title: Control retina C1 replicate3

city: Bangalore

first: Vishnu

last: Suresh Babu

state: Karnataka

address: NH Health city, Bommasandra

department: Narayana Nethralaya Foundation

institute: GROW Research Laboratory

description: miRNA expression in pediatric retina

source_name: Pediatric Control retina

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

extract_protocol: Total RNA was isolated from 9 Rb tumors and 2 control pediatric retina samples using Agilent Absolutely RNA miRNA kit (cat# 400814) according to the manufacturer’s instructions. Twenty-five nanograms of RNA from Rb tumors and control pediatric retina samples were labeled with Cy3 dye using an Agilent Low Input Quick Amp Labeling Kit

treatment_protocol: The study was conducted by the Declaration of Helsinki principles under a protocol approved by the institutional ethics committee of Narayana Nethralaya (EC Ref no: C/2013/03/02). Informed written consents were received from all parents before inclusion in the study. Histology confirmed Rb tumors (n=9) comprising of Group E and Group D of the age range 0.2 -4years and pediatric controls (n=2) of the age range (0.2-0.3 years) were used for the microarray

value: Pediatric Retina

tag: gender

value: Female


title: CAST/EiJ x BALB/c F1 aB YY1 Rep1

status: Public on Jul 21 2022

type: SRA

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

country: USA

institute: National Institutes of Health

library_source: genomic

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: aB

growth_protocol: Mature B and T cells were isolated by negative selection (StemCell Technologies)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen).

tag: cell type

value: aB

tag: background

value: CAST/EiJ x BALB/c F1

tag: experimental type

value: ChIP-Seq


title: Control retina C2 replicate1

type: RNA

country: India

description: miRNA expression in pediatric retina

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

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

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

molecule: total RNA

organism: Homo sapiens

tag: tissue


title: Retinoblastoma tumor P9 replicate2

description: miRNA expressions in tumors

source_name: Retinoblastoma tumor

value: Tumor

value: Male


title: Control retina C1 replicate2

description: miRNA expression in pediatric retina


title: Control retina C2 replicate2

description: miRNA expression in pediatric retina


title: Retinoblastoma tumor P9 replicate3

description: miRNA expressions in tumors


title: Retinoblastoma tumor P9 replicate1

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB SP1 Rep3


title: Lung, WT, SEB, 4 hrs 9SR35154B_H07

city: New Haven

first: Govindarajan

last: Rajagopalan

state: CT

address: 300 Cedar Street

institute: Yale University

description:
Lung, WT, SEB, 4 hrs
Gene expression profiling in the lungs

hyb_protocol: Hynridized with Mouse clariom S chips as per standard protocol

scan_protocol: GeneChips were scanned using GeneArray Scanner

data_processing: CEL data files were exported into Transcriptome Analysis Console (TAC, Applied Biosystems) software and analyzed as per recommended procedure.

label: Biotin

source_name: HLA-DR3,WT, Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were mainted in the vivarium as per standard procedure

extract_protocol: RNA were extracted using TRIZOL, cleaned using Qiagen RNA purification kit. Frozen RNAs were sent to THermoFisher Scienfitific Microarray lab for subsequent processing.

treatment_protocol: HLA-DR3, HLA-DR3.IL17A knockout and HLA-DR3.IFN-gamma knockout (KO) mice were challenged intraperitoneally with 10 microgram of staphylococcal enterotoxin B. 4 and 24 hours later mice were euthanized, lungs harvested, RNA extracted and processed for gene expression analysis using Clariom s arrays

tag: sample type

value: Lung, WT, SEB, 4 hrs


title: Lung, WT, SEB, 4 hrs 9SR35154B_H10


title: Lung, IFNgKO, SEB, 4 hrs 9SR35154B_H09

description:
Lung, IFNgKO, SEB, 4 hrs
Gene expression profiling in the lungs

source_name: HLA-DR3.IFNgKO, Lung

value: Lung, IFNgKO, SEB, 4 hrs


title: CAST/EiJ x BALB/c F1 aB SP1 Rep2


title: Lung, IFNgKO, SEB, 4 hrs 9SR35154B_H08


title: Lung, IFNgKO, SEB, 24 hrs 9SR35154B_H06

description:
Lung, IFNgKO, SEB, 24 hrs
Gene expression profiling in the lungs

value: Lung, IFNgKO, SEB, 24 hrs


title: Lung, IFNgKO, SEB, 4 hrs 9SR35154B_H12


title: Control retina C1 replicate1

description: miRNA expression in pediatric retina


title: CAST/EiJ x BALB/c F1 aB SP1 Rep1


title: Retinoblastoma tumor P8 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P8 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P7 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P6 replicate3

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB NRF1 Rep3


title: Retinoblastoma tumor P6 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P7 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P8 replicate3

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB NRF1 Rep2


title: Arid1b P3 heterozygous replicate 5

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

library_source: transcriptomic

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.4.1.1) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: genotype

value: Arid1b heterozygous

value: whole brain

tag: age

value: Postnatal day 3

tag: Sex

value: male


title: CAST/EiJ x BALB/c F1 aB Ikfz Rep3


title: Retinoblastoma tumor P4 replicate3

description: miRNA expressions in tumors


title: Retinoblastoma tumor P5 replicate2

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 T Cells Sp1 Rep3

description: library:ChIPCastXBalbcF1TCellS2AntiSp1Rep3

source_name: T Cells

value: T Cells


title: Retinoblastoma tumor P6 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P4 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P3 replicate2

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB Ikfz Rep2


title: Retinoblastoma tumor P5 replicate3

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB IRF4 Rep3


title: CAST/EiJ x BALB/c F1 aB Ikfz Rep1


title: Retinoblastoma tumor P3 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P2 replicate3

description: miRNA expressions in tumors


title: Retinoblastoma tumor P4 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P2 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P2 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P3 replicate3

description: miRNA expressions in tumors


title: CAST/EiJ x BALB/c F1 aB NRF1 Rep1


title: CAST/EiJ x BALB/c F1 aB IRF4 Rep2


title: CAST/EiJ x BALB/c F1 aB IRF4 Rep1


title: Retinoblastoma tumor P1 replicate2

description: miRNA expressions in tumors


title: Retinoblastoma tumor P1 replicate1

description: miRNA expressions in tumors


title: Retinoblastoma tumor P1 replicate3

description: miRNA expressions in tumors


title: Ch12 WT cell line Input none 2

description: library: ChIPCh12WtInputS2R1

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Ch12 cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).

treatment_protocol: Cultured CH12 B cells were treated with TGFb (5 ng/ml; 240-B R&D systems) for a period of 1h, 6 h or 24 h before harvesting.

value: Ch12 WT cell line

tag: treatment

tag: target

value: Input


title: Ch12 WT cell line Input for BirAS2

description: library: ChIPCh12WtBirAInputS2

value: treated with TGFb 24h


title: TGBC1 GemR_resistant_gemcitabine_biological rep 2

city: TEMUCO (CD)

first: Luis

last: Vergara

state: Araucania region

address: Alemania Avenue #0458, 4to Floor

department: Center of Excellence in Traslational Medicine (CEMT)

country: Chile

institute: Universidad de La Frontera

hyb_protocol: The labeled samples were then hybridized to GeneChip Human Transcriptome Array 2.0 containing > 6.0 million distinct probes at 45 °C for 16 h, according to the guidelines in the Affymetrix GeneChip WT Terminal Labeling and Hybridization User Manual.

scan_protocol: Genechips were scanned using the GeneChip Scanner 3000 7 G (Affymetrix, USA). Affymetrix GeneChip Command Console (AGCC) software was used for data management and quality controls checks.

data_processing:
AGCC Scan Control Software applying Affymetrix default analysis settings alings, computes and produce the raw data file (.CEL) wich was normalized using the default Robust Multichip Analysis (SST-RMA) algorithm using the Affymetrix Transcriptome Expression Console (TAC) software. The resulting RMA expression values were log2  transformed.
Signal intensity calculations on the pixel values. The resulting RMA expression values were log2  transformed.

label: biotin

source_name: Human GBC cell line, treated with gemcitabine, 6 months

label_protocol: The Ambion WT Expression Kit was used to synthesize double-stranded cDNA and the corresponding in vitro transcription cRNA. Then, the samples were labeled using Affymetrix GeneChip WT Terminal Labeling Kit following manufacturer's guidelines.

growth_protocol: TGBC1 GBC cell line was grown in Dulbecco's Modified Eagle Medium high glucose, supplemented with 5% fetal bovine serum and 10 units/mL penicillin and 10 mg/mL streptomycin. Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

extract_protocol: Total RNA was extracted using the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, USA) according to manufacturer's protocol

treatment_protocol: To establish the gemcitabine-resistant subline (TGBC1 GemR), during six months, TGBC1 cells was exposed to stepwise increased gemcitabine concentration until 500 nM. In brief, cells at sub-confluent density were exposed to gemcitabine starting at IC80 (~2 nM as determined previously by a dose-response curve). When surviving cells reached 70% confluency, the gemcitabine concentration was 2-fold increased until reach 128 nM. Then, the concentrations were stepwise increased at 200, 300, 400 and finally 500 nM

value: Gallbladder tumor epithelial cell line

tag: tumor of origin

value: Gallbladder carcinoma metastated to lymph node, cell morphology:epithelial-like.

tag: donor

value: Female


title: Ch12 WT cell line BirA for Smad3

description: library: ChIPCh12WtBirAAntiBirAS1

value: treated with TGFb 6h

value: BirA

value: ChIP-Seq


title: Ch12 WT cell line Input for BirAS1

description: library: ChIPCh12WtBirAInputS1


title: TGBC1 GemR_resistant_gemcitabine_biological rep 3


title: Ch12 WT cell line BirA for Smad7

description: library: ChIPCh12WtBirAAntiBirAS2


title: TGBC1_sensitive_gemcitabine_biological rep 3

source_name: Human GBC cell line, untreated with gemcitabine

value: Gallbladder tumor epithelial cell line  (RBRC-RCB1129)


title: TGBC1_sensitive_gemcitabine_biological rep 2


title: TGBC1_sensitive_gemcitabine_biological rep 1


title: Ch12 WT cell line Input treated with TGFb 24h

description: library: ChIPCh12WtBiotagSmad7InputS1


title: TGBC1 GemR_resistant_gemcitabine_biological rep 1

source_name: Human GBC cell line, treated with gemcitabine,6 months


title: NOZ GemR_resistant_gemcitabine_biological rep 2

growth_protocol: NOZ GBC cell line was grown in Dulbecco's Modified Eagle Medium high glucose, supplemented with 5% fetal bovine serum and 10 units/mL penicillin and 10 mg/mL streptomycin. Cells were maintained at 37 °C in a humidified atmosphere containing 5% CO2.

treatment_protocol: To establish the gemcitabine-resistant subline (NOZ GemR), during six months, NOZ cells was exposed to stepwise increased gemcitabine concentration until 500 nM. In brief, cells at sub-confluent density were exposed to gemcitabine starting at IC80 (~2 nM as determined previously by a dose-response curve). When surviving cells reached 70% confluency, the gemcitabine concentration was 2-fold increased until reach 128 nM. Then, the concentrations were stepwise increased at 200, 300, 400 and finally 500 nM

value: Moderately differentiated carcinoma with metastasis in  ascites, cell morphology:epithelial-like.

value: Female, 48 years old


title: Ch12 WT cell line Smad7 rep3

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S1Rep3


title: Ch12 WT cell line Smad7 rep2

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S1Rep2


title: Ch12 WT cell line Smad3 rep2

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S1Rep2


title: Ch12 WT cell line Input treated with TGFb 6h

description: library: ChIPCh12WtBiotagSmad3InputS1


title: Ch12 WT cell line Smad3 rep3

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S1Rep3


title: Ch12 WT cell line Smad7 rep1

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S1Rep1


title: NOZ_sensitive_gemcitabine_biological rep 3

value: Gallbladder tumor epithelial cell line (JCRB Number:JCRB1033)


title: NOZ_sensitive_gemcitabine_biological rep 2


title: Ch12 WT cell line Smad3 rep1

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S1Rep1


title: Ch12 WT cell line Yy1 rep3

description: library: ChIPCh12WtAntiYy1S2R3


title: NOZ_sensitive_gemcitabine_biological rep 1


title: 6mFB_406WW1_14

city: Santa Barbara

first: Stella

middle: M. K.

last: Glasauer

state: CA

address: Biological Sciences II

department: Neuroscience Research Institute

institute: University of California Santa Barbara

description: drop-seq

library_source: transcriptomic single cell

data_processing:
Gene expression matrices were generated using the drop-seq tools package version 1.13 (https://github.com/broadinstitute/Drop-seq/releases)
Assembly: hg19
Supplementary files format and content: matrix files

source_name: iPSC-derived cerebral organoid

growth_protocol: organoids were generated using the method describet in Yoon et al., 2019 (DOI: 10.1038/s41592-018-0255-0)

extract_protocol:
3-4 organoids were pooled for each dissociation and dissociated using the Worthington Papain Dissociation System (Worthington). Solutions were prepared according to the Manufacturer’s instructions. Organoids in FB “D” media were cut into pieces with a sterile scalpel blade and washed twice in PBS prior to dissociation. Incubation in papain/DNaseI solution was performed in a 15 ml conical tube with untightened lid and at 37°C and 5% CO2 with occasional agitation. After the first 30 min of incubation, organoids were triturated 10 times with a fire-polished glass Pasteur pipette, followed by further incubation and trituration every 15 min until dissociation was complete. The total incubation time in papain/DNaseI solution was 75 -90 min. After adding Inhibitor Solution and DNaseI in EBSS, the dissociated cells were pelleted by centrifugation for 5 min at 300 g. The cells were resuspended in ice-cold PBS/0.01% BSA and passed through a 35 µm cell strainer.
Following dissociation, cells were diluted to 110 cells/µl in PBS/0.01% BSA. Drop-seq was performed as described (Macosko et al., 2015, DOI: 10.1016/j.cell.2015.05.002). Briefly, cells and barcoded beads (Chemgenes, 132 beads/ul in lysis buffer) were ran on an aquapel-treated microfluidic drop-seq device (FlowJEM) for co-encapsulation in nanoliter-sized droplets. After droplet-breakage, reverse transcription and Exonuclease I treatment, beads were counted, and 2000 beads were apportioned per PCR tube for cDNA amplification. The amplified cDNA libraries were purified using SPRI beads (Beckman Coulter) and quantified on a Fragment Analyzer (Agilent). Tagmentations were performed using the Illumina Nextera XT kit (Illumina), and the resulting libraries were purified in two consecutive rounds of SPRI beads-based size selection (0.6x beads to sample ratio followed by 1x beads to sample ratio).

value: iPSC-derived cerebral organoid

tag: organoid age

value: 6 months

tag: cell line

value: MAPT 406W/W


title: 6mFB_337VV1_15

description: drop-seq

value: wild type


title: 6mFB_337VM1_15

description: drop-seq

value: MAPT 337V/M


title: 6mFB_337VM3_14

description: drop-seq


title: 4mFB_337VM1_13

description: drop-seq

value: 4 months


title: 4mFB_337VV1_13

description: drop-seq


title: NOZ GemR_resistant_gemcitabine_biological rep 1


title: 2mFB_337VM1_11

description: drop-seq

value: 2 months


title: 2mFB_337VV1_11

description: drop-seq


title: Ch12 WT cell line Yy1 rep1

description: library: ChIPCh12WtAntiYy1S2R1

value: Ch12 WT cell line


title: Ch12 WT cell line Yy1 rep2

description: library: ChIPCh12WtAntiYy1S2R2


title: 6mFB_337VV3B12_14

description: drop-seq


title: NOZ GemR_resistant_gemcitabine_biological rep 3

value: Gallbladder tumor epithelial cell line


title: 6mFB_337VM2_14

description: drop-seq


title: Ch12 WT cell line Nfyb rep3

description: library: ChIPCh12WtAntiYb1S2R3

value: Nfyb


title: 6mFB_406RW1_14

description: drop-seq

value: MAPT 406R/W


title: 6mFB_337VV2_14

description: drop-seq


title: Ch12 WT cell line Nfyb rep2

description: library: ChIPCh12WtAntiYb1S2R2


title: 6mFB_406RR1_14

description: drop-seq


title: Ch12 WT cell line Nfyb rep1

description: library: ChIPCh12WtAntiYb1S2R1


title: Ch12 WT cell line Nrf1 rep3

description: library: ChIPCh12WtAntiNrf1S2R3


title: 3mFB_337VV1_12

description: drop-seq

value: 3 months


title: 3mFB_337VM1_12

description: drop-seq


title: 4mFB_406WW1_12

description: drop-seq


title: 4mFB_337VV3B12_12

description: drop-seq


title: 4mFB_337VM3_12

description: drop-seq


title: 4mFB_337VV3F02_12

description: drop-seq


title: 4mFB_337VM2_12

description: drop-seq


title: 4mFB_406RR1_12

description: drop-seq


title: Ch12 WT cell line Input none

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoInputS1R1

value: Input

value: ChIP-Seq


title: 8mFB_406RW1_10_b

description: drop-seq

value: 8 months


title: 8mFB_406RR1_10_a

description: drop-seq


title: Ch12 WT cell line Nrf1 rep1

description: library: ChIPCh12WtAntiNrf1S2R1


title: 4mFB_337VV2_12

description: drop-seq


title: 4mFB_406RW1_12

description: drop-seq


title: 8mFB_406RW1_10_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Input for BirAS2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBirAInputS2

value: treated with TGFb 24h


title: 3mFB_406WW1_10

description: drop-seq


title: 8mFB_406RR1_10_b

description: drop-seq


title: 3mFB_337VV3F02_10

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a BirA for Smad7

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBirAAntiBirAS2

value: BirA


title: 3mFB_337VM3_10

description: drop-seq

value: iPSC-derived cerebral organoid


title: 3mFB_337VM2_10

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Input treated with TGFb 24h

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7InputS1


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a BirA for Smad3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBirAAntiBirAS1

value: treated with TGFb 6h


title: 3mFB_337VV3B12_10

description: drop-seq


title: 3mFB_337VV2_10

description: drop-seq


title: 3mFB_406RR1_10

description: drop-seq


title: 3mFB_406RW1_10

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad7 rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S1Rep3


title: 6mFB_337VM1_07_b

description: drop-seq

value: 6 months


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Input for BirAS1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBirAInputS1


title: 6mFB_337VM1_07_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad7 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S1Rep2


title: Ch12 WT cell line Nrf1 rep2

description: library: ChIPCh12WtAntiNrf1S2R2


title: 6mFB_337VV1_07_b

description: drop-seq

value: wild type


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad7 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S1Rep1


title: 6mFB_337VV1_07_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Input treated with TGFb 6h

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3InputS1


title: 4mFB_337VM1_07

description: drop-seq

value: MAPT 337V/M


title: 2mFB_337VM3_09

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad3 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S1Rep2


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad3 rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S1Rep3


title: 4mFB_337VV1_07

description: drop-seq

value: 4 months


title: 2moFB_337VV3B12_09

description: drop-seq

value: 2 months


title: 2mFB_406WW1_09

description: drop-seq

value: MAPT 406W/W


title: 2mFB_337VM2_09

description: drop-seq


title: 2mFB_337VV2_09

description: drop-seq


title: 2mFB_337VV3F02_09

description: drop-seq


title: 2mFB_406RW1_09_b

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Smad3 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3AntiSmad3S1Rep1


title: 2mFB_406RW1_09_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Yy1 rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYy1S1R3


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Yy1 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYy1S1R2


title: 2mFB_406RR1_09_a

description: drop-seq


title: 2mFB_406RR1_09_b

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Yy1 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYy1S1R1


title: 6mFB_337VM2_08_b

description: drop-seq


title: 6mFB_406RW1_06_b

description: drop-seq


title: 6mFB_337VV2_08_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nfyb rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYb1S1R2


title: 6mFB_406RW1_06_a

description: drop-seq


title: 6mFB_406RR1_06_b

description: drop-seq


title: 6mFB_406RR1_06_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nfyb rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYb1S1R3


title: 4mFB_337VM2_06

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nrf1 rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiNrf1S1R3


title: 4mFB_337VM1_05

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nrf1 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiNrf1S1R2


title: 4mFB_337VV1_05

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nrf1 rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiNrf1S1R1


title: 3mFB_406WW1_04

description: drop-seq


title: 4mFB_337VV2_06

description: drop-seq


title: CAST/EiJ x BALB/c F1 activated T cells rep3 [ATAC-Seq]

description: library: ATACCastBalbF1acTS3

data_processing:
Base calling: Illumina CASAVA 1.8.2
ATAC-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ATAC-Seq: Remove duplicates with picard.
ATAC-Seq: Remove mitochondria reads.
ATAC-Seq: Keep high-quality reads with MAPQ>=30.
ATAC-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ATAC-Seq: Call peak with MACS2.
Assembly: mm10

source_name: activated T cells

growth_protocol: Mature B cells were isolated from C57BL/6J mouse spleen by negative selection (StemCell Technologies)

extract_protocol:
ATAC-seq: To prepare nuclei for tagmentation, 100,000 cells were centrifuged at 500 × g for 5 minutes, then washed with 50 μL of cold 1x PBS and centrifugated at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were centrifuged at 500 × g for 10 minutes using a refrigerated centrifuge. Immediately following the nuclei prep, the pellets were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Zymo Clean and Concentrator kit. After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 4 cycles at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR, the PCR reaction was monitored using qPCR in order to stop amplification prior to saturation. A 5 μl aliquot of the PCR reaction was mixed with 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x, and a 20-cycles qPCR was run to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were then purified using the Zymo Clean and Concentrator kit.
ATAC-seq: DNA was prepared for single-end Illumina sequencing. Sequencing data were acquired on the Illumina NovaSeq 6000.

value: activated T cells

tag: background strain

value: CAST/EiJ x BALB/c F1

value: ATAC-Seq


title: 3mFB_406RW2_04_a

description: drop-seq

value: 3 months

value: MAPT 406R/W


title: 3mFB_406RW2_04_b

description: drop-seq


title: CAST/EiJ x C57BL/6 F1 activated B cells rep2 [ATAC-Seq]

description: library: ATACCastC57F1aBS2

source_name: activated B cells (LPS+IL4+aCD180 48h)

value: activated B cells (LPS+IL4+aCD180 48h)

value: CAST/EiJ x C57BL/6 F1


title: CAST/EiJ x BALB/c F1 activated T cells rep1 [ATAC-Seq]

description: library: ATACCastBalbF1acTS1


title: CAST/EiJ x BALB/c F1 activated T cells rep2 [ATAC-Seq]

description: library: ATACCastBalbF1acTS2


title: 6mFB_337VV2_08_b

description: drop-seq


title: 6mFB_337VM2_08_a

description: drop-seq


title: Ch12 QKO cell line, Klf16, Maz, Sp1, Zbtb7a Nfyb rep1

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoAntiYb1S1R1

value: Nfyb

value: ChIP-Seq


title: 1mFB_406RR2_02

description: drop-seq

value: iPSC-derived cerebral organoid

value: 1 month


title: 1mFB_406RW2_02

description: drop-seq


title: 2mFB_406WW1_03

description: drop-seq


title: CAST/EiJ x C57BL/6 F1 activated B cells rep1 [ATAC-Seq]

description: library: ATACCastC57F1aBS1


title: 3mFB_406RR2_04_b

description: drop-seq


title: CAST/EiJ x BALB/c F1 activated B cells rep3 [ATAC-Seq]

description: library: ATACCastBalbF1aBS3


title: 3mFB_406RR2_04_a

description: drop-seq


title: 2mFB_406RW2_03_b

description: drop-seq


title: Healthy control (N-CDK) [B26]

city: Shanghai

first: Zhixiang

last: Hua

address: 83 Fenyang Rd

department: Department of Ophthalmology and the Eye Institute, Eye and Ear, Nose, and Throat Hospital

country: China

institute: Fudan University

data_processing:
FASTQ files for each sample were generated using the bcl2fastq software (Illumina Inc.)
After quality control, the reads were 3’5'-adaptor trimmed and filtered 15 bp reads with cutadapt software
The trimmed reads were aligned to reference genome with bowtie software
For each sample, known miRNAs, and predicted novel miRNAs were identified and enumerated using miRDeep2 software package (Freedlander et al. Nature Biotechnology, 26, 407-415 (2008) )
Raw reads where normalized by dividing the number of reads by the total number of mapped reads in millions, i.e., RPM
Assembly: miRBase Release 22
Supplementary files format and content: #Gene biotype: miRNA  #Condition pair: Test_vs_Control    Column A: Mature_ID, The ID of mature miRNA.  Column B: Arm, The arm of miRNA.  Column C: Mature_Acc, The accession number of mature miRNA from miRBase.  Column D: Mature_Seq, The mature sequence of miRNA.  Column E: Seed, The seed sequence of miRNA.  Column F: Length, The length of mature miRNA.  Column G: High_Confidence, The high confidence microRNAs are robustly supported as authentic miRNA genes.  Column H: Type, The MirGeneDB annotated miRNA type based on expression level.  Column I: Canonical, The MirGeneDB annotated canconical mature miRNA type.  Column J: Pre_ID, The ID of precursor miRNA annotated in miRBase22.  Column K: Pre_Acc, The accession number of precursor miRNA from miRBase.  Column L: Pre_Seq, The sequence of precursor miRNA.  Column M: Pre_Locus, The chromosome site of precursor miRNA.  Column N: Family_AC, The family accession number of precursor miRNA from miRBase.  Column O: Family_ID, The family ID of precursor miRNA annotated in miRBase.  Column P: Clustered_miRNAs, A group of microRNA precursors with an inter-microRNA istance of <10 kb on the same chromosome an inter-microRNA distance of <10 kb n the same genomic strand.  Column Q: Promoter, The Fantom5 promoter of precursor miRNA (Only available for human nd mouse).  Column R: Primary_microRNA, The primary transcript of miRNA annotated in fantom5 (Only available for human and mouse).  Column S: log2FC, The difference in mean between two groups (Test_CPM vs Control_CPM) of negative binomial random variables.  Column T: Fold_Change, 2^(log2FC).  Column U: p_value, The p-value of the exact test by negative binomial distribution.  Column V: q_value, The FDR adjusted p-value. The q-value will be setted as 1 if any group in the comparison has no repilicate.  Column W, X: Group CPM, The average of log CPM scaled by qCML methods: log2(CPM) of gene in groups.  Column Y ~ AH: CPM, The counts per million reads of miRNA in samples.

source_name: Tears from eye

extract_protocol:
Care was taken to avoid touching the corneal and conjunctival surfaces. Tear samples were repeatedly collected after an interval and a few blinks until a sufficient volume (approximately 10 μl) was acquired.The tear samples were placed in cryo-tubes and stored at –80 ℃ until further examination.Total RNA from the tear samples was isolated using an EZB-RN2-serum RNA purification kit (EZBioscience, USA) according to the manufacturer’s instructions.Small RNA sequencing was performed by KangChen Biotech (Shanghai, China) using the Illumina Small RNA Sequencing platform (Illumina, USA).
1) 3’-adaptor ligation;2) 5’-adaptor ligation;3) cDNA synthesis;4) PCR amplification;5) size selection of 135   155 bp PCR amplified fragments (corresponding to 15   35 nt small RNAs).

value: Tears from eye

tag: condition

value: Healthy control (N-CDK)


title: 2mFB_406RW2_03_a

description: drop-seq


title: Healthy control (N-CDK) [B11]


title: 6mFB_337VV3F02_14

description: drop-seq

value: 6 months

value: wild type


title: 2mFB_406RR2_03_a

description: drop-seq

value: 2 months


title: Healthy control (N-CDK) [B5]


title: Healthy control (N-CDK) [B16]


title: Climatic droplet keratopathy (CDK) patients [E7]


title: CAST/EiJ x BALB/c F1 activated B cells rep1 [ATAC-Seq]

description: library: ATACCastBalbF1aBS1

tag: cell type


title: Climatic droplet keratopathy (CDK) patients [E5]


title: Climatic droplet keratopathy (CDK) patients [E4]


title: 2mFB_406RR2_03_b

description: drop-seq


title: C57BL/6 x BALB/c F1 activated B cells rep3 [ATAC-Seq]

description: library: ATACC57BalbF1aBS3

value: C57BL/6 x BALB/c F1


title: 48h SARS-CoV-2 DelARKSAP n3

city: Philadelphia

first: Erica

last: Korb

state: PENNSYLVANIA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania

data_processing:
Fastq files were aligned by Star
DESeq2 was used for differential gene expression analysis
Assembly: hg38
Supplementary files format and content: DESeq output

molecule: polyA RNA

extract_protocol:
Qiagen RNA extraction kits were used to isolate RNA
RNA libraries were prepared for sequencing using standard Illumina protocols

value: A549-ACE cells

value: lung cell line expressing the ACE receptor

tag: infection

value: SARS-CoV-2 DelARKSAP

tag: time

value: 48 hour


title: 48h SARS-CoV-2 DelOrf8 n3

value: SARS-CoV-2 DelOrf8


title: 48h SARS-CoV-2 DelARKSAP n1


title: 48h SARS-CoV-2 DelARKSAP n2


title: CAST/EiJ activated B cells rep2 [ATAC-Seq]

description: library: ATACCastaBS3

value: activated B cells (LPS+IL4+aCD180 48h)

value: CAST/EiJ

tag: experimental type

value: ATAC-Seq


title: CAST/EiJ x BALB/c F1 activated B cells rep2 [ATAC-Seq]

description: library: ATACCastBalbF1aBS2

value: CAST/EiJ x BALB/c F1


title: 48h SARS-CoV-2 DelOrf8 n2


title: 48h SARS-CoV-2 DelOrf8 n1


title: C57BL/6 x BALB/c F1 activated B cells rep1 [ATAC-Seq]

description: library: ATACC57BalbF1aBS1


title: Climatic droplet keratopathy (CDK) patients [E6]

tag: tissue


title: 48h SARS-CoV-2 WT n1

value: SARS-CoV-2 WT


title: 48h SARS-CoV-2 WT n2


title: CAST/EiJ activated B cells rep1 [ATAC-Seq]

description: library: ATACCastaBS1


title: 48h Mock n1

value: Mock


title: 24h SARS-CoV-2 DelARKSAP n3

value: 24 hour


title: 48h Mock n3


title: 24h SARS-CoV-2 DelOrf8 n2


title: C57BL/6 activated B cells rep1 [ATAC-Seq]

description: library: ATACC57aBS1


title: BALB/c activated B cells rep3 [ATAC-Seq]

description: library: ATACBalbaBS3

value: BALB/c


title: C57BL/6 activated B cells rep3 [ATAC-Seq]

description: library: ATACC57aBS3


title: C57BL/6 x BALB/c F1 activated B cells rep2 [ATAC-Seq]

description: library: ATACC57BalbF1aBS2


title: BALB/c activated B cells rep2 [ATAC-Seq]

description: library: ATACBalbaBS2


title: 24h SARS-CoV-2 DelOrf8 n1


title: BALB/c activated B cells rep1 [ATAC-Seq]

description: library: ATACBalbaBS1


title: 48h Mock n2


title: 24h Mock n2


title: 24h SARS-CoV-2 WT n2


title: CAST/EiJ x BALB/c F1 activated T cells TS3 rep2

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Assembly: mm10

extract_protocol:
mRNA-seq: Total RNA was extracted from 0.5 million cultured cells using RNAqueous™ Total RNA Isolation Kit (AM1912). mRNA was then isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina).

value: activated T cells

value: mRNA-Seq


title: C57BL/6 activated B cells rep2 [ATAC-Seq]

description: library: ATACC57aBS2


title: 24h Mock n3


title: 24h SARS-CoV-2 DelOrf8 n3


title: 48h SARS-CoV-2 WT n3


title: 24h SARS-CoV-2 WT n3


title: CAST/EiJ x BALB/c F1 activated T cells TS3 rep1


title: 24h SARS-CoV-2 DelARKSAP n2


title: 24h SARS-CoV-2 DelARKSAP n1


title: dOrf8_n3 (Set 3)

data_processing:
Fastq files were aligned by Bowtie2
IGVtools was used to generate TDF files
NGSplot was used to generate genome-wide analysis plots
bam files aligned by bowtie2
Assembly: hg38
Supplementary files format and content: tdf

extract_protocol:
Transfected cells were isolated by FACS and lysed in cell lysis buffer (10mM TrisHCl ph7.5, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 0.1% Tween20, 0.1% Digitonin
Transposition reactionx mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with Ampure beads used for cleanup

value: Orf8 deletion SARS-CoV-2 infection


title: dARKSAP_n3 (Set 3)

value: ARKSAP deletion SARS-CoV-2 infection


title: dOrf8_n1 (Set 3)


title: SKOV3, Vector, biol rep, 3

city: Jinan

first: Shuai

last: Xu

state: Shandong

address: 247 North Park Street

department: Obstetrics and Gynecology

institute: Second hospital of Shandong University

data_processing:
Illumina Casava 1.7 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 vO.12.2 with parameters
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
Assembly: mm8
Supplementary files format and content: tab-delimited text files include fpkm values for each sample

source_name: ovary

growth_protocol: SKOV3 cells were maintained in McCoy’s 5A supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s protocol. RNA purity and concentration were determined with a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The TIPE2-overexpression plasmid was constructed by cloning human TIPE2 cDNA into a lentivirus vector. SKOV3 cells were cultured in a 24- well plate overnight and transfected with lentivirus. The cells were selected with 2ug/ml puromycin for one week to establish stable TIPE2 overexpression cells.

value: ovary

value: ovarian cancer cell line

value: vector group

value: transfected with empty vector


title: dARKSAP_n2 (Set 3)


title: WT_n2 (Set 3)

value: WT SARS-CoV-2 infection


title: SKOV3, Vector, biol rep, 2


title: CAST/EiJ x BALB/c F1 activated T cells TS2 rep2


title: 24h SARS-CoV-2 WT n1

value: A549-ACE cells

value: lung cell line expressing the ACE receptor


title: CAST/EiJ x BALB/c F1 activated T cells TS3 rep3


title: 24h Mock n1


title: SKOV3, Vector, biol rep, 1


title: WT_n1 (Set 3)


title: CAST/EiJ x BALB/c F1 activated T cells TS2 rep3


title: dARKSAP_n1 (Set 3)


title: WT_n3 (Set 3)


title: Mock_n3 (Set 3)

value: Mock infection


title: CAST/EiJ x BALB/c F1 activated T cells TS2 rep1

value: CAST/EiJ x BALB/c F1


title: CAST/EiJ x BALB/c F1 activated T cells TS1 rep3


title: Mock_n2 (Set 3)


title: SKOV3, TIPE2, biol rep, 3

value: TIPE2 overexpression

value: transfected with lentivirus encoding TIPE2


title: Mock_n1 (Set 3)


title: SKOV3, TIPE2, biol rep, 2


title: CAST/EiJ x BALB/c F1 activated T cells TS1 rep1


title: CAST/EiJ x BALB/c F1 activated T cells TS1 rep2


title: dARKSAP_n2 (Set 2)


title: dOrf8_n2 (Set 2)


title: dARKSAP_n3 (Set 2)


title: dARKSAP_n1 (Set 2)


title: SKOV3, TIPE2, biol rep, 1


title: BCR Repertoire, patient 34

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

data_processing:
Basecalls and mapping performed using Cell Ranger ver 6.0
Assembly: GRCh38
Supplementary files format and content: TCR and BCR VDJ, barcodes, features and matrix tsv files
Library strategy: scVDJ-seq

source_name: PBMC

extract_protocol:
PBMC samples recovered from COVID-19 patients at admission (n=13) or within 10 days after admission (n=8), were stained with anti-human CD45 antibody. Propidium iodine was also added to samples to remove dead cells. Live CD45+ cells were sorted using a SONY SH800S (4,000-10,000 cells each, cell viability >98%) and then encapsulated into droplets.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics, CA, USA). The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 (Illumina, Inc., CA, USA)
Single cell RNA-seq, Single cell TCR and BCT V(D)J segments (scVDJ-seq)

value: PBMC

tag: method

value: BCR Repertoire

tag: individual

value: patient 34

tag: admission

value: admission

tag: disease state


title: dOrf8_n1 (Set 2)

value: Orf8 deletion SARS-CoV-2 infection


title: BCR Repertoire, patient 35

value: patient 35


title: dOrf8_n3 (Set 2)


title: CAST/EiJ x BALB/c F1 activated B cells rep3

value: activated B cells (LPS+IL4+aCD180 48h)

value: mRNA-Seq


title: BCR Repertoire, patient 33

value: patient 33

value: within 10 days after admission


title: Mock_n3 (Set 2)


title: Mock_n2 (Set 2)


title: WT_n1 (Set 2)

value: WT SARS-CoV-2 infection


title: CAST/EiJ x BALB/c F1 activated B cells rep1


title: BCR Repertoire, patient 32

value: patient 32


title: Mock_n1 (Set 2)


title: CAST/EiJ x BALB/c F1 activated B cells rep2


title: THP-1 cells, H2Ba1-3 2

city: Seoul

first: Lucy Eunju

last: Lee

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Division of Rheumatology, Department of Internal Medicine

institute: Yonsei University College of Medicine

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using BBDuk (> average Q20)
Trimmed sequence reads were mapped to GrCh37/hg19 using Bowtie2 and Bedtools
Read count extraction and normalization were performed using EdgeR
Assembly: hg19
Supplementary files format and content: tab-delimited text files include count values for each Sample

growth_protocol: THP-1 cells were cultured in RPMI-1640, supplemented with 25 mM HEPES, L-glutamate, heat-activated 10% FBS, and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was isolated from THP-1 cells using TRIzol reagent (Invitrogen), and samples of 3 μg of total RNA were prepared from each condition with three experimental replicates.
RNA libraries for RNA-seq were prepared using Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
THP-1 cells were seeded at a density of 1 × 10^5 cells/well in 96-well plates and differentiated into adherent macrophages with 25 ng/mL phorbol 12-myristate 13-acetate (PMA, Sigma-Aldrich, MO, USA) overnight.
THP-1 cells were treated with H2B-α1 peptide or cit-H2B-α1 peptide.

value: PMA-activated monocyte cells

tag: genotype

value: WT

tag: treatment

value: H2B-alpha1 peptide, citrullinated

value: 3 h


title: BCR Repertoire, patient 31

value: patient 31


title: CAST/EiJ x C57BL/6 F1 activated B cells rep1

value: CAST/EiJ x C57BL/6 F1


title: THP-1 cells, H2Ba1-3 1


title: BCR Repertoire, patient 30

value: PBMC

value: BCR Repertoire

value: patient 30


title: THP-1 cells, H2Ba1-0 3

value: H2B-alpha1 peptide


title: CAST/EiJ activated B cells rep3

value: CAST/EiJ


title: BCR Repertoire, patient 29

value: patient 29

value: admission


title: CAST/EiJ activated B cells rep1

value: activated B cells (LPS+IL4+aCD180 48h)

value: mRNA-Seq


title: THP-1 cells, Control 3


title: THP-1 cells, H2Ba1-0 1


title: THP-1 cells, H2Ba1-0 2


title: WT_n2 (Set 2)

value: WT SARS-CoV-2 infection


title: CAST/EiJ activated B cells rep2


title: BCR Repertoire, patient 28

value: patient 28


title: BCR Repertoire, patient 27

value: patient 27


title: THP-1 cells, Control 2

value: PMA-activated monocyte cells

value: WT


title: CAST/EiJ x C57BL/6 F1 activated B cells rep2


title: C57BL/6 x BALB/c F1 activated B cells rep3

value: C57BL/6 x BALB/c F1


title: BCR Repertoire, patient 25

value: patient 25


title: THP-1 cells, H2Ba1-3 3

value: H2B-alpha1 peptide, citrullinated

value: 3 h


title: BCR Repertoire, patient 26

value: PBMC

value: BCR Repertoire

value: patient 26

value: within 10 days after admission


title: C57BL/6 x BALB/c F1 activated B cells rep2


title: C57BL/6 x BALB/c F1 activated B cells rep1


title: TNF-alpha treated scaffold rep 6 [TNFa6]

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

data_processing:
2.11. Bioinformatic Analysis of RNA-seq Data  Raw read data were processed using a previously published MAPR-Seq pipeline and generate gene-wise read count data. In brief, sequencing data were quality controlled using FASTQC software. Read data were aligned against human reference genome (GRCh38) using STAR aligner. Gene expression counts were obtained using HTSeq software configured to use RefSeq human transcriptome (version 78) as reference transcriptome. Gene wise read counts observed in each sample were processed using edgeR software for obtaining differentially expressed genes between any two experimental groups. The software was configured to remove any genes with <100 counts in all samples across both groups. Read count data for the remaining genes were normalized using trimmed means of M-values method. Gene wise differential expression between groups was tested using a generalized linear model configured to use negative binomial distribution. Differential expression p-values were corrected using Benjamini-Hochberg method. Genes with an adjusted p-value <0.05 and an absolute log2 fold change ≥2.0 were considered as significantly differentially expressed and considered for further analyses
Assembly: GRCh38
Supplementary files format and content: Transcript metadata and respective read counts in tab-delimited file

source_name: Decellularized bovine ECM seeded with human endothelial cells

growth_protocol:
Tissue Harvest
Fresh bovine saphenous veins (SV) were harvested from young adult cattle (15-24 months, Spear Products, Coopersburg, PA, USA) and shipped on ice. Tissue was dissected to remove perivascular connective tissue and adventitia. Resultant SV was stored uncut in Dulbecco’s Modified Eagles Medium (DMEM) with 15% (v/v) dimethyl sulfoxide (DMSO) at -80°C.
Antigen Removal
All ECM scaffold generation steps were performed in 4 mL of solution at RT, 150 rpm and changed twice daily, unless otherwise stated. Previously frozen SV were thawed planarized by incising the vessel longitudinally and cut into discs using 14 mm biopsy punches, unless otherwise stated. All chemicals were added to a base buffer solution (0.5 mM Pefabloc, 1% v/v antibiotic antimycotic solution (AAS) in 10 mM Tris–HCl (pH 8.0)). Antigen removal (AR) samples (scaffolds) underwent sarcomeric relaxation ((2% amidosulfobetaine-14 (ASB-14), 120 mM potassium chloride (KCl), 4 mM MgCl2, 4 mM EDTA, 5.88 mM Na-ATP, 10 mM 2,3 Butanedione monoxime (BDM), 0.5 mM Pefabloc and 1% AAS in 10 mM Tris–HCl, pH 7.6) two times for 30 min each. Relaxed veins were incubated in lipophilic protein solubilization solution (3% ASB-16 in 100 mM dithiothreitol (DTT), 2 mM MgCl2 and 600 mM KCl, in base buffer) for 48 h. AR-scaffolds underwent sarcomeric disassembly by washing in base buffer twice for 15 min, followed by incubation in 50 nM Latranculin B (Cayman Chemical) in base buffer for 2 h. Washed again with base buffer twice for 15 min and incubated for 2 h in 0.6 M KCl in base buffer. Washed a final time with base buffer twice for 15 mins and incubated 2 h in 1 M potassium iodine (KI) in base buffer, followed by overnight incubation in base buffer alone. The KCl and KI steps were repeated the next day, followed by overnight incubation in base buffer. Scaffolds were then placed in lipophilic protein solubilization solution for 48 h, followed by 24 h incubation in hydrophilic protein removal solution (100 mM dithiothreitol (DTT), 2 mM MgCl2 and 600 mM KCl, in base buffer). Subsequently, scaffolds underwent 24 h of nuclease digestion (10 Kunitz units/mL DNase I, 15 Kunitz units/mL RNase A, 0.5 mM Pefabloc, 1% AAS, 0.15 M NaCl, 5 mM MgCl2–6H2O in 10 mM Tris–HCl, pH 7.6)) and 96 h of washout in base buffer at 4˚C.
EC recellularization
Human aortic endothelial cells (hAECs), GFP-labelled hAECs (GFP-hAECs), human umbilical Vein Cells (HUVECs) and GFP-labelled HUVECS (GFP-HUVECs, all cells from Angio-Proteomie, Boston, MA) were expanded to P4, unless otherwise stated, in a T-25 flask coated with Quick Coating Solution (Angio-Proteomie) at 37oC, 5% CO2. Cells were cultured in 7 mL of endothelial cell growth medium (Lonza, Allendale, NJ) with the solution changed at 24hr after thawing and once every 3 days. Cells were lifted using Accutase® solution, hAECs were re-seeded on scaffolds at a cell seeding density of 450 cells/mm2 and HUVECs were re-seeded at a cell density of 600 cells/mm2, unless otherwise stated and cultured under the same conditions. Before cell seeding, all scaffolds were incubated in 1% AAS in endothelial cell media overnight.

extract_protocol:
For RNA-sequencing, RNA was extracted via a Qiagen RNeasy mini kit, according to the manufacturer’s directions.
Total RNA concentration and quality were determined using Qubit fluorometry (Invitrogen). Sequencing libraries were prepared using the Illumina TruSeq® RNA Stranded Kit following the manufacturer’s instructions. The concentration and purity of the prepared libraries were checked using the Agilent TapeStation D1000. Libraries were sequenced at up to 8 samples per lane following Illumina’s standard protocol using the Illumina cBot and HiSeq 3000/4000 PE Cluster Kit. The flow cells were sequenced as 100 X 2 paired end reads on an Illumina HiSeq 4000 using the HiSeq Control Software HD 3.4.0.38 collection software. Base-calling was performed using Illumina’s RTA version 2.7.7.

treatment_protocol:
Endothelial Cell Activation/Quiescence Drug Treatment
For cell activation/quiescence assay, hAECs were seeded onto AR scaffolds using a 12 mm internal diameter stainless steel cylinder or seeding directly into the wells of a 24-well plate. The cells seeded onto tissue culture plastic were treated overnight with either 1 µM simvastatin, 5 ng/mL TNFα, or left untreated (Control).

value: Umblical vein cells and aortic endothelial cells

value: TNF-alpha treated


title: BALB/c activated B cells rep3

value: activated B cells (LPS+IL4+aCD180 48h)

value: BALB/c


title: TNF-alpha treated scaffold rep 5 [TNFa5]


title: 7SK WT, rep 4

city: Würzburg

first: Tom

last: Gräfenhan

address: Josef-Schneider-Str. 2, Bau D15

department: Core Unit SysMed

country: Germany

institute: University of Wuerzburg

data_processing:
Base calling with Illumina NextSeq RTA v2.11.3
FASTQ conversion with bcl2fastq v2.20.0.422
FASTQ quality and adapter trimming using Cutadapt (Martin, 2011) version 2.5 (cutadapt parameters: --nextseq-trim=20 -m 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC)
Alignment of trimmed reads to human genome (GRCh38.p13 primary assembly and mitochondrion) using STAR (Dobin et al., 2013) v2.7.2b with default parameters based on RefSeq annotation version 109.20210226
Calculation of read counts on exon level summarized for each gene (RefSeq annotation version 109.20210226 for GRCh38.p13) using featureCounts v1.6.4 from the Subread package (Liao et al., 2014). Multi-mapping and multi-overlapping reads were counted strand-specific and reversely stranded with a fractional count for each alignment and overlapping feature (command line parameters: -s 2 -t exon -M -O --fraction).
Assembly: GRCh38.p13 (primary assembly and mitochondrion)
Supplementary files format and content: Character (TAB) separated value file containing raw mRNA abundance measurements

source_name: HeLa

growth_protocol: HeLa cells were cultured at 37°C and 5% CO2 in high glucose Dulbecco's Modified Eagle Medium with GlutaMAX™ Supplement (DMEM; Gibco) supplemented with 1 mM sodium pyruvate (Gibco), 10% fetal calf serum (Linaris) and 1% Penicillin-Streptomycin (Gibco).

extract_protocol:
RNA was extracted using the NucleoSpin RNA kit (Macherey-Nagel).
RNA quality was checked using a 2100 Bioanalyzer with the RNA 6000 Nano kit (Agilent Technologies). The RIN for all samples was >9.6. cDNA libraries were prepared from 300 ng of total RNA with TruSeq mRNA Stranded Library Prep Kit from Illumina according to manufacturer’s instructions (1/2 volume). Libraries were quantified by QubitTM Flex Fluorometer (ThermoFisher) and quality was checked using Fragment Analyzer system 5200 with DNF-474 HS NGS Kit (Agilent).

value: HeLa


title: THP-1 cells, Control 1


title: 7SK KO, rep 2

value: 7SK KO


title: 7SK WT, rep 3


title: 7SK KO, rep 3


title: 7SK KO, rep 1


title: BCR Repertoire, patient 23

value: patient 23

value: admission


title: 7SK KO, rep 4


title: BALB/c activated B cells rep2

value: mRNA-Seq


title: TNF-alpha treated scaffold rep 4 [TNFa4]


title: BCR Repertoire, patient 24

value: patient 24


title: 7SK WT, rep 1

value: WT


title: TNF-alpha treated scaffold rep 3 [TNFa3]


title: 7SK WT, rep 2


title: BCR Repertoire, patient 22

value: patient 22


title: C57BL/6 activated B cells rep3


title: C57BL/6 activated B cells rep2


title: TNF-alpha treated scaffold rep 1 [TNFa1]


title: C57BL/6 activated B cells rep1


title: hnRNP R KO, rep 3

value: hnRNP R KO


title: BCR Repertoire, patient 19

value: PBMC

value: patient 19


title: hnRNP R KO, rep 4


title: BCR Repertoire, patient 20

value: BCR Repertoire

value: patient 20


title: Simvastatin treated scaffold rep 6 [Simvastatin6]

value: Umblical vein cells and aortic endothelial cells

value: Simvastatin treated


title: ADT_G9_2

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

description:
G9_2_filtered_feature_bc_matrix.tar.gz
G9_2_feature.csv

data_processing:
The sequencing data was processed using CellRanger software (version 3.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix
Supplementary_files_format_and_content: csv; feature barcodes

source_name: Cardiac CD45+ cells

extract_protocol:
Myocardial infarction (MI) was induced by permanent coronary artery ligation in Trem2+/+ (wildtype) and Trem2-/- mice. Non-infarcted wildtype mice (n=2), non-infarcted Trem2-/- mice (n=3), wildtype mice at day 5 after myocardial infarction (n=5) and Trem2-/- mice at day 5 after myocardial infarction (n=5received an i.v. injection of 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. # 109814) under isoflurane anesthesia. The heart was perfused via intracardiac injection of PBS, excised, the right ventricle removed, and the infarct, peri-infarct area, and adjacent viable myocardium were collected, weighed and digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506) , 60U/ml DNAse (Roche #11284932001). Cells were washed twice in MACS buffer (PBS+0.5% BSA+2mM EDTA) and incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml). Afterwards, cells were incubated with anti-VSIG4-PE (clone NLA-14, final concentration 2µg/ml, ThermoFisher #12-5752-82),  anti-LYVE1-Biotin (clone ALY7, 5µg/ml, ThermoFisher #13-0443-82), mouse CD45 microbeads (Miltenyi, 130-052-301, 1:10 final concentration), anti-mouse CD45.2-AlexaFluor488 (Trem2+/+ heart samples, clone 104, 2µg/ml, Biolegend) or anti-mouse CD45.2-Alexa700 (Trem2-/- heart samples, clone 104, 2µg/ml, Biolegend). After 10’ incubation at 4°C, TotalSeq-A hashtag antibodies were added as follows: Hashtag 1-2: WT no MI; Hashtag 3, 4 and 15: Trem2-/- no MI;  Hahstag 5, 6, 7, 8, 9: wildtype MI day 5; Hashtag 10, 11, 12, 13, 14: Trem2-/- MI day 5. Cells were incubated for an additional 15 minutes at 4°C, washed twice in MACS buffer, pooled, and magnetic selection was performed using LS Columns (Miltenyi (# 130-042-401) and MidiMACS separators (Miltenyi # 130-042-302). Sorted CD45+ cells were washed twice with PBS containing 0.04% BSA (Sigma-Aldrich A1595), and incubated for 25’ at 4°C in PBS/0.04% FCS containing Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Antibodies. Cells were washed with PBS/0.04% FCS, resuspended and sorted using a BD FACS Aria III with a 100µm nozzle. Cells from steady state hearts (~50% Trem2+/+ and ~50% Trem2-/-) and from day 5 post-MI hearts (~50% Trem2+/+ and ~50% Trem2-/-) were sorted separately and pooled post-sort so that steady state and day 5 post-MI cells represent ~30% and ~70% of the total cell pool, respectively. 20,000-25,000 cells were loaded in the 10x Genomics Chromium in duplicate lanes.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.

tag: strain

value: C57BL6/J background


title: hnRNP R KO, rep 2


title: Simvastatin treated scaffold rep 5 [Simvastatin5]


title: HTO_G9_2


title: BCR Repertoire, patient 17

value: patient 17

value: within 10 days after admission


title: BALB/c activated B cells rep1

value: activated B cells (LPS+IL4+aCD180 48h)

value: BALB/c


title: BCR Repertoire, patient 18

value: patient 18

value: admission


title: hnRNP R KO, rep 1

value: HeLa


title: ADT_G8_2

description:
G8_2_filtered_feature_bc_matrix.tar.gz
G8_2_feature.csv


title: BCR Repertoire, patient 21

value: patient 21


title: Simvastatin treated scaffold rep 3 [Simvastatin3]


title: TNF-alpha treated scaffold rep 2 [TNFa2]

value: TNF-alpha treated


title: HTO_G8_2


title: BCR Repertoire, patient 16

value: patient 16


title: Simvastatin treated scaffold rep 4 [Simvastatin4]


title: BCR Repertoire, patient 15

value: PBMC

value: patient 15


title: hnRNP R WT, rep 3

value: WT


title: BCR Repertoire, patient 14

value: BCR Repertoire

value: patient 14


title: hnRNP R WT, rep 2


title: G9_2


title: Simvastatin treated scaffold rep 2 [Simvastatin2]

value: Umblical vein cells and aortic endothelial cells

value: Simvastatin treated


title: BCR Repertoire, patient 13

value: patient 13


title: Untreated scaffold rep 5 [ScaffoldL5]

value: Untreated


title: G8_2

value: C57BL6/J background


title: hnRNP R WT, rep 4


title: BCR Repertoire, patient 12

value: patient 12


title: Simvastatin treated scaffold rep 1 [Simvastatin1]


title: Untreated scaffold rep 6 [ScaffoldL6]


title: HEK293T Orf8dARKSAP n1 RNA-seq

data_processing:
Fastq files were aligned by Star
DESeq2 was used for differential gene expression analysis
Genome_build: hg38
Supplementary_files_format_and_content: DESeq output

extract_protocol:
Zymo RNA extraction kits were used to isolate RNA
RNA libraries were prepared for sequencing using standard Illumina protocols


title: F1_2 [HTO]

data_processing:
The sequencing data was processed using CellRanger software (version 3.1.0).
Genome_build: mm10
Supplementary_files_format_and_content: h5; contains data corresponding to the observed molecules, as well as data about the libraries, feature set(s), and barcode lists used for the analysis
Supplementary_files_format_and_content: tar.gz; gene barcode matrices and feature barcode matrix

extract_protocol:
Mice were treated daily with a monoclonal anti-CCR2 (MC-21, i.p. 20µg/mouse/injection) or with an isotype control antibody (rat IgG2b, clone LTF-2, BioXcell # BE0090) starting 1 day before the induction of myocardial infarction (MI) to deplete circulating CCR2+ monocytes. Mi was induced by permanent coronary artery ligation. Control mice (steady state heart, n=3), day 5 post-MI isotype control treated mice (n=4), and day 5 post-MI anti-CCR2 treated mice (n=5) received an i.v. injection of 2.5µg anti-CD45.2 APC (clone 104, Biolegend, cat. # 109814) under isoflurane anesthesia. The heart was perfused via intracardiac injection of PBS, excised, the right ventricle removed, and the infarct, peri-infarct area, and adjacent viable myocardium were collected, weighed and digested for 1 hour at 37°C under agitation in RPMI containing 450U/ml collagenase I (Sigma-Aldrich, #C0130), 125U/ml Collagenase XI (Sigma-Aldrich C7657), 60U/ml Hyaluronidase (Sigma-Aldrich, H3506) , 60U/ml DNAse (Roche #11284932001). Cells were washed twice in MACS buffer (PBS+0.5% BSA+2mM EDTA) and incubated for 5 minutes on ice with TruStain FcX™ (anti-mouse CD16/32, Biolegend #101320, 10µg/ml). Afterwards, cells were incubated with anti-VSIG4-PE (clone NLA-14, final concentration 2µg/ml, ThermoFisher #12-5752-82),  anti-LYVE1-Biotin (clone ALY7, 5µg/ml, ThermoFisher #13-0443-82), mouse CD45 microbeads (Miltenyi, 130-052-301, 1:10 final concentration), anti-mouse CD45.2-eFluor506 (steady state heart samples, clone 104, 2µg/ml, ThermoFisher #69-0454-82), anti-mouse CD45.2-AlexaFluor488 (MI Day 5 isotype samples, clone 104, 2µg/ml, Biolegend #109816), anti-mouse CD45.2-BV421 (MI Day 5 isotype samples, clone 104, 2µg/ml, Biolegend #109832). After 10’ incubation at 4°C, TotalSeq-A hashtag antibodies (Biolegend, see table for CITE-seq panels) were added as follows: Hashtag 1 to 3: steady state heart; Hashag 4 to 7: MI Day 5, isotype control treated; Hashtag 8 to 12: MI Day 5, anti-CCR2 treated. Cells were incubated for an additional 15 minutes at 4°C, washed twice in MACS buffer, pooled, and magnetic selection was performed using LS Columns (Miltenyi (# 130-042-401) and MidiMACS separators (Miltenyi # 130-042-302). Sorted CD45+ cells were washed twice with PBS containing 0.04% BSA (Sigma-Aldrich A1595), and incubated for 25’ at 4°C in PBS/0.04% FCS containing Fixable Viability Dye eFluor™ 780 (ThermoFisher #65-0865-14, 1:1000) and anti-mouse TotalSeqA-Antibodies. Cells were washed with PBS/0.04% FCS, resuspended and sorted using a BD FACS Aria III with a 100µm nozzle. Number of sorted cells was adjusted so that cells from steady state hearts (CD45.2-e506+), MI Day 5 isotype-treated hearts, and MI day 5 anti-CCR2-treated hearts represent 20%, 40% and 40% of all cells, respectively. Cells were resuspended, counted (final concentration 1,200 cells/µl) and 20,000 cells were loaded in the 10x Genomics Chromium in duplicate lanes, and scRNA-seq ADT and HTO libraries were prepared.
Single cells were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.
Chromium Single Cell 3' v3 (10X Genomics)


title: E12_2 [HTO]


title: BCR Repertoire, patient 11

value: patient 11


title: HEK293T Orf8dARKSAP n2 RNA-seq


title: HEK293T Orf8 n3 RNA-seq


title: BCR Repertoire, patient 10

value: patient 10

value: admission


title: HEK293T Orf8 n2 RNA-seq


title: F1_2 [ADT]


title: E12_2 [ADT]


title: hnRNP R WT, rep 1

value: HeLa


title: Untreated scaffold rep 3 [ScaffoldL3]


title: BCR Repertoire, patient 9

value: patient 9


title: F1_2 [GEX]


title: BCR Repertoire, patient 8

value: patient 8

value: within 10 days after admission


title: BCR Repertoire, patient 7

value: PBMC

value: patient 7


title: Untreated scaffold rep 1 [ScaffoldL1]


title: Sham treated scaffold rep 6 [Control6]

value: Sham treated


title: Untreated scaffold rep 2 [ScaffoldL2]


title: E12_2 [GEX]


title: HEK293T GFP n1 RNA-seq

value: Control


title: BCR Repertoire, patient 6

value: BCR Repertoire

value: patient 6


title: Arid1b P120 vehicle wildtype 5

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.4.1.1) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes normalized read count metrix calculated by using DESeq2.

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage and the pups are weaned on P21.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq RNA Sample Prep Kit v2 (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: (P120 data only) Fluoxetine hydrochloride (0.1 mg/ml in 0.2 % saccharin-based drinking water) was delivered to dams to treat fluoxetine to pups via mammary milks. Dams in the vehicle group were fed with 0.2% saccharin water without fluoxetine. Drug treatment was done from postnatal day 3 to postnatal day 21. At postnatal day 21, mice were weaned and co-housed in cages with 3–6 mice in the same genetic background. After weaning, mice were fed with normal drinking water. Brain samples were collected at postnatal day 120.

value: whole brain

tag: age

value: Postnatal day 120

tag: Sex

value: male

value: Arid1b wildtype

value: vehicle


title: Arid1b P120 vehicle wildtype 4


title: BCR Repertoire, patient 5

value: patient 5


title: 48h SARS-CoV-2 Del n3 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 Del n3

source_name: iAT2 cells

value: iPSCs dfferentiated into AT2 cells

value: 48 hour

value: SARS-CoV-2 Orf8 Del


title: Sham treated scaffold rep 4 [Control4]

value: Umblical vein cells and aortic endothelial cells


title: 48h SARS-CoV-2 Del n2 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 Del n2


title: Sham treated scaffold rep 3 [Control3]


title: BCR Repertoire, patient 4

value: patient 4

value: within 10 days after admission


title: 48h SARS-CoV-2 Del n1 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 Del n1


title: Sham treated scaffold rep 2 [Control2]


title: BCR Repertoire, patient 3

value: PBMC

value: patient 3


title: 48h SARS-CoV-2 WT n3 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 WT n3

value: SARS-CoV-2 WT


title: Arid1b P120 vehicle wildtype 1


title: Arid1b P120 vehicle wildtype 2


title: BCR Repertoire, patient 2

value: BCR Repertoire

value: patient 2

value: admission


title: 48h SARS-CoV-2 WT n2 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 WT n2


title: Untreated scaffold rep 4 [ScaffoldL4]

value: Untreated


title: BCR Repertoire, patient 1

value: patient 1


title: Arid1b P120 vehicle hetero 5

value: whole brain

value: Postnatal day 120

value: male

value: Arid1b hetero


title: Arid1b P120 vehicle hetero 4

value: vehicle


title: HEK293T Orf8 n1 RNA-seq

tag: cell line


title: 48h SARS-CoV-2 WT n1 iAT2 cells RNA-Seq

description: 48h SARS-CoV-2 WT n1

value: iPSCs dfferentiated into AT2 cells

value: 48 hour


title: Sham treated scaffold rep 5 [Control5]

value: Umblical vein cells and aortic endothelial cells

value: Sham treated


title: TCR Repertoire, patient 35

value: PBMC

value: TCR Repertoire

value: patient 35


title: TCR Repertoire, patient 34

value: patient 34


title: 48h Mock n3 iAT2 cells RNA-Seq

description: 48h Mock n3

value: Mock infection


title: wild type YP KOAc 48h lane8185_CGATGT_DH_E61_2

city: Cambridge

first: Laura

last: Biggins

address: Babraham Research Campus

department: Bioinformatics

country: United Kingdom

institute: The Babraham Institute

description:
wild type YP KOAc 48h
Annotated Probe Report for All Probes - main paper datasets.txt

data_processing:
bcl2fastq version 1.8.4 was used for demultiplexing
Assembly: R64-1-1
After adapter and quality trimming using Trim Galore (v0.6.6), RNA-seq data was mapped to yeast genome R64-1-1 using HISAT2 v2.1.0 (Kim et al., 2019) by the Babraham Institute Bioinformatics Facility. Mapped data was imported into SeqMonk v1.47.0
Quantified for log2 total reads mapping to the antisense strand of annotated open reading frames (opposite strand specific libraries) including probes to the rDNA intergrenic regions. Read counts were adjusted by Size Factor normalisation for the full set of quantified probes.
Supplementary files format and content: Tab-separated file (Annotated SeqMonk Probe report) where the first columns are information about the gene (name, strand, start, end, chromosome, …), and the remaining columns are the samples (log2RPM counts).

organism: Saccharomyces cerevisiae

source_name: MEP diploid

growth_protocol: All cells were grown in YPx media (2% peptone, 1% yeast extract, 2% sugar) at 30°C with shaking at 200 rpm. Media components were purchased from Formedium and media was sterilised by filtration. MEP experiments were performed as described with modifications (Cruz et al., 2018): cells were inoculated in 4 ml YPx (where x is the sugar) and grown for 6-8 hours then diluted in 25 ml YPx and grown for 16-18 hours to 0.2-0.6x107 cells/ml in 50 ml Erlenmeyer flasks. 0.125x107 cells per aged culture were harvested by centrifugation (15 s at 13,000 g), washed twice with 125 µl PBS and re-suspended in 125 µl of PBS containing ~3 mg/ml Biotin-NHS (Pierce 10538723). Cells were incubated for 30 min on a wheel at room temperature, washed once with 125 µl PBS and re-suspended in 125 µl YPx then inoculated in 125 ml YPx at 1x104 cells/ml in a 250 ml Erlenmeyer flask (FisherBrand FB33132) sealed with Parafilm. 1 µM β-estradiol (from stock of 1 mM Sigma E2758 in ethanol) was added after 2 h (glucose, fructose), 3 h (galactose, sucrose) or 4 h (potassium acetate). An additional 0.125x107 cells were harvested from the log phase culture while biotin labelling reactions were incubating at room temperature. Cells were harvested by centrifugation for 1 min, 4600 rpm, immediately fixed by resuspension in 70% ethanol and stored at -80°C.

extract_protocol:
Cells were re-suspended in 50 µl Lysis/Binding Buffer (from mirVANA kit, Life Technologies AM1560), and 50 µl 0.5 µm zirconium beads (Thistle Scientific 11079105Z) added. Cells were lysed with 5 cycles of 30 s 6500 ms-1 / 30 s ice in an MP Fastprep bead beater or for 3 min at power 12 in a Bullet Blender (ThermoFisher) in cold room, then 250 µl Lysis/Binding buffer added followed by 15 µl miRNA Homogenate Additive and cells were briefly vortexed before incubating for 10 minutes on ice. 300 µl acid phenol : chloroform was added, vortexed and centrifuged 5 min at 13,000 g, room temperature before extraction of the upper phase. 400 µl room temperature ethanol and 2 µl glycogen (Sigma G1767) were added and mixture incubated for 1 hour at -30 °C before centrifugation for 15 minutes at 20,000 g, 4 °C. The pellet was washed with cold 70% ethanol and re-suspended in 10 µl water. 1 µl RNA was glyoxylated and analysed on a BPTE mini-gel, and RNA was quantified using a PicoGreen RNA kit (Life Technologies R11490) or Qubit® RNA HS Assay Kit.
150 ng RNA was used to prepare libraries using the NEBNext Ultra II Directional mRNAseq kit with poly(A)+ purification module (NEB E7760, E7490) as described with modifications: Reagent volumes for elution from poly(T) beads, reverse transcription, second strand synthesis, tailing and adaptor ligation were reduced by 50%; libraries were amplified for 13 cycles using 2 µl each primer per 50 µl reaction before two rounds of AMPure bead purification at 0.9x and elution in 11 µl 0.1x TE prior to quality control using a Bioanalyzer HS DNA ChIP (Agilent) and quantification using a KAPA Library Quantification Kit (Roche).

treatment_protocol: Percoll gradients (1-2 per sample depending on harvest density) were formed by vortexing 1 ml Percoll (Sigma P1644) with 110 µl 10x PBS in 2 ml tubes and centrifuging 15 min at 15,000 g, 4 °C. Ethanol fixed cells were defrosted and washed once with 1 volume of cold PBSE (PBS + 2 mM EDTA) before resuspension in ~100 µl cold PBSE per gradient and layering on top of the pre-formed gradients. Gradients were centrifuged for 4 min at 2,000 g, 4 °C, then the upper phase and brown layer of cell debris removed and discarded. 1 ml PBSE was added, mixed by inversion and centrifuged 1 min at 2,000 g, 4 °C to pellet the cells, which were then re-suspended in 1 ml PBSE per time point (re-uniting samples where split across two gradients). 25 µl Streptavidin microbeads (Miltenyi Biotech 1010007) were added and cells incubated for 5 min on a wheel at room temperature. Meanwhile, 1 LS column per sample (Miltenyi Biotech 1050236) was loaded on a QuadroMACS magnet and equilibrated with cold PBSE in 4 °C room. Cells were loaded on columns and allowed to flow through under gravity, washed with 1 ml cold PBSE and eluted with 1 ml PBSE using plunger. Cells were re-loaded on the same columns after re-equilibration with ~500 µl PBSE, washed and re-eluted, and this process repeated for a total of three successive purifications. After addition of Triton X-100 to 0.01% to aid pelleting, cells were split into 2 fractions in 1.5 ml tubes, pelleted 30 s at 20,000 g, 4 °C, frozen on N2 and stored at -70 °C.

value: MEP diploid

value: wild type

tag: media

value: YP KOAc


title: wild type YP KOAc 72h lane8185_TTAGGC_DH_E61_3

description:
wild type YP KOAc 72h
Annotated Probe Report for All Probes - main paper datasets.txt


title: HEK293T GFP n2 RNA-seq

value: Control


title: 48h Mock n2 iAT2 cells RNA-Seq

description: 48h Mock n2


title: Arid1b P120 vehicle hetero 2

source_name: Brain

value: whole brain

value: Postnatal day 120


title: Sham treated scaffold rep 1 [Control1]


title: Arid1b P120 vehicle wildtype 3

value: male

value: Arid1b wildtype


title: wild type YP raffinose 48h lane8185_CAGATC_DH_E61_6

description:
wild type YP raffinose 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YP raffinose


title: TCR Repertoire, patient 33

value: patient 33

value: within 10 days after admission


title: Arid1b P120 vehicle hetero 3

value: Arid1b hetero

value: vehicle


title: wild type YP KOAc log lane8185_ATCACG_DH_E61_1

description:
wild type YP KOAc log
Annotated Probe Report for All Probes - main paper datasets.txt

value: log


title: 24h SARS-CoV-2 Del n3 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 Del n3

value: iPSCs dfferentiated into AT2 cells

value: 24 hour

value: SARS-CoV-2 Orf8 Del


title: wild type YPD 72h lane8185_TGACCA_DH_E61_4

description:
wild type YPD 72h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: YPD


title: 48h Mock n1 iAT2 cells RNA-Seq

description: 48h Mock n1

value: 48 hour

value: Mock infection


title: Arid1b P120 vehicle hetero 1

value: whole brain


title: wild type YP raffinose log lane8185_ACAGTG_DH_E61_5

description:
wild type YP raffinose log
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type


title: Arid1b P120 fluoxetine-treated wildtype 5

value: Postnatal day 120

value: male

value: fluoxetine-treated


title: TCR Repertoire, patient 31

value: PBMC

value: TCR Repertoire

value: patient 31


title: 24h SARS-CoV-2 Del n2 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 Del n2


title: Arid1b P120 fluoxetine-treated wildtype 3

value: Arid1b wildtype


title: wild type YPD 48h wga high lane7430_GTGGCC_DH_E36_7_Wt_WGA_high

description:
wild type YPD 48h wga high
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h wga high


title: Arid1b P120 fluoxetine-treated wildtype 4


title: TCR Repertoire, patient 29

value: patient 29

value: admission


title: Pgpd-HAP4 YPD 48h WGA low lane7430_GTGATC_DH_E36_3_HAP4_GFP_high

description:
Pgpd-HAP4 YPD 48h WGA low
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA low


title: TCR Repertoire, patient 30

value: patient 30


title: 24h SARS-CoV-2 Del n1 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 Del n1

value: iPSCs dfferentiated into AT2 cells

value: 24 hour

value: SARS-CoV-2 Orf8 Del


title: TCR Repertoire, patient 28

value: patient 28


title: Pgpd-HAP4 YPD 48h WGA medium lane7430_CTATAC_DH_E36_2_HAP4_GFP_medium

description:
Pgpd-HAP4 YPD 48h WGA medium
Annotated Probe Report for All Probes - cell sorts.txt

value: MEP diploid

value: YPD

value: 48h WGA medium


title: 24h SARS-CoV-2 WT n3 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 WT n3

value: SARS-CoV-2 WT


title: Arid1b P120 fluoxetine-treated wildtype 1

value: whole brain

value: Postnatal day 120

value: male

value: fluoxetine-treated


title: TCR Repertoire, patient 27

value: PBMC

value: TCR Repertoire

value: patient 27


title: 24h SARS-CoV-2 WT n2 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 WT n2


title: 24h SARS-CoV-2 WT n1 iAT2 cells RNA-Seq

description: 24h SARS-CoV-2 WT n1


title: Pgpd-HAP4 YPD 48h WGA high lane7430_CTAGCT_DH_E36_1_HAP4_GFP_low

description:
Pgpd-HAP4 YPD 48h WGA high
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA high


title: Arid1b P120 fluoxetine-treated wildtype 2

value: Arid1b wildtype


title: 24h Mock n3 iAT2 cells RNA-Seq

description: 24h Mock n3

value: iPSCs dfferentiated into AT2 cells

value: Mock infection


title: TCR Repertoire, patient 26

value: patient 26

value: within 10 days after admission


title: wild type YPD 48h lane7129_TAGCTT_E30_1_3_Wt_48h

description:
wild type YPD 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: wild type


title: TCR Repertoire, patient 24

value: patient 24


title: TCR Repertoire, patient 25

value: patient 25

value: admission


title: wild type YPSucrose 48h lane7129_TAATCG_E34_9_SUC_48h

description:
wild type YPSucrose 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPSucrose


title: 24h Mock n1 iAT2 cells RNA-Seq

description: 24h Mock n1

value: 24 hour


title: 24h Mock n2 iAT2 cells RNA-Seq

description: 24h Mock n2


title: TCR Repertoire, patient 23

value: patient 23


title: Arid1b P120 fluoxetine-treated hetero 3

value: whole brain

value: Postnatal day 120

value: male

value: Arid1b hetero

value: fluoxetine-treated


title: TCR Repertoire, patient 32

value: PBMC

value: TCR Repertoire

value: patient 32


title: TCR Repertoire, patient 22

value: patient 22

value: within 10 days after admission


title: Arid1b P120 fluoxetine-treated hetero 1


title: wild type YPD log lane7129_GTGAAA_E34_1L_GLU_log

description:
wild type YPD log
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: wild type

value: YPD

value: log


title: TCR Repertoire, patient 21

value: patient 21

value: admission


title: Orf8 CUT&TAG

data_processing:
Fastq files were aligned by Bowtie2
IGVtools was used to generate TDF files
NGSplot was used to generate genome-wide analysis plots
Genome_build: hg38
Supplementary_files_format_and_content: tdf files generated by IGVtools from bam files aligned by bowtie2

source_name: HEK cells

extract_protocol:
Transfected cells were isolated by FACS and CUT&TAG was used with antibody H3K9ac Active Motif 39917
Transposition reactionx mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with Ampure beads used for cleanup

tag: treament

value: Orf8 transfection

tag: antibody

value: H3K9ac Active Motif 39917


title: Pgpd-HAP4 YPD 48h lane7129_GTCCGC_E30_2_4_HAP4_48h

description:
Pgpd-HAP4 YPD 48h
Annotated Probe Report for All Probes - main paper datasets.txt

tag: cell type


title: wild type YPD 48h WGA low lane7430_CCGTCC_DH_E36_6_Wt_WGA_low

description:
wild type YPD 48h WGA low
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA low


title: ARKSAP CUT&TAG

description: ARKSAP

value: Orf8 with ARKSAP deletion transfection


title: wild type YPD 24h lane7129_GGTAGC_E34_1_GLU_24h

description:
wild type YPD 24h
Annotated Probe Report for All Probes - main paper datasets.txt


title: GFP CUT&TAG

description: GFP

value: GFP transfection


title: Arid1b P10 wildtype 5

value: whole brain

value: Postnatal day 10

value: male

value: Arid1b wildtype


title: Arid1b P10 wildtype 4


title: Pgpd-HAP4 YPD 48h lane7129_GGCTAC_E30_1_4_HAP4_48h


title: ARKSAP_n2 HEK cells ATAC-Seq

data_processing:
Fastq files were aligned by Bowtie2
IGVtools was used to generate TDF files
NGSplot was used to generate genome-wide analysis plots
Genome_build: hg38
Supplementary_files_format_and_content: bam files aligned by bowtie2


title: TCR Repertoire, patient 20

value: PBMC

value: TCR Repertoire

value: patient 20


title: TCR Repertoire, patient 19

value: patient 19


title: Arid1b P10 wildtype 3


title: Pgpd-HAP4 YPD log lane7129_GCCAAT_E30_1_2l_HAP4_log

description:
Pgpd-HAP4 YPD log
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: YPD


title: ARKSAP_n1 HEK cells ATAC-Seq


title: wild type YPFructose log lane7129_GAGTGG_E34_3L_FRU_log

description:
wild type YPFructose log
Annotated Probe Report for All Probes - main paper datasets.txt

value: wild type

value: YPFructose

value: log


title: TCR Repertoire, patient 17

value: patient 17

value: within 10 days after admission


title: TCR Repertoire, patient 18

value: patient 18

value: admission


title: wild type YPD log lane7129_CTTGTA_E30_2_1l_Wt_log


title: Arid1b P10 wildtype 2

value: whole brain


title: Orf8_n2 HEK cells ATAC-Seq

value: Orf8 transfection


title: Arid1b P10 wildtype 1

value: Postnatal day 10

value: male


title: Orf8_n1 HEK cells ATAC-Seq


title: Arid1b P10 hetero 4

value: Arid1b hetero


title: TCR Repertoire, patient 15

value: PBMC

value: TCR Repertoire

value: patient 15


title: TCR Repertoire, patient 16

value: patient 16


title: GFP_n2 HEK cells ATAC-Seq

value: GFP transfection


title: GFP_n1 HEK cells ATAC-Seq


title: Arid1b P10 hetero 3


title: Arid1b P120 fluoxetine-treated hetero 4

value: Postnatal day 120

value: fluoxetine-treated


title: wild type YPD 48h lane7129_CCGTCC_E30_2_3_Wt_48h

value: MEP diploid

value: wild type

value: YPD


title: TCR Repertoire, patient 14

value: patient 14


title: 48h SARS-CoV-2 Del n3 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 Del n3

source_name: A549-ACE cells

value: lung cell line expressing the ACE receptor

tag: time

value: 48 hour


title: Arid1b P120 fluoxetine-treated hetero 2

value: whole brain


title: wild type YPFructose 48h lane7129_CCAACA_E34_8_FRU_48h

description:
wild type YPFructose 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPFructose


title: Arid1b P10 hetero 2

value: Postnatal day 10

value: male


title: TCR Repertoire, patient 13

value: PBMC

value: patient 13

value: within 10 days after admission


title: wild type YPGal 48h lane7129_CATTTT_E34_7_GAL_48h

description:
wild type YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPGal


title: 48h SARS-CoV-2 Del n2 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 Del n2


title: Arid1b P10 hetero 5

value: Arid1b hetero


title: 48h SARS-CoV-2 Del n1 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 Del n1


title: TCR Repertoire, patient 11

value: TCR Repertoire

value: patient 11

value: admission


title: TCR Repertoire, patient 12

value: patient 12


title: 48h SARS-CoV-2 WT n3 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 WT n3


title: wild type YPSucrose 24h lane7129_CACGAT_E34_4_SUC_24h

description:
wild type YPSucrose 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: wild type

value: YPSucrose


title: wild type YPGal log lane7129_CGTACG_E34_2L_GAL_log

description:
wild type YPGal log
Annotated Probe Report for All Probes - main paper datasets.txt

value: log


title: aB Rreb1

description: library: aBRreb1

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Genome_build: mm10

source_name: activated B cells

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on Illumina HiSeq 3000.

treatment_protocol: activated B cells were treated with mithramycin with 10nM, 50nM, and 100nM.

value: activated B cells

tag: target

tag: experimental type

value: ChIP-Seq


title: Arid1b P10 hetero 1

tag: tissue

value: whole brain

value: Postnatal day 10


title: TCR Repertoire, patient 10

value: PBMC

tag: method

tag: individual

value: patient 10


title: aB Input-2

description: library: ChIPaBInputS1

value: Input


title: 48h SARS-CoV-2 WT n2 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 WT n2

value: lung cell line expressing the ACE receptor

value: 48 hour


title: aB Input-1

description: library: ChIPaBInput


title: Pgpd-HAP4 YPD 24h lane7129_ATGTCA_E30_2_2_HAP4_24h

description:
Pgpd-HAP4 YPD 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPD


title: TCR Repertoire, patient 9

value: TCR Repertoire

value: patient 9

tag: admission

tag: disease state


title: Ch12 WT biotag Smad7 input

description: library: ChIPCh12WtBiotagSmad7InputS3

source_name: Ch12 cell line

treatment_protocol: CRISPR Cas9 engineering of CH12 B-cells: For complete deletion of respective transcription factor gene, two sgRNA were used per target gene. (a)sgRNA design: sgRNA targets were dresigned by the sgRNA online tool (https://crispr.zhaopage.com). Selected sgRNAs were cloned into px458 (Addgene #48138). (b) Nucleofection and cell sorting: Cultured CH12 B cells were nucleofected with 1 ug of plasmid per 1 million cells, using the SF Cell line 4D-Nucleofector X kit with the 4D-Nucleofector device (Pulse code: CM150). Cells were single cell-sorted for GFP expression into 96-well plates and allowed to recover for 7-10 days. Grown colonies were genotyped using respective primers, and clones with homozygous deletion were expanded for further experiments and analysis.

value: Ch12 cell line

tag: genotype

value: WT


title: 48h Mock n3 A549-ACE cells RNA-Seq

description: 48h Mock n3


title: TCR Repertoire, patient 8

value: patient 8

value: within 10 days after admission


title: TCR Repertoire, patient 7

value: patient 7

value: admission


title: wild type YPGal 24h lane7129_ATGAGC_E34_2_GAL_24h

description:
wild type YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

tag: strain

value: wild type

value: YPGal


title: Ch12 WT biotag Smad7 rep3

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S3R3

value: ChIP-Seq


title: wild type YPD 48h lane7129_CATGGC_E34_6_GLU_48h

tag: age


title: 48h Mock n2 A549-ACE cells RNA-Seq

description: 48h Mock n2


title: wild type YPD 24h lane7129_CAGATC_E30_1_1_Wt_24h


title: aB Egr1

description: library: aBEgr1

value: activated B cells


title: TCR Repertoire, patient 6

value: PBMC

value: patient 6


title: TCR Repertoire, patient 4

value: patient 4


title: 24h SARS-CoV-2 Del n2 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 Del n2

value: lung cell line expressing the ACE receptor

value: 24 hour


title: 24h SARS-CoV-2 Del n3 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 Del n3


title: 48h Mock n1 A549-ACE cells RNA-Seq

description: 48h Mock n1

value: 48 hour


title: wild type YPFructose 24h lane7129_CAACTA_E34_3_FRU_24h

description:
wild type YPFructose 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPFructose


title: Ch12 WT biotag Smad7 rep1

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S3R1

value: Ch12 cell line

value: WT


title: Pgpd-HAP4 YPD 24h lane7129_ACTTGA_E30_1_2_HAP4_24h

value: YPD


title: TCR Repertoire, patient 5

value: TCR Repertoire

value: patient 5

value: within 10 days after admission


title: TCR Repertoire, patient 3

value: patient 3


title: Arid1b P120 fluoxetine-treated hetero 5

value: whole brain

value: Postnatal day 120

tag: Sex

value: male

value: Arid1b hetero

tag: treatment

value: fluoxetine-treated


title: 48h SARS-CoV-2 WT n1 A549-ACE cells RNA-Seq

description: 48h SARS-CoV-2 WT n1


title: Ch12 WT biotag Smad3 input

description: library: ChIPCh12WtBiotagSmad3InputS3

value: ChIP-Seq


title: wild type YPSucrose log lane7129_ACTGAT_E34_4L_SUC_log

description:
wild type YPSucrose log
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: wild type

tag: media

value: YPSucrose

value: log


title: 24h SARS-CoV-2 Del n1 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 Del n1

value: lung cell line expressing the ACE receptor

value: 24 hour


title: Ch12 WT biotag Smad3 rep3

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S3R3

value: Ch12 cell line

value: WT


title: TCR Repertoire, patient 2

value: PBMC

value: TCR Repertoire

value: patient 2

value: admission


title: wild type YPD 24h lane7129_AGTTCC_E30_2_1_Wt_24h

value: YPD


title: Pgpd-HAP4 YPD 48h WGA low lane8144_CCGTCC_DH4_E66_Hap4-oe_low_WGA

description:
Pgpd-HAP4 YPD 48h WGA low
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA low


title: TCR Repertoire, patient 1

value: patient 1


title: 24h SARS-CoV-2 WT n2 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 WT n2


title: Pgpd-HAP4 YPD 48h WGA medium lane8144_AGTTCC_DH3_E66_Hap4-oe_medium_WGA

description:
Pgpd-HAP4 YPD 48h WGA medium
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA medium


title: Ch12 WT biotag Smad3 rep1

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S3R1

value: ChIP-Seq


title: Ch12 WT biotag Smad7 rep2

description: library: ChIPCh12WtBiotagSmad7AntiSmad7S3R2


title: Expression, patient 35

data_processing:
Basecalls and mapping performed using Cell Ranger ver 6.0
Assembly: GRCh38
Supplementary files format and content: TCR and BCR VDJ, barcodes, features and matrix tsv files

value: Expression

value: patient 35


title: Pgpd-HAP4 YPD log lane7129_AGTCAA_E30_2_2l_HAP4_log

description:
Pgpd-HAP4 YPD log
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid


title: 24h SARS-CoV-2 WT n1 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 WT n1


title: cat8 YPGal 24h lane7777_TTAGGC_E56_3_CAT8_24h

description:
cat8 YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: YPGal


title: 24h Mock n3 A549-ACE cells RNA-Seq

description: 24h Mock n3

value: lung cell line expressing the ACE receptor


title: Ch12 WT BirA only input rep1

description: library: ChIPCh12WtBiotagBirAInputS3


title: 24h Mock n2 A549-ACE cells RNA-Seq

description: 24h Mock n2

value: 24 hour


title: Pgpd-HAP4 YPD 48h WGA high lane8144_CTTGTA_DH2_E66_Hap4-oe_high_WGA

description:
Pgpd-HAP4 YPD 48h WGA high
Annotated Probe Report for All Probes - cell sorts.txt

value: 48h WGA high


title: Expression, patient 32

value: patient 32


title: 24h Mock n1 A549-ACE cells RNA-Seq

description: 24h Mock n1


title: 24h SARS-CoV-2 WT n3 A549-ACE cells RNA-Seq

description: 24h SARS-CoV-2 WT n3


title: cox9 gal80 YPGal 24h lane7777_TGACCA_E56_4_COX9_GAL80_24h

description:
cox9 gal80 YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt

value: cox9 gal80


title: Ch12 WT biotag Smad3 rep2

description: library: ChIPCh12WtBiotagSmad3AntiSmad3S3R2

value: Ch12 cell line

value: WT


title: cox9 gal80 YPGal 24h lane7777_TAGCTT_E56_10_COX9_GAL80_24h


title: gcn4 YPD log lane7777_GTTTCG_E57_1_GCN4_log

description:
gcn4 YPD log
Annotated Probe Report for All Probes - mutants not in paper.txt

value: log


title: Expression, patient 30

value: PBMC

value: patient 30

value: admission


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad7 input

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7InputS3

value: Klf16, Maz, Sp1, Zbtb7a Knockout


title: snf4 YPGal 24h lane7777_GTCCGC_E56_17_SNF4_24h

description:
snf4 YPGal 24h
Annotated Probe Report for All Probes - main paper datasets.txt


title: Del_n2 A549 ATAC-Seq

value: Orf8 deletion SARS-CoV-2 infection


title: snf4 YPGal 24h lane7777_GTGGCC_E56_19_SNF4_24h


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad7 rep3

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S3R3

value: ChIP-Seq


title: WT_n2 A549 ATAC-Seq

value: WT SARS-CoV-2 infection


title: Expression, patient 34

value: Expression

value: patient 34


title: Ch12 WT BirA only input rep2

description: library: ChIPCh12WtBiotagBirAInputS4


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad7 rep2

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad7AntiSmad7S3R2


title: Ch12 WT BirA only rep2

description: library: ChIPCh12WtBiotagBirAAntiBirAS4


title: Expression, patient 33

value: patient 33

value: within 10 days after admission


title: Expression, patient 27

value: patient 27


title: Expression, patient 31

value: patient 31


title: Ch12 Klf16,Maz,Sp1,Zbtb7a KO biotag Smad3 input

description: library: ChIPCh12Klf16MazSp1Zbtb7aKoBiotagSmad3InputS3


title: WT_n1 A549 ATAC-Seq


title: Expression, patient 28

value: patient 28


title: cox9 gal80 YPGal 48h lane7777_GCCAAT_E56_6_COX9_GAL80_48h

description:
cox9 gal80 YPGal 48h
Annotated Probe Report for All Probes - main paper datasets.txt

value: MEP diploid

value: cox9 gal80

value: YPGal


title: Ch12 WT BirA only rep1

description: library: ChIPCh12WtBiotagBirAAntiBirAS3

value: Ch12 cell line

value: WT


title: pmr1 YPD 24h lane7777_GTAGAG_E57_5_PMR1_24h

description:
pmr1 YPD 24h
Annotated Probe Report for All Probes - mutants not in paper.txt

value: YPD