 003, donor 8103 [17-mock]


title: 01 dpi, mock, batch 12, donor 7049 [20-mock-1dpi-07049]


title: 06 dpi, strain delta, batch 003, donor 8103 [17-delta-6dpi]

value: delta


title: 04 dpi, strain delta, batch 003, donor 8103 [17-delta-4dpi]


title: 04 dpi, strain omicron, batch 12, donor 7049 [20-omicron-4dpi-07049]


title: 03 dpi, strain delta, batch 003, donor 8103 [17-delta-3dpi]


title: 06 dpi, strain omicron, batch 002, donor 7049 [18-omicron-6dpi]


title: 04 dpi, strain omicron, batch 002, donor 7049 [18-omicron-4dpi]


title: 02 dpi, strain omicron, batch 002, donor 7049 [18-omicron-2dpi]


title: 05 dpi, strain delta, batch 003, donor 8103 [17-delta-5dpi]


title: 00 dpi, mock, batch 002, donor 7049 [18-mock]


title: 01 dpi, strain omicron, batch 002, donor 7049 [18-omicron-1dpi]


title: 03 dpi, strain omicron, batch 002, donor 7049 [18-omicron-3dpi]


title: 06 dpi, strain delta, batch 002, donor 7049 [18-delta-6dpi]


title: 04 dpi, strain delta, batch 002, donor 7049 [18-delta-4dpi]


title: 01 dpi, strain delta, batch 002, donor 7049 [18-delta-1dpi]


title: 00 dpi, mock, batch 23, donor 18564 [15-mock]


title: 02 dpi, strain delta, batch 002, donor 7049 [18-delta-2dpi]


title: 05 dpi, strain delta, batch 23, donor 18564 [15-delta-5dpi]


title: 01 dpi, strain omicron, batch 12, donor 7049 [20-omicron-1dpi-07049]


title: 04 dpi, mock, batch 12, donor 18224 [20-mock-4dpi-18224]


title: 04 dpi, strain delta, batch 23, donor 18564 [15-delta-4dpi]


title: 05 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-5dpi]

value: Wuhan


title: 02 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-2dpi]


title: 04 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-4dpi]


title: 06 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-6dpi]


title: 03 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-3dpi]


title: 03 dpi, strain delta, batch 23, donor 18564 [15-delta-3dpi]


title: 05 dpi, strain omicron, batch 002, donor 7049 [18-omicron-5dpi]


title: 05 dpi, strain delta, batch 002, donor 7049 [18-delta-5dpi]


title: 00 dpi, mock, batch 22, donor 7049 [12-mock]


title: 06 dpi, strain delta, batch 22, donor 7049 [12-delta-6dpi]


title: 03 dpi, strain delta, batch 22, donor 7049 [12-delta-3dpi]


title: 02 dpi, strain delta, batch 22, donor 7049 [12-delta-2dpi]


title: 05 dpi, strain delta, batch 22, donor 7049 [12-delta-5dpi]


title: 06 dpi, strain delta, batch 23, donor 18564 [15-delta-6dpi]


title: 01 dpi, strain delta, batch 22, donor 7049 [12-delta-1dpi]


title: 01 dpi, strain Wuhan, batch 22, donor 7049 [12-WT-1dpi]


title: 04 dpi, strain delta, batch 22, donor 7049 [12-delta-4dpi]


title: 02 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-2dpi]


title: 06 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-6dpi]


title: 01 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-1dpi]


title: 04 dpi, strain SA, batch 21, donor 8103 [11-SA-4dpi]

value: SA


title: 05 dpi, strain SA, batch 21, donor 8103 [11-SA-5dpi]


title: 06 dpi, strain SA, batch 21, donor 8103 [11-SA-6dpi]


title: 03 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-3dpi]


title: 03 dpi, strain delta, batch 002, donor 7049 [18-delta-3dpi]


title: 02 dpi, strain SA, batch 21, donor 8103 [11-SA-2dpi]


title: 04 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-4dpi]


title: 03 dpi, strain SA, batch 21, donor 8103 [11-SA-3dpi]


title: 00 dpi, mock, batch 21, donor 8103 [11-mock]


title: 05 dpi, strain Wuhan, batch 19, donor 7049 [9-WT-5dpi]


title: 03 dpi, strain Wuhan, batch 19, donor 7049 [9-WT-3dpi]


title: 01 dpi, strain Wuhan, batch 19, donor 7049 [9-WT-1dpi]


title: 06 dpi, strain Wuhan, batch 19, donor 7049 [9-WT-6dpi]


title: 06 dpi, strain SA, batch 19, donor 7049 [9-SA-6dpi]


title: 05 dpi, strain SA, batch 19, donor 7049 [9-SA-5dpi]


title: 04 dpi, strain SA, batch 19, donor 7049 [9-SA-4dpi]


title: 05 dpi, strain Wuhan, batch 21, donor 8103 [11-WT-5dpi]


title: 03 dpi, strain SA, batch 19, donor 7049 [9-SA-3dpi]


title: 05 dpi, strain Wuhan, batch 18, donor 8103 [8-WT-5dpi]


title: 00 dpi, mock, batch 18, donor 8103 [8-mock]


title: 06 dpi, strain Wuhan, batch 18, donor 8103 [8-WT-6dpi]


title: 00 dpi, mock, batch 19, donor 7049 [9-mock]


title: 03 dpi, strain Wuhan, batch 18, donor 8103 [8-WT-3dpi]


title: 01 dpi, strain SA, batch 19, donor 7049 [9-SA-1dpi]


title: 01 dpi, strain SA, batch 21, donor 8103 [11-SA-1dpi]


title: 04 dpi, strain Wuhan, batch 18, donor 8103 [8-WT-4dpi]


title: 06 dpi, strain Wuhan, batch 27, donor 18224 [ALI-SARScov-2-rep2-27]


title: 06 dpi, strain Wuhan, batch 27, donor 18224 [ALI-SARScov-2-rep1-27]


title: 04 dpi, strain Wuhan, batch 19, donor 7049 [9-WT-4dpi]


title: 06 dpi, strain Wuhan, batch 27, donor 18224 [ALI-SARScov-1-rep1-27]


title: 00 dpi, mock, batch 27, donor 18224 [ALI-ctrl-rep2-27]


title: 00 dpi, mock, batch 27, donor 18224 [ALI-ctrl-rep1-27]


title: 00 dpi, mock, batch 27, donor 18224 [ALI-ctrl-rep3-27]


title: TF ChIP-seq from HepG2 (ENCLB649TMU)

status: Public on Apr 30 2023

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR992KMO/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR992KMO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB649TMU
fragmentation methods: sonication (generic)

data_processing: See GSM*_README.txt supplementary file linked below

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens MTERF4

tag: antibody

tag: line

value: cell line

tag: biosample encode accession

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: age

value: 15 year

tag: lab

value: Richard Myers, HAIB

tag: source

value: Richard Myers

tag: link

value: ENCBS114SEW at ENCODE; https://www.encodeproject.org/ENCBS114SEW/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: TF ChIP-seq from WTC11 (ENCLB443BIV)

description:
https://www.encodeproject.org/experiments/ENCSR989LMJ/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR989LMJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB443BIV
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens RELA

value: RELA

value: male

value: adult

value: 30 year

value: ENCBS520SIL at ENCODE; https://www.encodeproject.org/ENCBS520SIL/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from HepG2 (ENCLB681HII)

description:
https://www.encodeproject.org/experiments/ENCSR998LUY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR998LUY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB681HII
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens TARDBP

value: TARDBP

value: ENCBS266OBE at ENCODE; https://www.encodeproject.org/ENCBS266OBE/


title: TF ChIP-seq from HepG2 (ENCLB363WKG)

description:
https://www.encodeproject.org/experiments/ENCSR992KMO/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR992KMO
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR615JHA
encode release date: 2023-01-10
lab: Richard Myers, HAIB
library encode accession: ENCLB363WKG
fragmentation methods: sonication (generic)

value: ENCBS379AWW at ENCODE; https://www.encodeproject.org/ENCBS379AWW/


title: TF ChIP-seq from K562 (ENCLB138PJP)

description:
https://www.encodeproject.org/experiments/ENCSR980ZWE/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR980ZWE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB138PJP
fragmentation methods: sonication (generic)

source_name: Homo sapiens K562 cell line genetically modified (insertion) using CRISPR targeting H. sapiens NR3C1

value: cell line

value: female

value: chronic myelogenous leukemia (CML)

value: 53 year

value: ENCBS569UMX at ENCODE; https://www.encodeproject.org/ENCBS569UMX/

value: derived from ENCODE donor ENCDO000AAD; https://www.encodeproject.org/ENCDO000AAD/


title: TF ChIP-seq from HepG2 (ENCLB224CJQ)

description:
https://www.encodeproject.org/experiments/ENCSR998LUY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR998LUY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR578XKJ
encode release date: 2022-08-31
lab: Richard Myers, HAIB
library encode accession: ENCLB224CJQ
fragmentation methods: sonication (generic)

value: hepatocellular carcinoma

value: child

value: 15 year

value: Richard Myers, HAIB

value: Richard Myers

value: ENCBS787WBX at ENCODE; https://www.encodeproject.org/ENCBS787WBX/


title: TF ChIP-seq from WTC11 (ENCLB860ZDJ)

description:
https://www.encodeproject.org/experiments/ENCSR987FPY/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR987FPY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB860ZDJ
fragmentation methods: sonication (generic)

source_name: Homo sapiens WTC11 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF6

value: male

value: adult

value: 30 year

value: ENCBS209CRY at ENCODE; https://www.encodeproject.org/ENCBS209CRY/


title: TF ChIP-seq from WTC11 (ENCLB363EGH)

description:
https://www.encodeproject.org/experiments/ENCSR987FPY/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR987FPY
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR922EQL
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB363EGH
fragmentation methods: sonication (generic)

value: ENCBS162EXV at ENCODE; https://www.encodeproject.org/ENCBS162EXV/

value: derived from ENCODE donor ENCDO882UJI; https://www.encodeproject.org/ENCDO882UJI/


title: TF ChIP-seq from K562 (ENCLB423DLT)

description:
https://www.encodeproject.org/experiments/ENCSR980ZWE/
***************
biological replicate number: 2
technical replicate number: 1
description: ChIP-Seq on K562
experiment encode accession: ENCSR980ZWE
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR144DXT
encode release date: 2022-09-13
lab: Richard Myers, HAIB
library encode accession: ENCLB423DLT
fragmentation methods: sonication (generic)

value: cell line

value: female

value: ENCBS582DDR at ENCODE; https://www.encodeproject.org/ENCBS582DDR/


title: TF ChIP-seq from WTC11 (ENCLB051GPM)

description:
https://www.encodeproject.org/experiments/ENCSR989LMJ/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on WTC11
experiment encode accession: ENCSR989LMJ
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR828IIG
encode release date: 2022-10-03
lab: Richard Myers, HAIB
library encode accession: ENCLB051GPM
fragmentation methods: sonication (generic)

value: RELA

value: ENCBS840CLJ at ENCODE; https://www.encodeproject.org/ENCBS840CLJ/


title: TF ChIP-seq from HepG2 (ENCLB115MLC)

description:
https://www.encodeproject.org/experiments/ENCSR979KHU/
***************
biological replicate number: 1
technical replicate number: 1
description: ChIP-Seq on HepG2
experiment encode accession: ENCSR979KHU
assay title: TF ChIP-seq
assembly: GRCh38
possible controls: ENCSR800SRA
encode release date: 2023-01-06
lab: Richard Myers, HAIB
library encode accession: ENCLB115MLC
fragmentation methods: sonication (generic)

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens ATF7

value: hepatocellular carcinoma

value: ENCBS143JPW at ENCODE; https://www.encodeproject.org/ENCBS143JPW/

value: derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/