title: C-T3_MAG-M_Gamb

source_name: Anopheles gambiae Mated Male accessor glands rep C 24 hr

tag: tissue

value: Male accessor glands

value: Male

value: Mated

value: 24 hr post-mating or time-matching virgins


title: AR-positive CRPC_vehicle_input

status: Public on Apr 20 2022

type: SRA

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

library_source: genomic

data_processing:
We used Trimmomatic-033 to trim and crop of Illumina (fastq) data by removing the sequences of adapters.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie-1.1.2 with parameters -a --best --strata -m 1 -v 2.
Generate alignments in the SAM format given single-end reads. Convert SAM to BAM files using samtools view command. samtools version is 0.1.19.
Signal scores in bed files were calculated using Model-based analysis of ChIP-seq (MACS; P-value < 10xE-4)
Genome_build: hg19
Supplementary_files_format_and_content: Bed files that summarized significant peak regions (P-value < 1.0xE-4)

molecule: genomic DNA

organism: Homo sapiens

source_name: AR-positive CRPC cells

growth_protocol:
For culturing organoids, PDXs were minced and digested in growth factor reduced, phenol red-free, ldEV-free Matrigel and cultured in advanced DMEM/F-12 media containing 1% penicillin-streptomycin, 2 mM Glutamax, 1 nM DHT, 1.25 mM N-acetylcysteine, 50 ng/ml EGF, 500 nM A83-01, 10 mM, nicotinamide, 10 μM SB202190, 2% B27, 100 ng/ml noggin, 10 ng/ml FGF10, 5 ng/ml FGF2, 1 μM prostaglandin E2 and 10% R-spondin 1 conditioned media. 10 μM Y-27632 dihydrochloride.
For 2D-culture, PDXs were minced and cultured in DMEM media containing 1% penicillin-streptomycin, 0.5ug/ml fungizone, 0.1mg gentamicin, 25mM HEPES buffer, 10% fetal calf serum, 225U/ml Collagenase Type 1, 25U/ml Hyaluronidase then cultured in advanced DMEM/F-12 media containing 1% penicillin-streptomycin, 2 mM Glutamax, 1 nM DHT, 1.25 mM N-acetylcysteine, 50 ng/ml EGF, 500 nM A83-01, 10 mM, nicotinamide, 10 μM SB202190, 2% B27, 100 ng/ml noggin, 10 ng/ml FGF10, 5 ng/ml FGF2, 1 μM prostaglandin E2 and 10% R-spondin 1 conditioned media. 10 μM Y-27632 dihydrochloride.

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
The Chromatin immunoprecipitated DNA fragments (approx.10 ng in 30 µl water) are end repaired by using T4 DNA polymerase, Klenow DNA polymerase and T4 polynucleotide kinase in the presence of dNTPs. And an ‘A’ base is added to the 3’end of the blunt phosphorylated DNA fragments, using the polymerase activity of Klenow fragment. Then, adaptors (Adaptor oligo mix, Illumina) are ligated to the ends of the DNA fragments. The resulting DNA fragments are purified by MinElute column (QIAGEN).
300 ~ 500 bp DNA fragments are purified by using E-Gel SizeSelect agarose Gels (Invitrogen) according to manufacturer’s instruction.
Size selected adaptor-modified DNA fragments are amplifiedand the resulting PCR products are purified by MinElute column (QIAGEN).
The size and amount of DNA fragments (libraries) are validated by Bioanalyzer (Agilent).

treatment_protocol: We treated cells with 10 µM OCT1-PI-polyamide (PI) for 48 h or vehicle (water). All cells were treated with 10 nM dehydrotestosterone（DHT) for 24 hours before collecting cells.

tag: cell type

value: AR-positive CRPC cells

tag: culture

value: 2D cultured from PDX

tag: treatment

value: DHT 10 nM for 24 h + vehicle  for 48 h

tag: chip antibody


title: osbzip47dsRNAI#14 rep1

city: Bangalore

first: Usha

last: Vijayraghavan

state: Karnataka

address: New biological Science building

department: Microbiology and cell biology

country: India

institute: Indian Institute of Science

library_source: transcriptomic

data_processing:
Illumina Hiseq. software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oryzastaiva (RAPDB) whole genome using STAR 2.5.3a with optimzed parameters
Trimed Mean of M-values (TMM) of each gene is calculated using the edgeR software (3.82.0).
Genome_build: RAPDB
Supplementary_files_format_and_content: tab-delimited excel file include TMM values for every sample
Supplementary_files_format_and_content: tab-delimited excel file with raw gene counts for every gene and every sample

molecule: total RNA

organism: Oryza sativa Japonica Group

source_name: Inflorescence

extract_protocol:
Total RNA was extracted using Trizol reagent.
1 ug of total RNA for the construction of sequencing libraries using RNA depletion-based NEB next UltraII RNA kit

tag: cultivar

value: Inflorescence

tag: length

tag: genotype

value: osbzip47 dsRNAi#14


title: CT3_HM_GAMB

city: Boston

first: Flaminia

last: Catteruccia

state: MA

address: 655 huntington ave

country: USA

institute: Harvard University

data_processing:
Alignment: hisat2/2.0.5. Parameters: -q -x --threads 4
Mapping quality filter: samtools/1.3.1. Parameters: view -bS -q 30
Sort mapped reads: samtools/1.3.1. Parameter: sort
Read count: htseq/0.9.1. Parameters: --stranded=no  --mode=union --quiet  -a 30
Assembly: Anopheles gambiae PEST AgamP4.12; Anopheles albimanus STECLA AalbS2.4
Supplementary files format and content: Processed data files format: Plain text file.  Content: Read counts

molecule: polyA RNA

organism: Anopheles gambiae

source_name: Anopheles gambiae Mated Head rep C 24 hr

extract_protocol:
Total RNA was extracted with TRI reagent (Thermo Fisher Scientific, MA) from pools of 10–12  tissues following the manufacturer’s instructions. RNA was treated with TURBO DNase (Thermo Fisher Scientific, MA), and purified with Qiagen RNeasy MinElute Cleanup Kit.
Illumina TruSeq Stranded mRNA kit

value: Head

tag: Sex

value: Female

tag: mating status

tag: replicate

value: C

tag: time point


title: WT rep2

value: wild type


title: AR-negative CRPC_AcH3

source_name: AR-negative CRPC organoid

value: AR-negative CRPC organoid

value: Organoid from PDX

value: DHT 10 nM for 24h


title: DT3_RBM_GAMB

source_name: Anopheles gambiae Mated Rest of the body (including thorax, wings, legs, fatbody, guts in both sexes and ovaries in females) rep D 24 hr

value: D


title: AR-positive CRPC_OCT1

value: OCT1 (abcam 15112)


title: WT rep1


title: DT3_HM_GAMB

source_name: Anopheles gambiae Mated Head rep D 24 hr


title: AR-positive CRPC_AcH3


title: ABL_Ser2_siCon_FP_inhibition_40min_ChIPSeq

city: Durham

first: Zhong

last: Chen

state: NC

address: 905 S. LaSalle Street

department: Pathology

institute: Duke University

data_processing:
ChIP-seq reads were aligned to the hg19 and mm10 genome assembly using bowtie-1.0.0 with the following parameters -v 3 -k 3 -m 2. And only those reads with unique or two mapped locations are remained for further analysis.
Each mapped reads has been extended into a 300 bp fragment (presumably coinciding with library size) in a direction from 5'-3' along with chromosome axis. And the bigwig files would be made on these processed alignments.
Genome_build: hg19 and mm10

source_name: prostate

growth_protocol: LNCaP-abl cells were cultured in RPMI 1640 (Invitrogen) supplemented with 10% charcoal-stripped FBS (Omega Scientific) and 1mM L-glutamine.

extract_protocol:
cells were grown to 70%-80% confluence, and crosslinked with 1% formaldehyde for 10 min at room temperature. After washing twice with cold PBS, cells were collected and resuspended in lysis buffer (1% SDS, 5 mM EDTA, 50 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). After sonication, the soluble chromatin was diluted in 1% Triton X-100, 2 mM EDTA, 150 mM NaCl, 20 mM Tris (pH 8.0), 1x protease and phosphatase inhibitors). Then samples were precleared and immunoprecipitated with the appropriate antibodies overnight at 4°C. The next day, protein A or G beads blocked with BSA were added for 2 h at 4°C, and then washed sequentially for 10 min with TSE I (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 150 mM NaCl), TSE II (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris (pH 8.0), 500 mM NaCl), buffer III (0.25 M LiCl, 1% NP-40, 1% deoxycholate, 1 mM EDTA, 10 mM Tris (pH 8.0), and TE buffer (10 mM Tris (pH 8.0), 1mM EDTA (pH 8.0)). DNA was eluted in Elution buffer (1% SDS, 0.1M NaHCO3) at room temperatue for 30 min. The crosslinking was reversed by incubation for 16 h at 65°C. During the purification, ChIP DNA was treated with DNase-free RNase for 30 min at 37°C.
Libraries were prepared according to NEBNext ChIP-Seq Library Prep Master Mix Set (E6240L). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 10 or 14 cycles and library fragments of ~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an E-gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the HiSeq2000 following the manufacturer's protocols.

treatment_protocol: Cells were treated with 300 nM FP for indicated time.

value: prostate cancer cells

tag: passages

tag: strain

value: LNCaP-abl

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: F2 DMSO1_WGBS

city: Gainesville

first: Tracie

middle: R

last: Baker

state: FL

institute: University of Florida

description:
F2_DMSO Sample 1
Control f2

data_processing:
Reads from 7 FO, 6 F1 and 6 F2 fish testes (3 controls and 3 descendants of TCDD-treated fish for each generation) were aligned (bismark 0.18.1; bowtie2 2.2.3) to the zebrafish genome (dR10) and differentially methylated sites were determined (methylKit 1.6.3) between conditions.
Methylated sites (percent methylation change > 5%; p-value ≤ 0.05) were annotated to the nearest gene. 5% methylation change was used as a cutoff based on previous studies.
Individual replicates from each condition were kept separate and not pooled.
Genome_build: zebrafish genome (danRer10/GRCz10)
Supplementary_files_format_and_content: bedGraph files

organism: Danio rerio

source_name: testicular tissue

growth_protocol: Zebrafish embryos (AB strain) were kept at 27-30 °C in lightly buffered water with a standard 14-h/10-h light/dark cycle as described by Westerfield (2000).

extract_protocol:
DNA isolation was performed using the BioRobot EZ1 workstation following the provided protocol from Qiagen (Hilden, Germany). Bisulfite conversion of methylated cytosines of DNA from zebrafish testes was performed using the EZ DNA Methylation Kit (Zymo, Irvine, CA, United States).
The bisulfite-converted ssDNA was converted to Illumina libraries with the TruSeq DNA Methylation Kit (Illumina, San Diego, CA, United States). DNA libraries were sequenced with 100 bp paired-end reads on an Illumina HiSeq 2500 run in high output mode.

treatment_protocol: F0 zebrafish were exposed for 1 hour to waterborne TCDD at 50 pg/ml or vehicle (DMSO) at both 3 and 7 wpf (weeks post fertilization; during sexual differentiation and gonad maturation). The next two generations were not exposed but were raised to adulthood and assessed.

value: AB

value: WT

value: Male

tag: age

value: 1 year

value: testicular tissue

value: DMSO (F0)

tag: generation


title: AR-positive CRPC_input

value: AR-positive CRPC cells

value: 2D cultured from PDX


title: BT3_HM_GAMB

source_name: Anopheles gambiae Mated Head rep B 24 hr

value: Head

value: Female

value: Mated

value: B

value: 24 hr post-mating or time-matching virgins


title: ABL_Ser2_siCon_FP_inhibition_20min_ChIPSeq


title: ABL_Ser2_siCon_FP_inhibition_30min_ChIPSeq


title: ABL_Ser2_siCon_FP_inhibition_0min_ChIPSeq


title: F2 DMSO3_WGBS

description:
F2_DMSO Sample 3
Control f2


title: BT1_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep B 3 hr

value: Virgin

value: 3 hr post-mating or time-matching virgins


title: ABL_Ser2_siCon_FP_inhibition_10min_ChIPSeq

value: prostate cancer cells

value: LNCaP-abl


title: DT1_HM_GAMB

source_name: Anopheles gambiae Mated Head rep D 3 hr

value: D


title: AR-negative CRPC_OCT1

value: AR-negative CRPC organoid

value: Organoid from PDX

value: DHT 10 nM for 24h

value: OCT1 (abcam 15112)


title: Lung_Tissue_pMed1_ChIPSeq

source_name: lung

value: lung tissue

value: lung

value: pMED1 (Yenzyme, Custom antibody)


title: DT1_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep D 3 hr

value: Head


title: Liver_Tissue_pMed1_ChIPSeq

source_name: liver

value: liver tissue

value: liver


title: AR-negative CRPC_input


title: BT3_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep B 24 hr

value: Female

value: B


title: F2 TCDD1_WGBS

description:
F2_TCDD Sample 1
Treatment f2

value: AB

value: WT

value: Male

value: 1 year

value: testicular tissue

value: TCDD (F0)


title: F2 DMSO2_WGBS

description:
F2_DMSO Sample 2
Control f2

value: DMSO (F0)


title: hALEC_d5_2

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
bulk RNAseq
hALEC_RNAseq_samples_raw_counts.txt

data_processing:
The Cell Ranger count pipeline (v.3.1.0) was used to align raw sequencing reads to the GRCh38 human genome (Single Cell 3' v3 chemistry).
For RNA-seq data, the Nextera adapter and poor qualities were removed with Trim Galore (v0.6.5). Trimmed files were aligned to the GRCh38 genome using HISAT2 (v2.1.0). Reads were quantitated using SeqMonk (v1.48.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X barcode file: Tsv files contain barcodes of detected cells.
Supplementary_files_format_and_content: 10X feature file: Tsv files contain IDs of detected genes.
Supplementary_files_format_and_content: 10X matrix file: Mtx files contain matrix of raw count values.
Supplementary_files_format_and_content: 10X cloupe file: The Cell Ranger cloupe file.
Supplementary_files_format_and_content: RNAseq_report: A SeqMonk (v1.48.0) Annotated Probe Report of raw read counts per gene (Ensembl).

source_name: differentiated hPSC

extract_protocol:
RNeasy extraction kit (Qiagen).
For bulk RNAseq, total RNA was purified using RNeasy kit (Qiagen) followed by treatment with Turbo DNase (Thermo Fisher Scientific). 500ng-1mg RNA was reverse transcribed with SuperScript II system and oligo-dT primer (Thermo Fisher Scientific), followed by 8 cycles of amplification using KAPA HiFi HotStart ReadyMix PCR Kit (KAPA Biosystems, Roche). 100-200pg of DNA were used for tagmentation performed with Nextera XT kit (Illumina), followed by 10 cycles amplification whereby iNext sequencing adaptors were added. The libraries were purified using AMPure XP magnetic beads (Beckman Coulter). The quality of the libraries was tested using Agilent Bioanalyzer system.

value: differentiated hPSC

value: MAPK and NODAL inhibitors


title: Prostate_Tissue_pMed1_ChIPSeq

value: prostate tissue

value: prostate


title: F1 DMSO3_WGBS

description:
F1_DMSO Sample 3
Control f1


title: CT1_HV_GAMB

source_name: Anopheles gambiae Virgin Head rep C 3 hr

value: Virgin

value: C

value: 3 hr post-mating or time-matching virgins


title: F2 TCDD2_WGBS

description:
F2_TCDD Sample 2
Treatment f2


title: F2 TCDD3_WGBS

description:
F2_TCDD Sample 3
Treatment f2


title: hALEC_d5_1


title: hALEC_d1_2


title: ABL_H3K27ac_rep2_ChIPSeq

value: prostate cancer cells

value: LNCaP-abl

value: H3K27ac (Abcam, ab4729)


title: hALEC_d1_1


title: F1 DMSO1_WGBS

description:
F1_DMSO Sample 1
Control f1

value: AB


title: ABL_H3K79Me2_ChIPSeq

value: H3K79me2 (Abcam, ab3594)


title: hALEC_d0_2

source_name: hPSC

value: hPSC


title: CT1_HM_GAMB

source_name: Anopheles gambiae Mated Head rep C 3 hr

value: Head

value: Female

value: Mated


title: ABL_MED31_Vehicle_rep2_ChIPSeq

value: MED31 (ThermoFisher, PA5-70247)


title: DT3_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep D 24 hr

value: Atria

value: D

value: 24 hr post-mating or time-matching virgins


title: ABL_Ser2_FP_1h_rep2_ChIPSeq

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: BT1_HM_GAMB

source_name: Anopheles gambiae Mated Head rep B 3 hr

value: B


title: DT1_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep D 3 hr

value: Virgin


title: T7_CT14_rep2

city: Bethesda

first: Samer

last: Hattar

state: MD

address: 35 Convent Drive, Bldg 35A

institute: National Institute of Mental Health

data_processing:
RNAseq reads were mapped to the mouse genome (mm10) using STAR aligner (v2.4.2a)
Aligned reads were counted using HTSeq-count (v0.9.1) with parameters --mode=union --stranded=no --idattr=gene_name, and the mm10 GTF annotation
Assembly: mm10
Supplementary files format and content: htseq-count output .txt files for each sample with feature counts mapped to gene_name

organism: Mus musculus

source_name: Perihabenular nucleus

extract_protocol:
Mice housed under T24 or T7 cycles were kept in darkness for 1 day prior to dissection to negate any acute effects of light. Brains were isolated and placed ventral side up on an ice-cold coronal slice brain matrix (Kent Scientific). A 1mm coronal slice of the brain was sectioned using ice-cold razor blades positioned caudal to the optic chiasm. PHb tissue was collected, immediately placed in ice-cold Qiazol lysis reagent (Qiagen) and stored at -80 C. Bilateral PHb tissue samples were pooled from 4 mice per replicate with a total of 4 replicates per condition. RNA isolation was performed with the Qiagen RNEasy Lipid Tissue Mini kit following manufacturer instructions. cDNA was prepared from total RNA using the Ovation RNASeq System V2 (Tecan) and end-repaired using the NEBNext End Repair Module (New England Biolabs).
RNA-Seq libraries were prepared from end-repaired cDNA with the TruSeq Stranded RNA Kit (Illumina). Libraries were pooled in an equimolar ratio prior to sequencing on an Illumina NovaSeq 6000 to a minimum depth of 128 million 150-bp paired-end reads per library.

value: Brain

tag: light cycle treatment

tag: circadian time


title: hALEC_d3_2

tag: cell type

value: differentiated hPSC

value: MAPK and NODAL inhibitors


title: BT3_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep B 24 hr

tag: tissue


title: F1 DMSO2_WGBS

description:
F1_DMSO Sample 2
Control f1

source_name: testicular tissue

value: WT

value: Male

value: 1 year

value: testicular tissue

tag: treatment

value: DMSO (F0)


title: hALEC_d3_1


title: DT3_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep D 24 hr

value: Female


title: CT3_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep C 24 hr

value: C


title: CMK+ARID3A_R2

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

country: Germany

institute: Goehte University Frankfurt

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. Clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
hisat 2 (v2.0.5.) was used to mapp to the reference genome (--dta --phred33)
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include read counts for each sample

source_name: CMK

extract_protocol:
Quick-RNA Miniprep (Zymo Research)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Doxycycline 1ug/mL for 48h

tag: source

value: Cell line

tag: transgene


title: AP8

description: 10X Chromium single-cell RNAseq

extract_protocol:
For 10X single-cell RNAseq, the cells were dissociated by incubating with 0.25% trypsin for 10min at 37°C, and then an equal volume of 0.1mg/ml collagenase IV (ThermoFisher Scientific) was added for further 20min incubation at 37°C. During this incubation, the cells were triturated by pipetting with 200ml tip every 10min. The cells were resuspended in DMEM/F12 supplemented with 0.1% BSA, washed twice and then filtered through 30mm mesh. 16,000 cells were resuspended in 47ml DMEM/F12 supplemented with 0.04% BSA for further processing.
Single-cell RNA-seq libraries were prepared in the Cancer Research UK Cambridge Institute Genomics Core Facility using the following: Chromium Single Cell 3′ Library & Gel Bead Kit v3 (10x Genomics, PN-1000075), Chromium Chip B Kit (10x Genomics, PN-1000073) and Chromium Single Cell 3' Reagent Kits v3 User Guide (Manual Part CG000183 Rev C, 10X Genomics). Cell suspensions were loaded on the Chromium instrument with the expectation of collecting gel-beads emulsions containing single cells. RNA from the barcoded cells for each sample was subsequently reverse-transcribed in a C1000 Touch Thermal cycler (Bio-Rad) and all subsequent steps to generate single-cell libraries were performed according to the manufacturer’s protocol with no modifications. cDNA quality and quantity were assessed with Agilent TapeStation 4200 (High Sensitivity 5000 ScreenTape) after which 25% of material was used for gene expression library preparation.


title: AP3

description: 10X Chromium single-cell RNAseq


title: hALEC_d0_1

value: hPSC


title: ABL_H3K27ac_rep1_ChIPSeq

source_name: prostate

value: prostate cancer cells

value: LNCaP-abl

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: CMK+ARID3A_R1


title: BT1_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep B 3 hr

value: Atria

value: Virgin

value: B

value: 3 hr post-mating or time-matching virgins


title: F1 TCDD2_WGBS

description:
F1_TCDD Sample 2
Treatment f1

value: AB

tag: genotype

value: WT

value: TCDD (F0)


title: CT3_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep C 24 hr

tag: Sex

value: Mated

value: 24 hr post-mating or time-matching virgins


title: ABL_Ser2_FP_1h_rep1_ChIPSeq

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: ABL_pMed1_FP_1h_rep2_ChIPSeq

value: pMED1 (Yenzyme, Custom antibody)


title: F1 TCDD1_WGBS

description:
F1_TCDD Sample 1
Treatment f1

value: Male

value: 1 year

value: testicular tissue


title: BT3_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep B 24 hr

value: Female

tag: mating status


title: F1 TCDD3_WGBS

description:
F1_TCDD Sample 3
Treatment f1


title: F0 DMSO3_WGBS

description:
F0_DMSO Sample 3
Control

value: DMSO


title: ABL_pMed1_FP_1h_rep1_ChIPSeq

value: prostate cancer cells

value: LNCaP-abl


title: CT1_GAMB_At_V

source_name: Anopheles gambiae Virgin Atria rep C 3 hr

value: Atria

value: Virgin

tag: replicate

value: C


title: F0 DMSO2_WGBS

description:
F0_DMSO Sample 2
Control

value: AB


title: CMK+LUC_R3

value: Doxycycline 1ug/mL for 48h

value: Cell line

value: LUC


title: ABL_pMed1_Vehicle_rep2_ChIPSeq


title: ABL_Ser2_Vehicle_rep1_ChIPSeq


title: ABL_MED31_Vehicle_rep1_ChIPSeq

value: MED31 (ThermoFisher, PA5-70247)


title: CMK+ARID3A_R3


title: F0 DMSO1_WGBS

description:
F0_DMSO Sample 1
Control

value: WT


title: F0 TCDD3_WGBS

description:
F0_TCDD Sample 3
Treatment

value: TCDD


title: BT1_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep B 3 hr

value: Mated

value: B

tag: time point

value: 3 hr post-mating or time-matching virgins


title: F0 TCDD4_WGBS

description:
F0_TCDD Sample 4
Treatment

value: Male

value: 1 year

value: testicular tissue


title: ABL_Ser2_Vehicle_rep2_ChIPSeq

value: prostate cancer cells

tag: passages

value: LNCaP-abl

value: phosphorylated RNA pol II (Abcam, phospho S2)


title: O1_negative_control_intermediate_10days_exp2

status: Public on Apr 19 2022

type: genomic

hyb_protocol: Samples were bisulphite converted and hybridised to the Infinium MethylationEPIC beadchip at the Barts and the London Genome Centre.

scan_protocol: Arrays were imaged with an Illumina iScan System and iScan Control Software with recommended Illumina scanner settings.

data_processing:
The array data was processed with the minfi R package and NOOB normalisation to generate beta values.
matrix processed value definition: NOOB normalized Average Beta

label: Cy3 and Cy5

source_name: Fibroblast

label_protocol: Standard Illumina protocol

growth_protocol: Dermal fibroblasts from middle age donors (38-53 years old) were purchased from Lonza. For lentiviral iPSC reprogramming, fibroblasts were expanded in fibroblast medium (DMEM-F12, 10% FBS, 1X Glutamax, 1X MEM-NEAA, 1X beta-mercaptoethanol, 0.2X Penicillin/Streptomycin, 16 ng/ml FGF2) before being spinfected with tetO-GFP-hOKMS and M2rtTA lentiviruses, where 10% virus supernatant and 8 µg/ml polybrene was added to the cells before centrifugation at 1000 rpm for 60 minutes at 32°C. Reprogramming was initiated 24 hours after lentiviral transduction by introducing doxycycline (2 µg/ml) to the media. Media was changed daily throughout the experiment subsequently. On day 2 of reprogramming, cells were flow sorted for viable GFP positive cells and then cultured on gelatine coated plates. On day 7 of reprogramming, cells were replated onto irradiated mouse embryonic fibroblasts (iMEFs) and on day 8 of reprogramming, the medium was switched to hES medium (DMEM-F12, 20% KSR, 1X Glutamax, 1X MEM-NEAA, 1X beta-mercaptoethanol, 0.2X Penicillin/Streptomycin, 8 ng/ml FGF2). For transient reprogramming, cells were flow sorted at day 10, 13, 15 or 17 of reprogramming for the CD13+ SSEA4- and CD13- SSEA4+ populations. These cells were then replated on iMEFs in fibroblast medium without doxycycline and subsequently maintained like fibroblasts without iMEFs.

extract_protocol: Genomic DNA was extracted from cell samples with the DNeasy blood and tissue kit (Qiagen) by following the manufacturer’s instructions and including the optional RNase digestion step. For intermediate reprogramming stage samples, genomic DNA was extracted alongside the RNA with the AllPrep DNA/RNA mini kit (Qiagen).

value: Negative control intermediate

tag: length of reprogramming phase (days)

tag: donor age (years)


title: DT1_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep D 3 hr

value: Atria

value: Female

value: D


title: O1_transient_reprogramming_intermediate_10days_exp2

value: Transient reprogramming intermediate


title: iPSC 21

value: iPSC


title: O3 Fib

value: Fibroblast


title: CMK+LUC_R2

value: Doxycycline 1ug/mL for 48h

value: Cell line

value: LUC


title: CMK+LUC_R1


title: F0 TCDD1_WGBS

description:
F0_TCDD Sample 1
Treatment

tag: strain

value: AB

value: WT

tag: age

value: TCDD

tag: generation


title: F0 TCDD2_WGBS

description:
F0_TCDD Sample 2
Treatment

value: Male

value: 1 year

value: testicular tissue


title: O1_failing_to_transiently_reprogram_intermediate_10days_exp2

tag: cell type

value: Failing to transiently reprogram intermediate


title: O2_negative_control_15days_exp2

value: Negative control fibroblast


title: ABL_pMed1_Vehicle_rep1_ChIPSeq

value: prostate cancer cells

value: LNCaP-abl

value: pMED1 (Yenzyme, Custom antibody)


title: O2_transient_reprogramming_intermediate_10days_exp2

value: Transient reprogramming intermediate


title: O2 Fib


title: iPSC 13

value: iPSC


title: O1_negative_control_15days_exp2


title: O2_transiently_reprogrammed_13days_exp2

value: Transiently reprogrammed fibroblast


title: O2_failed_to_transiently_reprogram_13days_exp2

value: Failed to transiently reprogram fibroblast


title: O3_negative_control_15days_exp2


title: O3_transiently_reprogrammed_15days_exp2


title: CT1_GAMB_At_M

source_name: Anopheles gambiae Mated Atria rep C 3 hr

tag: tissue

value: Atria

value: Female

value: Mated

value: C

value: 3 hr post-mating or time-matching virgins


title: O3_failed_to_transiently_reprogram_15days_exp2


title: O3_failed_to_transiently_reprogram_10days_exp2


title: O3_negative_control_13days_exp2


title: O1_failed_to_transiently_reprogram_15days_exp2


title: O3_failed_to_transiently_reprogram_13days_exp2


title: O3_transiently_reprogrammed_13days_exp2


title: O2_negative_control_13days_exp2


title: O1_failed_to_transiently_reprogram_10days_exp2


title: O1_transient_reprogramming_intermediate_15days_exp2


title: O3_negative_control_10days_exp2


title: O1_negative_control_13days_exp2


title: O3_negative_control_intermediate_13days_exp2

value: Negative control intermediate


title: O3_failing_to_transiently_reprogram_intermediate_13days_exp2


title: O3_transient_reprogramming_intermediate_13days_exp2


title: O2_negative_control_intermediate_13days_exp2


title: O2_failing_to_transiently_reprogram_intermediate_13days_exp2


title: O2_negative_control_10days_exp2


title: O1_negative_control_intermediate_13days_exp2


title: O3_failing_to_transiently_reprogram_intermediate_10days_exp2


title: O1_transient_reprogramming_intermediate_13days_exp2


title: O1_failing_to_transiently_reprogram_intermediate_13days_exp2


title: O3_transient_reprogramming_intermediate_10days_exp2


title: O2_failed_to_transiently_reprogram_10days_exp2


title: O2_failing_to_transiently_reprogram_intermediate_10days_exp2


title: O1_failed_to_transiently_reprogram_13days_exp2


title: O3_transiently_reprogrammed_10days_exp2


title: O3_negative_control_intermediate_15days_exp2


title: O1_transiently_reprogrammed_10days_exp2


title: O2_transiently_reprogrammed_10days_exp2


title: O2_failed_to_transiently_reprogram_15days_exp2


title: human-HUVEC-MAF-dox-JS_S23

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

state: NY

address: 1300 York Avenue

institute: Weill Cornell Medicine

description: HUVEC MAF Knockout

data_processing:
FastQC (v0.11.5) to check FASTQ quality.
Reads trimmed with Trimmomatic (v0.36)
TopHat2 v2.1.0; Bowtie2 v2.2.6 was used for alignment and genes quantified with HTSeq (v0.11.1)
Assembly: GRCh38
Supplementary files format and content: Gene count matrix

source_name: HUVEC KO 3

extract_protocol:
ECs were isolated by fluorescence-activated cell sorting and subjected to RNA extraction using RNeasy Mini Kit from Qiagen.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

value: HUVEC

value: MAF KO


title: human-HUVEC-MAF-dox-1_S21

description: HUVEC MAF Knockout

source_name: HUVEC KO 1


title: O1_negative_control_10days_exp2


title: O1_negative_control_intermediate_15days_exp2


title: O2_transient_reprogramming_intermediate_15days_exp2


title: human-HUVEC-Ctl-dox-JS_S20

description: HUVEC Control

source_name: HUVEC Ctl 3

value: Control


title: O3_transient_reprogramming_intermediate_17days_exp2


title: O3_negative_control_intermediate_10days_exp2


title: O2_failing_to_transiently_reprogram_intermediate_17days_exp2

value: Failing to transiently reprogram intermediate


title: O3_transient_reprogramming_intermediate_15days_exp2

data_processing:
Reads were trimmed with Trim Galore (version 0.6.2) and aligned to the human genome (GRCh38) with HISAT2 (version 2.1.0).
Genome_build: GRCh38
RNA-seq report: SeqMonk report with log2 RPM values for each each gene.

extract_protocol:
RNA was extracted from cell samples with the RNeasy mini kit (Qiagen) by following the manufacturer’s instructions.
RNA-Seq libraries were prepared at the Wellcome Sanger Institute and run on a HiSeq 2500 system (Illumina) for 50 bp single-end sequencing.


title: O1_failing_to_transiently_reprogram_intermediate_15days_exp2


title: O2_negative_control_intermediate_10days_exp2


title: O2_negative_control_intermediate_15days_exp2


title: O2_transient_reprogramming_intermediate_17days_exp2


title: human-HUVEC-MAF-dox-2_S22

description: HUVEC MAF Knockout

source_name: HUVEC KO 2


title: O1_transient_reprogramming_intermediate_17days_exp2


title: O3_negative_control_intermediate_17days_exp2


title: human-HUVEC-Ctl-dox-2_S19

description: HUVEC Control

source_name: HUVEC Ctl 2


title: O3_failing_to_transiently_reprogram_intermediate_17days_exp2


title: O1_failing_to_transiently_reprogram_intermediate_17days_exp2


title: human-HUVEC-Ctl-dox-1_S18

description: HUVEC Control

source_name: HUVEC Ctl 1


title: O3_transiently_reprogrammed_13days_exp2


title: O3_transiently_reprogrammed_10days_exp2


title: O2_negative_control_intermediate_17days_exp2


title: O2_negative_control_17days_exp2

value: Negative control fibroblast


title: O3_negative_control_intermediate_13days_exp2


title: O2_transient_reprogramming_intermediate_13days_exp2


title: O1_negative_control_17days_exp2


title: O3_failing_to_transiently_reprogram_intermediate_15days_exp2


title: O3_failed_to_transiently_reprogram_17days_exp2


title: O3_negative_control_10days_exp2


title: O1_negative_control_intermediate_17days_exp2


title: O3_transiently_reprogrammed_17days_exp1


title: O2_failed_to_transiently_reprogram_17days_exp1


title: O3_Fib

value: Fibroblast


title: O3_negative_control_17days_exp2


title: O3_negative_control_intermediate_15days_exp2


title: O2_failing_to_transiently_reprogram_intermediate_15days_exp2


title: O3_transiently_reprogrammed_17days_exp2


title: O2_failed_to_transiently_reprogram_17days_exp2


title: O1_failed_to_transiently_reprogram_17days_exp2


title: O3_transiently_reprogrammed_15days_exp2


title: O3_negative_control_15days_exp2


title: O3_negative_control_17days_exp1


title: O3_transient_reprogramming_intermediate_13days_exp2


title: O1 Fib


title: O3_negative_control_13days_exp1


title: O3_negative_control_intermediate_10days_exp2


title: O3_failed_to_transiently_reprogram_10days_exp2


title: O2_failed_to_transiently_reprogram_13days_exp1


title: O3_negative_control_13days_exp2


title: O2_negative_control_13days_exp1


title: O1_negative_control_17days_exp1


title: O3_failed_to_transiently_reprogram_17days_exp1


title: O2_negative_control_17days_exp1


title: O3_failing_to_transiently_reprogram_intermediate_10days_exp2


title: O2_transiently_reprogrammed_17days_exp1


title: O3_negative_control_17days_exp2


title: O2_transient_reprogramming_intermediate_10days_exp2


title: O1_transiently_reprogrammed_17days_exp1


title: O3_failing_to_transiently_reprogram_intermediate_17days_exp2


title: O3_failed_to_transiently_reprogram_13days_exp1


title: O2_transiently_reprogrammed_10days_exp2


title: O3_failed_to_transiently_reprogram_13days_exp2


title: O3_failing_to_transiently_reprogram_intermediate_13days_exp2


title: O3_failed_to_transiently_reprogram_15days_exp2


title: O2_transient_reprogramming_intermediate_17days_exp2


title: O3_transiently_reprogrammed_17days_exp2


title: O2_negative_control_intermediate_17days_exp2


title: O2_transient_reprogramming_intermediate_15days_exp2


title: O1_failed_to_transiently_reprogram_17days_exp1


title: O1_negative_control_15days_exp1


title: O3_transiently_reprogrammed_13days_exp1


title: O2_transiently_reprogrammed_13days_exp1


title: O2_negative_control_15days_exp2


title: O2_negative_control_13days_exp2


title: O1_failed_to_transiently_reprogram_13days_exp1


title: O3_transiently_reprogrammed_15days_exp1


title: O2_d11_CD13

growth_protocol: Human dermal fibroblasts were reprogrammed with the CytoTune™-iPS 2.0 Sendai Reprogramming kit (Invitrogen) as previously described (Milagre et al, 2017).

extract_protocol: Genomic DNA was extracted from cell samples with the DNeasy blood and tissue kit (Qiagen) by following the manufacturer’s instructions and including the optional RNase digestion step.

value: Failing to reprogram fibroblast

tag: donor age

tag: days of reprogramming


title: O2_negative_control_intermediate_15days_exp2


title: O3_failed_to_transiently_reprogram_15days_exp1


title: O2_negative_control_15days_exp1


title: O2_failing_to_transiently_reprogram_intermediate_15days_exp2


title: O2_d9_SSEA4

value: Reprogramming fibroblast


title: O2_negative_control_intermediate_10days_exp2


title: O2_failed_to_transiently_reprogram_15days_exp1


title: O1_negative_control_13days_exp1


title: O2_failing_to_transiently_reprogram_intermediate_10days_exp2


title: O2_negative_control_intermediate_13days_exp2


title: O2_transiently_reprogrammed_13days_exp2


title: Y2_d9_SSEA4


title: O2_negative_control_17days_exp2


title: Y1_d15_CD13


title: O2_d15_SSEA4


title: O3_negative_control_15days_exp1


title: O2_failed_to_transiently_reprogram_13days_exp2


title: O2_negative_control_10days_exp2


title: O2_Fib


title: O2_d15_CD13


title: O1_failed_to_transiently_reprogram_15days_exp1


title: O1_transient_reprogramming_intermediate_17days_exp2

value: Transient reprogramming intermediate


title: O2_failed_to_transiently_reprogram_15days_exp2


title: O2_d9_CD13


title: O2_d11_SSEA4


title: O2_failing_to_transiently_reprogram_intermediate_17days_exp2


title: O2_failing_to_transiently_reprogram_intermediate_13days_exp2


title: O2_failed_to_transiently_reprogram_17days_exp2


title: Y2_d9_CD13


title: O2_transient_reprogramming_intermediate_13days_exp2


title: Y1_d15_SSEA4


title: O2_failed_to_transiently_reprogram_10days_exp2


title: O1_d11_SSEA4


title: Y1_d11_CD13


title: O1_negative_control_intermediate_13days_exp2


title: O1_transient_reprogramming_intermediate_13days_exp2


title: Y1_d9_CD13


title: O1_transient_reprogramming_intermediate_15days_exp2


title: Y2_d15_SSEA4


title: Y1_d9_SSEA4


title: Y1_d11_SSEA4


title: O1_transient_reprogramming_intermediate_10days_exp2


title: O1_d15_SSEA4


title: Y2_d11_SSEA4


title: O1_d15_CD13


title: O1_transiently_reprogrammed_10days_exp2

value: Transiently reprogrammed fibroblast


title: O1_d11_CD13


title: O1_negative_control_intermediate_17days_exp2


title: O1_negative_control_intermediate_15days_exp2


title: O1_negative_control_15days_exp2


title: O1_negative_control_intermediate_10days_exp2


title: Y2_d15_CD13


title: rat cortical neurons_GRC327-CF-44_S6_Deltamethrin_1

city: RTP

first: Susan

last: Hester

address: 109 TW Alexander Dr

institute: US EPA

data_processing:
The sequencer output data files (FASTQ files) were “trimmed” to remove sequence adapters from the reads in Partek Flow (Build v4.0.16.0128, St. Louis, Missouri).
The files were inspected for pre- alignment and post-alignment quality control
The sequence was then aligned to a reference genome by using Spliced Transcripts Alignment to a Reference (STAR) software (STAR2.4.1d, Illumina).
post alignment QC metrics were conducted, and the reads were mapped to the transcriptome to determine which genes the sequence represents and annotation (gene level) in the Partek Flow software.
Transcript (genes) abundance from reads aligned to a rat genome were quantified using expectation-maximization algorithm (E/M) and normalized by dividing by counts per million (CPM) for the sample, adding 1 to all raw counts, and then log2 transforming
differentially expressed gene lists (DEGs) were identified using Partek Gene-specific analysis (GSA) on pairwise groups (control vs treated) followed by pathway mapping with statistical significance was ascribed to score values with a False Discovery Rate (FDR) value < 0.05 and a log2 fold change (FC) value of +/- 2.0.
Genome_build: Rat6

organism: Rattus norvegicus

source_name: rat cortical neurons

growth_protocol: Rat primary cortical cells were plated at 150K cells/well on multi-well MEA plates

extract_protocol:
Total RNA was collected using the Qiagen RNeasy Plus Kit. Two to three wells of identically-treated cultures were pooled, representing one sample. The experiment was repeated on two separate cultures.  A volume of 350 μL of lysis buffer with β-mercaptoethanol (Buffer RLT, Qiagen) was added (as described in RNeasy Plus Kit instructions) and mixed for complete lysis before being transferred to the next well to be pooled together. The lysate sample of pooled wells was transferred to a clean 1.5 mL RNase-free plastic tube and the homogenized lysate sample was then taken through the gDNA Eliminator spin column, centrifuged, and 350 to 600 μL 70% ethanol was added to the supernatant (as described in RNeasy Plus Kit instructions) to elute the RNA.
polyA-selected RNA-seq libraries following PrepX PolyA mRNA isolation kit instructions (Wafergen)

treatment_protocol: Each well was treated with vehicle or test compound beginnning 2 hr after plating. Media changes and renewal of test solutions was conducted after recordings on DIV 5, 7 and 9.

value: rat cortical neurons

tag: chemical

value: Deltamethrin

tag: concentration

tag: unit

value: uM


title: O1_failing_to_transiently_reprogram_intermediate_15days_exp2


title: O1_negative_control_13days_exp2


title: rat cortical neurons_GRC327-CF-43_S1_5-Fluorouracil_0


title: O1_negative_control_17days_exp2


title: O1_negative_control_10days_exp2


title: rat cortical neurons_GRC327-CF-41_S5_5-Fluorouracil_0.3


title: O1_Fib


title: Y2_d11_CD13


title: rat cortical neurons_GRC327-CF-46_S11_Deltamethrin_10


title: O1_failed_to_transiently_reprogram_17days_exp2

value: Failed to transiently reprogram fibroblast


title: O1_failing_to_transiently_reprogram_intermediate_17days_exp2


title: rat cortical neurons_GRC327-CF-45_S12_Deltamethrin_3


title: O1_failed_to_transiently_reprogram_15days_exp2


title: rat cortical neurons_GRC327-CF-38_S4_Cytosine arabinoside_1

value: Cytosine arabinoside


title: rat cortical neurons_GRC327-CF-39_S13_Cytosine arabinoside_0


title: iPSC_21

value: iPSC


title: rat cortical neurons_GRC327-CF-37_S17_Cytosine arabinoside_0.3


title: rat cortical neurons_GRC327-CF-36_S21_Cytosine arabinoside_0.1


title: O1_failing_to_transiently_reprogram_intermediate_13days_exp2


title: rat cortical neurons_GRC327-CF-42_S14_5-Fluorouracil_1


title: O3_transiently_reprogrammed_15days_exp1

data_processing:
Reads were trimmed with Trim Galore (version 0.6.2) and aligned to the human genome (GRCh38) with Hisat2 (version 2.1.0).
Genome_build: GRCh38
Supplementary_files_format_and_content: SeqMonk Annotated Probe reports of all genes with log2 RPM values in each sample

source_name: Transiently reprogrammed fibroblasts

value: Transiently reprogrammed fibroblasts


title: rat cortical neurons_GRC327-CF-47_S1_Deltamethrin_0


title: O1_failed_to_transiently_reprogram_13days_exp2


title: iPSC_13


title: O1_failed_to_transiently_reprogram_10days_exp2


title: O1_failing_to_transiently_reprogram_intermediate_10days_exp2


title: rat cortical neurons_GRC327-CF-40_S5_5-Fluorouracil_0.1


title: E6_MII_WT_paiso

city: Beijing

first: Zhuqing

last: Xiong

state: FOREIGN

address: Haidian District

country: China

institute: School of Life Science, Tsinghua Univers

data_processing:
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
After sequencing, CCS reads were extracted. The CCS reads were further split into different samples based on barcode and trimmed into clean reads. (The uploaded data are splitted and trimmed already). The clean reads were aligned to the mm9 genome using minimap. The poly(A) tail length of each transcript was calculated by the length of the clipped sequence. The poly(A) tail length of a gene was presented by the genomic mean of the poly(A) tail length of all the transcript as described44. For MII poly(A) tail length analysis, we merged WT and Btg4+/- data as MII control poly(A) tail length data to increase data depth after confirming their similarity.
Assembly: mm9
Library strategy: PAIso-seq

source_name: Oocyte

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/47 female mice mated with PWK/PhJ male mice.
Total RNA was extracted by TRIzol (life tech; 15596018) and further purified through isopropanal precipitation and resolved in 11 μl nuclease-free water. Total RNA is used for end extension with dU-containing end extension oligos by Klenow fragment (3'→ 5' exo-, NEB; M0212L). The end-extended RNAs (>200 nt) was cleaned up by RNA Clean & Concentrator-5 kit (Zymo; R1015) and eluted by 7 μl nuclease-free water. The cleaned RNA was reverse transcribed by SuperScript II similar to Smart-seq2 method. The amplified DNA was size selected by Ampure beads and made into SMRTbell Template library. The libraries were sequenced by Pacbio sequel II.

tag: genotype

value: WT

tag: developmental stage

value: MII oocyte

tag: molecule

value: Poly(A) tail length


title: rat cortical neurons_GRC327-CF-35_S19_Cypermethrin_0

value: Cypermethrin


title: O3_transiently_reprogrammed_17days_exp1


title: E6_MII_BTG4_KO_rep2_paiso

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/46 female mice mated with PWK/PhJ male mice.
Total RNA was extracted by TRIzol (life tech; 15596018) and further purified through isopropanal precipitation and resolved in 11 μl nuclease-free water. Total RNA is used for end extension with dU-containing end extension oligos by Klenow fragment (3'→ 5' exo-, NEB; M0212L). The end-extended RNAs (>200 nt) was cleaned up by RNA Clean & Concentrator-5 kit (Zymo; R1015) and eluted by 7 μl nuclease-free water. The cleaned RNA was reverse transcribed by SuperScript II similar to Smart-seq2 method. The amplified DNA was size selected by Ampure beads and made into SMRTbell Template library. The libraries were sequenced by Pacbio sequel II.

value: Btg4 KO


title: O3_negative_control_17days_exp1

source_name: Negative control fibroblasts

value: Negative control fibroblasts


title: O3_transiently_reprogrammed_13days_exp1


title: O3_failed_to_transiently_reprogram_17days_exp1

source_name: Failed to transiently reprogram fibroblasts


title: E6_MII_BTG4_Het_paiso

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/44 female mice mated with PWK/PhJ male mice.
Total RNA was extracted by TRIzol (life tech; 15596018) and further purified through isopropanal precipitation and resolved in 11 μl nuclease-free water. Total RNA is used for end extension with dU-containing end extension oligos by Klenow fragment (3'→ 5' exo-, NEB; M0212L). The end-extended RNAs (>200 nt) was cleaned up by RNA Clean & Concentrator-5 kit (Zymo; R1015) and eluted by 7 μl nuclease-free water. The cleaned RNA was reverse transcribed by SuperScript II similar to Smart-seq2 method. The amplified DNA was size selected by Ampure beads and made into SMRTbell Template library. The libraries were sequenced by Pacbio sequel II.

value: Btg4 Het


title: E6_FGO_WT_paiso

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/43 female mice mated with PWK/PhJ male mice.
Total RNA was extracted by TRIzol (life tech; 15596018) and further purified through isopropanal precipitation and resolved in 11 μl nuclease-free water. Total RNA is used for end extension with dU-containing end extension oligos by Klenow fragment (3'→ 5' exo-, NEB; M0212L). The end-extended RNAs (>200 nt) was cleaned up by RNA Clean & Concentrator-5 kit (Zymo; R1015) and eluted by 7 μl nuclease-free water. The cleaned RNA was reverse transcribed by SuperScript II similar to Smart-seq2 method. The amplified DNA was size selected by Ampure beads and made into SMRTbell Template library. The libraries were sequenced by Pacbio sequel II.

value: Full-grown oocyte SN


title: O3_failed_to_transiently_reprogram_15days_exp1

value: Failed to transiently reprogram fibroblasts


title: rat cortical neurons_GRC327-CF-33_S3_Cypermethrin_3


title: O2_transiently_reprogrammed_13days_exp1


title: O3_negative_control_13days_exp1


title: E6_MII_BTG4_KO_rep1_paiso

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/45 female mice mated with PWK/PhJ male mice.
Total RNA was extracted by TRIzol (life tech; 15596018) and further purified through isopropanal precipitation and resolved in 11 μl nuclease-free water. Total RNA is used for end extension with dU-containing end extension oligos by Klenow fragment (3'→ 5' exo-, NEB; M0212L). The end-extended RNAs (>200 nt) was cleaned up by RNA Clean & Concentrator-5 kit (Zymo; R1015) and eluted by 7 μl nuclease-free water. The cleaned RNA was reverse transcribed by SuperScript II similar to Smart-seq2 method. The amplified DNA was size selected by Ampure beads and made into SMRTbell Template library. The libraries were sequenced by Pacbio sequel II.


title: O3_failed_to_transiently_reprogram_13days_exp1


title: O2_transiently_reprogrammed_17days_exp1


title: O2_negative_control_13days_exp1


title: LPI_smart_rep2

data_processing:
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
After sequencing, CCS reads were extracted. The CCS reads were further split into different samples based on barcode and trimmed into clean reads. (The uploaded data are splitted and trimmed already). The clean reads were aligned to the mm9 genome using minimap. The poly(A) tail length of each transcript was calculated by the length of the clipped sequence. The poly(A) tail length of a gene was presented by the genomic mean of the poly(A) tail length of all the transcript as described44. For MII poly(A) tail length analysis, we merged WT and Btg4+/- data as MII control poly(A) tail length data to increase data depth after confirming their similarity.
Assembly: mm9

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/35 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: Late prometaphase I oocyte

value: polyA RNA


title: rat cortical neurons_GRC327-CF-31_S6_Deltamethrin_0

value: rat cortical neurons

value: Deltamethrin


title: FGO_smart_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/32 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously


title: rat cortical neurons_GRC327-CF-32_S12_Cypermethrin_1

value: uM


title: rat cortical neurons_GRC327-CF-30_S11_Deltamethrin_10


title: rat cortical neurons_GRC327-CF-34_S2_Cypermethrin_10


title: rat cortical neurons_GRC327-CF-29_S7_Deltamethrin_3


title: FGO_smart_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/33 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously


title: mouse514-graftL-contralateral

first: John

last: Connor

address: 620 Albany St.

department: National Emerging Infectious Diseases Laboratories

institute: Boston University

data_processing:
Base calling then pull from BGI cloud
Check quality with FastQC v0.11.7. Full command: fastqc --outdir 'fastqc-raw' $(ls *-r1.fq.gz)
Align to human (GRCh38, Ensembl 101), mouse (GRCm38, Ensembl 101), and SARS-CoV-2 (Wuhan-Hu-1 NC_045512.2) genomes using STAR v2.7.1a. Full command: STAR --runMode alignReads --genomeDir 'human-mouse-cov2-exon' --readFilesIn 'sampleID-r1.fq.gz' 'sampleID-r2.fq.gz' --readFilesCommand zcat --outFileNamePrefix 'sampleID/sampleID-' --outSAMtype BAM Unsorted --outSAMunmapped Within
Quantify expression with featureCounts v1.6.2 using a combined GTF file (GRCh30 and CRGm38 from Ensembl 101 and a custom SARS-CoV-2 GTF), the exon feature, and the gene_name meta-feature. Full command: featureCounts -O -M -p -t exon -g gene_name -a 'hsapiens-mmusculus-cov2.gtf' $(ls *.bam)
Check STAR and featureCounts output with MultiQC v1.10.1
Genome_build: Human: GRCh38, NCBI RefSeq GCF_000001405.39. Mouse: GRCm38, NCBI RefSeq GCF_000001635.26. SARS-CoV-2: Wuhan-Hu-1, NCBI RefSeq NC_045512.2.
Supplementary_files_format_and_content: counts.tsv: raw counts for all samples, output from featureCounts, tab-delimited matrix

organism:
Homo sapiens
Mus musculus

source_name: Fetal lung xenograft

growth_protocol: Fetal lung xenografts were engrafted in NRG mice.

extract_protocol:
Fetal lung xenografts were collected from mice and placed in 600 µL of RNAlater (Sigma-Aldrich; # R0901500ML) and stored at -80°C. For processing, 20–30 mg of tissue was taken and placed in into a 2 mL tube with 600 µL of RLT buffer with 1% β–mercaptoethanol and a 5 mm stainless steel bead (Qiagen; #69989). Tissues were then dissociated using a Qiagen TissueLyser II (Qiagen; Germantown, MD) with the following cycle: two-minute dissociation at 1800 oscillations/minute, one-minute rest, two-minute dissociation at 180 oscillations/minute. Samples were then subject to centrifugation at 13,000 rpm for 10 minutes and supernatant was transferred to a new 1.5 mL tube. RNA extractions were performed using a Qiagen RNeasy Plus Mini Kit (Qiagen #74134), according to the manufacturer’s instructions, with an additional on-column DNase treatment (Qiagen; #79256). RNA was eluted in 30 µL of RNase/DNase free water.
Total RNA was sent to BGI genomics (Hong Kong, China) for library preparation and sequencing (polyA selection, paired-end reads, 100bp, 20M reads per sample).

treatment_protocol: Ten to fifteen weeks post engraftment, NRG mice.

tag: sars-cov-2 innoculation dose

tag: group

value: Contralateral

tag: xenograft pair

value: Discordant

tag: viral copies/mg tissue

tag: sars-cov-2 ihc

tag: harvest dpi

tag: xenograft donor id


title: O2_negative_control_17days_exp1

tag: cell type

tag: length of reprogramming phase (days)

tag: donor age (years)


title: O2_negative_control_15days_exp1


title: O3_negative_control_15days_exp1


title: rat cortical neurons_GRC327-CF-28_S16_Deltamethrin_1

tag: tissue


title: O2_failed_to_transiently_reprogram_17days_exp1


title: rat cortical neurons_GRC327-CF-27_S8_Haloperidol_0

tag: chemical

value: Haloperidol


title: O2_failed_to_transiently_reprogram_13days_exp1


title: mouse062-graftR-contralateral


title: LPI_Ribo_rep2

data_processing:
Ribo-lite reads were trimmed with cutadapt v1.14 with parameters: cutadapt --trim-n -a GATCGGAAGAGCACACGTCTG -a AGAGCACACGTCTG <input.file> | cutadapt -u 3 -a A{100} --no-indels -e 0.16666666666666666 - | cutadapt -O 8 --match-read-wildcards -g GTTCAGAGTTCTACAGTCCGACGATCSSS -m 18 - -o <output.file> , and the trimmed reads were sequentially mapped to mouse/human rRNAs sequences (mm9/hg19) using Bowtie2 v2.2.2 with parameters --seedlen=23. Those aligned to rRNA were discarded, and the rest reads were mapped to transcriptome of mm9/hg19 using STAR v2.5.3a with parameters --outFilterMismatchNmax 2 --outFilterMultimapNmax 20 --outFilterMatchNmin 16 --alignEndsType EndToEnd. The gene expression level was then calculated by Cufflinks v2.2.1 based on the annotation of CDS region。
All mRNA-seq data were trimmed by Trim Galore v0.4.2 then mapped to transcriptome of mm9/hg19 by STAR v2.5.3a with parameters --outFilterMultimapNmax 20 --outSAMstrandField intronMotif. The gene expression level was calculated by Cufflinks v2.2.1.
After sequencing, CCS reads were extracted. The CCS reads were further split into different samples based on barcode and trimmed into clean reads. (The uploaded data are splitted and trimmed already). The clean reads were aligned to the mm9 genome using minimap. The poly(A) tail length of each transcript was calculated by the length of the clipped sequence. The poly(A) tail length of a gene was presented by the genomic mean of the poly(A) tail length of all the transcript as described44. For MII poly(A) tail length analysis, we merged WT and Btg4+/- data as MII control poly(A) tail length data to increase data depth after confirming their similarity.
Assembly: mm9
Library strategy: Ribo-lite

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/49 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8589G).

value: WT

value: Ribosome protected fragment


title: mouse059-graftL-contralateral


title: rat cortical neurons_GRC327-CF-26_S17_Haloperidol_3

tag: concentration


title: O1_transiently_reprogrammed_17days_exp1

value: Transiently reprogrammed fibroblasts


title: rat cortical neurons_GRC327-CF-25_S20_Haloperidol_1

tag: unit


title: mouse316-graftR-dpi7

description:
Rare pneumocyte; mild rare thromobisis edema hemorrhage and inflammation
sample17

tag: agent

value: Single


title: LPI_smart_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/34 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

tag: genotype

tag: developmental stage


title: LPI_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/48 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8588G).

tag: molecule


title: FGO_Ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/47 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8587G).


title: O1_negative_control_17days_exp1


title: O2_failed_to_transiently_reprogram_15days_exp1


title: FGO_Ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/46 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8586G).


title: mouse063-graftR-dpi7

description:
focal area of immunoreactivity; thrombosis with inflammation and hemorrhage
sample16

tag: sars-cov-2 innoculation dose

tag: group


title: O1_negative_control_15days_exp1

extract_protocol:
RNA was extracted from cell samples with the RNeasy mini kit (Qiagen) by following the manufacturer’s instructions.
RNA-Seq libraries were prepared at the Wellcome Sanger Institute and run on a HiSeq 2500 system (Illumina) for 50 bp single-end sequencing.


title: E5_MII_Btg4_Het_smart_rep2

value: MII oocyte


title: mouse042-graftR-dpi7

description:
IHC-rare individual epithelial cells in both; thrombosis on periphery  lung
sample14

tag: xenograft pair

value: Paired

tag: viral copies/mg tissue


title: mouse042-graftL-dpi7

description:
IHC-rare individual epithelial cells in both; thrombosis on periphery  lung
sample15

tag: sars-cov-2 ihc

tag: harvest dpi


title: O1_negative_control_13days_exp1

tag: cell type

value: Negative control fibroblasts


title: O1_failed_to_transiently_reprogram_17days_exp1

tag: length of reprogramming phase (days)


title: rat cortical neurons_GRC327-CF-22_S15_5-Fluorouracil_1


title: E5_MII_Btg4_KO_smart_rep2

value: Btg4 KO


title: rat cortical neurons_GRC327-CF-21_S10_5-Fluorouracil_0.3


title: rat cortical neurons_GRC327-CF-20_S4_5-Fluorouracil_0.1


title: mouse054-graftR-dpi7

description:
Severe coagulative necrosis attributed to thrombosis of large vessels
sample13

tag: xenograft donor id


title: rat cortical neurons_GRC327-CF-19_S8_Cytosine arabinoside_0

tag: tissue

value: Cytosine arabinoside


title: E5_MII_Btg4_KO_smart_rep1


title: mouse054-graftL-dpi7

description:
Severe coagulative necrosis attributed to thrombosis of large vessels
sample12


title: E5_MII_Btg4_Het_smart_rep1

value: Btg4 Het


title: rat cortical neurons_GRC327-CF-24_S22_Haloperidol_0.3

tag: chemical


title: O1_failed_to_transiently_reprogram_13days_exp1

value: Failed to transiently reprogram fibroblasts

tag: donor age (years)


title: O1_failed_to_transiently_reprogram_15days_exp1


title: E5_MII_Btg4_KO_ribo_rep3


title: mouse052-graftL-dpi7

description:
Severe edema and fibrin thrombosis
sample10


title: E5_MII_Btg4_Het_ribo_rep3

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/45 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8585G).


title: rat cortical neurons_GRC327-CF-17_S14_Cytosine arabinoside_0.3

extract_protocol:
Total RNA was collected using the Qiagen RNeasy Plus Kit. Two to three wells of identically-treated cultures were pooled, representing one sample. The experiment was repeated on two separate cultures.  A volume of 350 μL of lysis buffer with β-mercaptoethanol (Buffer RLT, Qiagen) was added (as described in RNeasy Plus Kit instructions) and mixed for complete lysis before being transferred to the next well to be pooled together. The lysate sample of pooled wells was transferred to a clean 1.5 mL RNase-free plastic tube and the homogenized lysate sample was then taken through the gDNA Eliminator spin column, centrifuged, and 350 to 600 μL 70% ethanol was added to the supernatant (as described in RNeasy Plus Kit instructions) to elute the RNA.
polyA-selected RNA-seq libraries following PrepX PolyA mRNA isolation kit instructions (Wafergen)

value: rat cortical neurons

tag: concentration

tag: unit


title: rat cortical neurons_GRC327-CF-23_S24_5-Fluorouracil_0


title: rat cortical neurons_GRC327-CF-18_S22_Cytosine arabinoside_1


title: Y2_d9_CD13_Sendai_Exp1

source_name: Failing to reprogram fibroblast

extract_protocol:
RNA was extracted alongside the genomic DNA with the AllPrep DNA/RNA mini kit (Qiagen).
Libraries were prepared as previously described (Milagre et al, 2017), and run on a Hiseq 2500 (Illumina) for 75 bp paired-end sequencing.

value: Failing to reprogram fibroblast

tag: donor age

tag: days of reprogramming


title: E5_MII_Btg4_Het_ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/44 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8584G).

tag: genotype

tag: developmental stage

tag: molecule


title: mouse514-graftR-dpi2

tag: sars-cov-2 innoculation dose

tag: agent

tag: group

tag: xenograft pair


title: Y2_d9_SSEA4_Sendai_Exp1

source_name: Reprogramming fibroblast

tag: cell type

value: Reprogramming fibroblast


title: rat cortical neurons_GRC327-CF-16_S7_Cytosine arabinoside_0.1

value: uM


title: mouse062-graftL-dpi2

value: Discordant

tag: viral copies/mg tissue

tag: sars-cov-2 ihc

tag: harvest dpi


title: E5_MII_Btg4_KO_ribo_rep2

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/43 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8583G).


title: rat cortical neurons_GRC327-CF-15_S13_Cypermethrin_10

tag: tissue

tag: chemical

value: Cypermethrin


title: Y2_d7_SSEA4_Sendai_Exp1


title: mouse052-graftR-dpi7

description:
Severe edema and fibrin thrombosis
sample11

tag: xenograft donor id


title: E5_MII_Btg4_KO_ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/42 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8582G).


title: rat cortical neurons_GRC327-CF-14_S10_Cypermethrin_3

tag: concentration

tag: unit


title: mouse059-graftR-dpi2

description:
Severe coagulative necrosis attributed to thrombosis of large vessels
sample07


title: E5_MII_Btg4_Het_ribo_rep1

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/41 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8581G).


title: E1_MII_20_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/42 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8581G).

value: WT


title: mouse061-graftR-dpi2


title: mouse654-graftL-pbs

value: Naive


title: Y2_d54_SSEA4_Sendai_Exp2

source_name: iPSC

value: iPSC

tag: donor age

tag: days of reprogramming


title: Y2_d47_SSEA4_Sendai_Exp2


title: Y2_Fib_Sendai_Exp2

source_name: Dermal fibroblast

value: Dermal fibroblast


title: rat cortical neurons_GRC327-CF-12_S16_Domoic Acid_0

value: Domoic Acid


title: E1_MII_19_Ribo

tag: genotype

tag: developmental stage

value: MII oocyte

value: Ribosome protected fragment


title: Y2_d40_SSEA4_Sendai_Exp2


title: rat cortical neurons_GRC327-CF-11_S23_Domoic Acid_1


title: mouse713-graftR1-naive

tag: sars-cov-2 innoculation dose


title: mouse713-graftR2-naive


title: E1_MII_18_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/40 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8580G).

tag: molecule


title: Y2_d34_SSEA4_Sendai_Exp2


title: rat cortical neurons_GRC327-CF-10_S3_Domoic Acid_0.3


title: Y2_d7_CD13_Sendai_Exp1


title: Y2_d29_SSEA4_Sendai_Exp2


title: mouse302-graftR2-naive

tag: group


title: rat cortical neurons_GRC327-CF-9_S9_Domoic Acid_0.1


title: E1_MII_17_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/39 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8579G).


title: mouse302-graftR1-naive

extract_protocol:
Fetal lung xenografts were collected from mice and placed in 600 µL of RNAlater (Sigma-Aldrich; # R0901500ML) and stored at -80°C. For processing, 20–30 mg of tissue was taken and placed in into a 2 mL tube with 600 µL of RLT buffer with 1% β–mercaptoethanol and a 5 mm stainless steel bead (Qiagen; #69989). Tissues were then dissociated using a Qiagen TissueLyser II (Qiagen; Germantown, MD) with the following cycle: two-minute dissociation at 1800 oscillations/minute, one-minute rest, two-minute dissociation at 180 oscillations/minute. Samples were then subject to centrifugation at 13,000 rpm for 10 minutes and supernatant was transferred to a new 1.5 mL tube. RNA extractions were performed using a Qiagen RNeasy Plus Mini Kit (Qiagen #74134), according to the manufacturer’s instructions, with an additional on-column DNase treatment (Qiagen; #79256). RNA was eluted in 30 µL of RNase/DNase free water.
Total RNA was sent to BGI genomics (Hong Kong, China) for library preparation and sequencing (polyA selection, paired-end reads, 100bp, 20M reads per sample).

tag: xenograft pair


title: rat cortical neurons_GRC327-CF-13_S19_Cypermethrin_1


title: E1_MII_16_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/38 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8578G).


title: Y2_d29_CD13_Sendai_Exp2

tag: cell type


title: E1_MII_15_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/37 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8577G).


title: rat cortical neurons_GRC327-CF-7_S23_Domoic Acid_1


title: Y2_d21_SSEA4_Sendai_Exp2


title: E1_MII_14_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/36 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8576G).


title: Y2_d21_CD13_Sendai_Exp2


title: Y2_d15_SSEA4_Sendai_Exp1


title: E1_MII_13_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/35 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8575G).


title: rat cortical neurons_GRC327-CF-5_S18_Domoic Acid_0.1


title: E1_MII_12_Ribo

extract_protocol:
To obtain oocytes or preimplantation embryos, 8-weeks-old or 5-weeks-old C57BL/6 female mice were intraperitoneally injected with pregnant mare’s serum gonadotropin (PMSG; 5 IU) and human chorionic gonadotrophin (hCG; 5 IU). Preimplantation embryos were collected from 5-weeks-old C57BL/34 female mice mated with PWK/PhJ male mice.
Samples was lysed in 310 μl ice-cold lysis buffer (20 mM Tris-HCL ph7.4; 150 mM NaCl; 5 mM MgCl2; 1mM DTT; 100 μg/ml Cycloheximide; 1% Triton; 25 U/ml Turbo Dnase Turbo DNase (Ambion, AM2239)) for 10 min. The lysate was clarified for 10 min at 20,000g at 4°C, then treated with 1 μl RNase I 100 U/ml (Ambion, AM2295) and incubated at room temperature for 45 min with gentle mixing. For 107 mESC and HEK293 cells, 7 μl RNase I was added. The digested extracts were stopped by the addition of 10 μl SUPERas•In (Ambion, AM2696) and were overlaid onto a 700 μl sucrose cushion of 1M sucrose in 20mM total Tris-HCL pH7.4; 150 mM NaCl; 5 mM MgCl2; 1 mM DTT; 100 μg/ml Cycloheximide; 20 U/ml SUPERas•In (Ambion, AM2696) for 4 hr at 76,400 rpm in a MLA-150 rotor in a Beckman Optima MAX-XP ultracentrifuge. The supernatant was removed and the pellet was resuspended in 50 μl pellet buffer (10 mM Tris (pH 7.5); 1% SDS). RNA was extracted from pellet buffer using TRIzol (life tech, 15596018), chloroform and aqueous phase was precipitated by at least one volume of isopropanol and 20 μg glycogen. Precipitation was carried out at -20°C overnight and RNA was then pelleted by centrifugation for 40 min at 12,000g, 4°C. RNA was resuspended in 6 μl Nuclease-free water and mix with 6 μl Gel Loading Buffer II (ThermoFisher, AM8574G).


title: rat cortical neurons_GRC327-CF-4_S21_Haloperidol_0

value: Haloperidol


title: Y2_d15_CD13_Sendai_Exp1


title: Y2_d13_SSEA4_Sendai_Exp1


title: noCOVID_noALI_rep9

type: RNA

city: New York

first: Stuart

last: Weisberg

address: 650 W 168th Street

department: Pathology and Cell Biology

institute: Columbia University

hyb_protocol: 300 ng total RNA was hybridized to gene-specific fluorescently barcoded reporter probes at 65˚C for 18 hours and then purified and deposited onto glass cartridges using the “high sensitivity” setting on the nCounter™ Prep Station (NanoString Technologies, Seattle, WA, USA).

scan_protocol: The number of barcodes hybridized to specific RNA targets on cartridges were directly counted by the nCounter™ Digital Analyzer with 555 fields of view setting.

data_processing: Normalization of RNA loading was performed using the NanoString nCounter® Advanced Analysis protocol based on the geometric mean of 12 internal reference genes (housekeeping genes; ABCF1, G6PD, GUSB, NRDE2, OAZ1, POLR2A, PPIA, SDHA, STK11IP, TBC1D10B, TBP, and UBB).

source_name: formalin fixed paraffin embedded lung, from uninfected organ donor lung

extract_protocol: The RNA was extracted from a 20 µm thick tissue section using the RNeasy FFPE Kit (Qiagen) according to the manufacturer’s instructions by the Molecular Pathology Shared Resource core facility at CUIMC. The RNA concentration and size distribution for each sample was assessed using NanoDrop (ThermoFisher Scientific) and Bioanalyzer (Agilent).

value: lung

tag: symptomatic interval (days)