title: UM90-14 Ly209 + Xenofree media Passage 28

city: Ann Arbor

first: Sundeep

last: Kalantry

state: Michigan

address: 1241 E Catherine Street

department: Human Genetics

institute: University of Michigan

data_processing:
Quality Control, FastQC
Read alignment, STAR
Peak calling, FeatureCounts
Genome_build: hg19
Supplementary_files_format_and_content: .txt files containing raw and normalized read counts

growth_protocol: Cells were cultured on human fibroblast feeders in the indicated media formulation (Xenofree, mTeSR). GSK-3 inhibitors were added to some samples, as indicated (BIO, Ly209, LiCl).

extract_protocol:
Total RNA was collected from TRIzol according to the manufacturer's instructions.
cDNA libraries were created and sequencing was performed by Girihlet Inc.

treatment_protocol: Some samples were treated with GSK-3 inhibitors, as indicated.

value: hESC

tag: growth

value: Ly209 + Xenofree media Passage 28


title: NeuNT/H1074R tumor 3863

status: Public on Mar 11 2022

type: RNA

city: Montreal

first: Tung

last: Bui

state: Quebec

address: 1160 Pine Ave. W, R507

department: Biochemistry

country: Canada

institute: McGill University

hyb_protocol: 3.5 mg DNA target was hybridized on the GeneChip Mouse Gene 2.0 ST Array (Affymetrix)

scan_protocol: The microarrays were finally scanned on the GeneChip Scanner 3000 (Affymetrix).

data_processing: Raw data were first processed to perform gene-level normalization and quality control using Affymetrix Expression Console software (Affymetrix). Processed data were next subjected to gene-level differential expression analysis using Affymetrix Transcriptome Analysis Console software with filter criteria as following: linear fold change < 2 or > 2 and ANOVA P value (condition pair) < 0.05.

label: biotin

molecule: total RNA

organism: Mus musculus

source_name: mammary tumor

label_protocol: Fragmentation and labeling were performed to produce ssDNA with the Affymetrix GeneChip WT Terminal Labeling Kit according to the manufacturer’s instructions (Affymetrix)

growth_protocol: Primary mammary tumors collected from transgenic mice

extract_protocol: Total tumor RNA extracted using Rneasy kit (Qiagen)

tag: strain

value: FVB

tag: tissue

value: mammary tumor

tag: genotype


title: NeuNT/H1074R tumor 149


title: NeuNT tumor 1000

value: NeuNT


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-257

type: SRA

city: Seattle

first: Chengxiang

last: Qiu

state: WA

address: William H. Foege Hall, 3720 15th Ave NE

department: Genome Sciences

country: USA

institute: University of Washington

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library

library_source: transcriptomic

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file (using scanpy.read_loom to open)

molecule: polyA RNA

source_name: mouse embryos

growth_protocol: The C57BL/6 mice were obtained from The Jackson Laboratory (Bar Harbor, ME) and plug matings were set up. Noon on the day of the vaginal plug was considered as embryonic day (E) 0.5. Dissections were done as previously described76 and all embryos were immediately snap frozen in liquid nitrogen. All animal procedures were in accordance with institutional, state, and government regulations (IACUC protocol 4378-01).

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer.
The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%. Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping. The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi).
Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer. Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well.
Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes). After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including 4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.
After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen).
1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter).
In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate. For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.

tag: developmental stage


title: UM90-14 BIO + Xenofre media Passage 28

organism: Homo sapiens

tag: cell type

tag: cell line

value: BIO + Xenofre media Passage 28


title: NeuNT/H1074R tumor 9918


title: NeuNT tumor 2589


title: NeuNT tumor 1001


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-237


title: UM90-14 mTeSR media Passage 28

value: mTeSR media Passage 28


title: NeuNT/H1074R tumor 3862


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-235


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-249


title: NeuNT tumor 1807


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-234


title: HFF Passage 28

source_name: HFF

value: human foreskin fibroblast feeders

value: HFF Passage 28


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-254


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-255


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-245


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-233


title: HFF Passage 6

value: HFF Passage 6


title: UM90-14 Xenofree media Passage 28

value: Xenofree media Passage 28


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-232


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-231


title: UM90-14 Xenofree media Passage 6

value: Xenofree media Passage 6


title: UM90-14 LiCl + Xenofree media Passage 28

value: LiCl + Xenofree media Passage 28


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-240


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-230


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-229


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-236


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-227


title: SN_d5

city: Verona

first: Francisco

middle: Miguel Angel

last: Bianchetto-Aguilera

state: VR

address: Strade le Grazie, 8

department: Department of Medicine

country: Italy

institute: University of Verona

data_processing:
Reads were quality-filtered according the Illumina pipeline
reads were mapped onto the Ensembl human transcriptome (version 96) and quantified at the transcript level using kallisto
transcripts were combined to gene level using tximport packages
Gene counts were normalized among various samples using DESeq2
Gene abundance was indicated as FPKM, and genes with FPKM equal or higher than 1 in at least one sample were considered as expressed and further analysed
Differentially expressed genes were identified using DESeq2, by using as selection parameter an adjusted p-values (padj) lower than 0.01
Genome_build: Ensembl human transcriptome (version 96)
Supplementary_files_format_and_content: tab-delimited text files include sample specific read counts per gene in FPKM

source_name: bone marrow

extract_protocol:
Total RNA was extracted after cell lysis by the RNeasy Mini Kit (Qiagen). To completely remove any possible contaminating DNA, an on-column DNase digestion with the RNase-free DNase set (Qiagen) was performed during total RNA isolation.
Libraries for transcriptome analysis were prepared using Smart-seq2 protocol (PMID: 24056875)

value: segmented neutrophils

value: bone marrow

tag: donor id


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-225


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-224


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-223


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-222


title: BC_d5

value: band cells


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-226


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-220


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-221


title: MCF-7_siRNA1

city: Guangzhou

first: LiuTao

last: Chen

address: Waihuan West Road 132, University TownHigher Education Mega Center

country: China

institute: The Sun YAT-SEN UNIVERSITY

data_processing:
Library strategy: IVT-SAPAS
Filtering and trimming of the reads was performed with Perl scripts
reads were mapped to the human genome (hg19) with Bowtie
Cleavage sites were cluster.txted into poly(A) sites as described previously
3' UTR switching for each gene between the cancer cell lines and the normal cell line was detected by a test of linear trend alternative to independence
Assembly: hg19
Supplementary files format and content: tab-delimited text files with raw gene counts for every gene and every sample

growth_protocol: Human HEK293T cells were cultured in DMEM supplemented with 10% FBS. The human breast cancer cell line MCF-7 was cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 10 µg/ml human recombinant insulin.

extract_protocol:
total RNA were extracted by TRIZOL following the manufacturer’s instructions
Genomic DNA was digested with DNase I (Ambion), and total RNA was fragmented by heating at 95 °C for 25 mins. The first strand cDNA was transcribed by an anchored oligo d(T) tagged with Illumina A adaptor and T7 promoter, and then the second strand was synthesized to perform in vitro transcription. The second round of reverse transcription was performed with random primers, and then cDNA was used as a template to perform PCR with 15 cycles to amplify the library. Finally, 200-500 bp fragments of the PCR product purified with AMPure XP Beads (Beckman Coulter) were selected for size selection. The final pooled libraries were quantified and sequenced with HiSeq 2500.

treatment_protocol: Two different siRNA for 48h

value: breast

value: epithelial cells

tag: age

value: 69 years

tag: knockdown

value: YTHDC1 siRNA


title: MCF-7_siRNA2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-217


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-219


title: BC_d4


title: MCF-7_NC

value: control


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-218


title: HEK293T_siRNA2

value: kidney

value: epithelial-derived stem cells

value: fetus


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-215


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-213


title: HEK293T_siRNA1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-212


title: PMN_d8

source_name: blood

value: neutrophil

value: blood


title: MM_d5

value: metamyelocytes


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-210


title: HEK293T_NC


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-211


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-207


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-208


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-209


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-228


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-205


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-206


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-204


title: SN_d4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-203


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-202


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-200


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-199


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-198


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-201


title: MY_d4

value: myelocytes


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-197


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-194


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-195


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-196


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-193


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-216


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-192


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-190


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-214


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-189


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-191


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-188


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-184


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-182


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-185


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-186


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-183


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-181


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-187


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-177


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-175


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-178


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-179


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-174


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-176


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-172


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-173


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-171


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-169


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-170


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-168


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-167


title: CMP_d3

value: common myeloid progenitors (CMPs)


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-166


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-165


title: Nsp14_MPA_rep_3

city: Waltham

first: Sebastian

last: Kadener

state: MA

address: 415 South Street

institute: Brandeis University

description:
RNA-seq polyA+
Nsp14 transfected HEK293T and treated with MPA 0.5uM 8h after transfection
NM3_S12_new
normalized_counts_MPA

data_processing:
Alignment to the human genome (hg38) using STAR
CircRNA expression anlysis using find_circ.py (Memczak S et al 2013)
Counting number of reads for each gene using ESAT for polyA data and featureCounts for total RNA data
Genome_build: hg38
Supplementary_files_format_and_content: Table with reads counts for each gene.
Supplementary_files_format_and_content: Table with  back-spliced reads and linear spliced reads for total RNA data

growth_protocol: HEK293T cells were a kind gift from Dr. Marr at Brandeis University. HEK293T were maintained in Dulbecco's Modified Eagle's Medium (Genesee Scientific, 25-500), supplemented with 10% serum (FetalPlex, Gemini Bio/Fisher, # 100-602), and 1X Penicillin-Streptomycin (Penicillin-Streptomycin 100x, Genesee Scientific, 25-512).

extract_protocol:
Total RNA was extracted using Trizol reagent (Sigma) and treated with DNase I (NEB) following the manufacturer's protocol.
For 3' RNA sequencing libraries, 75ng of RNA were used as input  following CelSeq2(Hashimshony et al., 2016) protocol, changing the UMI to 6 bases. Sequencing was performed on Illumina NextSeq 500. For total RNA libraries 40ng of rRNA depleted RNA was used as a starting material for library preparation. NEBNext rRNA Depletion kit( NEB #E7405) was used to deplete ribosomal RNA. Libraries were prepared using the NEXTFLEX® Rapid Directional RNA-Seq Kit 2.0 by PerkinElmer, following the manufacturer’s instructions. The samples were sequenced by Novogene (Novogene Corporation Inc. 8801 Folsom BLVD, Suite 290, Sacramento, CA 95826) with Hiseq-4000.
3' RNA sequencing libraries stranded, CelSeq2 based. For total RNA libraries, stranded  ligation-based.

treatment_protocol:
Plasmids pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Puro proteins are a gift from Nevan Krogan (Addgene)(Gordon et al., 2020). The day before transfection, 0.35*106 cells per well were plated in 12 well-plates. Then, cells were transfected with PEI (Polyethylenimine 25kD linear from Polysciences, cat# 23966-2). Briefly, 1500ng of total DNA (1200 ng of pLVX-EF1alpha-SARS-CoV-2-proteins-2xStrep-IRES-Pur + 300ng of pLVX-EF1alpha-eGFP-2xStrep-IRES-Puro ) were incubated at RT for 20 min with PEI, with a ratio 3 1=PEI
DNA in 100ul of serum free medium, and the mixture was added to the cells.  RNA extraction was performed at the indicated timepoint after transfection, or at 48h if not indicated.

tag: transfection

tag: timepoint

value: 48h post transfection

tag: treatment

value: MPA 0.5uM


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-164


title: Nsp14_MPA_rep_2

description:
RNA-seq polyA+
Nsp14 transfected HEK293T and treated with MPA 0.5uM 8h after transfection
NM2_S11_new
normalized_counts_MPA


title: Nsp14_MPA_rep_1

description:
RNA-seq polyA+
Nsp14 transfected HEK293T and treated with MPA 0.5uM 8h after transfection
NM1_S10_new
normalized_counts_MPA


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-162


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-163


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-160


title: Nsp14_DMSO_rep_3

description:
RNA-seq polyA+
Nsp14 transfected HEK293T
ND3_S9_new
normalized_counts_MPA

value: DMSO


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-161


title: Nsp14_DMSO_rep_2

description:
RNA-seq polyA+
Nsp14 transfected HEK293T
ND2_S8_new
normalized_counts_MPA


title: Nsp14_DMSO_rep_1

description:
RNA-seq polyA+
Nsp14 transfected HEK293T
ND1_S7_new
normalized_counts_MPA


title: Control_MPA_rep_3

description:
RNA-seq polyA+
GFP transfected HEK293T and treated with MPA 0.5uM 8h after transfection
GM3_S6_new
normalized_counts_MPA

value: eGFP


title: Farm.EO_fish1

city: ST JOHN'S

first: Shahinur

middle: S.

last: Islam

state: Newfoundland and Labrador

address: 230 Elizabeth Avenue

institute: Memorial University of Newfoundland

hyb_protocol: Equal quantities (825 ng) of labeled aRNA from each experimental sample and the common reference were fragmented and co-hybridized to a microarray, as per manufacturer protocols (Agilent, Mississauga, ON, CA). Hybridizations were conducted at 65oC for 17 h at 10 rpm rotation in an Agilent hybridization oven. Array slides were then washed with Gene Expression Wash Buffer 1 and 2 (Agilent) immediately after hybridization according to the manufacturer’s guidelines, and residual wash buffer was removed by centrifuging at 200 x g for 5 min at room temperature.

scan_protocol: Each microarray slide was scanned (at 5 µm resolution and 90% of laser power) using a ScanArray Gx Plus scanner and ScanArray Express software (v.4.0; Perkin Elmer, Waltham, MA, USA). The Cy5 and Cy3 photomultiplier tube (PMT) sensitivities were adjusted to balance the fluorescence signal.

data_processing: The TIFF images were extracted using Imagene software (v.9.0; Biodiscovery Inc., El Segundo, CA, USA). The removal of low-quality/flagged spots, background signal correction, LOWESS normalization, and data transformation (log2) were performed using R software version 3.6.1 and the Bioconductor package mArray.

organism: Salmo salar

source_name: Whole fry tissue, Farm.EO, individual fish

label_protocol: Differences among the six cross types in the whole-body transcriptome were assessed by contrasting individual RNA samples against a common reference pool of equal quantities of RNA from all 36 fry. In short, anti-sense amplified RNA (aRNA) was prepared using Ambion’s Amino Allyl MessageAmp II aRNA Amplification kit (Life Technologies). The aRNA samples were column-purified and subjected to the quality and quantity assessment by agarose gel electrophoresis and Nanodrop UV spectrophotometry. A common reference was prepared by pooling 10 µg of each of the 36 experimental aRNA samples. Twenty micrograms of each experimental and common reference aRNA sample was then precipitated overnight following standard molecular biology procedures and re-suspended in coupling buffer. Subsequently, individual and common reference aRNA were labeled with Cy5 and Cy3 (GE HealthCare, Mississauga, ON, CA), respectively. The labeling efficiency was quantified using the “microarray” function in the ND-1000 Nanodrop UV spectrophotometer.

extract_protocol: Frozen whole fry were homogenized individually in TRIzol Reagent (Invitrogen/Life Technologies, Burlington, CA) with stainless steel beads (5 mm; QIAGEN, Mississauga, ON, CA) using a TissueLyser (QIAGEN), following the manufacturer’s instructions, then further disrupted using QIAshredder spin columns (QIAGEN), and then subjected to RNA extraction. The resulting 30 μg of each total RNA samples were treated with DNase I (6.8 Kunitz units; RNase-free DNase Set, QIAGEN) with the manufacturer’s buffer (1 x final concentration) to degrade residual genomic DNA, and then purified using the RNeasy Mini Kit (QIAGEN) following the manufacturer’s instructions. RNA integrity was confirmed by 1% agarose gel electrophoresis, and RNA purity was assessed using A260/280 and A260/230 via NanoDrop UV spectrophotometry (NanoDrop, Wilmington, DE, USA) at both the pre-cleaned and the cleaned RNA stages. Only high-purity (A260/280 > 2.0, A260/230 > 1.8) column-cleaned RNA samples were used in RNA amplification and cDNA synthesis reactions.

treatment_protocol: The microarray experiment comprised 36 arrays: 6 cross types (Farm.NA, Hyb.NAff, Wild, Hyb.EOwf, Hyb.EOff, and Farm.EO) x 3 families per cross type x 2 biological replicates per family. The origin of Farm.NA is the Saint John River, New Brunswick, Canada. Farm.NA gametes were collected from the aquaculture company Northern Harvest, based in Southern Newfoundland, Canada. Farm.EO, a Norwegian origin farm strain, is now produced at an Icelandic facility (StofnFiskur), from where the gametes were shipped by air for the experimental crosses. The wild population was derived from the Northeast Placentia River, Newfoundland, Canada. F1 Farm.NA(f)-x-Wild(m) hybrid (referred to as “Hyb.NAff”); F1 Farm.EO(m)-x-Wild(f) hybrid (referred to as “HybEOwf”); and F1 Farm.EO(f)-x-Wild(m) hybrid (referred to as “Hyb.EOff”). Atlantic salmon whole fry were euthanized with AQUALIFE TMS (MS-222; 400 mgl-1, buffered with 0.1 M sodium bicarbonate), immediately flash-frozen in liquid nitrogen and stored at -80 ºC until homogenized.

value: Whole fry

tag: life stage

value: Fry

source_name: pool of RNAs from whole fry tissues invovled in the microarray experiment


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-158


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-159


title: Farm.EO_fish3


title: Control_MPA_rep_2

description:
RNA-seq polyA+
GFP transfected HEK293T and treated with MPA 0.5uM 8h after transfection
GM2_S5_new
normalized_counts_MPA


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-157


title: Farm.EO_fish5


title: Farm.EO_fish4


title: Farm.EO_fish2


title: Hyb.EOff_fish5

source_name: Whole fry tissue, Hyb.EOff, individual fish


title: Hyb.EOff_fish4


title: Hyb.EOff_fish6


title: Hyb.EOff_fish2


title: Hyb.EOff_fish1


title: Control_MPA_rep_1

description:
RNA-seq polyA+
GFP transfected HEK293T and treated with MPA 0.5uM 8h after transfection
GM1_S4_new
normalized_counts_MPA


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-156


title: Control_DMSO_rep_3

description:
RNA-seq polyA+
GFP transfected HEK293T
GD3_S3_new
normalized_counts_MPA


title: Abdomino-pelvic adipose tissue from patient3

city: Toulouse

first: David

last: Estève

address: 205 route de narbonne

country: France

institute: Institut de pharmacologie et de biologie structurale-IPBS

data_processing:
Reads were preprocessed in order to remove adapter and low-quality sequences (Phred quality score below 20). After this preprocessing, reads shorter than 40 bases were discarded for further analysis. These preprocessing steps were performed using cutadapt version 1.10.
Reads were mapped to rRNA sequences using bowtie version 2.2.8, and reads mapping to rRNA sequences were removed for further analysis. Reads were mapped to spike sequences using bowtie version 2.2.8, and reads mapping to spike sequences were removed for further analysis.
Preprocessed reads were mapped onto the Homo sapiens genome assembly hg38 by using STAR v2.5.3a
Gene expression quantification was performed from uniquely aligned reads using htseq-count [6] version 0.6.1p1, with annotations from Ensembl version 91
Raw count and Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.  In short, exons from all isoforms of a gene were merged to calculate the median of transcript length. The number of reads falling in the exons were counted and normalized by the median of transcript length and by the size of the library
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts, RPKM values and medianof transcript length for each Sample

source_name: Adipose tissue

extract_protocol:
RNA were harvested with qiazol and Rneasy minikit
RNA-Seq libraries were generated from 400 ng of total RNA by using the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA), according to the manufacturer's instructions

treatment_protocol: Samples were frozed in liquid nitrogen and stored at -80°C until RNA extraction

tag: individual

value: Abdomino pelvic adipose


title: Control_DMSO_rep_2

description:
RNA-seq polyA+
GFP transfected HEK293T
GD2_S2_new
normalized_counts_MPA


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-154


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-155


title: Hyb.EOwf_fish6

source_name: Whole fry tissue, Hyb.EOwf, individual fish


title: Abdomino-pelvic adipose tissue from patient2


title: Hyb.EOwf_fish5


title: Abdomino-pelvic adipose tissue from patient1


title: Control_DMSO_rep_1

description:
RNA-seq polyA+
GFP transfected HEK293T
GD1_S1_new
normalized_counts_MPA


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-153


title: Hyb.EOff_fish3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-152


title: Periprostatic adipose tissue from patient3

value: Periprostatic adipose


title: Nsp14_48hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_48hrs_3_S30_
nsp14_timepoints_normalized_counts

value: no treatment


title: Nsp14_48hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_48hrs_2_S29_
nsp14_timepoints_normalized_counts


title: Hyb.EOwf_fish4


title: Periprostatic adipose tissue from patient2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-150


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-151


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-149


title: Hyb.EOwf_fish1


title: Periprostatic adipose tissue from patient1


title: Ctrl_48hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ctrl_48hrs_3_S27_
nsp14_timepoints_normalized_counts


title: MDS iPSC TP53 R209fs-/+ , del5q HPC 2

first: Sergei

last: Doulatov

address: 1705 N.E. Pacific Street

department: Hematology

description:
11-P53-15-d23.12-P53-15.merge.hic
11-P53-15-d23.PC1.bw
11-P53-15-d23.12-P53-15.insulationScore.bw
11-P53-15-d23.12-P53-15.TAD.2D.bed
11-P53-15-d23.loop.2D.bed

library_source: genomic

data_processing:
Hi-C data were processed using Juicer (Durand et al., 2016) with the default parameters. For each of the 12 libraries, the .fastq files from two runs were merged. Adapter trimming (adapter sequence: 5'GGTGAGGCTGAGGGATC3') was performed by cutadapt and reads shorter than 20bp after adapter removal were discarded. Reads were mapped to reference human genome assembly hg38 using BWA. PCR duplicates or reads with mapping quality score (MAPQ) <30 were removed. Then the valid read pairs were binned and counted in matrices of 5kb, 10kb, 25kb, 50kb, 100kb, and 250kb resolution. KR normalization was used to correct bias and generate balanced Hi-C interaction matrices for subsequent analyses. Contact matrices and virtual 4C tracks by pileup of 5kb bins were generated using Juicebox (Robinson et al., 2018). A/B compartments calling were performed per chromosome from KR normalized intra-chromosomal Hi-C matrix at 100kb resolution. First, O/E (observed/expected) matrix was calculated. Then we transformed the O/E matrix into a z-score matrix, which was then converted to a Pearson correlation matrix. PCA (principal component analysis) was performed on the correlation matrix and the first eigenvector (PC1) of the PCA was used to identify A/B compartments. For each chromosome, the assigning of eigenvector sign orientation (positive or negative) to correct A/B compartments was done by counting gene density such that A compartment was more gene-rich than B compartment. We used both insulation score and directionality index (DI) to call TADs (topologically associating domains). Insulation score analysis was performed as previously reported (Crane et al., 2015). Hi-C interaction matrices at 10kb resolution were used. As for parameters, insulation delta span (-ids) was set to 250kb, and insulationSquareSize (-is) was set to 100kb. Other parameters were the same as the original paper. We also calculated directionality index (DI) as previously reported (Dixon et al., 2012) to identify TADs. The directionality index is calculated as the degree of upstream or downstream bias. Similar to the insulation score, Hi-C interaction matrices at 10kb resolution were used and the window size of upstream/downstream patterns is set to 1Mb. Then we used a hidden Markov model (HMM) to determine the directionality bias and TADs from the calculated directionality index. The mean insulation score at TAD boundaries was generated using the deepTools package (Ramírez et al., 2016). HOMER (Heinz et al., 2010) was used to identify chromatin loops from Hi-C data. Briefly, loops are identified as significant interactions as two regions interact at a high frequency with one another. Hi-C interaction matrices at 10kb resolution were used. Overlapping window size (-window) was set to 25kb and maximum interaction distance (-maxDist) was set to 5Mb.
.hic matrices (Juicer), .bw PC1 scores, .bw insulation socre, .bed TAD , .bed loops
STAR, Subread, DESeq2
BWA, Juicer, HOMER
CellRanger, Monocle 3
Genome_build: hg38
Supplementary_files_format_and_content: .csv, .bw, .bed, .hic, .rds

molecule: genomic DNA

source_name: Differentiated and immortalized progenitor cells

extract_protocol: Bone marrow cells were obtained from MDS patients according to the institutional guidelines approved by the University of Washington. iPSC reprogramming, differentiation, and MDS HPC cell line generation was performed as described previously(Hsu et al., 2019). iPSC-MDS HPCs were cultured in StemSpan SFEM (StemCell Technologies) plus 50 ng/mL SCF, 50 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL-6, 10 ng/ml IL-3 (Peprotech), and doxycycline (2 μg/ml) (Sigma). Cells were maintained at 1x106 cells/ml and medium changed every 3 to 4 days.


title: Ctrl_48hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ctrl_48hrs_2_S26_
nsp14_timepoints_normalized_counts


title: Nsp14_48hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_48hrs_1_S28_
nsp14_timepoints_normalized_counts


title: Hyb.EOwf_fish3


title: Hyb.EOwf_fish2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-148

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: MDS iPSC TP53 R209fs-/+ , del5q HPC 1

value: Differentiated and immortalized progenitor cells


title: Ctrl_48hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ctrl_48hrs_1_S25_
nsp14_timepoints_normalized_counts


title: MDS iPSC TP53 R209fs-/+ HPC 2

description:
9-P53-5-d29.10-P53-2.merge.hic
9-P53-5-d29.PC1.bw
9-P53-5-d29.10-P53-2.insulationScore.bw
9-P53-5-d29.10-P53-2.TAD.2D.bed
9-P53-5-d29.loop.2D.bed


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-146


title: MY_d5

value: bone marrow


title: MDS iPSC TP53 R209fs-/+ HPC 1


title: Nsp14_24hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_24hrs_3_S24_
nsp14_timepoints_normalized_counts

value: 24h post transfection


title: Wild_fish6

source_name: Whole fry tissue, Wild, individual fish


title: Nsp14_24hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_24hrs_2_S23_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-145


title: NT HiC LMNB1 2

description:
7-LB1-3.8-L3-NT.merge.hic
7-LB1-3.PC1.bw
7-LB1-3.8-L3-NT.insulationScore.bw
7-LB1-3.8-L3-NT.TAD.2D.bed
7-LB1-3.loop.2D.bed

source_name: Neutrophils in vitro differentiated from cord blood

extract_protocol: CB CD34+ cells were cultured in IMDM (ThermoFisher, cat. # 12440-053) + 20% FBS (Sigma, cat. # F0926) and 100 ng/mL G-CSF (Peprotech) for 12 days. Media was changed every 3-4 days. iPSC-MDS HPCs were cultured without doxycycline for 4 days in StemSpan SFEM  + 50 ng/mL SCF, 50 ng/mL FLT3, 50 ng/mL TPO, 50 ng/mL IL-6, and 10 ng/mL IL-3. Cells were then transferred to IMDM + 20% FBS (Sigma) and 100 ng/mL G-CSF (Peprotech) for 6 days, with one media change at day 3. At the end of differentiation, neutrophils were labeled with CD66b-PE (BD, cat. # 561650) by incubating with the antibody for 10 min at RT, and neutrophils purified using the MACS CD66b+ selection column following kit protocol (Miltenyi, cat. # 130-048-801).

tag: shRNA lentivirus

value: LB1 LMNB1 shRNA Sigma, TRCN0000029271


title: Wild_fish4


title: Wild_fish3


title: Nsp14_24hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_24hrs_1_S22_
nsp14_timepoints_normalized_counts


title: Wild_fish2


title: NT HiC LMNB1 1

value: Neutrophils in vitro differentiated from cord blood


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-144


title: NT RNAseq LMNB1 2

data_processing:
RNA sequencing was performed at Genewiz using the standard pipeline. Samples were processed on the Illumina HiSeq platform in the 2x150bp configuration with 20-30 million reads per sample. Gene set enrichment analysis (GSEA) was performed on the Gene Ontology datasets available in the Broad MSigDB (https://www.broadinstitute.org/msigdb). Datasets with FDR < 0.05 were considered significantly enriched.
normalized counts (DESeq2)
STAR, Subread, DESeq2
BWA, Juicer, HOMER
CellRanger, Monocle 3
Genome_build: hg38
Supplementary_files_format_and_content: .csv, .bw, .bed, .hic, .rds


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-143


title: Ctrl_24hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ctrl_24hrs_3_S21_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-142


title: NT RNAseq LMNB1 1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-180


title: Wild_fish5


title: Hyb.NAff_fish5

source_name: Whole fry tissue, Hyb.NAff, individual fish


title: NT HiC Control 2

description:
5-C11.6-C11-NT.merge.hic
5-C11.PC1.bw
5-C11.6-C11-NT.insulationScore.bw
5-C11.6-C11-NT.TAD.2D.bed
5-C11.loop.2D.bed

value: C11 Luciferase shRNA


title: NT RNAseq Control 2


title: Hyb.NAff_fish6


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-141


title: Ctrl_24hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ctrl_24hrs_1_S19_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-147


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-140


title: Hyb.NAff_fish4


title: Nsp14_12hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_12hrs_3_S18_
nsp14_timepoints_normalized_counts

value: 12h post transfection


title: Nsp14_12hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_12hrs_2_S17_.1
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-139


title: Nsp14_12hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_12hrs_2_S17_
nsp14_timepoints_normalized_counts


title: NT HiC Control 1


title: Farm.EO_fish6


title: Hyb.NAff_fish3


title: Wild_fish1


title: Hyb.NAff_fish2


title: NT RNAseq Control 1


title: Ctrl_12hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ctrl_12hrs_3_S15_
nsp14_timepoints_normalized_counts


title: Ctrl_24hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ctrl_24hrs_2_S20_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-137


title: CB CD34 LMNB1 2

description:
3-L3-CB1.4-L3-CB2.merge.hic
3-L3-CB1.PC1.bw
3-L3-CB1.4-L3-CB2.insulationScore.bw
3-L3-CB1.4-L3-CB2.TAD.2D.bed
3-L3-CB1.loop.2D.bed

source_name: CD34+ cord blood

extract_protocol: Cryopreserved CD34+ HSPCs were thawed following the Lonza Poietics protocol (www.lonza.com), and cultured for 4 hours in X-VIVO 10 media (Lonza) + 1% BSA, 1 mM L-glutamine, penicillin/streptomycin, 100 ng/ml SCF, 100 ng/ml FLT3, 50 ng/ml TPO, and 20 ng/ml IL-6 (Peprotech). Lentiviral transduction was carried out on Retronectin-coated (Takara) non-tissue culture treated 96-well plates in complete X-VIVO 10 media at MOI = 50 and a total volume of 150 μl. Virus was concentrated onto cells by centrifuging the plate at 2500 rpm for 30 min at RT. After 24 hours, cells were washed in PBS and cultured in X-VIVO with cytokines for another 48 hours. CD34+/GFP+ cells were sorted on the BD Aria III flow sorter and subsequently cultured in StemSpan SFEM (StemCell Technologies) plus 100 ng/ml SCF, 100 ng/ml FLT3, 50 ng/ml TPO, 50 ng/ml IL-6, and 20 ng/ml IL-3.

value: CD34+ cord blood


title: CB CD34 RNAseq LMNB1 2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-136


title: Ctrl_12hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ctrl_12hrs_1_S13_
nsp14_timepoints_normalized_counts


title: Farm.NA_fish6

source_name: Whole fry tissue, Farm.NA, individual fish


title: CB CD34 HiC LMNB1 1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-135

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: Nsp14_8hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_8hrs_3_S12_
nsp14_timepoints_normalized_counts

value: 8h post transfection


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-134


title: Farm.NA_fish5


title: CB CD34 RNAseq LMNB1 1


title: Farm.NA_fish4


title: Nsp14_8hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_8hrs_2_S11_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-133


title: CB CD34 HiC Control 2

description:
1-C11-CB1.2-C11-CB2.merge.hic
1-C11-CB1.PC1.bw
1-C11-CB1.2-C11-CB2.insulationScore.bw
1-C11-CB1.2-C11-CB2.TAD.2D.bed
1-C11-CB1.loop.2D.bed


title: Nsp14_8hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_8hrs_1_S10_
nsp14_timepoints_normalized_counts


title: CB CD34 RNAseq Control 2


title: Farm.NA_fish3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-138


title: Ctrl_8hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ctrl_8hrs_3_S9_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-131


title: CB CD34 HiC Control 1

data_processing:
Hi-C data were processed using Juicer (Durand et al., 2016) with the default parameters. For each of the 12 libraries, the .fastq files from two runs were merged. Adapter trimming (adapter sequence: 5'GGTGAGGCTGAGGGATC3') was performed by cutadapt and reads shorter than 20bp after adapter removal were discarded. Reads were mapped to reference human genome assembly hg38 using BWA. PCR duplicates or reads with mapping quality score (MAPQ) <30 were removed. Then the valid read pairs were binned and counted in matrices of 5kb, 10kb, 25kb, 50kb, 100kb, and 250kb resolution. KR normalization was used to correct bias and generate balanced Hi-C interaction matrices for subsequent analyses. Contact matrices and virtual 4C tracks by pileup of 5kb bins were generated using Juicebox (Robinson et al., 2018). A/B compartments calling were performed per chromosome from KR normalized intra-chromosomal Hi-C matrix at 100kb resolution. First, O/E (observed/expected) matrix was calculated. Then we transformed the O/E matrix into a z-score matrix, which was then converted to a Pearson correlation matrix. PCA (principal component analysis) was performed on the correlation matrix and the first eigenvector (PC1) of the PCA was used to identify A/B compartments. For each chromosome, the assigning of eigenvector sign orientation (positive or negative) to correct A/B compartments was done by counting gene density such that A compartment was more gene-rich than B compartment. We used both insulation score and directionality index (DI) to call TADs (topologically associating domains). Insulation score analysis was performed as previously reported (Crane et al., 2015). Hi-C interaction matrices at 10kb resolution were used. As for parameters, insulation delta span (-ids) was set to 250kb, and insulationSquareSize (-is) was set to 100kb. Other parameters were the same as the original paper. We also calculated directionality index (DI) as previously reported (Dixon et al., 2012) to identify TADs. The directionality index is calculated as the degree of upstream or downstream bias. Similar to the insulation score, Hi-C interaction matrices at 10kb resolution were used and the window size of upstream/downstream patterns is set to 1Mb. Then we used a hidden Markov model (HMM) to determine the directionality bias and TADs from the calculated directionality index. The mean insulation score at TAD boundaries was generated using the deepTools package (Ramírez et al., 2016). HOMER (Heinz et al., 2010) was used to identify chromatin loops from Hi-C data. Briefly, loops are identified as significant interactions as two regions interact at a high frequency with one another. Hi-C interaction matrices at 10kb resolution were used. Overlapping window size (-window) was set to 25kb and maximum interaction distance (-maxDist) was set to 5Mb.
.hic matrices (Juicer), .bw PC1 scores, .bw insulation socre, .bed TAD , .bed loops
STAR, Subread, DESeq2
BWA, Juicer, HOMER
CellRanger, Monocle 3
Genome_build: hg38
Supplementary_files_format_and_content: .csv, .bw, .bed, .hic, .rds


title: Farm.NA_fish2


title: Farm.NA_fish1


title: Ctrl_12hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ctrl_12hrs_2_S14_
nsp14_timepoints_normalized_counts


title: Hyb.NAff_fish1


title: CB CD34 RNAseq Control 1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-130


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-128


title: Ctrl_8hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ctrl_8hrs_1_S7_
nsp14_timepoints_normalized_counts


title: EVs_c

city: Rionero in Vulture

first: Luciana

last: De Luca

address: Via Padre Pio, 1

institute: IRCCS - CROB

description: replicate 3

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan system

data_processing: The data were normalised using neqc() quantile normalization with limma in R

source_name: EVs

label_protocol: Biotinylated cRNA were prepared with the Ambion kit for Illumina arrays

extract_protocol: RNA was extracted with RNA/DNA/PROTEIN Purification Plus Micro Kit (Norgen Biotek). Quality control was performed with Agilent Bioanalyzer.

tag: sample group

value: EVs


title: ChIP-seq_HNF1B_OS-LM1_input_3

city: Helsinki

first: Sakari

last: Vanharanta

address: Haartmaninkatu 8

department: Translational Cancer Medicine Program

country: Finland

institute: University of Helsinki

data_processing:
Pre-processing fastq files: Cutadapt (version 1.10.0) was used to remove adapter contaminations identified by FastQC (version 0.11.7), trim low quality bases from read ends (<20) and discard reads shorter than 10 bases.
Mapping to mouse genome: Reads were mapped to mm10 genome using Bowtie2 (version 2.3.4.3) and only the reads which did not map to mm10 were used for futher analysis.
Mapping to human genome: Reads which did not map to mm10 were mapped to hg38 including regions in 'sponge database' described in Miga et al. 2015 using Bowtie2.
File formatting: The output SAM files were converted to bigwig format using samtools (version 1.2) (SAM -> BAM). Reads which mapped to blacklisted regions and reads which did not map to chr1-22, X and Y were removed. Reads with low mapping quality (MAPQ<20) were also removed. DeepTools (version 3.5.0) was used to convert BAM into bigwig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: ccRCC xenograft

growth_protocol: Xenograft tumors formed by human cancer cells in immunocompromised athymic mice.

extract_protocol:
Approximately 30mg of tumor tissue was homogenized in the Precellys (Bertin instruments) for 30sec and crosslinked with 1% formaldehyde-supplemented media for 10 minutes. The reaction was quenched with 0.125M glycine for 5 minutes and followed by PBS washes twice. The cells were either pelleted and stored at -80oC or subjected to immunoprecipitation. For IP, the protein A/G magnetic beads (Thermo, 26162) were first equilibrated by washing the beads with 0.5% BSA in PBS three times. The beads were then incubated with antibodies in 0.5% BSA in PBS at 4oC while rotating for a minimum of 4 hours. The crosslinked cells were resuspended and dounced in lysis buffer (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2mM EDTA pH 8.0, 0.1% SDS and 1% Triton X-100), followed by sonication in the Bioruptor (Diagenode) for 14 cycles, 30” on / 30” off. The lysates were spun down at 4oC for 20 minutes at 14000 rpm. The supernatants were added onto the antibody-conjugated magnetic beads and incubated overnight at 4oC while rotating. On the following day, the beads were washed three times with low salt buffer (50 mM HEPES pH 7.5, 140 mM NaCl, 1% Triton) and high salt buffer (50 mM HEPES pH 7.5, 500 mM NaCl, 1% Triton) once. The DNA bound to the antibody-conjugated beads was eluted with elution buffer (50 mM NaHCO3, 1% SDS) and de-crosslinked by shaking at 1000 rpm for 3 hours at 65oC. De-crosslinked DNA was purified using the QuickClean II PCR Extraction Kit (Genescript L00419-100) according to the manufacturer’s recommendations.
Purified ChIP DNA was subjected to Illumina sequencing. Sequencing libraries were prepared by using the KAPA Hyper Prep Kit (KR0961) according to the manufacturer’s recommendations. Adapter-ligated libraries were size-selected using Agencourt AmPure XP beads (Beckman Coulter A63880) to obtain fragments of 150-350bp. Size-selected fragments were amplified for 15 cycles using the KAPA HiFi HotStart Ready mix and the amplified libraries were pooled in equimolar concentration for Illumina sequencing on a HiSeq4000 instrument.

value: ccRCC xenograft

tag: chip antibody


title: Nsp14_6hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_6hrs_2_S5_
nsp14_timepoints_normalized_counts

value: 6h post transfection


title: CTRL_c

description: replicate 3

source_name: CTRL

value: CTRL


title: ChIP-seq_HNF1B_OS-LM1_input_2


title: EVs_b

description: replicate 2


title: ChIP-seq_HNF1B_OS-LM1_input_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-132

source_name: mouse embryos

tag: strain


title: Nsp14_6hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_6hrs_1_S4_
nsp14_timepoints_normalized_counts


title: CTRL_b

description: replicate 2


title: EVs_a

description: replicate 1


title: ChIP-seq_HNF1B_OS-LM1_3

tag: tissue

value: HNF1B (Human Protein Atlas, HPA002083)


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-126


title: Ctrl_8hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ctrl_8hrs_2_S8_
nsp14_timepoints_normalized_counts

value: eGFP


title: Ctrl_6hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ctrl_6hrs_3_S3_
nsp14_timepoints_normalized_counts


title: CTRL_a

description: replicate 1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-125


title: ChIP-seq_HNF1B_OS-LM1_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-124


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-129


title: ChIP-seq_HNF1B_OS-LM1_1


title: Ctrl_6hr_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ctrl_6hrs_2_S2_
nsp14_timepoints_normalized_counts


title: ChIP-seq_HNF1B_786-M1A_input_3


title: Ctrl_6hr_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ctrl_6hrs_1_S1_
nsp14_timepoints_normalized_counts


title: Nsp14_6hr_rep_3

description:
RNA-seq polyA+
transfected HEK293T
NSP14OE_6hrs_3_S6_
nsp14_timepoints_normalized_counts


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-123


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-127


title: Nsp14_D273A_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp1014_3_
Nsp14_ExoN_mutant_normalized

value: Nsp14 D273A-SARS-CoV-7

value: 48h post transfection


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-122


title: ChIP-seq_HNF1B_786-M1A_input_2


title: KG1_b

description: replicate 2


title: Nsp14_D273A_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp1014_2_
Nsp14_ExoN_mutant_normalized

value: Nsp14 D273A-SARS-CoV-6

value: no treatment


title: MC3T3-E1 cells, met rep2

city: shenyang

first: Keda

last: Yang

state: --- Select One ---

address: North Nanjing Street 155

institute: The First Affiliated Hospital of China Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: RPKM values for each sample

source_name: MC3T3-E1 cells

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

value: Osteoblasts

tag: growth protocol

value: osteogenic medium

value: metformin


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-121

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library

tag: developmental stage


title: MC3T3-E1 cells, nc rep3

tag: cell type

value: control


title: KG1_a

description: replicate 1


title: Nsp14_D273A_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp1014_1_
Nsp14_ExoN_mutant_normalized

tag: cell line

value: Nsp14 D273A-SARS-CoV-5


title: KG1_c

description: replicate 3


title: ChIP-seq_HNF1B_786-M1A_3


title: ChIP-seq_HNF1B_786-M1A_input_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-119


title: MC3T3-E1 cells, nc rep2


title: ChIP-seq_HNF1B_786-M1A_2


title: MC3T3-E1 cells, met rep3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-120


title: Nsp14_D90A_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_2_
Nsp14_ExoN_mutant_normalized

value: Nsp14 D90A-G92A-SARS-CoV-3


title: MC3T3-E1 cells, nc rep1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-118


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-117


title: ChIP-seq_HNF1B_786-M1A_1


title: Nsp14_D90A_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_1_
Nsp14_ExoN_mutant_normalized

value: Nsp14 D90A-G92A-SARS-CoV-2


title: ChIP-seq_PAX8_OS-LM1_input_4


title: d2_MRC_Aged_5

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

description:
MRC_expressed_genes_log2RPM.txt
Stromal cells were isolated from lymph nodes by enzymatic digestion and were enriched by magnetic depletion of CD45+ cells
FDCs and MRCs were purified by cell sorting based on cell surface marker expression. Cells were sorted directly into 8.5uL of lysis buffer supplied with the SMART-Seq v4 Ultra low Input RNA kit for Sequencing

data_processing:
Standard Illumina base-calling pipeline.
Sequenced RNA-seq reads were trimmed for the Nextera adaptor sequence and low-quality sequence with Trim Galore (v0.4.4), and then mapped to the GRCm38 genome using HISAT2 v2.1.0 with parameters --dta --no-softclip --no-mixed --no-discordant. The resulting hits were filtered to remove mappings with a MAPQ scores of < 20.
Genome_build: GRCm38
The RNAseq report was generated by SeqMonk (v1.46.0). It is a tab delimited text file showing log2RPM values for each sample

source_name: lymph node

extract_protocol: Libraries were prepared with 400pg of cDNA per sample using the Illumina Nextera XT kit. cDNA and sequencing library quality were determined using Agilent BioAnalyser High Sensitivity DNA chips, Qubit dsDNA High sensitivity Assay kit on a Qubit 4 fluorometer (Invitrogen), and a KAPA library quantification kit. Samples were sequenced on a HiSeq 2500 as 100bp single-end reads.

treatment_protocol: cDNA from sorted cells was generated using the SMART-Seq v4 Ultra low input RNA kit according to manufacturer’s instructions.

value: lymph node

value: Marginal reticular cell

value: 98 week old

tag: immunisation state

value: day 2; 50ug NP-KLH in Alum


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-116


title: Nsp14_WT_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_3_
Nsp14_ExoN_mutant_normalized


title: ChIP-seq_PAX8_OS-LM1_input_3

value: ccRCC xenograft


title: MC3T3-E1 cells, met rep1


title: d2_MRC_Aged_3

tag: age


title: Nsp14_WT_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_2_
Nsp14_ExoN_mutant_normalized


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-115


title: ChIP-seq_PAX8_OS-LM1_input_2


title: d2_MRC_Aged_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-114


title: d2_MRC_Aged_1


title: GFP_mut_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Ctrl_3_
Nsp14_ExoN_mutant_normalized

value: eGFP


title: ChIP-seq_PAX8_OS-LM1_input_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-113


title: d2_MRC_Adult_5

value: 8 week old


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-112


title: GFP_mut_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Ctrl_2_
Nsp14_ExoN_mutant_normalized

value: 48h post transfection


title: ChIP-seq_PAX8_OS-LM1_2

value: PAX8 (ProteinTech 10336-1-AP)


title: GFP_mut_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Ctrl_1_
Nsp14_ExoN_mutant_normalized

value: no treatment


title: d2_MRC_Adult_4


title: d2_MRC_Aged_4


title: GFP_L4_rep_3

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_3_all_S99_
CovidProteinCounts_normalized_L4


title: ChIP-seq_PAX8_OS-LM1_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-110


title: d2_MRC_Adult_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-109


title: ChIP-seq_PAX8_786-M1A_input_3


title: GFP_L4_rep_2

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_2_all_S98_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-111


title: GFP_L4_rep_1

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_1_all_S97_
CovidProteinCounts_normalized_L4


title: Nsp14_WT_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_1_
Nsp14_ExoN_mutant_normalized


title: ChIP-seq_PAX8_786-M1A_input_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-108


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-107


title: d2_FDC_Aged_5

description:
FDC_expressed_genes_log2RPM.txt
Stromal cells were isolated from lymph nodes by enzymatic digestion and were enriched by magnetic depletion of CD45+ cells
FDCs and MRCs were purified by cell sorting based on cell surface marker expression. Cells were sorted directly into 8.5uL of lysis buffer supplied with the SMART-Seq v4 Ultra low Input RNA kit for Sequencing

value: Follicular dendritic cell


title: d2_FDC_Aged_4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-106


title: GFP_L3_rep_2

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_2_all_S71_
CovidProteinCounts_normalized_L3


title: ChIP-seq_PAX8_786-M1A_3


title: ChIP-seq_PAX8_OS-LM1_3


title: ChIP-seq_PAX8_786-M1A_2


title: d2_FDC_Aged_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-105


title: GFP_L3_rep_1

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_1_all_S70_
CovidProteinCounts_normalized_L2


title: ChIP-seq_PAX8_786-M1A_1


title: d2_FDC_Aged_2


title: d2_MRC_Adult_2


title: GFP_L2_rep_2

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_2_all_S47_
CovidProteinCounts_normalized_L2


title: ChIP-seq_HIF2A_OS-LM1_input_3


title: d2_FDC_Aged_1


title: ChIP-seq_HIF2A_OS-LM1_input_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-103

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: d2_FDC_Adult_5


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-102


title: d2_MRC_Adult_1


title: ChIP-seq_PAX8_786-M1A_input_1


title: ChIP-seq_HIF2A_OS-LM1_input_1


title: d2_FDC_Adult_4


title: GFP_L3_rep_3

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_3_all_S72_
CovidProteinCounts_normalized_L3


title: d2_FDC_Adult_3


title: GFP_L1_rep_3

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_3_all_S21_
CovidProteinCounts_normalized_L1


title: GFP_L1_rep_2

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_2_all_S20_
CovidProteinCounts_normalized_L1


title: ChIP-seq_HIF2A_OS-LM1_3

value: HIF2A (Novus Biologicals NB100-122)


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-101


title: d2_FDC_Adult_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-100


title: GFP_L2_rep_3

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_3_all_S48_
CovidProteinCounts_normalized_L2


title: GFP_L1_rep_1

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_1_all_S19_
CovidProteinCounts_normalized_L1


title: ChIP-seq_HIF2A_OS-LM1_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-104


title: d2_FDC_Adult_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-098


title: ORF9b_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF9b_3_all_S96_
CovidProteinCounts_normalized_L4


title: ChIP-seq_HIF2A_OS-LM1_2


title: d0_MRC_Aged_4

description:
MRC_expressed_genes_log2RPM.txt
Stromal cells were isolated from lymph nodes by enzymatic digestion and were enriched by magnetic depletion of CD45+ cells
FDCs and MRCs were purified by cell sorting based on cell surface marker expression. Cells were sorted directly into 8.5uL of lysis buffer supplied with the SMART-Seq v4 Ultra low Input RNA kit for Sequencing

value: unimmunised


title: d0_MRC_Aged_5


title: GFP_L2_rep_1

description:
RNA-seq polyA+
transfected HEK293T
GFPctrl_1_all_S46_
CovidProteinCounts_normalized_L2


title: ORF9b_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF9b_2_all_S95_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-096


title: ChIP-seq_HIF2A_786-M1A_input_2


title: ChIP-seq_HIF2A_786-M1A_input_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-097


title: d0_MRC_Aged_3


title: ChIP-seq_HIF2A_786-M1A_input_1


title: Nsp14_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_3_all_S93_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-094


title: d0_MRC_Aged_2


title: Nsp14_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_1_all_S91_
CovidProteinCounts_normalized_L4


title: ChIP-seq_HIF2A_786-M1A_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-095


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-099


title: d0_MRC_Aged_1


title: Nsp14_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_2_all_S92_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-093


title: d0_MRC_Adult_5


title: ChIP-seq_HIF2A_786-M1A_2


title: ChIP-seq_HIF2A_786-M1A_input_4


title: ChIP-seq_HIF2A_786-M1A_1


title: Nsp9_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp9_3_all_S90_
CovidProteinCounts_normalized_L4


title: Nsp9_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp9_2_all_S89_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-092


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-091


title: d0_MRC_Adult_4


title: ATAC-seq_PAX8_Ren_Rep6

data_processing:
Pre-processing fastq files: Cutadapt (version 2.10) was used to remove adapter contaminations identified by FastQC (version 0.11.9), trim low quality bases from read ends (<20) and discard reads shorter than 10 bases.
Mapping to human genome: Reads were mapped to hg38 using BWA (version 0.7.17).
File formatting: The output SAM files were converted to bigwig format using samtools (version 1.9) (SAM -> BAM). Reads which mapped to blacklisted regions and reads which did not map to chr1-22, X and Y were removed. Reads with low mapping quality (MAPQ<20) were also removed. Reads were corrected for the Tn5 offset (+ve strand: +4bp, -ve strand: -5bp). DeepTools (version 3.5.0) was used to convert BAM into bigwig.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files

source_name: ccRCC cell line

growth_protocol: Cells grown under standard tissue culture conditions in RPMI + 10% FBS.

extract_protocol:
Cells at 75% confluency were trypsinised, counted and 50,000 cells were subjected to ATAC-seq protocol directly as previously described (Buenrostro et al., 2013).
Libraries were prepared using the Illumina Nextera DNA library preparation kit (FC-121-1030) and purified using the minElute PCR purification kit (Qiagen 28004). Following purification, library fragments were amplified using NEBNext PCR master mix and custom Nextera PCR primers. Libraries were amplified for a total of 8-12 cycles and cleaned-up using the Agencourt AMPureXP reagent (A63880) according to manufacturer's recommendations, and pooled in equimolar concentrations prior to sequencing.

treatment_protocol: 1μg/ml doxycycline for 10 days to induce the expression of shRNA constructs.

tag: construct

value: shRen


title: Nsp9_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp9_1_all_S88_
CovidProteinCounts_normalized_L4

tag: transfection


title: d0_MRC_Adult_2


title: d0_MRC_Adult_3


title: ATAC-seq_PAX8_Ren_Rep5


title: ORF9b_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF9b_1_all_S94_
CovidProteinCounts_normalized_L4

tag: timepoint


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-090

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-089


title: ORF7a_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF7a_2_all_S86_
CovidProteinCounts_normalized_L4

tag: treatment


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-088


title: ATAC-seq_PAX8_Ren_Rep4


title: ORF7a_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF7a_3_all_S87_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-087


title: ATAC-seq_PAX8_Ren_Rep3


title: d0_MRC_Adult_1


title: ORF7a_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF7a_1_all_S85_
CovidProteinCounts_normalized_L4


title: d0_FDC_Aged_4

description:
FDC_expressed_genes_log2RPM.txt
Stromal cells were isolated from lymph nodes by enzymatic digestion and were enriched by magnetic depletion of CD45+ cells
FDCs and MRCs were purified by cell sorting based on cell surface marker expression. Cells were sorted directly into 8.5uL of lysis buffer supplied with the SMART-Seq v4 Ultra low Input RNA kit for Sequencing


title: ORF3b_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF3b_3_all_S81_
CovidProteinCounts_normalized_L4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-086


title: ATAC-seq_PAX8_Ren_Rep1


title: d0_FDC_Aged_3


title: d0_FDC_Aged_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-085


title: ATAC-seq_PAX8_Ren_Rep2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-084


title: ORF3b_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF3b_1_all_S79_
CovidProteinCounts_normalized_L4


title: ATAC-seq_shPAX8-2_Rep2


title: ORF3b_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF3b_2_all_S80_
CovidProteinCounts_normalized_L4


title: ATAC-seq_shPAX8-2_Rep3


title: d0_FDC_Aged_1


title: Nsp1_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp1_3_all_S78_
CovidProteinCounts_normalized_L4


title: Nsp1_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp1_2_all_S77_
CovidProteinCounts_normalized_L4


title: d0_FDC_Adult_5


title: Nsp14_D90A_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp14_3_
Nsp14_ExoN_mutant_normalized

value: Nsp14 D90A-G92A-SARS-CoV-4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-083


title: ATAC-seq_shPAX8-2_Rep1


title: ATAC-seq_shPAX8-1_Rep2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-082


title: d0_FDC_Adult_4


title: ATAC-seq_shPAX8-1_Rep3


title: Nsp1_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp1_1_all_S76_
CovidProteinCounts_normalized_L4


title: d0_FDC_Adult_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-081


title: d0_FDC_Adult_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-078


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-080


title: Nsp8_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp8_3_all_S66_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-077


title: d0_FDC_Adult_1


title: ORF7b_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF7b_2_all_S68_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-079


title: ATAC-seq_shPAX8-1_Rep1


title: ATAC-seq_HNF1B_Ren_Rep4


title: ATAC-seq_HNF1B_Ren_Rep5


title: ATAC-seq_HNF1B_Ren_Rep3


title: Nsp8_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp8_1_all_S64_
CovidProteinCounts_normalized_L3


title: ORF7b_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF7b_1_all_S67_
CovidProteinCounts_normalized_L3


title: Nsp8_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp8_2_all_S65_
CovidProteinCounts_normalized_L3


title: ATAC-seq_HNF1B_Ren_Rep1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-075

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: Nsp5_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp5_3_all_S63_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-076


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-074


title: ATAC-seq_HNF1B_Ren_Rep2


title: ATAC-seq_shHNF1B-2_Rep3


title: ORF7b_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF7b_3_all_S69_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-073


title: Nsp5_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp5_2_all_S62_
CovidProteinCounts_normalized_L3


title: Nsp5_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp5_1_all_S61_
CovidProteinCounts_normalized_L3


title: Nsp11_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp11_3_all_S60_
CovidProteinCounts_normalized_L3


title: ATAC-seq_shHNF1B-2_Rep2


title: Nsp11_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp11_2_all_S59_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-072


title: ATAC-seq_shHNF1B-2_Rep1


title: ATAC-seq_shHNF1B-1_Rep1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-070


title: Nsp11_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp11_1_all_S58_
CovidProteinCounts_normalized_L3


title: ATAC-seq_shHNF1B-1_Rep3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-068


title: Nsp15_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp15_2_all_S56_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-069


title: Nsp15_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp15_3_all_S57_
CovidProteinCounts_normalized_L3


title: Nsp2_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp2_3_all_S54_
CovidProteinCounts_normalized_L3


title: 786-M1A-shRen_REP_4

data_processing:
Fastq files were mapped to the human transcriptome using Bowtie2.
Relative gene expression was determined using RSEM.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: *.genes.results.txt: Gene-level RSEM output files.

extract_protocol:
RNA was extracted from 80% confluent cells using the RNeasy Mini Kit (Qiagen 74104) following the manufacturer’s recommendations. RNA quality was assessed with the RNA Nano 6000 kit (Agilent 5067-1511) and Agilent Bioanalyzer 2100 instrument.
Purified RNA (1µg) was used to prepare Illumina multiplexed sequencing libraries. Libraries were prepared following the KAPA Stranded mRNA-seq Kit (KR0960) Illumina platforms sample preparation protocol (v3.15). Briefly, poly(A) RNA was captured with magnetic oligo-dT beads and heat fragmented (94°C) to a size of 200-300bp. Fragmented RNA was used for 1st strand cDNA synthesis, generating cDNA-RNA hybrids which were used for 2nd strand synthesis and marking to obtain dscNDA marked with dUTP. Newly synthesized fragments were end-repaired and A-tailed to add dAMP to the 3’-end of dscDNA fragments. These 3’-dA-tailed library fragments were then ligated with 3’-dTMP adapters. After adapter ligation, libraries were cleaned up using the Agencourt AMPure XP reagent (A63880) according to manufacturer’s recommendations. Purified, adapter-ligated DNA was amplified for 15 cycles. PCR libraries were pooled in equimolar concentrations and sequenced.


title: ATAC-seq_shHNF1B-1_Rep2


title: 786-M1A-shRen_REP_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-067


title: Nsp15_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp15_1_all_S55_
CovidProteinCounts_normalized_L3


title: 786-M1A-shRen_REP_3


title: Nsp2_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp2_2_all_S53_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-065


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-064


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-063


title: 786-M1A-shRen_REP_2


title: 786-M1A-shPAX8-1_REP_4


title: ORF8_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF8_3_all_S45_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-062


title: 786-M1A-shPAX8-1_REP_2


title: ORF8_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF8_2_all_S44_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-066


title: 786-M1A-shPAX8-1_REP_1


title: ORF8_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF8_1_all_S43_
CovidProteinCounts_normalized_L2


title: 786-M1A-shPAX8-2_REP_4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-059


title: 786-M1A-shPAX8-1_REP_3


title: hek293t cells-sunflower calathide extract [SCE1]

city: Changchun

first: ning

middle: Hui

last: Dai

state: Jilin

address: Qianjin Street

department: Life Sciences

institute: Jilin university

data_processing:
Agilent 2100 bioanalyzer (Agilent Technologies, CA, USA) was applied to accurately detect the integrity and total amount of RNA.
The library fragments of preferentially 370 ~ 420 bp in length were purified with AMPure XP beads(Beckman Coulter, Beverly, USA)
Assessed the library's quality using the Agilent bioanalyzer 2100 system.
Mapping to genome of Homo sapiens and using featureCounts v1.5.0 - p 3 to evaluate gene expression levels
Assembly: GRCh38.p13
Supplementary files format and content: FPKM values of all the groups

source_name: hek293t cells

growth_protocol: cultured in DMEM high glucose medium with 10% fetal bovine serum and 1% penicillin/streptomycin

extract_protocol:
The total RNA was extracted based on the instruction manual of TRIzol reagent by Novogene Technology Co., Ltd.
The library preparations were sequenced on an Illumina Novaseq platform

treatment_protocol: pretreated with SCE and abietic acid for 3h before uric acid-induced for 24h

value: human embryonic  kidney

value: 300µg/ml SCE pretreated for 3h +1mM uric acid for 24h


title: hek293t cells-sunflower calathide extract [SCE3]


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-060


title: hek293t cells-sunflower calathide extract [SCE2]


title: hek293t cells-abietic acid [AA3]

value: 132µM abietic acid pretreated for 3h +1mM uric acid for 24h


title: ORF6_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF6_3_all_S42_
CovidProteinCounts_normalized_L2


title: 786-M1A-shPAX8-2_REP_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-058

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: hek293t cells-abietic acid [AA2]


title: ORF6_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF6_1_all_S40_
CovidProteinCounts_normalized_L2


title: 786-M1A-shPAX8-2_REP_1


title: hek293t cells-abietic acid [AA1]


title: Nsp12_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp12_3_all_S39_
CovidProteinCounts_normalized_L2


title: ORF6_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF6_2_all_S41_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-056


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-057


title: OS-LM1-shRen_REP_4


title: Nsp2_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp2_1_all_S52_
CovidProteinCounts_normalized_L3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-061


title: hek293t cells-uric acid [UA3]

value: 1mM uric acid for 24h


title: Nsp12_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp12_2_all_S38_
CovidProteinCounts_normalized_L2


title: OS-LM1-shRen_REP_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-055


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-071


title: hek293t cells-control [Control3]

value: untreated


title: OS-LM1-shRen_REP_2


title: Nsp10_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_2_all_S35_
CovidProteinCounts_normalized_L2


title: hek293t cells-uric acid [UA2]


title: Nsp10_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_1_all_S34_
CovidProteinCounts_normalized_L2


title: OS-LM1-shPAX8-1_REP_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-050


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-054


title: 786-M1A-shPAX8-2_REP_3


title: ORF9c_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF9c_3_all_S33_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-053


title: hek293t cells-uric acid [UA1]


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-049


title: OS-LM1-shPAX8-1_REP_1


title: OS-LM1-shRen_REP_1


title: ORF8_4

city: Cleveland

first: Xin

last: Wu

email: xinwu628@gmail.com, wux2@ccf.org

state: OH

address: 9500 Euclid Ave., NE2-251

department: Cancer Biology

institute: Cleveland Clinic Lerner Research Institute

data_processing:
Fastq files were analyzed with Partek Flow (Build 10.0.21.1026). This includes quality control, alignment to hg38, peak filtering, normalization, and differential gene expression.
Genome_build: hg38

source_name: Monocytes

extract_protocol:
Peripheral blood specimens for RNA-Seq were obtained from healthy donors aged 21 to 50 years old and stored temporarily at 37 °C in lithium heparin-containing tubes (BD) prior to treatment. All procedures were approved by the Cleveland clinic Institutional Review Board and Internal Biosafety Committee. Total RNA was isolated with RNeasy Micro Kit (74004) from QIAGEN.
The RNA-seq library was prepared using the KAPA mRNA HyperPrep Kit (KR1352), according to manufacturers’ instructions.

value: Monocytes


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-052

data_processing:
Base calls were converted to fastq format using Illumina’s bcl2fastq/v2.20 and demultiplexed based on PCR i5 and i7 barcodes using maximum likelihood demultiplexing package deML (Renaud et al. 2015) with default settings. Downstream sequence processing and single cell digital expression matrix generation were similar to sci-RNA-seq (Cao et al. 2017) except that RT index was combined with hairpin adaptor index, and thus the mapped reads were split into constituent cellular indices by demultiplexing reads using both the RT index and ligation index (Levenshtein edit distance (ED) < 2, including insertions and deletions).
Briefly, demultiplexed reads were filtered based on RT index and ligation index (ED < 2, including insertions and deletions) and adaptor-clipped using trim_galore/v0.6.5 with default settings. Trimmed reads were mapped to the mouse reference genome (mm10) for mouse embryo nuclei, using STAR/v2.6.1d (Dobin et al. 2013) with default settings and gene annotations (GENCODE VM12 for mouse). Uniquely mapping reads were extracted, and duplicates were removed using the unique molecular identifier (UMI) sequence (ED < 2, including insertions and deletions), reverse transcription (RT) index, hairpin ligation adaptor index and read 2 end-coordinate (i.e. reads with UMI sequence less than 2 edit distance, RT index, ligation adaptor index and tagmentation site were considered duplicates).
Finally, mapped reads were split into constituent cellular indices by further demultiplexing reads using the RT index and ligation hairpin (ED < 2, including insertions and deletions). To generate digital expression matrices, we calculated the number of strand-specific UMIs for each cell mapping to the exonic and intronic regions of each gene with python/v2.7.13 HTseq package (Anders, Pyl, and Huber 2015). For multi-mapped reads, reads were assigned to the closest gene, except in cases where another intersected gene fell within 100 bp to the end of the closest gene, in which case the read was discarded. For most analyses we included both expected-strand intronic and exonic UMIs in per-gene single-cell expression matrices.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files include a cell annotation csv  file, gene annotation csv file, and a gene count sparse matrix file (using scanpy.read_loom to open)

extract_protocol:
Mouse embryos from different development stages were processed together to reduce batch effect. Each mouse embryo was minced into small pieces by blade in 1 mL ice-cold cell lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630 from77, modified to also include 1% SUPERase In and 1% BSA) and transferred to the top of a 40um cell strainer (Falcon). Tissues were homogenized with the rubber tip of a syringe plunger (5ml, BD) in 4ml cell lysis buffer. The filtered nuclei were then transferred to a new 15ml tube (Falcon) and pelleted by centrifuge at 500xg for 5min and washed once with 1ml cell lysis buffer. The nuclei were fixed in 4ml ice cold 4% paraformaldehyde (EMS) for 15min on ice. After fixation, the nuclei were washed twice in 1ml nuclei wash buffer (cell lysis buffer without IGEPAL), and re-suspended in 500ul nuclei wash buffer.
The samples were split to two tubes with 250ul in each tube and flash frozen in liquid nitrogen. We estimated the nuclei extraction efficiency based on extracted nuclei number vs. expected total nuclei number in each embryo and the nuclei extraction efficiency range from 60% to 85%. Thawed nuclei are permeabilized with 0.2% tritonX-100 (in nuclei wash buffer) for 3 minutes on ice, and briefly sonicated (Diagenode, 12s on low power mode) to reduce nuclei clumping. The nuclei were then washed once with nuclei wash buffer and filtered through 1ml Flowmi cell strainer (Flowmi).
Filtered nuclei were spun down at 500xg for 5min and resuspended in nuclei wash buffer. Nuclei from each mouse embryo were then distributed into several individual wells in four 96-well plates. The links between well id and mouse embryo were recorded for downstream data processing. For each well, 80,000 nuclei (16 µL) were mixed with 8 µl of 25 µM anchored oligo-dT primer (5′- /5Phos/CAGAGCNNNNNNNN[10bp barcode]TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT-3′, where “N” is any base; IDT) and 2 µL 10 mM dNTP mix (Thermo), denatured at 55°C for 5 min and immediately placed on ice. 14 µL of first-strand reaction mix, containing 8 µL 5X Superscript IV First-Strand Buffer (Invitrogen), 2 µl 100 mM DTT (Invitrogen), 2 µl SuperScript IV reverse transcriptase (200 U/μl, Invitrogen), 2 μL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen), was then added to each well.
Reverse transcription was carried out by incubating plates by gradient temperature (4°C 2 minutes, 10°C 2 minutes, 20°C 2 minutes, 30°C 2 minutes, 40°C 2 minutes, 50°C 2 minutes and 55°C 10 minutes). After ligation reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 500xg for 10min. Nuclei were then resuspended in nuclei wash buffer and redistributed into another four 96-well plates with each well including 4µL T4 ligation buffer (NEB), 2µL T4 DNA ligase (NEB), 4µL Betaine solution (5M, Sigma-Aldrich), 6µL nuclei in nuclei wash buffer, 8µL barcoded ligation adaptor (100uM, 5’- GCTCTG[9bp or 10bp barcode A]/ideoxyU/ACGACGCTCTTCCGATCT[reverse complement of barcode A]-3’) and 16µL 40% PEG 8000 (Sigma-Aldrich). The ligation reaction was done at 16°C for 3 hours.
After RT reaction, 60µL nuclei dilution buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 1% BSA) was added into each well. Nuclei from all wells were pooled together and spun down at 600xg for 10min. Nuclei were washed once with nuclei wash buffer and filtered with 1ml Flowmi cell strainer (Flowmi) twice, counted and redistributed into eight 96-well plates with each well including 2,500 nuclei in 5µL nuclei wash buffer and 5µL elution buffer (Qiagen).
1.33 μl mRNA Second Strand Synthesis buffer (NEB) and 0.66 μl mRNA Second Strand Synthesis enzyme (NEB) were then added to each well, and second strand synthesis was carried out at 16°C for 180 min. For tagmentation, each well was mixed with 11 μL Nextera TD buffer (Illumina) and 1 μL i7 only TDE1 enyzme (62.5nM, Illumina), and then incubated at 55°C for 5 min to carry out tagmentation. The reaction was then stopped by adding 24 μL DNA binding buffer (Zymo) per well and incubating at room temperature for 5 min. Each well was then purified using 1.5x AMPure XP beads (Beckman Coulter).
In the elution step, each well was added with 8µL nuclease free water, 1µL 10X USER buffer (NEB), 1µL USER enzyme (NEB) and incubated at 37°C for 15 min. Another 6.5µL elution buffer was added into each well. The AMPure XP beads were removed by magnetic stand and the elution product was transferred into a new 96-well plate. For PCR amplification, each well (16µL product) was mixed with 2μL of 10 μM indexed P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC[i5]ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3′; IDT), 2 μL of 10 μM P7 primer (5′-CAAGCAGAAGACGGCATACGAGAT[i7]GTCTCGTGGGCTCGG-3′, IDT), and 20 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB). Amplification was carried out using the following program: 72°C for 5 min, 98°C for 30 sec, 12-14 cycles of (98°C for 10 sec, 66°C for 30 sec, 72°C for 1 min) and a final 72°C for 5 min.


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-051


title: OS-LM1-shPAX8-1_REP_4


title: hek293t cells-control [Control1]


title: Nsp4_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp4_3_all_S30_
CovidProteinCounts_normalized_L2


title: IL-17A_4


title: OS-LM1-shPAX8-1_REP_2


title: ORF9c_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF9c_2_all_S32_
CovidProteinCounts_normalized_L2


title: Nsp12_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp12_1_all_S37_
CovidProteinCounts_normalized_L2


title: Nsp10_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp10_3_all_S36_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-046


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-048


title: ORF9c_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF9c_1_all_S31_
CovidProteinCounts_normalized_L2


title: hek293t cells-control [Control2]


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-044


title: OS-LM1-shPAX8-2_REP_4


title: Control_4

value: mock


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-047


title: IL-17A_3


title: IL-17A_2


title: OS-LM1-shPAX8-2_REP_3


title: OS-LM1-sgNTC18_REP_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-043


title: Nsp4_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp4_2_all_S29_
CovidProteinCounts_normalized_L2


title: Nsp7_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp7_1_all_S25_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-042


title: ORF8_3


title: ORF8_2


title: Nsp4_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp4_1_all_S28_
CovidProteinCounts_normalized_L2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-045

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: OS-LM1-shPAX8-2_REP_2


title: Nsp13_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp13_3_all_S18_
CovidProteinCounts_normalized_L1


title: OS-LM1-shPAX8-2_REP_1


title: Control_3


title: Nsp7_rep_3

description:
RNA-seq polyA+
transfected HEK293T
Nsp7_3_all_S27_
CovidProteinCounts_normalized_L2


title: OS-LM1-sgNTC18_REP_4


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-040


title: Nsp7_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp7_2_all_S26_
CovidProteinCounts_normalized_L2


title: Control_2


title: OS-LM1-sgHNF1B_8_REP_2


title: ORF10_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF10_2_all_S14_
CovidProteinCounts_normalized_L1


title: ATAC-seq_HK2_HIF2A_Rep3

source_name: renal epithelial cell line


title: OS-LM1-sgNTC18_REP_2


title: OS-LM1-sgNTC18_REP_1


title: ORF10_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF10_1_all_S13_
CovidProteinCounts_normalized_L1


title: OS-LM1-sgHNF1B_8_REP_1


title: Nsp13_rep_2

description:
RNA-seq polyA+
transfected HEK293T
Nsp13_2_all_S17_
CovidProteinCounts_normalized_L1


title: IL-17A_1


title: OS-LM1-sgHNF1B_2_REP_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-035


title: OS-LM1-sgHNF1B_8_REP_4


title: Nsp13_rep_1

description:
RNA-seq polyA+
transfected HEK293T
Nsp13_1_all_S16_
CovidProteinCounts_normalized_L1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-039


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-041


title: ORF3a_rep_2

description:
RNA-seq polyA+
transfected HEK293T
ORF3a_2_all_S11_
CovidProteinCounts_normalized_L1


title: OS-LM1-sgHNF1B_8_REP_3


title: ORF10_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF10_3_all_S15_
CovidProteinCounts_normalized_L1


title: Control_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-037


title: ORF3a_rep_1

description:
RNA-seq polyA+
transfected HEK293T
ORF3a_1_all_S10_
CovidProteinCounts_normalized_L1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-038


title: ATAC-seq_HK2_EV_Rep1

value: Empty vector


title: OS-LM1-sgHNF1B_2_REP_1


title: M_rep_3

description:
RNA-seq polyA+
transfected HEK293T
M_3_all_S9_
CovidProteinCounts_normalized_L1


title: ATAC-seq_HK2_HIF2A_Rep2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-031


title: ATAC-seq_RCCJF_Rep3

value: RCC-JF


title: ORF3a_rep_3

description:
RNA-seq polyA+
transfected HEK293T
ORF3a_3_all_S12_
CovidProteinCounts_normalized_L1

value: 48h post transfection


title: 786-M1A-sgNTC18_REP_4


title: OS-LM1-sgHNF1B_2_REP_4


title: ATAC-seq_HK2_HIF2A_Rep1


title: ORF8_1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-036


title: 786-M1A-sgNTC18_REP_3


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-032


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-034


title: ATAC-seq_HK2_EV_Rep2


title: OS-LM1-sgHNF1B_2_REP_2


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-033


title: ATAC-seq_RCCJF_Rep2


title: ATAC-seq_HK2_EV_Rep3


title: M_rep_1

description:
RNA-seq polyA+
transfected HEK293T
M_1_all_S7_
CovidProteinCounts_normalized_L1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-030


title: E_rep_3

description:
RNA-seq polyA+
transfected HEK293T
E_3_all_S6_
CovidProteinCounts_normalized_L1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-029


title: 786-M1A-sgHNF1B_8_REP_4


title: 786-M1A-sgNTC18_REP_2


title: E_rep_2

description:
RNA-seq polyA+
transfected HEK293T
E_2_all_S5_
CovidProteinCounts_normalized_L1


title: 786-M1A-sgNTC18_REP_1


title: M_rep_2

description:
RNA-seq polyA+
transfected HEK293T
M_2_all_S8_
CovidProteinCounts_normalized_L1


title: N_rep_3

description:
RNA-seq polyA+
transfected HEK293T
N_3_all_S3_
CovidProteinCounts_normalized_L1


title: sci-RNA-seq3 with mouse embryo atlas (deeper sequencing) sci3-me-027

description:
sci-RNA-seq3 with mouse embryo atlas (deeper sequencing)
sci-RNA-seq3 library


title: E_rep_1

description:
RNA-seq polyA+
transfected HEK293T
E_1_all_S4_
CovidProteinCounts_normalized_L1