title: E1_MII_11_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/33 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, AM8573G).


title: noCOVID_noALI_rep10

status: Public on Apr 19 2022

type: RNA

city: New York

first: Stuart

last: Weisberg

state: NY

address: 650 W 168th Street

department: Pathology and Cell Biology

country: USA

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).

molecule: total RNA

organism: Homo sapiens

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).

tag: tissue

value: lung

tag: symptomatic interval (days)


title: rat cortical neurons_GRC327-CF-3_S2_Haloperidol_3

type: SRA

city: RTP

first: Susan

last: Hester

state: NC

address: 109 TW Alexander Dr

institute: US EPA

library_source: transcriptomic

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: Haloperidol

tag: concentration

tag: unit

value: uM


title: rat cortical neurons_GRC327-CF-8_S20_Domoic Acid_0

value: Domoic Acid


title: noCOVID_noALI_rep7


title: rat cortical neurons_GRC327-CF-2_S9_Haloperidol_1


title: Y2_d13_CD13_Sendai_Exp1

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

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: Failing to reprogram fibroblast

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:
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.

tag: cell type

value: Failing to reprogram fibroblast

tag: donor age

tag: days of reprogramming


title: E1_MII_10_Ribo

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: Ribo-lite

organism: Mus musculus

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/32 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, AM8572G).

tag: genotype

value: WT

tag: developmental stage

value: MII oocyte

tag: molecule

value: Ribosome protected fragment


title: E1_MII_9_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/31 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, AM8571G).


title: Y2_d11_SSEA4_Sendai_Exp1

source_name: Reprogramming fibroblast

value: Reprogramming fibroblast


title: Y2_d11_SSEA4_Sendai_Exp2


title: noCOVID_noALI_rep5


title: rat cortical neurons_GRC321-ONT25_S4_5-Fluorouracil_1


title: noCOVID_noALI_rep8


title: E1_MII_7_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/29 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, AM8569G).


title: E1_MII_8_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/30 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, AM8570G).


title: rat cortical neurons_GRC327-CF-6_S15_Domoic Acid_0.3


title: noCOVID_noALI_rep4


title: noCOVID_noALI_rep3


title: rat cortical neurons_GRC327-CF-1_S18_Haloperidol_0.3


title: E1_MII_6_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/28 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, AM8568G).


title: rat cortical neurons_GRC321-ONT23_S7_5-Fluorouracil_0.1


title: rat cortical neurons_GRC321-ONT24_S22_5-Fluorouracil_0.3


title: Y1_Fib_Sendai_Exp2

source_name: Dermal fibroblast

value: Dermal fibroblast


title: E1_MII_5_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/27 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, AM8567G).


title: noCOVID_noALI_rep6


title: Y2_d11_CD13_Sendai_Exp2


title: rat cortical neurons_GRC321-ONT22_S19_Cytosine Arabinoside_1

value: Cytosine Arabinoside


title: rat cortical neurons_GRC321-ONT21_S1_Cytosine Arabinoside_0.3


title: E1_MII_4_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/26 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, AM8566G).


title: Y1_d9_SSEA4_Sendai_Exp1


title: COVID_noALI_rep7

source_name: formalin fixed paraffin embedded lung, from COVID-19 case autopsy without acute lung injury


title: E1_MII_3_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/25 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, AM8565G).


title: COVID_noALI_rep6


title: rat cortical neurons_GRC321-ONT20_S10_Cytosine Arabinoside_0.1


title: Y1_d7_SSEA4_Sendai_Exp1


title: E1_MII_2_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/24 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, AM8564G).


title: COVID_noALI_rep5


title: noCOVID_noALI_rep2


title: Y2_d11_CD13_Sendai_Exp1


title: rat cortical neurons_GRC321-ONT19_S17_Cytosine Arabinoside_0


title: E1_MII_1_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/23 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, AM8563G).


title: noCOVID_noALI_rep1


title: Y1_d54_SSEA4_Sendai_Exp2

source_name: iPSC

value: iPSC


title: Y1_d7_CD13_Sendai_Exp1


title: rat cortical neurons_GRC321-ONT18_S23_Cypermethrin_10

value: Cypermethrin


title: COVID_noALI_rep4


title: Y1_d47_SSEA4_Sendai_Exp2


title: E1_FGO_18_Ribo

value: Full-grown oocyte


title: COVID_noALI_rep3


title: rat cortical neurons_GRC321-ONT17_S5_Cypermethrin_3


title: E1_FGO_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/21 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, AM8561G).


title: E1_FGO_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/22 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, AM8562G).


title: rat cortical neurons_GRC321-ONT16_S8_Cypermethrin_1


title: COVID_noALI_rep1


title: COVID_noALI_rep2


title: Y1_d9_CD13_Sendai_Exp1


title: COVID_ALI_rep7

source_name: formalin fixed paraffin embedded lung, from COVID-19 case autopsy with acute lung injury


title: rat cortical neurons_GRC321-ONT14_S3_Cypermethrin_0


title: Y1_d34_SSEA4_Sendai_Exp2


title: rat cortical neurons_GRC321-ONT13_S13_Deltamethrin_10

value: Deltamethrin


title: E1_FGO_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/19 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, AM8559G).


title: Y1_d21_CD13_Sendai_Exp2


title: E1_FGO_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/18 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, AM8558G).


title: rat cortical neurons_GRC321-ONT12_S20_Deltamethrin_3


title: rat cortical neurons_GRC321-ONT11_S16_Deltamethrin_1


title: Y1_d21_SSEA4_Sendai_Exp2


title: COVID_ALI_rep6

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).


title: COVID_ALI_rep4


title: Y1_d15_SSEA4_Sendai_Exp1


title: Y1_d15_CD13_Sendai_Exp1


title: E1_FGO_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/17 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, AM8557G).


title: Y1_d40_SSEA4_Sendai_Exp2

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.


title: rat cortical neurons_GRC321-ONT10_S11_Deltamethrin_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)


title: E1_FGO_11_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/16 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, AM8556G).


title: COVID_ALI_rep2


title: rat cortical neurons_GRC321-ONT9_S18_Deltamethrin_0


title: COVID_ALI_rep3


title: E1_FGO_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/20 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, AM8560G).


title: Y1_d13_SSEA4_Sendai_Exp1


title: E1_FGO_10_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/15 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, AM8555G).


title: rat cortical neurons_GRC321-ONT8_S24_Domoic Acid_1


title: DF_KD_0317_16

city: Boston

first: Single Cell

last: Sequencing Core

address: 72 E. Concord St

institute: BU Single Cell Sequencing Core

description: scRNA

data_processing:
BaseCalls performed using Illumina
Demultiplexing performed using Cell Ranger v4.0.0 with default settings
Reads were aligned to multiple reference genomes:  GRCh38 & mm10, GRCh38, mm10, and a custom SARS-CoV-2 reference genome using Cell Ranger v4.0.0 with --expect-cells=6000
DecontX was used on the GRCh38 & mm10 reference alignment to classify mouse and human cells
Genome_build: GRCh38 & mm10, GRCh38, mm10, custom SARS-CoV-2
Supplementary_files_format_and_content: matrix table with raw gene counts for all genes and samples

molecule: polyA RNA

organism:
Homo sapiens
Mus musculus
Severe acute respiratory syndrome coronavirus 2

source_name: Fetal lung xenograft

growth_protocol: Fetal lung xenografts were engrafted in NRG or NRG-Flk2-/- mice co-engrafted with human hematopoeitic stem cells.

extract_protocol:
fLX were processed as single cell suspension (HBSS minus Ca2+, Mg2+, and phenol red, 0.5 mg/mL Liberase TM, 1 mg/mL DNase I) and incubated at 37°C for 30 min with agitation every 10 min. Minced pieces were transferred to a 70 µm strainer on a 50 mL tube and mashed through using the plunger of a 3 mL syringe plunger. The strainer was washed two times with 1 mL of FACS buffer (1X PBS with 1% (v/v) FBS) and the cell suspension was centrifuged at 300 x g for 5 min at 4°C. The cell pellet was resuspended in 1 mL of ACK lysing buffer (ThermoFisher Scientific; #A1049201) and incubated for 2 min at room temperature. After incubation, 9 mL of FACS buffer was added to quench the lysis, samples were centrifuged at 300 x g for 5 min at 4°C, and the cell pellet was resuspended in 1 mL of a PBS 1%FBS solution. Cells were frozen down in a 90% FBS (Bio-Techne, R&D systems) 10% DMSO solution (ThermoFisher Scientific) and kept at -80°C. Four to five days following freezing, cells were thawed, and viability was assessed using Trypan blue (Fisher Scientific). Samples with ≥90% viability were then processed using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, as per manufacturer instructions, and single cell barcoding was performed using a Chromium instrument (10x genomics) located in the NEIDL BSL-3.
Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. Enzyme fragmentation, A tailing, adaptor ligation and PCR were then performed at the Boston University single-cell sequencing core to obtain final libraries containing P5 and P7 primers used in Illumina bridge amplification. Size distribution and molarity of resulting cDNA libraries were assessed via Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA). All cDNA libraries were sequenced on an Illumina NextSeq 500 instrument at the Boston University microarray and sequencing core according to Illumina and 10x Genomics guidelines with 1.4-1.8pM input and 1% PhiX control library spike-in (Illumina, USA).

treatment_protocol: Ten to fifteen weeks post engraftment, NRG or NRG-Flk2-/-

tag: mouse strain

value: NRG Flk2-/-

tag: engraftment

value: CD34+ Human HSC ; Fetal lung tissue

tag: cd34+ hsc donor

tag: fetal lung tissue donor

tag: treatment

tag: group

value: Naive

tag: infectious agent

value: SARS-CoV-2 WA-isolate

tag: inoculation dose

tag: time point post infection


title: E1_FGO_9_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/14 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, AM8554G).


title: Y1_d13_CD13_Sendai_Exp1


title: rat cortical neurons_GRC321-ONT7_S9_Domoic Acid_0.3

tag: tissue

value: rat cortical neurons

tag: chemical

tag: concentration

value: uM


title: COVID_ALI_rep1

value: lung

tag: symptomatic interval (days)


title: COVID_ALI_rep5


title: DF_KD_0317_15

description: scRNA

value: 2 days post infection


title: E1_FGO_7_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/12 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, AM8552G).

value: WT


title: DF_KD_0317_14

description: scRNA


title: Y1_d11_SSEA4_Sendai_Exp2

tag: cell type

tag: donor age

tag: days of reprogramming


title: rat cortical neurons_GRC321-ONT6_S14_Domoic Acid_0.1

value: Domoic Acid

tag: unit


title: rat cortical neurons_GRC321-ONT5_S21_Domoic Acid_0


title: E1_FGO_6_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/11 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, AM8551G).

tag: genotype

tag: developmental stage

tag: molecule

value: Ribosome protected fragment


title: Y1_d11_SSEA4_Sendai_Exp1

value: Reprogramming fibroblast


title: rat cortical neurons_GRC321-ONT3_S2_Haloperidol_1

value: Haloperidol


title: Y1_d11_CD13_Sendai_Exp1

value: Failing to reprogram fibroblast


title: DF_KD_0317_13

description: scRNA

tag: mouse strain

tag: engraftment

tag: cd34+ hsc donor

tag: fetal lung tissue donor

value: 7 days post infection


title: Y1_d11_CD13_Sendai_Exp2


title: E1_FGO_5_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/10 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, AM8550G).

value: Full-grown oocyte


title: rat cortical neurons_GRC321-ONT4_S15_Haloperidol_3


title: DF_KD_0317_11

description: scRNA

tag: treatment

tag: group

tag: infectious agent

tag: inoculation dose


title: rat cortical neurons_GRC321-ONT2_S12_Haloperidol_0.3

tag: tissue

tag: chemical

tag: concentration


title: E1_FGO_3_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/8 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, AM8548G).


title: rat cortical neurons_GRC321-ONT1_S6_Haloperidol_0


title: E1_FGO_8_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/13 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, AM8553G).


title: DF_KD_0317_9

description: scRNA

tag: time point post infection


title: E1_FGO_4_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/9 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, AM8549G).


title: O2_d9_CD13_Sendai_Exp1

tag: cell type

tag: donor age

tag: days of reprogramming


title: E1_FGO_2_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/7 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, AM8547G).

tag: genotype

tag: developmental stage


title: DF_KD_0317_10

description: scRNA

tag: mouse strain


title: E1_FGO_1_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/6 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, AM8546G).

tag: molecule


title: DF_KD_0317_8

description: scRNA

tag: engraftment

tag: cd34+ hsc donor


title: O2_d9_SSEA4_Sendai_Exp1


title: DF_KD_0317_12

description: scRNA

tag: fetal lung tissue donor

tag: treatment


title: DF_KD_0317_7

description: scRNA

value: NRG

value: Fetal lung tissue

tag: group

tag: infectious agent


title: O2_d7_CD13_Sendai_Exp1


title: O2_d7_SSEA4_Sendai_Exp1


title: O2_Fib_Sendai_Exp2

value: Dermal fibroblast


title: O2_d54_SSEA4_Sendai_Exp2

value: iPSC


title: E4_MII_Cnot6l_Het_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.
Genome_build: mm9

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep14 as control.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: Cnot6l Het

value: MII oocyte

value: polyA RNA


title: O2_d47_SSEA4_Sendai_Exp2


title: DF_KD_0317_5

description: scRNA

value: Naive

value: SARS-CoV-2 WA-isolate

tag: inoculation dose


title: O2_d34_SSEA4_Sendai_Exp2


title: E4_MII_Cnot6l_Het_smart_rep1

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep12 as control.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously


title: KI-023

city: Solna

first: Yizhou

last: Hu

state: Stockholm

address: C6 , Biomedicum Karolinska, Solnavägen 9,

country: Sweden

institute: Karolinska Institute

data_processing:
library strategy: single cell RNA-Seq: STRTseq
Read processing was performed as described (Islam et al., Nat Methods. 2014 Feb;11(2):163-6), except that we removed any RNA molecule (i.e. Unique Molecular Identifier) supported only by a single read ("singleton molecules"). This removed a large number of false positive molecules, artefacts that can arise by sequencing error, PCR-induced mutations or translocations and cross-contamination.
The first 6 bases of each read represent the random Unique Molecular Identifier used for molecule counting. After follows three or more Gs, stemming from the template switching at the mRNA 5' end during first strand cDNA synthesis. In some reads, one of the three Gs has been replaced by an A by the Illumina HiSeq software, representing failed base calling at that position.
We rejected cells that had less than 2000 mRNA molecules, more than 26,000 mRNA molecules (putative doublets) as well as cells that formed a separate cluster with no specific gene expression (putative damaged or dead cells). Genes that were detected at less than 4 molecules in the whole datasets were eliminated.
Genome_build: UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
Supplementary_files_format_and_content: HDF5 Loom file include raw counts and patient ID for each Sample

source_name: Glioma

growth_protocol: Surgical tissue samples of glioma patients were obtained in accordance with the protocol approved by regional ethical review board. Human glioblastoma tissues were minced with a scalpel, digested in Accutase/TrypLE (1:1) at 37°C for 15 min and triturated through 18 g and 21 g needles. The dissociated cells were resuspended in Neurocult NS-a basal medium (Stemcell) with addition of 1% B27 (Invitrogen), 0.5% N2 (Invitrogen), 10 ng/ml each of EGF and FGF2 (Peprotech) and plated on laminin-coated Primaria dishes (Corning) and cultured as adherent cells.

extract_protocol:
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.
Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase (‘tagmentation’). 1 μl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in Binding and Blocking buffer (10 mM Tris, 250 mM NaCl, 5 mM EDTA, 0.5% SDS) at the ratio of 1:20 and then added to each well. After incubation at room temperature for 15 min, all wells were pooled, the beads washed once with 100 μl Washing buffer (10 mM Tris-150 mM NaCl, 0.02% Tween), once with 100 μl QIAGEN Qiaquick PB and then twice with 100 μl Washing buffer. Restriction was performed to cleave 3′ fragments: the beads were incubated in 100 μl restriction mix (1x NEB CutSmart, 0.4 U/μl PvuI-HF enzyme) for 1 hour at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 μl to remove short fragments. The molar concentrations of the libraries were determined with KAPA Library Quant qPCR (Kapa Biosystems) and size distribution was evaluated after PCR (12cycles) using an Agilent BioAnalyzer. Sequencing was performed on an Illumina HiSeq 2000 with C1-P1-PCR2 as read 1 primer and C1-TN5-U as index read primer. Reads of 50 bp as well as 8 bp index reads corresponding to the cell-specific barcodes were generated.

tag: tissue

value: Brain

tag: tissue type

value: Glioma

tag: age

value: IDH-wt

value: human glioblastoma cells


title: KI-024

tag: cell type


title: KI-021


title: E4_MII_Cnot6l_KO_smart_rep2

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep18 as control.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

value: Cnot6l KO


title: E4_MII_Cnot6l_KO_smart_rep1

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep16 as control.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously


title: KI-020


title: O2_d40_SSEA4_Sendai_Exp2

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: Reprogramming fibroblast

tag: donor age


title: E4_MII_Cnot6l_Het_Ribo_re1

data_processing:
Library strategy: Ribo-seq
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.
Genome_build: mm9

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep4 as control.
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, AM8559G).

value: Ribosome protected fragment


title: O2_d29_SSEA4_Sendai_Exp2

tag: days of reprogramming


title: E4_MII_Cnot6l_KO_Ribo_re1

extract_protocol:
Oocytes were collected from 4-5 weeks old Cnot6l-/- and Cnot6l+/- female mice. The MI oocytes and MII oocytes were similarly collected as described above. Due the limited number of Cnot6l+/- mice, we used C57BL/6 mice as control for Ribo-seq of FGOs, also as control for mRNA-seq of FGOs. Due to data quality, we used MI oocytes Ribo-seq rep5 as control.
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, AM8560G).

tag: genotype


title: tdp1-/-_biological_rep_3

city: Sheffield

first: Sherif

last: El-Khamisy

state: South Yorkshire

address: Firth Court, Western Bank

department: Department of Molecular Biology and Biotechnology

institute: The University of Sheffield

description: Gene expression data from 5 dpf CPT-treated zebrafish embryos

hyb_protocol: Samples were hybridized using the Affymetrix standard protocol and the Hybridization, wash and stain solutions. Hybridization took place overnight in a rotating hybridization platform at 45°C for 16 hours. Post hybridization stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions

scan_protocol: Scanned on an Affymetrix® GeneChip Scanner 3000 according to manufacturer's protocols

data_processing: Data was processed and RMA normalized using the TAC 4.0 programme

label: Biotin

organism: Danio rerio

source_name: 5 dpf zebrafish embryos

label_protocol: Samples were porcessed using the Affymetrix WT plus protocol. 200ng of total RNA was taken forward to biotin labelling.

growth_protocol: Zebrafish embryos were raised in petri dishes in E3 media at 28C

extract_protocol:
At 5 dpf, embryos were harvested in trizol reagent, according to Peterson and Freeman (2009)
Peterson S.M., Freeman J.L. (2009). RNA Isolation from Embryonic Zebrafish and cDNA Synthesis for Gene Expression Analysis. JoVE. 30.http://www.jove.com/details.php?id=1470, doi: 10.3791/1470

treatment_protocol: At 5pm on 4 dpf, zebrafish embryos were transferred to 20ml of 500nM CPT in E3

value: 5 days post-fertilization

value: whole embryo

value: camptothecin (CPT)


title: O2_d29_CD13_Sendai_Exp2

value: Failing to reprogram fibroblast


title: DF_KD_0317_6

description: scRNA

extract_protocol:
fLX were processed as single cell suspension (HBSS minus Ca2+, Mg2+, and phenol red, 0.5 mg/mL Liberase TM, 1 mg/mL DNase I) and incubated at 37°C for 30 min with agitation every 10 min. Minced pieces were transferred to a 70 µm strainer on a 50 mL tube and mashed through using the plunger of a 3 mL syringe plunger. The strainer was washed two times with 1 mL of FACS buffer (1X PBS with 1% (v/v) FBS) and the cell suspension was centrifuged at 300 x g for 5 min at 4°C. The cell pellet was resuspended in 1 mL of ACK lysing buffer (ThermoFisher Scientific; #A1049201) and incubated for 2 min at room temperature. After incubation, 9 mL of FACS buffer was added to quench the lysis, samples were centrifuged at 300 x g for 5 min at 4°C, and the cell pellet was resuspended in 1 mL of a PBS 1%FBS solution. Cells were frozen down in a 90% FBS (Bio-Techne, R&D systems) 10% DMSO solution (ThermoFisher Scientific) and kept at -80°C. Four to five days following freezing, cells were thawed, and viability was assessed using Trypan blue (Fisher Scientific). Samples with ≥90% viability were then processed using the Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1, as per manufacturer instructions, and single cell barcoding was performed using a Chromium instrument (10x genomics) located in the NEIDL BSL-3.
Full-length, barcoded cDNAs were then amplified by PCR to generate sufficient mass for library construction. Enzyme fragmentation, A tailing, adaptor ligation and PCR were then performed at the Boston University single-cell sequencing core to obtain final libraries containing P5 and P7 primers used in Illumina bridge amplification. Size distribution and molarity of resulting cDNA libraries were assessed via Bioanalyzer High Sensitivity DNA Assay (Agilent Technologies, USA). All cDNA libraries were sequenced on an Illumina NextSeq 500 instrument at the Boston University microarray and sequencing core according to Illumina and 10x Genomics guidelines with 1.4-1.8pM input and 1% PhiX control library spike-in (Illumina, USA).

value: NRG

value: Fetal lung tissue

tag: time point post infection


title: tdp1-/-_biological_rep_2


title: tdp1WT_biological_rep_3


title: tdp1WT_biological_rep_2


title: tdp1-/-_biological_rep_1


title: KI-017


title: tdp1WT_biological_rep_1


title: E2_Ctr_L2C_fromPN5_L2C_smart

source_name: Preimplantation embryo

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/64 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 13-cell stage.

value: WT

tag: developmental stage

value: late 2-cell


title: E2_Ctr_L2C_fromPN3_L2C_smart

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/61 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 10-cell stage.

tag: molecule

value: polyA RNA


title: O2_d21_SSEA4_Sendai_Exp2


title: KI-016


title: O2_d21_CD13_Sendai_Exp2


title: O2_d15_SSEA4_Sendai_Exp1


title: E2_CHX_L2C_fromPN5_L2C_smart

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/57 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 6-cell stage.

value: late 2-cell stage


title: E2_CHX_L2C_fromPN3_L2C_smart

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/56 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 5-cell stage.


title: KI-015

value: Brain


title: O2_d15_CD13_Sendai_Exp1


title: E2_Ctr_L2C_fromE2C_L2C_smart

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/60 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 9-cell stage.


title: KI-014

value: Glioma


title: KI-013

value: IDH-wt


title: E2_CHX_L2C_fromE2C_L2C_smart

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/53 female mice mated with PWK/PhJ male mice.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN3/PN5 zygotes or early 2-cell embryos were collected and cultured in KSOM (Millipore; MR-121-D) containing either 0.1% DMSO or 25μg/ml CHX (Sigma; C4859), and released till embryos entering late 2-cell stage.


title: O2_d13_SSEA4_Sendai_Exp1


title: O2_d13_CD13_Sendai_Exp1


title: PC-3, rBC2LCN-positive subpopulation_3

city: Tsukuba

first: Yuzuru

last: Ito

state: Ibaraki

address: Central 6, Higashi 1-1-1

department: Biotechnology Research Institute for Drug Discovery

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Gene expression in human prostate cancer

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 ul of 2x HiRPM Hybridization Buffer was added to the fragmentation mixture and 480 ng cRNA was hybridized to Agilent SurePrint G3 Human GE 8x60K Microarray Kit (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60k array slides.

data_processing:
The scanned images were analyzed with Feature Extraction Software GX14.9.1 (Agilent) using default parameters.
Signal intensities of <1 were set to 1, and each chip was normalized to the 75th percentiles of all measurements from that chips. Baseline transformation of these data was not performed.

source_name: PC-3, passage 29, rBC2LCN-positive subpopulation

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng of total RNA using Low Input Quick Amp Labeling Kit (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: PC-3 cells were maintained in F-12K medium (ATCC, 30-2004) supplemented with 10 % FBS (GIBCO, 12483-020) and 1 % Penstrep (SIGMA, I0516-5ML). The cultures were incubated at 37 ºC in a humidified incubator with 5% CO2.

extract_protocol: Total RNA was prepared by using ISOGEN (Nippon Gene) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 spectrophotometer.

treatment_protocol: PC-3 cells were separated into rBC2LCN-positive and -negative subpopulations by live cell sorting using HiLyte Fluor 647-conjugated rBC2LCN.

value: Human prostate cancer

tag: cell line

tag: passage number

tag: rbc2lcn status

value: positive


title: E3_DRB_L2C_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/50 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, AM8557G).

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 11-cell stage.


title: O2_d11_SSEA4_Sendai_Exp2

value: Reprogramming fibroblast


title: KI-012

value: human glioblastoma cells


title: 70925-41

first: Tong

last: Lian

address: Zhongguancun South Street

department: Biotechnology Research Institute

institute: CAAS

data_processing:
All libraries were sequenced using the Sanger method by Illumina 1.9 Platform. The adapters, low-quality reads, and the reads containing poly-N were removed to obtain clean reads
The clean-reads were mapped to Zea mays B73 genome by using Hisat software (v2.1.0) with setting non-strand-specific and other default parameters
The clean reads were assembled using Sam tools software, Cufflink software (v2.2.1) and Cuffcompare software (v2.2.1).
The counts were output using htseq-count(v0.11.2)
The annotation of genes refer to Zea mays B73 genome by Trinotate (v3.2.0).
Genome_build: Zea mays B73 genome
Supplementary_files_format_and_content: normalized_counts for each transcript and sample,  location of transcripts, annotation of transcripts

organism: Zea mays

source_name: JI63-Mature kernel

growth_protocol: DAN3130 and JI63 inbred lines are originated from China, belonging to the NSS subpopulation, JI63 with pedigree being (127-32 ×Tie84) × (Wei24 × Wei20) and DAN3130 with pedigree being American hybrid P78599. They were grown at Langfang, Hebei province, in the summer of 2018. Fresh kernel samples were collected on 24, 35 days after pollination then frozen in liquid nitrogen immediately. Mature kernel samples were harvested after all plants turned yellow. Three biological replicates of each stage were harvested.

extract_protocol:
Total RNA of DAP 24, DAP 35 and mature kernels were extracted using BAIXU Maize Kernel Total RNA Extraction Kit (Beijing, China). To eliminate any residual genomic DNA, total RNA was treated with RNase-free DNase I (New England Biolabs) and the concentration of RNA were determined using Nanodrop-2000. Total RNA was used to synthesize ﬁrst-strand complementary DNA (cDNA) using the RevertAid First Strand cDNA Synthesis kit (Fermentas).
RNA-Seq library preparation and sequencing were carried out by BEIJING BAIXU BIOTECH CO., LTD, Beijing, China. All libraries were sequenced using the Sanger method by Illumina 1.9 Platform. The adapters, low-quality reads, and the reads containing poly-N were removed to obtain clean reads. Then the clean-reads were mapped to Zea mays B73 genome by using Hisat software (v2.1.0) with setting non-strand-specific and other default parameters. Afterwards, the clean reads were assembled using Sam tools software, Cufflink software (v2.2.1) and Cuffcompare software (v2.2.1).

tag: cultivar

value: kernel

value: Mature kernel


title: E3_DRB_E2C_smart

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.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 10-cell stage.

value: early 2-cell


title: PC-3, rBC2LCN-positive subpopulation_4

source_name: PC-3, passage 30, rBC2LCN-positive subpopulation


title: KI-009

extract_protocol:
Fluidigm C1 Autoprep System  Cells medium (10-17 micrometer) microfluidic was used to capture the cells. 14 microlitre of cell suspension (approx. 800 cells/microlitre in N2 culturing medium with DNaseI) was mixed with 7 microlitre C1 Suspension Reagent after filtering. Single-cells were then captured for 30 min at 4°C. The protocol for Lysis, RT and PCR was performed as previously described  (Islam et al., Nat Methods. 2014 Feb;11(2):163-6). Amplified cDNA was harvested with 13 microlitre Harvest Reagent and cDNA library quality was measured on an Agilent BioAnalyzer. Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase as described previously. 1 microlitre Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in 20 microlitre Binding and Blocking buffer (10mM Tris, 250mM NaCl, 5mM EDTA, 0.5% SDS) and added to each well. After 15 min incubation at room temperature, all wells were pooled, the beads washed once with 100 microlitre Washing buffer (10mM Tris-150mM NaCl, 0.02% Tween), once in 100 microlitre Qiagen Qiaquick PB and then twice using 100 microlitre Washing buffer. Restriction was performed to cleave fragments: the beads were incubated in 100 microlitre restriction mix (1x NEB CutSmart, 0.4 U/microlitre PvuI-HF enzyme) for 1h at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 microlitre to remove short fragments.
Cell barcoding and fragmentation was performed in a single step using Tn5 DNA transposase (‘tagmentation’). 1 μl Dynabeads MyOne Streptavidin C1 beads (Invitrogen) were resuspended in Binding and Blocking buffer (10 mM Tris, 250 mM NaCl, 5 mM EDTA, 0.5% SDS) at the ratio of 1:20 and then added to each well. After incubation at room temperature for 15 min, all wells were pooled, the beads washed once with 100 μl Washing buffer (10 mM Tris-150 mM NaCl, 0.02% Tween), once with 100 μl QIAGEN Qiaquick PB and then twice with 100 μl Washing buffer. Restriction was performed to cleave 3′ fragments: the beads were incubated in 100 μl restriction mix (1x NEB CutSmart, 0.4 U/μl PvuI-HF enzyme) for 1 hour at 37°C. Finally, the beads were washed three times with Washing buffer, then resuspended in 30 μl ddH2O and incubated for 10 min at 70°C to elute the DNA. AMPure beads XP (Beckman Coulter) were used at 1.8x volume and eluted in 30 μl to remove short fragments. The molar concentrations of the libraries were determined with KAPA Library Quant qPCR (Kapa Biosystems) and size distribution was evaluated after PCR (12cycles) using an Agilent BioAnalyzer. Sequencing was performed on an Illumina HiSeq 2000 with C1-P1-PCR2 as read 1 primer and C1-TN5-U as index read primer. Reads of 50 bp as well as 8 bp index reads corresponding to the cell-specific barcodes were generated.


title: 70925-40


title: PC-3, rBC2LCN-positive subpopulation_2

source_name: PC-3, passage 34, rBC2LCN-positive subpopulation


title: KI-008


title: PC-3, rBC2LCN-negative subpopulation_3

source_name: PC-3, passage 29, rBC2LCN-negative subpopulation

value: negative


title: PC-3, rBC2LCN-negative subpopulation_4

source_name: PC-3, passage 30, rBC2LCN-negative subpopulation


title: 70925-39


title: O2_d11_CD13_Sendai_Exp2

source_name: Failing to reprogram fibroblast

value: Failing to reprogram fibroblast


title: 70925-35

source_name: DAN3130-Mature kernel


title: E3_Ctr_L2C_smart

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.
The RNA-seq libraries were generated using the Smart-seq2 protocol as described previously

treatment_protocol: PN5 zygotes were obtained and cultured in KSOM containing either 0.1% DMSO or 60 μM DRB (Sigma; D1916). DRB was washed it away at the early 2-cell stage and embryos were continued to be cultured in KSOM till late 7-cell stage.