title: Volunteer AE0DC Sample 33AC


title: Volunteer B04EC Sample 3330

status: Public on Apr 04 2022

type: protein

city: Irvine

first: Rafael

last: de Assis

state: CA

address: 3800 PARKVIEW LN APT 38A, Irvine, CA 92612

country: USA

institute: University of California Irvine

hyb_protocol: Antibodies were detected using Qdot (Q800) -conjugated anti-human IgG

scan_protocol: Slides were imaged using the ArrayCam system (https://gracebio.com/) for 300ms and images processed using ScanArray Express.

data_processing:
Raw data was normalized by re-scaling based on the positive control spots as descibed by Duarte J. 2013; Causton 2004 and Bolstad 2003
processed.xls: Normalized signal Intensity

molecule: protein

organism: Homo sapiens

source_name: Sera

label_protocol: No labeling

extract_protocol: Sera samples were extracted from finger pricks using a lancet and collected by capilary. Sera was then separated from the blood cells by centrifugation.

tag: volunteer id

tag: age

tag: gender

value: Female

tag: ethnicity

value: Asian

tag: job/role

value: Administrative

tag: first vaccination

tag: second vaccination

tag: days since vaccine


title: AB8457

type: SRA

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

library_source: transcriptomic

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Well-barcode-RMT are extracted from the 9 first base pairs in the R2 fastq sequences. Unique-molecular-identifier are extracted from the subsequent 8 base pairs in the R2 sequences. R1 contains the genomic sequences.
Reads were separated by POOL_BARCODE_WELL_BARCODE header data, allowing 1 sequencing error. This process created a single fastq file for each source well.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include mRNA molecule count values for each Sample

molecule: polyA RNA

source_name: Peripheral blood

extract_protocol:
human sample collection: skin samples were obtained through punch biopsy (4 mm), 10 cm distal to the elbow and placed in saline containing tubes on ice and then transferred to cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS). Whole blood samples were collected at the time of skin biopsy, were placed in EDTA-containing tubes (Beckton Dickenson) on ice and diluted 1:1 with ice cold FACS buffer. Skin and blood samples immediately transported to the lab.
Skin cell suspension and blood mononuclear cells were stained with the following antibodies: CD45 (PerCp/Cyanine, 3040285.5, Biolegend), CD90 (PE 328144, Biolegend), LGR5 (PE, 373803, Biolegend), CD55 (FITC, 311306, Biolegend). All FACS antibodies were used with a 1:100 dilution. Samples were filtered through a 40μm strainer before commencing sorting. Single cell sorting was performed using FACSAria Fusion cell sorter (BD Biosciences, San Jose, CA). After doublets exclusion, isolated live cells were single-cell sorted into 384-well cell capture plates containing 2μL of lysis solution and barcoded poly(T) reverse-transcription (RT) primers for single-cell RNA-seq. Four empty wells were kept in each 384-well plate as a no-cell control for data analysis. Immediately after sorting, each plate was spun down to ensure cell immersion into the lysis solution, snap frozen on dry ice, and stored at –80°C until processed. Cells were analyzed using BD FACSDiva software (BD Bioscience) and FlowJo software (FlowJo, LLC).
Single-cell RNA-seq libraries were prepared as previously described {Jaitin, 2014}. In brief, mRNA from single cells sorted into capture plates were barcoded and converted into cDNA and then pooled using an automated pipeline. The pooled sample was linearly amplified by T7 in vitro transcription, and the resulting RNA was fragmented and converted into a sequencing-ready library by tagging the samples with pool barcodes and Illumina sequences during ligation, RT, and PCR. Each pool of cells was tested for library quality and concentration as described previously {Jaitin, 2014}

treatment_protocol:
treatment protocol (1): To generate gentle and efficient single-cell suspensions from human skin tissue, we used Miltenyi human whole skin dissociation kit (catalog num. 130-101-540), which combines mechanical dissociation with enzymatic degradation of the extracellular adhesion proteins. In short, first we cut the skin biopsy into small pieces (< 1mm) and transferred them into gentleMACS C Tube containing 435µL of Buffer and 65 µL of enzyme mix. Next, samples were incubated in a water bath at 37 °C for 1h. After incubation we diluted the samples by adding 0.5 mL of cold cell culture medium, tightly closed C Tube and attached it upside down onto the sleeve of the gentleMACS dissociator, and run the gentleMACS Program h_skin_01. After a short centrifugation step to collect the sample material at the tube bottom, we applied the cell suspension to a 70 µm pre-separation filter, placed on a 15 mL tube, and washed with ice cold FACS buffer. Then, we centrifuged the cell suspension at 300×g for 10 minutes at 4°C and aspirated the supernatant completely. Finally, after red blood cell lysis (Sigma) for 5min at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.
treatment protocol (2): Blood mononuclear cell separation was performed by density centrifugation media (Ficol-paque, GE Life Sciences) in a 1:1 ratio with blood cells. Centrifugation (460g, 25min) was performed at 10°C, and the mononuclear cells were carefully aspirated and washed with ice cold FACS buffer. After red blood cell lysis (Sigma) for 5 minutes at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.

tag: tissue

value: Blood

tag: selection marker

tag: patient id


title: Primed leaf, Botrytis inoculated, t= 12 h; replicate 3

type: RNA

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

hyb_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Biotin Labelled cRNA using Affymetrix GeneChip Hybridization, Wash and Stain Kit, according to guidelines set out by Affymetrix, Santa Clara, CA

scan_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Scanned according to guidelines set out by Affymetrix, Santa Clara, CA.

data_processing: Normalisation performed using RMA algorithm in the R Bioconductor Suite

label: biotin

molecule: total RNA

organism: Solanum lycopersicum

label_protocol: Labelling, hybridisation and scanning were outsourced to a commercial provider (Nottingham Arabidopsis Stock Centre Affymetrix Service - http://arabidopsis.info/affy). Labelled using protocol described in Affymetrix manual 3' IVT Express Kit User Manual

growth_protocol: Plants were grown in a peat-based compost mixture (Levingtons M3) and cultivated in a heated, passively ventilated glasshouse (min 18 °C+/- 2  max 25 °C+/- 3) with supplementary lighting (Osram Greenpower 600 W high pressure sodium lamps) to a minimum 250±25 μmol m-2s-1 PAR at the canopy. A minimum 16-hour photoperiod was maintained.

extract_protocol: RNA was extracted essentially as described by Verwoerd et. al. (Verwoerd TC, Dekker BMM, Hoekema A (1989) Nucleic Acids Research 17: 2362), scaled up accordingly and then purified using Qiagen RNeasy spin columns (Qiagen.com).

treatment_protocol: Seven-day-old seedlings were root-drenched with a volume of 5 mM BABA equivalent to one tenth of the volume of the compost growing medium to achieve a final concentration of 0.5 mM BABA around the root system. One week later, seedlings were gently removed from the compost, their root systems rinsed in water and then re-potted to new compost. Control plants were similarly treated but given a water root drench rather than BABA. Inoculations of tomato leaves with Botrytis cinerea were performed as previously described (Worrall et al., (2012) New Phytol 193: 770-778. doi: 10.1111/j.1469-8137.2011.03987.x).

value: leaf

tag: cultivar

value: Money Maker

tag: treatment

value: Botrytis inoculated, t= 12 h


title: AB8459

source_name: Forearm skin

value: Skin


title: AB8458


title: Volunteer G30F4 Sample 33DB

value: Nurse

tag: vaccine

value: Pfizer


title: Volunteer A3GEA Sample 3343


title: Volunteer GBG0D Sample 33DD


title: AB8456


title: Volunteer AEBD0 Sample 33CG


title: AB8455


title: Primed leaf, Botrytis inoculated, t= 12 h; replicate 2


title: Volunteer EBFBD Sample 3DE4

value: EBFBD


title: Volunteer ADECF Sample 3G44

value: ADECF


title: Control leaf, mock inoculated, t= 0 h; replicate 1

source_name: Control leaf, mock inoculated, t= 0 h

value: mock inoculated, t= 0 h


title: Primed leaf, Botrytis inoculated, t= 12 h; replicate 1


title: AB8453


title: Primed leaf, mock inoculated, t= 12 h; replicate 2

source_name: Primed leaf, mock inoculated, t= 12 h

value: mock inoculated, t= 12 h


title: Volunteer G30CB Sample 33DF

value: Other


title: Volunteer BA3E4 Sample 3DGG


title: AB8454


title: AB8452


title: Primed leaf, mock inoculated, t= 12 h; replicate 1


title: Volunteer GBC0G Sample 3G3E


title: Volunteer ABBFF Sample 3G3G

value: ABBFF


title: Primed leaf, mock inoculated, t= 12 h; replicate 3


title: Volunteer B30CE Sample 33BE

value: Male

value: White


title: Volunteer A3D3G Sample 3400


title: Volunteer EBD0B Sample 3G43

value: Female

value: Asian

value: Pfizer-BioNTech


title: Volunteer A3C3A Sample 3GD0

value: Clinical staff


title: Primed leaf, Botrytis inoculated, t= 9 h; replicate 3

value: leaf

value: Money Maker

value: Botrytis inoculated, t= 9 h


title: AB8450

value: Skin


title: Volunteer GA3CF Sample 33F0

value: Moderna


title: Primed leaf, mock inoculated, t= 9 h; replicate 2

source_name: Primed leaf, mock inoculated, t= 9 h

value: mock inoculated, t= 9 h


title: Primed leaf, Botrytis inoculated, t= 9 h; replicate 1


title: Volunteer A44GA Sample 33B0

value: Administrative


title: Volunteer ABEFA Sample 33GD

value: ABEFA


title: Volunteer G3C4B Sample 3G4F

value: Nurse

value: Pfizer


title: Primed leaf, Botrytis inoculated, t= 9 h; replicate 2


title: Primed leaf, mock inoculated, t= 9 h; replicate 1


title: Volunteer GC4A4 Sample 33GA


title: AB8449


title: Volunteer AFG33 Sample 33G0


title: Volunteer FCEDA Sample 334B

value: FCEDA


title: Volunteer BBAAB Sample 334C

value: BBAAB


title: AB8451


title: Volunteer ACA0E Sample 334D


title: AB8448


title: Volunteer ACEFG Sample 333B

value: ACEFG

value: Latino


title: AB8447


title: AB8334

value: Blood


title: Volunteer AB4B3 Sample 333F

value: Female

value: Asian


title: AB8446


title: Primed leaf, mock inoculated, t= 9 h; replicate 3

value: leaf


title: Volunteer GCDEE Sample 333G

value: GCDEE


title: Primed leaf, Botrytis inoculated, t= 6 h; replicate 3

value: Money Maker

value: Botrytis inoculated, t= 6 h


title: AB8330

value: Skin


title: Volunteer AF0E0 Sample 3334

value: Student

value: moderna


title: AB8329


title: Volunteer EBC0C Sample 333D

value: Moderna


title: Volunteer GEF0A Sample 333C


title: Primed leaf, mock inoculated, t= 6 h; replicate 2

source_name: Primed leaf, mock inoculated, t= 6 h

value: mock inoculated, t= 6 h


title: Volunteer AEC40 Sample 334E

value: White

value: Other


title: Primed leaf, mock inoculated, t= 6 h; replicate 3


title: Volunteer FGAAE Sample 33D3

value: FGAAE

value: Pfizer


title: Primed leaf, Botrytis inoculated, t= 6 h; replicate 1


title: Primed leaf, Botrytis inoculated, t= 6 h; replicate 2


title: Volunteer FAAB3 Sample 333A


title: AB8328


title: Volunteer AG3BC Sample 33C4


title: Volunteer B3CGC Sample 33C3

value: Physician


title: AB8327

value: Blood


title: Volunteer AFA3G Sample 33CC

value: Female


title: Volunteer DAE3 Sample 33C0

value: Asian

value: Nurse


title: AB8326


title: AB8325


title: Volunteer EEAE3 Sample 3304


title: Primed leaf, Botrytis inoculated, t= 0 h; replicate 3

value: leaf

value: Botrytis inoculated, t= 0 h


title: Primed leaf, mock inoculated, t= 6 h; replicate 1

value: Money Maker


title: Primed leaf, Botrytis inoculated, t= 0 h; replicate 2


title: Volunteer F4BA0 Sample 330C

value: Male


title: AB8324

value: Skin


title: Primed leaf, mock inoculated, t= 0 h; replicate 3

source_name: Primed leaf, mock inoculated, t= 0 h

value: mock inoculated, t= 0 h


title: Volunteer AB44D Sample 3DBE

value: Moderna


title: Primed leaf, Botrytis inoculated, t= 0 h; replicate 1


title: Volunteer B40CF Sample 3DAA

value: Administrative


title: Volunteer AB03E Sample 3DBD


title: Volunteer GGBDA Sample 3300

value: GGBDA


title: Primed leaf, mock inoculated, t= 0 h; replicate 2


title: AB8321


title: Volunteer EAEFG Sample 3DBG

value: EAEFG


title: Volunteer A30G3 Sample 3DB0

value: Latino

value: Other


title: Volunteer EFGEB Sample 3DA3

value: EFGEB

value: Pfizer


title: Volunteer BBCDE Sample 330F

value: BBCDE


title: Volunteer A4003 Sample 3DBC

value: White


title: AB8322


title: Volunteer BG3EE Sample 3DFE


title: Volunteer A33FE Sample 3DFG


title: AB8318

value: Blood


title: Volunteer ED043 Sample 330G

value: Female

value: Asian


title: Volunteer AEG34 Sample 3DEE


title: AB8323


title: AB8319


title: Primed leaf, mock inoculated, t= 0 h; replicate 1

value: leaf

value: Money Maker


title: AB8320

value: Skin


title: H0296_BXD87_CD_F

type: genomic

city: Memphis

first: Khyobeni

last: Mozhui

state: TN

address: 66 N. Pauline Street, #631

department: Preventive Medicine

institute: University of Tennessee Health Science Center

hyb_protocol: Bisulphite converted DNA hybridised to the Illumina HorvathMammalMethylChip40 Beadchip using standard Illumina protocol

scan_protocol: Illumina scaner

data_processing: SeSame normalized beta-values

label: cy3, cy5

molecule: genomic DNA

organism: Mus musculus

source_name: Liver

label_protocol: Standard protocol for Illumina Infinium DNA methylation arrays

growth_protocol: Aging under standard laboratory diet of high fat diet

extract_protocol: DNA was extracted using the DNeasy Blood & Tissue Kit from Qiagen. Nucleic acid purity was inspected with a NanoDrop spectrophotometer, and quantified using a Qubit fluorometer dsDNA BR Assay.

treatment_protocol: No treatment; normative aging study

tag: age (days)

tag: strain

tag: Sex

value: F

tag: diet

value: CD

tag: weight (g)


title: H0770_BXD29_CD_F


title: Volunteer BCCB0 Sample 3DEC

tag: volunteer id

tag: age

tag: gender

value: Nurse


title: Volunteer BAFFF Sample 3DF3

value: BAFFF

tag: ethnicity

tag: job/role

tag: first vaccination


title: Volunteer A0DEA Sample 3DGA

value: Administrative

tag: second vaccination

tag: days since vaccine


title: H0820_BXD63_CD_F


title: Volunteer BD0GB Sample 3DGF

value: Not reported

value: Physician


title: H1903_BXD70_CD_F


title: H0178_BXD89_HFD_F

value: HFD


title: AB8315

tag: tissue

tag: selection marker

tag: patient id


title: AB8317


title: Volunteer BD30B Sample 3DF0


title: Volunteer A03EB Sample 3G4D

tag: vaccine

value: Pfizer


title: Volunteer AB4DC Sample 3G3B

value: Moderna


title: H1270_BXD95_CD_F

tag: age (days)


title: AB8316


title: Volunteer ACGBB Sample 3G4B

value: ACGBB


title: Volunteer G3CG3 Sample 3G4C


title: AB8313

value: Blood


title: Volunteer EFECE Sample 3G4E

value: EFECE

value: Male

value: Latino

value: Other


title: Volunteer AD3A3 Sample 3G3F

value: Female

value: White


title: AB8314

value: Skin


title: Volunteer AACGD Sample 3G40

value: AACGD


title: Volunteer GCEBF Sample 3G4G

value: GCEBF


title: Volunteer EDED0 Sample 3G34

value: Asian


title: AB8312


title: Volunteer AAC43 Sample 3G33


title: H0821_BXD63_CD_F

tag: strain

value: F

value: CD


title: H0254_BXD86_CD_F

tag: Sex


title: H1275_BXD95_HFD_F

tag: diet

value: HFD


title: Volunteer ABFEC Sample 3G3D

value: ABFEC

value: Pfizer


title: H1361_BXD102_HFD_F

tag: weight (g)


title: AB8053


title: Volunteer GACBE Sample 3G3C

tag: volunteer id

value: GACBE


title: AB8052


title: Volunteer AECG3 Sample 3G30

tag: age


title: Volunteer ACFBC Sample 3DFC

value: ACFBC


title: Volunteer BA400 Sample 3GDB

tag: gender

value: Physician


title: Volunteer G3CE4 Sample 3GDF

tag: ethnicity

value: Nurse


title: AB8051


title: Volunteer AAC3D Sample 3GDE

value: Male

value: Latino

tag: job/role


title: Volunteer ABC3F Sample 3GDG

value: Female

value: Clinical staff

tag: first vaccination


title: AB8054

value: Blood


title: AB8050

value: Skin


title: Volunteer BAEA4 Sample 3GD4

tag: second vaccination


title: AB8049


title: AB8048


title: Volunteer G30GC Sample 33AE

tag: days since vaccine


title: Volunteer A3EDE Sample 3GCF

value: White

value: Other


title: Volunteer G34BE Sample 3GCG


title: AB8047

tag: tissue


title: Volunteer BABGF Sample 33AF

value: BABGF


title: Volunteer BDFEE Sample 33BC

value: BDFEE


title: H0778_BXD27_CD_F

value: F

value: CD


title: H2519_BXD27_CD_F


title: H0252_BXD86_CD_F


title: AB8046

tag: selection marker


title: Volunteer AE4GD Sample 334F

value: Administrative


title: H1043_BXD29_HFD_F

value: HFD


title: Volunteer AD4F3 Sample 334G

value: Pfizer


title: Volunteer G44E0 Sample 3GD3


title: Volunteer A3FF4 Sample 3344


title: Volunteer AG0FG Sample 3GCA

value: Physician


title: AB8045

tag: patient id


title: Volunteer BABEA Sample 3333

value: BABEA

value: Asian

value: Nurse

tag: vaccine

value: Moderna


title: Volunteer ABDF3 Sample 33CB


title: H0772_BXD29_CD_F

tag: age (days)


title: Volunteer ABCFF Sample 33CE

value: ABCFF


title: H0223_BXD66_HFD_F

tag: strain


title: H0629_BXD98_HFD_F

tag: Sex


title: AB8043


title: H1315_BXD62_HFD_F

tag: diet


title: H0628_BXD98_HFD_F

tag: weight (g)


title: H1751_BXD63_HFD_F


title: Volunteer BCBFE Sample 33CF

tag: volunteer id

value: BCBFE


title: H0755_BXD90_CD_F


title: Volunteer BBGA0 Sample 33CD

tag: age


title: AB8044

value: Skin


title: AB8042

value: Blood


title: Volunteer AFEBB Sample 330E

value: AFEBB


title: Volunteer ACC4C Sample 3303

tag: gender

value: Male

value: White


title: Volunteer AEGGD Sample 3DAE

value: AEGGD


title: AB8041


title: H1724_BXD61_CD_F

value: F

value: CD


title: AB8040


title: Volunteer AD4E3 Sample 3DAF

tag: ethnicity

value: Food/EVS

value: Pfizer-BioNTech


title: H1206_BXD62_CD_F


title: H1271_BXD95_CD_F


title: Volunteer BDCDA Sample 3DAG

value: BDCDA

value: Pfizer


title: AB8039


title: Volunteer G3CAC Sample 3DAD

value: Female

value: Asian

tag: job/role


title: H0701_BXD62_HFD_F

value: HFD


title: Volunteer BE43A Sample 3DEB

tag: first vaccination


title: Volunteer FAA44 Sample 3DAC

value: Nurse

tag: second vaccination


title: Volunteer EBGDF Sample 3DFF

value: EBGDF

tag: days since vaccine


title: AB8038

tag: tissue

value: Skin


title: Volunteer AFGBG Sample 3DE3

value: AFGBG

value: Clinical staff


title: H0734_BXD29_HFD_F


title: AB8036

tag: selection marker


title: AB8037

tag: patient id


title: H0704_BXD51_CD_F


title: Volunteer A4ABD Sample 3E00

value: Male

value: Physician

tag: vaccine


title: Volunteer FABG3 Sample 3FAB


title: AB8035


title: Volunteer AFCGF Sample 3FEA

value: AFCGF


title: Volunteer GDD3B Sample 3DBB

value: Moderna


title: Volunteer ACCGE Sample 340F

value: ACCGE


title: AB8034


title: Volunteer G3C3B Sample 3FA4

value: Latino

value: Administrative


title: Volunteer ABEFA Sample 3FAF

value: ABEFA

value: White


title: AB8032


title: Volunteer EBD3F Sample 3DEF

value: Pfizer


title: Volunteer BF330 Sample 3DGE


title: H0532_DBA/2J_HFD_F

tag: age (days)

value: F


title: H0451_BXD70_HFD_F

tag: strain

value: HFD


title: H1098_BXD90_HFD_F

tag: Sex


title: Volunteer G30F4 Sample 3FEG

value: Female

value: Asian

value: Nurse


title: H0818_BXD63_CD_F

tag: diet

value: CD


title: H0854_BXD53_CD_F

tag: weight (g)


title: Volunteer BAEA4 Sample 3FE4

tag: volunteer id

value: Clinical staff


title: Volunteer G3CAC Sample 3FE3

tag: age


title: Volunteer BDFCC Sample 3FE0

value: BDFCC

tag: gender


title: Volunteer ABEAB Sample 3FFA

value: ABEAB


title: AB8030

source_name: Leg skin

value: Skin


title: AB8029


title: AB8033


title: Volunteer A0DEA Sample 3FEF

tag: ethnicity


title: Volunteer ABC3F Sample 33GE

tag: job/role


title: Volunteer EDED0 Sample 3FFF

value: Other

tag: first vaccination


title: AB8028


title: H1522_BXD98_HFD_F


title: Volunteer GBG0D Sample 33GG

tag: second vaccination


title: AB8027


title: Volunteer AD0CE Sample 33GF

tag: days since vaccine


title: Volunteer AEF3F Sample 33G4

value: Food/EVS


title: AB8031

tag: tissue


title: AB8026

tag: selection marker


title: H0179_BXD89_HFD_F


title: H0703_BXD51_CD_F


title: Volunteer BD4FF Sample 3FBE

value: Latino


title: Volunteer EEB00 Sample 3FB4


title: Volunteer A4BEF Sample 3FAD

value: Moderna


title: Volunteer EE404 Sample 3G3A


title: Volunteer B4E44 Sample 3G0F


title: Volunteer BAD3D Sample 3FEB

value: Administrative


title: Volunteer G3CBG Sample 3G0E

value: White


title: AB8024

tag: patient id


title: H0857_BXD95_HFD_F


title: AB8023


title: Volunteer FABG3 Sample 3G0G

tag: vaccine

value: Pfizer-BioNTech


title: H0847_BXD53_CD_F

tag: age (days)

value: F


title: Volunteer AD0CE Sample 3G03

value: Pfizer


title: Volunteer AFFGB Sample 3G0D

value: AFFGB

value: Female


title: AB8025


title: AB8022


title: H1093_BXD90_HFD_F

tag: strain

value: HFD


title: H0851_BXD53_CD_F

tag: Sex

value: CD


title: H0221_BXD66_HFD_F

tag: diet


title: H0742_BXD29_CD_F

tag: weight (g)


title: Volunteer AEC40 Sample 33GB

tag: volunteer id


title: AB8021


title: Volunteer FFAFE Sample 3FFD

value: FFAFE

tag: age

value: Clinical staff


title: Volunteer G30F4 Sample 3FGB

tag: gender

value: Asian

value: Nurse


title: Volunteer ADDEF Sample 3FGA

value: ADDEF

tag: ethnicity


title: Volunteer ADECG Sample 3FGD

value: ADECG

tag: job/role


title: Volunteer ABDG3 Sample 3FG3

tag: first vaccination


title: AB8019

value: Skin


title: AB8020


title: Volunteer ADECF Sample 3FGC

value: ADECF

tag: second vaccination


title: AB8018


title: Volunteer EEF0A Sample 3G04

tag: days since vaccine


title: Volunteer GF0DE Sample 330A

value: Male

value: Latino

value: Other


title: Volunteer EGBDD Sample 3DG4

value: EGBDD

value: White


title: AB8017

tag: tissue


title: H0298_BXD87_CD_F

value: F


title: H0669_BXD29_HFD_F


title: Volunteer AEC40 Sample 3FF3

value: Female

value: Moderna


title: Volunteer BABD4 Sample 3D43

value: Physician

value: Pfizer


title: H1181_BXD51_HFD_F

value: HFD


title: Volunteer ABB0F Sample 3FA3


title: AB8016

tag: selection marker


title: AB8015

tag: patient id


title: H2092_BXD63_CD_F

value: CD


title: Volunteer EFECE Sample 3FF0

value: EFECE

tag: vaccine


title: H0737_BXD90_HFD_F

tag: age (days)


title: Volunteer G3CAC Sample 3FGE

value: Asian

value: Nurse


title: AB8014

value: Skin


title: Volunteer BAEA4 Sample 3FGF

value: Clinical staff


title: Volunteer ABC3F Sample 3DGC


title: AB8013


title: H0465_BXD101_HFD_F

tag: strain


title: Volunteer EDED0 Sample 3DG0


title: H1827_BXD45_CD_F

tag: Sex


title: H0547_BXD87_HFD_F

tag: diet


title: H1841_BXD61_CD_F

tag: weight (g)


title: Volunteer E4FA3 Sample 3D4B

tag: volunteer id


title: H1812_DBA/2J_CD_F


title: H1182_BXD51_HFD_F


title: AB8012


title: H0819_BXD63_CD_F


title: Volunteer BDFCC Sample 3D4D

value: BDFCC

tag: age


title: Volunteer ABEFA Sample 3FFC

value: ABEFA

tag: gender


title: Volunteer G3C3B Sample 3FG4

tag: ethnicity

value: Latino

value: Administrative


title: H1722_BXD61_HFD_F


title: AB8009


title: AB8010


title: AB8011


title: Volunteer A04B3 Sample DF4D

value: Male

tag: job/role


title: Volunteer AEDBB Sample 3D4F

value: AEDBB

tag: first vaccination


title: Volunteer F00D0 Sample DDGG

value: Female

tag: second vaccination


title: Volunteer GBG0D Sample 3D44

tag: days since vaccine


title: Volunteer AECAA Sample DD4G

value: AECAA

value: White


title: Volunteer AB4AC Sample 3G0C

value: Pfizer


title: H0548_BXD87_HFD_F

value: F

value: HFD


title: Volunteer ADEG3 Sample DC34

value: Other


title: H0856_BXD95_HFD_F


title: Volunteer A0DEA Sample 3D4E


title: H0555_BXD89_CD_F

value: CD


title: AB8007

tag: tissue


title: Volunteer AEBA0 Sample D0GF


title: H0514_C57BL/6J_HFD_F


title: Volunteer AG4EB Sample CAGG

value: Nurse


title: Volunteer AEGCD Sample CAGD

value: AEGCD


title: AB8008

value: Skin

tag: selection marker


title: Volunteer AGFGD Sample CA4B

value: AGFGD


title: H0087_BXD32_CD_F


title: Volunteer AGBBC Sample CAC3

value: AGBBC


title: AB7770

value: Blood

tag: patient id


title: Volunteer G34AC Sample CA3A

value: Asian


title: AB7769


title: Volunteer AE3G3 Sample CA0A

tag: vaccine


title: Volunteer B0CB3 Sample CBAE

value: Student


title: H1376_C57BL/6J_HFD_M

tag: age (days)

value: M


title: AB7768


title: Volunteer AE3GB Sample CBA3

value: Female


title: AB7766


title: H0466_BXD101_HFD_F

tag: strain


title: Volunteer E0EEC Sample CE40

value: Latino

value: Administrative


title: H0848_BXD53_CD_F

tag: Sex


title: AB7765


title: Volunteer A4EE0 Sample 3G0B

value: Moderna


title: Volunteer AB4B3 Sample 3DDE


title: H0554_BXD89_CD_F

value: F

tag: diet


title: AB7764


title: Volunteer FB4BE Sample 3DD3


title: Volunteer G3CAC Sample 3D0A

value: Pfizer


title: AB7767


title: AB7763


title: Volunteer AAC3D Sample 3D0E

value: Male


title: Volunteer AFAA4 Sample 3D0F


title: Volunteer AD0CE Sample 3CFG

value: Other


title: H0756_BXD90_CD_F

value: CD

tag: weight (g)


title: AB7762


title: Volunteer A33FE Sample 3CE3

tag: volunteer id


title: Volunteer BA3DC Sample 3FGG

tag: age

value: White

value: Clinical staff


title: AB7761

value: Skin


title: H0169_BXD60_CD_F


title: H0615_BXD86_CD_F


title: Volunteer AD3FB Sample 3GCD


title: Volunteer BBE0C Sample 3D34

tag: gender

value: Nurse


title: Volunteer EC0F3 Sample 3D4C

tag: ethnicity


title: AB7760


title: Volunteer F0CCG Sample 3D33


title: Volunteer A0BAC Sample 3D3C


title: AB7759


title: H1799_BXD100_CD_F


title: H1564_BXD95_CD_F


title: Volunteer BBGA4 Sample 3DD4

tag: job/role


title: H1486_BXD70_CD_F


title: H2085_BXD100_HFD_F

value: HFD


title: Volunteer A40FD Sample 3DCE

tag: first vaccination


title: AB7758


title: Volunteer F0CC3 Sample 3DCG

value: Asian

tag: second vaccination


title: H2086_BXD100_CD_F


title: AB7757


title: Volunteer BAFC4 Sample 3CBC

tag: days since vaccine


title: Volunteer BGFGC Sample 3CEB

value: BGFGC


title: Volunteer ACBBC Sample 3CBF

value: ACBBC


title: AB7756

tag: tissue

value: Blood


title: Volunteer EBC0C Sample 3CFB


title: Volunteer ACCEF Sample 3CEF

value: ACCEF

value: Female


title: AB7754

tag: selection marker


title: Volunteer GEF0A Sample 3CGF


title: Volunteer AG4F0 Sample 3CFF

value: Moderna


title: AB7753

tag: patient id


title: AB7755


title: H1885_DBA/2J_CD_F

value: F


title: Volunteer GA3B4 Sample 3CD4

tag: vaccine


title: Volunteer FBAEA Sample 3CCA

value: FBAEA

value: Latino

value: Administrative

value: Pfizer


title: H1597_BXD65b_HFD_F

tag: age (days)


title: Volunteer B0GBC Sample 3CDD


title: AB7752


title: H1491_BXD70_CD_F

tag: strain

value: CD


title: H1886_DBA/2J_CD_F

tag: Sex


title: Volunteer ABF4E Sample 3CCE


title: Volunteer A0BBA Sample 3CC4


title: Volunteer ABC3F Sample 3CC0

value: White

value: Clinical staff


title: H1487_BXD70_CD_F

tag: diet


title: H1936_BXD70_CD_F

tag: weight (g)


title: AB7751

value: Skin


title: Volunteer BABD4 Sample 3C0C

tag: volunteer id

value: Male

value: Physician


title: Volunteer ADD4D Sample 3CGG

tag: age

value: Asian


title: Volunteer ABDG3 Sample 30A0


title: AB7750


title: Volunteer ABA3A Sample 30BA

tag: gender


title: Volunteer EG44B Sample 30B3

tag: ethnicity

value: Other


title: H2124_BXD66_HFD_F

value: HFD


title: AB7748


title: H1855_BXD70_CD_F


title: Volunteer EBD0B Sample 30BD

tag: job/role

value: Nurse

value: Pfizer-BioNTech


title: H1350_C57BL/6J_CD_M

value: M


title: Volunteer AB44D Sample 30EG

tag: first vaccination

value: Moderna


title: Volunteer AF3DG Sample 30ED

tag: second vaccination


title: Volunteer ADCDC Sample 30F4

value: ADCDC

tag: days since vaccine


title: H1598_BXD65b_HFD_F

value: F


title: Volunteer A3C3A Sample 304C

value: Female


title: AB7745

tag: tissue


title: AB7749

tag: selection marker


title: H1266_C57BL/6J_HFD_M


title: AB7746

tag: patient id


title: Volunteer AE0FA Sample 3C00

value: Latino

tag: vaccine

value: Pfizer


title: Volunteer ABAFA Sample 3044

value: ABAFA


title: Volunteer ABFF3 Sample DAGB


title: H2014_C57BL/6J_HFD_M

tag: age (days)


title: H2015_C57BL/6J_HFD_M

tag: strain


title: AB7744


title: Volunteer G40GA Sample 30EB


title: H1847_BXD62_CD_F

tag: Sex

value: CD


title: AB7747

value: Skin


title: Volunteer ADEDG Sample 3DB4

value: ADEDG


title: AB7743


title: Volunteer EEEEC Sample 3D40

value: EEEEC


title: H2125_BXD66_HFD_F

tag: diet


title: Volunteer AE04A Sample 3DDD


title: H2035_BXD32_CD_F

tag: weight (g)


title: Volunteer BD4FF Sample 3D3E

tag: volunteer id

value: Food/EVS


title: Volunteer AE4GD Sample 3DCD

tag: age

value: White

value: Administrative


title: Volunteer EBF3F Sample 3CED

tag: gender

value: Male

value: Other


title: H1848_BXD62_CD_F


title: Volunteer AA0FD Sample 3DCC

tag: ethnicity

value: Nurse


title: Volunteer ABEFA Sample 3CGE

value: ABEFA

tag: job/role

value: Clinical staff

value: Moderna


title: AB7708

value: Blood


title: Volunteer ACF3B Sample 3C30

value: Female

value: Latino

tag: first vaccination


title: AB7741


title: AB7707


title: Volunteer AFG33 Sample 3CFE

tag: second vaccination


title: Volunteer EDED0 Sample 3CD0

value: Asian

value: Pfizer

tag: days since vaccine


title: Volunteer E0F00 Sample 3CDC

value: Pfizer-BioNTech


title: H1422_BXD101_HFD_F

value: F

value: HFD


title: AB7705

tag: tissue

value: Skin


title: Volunteer AG3BC Sample 3CCF


title: Volunteer AG3B0 Sample 3CCG


title: AB7706

tag: selection marker


title: Volunteer A4CBB Sample 3C0A


title: AB7742

tag: patient id


title: Volunteer AFDBD Sample 3C0B

value: AFDBD

value: White

tag: vaccine


title: AB7704


title: H1434_BXD62_HFD_F

tag: age (days)


title: H1426_BXD101_CD_F

tag: strain

value: CD


title: Volunteer A3BCD Sample 3C0E

value: Male


title: AB7703


title: Volunteer EC33D Sample 3C0F

value: Physician


title: Volunteer BAEBC Sample 30AB

value: BAEBC


title: H1800_BXD29_CD_F

tag: Sex


title: H0777_BXD27_CD_F

tag: diet


title: Volunteer A44GG Sample 30AE

value: Nurse


title: H0474_BXD63_HFD_F

tag: weight (g)


title: Volunteer GGBDG Sample 30AF

tag: volunteer id

value: GGBDG


title: AB7702


title: AB7701


title: H0186_BXD70_HFD_F


title: Volunteer GGBDA Sample 30AG

value: GGBDA

tag: age


title: Volunteer A3EDE Sample 30B4

tag: gender

value: Female

value: Other


title: Volunteer EAEFG Sample 30A3

value: EAEFG


title: Volunteer FEF0F Sample 30AD

value: Pfizer


title: AB7700


title: AB7699


title: Volunteer AF0E0 Sample 30A4

tag: ethnicity

value: Asian

value: Student

value: moderna


title: AB7698

value: Skin


title: Volunteer AAC43 Sample 30BB


title: H1716_BXD63_HFD_F

value: F

value: HFD


title: H1488_BXD40_HFD_F


title: Volunteer BB03G Sample 30BC


title: H1840_BXD61_CD_F

value: CD


title: H1826_BXD45_CD_F


title: H1358_BXD102_HFD_F


title: Volunteer ACC4C Sample 30EE

value: Male

value: White

tag: job/role


title: Volunteer F4BA0 Sample 30E0

tag: first vaccination


title: Volunteer A30E4 Sample 30EF

tag: second vaccination


title: Volunteer AD3A3 Sample 30E4

tag: days since vaccine


title: Volunteer BEGCE Sample 30FG

value: BEGCE


title: H1688_BXD40_HFD_F


title: AB7696

tag: tissue


title: AB7695

tag: selection marker


title: Volunteer BACFC Sample 30F3

value: BACFC

value: Physician


title: Volunteer 3GDD Sample 30FD

value: Nurse


title: AB7697

tag: patient id


title: Volunteer A3GEA Sample 30FC

tag: vaccine


title: Volunteer AEG34 Sample 30GA


title: Volunteer BB4C4 Sample 30GE

value: Female


title: Volunteer B03GC Sample 30GF


title: AB7693


title: Volunteer ABE4G Sample 304B

value: Moderna


title: H1321_BXD89_HFD_F

tag: age (days)


title: AB7629


title: AB7628


title: Volunteer BGG4E Sample 303A

value: Other


title: AB7694


title: Volunteer BDFCC Sample 303E

value: BDFCC

value: Clinical staff

value: Pfizer


title: AB7627


title: Volunteer BABEF Sample 3034

value: BABEF


title: H1362_BXD102_HFD_F

tag: strain


title: H1518_BXD51_CD_F

tag: Sex


title: H1844_BXD62_CD_F

tag: diet


title: Volunteer ABBG3 Sample 30CB

value: Latino

value: Administrative


title: Volunteer EFCA4 Sample 30D4


title: H1320_BXD89_HFD_F

value: F

value: HFD

tag: weight (g)


title: H1565_BXD95_CD_F

value: CD


title: Volunteer A4AFF Sample 30C4

tag: volunteer id

value: Asian


title: AB7623

value: Skin


title: AB7624


title: Volunteer B0CBD Sample 3040

tag: age


title: Volunteer AB03E Sample 3004


title: Volunteer A04AF Sample 300F

tag: gender

value: White


title: AB7562


title: H2251_BXD98_CD_F


title: Volunteer AFEFE Sample 3003

value: AFEFE

tag: ethnicity


title: Volunteer AB4DC Sample 3033


title: H1420_BXD101_HFD_F


title: Volunteer A30G3 Sample DAAA

tag: job/role


title: H2452_BXD86_CD_F


title: H1905_BXD70_HFD_F


title: AB7625


title: Volunteer ABA4F Sample DABB

value: Male

value: Nurse

tag: first vaccination


title: Volunteer BBCDE Sample DAA4

value: BBCDE

tag: second vaccination


title: Volunteer EB4GA Sample DABE

value: Female

tag: days since vaccine


title: Volunteer AEBD0 Sample 30C0


title: AB7559

tag: tissue


title: H1689_BXD40_HFD_F


title: H2146_BXD61_CD_F


title: H1802_BXD32_CD_F


title: Volunteer G3CFC Sample DAB4


title: AB7558

tag: selection marker


title: Volunteer FEGED Sample DAEG

value: FEGED


title: AB7498

tag: patient id


title: AB7561


title: AB7560


title: Volunteer GBG0D Sample DAFF

tag: vaccine


title: H2078_BXD89_CD_F

tag: age (days)


title: Volunteer EA4BE Sample DAE0


title: Volunteer EEGDB Sample DA4F

value: EEGDB


title: Volunteer ABB40 Sample DAGG

value: Pfizer


title: Volunteer BEC3E Sample DA34


title: AB7496


title: Volunteer BG3EE Sample DAAG


title: AB7497


title: Volunteer ABADG Sample DADB

value: ABADG


title: Volunteer B000A Sample DAGE


title: H1322_BXD39_CD_F

tag: strain


title: Volunteer G3C4B Sample DACB


title: Volunteer AEDCA Sample DABG

value: AEDCA


title: H1742_BXD95_CD_F

tag: Sex


title: Volunteer A0CEF Sample DAC0


title: Volunteer ABADB Sample DAC4

value: ABADB


title: AB7494


title: Volunteer ABCG3 Sample DA03


title: Volunteer FFGCG Sample DA0D

value: FFGCG


title: H1728_BXD70_HFD_F

value: F

tag: diet

value: HFD


title: H1801_BXD32_CD_F

value: CD

tag: weight (g)


title: Volunteer A3D3G Sample 3DCB

tag: volunteer id


title: AB7493

value: Skin


title: Volunteer EAEA4 Sample DBEE

tag: age


title: Volunteer B30CE Sample 3D0B

tag: gender

value: White


title: Volunteer ACBBA Sample 3DC3

value: ACBBA

tag: ethnicity

value: Asian

value: Clinical staff


title: Volunteer BG443 Sample 3DDC

tag: job/role

value: Student


title: AB7491


title: AB7492


title: Volunteer BD0D0 Sample 3C33

tag: first vaccination


title: AB7495


title: AB7469


title: Volunteer A0F4G Sample 3C3D

tag: second vaccination


title: H2063_BXD61_HFD_F


title: H2145_BXD61_CD_F


title: Volunteer A4E03 Sample 3CDE

tag: days since vaccine


title: H1481_BXD40_HFD_F


title: Volunteer G3C3F Sample 3C0G

value: Female

value: Other

value: Nurse


title: Volunteer A4E0D Sample 3CDG

value: Pfizer


title: Volunteer AADBA Sample 3C03

value: AADBA


title: AB7467

tag: tissue


title: H2149_BXD61_HFD_F


title: AB7466

tag: selection marker


title: Volunteer AEA4D Sample 30AA


title: Volunteer BEE0G Sample 30BE


title: H2077_BXD89_CD_F


title: Volunteer G4C4D Sample 30FB


title: Volunteer FAAB3 Sample 30FE


title: H2148_BXD61_HFD_F


title: Volunteer FCEDA Sample 30BF

value: FCEDA


title: AB7465

tag: patient id


title: AB7468


title: Volunteer BAEA4 Sample 30F0

value: Male

tag: vaccine


title: Volunteer GCEBF Sample 30GG

value: GCEBF


title: Volunteer ABDF3 Sample 30FF


title: H2076_BXD89_HFD_F

tag: age (days)

value: F


title: AB7463


title: H2349_BXD29_HFD_F

tag: strain

value: HFD


title: AB7462


title: Volunteer BAGE4 Sample 30G4


title: Volunteer B04GC Sample 30G3

value: Pfizer-BioNTech


title: H1407_BXD65b_HFD_F

tag: Sex


title: H1843_BXD61_HFD_F

tag: diet


title: AB7461

value: Blood


title: AB7464

value: Skin


title: Volunteer ABG3A Sample 303G


title: Volunteer AF0G3 Sample 303C

value: Latino


title: AB7459


title: AB7460


title: Volunteer BAD0E Sample 30DB


title: H1713_BXD65b_HFD_F

tag: weight (g)


title: AB7458


title: H2252_BXD98_CD_F

value: CD


title: Volunteer BD30B Sample 30DE

tag: volunteer id

value: Asian


title: H1818_DBA/2J_CD_F


title: Volunteer AA3FA Sample 30DF

tag: age

value: White


title: AB7457


title: Volunteer EAFG0 Sample 30D3

tag: gender

value: Female


title: H1560_BXD66_HFD_F


title: Volunteer G3C3B Sample 30GD

tag: ethnicity

value: Administrative

value: Moderna


title: Volunteer ABF3A Sample 30D0

tag: job/role

value: Nurse


title: Volunteer G3033 Sample 30G0

tag: first vaccination

value: Pfizer


title: Volunteer AD4E3 Sample 30CA

value: Food/EVS

tag: second vaccination


title: Volunteer BDFCG Sample 30CE

value: BDFCG

tag: days since vaccine


title: H1741_BXD63_CD_F


title: AB7456

tag: tissue


title: AB7455

tag: selection marker


title: Volunteer BAD0F Sample 30CF


title: H2494_BXD32_CD_F


title: H1436_BXD62_CD_F


title: Volunteer B3CGC Sample 30C3

value: Physician


title: AB7454

tag: patient id


title: H1143_DBA/2J_HFD_F

value: F


title: H2091_BXD63_HFD_F

value: HFD


title: Volunteer ADACF Sample 30CD

value: ADACF


title: Volunteer AECG3 Sample 300E

value: Male

value: Other

tag: vaccine


title: H1424_BXD101_CD_F

tag: age (days)


title: AB7453

value: Skin


title: Volunteer G34BE Sample 30CC


title: H1594_BXD40_HFD_F

tag: strain


title: Volunteer B0BFF Sample 300D


title: Volunteer FBEDG Sample DAAE

value: FBEDG

value: Latino


title: AB7452


title: AB7451


title: Volunteer G44E0 Sample DAA3


title: Volunteer BDG4C Sample DAAF


title: Volunteer BBG3E Sample 300G


title: Volunteer BBGDE Sample DAA0

value: BBGDE


title: AB7450


title: AB7448


title: Volunteer E0FCC Sample DABF

value: Female


title: AB7449


title: Volunteer E43G0 Sample 3000


title: Volunteer A0FDE Sample DAEB


title: Volunteer AD44B Sample DAB0


title: Volunteer AA3G4 Sample DAEE


title: AB7447


title: Volunteer G3CE4 Sample 300C

value: White


title: H1524_BXD98_CD_F

tag: Sex

value: CD


title: Volunteer ACA0E Sample DAEF


title: H1147_DBA/2J_CD_F

tag: diet


title: H1213_BXD100_CD_F

tag: weight (g)


title: H1095_BXD90_HFD_F


title: Volunteer BE43A Sample DAFB

tag: volunteer id


title: AB7446


title: H1297_BXD100_CD_F


title: AB7361

value: Blood


title: Volunteer GGGBB Sample DAFE

value: GGGBB

tag: age

value: Pfizer


title: H1916_BXD102_HFD_F


title: H0480_BXD100_CD_F


title: Volunteer A4D34 Sample DAEC

tag: gender

value: Nurse


title: Volunteer BF330 Sample DAFG

tag: ethnicity

value: Administrative


title: Volunteer EBD3F Sample DAF4


title: AB7360


title: H1193_BXD100_HFD_F

value: F


title: Volunteer ABGDD Sample DAF0

value: ABGDD


title: Volunteer B0C0D Sample DAGA

tag: job/role


title: H0222_BXD66_CD_F


title: Volunteer F0BAC Sample DA40

tag: first vaccination


title: AB7359


title: Volunteer A03FG Sample DAFD

tag: second vaccination


title: H0234_BXD60_CD_F


title: Volunteer AFA3G Sample DA4D

value: Student

tag: days since vaccine


title: AB7357

tag: tissue


title: H1187_BXD100_HFD_F

value: HFD


title: Volunteer EFC0G Sample DA33

value: Asian


title: Volunteer A4CDE Sample DA4G


title: H0235_BXD60_CD_F


title: H0224_BXD66_CD_F


title: Volunteer E434B Sample DA3E


title: Volunteer BBCBF Sample DA3D

value: BBCBF


title: Volunteer FAAGA Sample DADE

value: FAAGA


title: AB7354

tag: selection marker


title: AB7358

tag: patient id


title: Volunteer GF4A0 Sample DA4E

tag: vaccine


title: Volunteer AEGGD Sample DADD

value: AEGGD


title: AB7353


title: Volunteer 3FAG Sample DAD3


title: AB7356


title: H2127_BXD66_CD_F

tag: age (days)


title: H1558_BXD66_CD_F

tag: strain


title: H2128_BXD66_CD_F

tag: Sex


title: H1425_BXD101_CD_F

tag: diet


title: AB7355


title: Volunteer GBGEF Sample DACE

value: GBGEF


title: AB7352


title: Volunteer AEBGC Sample DA3C

value: AEBGC

value: Male


title: Volunteer G4CA4 Sample DACF

value: Female

value: Other

value: Pfizer-BioNTech


title: AB7347

value: Skin


title: AB7348


title: Volunteer BBCAG Sample DA0B

value: BBCAG

value: Clinical staff

value: Moderna


title: Volunteer BAGAC Sample DA0E

value: BAGAC

value: Pfizer


title: Volunteer ABE30 Sample DA04


title: AB7346


title: H1037_BXD29_HFD_F

value: F

value: HFD

tag: weight (g)


title: Volunteer A0DEA Sample DA00

tag: volunteer id

value: White

value: Administrative


title: Volunteer G3CAC Sample DBAB

tag: age

value: Asian

value: Nurse


title: AB7345


title: Volunteer B4CGD Sample DBAE


title: H1190_BXD100_CD_F

value: CD


title: Volunteer G30CB Sample DACG

tag: gender


title: Volunteer A4A40 Sample DADC

tag: ethnicity


title: H1683_BXD79_HFD_F


title: H1781_BXD79_HFD_F


title: Volunteer BD0GB Sample DBAF

value: Not reported

tag: job/role

value: Physician


title: Volunteer BGG4B Sample DBA4

tag: first vaccination


title: H1684_BXD79_HFD_F


title: AB7344


title: Volunteer ECCDF Sample DBAD

value: ECCDF

value: Female

value: Latino

value: Student

tag: second vaccination


title: Volunteer BBGEA Sample DBA0

value: BBGEA

tag: days since vaccine


title: AB7343

tag: tissue

value: Skin


title: AB7342

tag: selection marker


title: Volunteer BBEAA Sample DBE4

value: BBEAA


title: Volunteer A300B Sample DBB0

value: Pfizer


title: Volunteer FCBBC Sample DBBF

value: FCBBC


title: Volunteer GD4EC Sample DBG3


title: H1593_BXD40_HFD_F

value: F

value: HFD


title: Volunteer BADGG Sample DBEB

value: BADGG


title: AB7339

tag: patient id


title: AB7341


title: Volunteer B0CDA Sample DBFB

tag: vaccine


title: Volunteer A443E Sample 3030


title: Volunteer AB444 Sample 3D3F

value: Moderna


title: Volunteer EE404 Sample 3CCC

value: Asian

value: Nurse


title: H1733_BXD79_HFD_F

tag: age (days)


title: AB7340


title: H1589_C57BL/6J_CD_M

tag: strain

value: M

value: CD


title: AB7283


title: H1406_BXD65b_HFD_F

tag: Sex


title: Volunteer B3EBE Sample DBFE

value: Male

value: White

value: Physician


title: Volunteer AFG33 Sample 304D

value: Female


title: Volunteer FAGAC Sample 30DG

value: FAGAC


title: Volunteer GBGCD Sample DGBD

value: GBGCD


title: Volunteer A0FEE Sample DAFC


title: H0526_C57BL/6J_CD_F

tag: diet


title: Volunteer GDF0F Sample 30AC


title: H0550_BXD87_CD_F

tag: weight (g)


title: AB7282

value: Skin


title: Volunteer AFGE4 Sample DA30

tag: volunteer id

value: Pfizer


title: H1512_BXD70_CD_F


title: H0243_BXD87_HFD_F


title: H0549_BXD87_CD_F


title: Volunteer EEB00 Sample 3CDF

tag: age


title: AB7281


title: AB7279


title: AB7278


title: H0469_BXD101_CD_F


title: AB7280


title: Volunteer FAGA0 Sample DABA


title: AB7276


title: Volunteer AE44E Sample DBAC


title: Volunteer AG40C Sample DADF

tag: gender

value: Clinical staff


title: H1301_C57BL/6J_HFD_F

value: F


title: Volunteer A3CBG Sample DA0F


title: Volunteer A3FF4 Sample DADA


title: Volunteer A0C0D Sample DADG

tag: ethnicity


title: Volunteer BCBFE Sample 300A

value: BCBFE


title: AB7277


title: Volunteer B4E44 Sample DBDA

tag: job/role


title: H0468_BXD101_CD_F


title: Volunteer BBADA Sample DBEC

value: BBADA

tag: first vaccination


title: AB7275


title: Volunteer ABD3G Sample DBED

tag: second vaccination


title: Volunteer BBGA0 Sample DBE3

tag: days since vaccine


title: AB7274

tag: tissue


title: Volunteer BCEA3 Sample 3D04

value: Moderna


title: H0582_BXD79_HFD_F

value: HFD


title: Volunteer AA0FF Sample 3GCC

value: Latino

value: Food/EVS


title: Volunteer BD4FF Sample DAB3


title: Volunteer ABE0E Sample DAGD


title: AB7272

tag: selection marker


title: H0170_BXD60_CD_F

value: CD


title: H0171_BXD60_CD_F


title: H0591_BXD69_CD_F


title: Volunteer ABCF3 Sample DAG0


title: HS96_SCAHT16_CMA3+_donor

city: Geneva

first: Ludwig

last: Stenz

address: Rue Michel-Servet 1

department: Department of Genetic Medecine and Development

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
RRBS librairies were sequenced in paired-end mode of 50 bases on an Illumina NovaSeq6000.
reads were trimmed using TrimGalore (version 0.6.0) with option: --non-directional, --paired, --rrbs, --phred33, as well as with cutadapt (version 2.3) using options: --quality 30, --length 35.
Trimmed reads were mapped against the human bisulfite genome (assembly GRCH38) using Bismark (version 0.22.1) running with Bowtie 2 (version 2.3.5.1) and with the specified options: --q, --phred33, --score-min L,0,-0.2, --ignore-quals, --no-mixed, --no-discordant, --devtail, --maxins 1000, option --non-directional
Methylation calls were performed using the Bismark methylation extractor with options --paired-end, --gzip, --bedGraph, --multicore 10, --cytosine_report, --ignore 3, --ignore_r2 3, --ignore_3prime_r2
Cmeth and Cunmeth located within known C to T polymorphisms were removed using a bash script.
fisherTests of the Bsseq package were used to test methylation differences between two groups for each of the three comparisons at the single CpG level.
CpG with a p-value <2e-9 and with a finite value for the logarithm in base 2 of the odd ratio were kept.
BSmooth was used to analyse differentially methylated regions (DMR) cf: Genome Biology volume 13, Article number: R83 (2012) https://doi.org/10.1186/gb-2012-13-10-r83.
Quantile-based cutoff of the t-statistic were setup at 0.025 and 0.975 and methylation changes should be present in at least 3 samples of the group with an absolute change in methylation of 0.25 or higher.
bsseq::dmrFinder function identify the DMR reported with the meanDiff and the areaStat parameters.
We kept DMR and significant CpG overlapping each other.
We check overlaps with ALU repeats and ESR1 binding sites.
Assembly: GRCH38
Supplementary files format and content: bismark.cov.gz files containing methylation data after C/T SNP filtration.

source_name: Human semen samples

extract_protocol:
Puregene Gentra kit with modification (overnight lysis with DL-Dithiothreitol and proteinase K in the lysis buffer). Final re-suspention in water.
MspI-derived RRBS libraries prepared with the Diagenode® Premium RRBS technology (Service Cat. G02020000) as referenced in Nat Methods 13, i–ii (2016). https://doi.org/10.1038/nmeth.f.391

treatment_protocol: Masturbation, 30 minutes at 37 ºC, swim-up, wash, Ham’s F-10 media. Staining with 0.2 µM YO-PRO-1 dye (Thermo Fisher Scientific) and 1 µg/ml Hoechst 33342 or 0.25 mg/ml CMA3 (Sigma Aldrich) and 1 µg/ml Hoechst 33342. Sorted using a BD Influx cell sorter.

tag: technic

value: RRBS

tag: condition

value: donor

tag: facs


title: HS98_SCAHT17_CMA3+_donor


title: HS99_SCAHT18_CMA3-_patient

value: patient


title: HS97_SCAHT17_CMA3-_donor


title: AB7271

tag: patient id


title: HS93_SCAHT15_CMA3-_patient


title: H0583_BXD79_HFD_F

tag: age (days)

tag: strain

tag: Sex


title: AB7270


title: Volunteer AE0AA Sample 3C3C

tag: volunteer id

value: Male

tag: vaccine


title: Fast16liver_C57BL/6J_CD_F

tag: diet

tag: weight (g)


title: AB7267


title: AB7269


title: HS94_SCAHT15_CMA3+_patient


title: HS92_SCAHT14_CMA3+_patient


title: AB7268


title: HS91_SCAHT14_CMA3-_patient


title: Fast18liver_C57BL/6J_CD_F


title: AB7273


title: HS89_SCAHT13_CMA3-_donor


title: HS95_SCAHT16_CMA3-_donor


title: HS90_SCAHT13_CMA3+_donor


title: AB7266


title: AB7219


title: HS88_SCAHT12_CMA3+_patient


title: Fast14liver_C57BL/6J_CD_F


title: Fast11liver_BXD216_CD_F


title: H0927_C57BL/6J_CD_F


title: HS87_SCAHT12_CMA3-_patient


title: Fast17liver_C57BL/6J_CD_F


title: AB7218


title: Fast13liver_C57BL/6J_CD_F


title: HS85_SCAHT11_CMA3-_patient


title: HS84_SCAHT20_YOPRO+_donor

value: YOPRO+


title: AB7216


title: HS83_SCAHT20_YOPRO-_donor

value: YOPRO-


title: AB7217

value: Skin


title: HS82_SCAHT19_YOPRO+_donor


title: AB7215


title: HS81_SCAHT19_YOPRO-_donor


title: HS78_SCAHT17_YOPRO+_donor


title: Fast6liver_BXD176a_CD_F


title: HS79_SCAHT18_YOPRO-_patient


title: Fast10liver_BXD219_CD_F


title: HS86_SCAHT11_CMA3+_patient


title: AB7214


title: Fast2liver_BXD199_CD_F


title: HS76_SCAHT16_YOPRO+_donor


title: H1169_D2B6F1_CD_F


title: AB7213


title: HS75_SCAHT16_YOPRO-_donor


title: HS74_SCAHT15_YOPRO+_patient


title: HS73_SCAHT15_YOPRO-_patient


title: HS72_SCAHT14_YOPRO+_patient


title: AB7212


title: HS80_SCAHT18_YOPRO+_patient


title: AB7211


title: H1411_BXD65b_CD_F


title: HS71_SCAHT14_YOPRO-_patient


title: AB7197

value: Blood


title: H0069_BXD48a_CD_F


title: HS70_SCAHT13_YOPRO+_donor


title: HS69_SCAHT13_YOPRO-_donor


title: HS68_SCAHT12_YOPRO+_patient


title: HS77_SCAHT17_YOPRO-_donor


title: H1216_B6D2F1_HFD_M

value: M


title: AB7196


title: H1217_B6D2F1_HFD_M


title: HS67_SCAHT12_YOPRO-_patient


title: AB7195


title: H0330_BXD77_HFD_F

value: F


title: AB7194


title: H0699_BXD48a_HFD_F


title: HS64_Donor3_YOPRO-_donor


title: HS65_SCAHT11_YOPRO-_patient


title: AB7193


title: HS62_Donor3_CMA3-_donor


title: HS58_Patient4_YOPRO+_patient


title: HS54_Patient3_YOPRO-_patient


title: AB7190


title: H1058_BXD40_CD_F


title: AB7189


title: HS66_SCAHT11_YOPRO+_patient


title: H0679_BXD40_CD_F


title: H0680_BXD40_CD_F


title: H0301_BXD83_CD_F


title: HS43_Patient2_YOPRO+_patient


title: HS53_Patient3_YOPRO+_patient


title: HS37_Patient1_CMA3-_patient


title: HS63_Donor3_YOPRO+_donor


title: HS36_Patient1_CMA3-_patient


title: HS59_Patient4_YOPRO-_patient


title: HS33_Donor1_YOPRO+_donor


title: AB7191


title: HS35_Patient1_CMA3+_patient


title: AB7192


title: HS38_Patient1_YOPRO+_patient


title: H1162_D2B6F1_CD_F


title: HS40_Patient2_CMA3+_patient


title: HS31_Donor1_CMA3+_donor


title: H0146_BXD77_CD_F


title: H0299_BXD83_CD_F


title: AB7188


title: AB7186


title: H0588_BXD48_HFD_F


title: AB7187


title: HS28_EPIStu8_CMA3-_patient


title: HS25_EPIStu6_CMA3+_patient


title: HS30_EPIStu8_YOPRO+_patient


title: H0148_BXD77_CD_F


title: H2040_BXD40_CD_F


title: H1221_B6D2F1_CD_M


title: HS23_EPIStu6_YOPRO+_patient


title: HS29_EPIStu8_CMA3+_patient


title: HS32_Donor1_CMA3-_donor


title: HS27_EPIStu8_YOPRO-_patient


title: AB7184


title: H1222_B6D2F1_CD_F


title: AB7185


title: AB7181


title: HS21_EPIStu4_YOPRO-_donor


title: HS24_EPIStu6_YOPRO-_patient


title: HS26_EPIStu6_CMA3-_patient


title: H1224_B6D2F1_CD_F


title: HS18_EPIStu3_YOPRO+_donor


title: AB7180


title: HS17_EPIStu3_YOPRO-_donor


title: HS22_EPIStu4_CMA3+_donor


title: HS16_EPIStu3_CMA3+_donor


title: HS15_EPIStu3_CMA3-_donor


title: HS19_EPIStu4_YOPRO+_donor


title: AB7183


title: HS20_EPIStu4_CMA3-_donor


title: HS14_EPIStu1_YOPRO+_donor


title: H1232_B6D2F1_CD_F


title: AB7182


title: H1154_D2B6F1_CD_F


title: H1237_B6D2F1_HFD_M


title: AB7179


title: HS12_EPIStu1_YOPRO-_donor


title: H1285_BXD65_HFD_F


title: H0646_D2B6F1_CD_F


title: HS11_EPIStu1_CMA3-_donor


title: AB7177


title: AB7178


title: HS104_SCAHT20_CMA3+_donor


title: HS102_SCAHT19_CMA3+_donor


title: HS100_SCAHT18_CMA3+_patient


title: AB7176


title: HS103_SCAHT20_CMA3-_donor


title: HS13_EPIStu1_CMA3+_donor


title: AB7175


title: H0132_BXD48_CD_F


title: AB7174


title: HS101_SCAHT19_CMA3-_donor


title: AB7172


title: AB7083


title: H0645_D2B6F1_CD_F


title: HSC - Hypoxia_rep2

city: Beijing

first: Cheng

last: Quan

state: Beijing

address: Beijing Taiping Road No.27

country: China

institute: Beijing Institute of Radiation Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STAR v2.7.6a with parameters --twopassMode Basic --quantMode TranscriptomeSAM --outSAMstrandField intronMotif --readFilesCommand zcat
Estimate gene and isoform expression from RNA-Seq data using rsem-calculate-expression with parameters --paired-end --bam --no-bam-output --forward-prob 0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts/FPKM/TPM values for each Sample

source_name: HSC

extract_protocol:
Cells were harvested, and total RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: treatment

value: Hypoxia

tag: cellline

value: HSC


title: HSC - Hypoxia_rep3


title: H1303_B6D2F1_HFD_F


title: AB7173


title: H1153_D2B6F1_CD_F


title: K562 cells - Normoxia_rep2

value: Normoxia


title: Healthy_multiome_mrna

description: Processed data included in "Healthy_atac.tar" on GSM5884742

data_processing:
bcl2fastq/2.15.0.4
cellranger-arc/2.0.0
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include ATAC peak read count values and mRNA molecule count values for each Sample

source_name: Forearm skin rna-seq

extract_protocol:
human samples: skin samples were obtained through punch biopsy (4 mm), 10 cm distal to the elbow and placed in saline containing tubes on ice and then transferred to cold FACS buffer (EDTA pH8.0 2mM, BSA 0.5% in PBS). Whole blood samples were collected at the time of skin biopsy, were placed in EDTA-containing tubes (Beckton Dickenson) on ice and diluted 1:1 with ice cold FACS buffer. Skin and blood samples immediately transported to the lab.
To generate gentle and efficient single-cell suspensions from human skin tissue, we used Miltenyi human whole skin dissociation kit (catalog num. 130-101-540), which combines mechanical dissociation with enzymatic degradation of the extracellular adhesion proteins. In short, first we cut the skin biopsy into small pieces (< 1mm) and transferred them into gentleMACS C Tube containing 435µL of Buffer and 65 µL of enzyme mix. Next, samples were incubated in a water bath at 37 °C for 1h. After incubation we diluted the samples by adding 0.5 mL of cold cell culture medium, tightly closed C Tube and attached it upside down onto the sleeve of the gentleMACS dissociator, and run the gentleMACS Program h_skin_01. After a short centrifugation step to collect the sample material at the tube bottom, we applied the cell suspension to a 70 µm pre-separation filter, placed on a 15 mL tube, and washed with ice cold FACS buffer. Then, we centrifuged the cell suspension at 300×g for 10 minutes at 4°C and aspirated the supernatant completely. Finally, after red blood cell lysis (Sigma) for 5min at 4°C, centrifugation at 300×g for 10 minutes at 4°C, and washing, we resuspended the cells for FACS staining and sorting.
Skin cell suspension was stained with the following antibodies: CD45 (PerCp/Cyanine, 3040285.5, Biolegend), CD90 (PE 328144, Biolegend). All FACS antibodies were used with a 1:100 dilution. Cells were bulk sorted on FACS Symphony S6, cell sorter (BD Biosciences) using 100 nozzle and flowrate of 2 for 3 hours and pooled together. 75.000 and 40000 cells were obtained equally from 9 healthy and 9 dSSc patients, respectively.
Sorted cells were processed according to 10x Genomics Chromium Single Cell Multiome ATAC+ Gene Expression low cell number protocol according to protocol number CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevB used for cell lysis (0.1x lysis buffer and lysed for 7 min) to obtain intact nuclei. Single cell ATAC and RNA-seq libraries were prepared using the Chromium single cell multiome ATAC + gene expression platform (10x Genomics). Nuclei were prepared and counted to ensure quality and concentration. Nuclei were then transposed according to the manufacturer’s protocol.  Transposed nuclei suspension was loaded onto Next GEM Chip J targeting 5000 nuclei and then ran on a Chromium Controller instrument to generate GEM emulsion (10x Genomics). Single-cell gene expression libraries, as well as single cell ATAC-seq libraries, were generated according to the manufacturer’s protocol using the Chromium Next GEM Single Cell multiome ATAC+ gene expression kit. Final libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB) and high sensitivity D1000 TapeStation (Agilent). Each library was sequenced separately on a NovaSeq 6000 instrument using an SP 100 cycles reagent kit (Illumina), targeting 25,000 reads/nuclei for ATAC-seq and a minimum of 20,000 reads/nuclei for gene expression.

value: Ctrl


title: H0136_BXD48_CD_F


title: HSC - Hypoxia_rep1


title: H1236_B6D2F1_HFD_M

value: HFD


title: AB7080


title: HSC - Normoxia_rep3


title: HSC - Normoxia_rep1


title: AB7079


title: Patients_multiome_mrna

description: Processed data included in "Patients_atac.tar" on GSM5884740

value: dSSc


title: K562 cells - Hypoxia_rep2


title: AB7082


title: AB7078


title: K562 cells - Hypoxia_rep1


title: H0031_BXD77_CD_F

value: CD


title: H2290_B6D2F1_HFD_F


title: H1159_D2B6F1_CD_M


title: H1165_D2B6F1_CD_F


title: week_5.1

city: Vienna

first: Irina

last: Poverennaya

state: Österreich

address: Spitalgasse 4 / Medizinishe Universitat Wien, Zentrum fur Hirnforschung

department: Neuroimmunology

country: Austria

institute: Medical University of Vienna

data_processing:
Sequenced bcl files were converted to fastq files with Cell Ranger 3.1.0.
The sequenced 10X libraries from 5 samples were mapped to GRCh38-3.0.0 human genome and assigned to droplets with Cell Ranger software (version 3.1.0) with default parameters.
The obtained read count matrices were analyzed with Seurat 4.0.2.
Genome_build: Cell Ranger GRCh38-3.0.0
Supplementary_files_format_and_content: h5 datasets with raw gene expression counts filtered by CellRanger.

source_name: Aorta-gonad-mesonephros region

extract_protocol:
Human pre-natal tissue was obtained from clinical routine abortions with oral and written consent from the patient. The acquisition of human pre-natal tissue was approved by the Swedish Ethical Research Authority and the National Board of Health and Welfare (ethical reference is 2018/769-31) for research purposes. The material was donated for a general research purpose especially with the focus on neuronal and nervous system related cell types. Measurement of crown-rump-length (CRL) and anatomical landmarks were used to determine the post-conception age. The tissue was received in ice-cold PBS and enzymatically digested to obtain the single cell suspension. For this, tissue cut into smaller pieces was incubated with 500 ul 0.05% Trypsin/0.02% EDTA (Sigma, 59417-C) for 15 min at 37°C with gentle swirling every 5 min. Gentle pipetting up and down was used to mechanically dissociate bigger pieces if any. 500 ul 10% FBS in PBS was added to cell suspension and the cells were pelleted at 500 rcf for 5 min at 4°C. Cells were washed two times with 1000 uL PBS, passed though the 35 um cell strainer (Falcon, 352235), pelleted at 500 rcf for 5 min at 4°C and re-suspended in 100 ul 0.04% BSA in PBS. Ice-cold methanol (400 uL was added for fixation of the cells and the cells were stored at -80°C.
For the preparation of the library the cells were brought to +4°C and pelleted at 1000 rcf for 10 min at 4°C. Cell pellet was re-suspended in 500 uL of rehydration buffer (1X DPBS (Gibco 14190144) containing 1.0% BSA (Sigma, B4287) and 0.5U/μl RNase Out (ThermoFisher Scientific, 10777019)) followed by two washes with 500 uL of rehydration buffer. The rehydrated cell suspension was sorted to remove debris with BD FACS Aria Fusion instrument (BD Biosciences, San Jose, CA) equipped with 100 um nozzle. After FACS cells were pelleted to obtain concentrated cell suspension with 700-1200 cells/uL. 10x Genomics Chromium Single Cell 3ʹ protocol for Reagent Kits v3 was used for library preparation aiming to recover 5000-8000 cells.

value: Aorta-gonad-mesonephros region

tag: developmental stage

value: 5 weeks


title: K562 cells - Normoxia_rep3


title: AB7076


title: week_7.1

source_name: Adrenal gland

value: Adrenal gland

value: 7 weeks


title: K562 cells - Normoxia_rep1


title: week_7.2


title: week_5.2


title: AB7081


title: week_6

value: 6 weeks


title: AB9433


title: Patients_multiome_atac

source_name: Forearm skin atac-seq


title: AB9432


title: AB7077


title: AB9431


title: AB9434


title: AB7075


title: AB7073


title: H0145_BXD77_HFD_F


title: AB7074


title: AB7072


title: H1866_BXD77_HFD_F


title: AB9429


title: H1302_B6D2F1_HFD_F


title: H1766_BXD65b_CD_F


title: H0216_BXD48a_HFD_F


title: H2287_B6D2F1_HFD_F


title: AB9430


title: H1295_B6D2F1_HFD_F


title: H1298_BXD65_HFD_F


title: AB7069


title: AB9422


title: AB9423


title: AB9421


title: AB9420


title: AB7068


title: H1223_B6D2F1_CD_F


title: H0214_BXD48a_HFD_F


title: AB7067


title: AB9418


title: AB9424


title: AB9419


title: AB9116


title: AB9428


title: H0825_BXD79_CD_F


title: AB9115


title: AB7066


title: AB9113


title: AB9111


title: H1180_BXD73b_HFD_F


title: AB9110


title: AB9114


title: H1554_BXD79_CD_F


title: AB7065


title: AB9112


title: AB7064


title: AB9109


title: AB7063


title: H2071_BXD73_HFD_F


title: AB9108


title: H1398_BXD77_CD_F


title: H1859_BXD73_CD_F


title: AB9107


title: AB7061


title: AB9106


title: AB9104


title: H1327_BXD40_CD_F


title: AB9102


title: AB9101


title: AB6917


title: AB6916


title: H2046_BXD48_HFD_F


title: AB9100


title: AB9097


title: AB9098


title: AB7060


title: AB6915


title: AB7062


title: AB6914


title: AB8945


title: AB9099


title: AB8944


title: AB9105


title: AB6913


title: AB8943


title: AB9103


title: AB8941


title: K562 cells - Hypoxia_rep3


title: AB8942


title: AB8939


title: AB8940


title: AB6912


title: AB8937


title: AB6910


title: AB6911


title: AB8935


title: AB8938


title: AB6909


title: AB8936


title: AB6908


title: AB8933


title: AB8934


title: H1822_BXD44_CD_F


title: H2054_BXD48_CD_F


title: AB8932


title: AB8919


title: H1160_D2B6F1_CD_M


title: H1057_BXD40_CD_F


title: H2072_BXD73_CD_F


title: AB8918


title: H2053_BXD48_HFD_F


title: AB8917


title: AB6907


title: AB8916


title: AB6868


title: AB8915


title: AB6867

value: NONB/T


title: AB8914

value: Skin


title: H1170_D2B6F1_CD_F


title: AB8913


title: AB6866

value: Blood


title: AB8912


title: AB8911


title: Healthy_multiome_atac


title: HSC - Normoxia_rep2


title: H1352_B6D2F1_CD_M

value: M


title: H0328_BXD77_HFD_F

value: F


title: AB8910


title: AB6865


title: AB8909


title: AB6864


title: H1743_BXD102_CD_M


title: H1445_B6D2F1_HFD_F


title: AB8785


title: AB8783


title: AB6863


title: AB8784


title: AB8782


title: H1441_D2B6F1_CD_M


title: H1823_BXD44_CD_F


title: AB8780


title: H1378_BXD48_HFD_F


title: H1440_D2B6F1_CD_M


title: AB8779


title: AB6861


title: H1444_B6D2F1_HFD_F


title: H0210_BXD48a_HFD_F


title: AB8775


title: H1454_BXD48a_CD_F


title: AB8778


title: H1455_BXD48a_CD_F


title: H1377_BXD48_HFD_F


title: AB8774


title: AB6859


title: AB8772


title: AB8773


title: AB6858


title: AB8771


title: AB6857


title: AB6860


title: AB8781


title: AB8770


title: AB6862


title: AB6856


title: AB8769


title: AB8776


title: AB8768


title: AB8767


title: AB6855


title: AB8766


title: H1482_BXD40_CD_F


title: H1452_BXD48a_HFD_F


title: H0459_BXD65_HFD_F


title: AB8765


title: H1453_BXD48a_HFD_F


title: H0070_BXD48a_CD_F


title: AB6854


title: AB8762


title: AB8681


title: H1369_BXD102_CD_M


title: AB6853


title: AB8763


title: AB8682


title: AB8764


title: AB6852


title: AB6850


title: AB8677


title: AB8678


title: AB6851


title: AB6849


title: AB8676


title: AB8675


title: AB8680


title: H2288_B6D2F1_HFD_F


title: AB8679


title: H1714_BXD65b_CD_F


title: H1784_BXD65_HFD_F


title: H2089_BXD73b_CD_F


title: H1906_BXD73_CD_F


title: AB6848


title: AB8672


title: AB8670


title: AB8669


title: AB8671


title: AB6847


title: AB8668


title: AB6843


title: AB6838


title: AB8667


title: AB7896


title: AB6837


title: AB7894


title: H1506_BXD73_HFD_F


title: H1913_BXD48_CD_F


title: AB6701


title: H1907_BXD73_CD_F


title: AB8674


title: AB7893


title: H1483_BXD40_CD_F


title: H1410_BXD65b_CD_F


title: AB7878


title: H2577_BXD9_CD_F


title: AB6696


title: AB7875


title: H2578_BXD9_CD_F


title: AB7874


title: AB7873


title: H1188_BXD48a_CD_F


title: AB6695


title: AB7872


title: AB6694


title: H1239_BXD48a_HFD_F


title: AB7871


title: AB7870


title: AB6697


title: AB7869


title: AB7876


title: AB6692


title: AB7868


title: AB7895


title: AB7865


title: H1794_BXD65b_CD_F


title: AB6689


title: AB7866


title: H2107_BXD65b_CD_F


title: H1793_BXD65b_CD_F


title: AB6688


title: AB7860


title: AB7861


title: AB7859


title: AB7858


title: AB7857


title: AB14264

value: skin


title: H1227_B6D2F1_CD_F


title: AB7867


title: H1448_BXD73_HFD_F


title: AB7855


title: AB7854


title: H1413_BXD65b_CD_F


title: AB7856


title: H0182_BXD73b_CD_F


title: AB7853


title: H1363_BXD102_CD_F


title: AB14265


title: AB7849


title: H0450_BXD102_CD_F


title: AB6693


title: AB14260


title: AB14263


title: AB7850


title: AB7848


title: H1364_BXD102_CD_F


title: AB7847


title: H0184_BXD73b_CD_F


title: AB14262


title: AB7852


title: AB7844


title: AB14138


title: AB14258


title: AB7851


title: AB7846


title: AB14139


title: AB7845


title: AB14256


title: AB14127


title: AB14259


title: AB13858


title: AB14137


title: AB13855

value: Control


title: AB14126


title: AB14135


title: AB13853


title: AB14257


title: AB14261


title: AB14121


title: AB14120


title: AB13843


title: AB14117


title: AB14119


title: H0183_BXD73b_HFD_F


title: AB14136


title: AB14118


title: H0231_BXD102_CD_F


title: H0229_BXD102_CD_F


title: H2098_BXD65_CD_F


title: H0181_BXD73b_HFD_F


title: AB13842


title: AB14116


title: H0265_BXD73b_CD_F


title: AB13454


title: H1429_BXD79_CD_F


title: AB13455


title: H1720_BXD65_CD_F


title: AB13840


title: AB13453


title: AB13841


title: AB13450


title: AB13452


title: AB8673


title: AB13451


title: AB13449


title: AB13839


title: AB13448


title: AB13838


title: AB13447


title: H1447_BXD73_HFD_F


title: AB13446


title: AB13836


title: AB13837


title: H1451_BXD73_CD_F


title: H1450_BXD73_CD_F


title: H1412_BXD65b_CD_F


title: AB13445


title: AB13442


title: AB13835


title: AB13441


title: AB13443


title: AB7877


title: H1504_BXD44_CD_F


title: AB13439


title: AB13440


title: AB13438


title: AB13437


title: H0365_BXD9_CD_F


title: AB13444


title: AB13834


title: H0823_BXD79_CD_F


title: H0209_BXD48a_CD_F


title: AB13830


title: AB13832


title: AB13436


title: AB13435


title: AB13831


title: AB13433


title: AB13434


title: AB13432


title: AB13343


title: AB13431


title: AB13829


title: AB13828


title: AB13430


title: AB13827


title: AB13833


title: H1862_BXD73_HFD_F


title: AB13342


title: H0211_BXD48a_CD_F


title: H0005_BXD48_CD_F


title: H0826_BXD79_CD_F


title: AB13341


title: AB13826


title: AB13340


title: AB13825


title: AB13339


title: H0824_BXD79_CD_F


title: H0004_BXD48_CD_F


title: H1198_BXD73b_HFD_F


title: AB13824


title: AB13338


title: H0831_BXD79_CD_F


title: AB13823


title: AB13337


title: AB13822


title: H1197_BXD73b_HFD_F


title: AB13336


title: AB13821


title: H0832_BXD79_CD_F


title: H1284_BXD65_CD_F


title: metastasis, sample 6

city: Rennes

first: Frédéric

last: Chalmel

state: France

address: 9 avenue du Pr. Léon Bernard

department: Physiology and physiopathology of the urogenital tract

country: France

institute: Inserm U1085-Irset

description: Gene expression data from a metastasis of the right adrenal gland

hyb_protocol: Total RNA samples were hybridized to Human Transcriptome Array 2.0 GeneChips as recommended by the manufacturer (Affymetrix, Santa Clara, USA). Sample processing, labeling and hybridization were performed using the GeneChip WT PLUS Reagent Kit and the GeneChip Hybridization/Wash/Stain Kit, according to the manufacturer's guidelines (ThermoFischer Scientific). Scanning and data extraction of the microarray were followed by the transformation of fluorescence data into CEL files employing the Affymetrix GeneChip Command Console (AGCC) software.

scan_protocol: The resulting CEL files were processed using the oligo package available performed in R/Bioconductor (3). The SCAN.UPC package were then employed for data normalization and background correction using the BRAINARRAY custom CDF file for directly mapping Affymetrix probe to Entrez gene identifiers (hta20_Hs_ENTREZG version 21.0.0) (4). The signal distribution was further quality controlled by box plots as implemented in R (Fig. S1, panel B ).

data_processing: the statistical filtration of the genes differentially expressed (DE) among the three sample classes (C1-C3) was performed using AMEN (7) (Table S2, Fig. S2, panel B). Briefly, we first filtered genes with at least one signal above the background expression cutoff (BEC = 0.189, corresponding to the overall median intensity) and with a minimal fold change of 1.5 across sample classes. Finally, a statistical test implemented in the LIMMA package (F-value adjusted with the false discovery rate method: P ≤ 0.05) was used to identify significantly DE genes across sample classes (8). The resulting genes were then partitioned into three gene expression clusters (named G1 to G3) using the k-means method (k = 3) implemented in R.

source_name: metastasis, right adrenal gland

label_protocol: Tissues were homogenized in RLT buffer using TissueLyser (Qiagen) followed by passing the lysate through a blunt 23-gauge. Genomic DNA purification and RNA isolation were performed according to the manufacturer's instructions. DNase digestion done also for RNA and integrity was checked using RNA 6000 NanoChips with the Agilent 2100 Bioanalyzer (Agilent, Diegem, Belgium). Only RNA preparations with a RNA integrity number (RIN) >6.9 were considered for further microarray analysis.

extract_protocol: Total RNA was extracted from biological samples using AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions with a maximum of 30 mg frozen tissue.

treatment_protocol: no treatment was induced

tag: type

value: tumor tissue

tag: site

tag: organ

value: adrenal gland

tag: side

value: right


title: AB13335

tag: tissue

tag: selection marker


title: H1283_BXD65_CD_F


title: AB13820

tag: patient id


title: metastasis, sample 9

description: Gene expression data from a metastasis of the left adrenal gland

source_name: metastasis, left adrenal gland

value: left


title: AB13334


title: metastasis, sample 8


title: AB13819


title: metastasis, sample 4


title: AB13333

value: Hip


title: AB13818


title: metastasis, sample 7


title: H0267_BXD73b_CD_F

tag: age (days)

value: CD


title: metastasis, sample 5


title: metastasis, sample 3


title: H0807_BXD65_CD_F

tag: strain


title: AB13332


title: H0808_BXD65_CD_F

tag: Sex


title: metastasis, sample 2

description: Gene expression data from tumor thrombus of the vena cava

source_name: tumor thrombus

value: thrombus


title: AB13817

source_name: Forearm skin


title: AB13331


title: AB13816


title: H0883_BXD91_CD_F


title: AB13815


title: metastasis, sample 1


title: H0881_BXD91_HFD_F

value: HFD


title: AB13330


title: AB13814


title: AB13329


title: primary tumor, sample 5

description: Gene expression data from primary tumor of a clear cell renal cell carcinoma

source_name: primary tumor, right kidney

value: primary

value: kidney


title: S. hominis C5 + 100uM Apicidin rep 2

city: Aurora

first: Morgan

last: Severn

state: CO

institute: University of Colorado Anschutz Medical Campus

data_processing:
RNA-seq data analysis was performed with the CLC Genomics Workbench (Qiagen version 20.0.4) using a four-fold cut-off for differential gene expression and False Discovery Rate p-value <0.05. Read mapping was performed with standard parameters (mismatch cost = 2; insertion cost = 3; deletion cost = 3; length fraction = 0.8; similarity fraction = 0.8). RNA-seq analysis was performed with standard program parameters for microarray analysis (total count filter cutoff = 5; estimate tagwise dispersion = yes; comparisons = all pairs; Bonferroni corrected = yes; FDR corrected = yes; Normalization = quantile; normalized data = original expression values; observations are paired.)
Assembly: S. hominis C5 Genbank CP093539

organism: Staphylococcus hominis

source_name: Bacterial

growth_protocol: Two days prior to experimentation, S. hominis C5 was struck to isolated colonies from a freezer stock and grown ON at 37c on tryptic soy agar. The day before experimentation, one colony was inoculated into 5mL tryptic soy broth for a total of 3 biological replicates. The day of the experiment, each biological replicate was used for a paired comparison with DMSO or Apicidin treatment.

extract_protocol:
RNA from each sample was prepared with the Qiagen RNeasy mini kit (Qiagen) following manufacturer’s guidelines. RNA was DNase treated with the TURBO DNase kit (Thermo Scientific) following standard manufacturer’s guidelines
Illumina stranded RNA library preparation with RiboZero Plus rRNA depletion at the Microbial Genome Sequencing Center (MiGS, Pittsburg, PA) following standard Illumina protocols.

treatment_protocol: S. hominis C5 grown in TSB were sub-cultured 1:200 in fresh TSB with 100 M apicidin (diluted in DMSO) or equivalent volume of DMSO in biological triplicate in a 24-well plate (Corning). The plate was incubated at 37C shaking at 1000 RPM in a Stuart humidified shaker for 8 hours (optical density of 3 at 600 nm). Cultures were harvested by adding 2 mL RNAprotect Bacteria (2:1 v/v) (Qiagen), incubated for 5 minutes at room temperature, then pelleted. Pellets were stored at -80°C until RNA purification.

value: 100uM Apicidin


title: AB13321

value: Skin


title: S. hominis C5 + 100uM Apicidin rep 3


title: AB13813


title: S. hominis C5 + 100uM Apicidin rep 1


title: AB13320


title: S. hominis C5 + DMSO rep 3

value: DMSO


title: AB13812


title: AB13319


title: primary tumor, sample 4


title: H882_BXD91_HFD_F


title: S. hominis C5 + DMSO rep 2


title: AB13811


title: H0884_BXD91_CD_F


title: primary tumor, sample 2


title: H1145_DBA/2J_HFD_F


title: H1200_BXD64_HFD_F


title: AB13318


title: primary tumor, sample 1


title: S. hominis C5 + DMSO rep 1


title: H1860_BXD73_CD_F


title: AB13809


title: H1096_BXD90_CD_F


title: AB13810


title: AB13317


title: AB13316


title: H2498_BXD87_CD_F


title: AB13801


title: primary tumor, sample 3


title: AB13808


title: H2495_BXD32_CD_F


title: AB13315


title: H1769_BXD98_CD_F


title: H1502_BXD44_HFD_F


title: H0675_BXD39_CD_F


title: 20210715_MS-1_11~9o-2_11

city: Stanford

first: Anusha

last: Kalbasi

address: 269 Campus Drive

department: Radiation Oncology

institute: Stanford

description: in vitro T cell culture

hyb_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12

data_processing: no further processing of data -- raw counts were used in analysis (not normalized data)

source_name: CAR-o9R + MSA-oIL2

growth_protocol: Murine CD3 positive T cells activated and retrovirally transduced over a 5 day period

extract_protocol: Total RNA was extracted from T cells using the RNeasy mini Kit (Qiagen)

treatment_protocol: 1 million T cells cultured for 48 hours with orthogonal or wild-type IL-2

tag: cell type

value: CAR T cells

tag: transduced with


title: AB13314


title: 20210715_MS-1_12~9o-3_12

description: in vitro T cell culture

scan_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12


title: 20210715_MS-1_9~9wt-3_09

description: in vitro T cell culture

source_name: CAR-o9R + MSA-IL2

label_protocol: According to manufacturer's protocol (Nanostring); used commercially available kit catalog number XT-CSO-MIM1-12


title: AB13312


title: AB13313


title: FERONIA mutant rep 2

city: Ames

first: Natalie

middle: M

last: Clark

state: IA

address: Advanced Teaching and Research Building 2213 Pammel Drive

department: Plant Pathology and Microbiology

institute: Iowa State University

data_processing:
Adapters trimmed using bbtools
Reads aligned using STAR Aligner
Counts obtained using HTSeq
TMM normalization performed using edgeR
Differential expression performed using PoissonSeq
Genome_build: TAIR10
Supplementary_files_format_and_content: .csv file of  TMM expression in all samples

organism: Arabidopsis thaliana

source_name: Rosette tissue

growth_protocol: Seeds were germinated on 1/2MS with constant light (24hr light) for 10 days. Then, plants were transferred to soil and grown under short day condition (8-hour light and 16-hour dark) at 22C for another 3 weeks (21 days). Samples were 4 weeks old when collected

extract_protocol:
RNA was extracted from rosette leaves using Qiagen RNEasy Mini prep kit
Library was constructed using QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina
Sequencing was performed on a HiSeq4000 with 50bp single end reads. All libraries were run twice, and reads were merged prior to data processing.

tag: genotype

value: fer mutant


title: 20210715_MS-1_10~9o-1_10

description: in vitro T cell culture


title: FERONIA mutant rep 3


title: AB13797


title: AB13798


title: 20210715_MS-1_7~9wt-1_07

description: in vitro T cell culture


title: AB13311


title: FERONIA mutant rep 1


title: Wild type rep 3

value: Wild type


title: AB13799


title: H1045_BXD29_CD_F

source_name: Liver

value: F

tag: diet

tag: weight (g)


title: 20210715_MS-1_8~9wt-2_08

description: in vitro T cell culture

tag: treatment


title: 20210715_MS-1_6~2o-3_06

description: in vitro T cell culture

source_name: CAR-o2R + MSA-oIL2


title: AB13796


title: 20210715_MS-1_5~2o-2_05

description: in vitro T cell culture


title: AB13309


title: AB13795


title: AB13800


title: Wild type rep 2


title: 20210715_MS-1_4~2o-1_04

description: in vitro T cell culture


title: AB13308


title: AB13794


title: AB12599


title: AB13307


title: 20210715_MS-1_3~2wt-3_03

description: in vitro T cell culture

source_name: CAR o2R + MSA-IL2


title: AB13310


title: H1228_B6D2F1_CD_F


title: 20210715_MS-1_2~2wt-2_02

description: in vitro T cell culture


title: FLL3

city: Aarhus N

first: Paul

middle: Vinu

last: Salachan

state: Aarhus

address: Brendstrupgårdsvej 21A

country: Denmark

institute: Aarhus University

description: sampled at low temperature point after 6 fluctuation cycles during larval stage

data_processing:
The raw reads were checked for quality using FastQC (Andrews, 2010) and trimmed using trimmomatic based on a minimum length of 80 bp. Alignment of the trimmed reads was done using HISAT2 with default settings (Kim et al., 2015). StringTie (Pertea et al., 2015) was used to assemble the transcripts based on Drosophila melanogaster reference genome. All the transcripts were further merged using StringTie merge. The StringTie was run again with the B option on the merged transcripts to produce Ballgown input table files.
hisat2 -p 19 --dta -t -q -x
stringtie align_1/${sample}.bam -o align_1/${sample}.gtf -p 19 -G drosGTF/Dros_mel.BDGP6.92.chr.gtf
stringtie --merge -p 19 -o align_1/stringtie_merged.gtf -G drosGTF/Dros_mel.BDGP6.92.chr.gtf align_1/mergelist.txt
stringtie -e -B align_1/${sample}.bam -o align_1/ballgown/${sample}/${sample}.gtf -p 19 -G align_1/stringtie_merged.gtf
Genome_build: BDGP6
Supplementary_files_format_and_content: .csv file containing count data for all samples, generated using a python script provided by the developers of StringTie

organism: Drosophila melanogaster

source_name: Whole organism

growth_protocol: Experimental animals were kept in vials with 7ml standard Drosophila food medium. Adult flies were tipped to fresh food containing vials every second day

extract_protocol:
Extrraction and Library construction performed by Novogene using standard protocols.
mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: Experimental animals subjected to constant temperature at 19 degree centigrade or a fluctuating temperature with a mean of 19 and an amplitude of plus or minus 8 degree centigrade. The treatment was continued for 7 days during larval development and for 13 days during adult stage, during which animals were taken for RNA sequencing at different timepoints

value: fluctuating

value: unknown

tag: timepoint

tag: lifestage

value: larvae


title: FLL2


title: AB13792


title: FLL4


title: AB13793


title: AB13790


title: AB12597


title: AB13791


title: FLH4

description: sampled at high temperature point after 6 fluctuation cycles during larval stage


title: Wild type rep 1


title: 20210715_MS-1_1~2wt-1_01

description: in vitro T cell culture


title: KO liver sample 3 from ethanol-fed

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

data_processing:
Sequencing was done on BGISEQ-500 platform
The reads were mapped to the mouse genome using STAR (v2.5) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v1.5.3) with the following parameters: “-s 2 –p –Q 10”.
The data was filtered using read count per million (CPM) > 0.5 in more than 4 of the samples, normalized using TMM (trimmed mean of M values) method and subjected to differential expression analysis using edgeR (v3.20.8).
Genome_build: mm10
Supplementary_files_format_and_content: Raw counts and analysis (excel) from edgeR

source_name: liver

extract_protocol:
Mouse livers were dissected and snap frozen in liquid nitrogen. Total RNAs were isolated using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice were treated with with an isocaloric control diet or a 5% Lieber-DeCarli diet for 10 days plus a single binge of maltose dextrin or ethanol (5 g/kg)

value: liver

tag: age

value: 3 months

tag: agent

value: ethanol-fed

tag: genotype/variation

value: Sirt6 liver-specific knockout

value: Female


title: KO liver sample 2 from ethanol-fed

tag: tissue


title: AB12595

tag: selection marker


title: AB12596

tag: patient id


title: AB13789


title: KO liver sample 1 from ethanol-fed


title: FLH3


title: FLH2


title: AB13788


title: FLL1


title: AB13787


title: AB11885


title: AB12598


title: AB11884


title: AB13786


title: FLH1


title: AB13785


title: FAL8F

description: sampled at low temperature point after 12 fluctuation cycles during adult stage

value: female

value: adult


title: AB11883

source_name: Peripheral blood

value: Blood


title: AB13784

value: Skin


title: WT liver sample 1 from ethanol-fed

value: wildtype


title: FAL8M

value: male


title: KO liver sample 2 from pair-fed

value: pair-fed


title: AB11882


title: KO liver sample 1 from pair-fed


title: AB11881


title: WT liver sample 3 from ethanol-fed


title: AB11880


title: AB13783


title: FAL7M


title: FAL7F


title: AB13781


title: AB13782


title: WT liver sample 2 from pair-fed


title: AB11879


title: FAL6M


title: KO liver sample 3 from pair-fed


title: WT liver sample 2 from ethanol-fed


title: AB13780


title: WT liver sample 3 from pair-fed


title: FAL5M


title: WT liver sample 1 from pair-fed


title: FAL6F


title: AB13778


title: AB11877


title: T7dpa-3

city: xinxiang

first: jing

last: li

state: henan

address: No. 46, Jianshe East Road

institute: henan normal university

description: tissue

data_processing:
Basecalls performed using  Solexa pipeline v1.8
The trimmed reads (trimmed 5’,3’-adaptor bases using cutadapt) were aligned to reference genome using tophat2 version 2.0.3.12)software
The transcript abundances for each sample was estimated with RSEM
the FPKM value for gene and transcript level were calculated with R package edgeR
The circRNA reads were aligned to reference genome using (tophat2)detecting backesplicec junction reads with find_circ
Genome_build: Homo sapiens (hg38)
Supplementary_files_format_and_content: circRNA matrix.txt, lncRNA matrix.txt, mRNA matrix.txt

organism: Danio rerio

source_name: caudal fin

extract_protocol:
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.

treatment_protocol: Wild-type zebrafish were kept in a closed recirculating aquacultural system.The intact caudal fins (CK0dpa) were used as control and the regenerated caudal fins at corresponding stages (T3dpa and T7dpa) were used as treatment group.

value: caudal fin removal

tag: time

value: caudal fin (regenerating)


title: FAL5F

value: fluctuating


title: AB11875


title: AB11878


title: AB11876


title: T7dpa-1

description: tissue

growth_protocol: Wild-type zebrafish were kept in a closed recirculating aquacultural system.


title: AB13777


title: AB13779


title: T7dpa-2

description: tissue


title: FAL3M

description: sampled at low temperature point after 6 fluctuation cycles during adult stage


title: FAL4F


title: FAL4M


title: AB13776


title: FAL2M


title: AB11873


title: FAL3F


title: AB11871


title: AB11874


title: CK0dpa-3

description: tissue

value: control

value: caudal fin


title: T3dpa-3

description: tissue


title: FAL2F


title: AB11870


title: AB13775


title: AB11872


title: T3dpa-1

description: tissue


title: CK0dpa-2

description: tissue


title: T3dpa-2

description: tissue


title: AB11429


title: FAL1M


title: FAL1F


title: D94_AlgGroup_2D

city: Bergen

first: Helge

last: Ræder

address: Dept of Pediatrics, Haukeland University Hospital

department: Department of Clinical Science

country: Norway

institute: University if Bergen

description:
Sample 25
Alg_Expression_raw_counts.csv

data_processing:
Raw data was de-multiplexed and FASTQ files for each sample were generated using the bcl2fastq2 software (Illumina inc.).
The “Demultiplex QIAseq UPX 3’ reads” tool of the CLC Genomics Workbench 21.0.4 was used to demultiplex the raw sequencing reads according to the sample indices.
The reads were then mapped to the Human genome GRCh38 and annotated using the ENSEMBL GRCh38 v. 98 gene annotation.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: hiPSC-derived beta like cells at Stage7

growth_protocol: The directed differentiation of hiPSCs to β-like cells was performed as previously described (7, 8). To reduce variability between different differentiations we performed the original differentiation in parallel in the same multiwell-plate for all conditions with the same batch of differentiation cocktail. At the end of Stage 5, 5.0 million cells were embedded in alginate beads, as previously described (13), 2.4 million cells were used to form cell aggregates (11) and approximately 5 million were kept in adherent culture. The beads, aggregates and planar cultures were differentiated until ST7 as previously described (7, 14).

extract_protocol:
RNA from cell clusters were isolated using  Qiagen RNeasy kit. RNA from alginate capsules were snap freeze in the kit lysis buffer, without de-algination, RNA were then isolated by following the recommended process.
The library preparation was done using the QIAseq UPX 3’ Transcriptome Kit (QIAGEN). A total of 10 ng (sample 1-7), 2.5 ng (sample 8-14) purified RNA was converted into cDNA NGS libraries. During reverse transcription, each sample was tagged with a unique ID, and each RNA molecule was tagged with a unique molecular index (UMI). The samples were then pooled into one tube for downstream processing. Quality control of the library preparation was performed using capillary electrophoresis (Agilent DNA 7500 Chip) and the libraries were quantified using qPCR.

treatment_protocol: Different cell lins were differentiated in Aggrewell plates (3D), encapsulated in Alginate, or in 2D conditation respectively.

tag: condition

value: Alginate Group_2D

tag: iPSc cell line


title: D13_AlgGroup_2D

description:
Sample 23
Alg_Expression_raw_counts.csv


title: E87_Alg

description:
Sample 28
Alg_Expression_raw_counts.csv

value: Alginate Group


title: HKU16 gshT mutant in THY_rep3

city: Parkville

first: Magnus

middle: Ganer

last: Jespersen

state: Victoria

address: 792 Elizabeth street

country: Australia

institute: The University of Melbourne

description: HKU16 strain with deletion of gshT harvested in late logartihmic phase of growth

data_processing:
Size filtering using cutadapt verison 2.8, special parameters: -n 0 -U 0 --action none -m 45
rRNA read filtering using database comprised of rRNA from S. pyogenes SF370, 5448, and HKU488 and SortMeRNA version 4.3.4, special parameters: --fastx
Alignment of reads against HKU16 (GCF_000275625.1) using BWA-mem, bwa version 0.7.17
Read counting using FeatureCounts, subreads version 2.0.0, special parameters: -s 1 --largestOverlap -B -t gene -g ID
Differential expression analysis using Deseq2 v.1.32.0 in R v. 4.0.0. HKU16ΔgshT compared to WT HKU16
Genome_build: GCF_000275625.1
Supplementary_files_format_and_content: Xlsx and csv format

organism: Streptococcus pyogenes

source_name: Bacterial culture

growth_protocol: Bacteria were statically grown to late-logarithmic growth phase in Todd Hewitt broth supplemented with 1% yeast extract (THY) at 37˚C

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen). Briefly, bacteria were grown to late-logarithmic growth phase in THY. Two volumes of RNAprotect (Qiagen) were added to the cultures and the samples were then centrifuged at 5,000 x g for 25 min at 4°C to pellet cells. RNA was isolated from the dry pellet as per the manufacturer’s instructions with an additional mechanical lysis step using Lysing Matrix B tubes (MP Biomedicals) on the FastPrep-2 5G bead beating grinder and lysis system (MP Biomedicals). To ensure complete removal of DNA, the RNA was then further purified using the TURBO DNA-free kit (Thermo Fisher Scientific) according to the manufacturer’s instructions.
RNAseq analysis was performed at the Australian Centre for Ecogenomics (University of Queensland, Brisbane, Australia). cDNA libraries were prepared from total RNA using TruSeq Stranded Total RNA Library Prep with Ribo-Zero Plus rRNA Depletion kit (Illumina). Sequencing of the cDNA libraries was performed on the NovaSeq 6000 System (Illumina) on a 2x150 bp SP flowcell run generating an average of 20 million reads per sample.

treatment_protocol: No treatment

tag: strain

value: GAS emm12 HKU16[delta]gshT

tag: growth phase

value: Late-logarithmic


title: HKU16 gshT mutant in THY_rep2


title: HKU16 gshT mutant in THY_rep1


title: FAH8F

description: sampled at high temperature point after 12 fluctuation cycles during adult stage

tag: Sex


title: HKU16 in THY_rep3

description: Wild-type HKU16 strain harvested in late logartihmic phase of growth

value: GAS emm12 HKU16


title: E75_Alg

description:
Sample 26
Alg_Expression_raw_counts.csv

tag: genotype


title: FAH7F

value: female


title: FAH7M

value: adult


title: AB11426


title: D13_Alg

description:
Sample 22
Alg_Expression_raw_counts.csv


title: AB11428


title: E87_AlgGroup_2D

description:
Sample 20
Alg_Expression_raw_counts.csv


title: AB11425


title: 6F_AlgGroup_2D

description:
Sample 21
Alg_Expression_raw_counts.csv


title: D94_Alg

description:
Sample 24
Alg_Expression_raw_counts.csv


title: HKU16 in THY_rep1


title: AB11427


title: 6F_Alg

description:
Sample 19
Alg_Expression_raw_counts.csv


title: AB11423


title: E75_AlgGroup_2D

description:
Sample 27
Alg_Expression_raw_counts.csv


title: FAH6M


title: AB11424


title: HKU16 in THY_rep2


title: FAH6F


title: CK0dpa-1

description: tissue


title: AB11422


title: FAH5M


title: FAH8M


title: 6A_AlgGroup_2D

description:
Sample 16
Alg_Expression_raw_counts.csv


title: AB11338


title: 6D_AlgGroup_2D

description:
Sample 18
Alg_Expression_raw_counts.csv


title: 6A_Alg

description:
Sample 15
Alg_Expression_raw_counts.csv


title: Over3720_RNAseq Over37203

city: xian

first: Miaomiao

last: Jin

address: yangling

institute: northwest A&F university

data_processing:
TopHat (version 2.0.12) was used to map the paired-end clean reads to the reference goat genome and to build the index of the reference genome with Bowtie (Version 2.2.3)
Cufflinks (version 2.1.1) was used to assemble the mapped reads from TopHat2 (version 2.0.12)
Cuffdiff was used to calculate FPKM of the lncRNAs and coding genes in all libraries
Assembly: ASM170441v1
Supplementary files format and content: gtf were generated by cufflinks. FPKM were caculated by cuffdiff.

organism: Capra hircus

source_name: Ear marginal tissue

extract_protocol:
Total RNA was isolated from in vitro fertilization (IVF) goat embryos at the two-cell and eight-cell stages and somatic cell nuclear transfer(SCNT) 8-cell embyos. We used the Qubit® RNA Assay Kit and Qubit® 2.0 Fluorometer (Life Technologies, CA, USA) to detect RNA concentration. RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA) was employed for RNA integrity evaluation, and SMART-SeqTM v4 UltraTM Low RNA Kit for Sequencing (Clontech) was used to obtain the amplified cDNA in accordance with the manufacturer’s instructions.
The Covaris system sheared the cDNA samples prior to library preparation. Moreover, sequencing libraries (IVF-2c  IVF-8c and SCNT-8c) were generated using NEBNext® UltraTM DNA Library Prep Kit for Illumina® (NEB, USA) in accordance with the manufacturer’s instructions, and index codes were added to attribute sequences to each sample. Clustering of the index-coded samples was conducted on a cBot Closter Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) in accordance with the manufacturer’s instructions. After cluster generation, library preparations were sequenced on an Illumina HiseqTM 2500 platform, and 125-bp paired-end reads were generated.

value: Ear marginal tissue

tag: cell type

value: GFFs cells

value: Overexpress

value: transfected with pcDNA3.1(+)-lncRNA3720 using Lipofectamine 3000


title: Control_RNAseq C3

value: Control

tag: treatment

value: transfected with pcDNA3.1 using Lipofectamine 3000


title: Over3720_RNAseq Over37201


title: FAH4M

description: sampled at high temperature point after 6 fluctuation cycles during adult stage

value: male

tag: timepoint