title: DNAmethylation_patient56 [205023290052_R03C01]

description:
tumor sample 49
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 145

status: Public on Jul 17 2024

type: SRA

city: Basel

first: Simona

last: Baghai Sain

address: Schanzenstrasse 44

department: Department of Biosystems Science and Engineering

country: Switzerland

institute: ETH Zurich

library_source: other

data_processing:
library strategy: Amplicon sequencing of genomic DNA
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. The number of sgRNAs in each sample was counted by the count command from the MAGeCK package.
processed data files format and content: Count matrix of sgRNAs (represented by the gene symbol of their target gene). Gene symbols on rows, samples on columns.
Assembly: mm10

molecule: other

organism: Mus musculus

source_name: mouse epidermis

extract_protocol:
DMBA/TPA-induced tumors (which were not used for neither scRNA-seq nor spatial analysis) were minced and genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit.
The sgRNA region was amplified in a nested PCR. In PCR1, we used 12.5 µl KAPA HiFi HotStart ReadyMix (Roche, 07958935001), 0.75 µl forward primer (5‘ CTTGTGGAAAGGACGAAACACCG 3’, 10μM), 0.75 µl reverse primer (5‘ GTGTCTCAAGATCTAGTTACGCCAAGC 3’ 10μM), 1 µl of extracted genomic tumor DNA (with a concentration between 50-100 ng/μl) and 10 μl nuclease-free water for a total volume of 25 μl per tumor. PCR1 was performed using the following conditions: Initial denaturation at 98°C for 2:30 min, followed by 22 cycles of denaturation 98°C -– 20 s, annealing 62°C -– 30 s, extension 72°C -– 30 s. PCR1 products for each tumor were individually column-purified with a GenElute™ PCR Clean-Up Kit (Sigma-Aldrich NA1020-1KT). For PCR2, 1 μl of cleaned up PCR1 was used as template along with 0.75 μl forward barcoded i5 primer (see Supplementary Information Table 1, 10 μM), 0.75 μl reverse barcoded i7 primer (see table, 10 μM), 10 μl nuclease free-water, along with 12.5 μl of KAPA HiFi HotStart ReadyMix for a total volume of 25 μl. Eight different i5 and i7 primers allowed for a total of 64 different combinations. PCR2 was performed under following conditions: Initial denaturation at 95°C for 3 min, followed by 32 cycles of denaturation 98°C -– 30 s, annealing 62°C – 30 s, extension 72°C – 30 s. PCR2 products for a maximum of 64 individually barcoded tumor amplifications were pooled and cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to manufacturer’s instructions before sequencing.

treatment_protocol: DMBA/TPA chemical carcinogenesis: Two-stage cutaneous chemical carcinogenesis was performed as previously described by Filler et al. (2007). In brief: the back of 6-8 week old animals were shaved with electric hair clippers and treated once with 400 nmol 7,12-dimethylbenz[a]anthracene (DMBA)(Sigma-Aldrich D3254) per 100 µl (dissolved in acetone) application as an initiator mutagen. After a two-week rest period, 40 nmol 2-o-tetradecanoylphorbol-13-acetate (TPA)(Sigma-Aldrich 79346) dissolved in 100 µl 100% Ethanol was applied twice a week. Tumor formations were monitored regularly by visual inspection and mice were euthanized after 12 weeks of treatment or when tumors reached a cumulative length of 2cm.

tag: tissue

value: mouse epidermis

tag: treatment

value: DMBA/TPA carcinogenesis

tag: strain

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J

tag: age

value: 144 days post natal


title: DNAmethylation_patient55 [205023290052_R02C01]

type: genomic

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

country: Germany

institute: Childens Cancer Center - University hospital Augsburg

description:
tumor sample 48
genomic DNA

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
Data was processed as described in Johann, Pascal D., et al. "Atypical teratoid/rhabdoid tumors are comprised of three epigenetic subgroups with distinct enhancer landscapes." Cancer cell 29.3 (2016): 379-393.
eMRTbetas.csv: normalized beta values

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: formalin-fixed paraffin-embedded tumor sample

label_protocol: standard protocol

extract_protocol: standard protocol

treatment_protocol: DNA was isolated from FFPE tumor samples, purification and bisulfite conversion were performed as described in:  Holdhof D, Johann PD, Spohn M, Bockmayr M, Safaei S, Joshi P, et al. Atypical teratoid/rhabdoid tumors (ATRTs) with SMARCA4 mutation are molecularly distinct from SMARCB1-deficient cases. Acta Neuropathologica. 2021;141(2):291-301.

value: extracranial malignanat rhabdoid tumor

tag: subgroup

tag: status (0=alive, 1=deceased)


title: DNAm postmortem brain s32

city: Munich

first: Natan

last: Yusupov

address: Kraepelinstr. 2-10

department: Dept. Genes and Environment

institute: Max Planck Institute of Psychiatry

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC v1.0 BeadChip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Minfi pipline with stratified quantile normalization and subsequently beta-mixture quantile normalization.

source_name: postmortem brain

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted from fresh-frozen postmorten brain samples according to standard procedures

tag: Sex

value: Male

tag: hemisphere

value: Right

tag: pmi

value: no

value: Current


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 140


title: DNAmethylation_patient54 [205023290051_R08C01]

description:
tumor sample 47
genomic DNA


title: DNAmethylation_patient53 [205023290051_R07C01]

description:
tumor sample 46
genomic DNA


title: DNAm postmortem brain s92

value: Female


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 138


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 139


title: DNAmethylation_patient52 [205023290051_R06C01]

description:
tumor sample 45
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 150


title: DNAmethylation_patient51 [205023290051_R05C01]

description:
tumor sample 44
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 136


title: DNAmethylation_patient50 [205023290051_R03C01]

description:
tumor sample 43
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 134


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 135


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 137


title: DNAmethylation_patient5 [200876170045_R06C01]

description:
tumor sample 42
genomic DNA


title: DNAmethylation_patient48 [205023290049_R08C01]

description:
tumor sample 40
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 133


title: Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA)

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using iSCAN using standard recommended Illumina scanner setting

data_processing: lumi

label: Cy3 and Cy5

source_name: FFPE tumor tissue of a 19 year old male

extract_protocol: genomic DNA was extracted and purified from tumor sample using QIAamp DNA FFPE tissue (Qiagen)

treatment_protocol: tumor tissue was formalin-fixed and paraffin embedded

value: tumor tissue


title: DNAmethylation_patient49 [205023290051_R02C01]

description:
tumor sample 41
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 141


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 132


title: DNAmethylation_patient47 [205023290049_R07C01]

description:
tumor sample 39
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 131


title: DNAmethylation_patient45 [205023290049_R05C01]

description:
tumor sample 37
genomic DNA


title: DNAmethylation_patient46 [205023290049_R06C01]

description:
tumor sample 38
genomic DNA


title: DNAm postmortem brain s37

value: Never


title: DNAm postmortem brain s44

value: Left


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 130


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 129


title: DNAmethylation_patient44 [205023290049_R04C01]

description:
tumor sample 36
genomic DNA


title: DNAm postmortem brain s80


title: DNAmethylation_patient42 [205023290049_R02C01]

description:
tumor sample 34
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 125


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 127


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 123


title: DNAmethylation_patient40 [205023290048_R08C01]

description:
tumor sample 32
genomic DNA


title: DNAmethylation_patient4 [200876170045_R03C01]

description:
tumor sample 31
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 124


title: DNAmethylation_patient38 [203952880054_R05C01]

description:
tumor sample 30
genomic DNA


title: DNAmethylation_patient39 [200848860134_R04C01]

description:
tumor sample 79
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 121


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 122


title: DNAmethylation_patient37 [200848860134_R03C01]

description:
tumor sample 78
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 120


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 128


title: DNAmethylation_patient36 [202128330008_R04C01]

description:
tumor sample 29
genomic DNA


title: DNAmethylation_patient43 [205023290049_R03C01]

description:
tumor sample 35
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 119


title: DNAmethylation_patient35 [200848860134_R02C01]

description:
tumor sample 77
genomic DNA


title: DNAmethylation_patient33 [200928190107_R08C01]

description:
tumor sample 27
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 118


title: DNAmethylation_patient32 [200928190107_R07C01]

description:
tumor sample 26
genomic DNA


title: DNAmethylation_patient41 [205023290049_R01C01]

description:
tumor sample 33
genomic DNA


title: DNAmethylation_patient34 [200876170042_R02C01]

description:
tumor sample 28
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 116


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 117


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 126


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 115


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 114


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 113


title: DNAmethylation_patient3 [200876170042_R06C01]

description:
tumor sample 23
genomic DNA


title: DNAmethylation_patient30 [200928190107_R05C01]

description:
tumor sample 24
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 112


title: DNAmethylation_patient70 [205023290087_R07C01]

description:
tumor sample 65
genomic DNA


title: DNAmethylation_patient31 [200928190107_R06C01]

description:
tumor sample 25
genomic DNA


title: DNAmethylation_patient28 [200928190107_R03C01]

description:
tumor sample 21
genomic DNA


title: DNAmethylation_patient29 [200928190107_R04C01]

description:
tumor sample 22
genomic DNA


title: DNAmethylation_patient69 [205023290087_R06C01]

description:
tumor sample 63
genomic DNA


title: DNAmethylation_patient27 [200928190107_R02C01]

description:
tumor sample 20
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 111


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 110


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 109


title: DNAmethylation_patient26 [200928190107_R01C01]

description:
tumor sample 19
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 107


title: DNAmethylation_patient25 [200928190026_R04C01]

description:
tumor sample 18
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 108


title: DNAmethylation_patient22 [200925700164_R08C01]

description:
tumor sample 15
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 106


title: DNAmethylation_patient23 [200928190026_R02C01]

description:
tumor sample 16
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 104


title: DNAmethylation_patient65 [205023290054_R05C01]

description:
tumor sample 59
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 105


title: DNAmethylation_patient20 [200925700164_R05C01]

description:
tumor sample 13
genomic DNA


title: DNAmethylation_patient2 [200876170042_R05C01]

description:
tumor sample 12
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 103


title: DNAmethylation_patient19 [200925700164_R04C01]

description:
tumor sample 11
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 102


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 100


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 99


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 101


title: DNAmethylation_patient16 [200925700164_R01C01]

description:
tumor sample 8
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 98


title: DNAmethylation_patient17 [200925700164_R02C01]

description:
tumor sample 9
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 96


title: DNAmethylation_patient24 [200928190026_R03C01]

description:
tumor sample 17
genomic DNA


title: DNAmethylation_patient14 [200925700162_R06C01]

description:
tumor sample 6
genomic DNA


title: DNAmethylation_patient15 [200925700162_R07C01]

description:
tumor sample 7
genomic DNA


title: DNAmethylation_patient21 [200925700164_R06C01]

description:
tumor sample 14
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 95


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 94


title: DNAmethylation_patient12 [200925700162_R03C01]

description:
tumor sample 4
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 97


title: DNAmethylation_patient10 [200925700161_R08C01]

description:
tumor sample 2
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 92


title: DNAmethylation_patient11 [200925700162_R02C01]

description:
tumor sample 3
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 91


title: DNAmethylation_patient1 [200876170042_R04C01]

description:
tumor sample 1
genomic DNA


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 93


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 90


title: genomic DNA from ID CLZ1022 for 'a' visit

city: Exeter

first: Emma

last: Walker

address: RILD Barrack Rd

country: United Kingdom

institute: University of Exeter

description:
CLZ1022a
204026590037_R03C01

hyb_protocol: standard Illumina protocol

scan_protocol: illumina iScan

data_processing:
waterMelon
wateRmelon::dasen() normalised Average Beta

source_name: peripheral whole blood

label_protocol: KCL samples were profiled using the Illumina Infinium HumanMethylation450 BeadChip and UMC samples were profiled using the Illumina Infinium HumanMethylationEPIC BeadChip

extract_protocol: Approximately 500ng of blood-derived DNA from each sample was treated with sodium bisulfite in duplicate, using the EZ-96 DNA methylation kit (Zymo Research, CA, USA)

tag: visit

value: a

tag: institute

value: Utrecht

value: M

tag: bcell

tag: gran

tag: mono

tag: nk

tag: smokingscore


title: DNAmethylation_patient18 [200925700164_R03C01]

description:
tumor sample 10
genomic DNA


title: genomic DNA from ID CLZ1022 for 'b' visit

description:
CLZ1022b
204026590037_R02C01

value: b


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 87

value: mouse epidermis


title: genomic DNA from ID CLZ1022 for 'c' visit

description:
CLZ1022c
204026590037_R01C01

value: c


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 88

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 89

value: 144 days post natal


title: genomic DNA from ID CLZ1024 for 'a' visit

description:
CLZ1024a
204026590024_R07C01


title: genomic DNA from ID CLZ1024 for 'b' visit

description:
CLZ1024b
204026590024_R06C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 86


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 85


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 83


title: genomic DNA from ID CLZ1021 for 'b' visit

description:
CLZ1021b
204026590024_R04C01

value: F


title: genomic DNA from ID CLZ1021 for 'c' visit

description:
CLZ1021c
204026590024_R05C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 82


title: genomic DNA from ID CLZ1021 for 'a' visit

description:
CLZ1021a
204026590024_R03C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 81


title: genomic DNA from ID CLZ1014 for 'c' visit

description:
CLZ1014c
204026590024_R02C01


title: genomic DNA from ID CLZ1014 for 'a' visit

description:
CLZ1014a
204026590024_R01C01


title: genomic DNA from ID CLZ1011 for 'b' visit

description:
CLZ1011b
204026590021_R08C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 79


title: genomic DNA from ID CLZ1012 for 'a' visit

description:
CLZ1012a
204026590021_R04C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 75


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 77


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 76


title: genomic DNA from ID CLZ1012 for 'c' visit

description:
CLZ1012c
204026590021_R03C01


title: DNAmethylation_patient58 [205023290052_R05C01]

description:
tumor sample 51
genomic DNA

value: extracranial malignanat rhabdoid tumor


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 73


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 72


title: genomic DNA from ID CLZ1013 for 'a' visit

description:
CLZ1013a
204026590021_R05C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 71


title: genomic DNA from ID CLZ1011 for 'a' visit

description:
CLZ1011a
204026590024_R08C01


title: genomic DNA from ID CLZ1007 for 'c' visit

description:
CLZ1007c
204026590017_R08C01


title: genomic DNA from ID CLZ1011 for 'c' visit

description:
CLZ1011c
204026590017_R07C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 84


title: genomic DNA from ID CLZ1012 for 'b' visit

description:
CLZ1012b
204026590021_R02C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 70


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 80


title: genomic DNA from ID CLZ1008 for 'c' visit

description:
CLZ1008c
204026590017_R03C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 69


title: genomic DNA from ID CLZ1008 for 'b' visit

description:
CLZ1008b
204026590017_R02C01


title: genomic DNA from ID CLZ1013 for 'b' visit

description:
CLZ1013b
204026590021_R07C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 78


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 68


title: genomic DNA from ID CLZ1007 for 'a' visit

description:
CLZ1007a
204026590013_R08C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 67


title: genomic DNA from ID CLZ1008 for 'a' visit

description:
CLZ1008a
204026590017_R01C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 74


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 66


title: genomic DNA from ID CLZ1007 for 'b' visit

description:
CLZ1007b
204026590013_R07C01


title: genomic DNA from ID CLZ1014 for 'b' visit

description:
CLZ1014b
204026590021_R01C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 64


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 65


title: genomic DNA from ID CLZ1005 for 'b' visit

description:
CLZ1005b
204026590013_R04C01


title: genomic DNA from ID CLZ1005 for 'a' visit

description:
CLZ1005a
204026590013_R03C01


title: genomic DNA from ID CLZ1002 for 'b' visit

description:
CLZ1002b
204026590006_R08C01


title: genomic DNA from ID CLZ1005 for 'c' visit

description:
CLZ1005c
204026590013_R02C01


title: genomic DNA from ID CLZ1002 for 'a' visit

description:
CLZ1002a
204026590006_R07C01


title: genomic DNA from ID CLZ1002 for 'c' visit

description:
CLZ1002c
204026590006_R06C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 61


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 60


title: genomic DNA from ID CLZ1001 for 'b' visit

description:
CLZ1001b
204026590006_R04C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 59


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 57


title: genomic DNA from ID CLZ1001 for 'a' visit

description:
CLZ1001a
204026590006_R03C01


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 56


title: Stag2-R370Q Atrx-Luc/bGal (FITC positive)

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

description: 10x Genomics Chromium

library_source: transcriptomic single cell

data_processing:
Demultiplexing, barcoding, alignment, and feature counting were performed with 10x Genomics CellRanger software v5.0.1 mkfastq and count commands.
Assembly: GRCm38
Supplementary files format and content: Tab-separated values files
Supplementary files format and content: Matrix files

molecule: total RNA

source_name: Bone marrow

extract_protocol:
Cells were partitioned and barcoded using the 10X Genomics Chromium Controller, according to the manufacturer’s instructions. The harvested cDNA was assessed and quantified using the Agilent 2100 Bioanalyser and library construction performed using the 10X Single Cell 3' Library Kit v3.1. Libraries were quality controlled by shallow sequencing, balanced, and deep-sequenced using an Illumina NextSeq 2000 system.
scRNA-Seq libraries were prepared according to the manufacturer's instructions using the 10X Single Cell 3' Library Kit v3.1

treatment_protocol: Bone marrow cells isolated from heterozygous Stag2-WT x Stag2-R370Q Atrx-Luc/bGal female mice were depleted of lineage markers. Lineage-negative cells were stained with Sca-1, c-kit, FLT-3 and CD127 antibodies and FITC+ (Stag2-R370Q) and FITC- (Stag2-WT) Lin−cKit+Sca-1+Flt3+CD127+ cells were sorted and analyzed by scRNAseq.

value: Bone marrow

tag: cell type

tag: genotype

value: Stag2-WT x Stag2-R370Q Atrx-Luc/bGal


title: Stag2-WT  (FITC negative)

description: 10x Genomics Chromium

tag: tissue

value: Female


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 58

tag: treatment

tag: strain


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 55

tag: age


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 54


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 62


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 63


title: cra2, shoot, satiety, rep3

city: Gif-sur-Yvette

first: Thomas

last: Blein

address: Avenue des Sciences

country: France

institute: CNRS

library_source: transcriptomic

data_processing:
The raw reads were trimmed using Cutadapt to remove the sequencing adapter (TGGAATTCTCGGGTGCCAAGG) at the 3’-end. Additionally, four bases were also trimmed from the 5’-end and 3’-end of the reads as described in the manual of the NEXTFLEX Small RNA-Seq Kit v3 (Perkin-Elmer).
The amount of each mature miRNA was computed as the number of mature reads exactly corresponding to the mature sequence.
Assembly: miRBase (v22, Medicago mature miRNAs) and MIRMED (Formey et al. 2009)
Supplementary files format and content: tab-delimited text files include raw count values for each known miRNAs

organism: Medicago truncatula

source_name: shoot

growth_protocol: Seeds were scarified and sterilized in Bayrochlore and stratified for 4 days. Plants were grown in a growth chamber with 16h of light with a 250 μmole.m 2 -.s -1 intensity, a 70% relative humidity, and 22 °C day/20 °C night, into hydroponic tanks containing a vigorously aerated HY basal nutrient solution supplemented with 0.5 mM KNO 3 as sole mineral N source and with a pH 5.8, which was renewed every four days. After one week, the primary root tips of plantlets were cut to promote branching of the root system. The root systems of three-week-old plants were separated into two parts and grown in a split-root system.

extract_protocol:
Total RNAs were extracted using the miRNeasy mini kit (Qiagen).
Libraries were prepared using the NEXTFLEX Small RNA-seq kit v3 (PerkinElmer) following the manufacturer’s instructions. The resulting barcoded library was size-selected (137-187 bp) using a Pippin HT (SAGE Science) with a 3 % agarose cassette (#HTG3004).

treatment_protocol: Four days before harvest, the differential local N treatments were then applied using HY supplemented with high mineral N (10 mM NH 4 NO 3 ) or low mineral N (0.05 mM KNO 3 ), whereas systemic root compartments were supplied with HY without mineral.  Four-week-old plants were harvested in the middle of the day period.

value: shoot

value: nitrogen satiety


title: cra2, shoot, satiety, rep2


title: cra2, shoot, satiety, rep1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 53


title: T2D_Participant_12_w52

city: Nuthetal

first: Heike

last: Vogel

state: BRB

address: Arthur-Scheunert-Allee 114-116

department: Department of Experimental Diabetology

institute: German Institute of Human Nutrition Potsdam-Rehbruecke

data_processing:
adapters and low-quality reads have been filtered by BGI
alignment to reference with STARv2.7.0f
Read count extraction via STRINGTIE v1.3.6 and prepDE.py (following Protocol stringtie webpage)
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: skeletal muscle

extract_protocol:
total RNA was extracted using the miRNAeasy Mini Kit (Qiagen, Germany) as per the manufacturer's protocol, with additional DNase treatment
done by BGI (Yantian District, Shenzhen, China)

value: skeletal muscle

value: female

tag: timepoint

value: 52 weeks post metabolic surgery

tag: group

value: Obese diabetic


title: T2D_Participant_13_w52

tag: Sex

value: male


title: T2D_Participant_11_w52


title: T2D_Participant_10_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 52

value: mouse epidermis


title: cra2, shoot, deficit, rep1

value: nitrogen deficient


title: genomic DNA from ID CLZ1001 for 'c' visit

description:
CLZ1001c
204026590006_R05C01

value: c

value: Utrecht

value: M


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 51

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J

value: 144 days post natal


title: cra2, root, satiety, rep3

source_name: root

value: root


title: cra2, shoot, deficit, rep2


title: T2D_Participant_9_w52


title: cra2, root, satiety, rep1


title: Glioneuronal tumor with ATRX alteration, kinase fusion and anaplastic features (GTAKA)

data_processing:
Raw reads were aligned to the reference human genome (UCSC-Build38) using STAR (2.5.3a) algorithm.
Arriba pipeline was used for fusion detection.
Assembly: GRCh38
Supplementary files format and content: tsv format, contains details about the detected fusions

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded tumour tissue using the Maxwell CSC instrument (Promega) according to the manufacturer’s protocol.
RNA sequencing libraries were obtained using the SureSelect XT HS2 RNA kit (Agilent Technologies) from 300 nanograms of total RNA according to the manufacturer's protocol.

value: FFPE tumor tissue of a 19 year old male


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 50


title: T2D_Participant_8_w52


title: cra2, root, deficit, rep3


title: cra2, root, deficit, rep2


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 49


title: DNAmethylation_patient13 [200925700162_R04C01]

description:
tumor sample 5
genomic DNA

value: extracranial malignanat rhabdoid tumor

tag: subgroup

tag: status (0=alive, 1=deceased)


title: cra2, shoot, deficit, rep3

value: shoot


title: T2D_Participant_6_w52

value: skeletal muscle


title: cra2, root, deficit, rep1


title: A17, shoot, satiety, rep3

value: nitrogen satiety


title: T2D_Participant_5_w52

value: female

value: 52 weeks post metabolic surgery


title: A17, shoot, satiety, rep1


title: A17, shoot, satiety, rep2


title: T2D_Participant_4_w52

value: male

value: Obese diabetic


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 48

value: mouse epidermis


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 46


title: A17, shoot, deficit, rep3

value: nitrogen deficient


title: T2D_Participant_2_w52


title: T2D_Participant_3_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 45


title: A17, shoot, deficit, rep2


title: A17, root, satiety, rep1


title: T2D_Participant_7_w52


title: A17, root, deficit, rep3


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 44


title: A17, root, satiety, rep2


title: A17, root, deficit, rep1


title: A17, root, satiety, rep3


title: cra2, root, satiety, rep2


title: T2D_Participant_13_w0

value: Before metabolic surgery


title: RNA-seq of sheep: omega-3 fatty acids 6

city: Columbus

first: Jinsoo

last: Ahn

address: 2029 Fyffe Rd

country: USA

institute: Ohio State Univesity

data_processing:
The raw sequencing reads were trimmed and filtered using Trimmomatic (v0.38) with default settings (Bolger et al., 2014), and the quality of reads was checked using FastQC (v0.11.8). The clean reads were quantified using the default mapping-based mode of Salmon for pseudo-alignment with an index (v1.5.2).
Assembly: ARS-UI_Ramb_v2.0
Supplementary files format and content: Transcript quantification files (.sf format)  generated using Salmon. The files contain name, length, effective length, TPM, and NumReads.

organism: Ovis aries

source_name: hypothalamus

extract_protocol:
Lamb hypothalamus RNA was extracted using RNAzol RT (Molecular Research Center; Cincinnati, OH) according to the manufacturer’s procedure.
The concentration of RNA was measured using UV spectroscopy (Nanodrop Technologies). Sizing, quantitation, integrity, and purity from RNA was were assessed using a BioAnalyzer 2100 and RNA NanoChip assay (Agilent Technologies). Quantified and qualified RNA samples were sent out to BGI for DNBSEQ library construction.

value: hypothalamus

value: omega-3 fatty acids supplementation


title: T2D_Participant_1_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 47

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: A17, root, deficit, rep2

value: root


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 42

value: 144 days post natal


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 41


title: A17, shoot, deficit, rep1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 40


title: RNA-seq of sheep: omega-3 fatty acids 2


title: RNA-seq of sheep: omega-3 fatty acids 4


title: RNA-seq of sheep: omega-3 fatty acids 3


title: T2D_Participant_10_w0


title: T2D_Participant_12_w0


title: T2D_Participant_11_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 39


title: RNA-seq of sheep: methionine6

value: methionine supplementation


title: RNA-seq of sheep: methionine4


title: T2D_Participant_9_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 43


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 38


title: T2D_Participant_8_w0


title: RNA-seq of sheep: methionine3


title: RNA-seq of sheep: methionine1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 36


title: RNA-seq of sheep: omega-3 fatty acids 5


title: RNA-seq of sheep: methionine2


title: RNA-seq of sheep: control5

value: control


title: T2D_Participant_7_w0

value: skeletal muscle


title: T2D_Participant_6_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 35


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 37


title: RNA-seq of sheep: control4


title: RNA-seq of sheep: control1


title: RNA-seq of sheep: control3


title: RNA-seq of sheep: control2


title: RNA-seq of sheep: omega-3 fatty acids 1


title: RNA-seq of sheep: methionine5


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 34


title: IgG ChIP

city: Philadelphia

first: Emily

last: Feierman

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

library_source: genomic

data_processing:
Fastq files were aligned by Bowtie2
bam files were generated using SAMtools
NGSplot was used to generate metaplots
bigwig files were generated using deepTools
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2

source_name: primary cortical neurons

extract_protocol:
At 12DIV, primary cortical neurons were fixed and collected for ChIP
Illumina TruSeq Library Preparation Kit

value: primary cortical neurons

value: WT


title: T2D_Participant_5_w0

value: female


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 33


title: IgG input


title: T2D_Participant_4_w0

value: male


title: input biol rep 2


title: T2D_Participant_3_w0

value: Obese diabetic


title: H2BE ChIP biol rep 1


title: H2BE-L3P biol rep 2

data_processing:
Fastq files were aligned by Bowtie2
bam files from biological replicates within each condition were merged, and 30 million reads were subset for each group
NGSplot was used to generate metaplots
deepTools was used to generate bigwig files
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2

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


title: H2BE ChIP biol rep 2


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 31

value: mouse epidermis


title: T2D_Participant_1_w0


title: input biol rep 1


title: WT H2BE biol rep 2

value: WT H2BE


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 32


title: T2D_Participant_2_w0

value: Before metabolic surgery


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 30


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 29


title: WT H2BE biol rep 1


title: GFP biol rep 1

value: GFP


title: KO biol rep 3

data_processing:
Fastq files were aligned by Star
DESeq2 was used for differential gene expression analysis
Assembly: mm10
Supplementary files format and content: csv of DESeq output

molecule: polyA RNA

extract_protocol:
Zymo Quick-RNA Minprep kits were used to isolate RNA
RNA libraries were prepared for sequencing using TruSeq stranded mRNA library prep kit


title: OB_Participant_11_w52

value: 52 weeks post metabolic surgery

value: Obese non diabetic


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 27

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: GFP biol rep 2


title: WT biol rep 4


title: OB_Participant_12_w52


title: WT biol rep 3


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 26

value: 144 days post natal


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 28


title: KO biol rep 4


title: KO biol rep 2


title: OB_Participant_10_w52


title: KO biol rep 1


title: OB_Participant_9_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 25


title: OB_Participant_13_w52


title: WT biol rep 2


title: OB_Participant_8_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 24


title: OB_Participant_7_w52


title: OB_Participant_6_w52


title: FP_rep3_RNAseq

city: Beijing

first: Zejia

last: Wang

address: Yanyuan Street

country: China

institute: Peking University

data_processing:
For RNA-seq analysis, adaptors of the raw reads were trimmed off using fastp v0.20.1. The trimmed reads were aligned to the Vaccinium corymbosum cv ‘Draper’ genome using HISAT2 v2.2.1 under default settings. Since “Draper” is tetraploid, we selected largest scaffolds of each of the 12 homoeologous groups to represent the genome. The expression level of each gene, measured as TPM (Transcripts Per kilobase of exon model per Million mapped reads) values, were counted using featureCounts of the Subread package v2.0.2  with default parameters.
Assembly: V_corymbosum_v1.0
Supplementary files format and content: The processed data is generated  by HISAT2

organism: Vaccinium corymbosum

source_name: fruit

extract_protocol: The total RNA was isolated from the strain using the Trizol reagent according to manufacturer’s instructions (Invitrogen) and sent to Novogene (Tianjin, China) for library   preparation and deep sequencing.

value: fruit

tag: cell line

value: wild type

value: no

tag: time

value: 63 days after anthesis


title: MG_rep3_RNAseq

value: 42 days after anthesis


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 22


title: OB_Participant_5_w52

value: skeletal muscle

value: female


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 21


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 20


title: FP_rep2_RNAseq


title: PP_rep2_RNAseq

value: 56 days after anthesis


title: OB_Participant_4_w52


title: OB_Participant_3_w52


title: LG_rep2_RNAseq

value: 49 days after anthesis


title: SG_rep2_RNAseq

value: 35 days after anthesis


title: FP_rep1_RNAseq


title: WT biol rep 1

value: primary cortical neurons

value: WT


title: LG_rep1_RNAseq


title: MG_rep1_RNAseq


title: PP_rep1_RNAseq


title: H2BE-L3P biol rep 1


title: PP_rep3_RNAseq


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 23

value: mouse epidermis


title: OB_Participant_1_w52

value: 52 weeks post metabolic surgery

value: Obese non diabetic


title: OB_Participant_2_w52


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 18

value: DMBA/TPA carcinogenesis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: OB_Participant_13_w0

value: Before metabolic surgery


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 16

value: 144 days post natal


title: mlaA_mutant-pJV300-3

city: Shanghai

first: Kejing

last: Wu

address: 320 Yueyang Road

institute: Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences

data_processing:
Clean reads were generated from raw sequencing reads by removing adaptor sequences (5' Adapter: 5'-AATGATACGGCGACCACCGAGATCTACAC(i5Index)ACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; 3' Adapter: 5'-CAAGCAGAAGACGGCATACGAGAT(i7Index reversed)GTGACTGGAGTTCAGACGTGTGCTCTTCCGATC-3') and low-quality sequences using cutadapt (Version 2.10) and FASTXToolkit (Version 0.0.14), and reads less than 25 nt were discarded.
Reads were aligned to the reference genome K. pneumoniae ATCC 43816 (GenBank: NZ_CP009208.1) by BWA (Version: 0.7.17-r1198-dirty) with the default setting. Reads only unambiguously aligned to unique position were preserved to calculate reads number, CPM (counts per million) and RPKM (reads per kilobase and per million) for each gene.
Differential expression between the conditions was tested using DESeq2 in R packages. For each gene, significance p-value and FDR were obtained based on the model of negative binomial generalized linear model. Fold changes of gene expression were also estimated within the DESeq2 statistical package.
Assembly: NZ_CP009208.1
Supplementary files format and content: Tab-delimited text include counts of mapped reads

organism: Klebsiella pneumoniae subsp. pneumoniae ATCC 43816

source_name: Bacterial cells

growth_protocol: K. pneumoniae strains were grown in LB media containing IPTG (final concentration 1 mM) as sRNA expression inducer with 220 rpm at 37 °C.

extract_protocol:
Cells at OD600 3 were harvested by addition of 0.2 volumes of stop mix (95% ethanol, 5% (v/v) phenol) and snap-frozen in liquid nitrogen.
Total RNA was used as input material for the RNA sample preparations. mRNA was purified from total RNA using probes to remove rRNA. Fragmentation was carried out using divalent cations under elevated temperature. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER® enzyme digestion, amplification, and purification.

value: Bacterial cells


title: LG_rep3_RNAseq

value: fruit

value: wild type

value: no


title: mlaA_mutant-pJV300-1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 17


title: OB_Participant_12_w0

value: skeletal muscle

value: female


title: arcZ_mutant-ArcZ_M5-2


title: SG_rep1_RNAseq


title: arcZ_mutant-ArcZ_M5-3


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 15


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 13


title: arcZ_mutant-ArcZ-1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 11


title: arcZ_mutant-pJV300-1


title: WT-pJV300-2


title: WT-pJV300-3


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 10


title: OB_Participant_8_w0


title: OB_Participant_10_w0


title: OB_Participant_9_w0


title: arcZ_mutant-ArcZ-3


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 9


title: arcZ_mutant-ArcZ_M5-1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 14


title: OB_Participant_11_w0


title: arcZ_mutant-pJV300-2


title: IgG-2

data_processing:
Clean reads were generated from raw sequencing reads by removing adaptor sequences and low-quality sequences using FASTXToolkit (Version 0.0.13), and reads less than 25 nt were discarded.
The first 25 nucleotides of each remaining paired read were mapped to the genome of K. pneumoniae ATCC 43816 (GenBank: NZ_CP009208.1 using the BWA software (Version: 0.7.17-r1198-dirty) with default parameters.
Fragments that mapped within a distance of 1,000 nt were considered single, whereas fragments that mapped to two different loci were considered chimeric.
To identify over-represented chimeras, we divided the genome into non-overlapping 100 nt-long windows and counted the number of sequenced fragments showing fusion between each window pair. If neighboring windows of windows appear in chimeric fragments, the size of tested windows were increased gradually in leaps of 100 nt up to 500 nt (from four windows upstream each original window to four windows downstream). We applied Fisher’s exact test to test if the chimeric fragments between two windows were statistically significantly more than expected at random based on the number of single and chimeric fragments mapped to each window. The p-values were corrected using the Bonferroni method. Chimeras with Padj-value < 0.05, odds ratio value > 1 and chimeric fragments > 10 were considered significant and termed S-chimeras.
Assembly: NZ_CP009208.1
Supplementary files format and content: Tab-delimited text include counts of statistically significant chimeras

growth_protocol: K. pneumoniae hfq::3xFLAG strain containing the plasmid pBAD-t4rnl1 was grown in LB medium with 220 rpm at 37 °C.

extract_protocol:
Bacterial samples (about 100 OD) were collected by centrifugation at 6,000 rpm for 20 min at 4 °C. The bacterial pellets were resuspended in 500 µl ice-cold lysis buffer (20 mM Tris pH 8.0, 150 mM KCl, 1 mM of MgCl2, 1 mM DTT, 0.05% Tween-20), and broke with 500 µl glass beads using the Cryolys Evolution instrument, at 7,200 rpm for 15 min at 4 °C. Lysates were collected by centrifugation at 13,000 rpm for 30 min at 4 °C, and divided into new tubes equally. Cleared lysates were respectively incubated with anti-FLAG antibody (Sigma) or IgG isolate control (Invitrogen) conjugated on the protein-G magnetic beads (Thermo-Fisher) for 1 hour at 4 °C with rotation. The beads were collected by the magnet, and washed five times with 500 µl lysis buffer and resuspended in 50 µl lysis buffer. The Hfq-bound RNA was extracted by RNA clean & concentrator columns (Sangon, Shanghai). The purified RNA was resuspended in nuclease-free water.
LiRIP-seq libraries were constructed using the RNAtag-seq method as described previously (Liu et al., 2023; Melamed et al., 2018), with a few modifications. Briefly, fragmented RNA was treated with DNase I and FastAP. RNA then was ligated to the 3’ barcoded adaptor, and depleting Ribosomal RNA by Ribo-off rRNA depletion Kit (#N407-01, Vazyme). First strand cDNA was synthesized by HiScript II 1st Strand cDNA Synthesis Kit (#R211-01, Vazyme), and RNA was degraded after reverse transcription by 1 M NaOH and 0.5M acetic acid. The cDNA was ligated to a second adaptor. Every step needed to purify the sample with 2.5x Agencourt AMPure XP beads and 1.5x isopropanol. Libraries were constructed by PCR with Illumina P5 and P7 primers using Q5 High-Fidelity DNA Polymerase (#M0491L, NEB), and purified with 1.5x AMPure XP beads. The libraries were sequenced by 150 bp paired-end sequencing with an Illumina NovaSeq instrument.

treatment_protocol: Strains expressing Hfq-FLAG were induced to express the T4 RNA ligase for 30 min and grown to OD600~3.0, and cell lysates were prepared.


title: WT-pJV300-1


title: IgG-3


title: OB_Participant_5_w0


title: IgG-1


title: arcZ_mutant-ArcZ-2


title: OB_Participant_6_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 8


title: Hfq-3


title: arcZ_mutant-pJV300-3


title: OB_Participant_4_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 12


title: Hfq-2


title: Hfq-1


title: OB_Participant_3_w0


title: PP1-7_+Tet_C

city: Athens

first: Haidong

last: Yan

state: Georgia

address: 220 Mark Twain Cir Apt D

institute: University of Georgia

data_processing:
Raw reads were trimmed with the default settings of fastp (v0.19.5)
alignment: Bowtie2 v2.3.4.1 using sensitive local alignment mode
sorting: Samtools v1.2 using default parameters
expression levels: DESeq2 variance stabilized counts
Assembly: Trypanosoma brucei Lister 427 (v9.0 from TriTrypDB.org)
Supplementary files format and content: tab-delimited text file, see metafile for column headers

organism: Trypanosoma brucei

source_name: Blood Stream Form Single Marker Cell line

extract_protocol:
Total RNA was isolated from T. brucei cultures using TriPure, according to the manufacturer’s instructions. 5x107 cells were used for each prep.
For mRNA-seq, total RNA was isolated from T. brucei RNAi cultures grown in presence or absence of tetracycline for two days using TriPure. Six mRNA-seq libraries were constructed for each of the PP1 RNAi cell lines (triplicate samples for plus and minus tetracyclin) using Illumina TruSeq Stranded RNA LT Kit following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 µg, and all volumes were reduced to a third of the described quantity. High throughput sequencing was performed on an Illumina Novaseq6000 instrument.


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 19

data_processing:
library strategy: Amplicon sequencing of genomic DNA
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. The number of sgRNAs in each sample was counted by the count command from the MAGeCK package.
processed data files format and content: Count matrix of sgRNAs (represented by the gene symbol of their target gene). Gene symbols on rows, samples on columns.
Assembly: mm10

extract_protocol:
DMBA/TPA-induced tumors (which were not used for neither scRNA-seq nor spatial analysis) were minced and genomic DNA was extracted using the Qiagen DNeasy Blood and Tissue Kit.
The sgRNA region was amplified in a nested PCR. In PCR1, we used 12.5 µl KAPA HiFi HotStart ReadyMix (Roche, 07958935001), 0.75 µl forward primer (5‘ CTTGTGGAAAGGACGAAACACCG 3’, 10μM), 0.75 µl reverse primer (5‘ GTGTCTCAAGATCTAGTTACGCCAAGC 3’ 10μM), 1 µl of extracted genomic tumor DNA (with a concentration between 50-100 ng/μl) and 10 μl nuclease-free water for a total volume of 25 μl per tumor. PCR1 was performed using the following conditions: Initial denaturation at 98°C for 2:30 min, followed by 22 cycles of denaturation 98°C -– 20 s, annealing 62°C -– 30 s, extension 72°C -– 30 s. PCR1 products for each tumor were individually column-purified with a GenElute™ PCR Clean-Up Kit (Sigma-Aldrich NA1020-1KT). For PCR2, 1 μl of cleaned up PCR1 was used as template along with 0.75 μl forward barcoded i5 primer (see Supplementary Information Table 1, 10 μM), 0.75 μl reverse barcoded i7 primer (see table, 10 μM), 10 μl nuclease free-water, along with 12.5 μl of KAPA HiFi HotStart ReadyMix for a total volume of 25 μl. Eight different i5 and i7 primers allowed for a total of 64 different combinations. PCR2 was performed under following conditions: Initial denaturation at 95°C for 3 min, followed by 32 cycles of denaturation 98°C -– 30 s, annealing 62°C – 30 s, extension 72°C – 30 s. PCR2 products for a maximum of 64 individually barcoded tumor amplifications were pooled and cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to manufacturer’s instructions before sequencing.


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 6


title: PP1-7_+Tet_B

value: Blood Stream Form Single Marker Cell line


title: OB_Participant_2_w0


title: PP1-7_-Tet_C


title: PP1-7_+Tet_A


title: OB_Participant_1_w0


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 3


title: BMSCs, AI-FGF9, Day4, Rep3

first: Mingmei

last: Chen

address: 197 Ruijin Road II, Building #17

institute: Shanghai Jiao Tong University

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1)
Expression analysis: In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: all.fpkm_anno text file includes raw counts and FPKM for each sample.

source_name: bone marrow

extract_protocol:
Total RNA was extracted from BMSCs using R0.RNA Reagent kit (Lot: AJ15RK01).
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: bone marrow

value: BMSCs

value: mesenchymal stem cell

value: wt

value: adipogenic induction


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 5

value: mouse epidermis


title: PP1-1_+Tet_C


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 4

value: DMBA/TPA carcinogenesis


title: BMSCs, AI-FGF9, Day4, Rep2


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 2

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: PP1-1_+Tet_B


title: BMSCs, AI-FGF9, Day4, Rep1


title: PP1-1_+Tet_A


title: PP1-7_-Tet_B


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 1


title: BMSCs, AI-Control, Day4, Rep3


title: PP1-7_-Tet_A


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 7, posterior back skin

data_processing:
library strategy: Amplicon sequencing of genomic DNA
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. The number of sgRNAs in each sample was counted by the count command from the MAGeCK package.
processed data files format and content: Count matrix of sgRNAs (represented by the gene symbol of their target gene). Gene symbols on rows, samples on columns. Additional sample information in 'bulk_sequencing_keratinocytes_and_immune_depletion_Info.txt'.
Assembly: mm10

extract_protocol:
P60 back skin was harvested with surgical scissors and placed dermis-facing up on a styrofoam tray with pins. Fat and subcutis were scraped off with a scalpel. Fat-free skin was then washed, dermis-side facing down in 1xPBS. Skin was then placed in the same orientation in 0.5% Trypsin-EDTA (10X, Gibco; 15400054) and incubated at 37°C on an orbital shaker for 25 (females) or 50 min (males). Using a glass microscopy slide, skin was secured to the bottom of the dish and scraped again with a scalpel until it started to break. Excess cold PBS with 2% chelexed FBS (FBS(-)) was added to neutralize trypsin. Cell suspension was strained on ice first through a 70 µm filter, washed with an additional 15 mL of cold 1X PBS with 2% FBS(-) and then filtered through a 40 µm filter. Cell suspension was spun down at 400 x g for 10 min. Genomic DNA was extracted with Qiagen DNEasy genomic DNA isolation kit.
The sgRNA region was  amplified in a nested PCR. In PCR1, we used 12.5 µl KAPA HiFi HotStart ReadyMix (Roche, 07958935001), 0.75 µl forward primer (5‘ CTTGTGGAAAGGACGAAACACCG 3’, 10μM), 0.75 µl reverse primer (5‘ GTGTCTCAAGATCTAGTTACGCCAAGC 3’ 10μM), 1 µl of extracted genomic DNA (with a concentration between 50-100 ng/μl) and 10 μl nuclease-free water for a total volume of 25 μl per tumor. PCR1 was performed using the following conditions: Initial denaturation at 98°C for 2:30 min, followed by 22 cycles of denaturation 98°C -– 20 s, annealing 62°C -– 30 s, extension 72°C -– 30 s. PCR1 products for each tumor were individually column-purified with a GenElute™ PCR Clean-Up Kit (Sigma-Aldrich NA1020-1KT). For PCR2, 1 μl of cleaned up PCR1 was used as template along with 0.75 μl forward barcoded i5 primer (see Supplementary Information Table 1, 10 μM), 0.75 μl reverse barcoded i7 primer (see table, 10 μM), 10 μl nuclease free-water, along with 12.5 μl of KAPA HiFi HotStart ReadyMix for a total volume of 25 μl. Eight different i5 and i7 primers allowed for a total of 64 different combinations. PCR2 was performed under following conditions: Initial denaturation at 95°C for 3 min, followed by 32 cycles of denaturation 98°C -– 30 s, annealing 62°C – 30 s, extension 72°C – 30 s. PCR2 products for a maximum of 64 individually barcoded tumor amplifications were pooled and cleaned up with Agencourt AMPure XP beads (Beckman Coulter, A63881) according to manufacturer’s instructions before sequencing.

value: 60 days post natal


title: BMSCs, AI-Control, Day4, Rep2


title: PP1-1_-Tet_B


title: BMSCs, OI-FGF9, Day4, Rep3

value: osteogenic induction


title: BMSCs, OI-FGF9, Day4, Rep2


title: BMSCs, AI-Control, Day4, Rep1


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 6, anterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 6, posterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 7, anterior back skin


title: BMSCs, OI-FGF9, Day4, Rep1


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 5, anterior back skin


title: PP1-1_-Tet_C


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 4, anterior back skin


title: BMSCs, OI-Control, Day4, Rep3


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch2, mouse 5, posterior back skin


title: BMSCs, OI-Control, Day4, Rep1


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 4, posterior back skin


title: BMSCs, OI-Control, Day4, Rep2


title: BMSCs, CM-FGF9, Day4, Rep3

value: culture medium


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 3, posterior back skin


title: BMSCs, CM-FGF9, Day4, Rep2


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 2, posterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 3, anterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 2, anterior back skin


title: OB_Participant_7_w0

value: Before metabolic surgery

value: Obese non diabetic


title: BMSCs, CM-Control, Day4, Rep2


title: BMSCs, CM-FGF9, Day4, Rep1


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 1, anterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion, IgG isotype control, batch1, mouse 1, posterior back skin


title: MMRF_2614

city: St. Louis

first: Jessica

last: Silva-Fisher

address: 425 Euclid

institute: Washington University in St. Louis

data_processing:
The assembled data was integrated with supplementary contigs, including the complete repeating unit of ribosomal DNA, cancer-related viruses, and data from the external RNA Control Consortium.
For gene and transcript models, Ensemble version 74 was used, along with additional annotations provided in the GTF file (https://github.com/tgen/MMRF_CoMMpass.git).
TopHat 2.0.11.Linux_x86_84 was used for generating the transcriptome and Salmon was utilized to quantify expression levels
Picard Tools suite, with the 'SAMtools faidx' function, was applied to create an index for the reference genome
For sequence alignment, Bowtie, Bowtie 2, and Salmon (p – 12 and type - Quasi), were used, followed by STAR 2.3.12
BAM files were subsequently generated using SAMtools v.1.19
Quality control checks on the RNA BAM files using Picard RNA metrics and BamTools Ig Counts
Assembly: GRCh37 reference genome (hs37d5 version)
Supplementary files format and content: Comma Separated Values text file with normalized counts for each sample

source_name: Bone marrow aspirates

extract_protocol:
RNA isolation
TSMRU - Illumina TruSeq mRNA Unstranded Library Prep

value: Bone marrow aspirates

tag: experimental group

value: Responders


title: BMSCs, CM-Control, Day4, Rep1


title: MMRF_2611


title: MMRF_2597


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 6, posterior back skin


title: MMRF_2564


title: MMRF_2570


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 6, anterior back skin


title: MMRF_2559


title: MMRF_2532


title: JG024 24min rep2

city: Berlin

first: Magdalena

last: Bürkle

address: Chritéplatz 1

institute: Charité

data_processing:
cDNA reads were imported into CLC Genomics Workbench v 22.0.2 (Qiagen) and analysed using standard parameters. 3'adaptor- and quality trimming was performed using the trim reads command with the following settings: 3´ trim: AGATCGGAAGAGCACACGTCTGAACTCCAGTCA; Trim quality scores limit 0.05, Trim ambiguous nucleotides
The trimmed reads were checked for quality and mapped to theP. aeruginosa, JG024 and JG005 reference genomes (NCBI accession numbers:AE004091, NC_017674, PP712940)using the following settings: Mismatch cost = 2, Insertion cost = 3, Deletion cost = 3, Length fraction = 0.8, Similarity fraction = 0.8, Global alignment = Yes, Strand specific = Forward, Library type= Bulk, Maximum number of hits for a read = 10, expression value= TPM.
Reads mapping to CDS were counted and fold enrichment in phage-infected samples over untreated control samples was calculated using the CLC "Differential expression for RNA-seq" tool
Genes with a fold change ≥ 1.5 and an FDR-adjusted p-value ≤ 0.05 were defined as differentially expressed.
Assembly: NCBI accession numbers:PAO1 - AE004091, JG024 - NC_017674, JG005 - PP712940)
Supplementary files format and content: Excel sheet Fold change, and FDR p-value, TPM and RPKM

organism: Pseudomonas aeruginosa PAO1

source_name: bacterial + phage

growth_protocol: PAO1 was grown over night in LB medium (Roth) at 37 °C in shaking conditions.

extract_protocol:
RNA was extracted using hot-phenol method and digested with TURBO DNase (Thermo Fisher Scientific). Ribosomal RNA was depleted using rRNA-specific biotinylated probes (Culviner et al., 2020, https://doi.org/10 .1128/mBio.00010-20.)
RNA libraries for RNA-Seq were prepared with NEBNext® Small RNA Library Prep Set for Illumina (NEB; #E7300L).
Illumina NextSeq1000 system in single-read mode for 100 cycles

treatment_protocol: PAO1-overnight culture was diluted to OD600 of 0.1 and grown to 0.3 before infection. Phage infection was performed at phage-to-bacterium ratio of 5:1

value: bacterial + phage

value: wild-type

value: JG024 24 min


title: JG024 24min rep1


title: MMRF_2516


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 5, anterior back skin

source_name: mouse epidermis


title: JG005+JG024 24min rep2


title: MMRF_2501


title: MMRF_2498


title: JG005+JG024 24min rep1


title: BMSCs, CM-Control, Day4, Rep3

value: bone marrow

value: BMSCs


title: MMRF_2488


title: untreated 24min rep2

source_name: bacterial

value: bacterial

value: uninfected 24 min


title: MMRF_2464


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 4, posterior back skin

value: mouse epidermis


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 4, anterior back skin


title: MMRF_2468


title: MMRF_2459


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 3, posterior back skin


title: MMRF_2440


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 3, anterior back skin


title: MMRF_2429


title: MMRF_2352


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch2, mouse 5, posterior back skin


title: MMRF_2273


title: JG024 8min II rep1

value: JG024 8 min


title: MMRF_2265


title: JG005+JG024 8min rep2


title: MMRF_2224


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 2, anterior back skin

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: MMRF_2213


title: JG005+JG024 8min rep1


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 1, posterior back skin

value: 60 days post natal


title: untreated 24min rep1


title: Amplicon sequencing of genomic DNA, DMBA/TPA-induced tumors, replicate 7

value: DMBA/TPA carcinogenesis

value: 144 days post natal


title: MMRF_2211


title: SG_rep3_RNAseq

value: fruit

value: wild type

value: no

value: 35 days after anthesis


title: untreated 8min rep2

value: uninfected 8 min


title: JG024 8min rep2

value: bacterial + phage

value: wild-type


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 1, anterior back skin


title: untreated 8min rep1


title: MMRF_2074

value: Bone marrow aspirates

value: Responders


title: MMRF_2080


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD4+ and CD8+ T cells, batch1, mouse 2, posterior back skin


title: MMRF_2056


title: MMRF_2043


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 7, anterior back skin


title: MMRF_2232


title: non-SjD Sicca, Patient6, scRNAseq

city: Birmingham

first: Jason

middle: Dale

last: Turner

address: Queen Elizabeth Hospital

department: Rheumatology research group

institute: University of Birmingham

description:
10x Genomics
SICCA_H

data_processing:
Cellranger v3.0.2 used to generate count matricies and aggregate samples.
Assembly: hg38
Supplementary files format and content: Tab separated values and matrix files

source_name: Minor labial salivary gland

extract_protocol:
Minor salivary gland biopsies were taken surgically from the lip and frozen in 1mL of CryoStor® CS10 (StemCell Technologies) at −80°C. For preparation of single-cell suspension, firstly the frozen tissue sample in Cryotube were quickly thawed in water bath at 37°C and washed twice in pre-warmed 5%FBS RPMI media. The salivary gland biopsies were then enzymatically digested as previously described. Dead cells were removed using the EasySepTM Dead Cell Removal (Annexin V) kit from the digested samples following manufacturer’s instructions before proceeding for the scRNA sequencing using the 10x platform.
Library preparation and sequencing was completed by Oxford Genomics Centre. Cell counts in each sample were quantified using the Bio-Rad TC20. 10,000 cells per sample were used to generate libraries with the 10x Genomics v3 Single Cell 3’ kit before sequencing to a minimum depth of 50,000 reads per cell using the NovaSeq 6000.

value: Minor labial salivary gland

value: Female

value: All primary isolated cells

tag: rhoautoab

value: Negative


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 6, posterior back skin

first: Simona

last: Baghai Sain

address: Schanzenstrasse 44

institute: ETH Zurich

value: mouse epidermis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: MMRF_2005


title: non-SjD Sicca, Patient5, scRNAseq

description:
10x Genomics
SICCA_G

value: Male


title: MMRF_1927


title: non-SjD Sicca, Patient4, scRNAseq

description:
10x Genomics
SICCA_F


title: MMRF_1921


title: MMRF_2140


title: non-SjD Sicca, Patient3, scRNAseq

description:
10x Genomics
SICCA_D


title: MMRF_1918


title: MMRF_2091


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 7, posterior back skin

value: 60 days post natal


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 5, posterior back skin


title: MMRF_1911


title: non-SjD Sicca, Patient2, scRNAseq

description:
10x Genomics
SICCA_B


title: MMRF_1893


title: MMRF_2038


title: MMRF_1881


title: MMRF_1854


title: SjD, Patient7, scRNAseq

description:
10x Genomics
PSS_H

value: Positive


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 5, anterior back skin


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 4, anterior back skin


title: MMRF_1846


title: SjD, Patient6, scRNAseq

description:
10x Genomics
PSS_G


title: PP1-1_-Tet_A

value: Blood Stream Form Single Marker Cell line


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 3, posterior back skin


title: MMRF_1837


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 4, posterior back skin


title: MMRF_1839


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch2, mouse 6, anterior back skin


title: MMRF_1824


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 3, anterior back skin


title: SjD, Patient5, scRNAseq

description:
10x Genomics
PSS_F


title: MMRF_1792


title: MMRF_1766


title: MMRF_1750


title: MMRF_1786


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 2, posterior back skin


title: MMRF_1865


title: SjD, Patient3, scRNAseq

description:
10x Genomics
PSS_D


title: non-SjD Sicca, Patient1, scRNAseq

description:
10x Genomics
SICCA_A


title: SjD, Patient4, scRNAseq

description:
10x Genomics
PSS_E


title: MMRF_1690


title: MMRF_1665


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 2, anterior back skin


title: MMRF_1698


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 1, posterior back skin


title: MMRF_1652


title: MMRF_1805


title: MMRF_1624


title: SjD, Patient1, scRNAseq

description:
10x Genomics
PSS_A


title: MMRF_1686


title: SjD, Patient2, scRNAseq

description:
10x Genomics
PSS_B


title: MMRF_1630


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 24Hr, rep3

city: Indianapolis

first: Frank

middle: Charles

last: Dorsey

state: IN

address: Eli Lilly and Company

department: Department of Immunology and Biotechnology

institute: Eli Lilly and Company

data_processing:
Raw FastQ files were quality- and adapter-trimmed using cutadapt (cutadapt-1.9.1) and aligned using GSNAP (v2013-11-27) to build 37.p5 of the human genome.
Read counts were generated against exons annotated in NCBI gene models (NCBI h37.p13 annotation) using a custom Perl script, then summarized at the gene level as the log2 of mean exon reads and quantile-normalized using a custom R script.
Gene-level relative expression levels were estimated using log2 transformed mapped read counts for each exon associated with the gene and fitting a robust linear regression model of the form: log2(countsi,j) ~ Samplei + Exonj + ei,j using the rlm function in R. Sample-level estimates of relative gene expression were obtained from the least squares means estimate from the model fit. These estimates of relative gene expression were then normalized using a quantile normalization procedure.
Assembly: GRCh37.p5
Supplementary files format and content: tab-delimited .txt file contains log2 quantile normalized counts for each sample

growth_protocol: WT and IRG1 KO THP-1 cells were cultured in RPMI 1640 (RPMI; Gibco; A10491-01) with 1X βME and 10% Heat Inactivated Fetal Bovine Serum (HI FBS; Gibco; 10082-147) up to a confluency of 1.0 x 106 cells/mL.

extract_protocol:
RNA extracted using Qiagen Rneasy
Libraries were constructed using Roche KAPA HyperPrep with RiboErase mRNA Library Prep Kit

treatment_protocol: Prior to stimulation, cells were differentiated with PMA (100 nM) for 72 hr at a ratio of 800,000 cells/ 1 mL. WT and IRG1 KO THP-1 cells were stimulated with vehicle control or LPS (200 ng/mL) and IFN-γ (200 ng/mL) for 6, 12, and 24 hr.

value: IRG1 KO

value: LPS + IFNg


title: THP-1, IRG1 KO, Vehicle, 24Hr, rep3

value: Vehicle


title: Amplicon sequencing of genomic DNA, Immune cell depletion of CD115+ macrophages, batch1, mouse 1, anterior back skin

city: Basel


title: MMRF_1621


title: MMRF_1605


title: THP-1, WT, LPS&IFNg Stimulated, 24Hr, rep3

value: WT


title: MMRF_1589


title: MMRF_1577


title: THP-1, WT, Vehicle, 24Hr, rep3


title: MMRF_1572


title: DMBA/TPA-induced skin tumor Visium Spatial Transcriptomics, replicate 2 (A1_231204)

data_processing:
library strategy: Spatial Transcriptomics
The raw sequencing data comprising the BCL files were demultiplexed into FASTQ files using the Illumina bcl2fastq program v2.20 with default options allowing one mismatch of the sample barcode sequences. FASTQ files were processed using Space Ranger software (version 2.0.1, 10x Genomics). Reads were aligned with the ‘spaceranger count’ pipeline to the pre-built mouse reference genome provided by 10x Genomics version 2020-A (comprising the STAR-indexed mm10 mouse genome and the GTF gene annotation from GENCODE version M23 (Ensembl 98)), and the probe set reference CSV file (Visium Mouse Transcriptome Probe Set v1.0) was provided for filtering of valid genes. The resulting filtered count matrix of features (i.e. genes) per spot barcodes were employed for the downstream analysis.
genome build/assembly: mm10
processed data files format and content: *_barcodes.tsv.gz:  list of spatial barcodes; *_features.tsv.gz:  list of gene IDs; *_matrix.mtx.gz:  gene-barcode expression count data in Matrix Market Exchange Format; *_aligned_fiducials.jpg:  aligned fiducials of the tissue image; *_detected_tissue_image.jpg:  image of tissue and spots; *_scalefactors_json.json:  scalefactors in JSON format; *_tissue_hires_image.png:  hi-res image of tissue; *_tissue_lowres_image.png:  low-res image of tissue; *_tissue_positions_list.csv.gz:  list of spatial barcodes and the coordinates specifying spots
Assembly: mm10

extract_protocol:
A microarray of fresh-frozen DMBA/TPA-induced squamous cell carcinoma samples, surgically removed from mouse back skin, was cryo-sectioned with a 10µm thickness (Leica, CM3050S) and placed on the capture area of a spatial gene expression slide (10x Genomics, 1000188), resulting in 4 different tumors on a single capture area. Samples were stored in -80°C before processing.
The workflow of Mirzazadeh et al. (2023) for RNA-Rescue Spatial Transcriptomics (RRST) was followed to overcome low RNA integrity number (RIN) score. The samples were fixed with 4% PFA and hematoxylin and eosin (H&E) staining was performed. The spatial libraries were then generated from the probe hybridization step (10x Genomics, 1000365) according to Visium Spatial Gene Expression Reagent Kits for FFPE (10x Genomics, User Guide CG000407 Rev D, 1000361). The resulting libraries were sequenced by the Genomics Facility Basel. The sequencing was performed in a paired-end manner with dual indexing (10x Genomics, 1000251) on a NovaSeq 6000 (Illumina) with a SP flow cell (51bp read length).

value: DMBA/TPA carcinogenesis

value: 144 days post natal


title: MMRF_1522

value: Bone marrow aspirates

value: Responders


title: MMRF_1520


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 12Hr, rep3


title: Re_24h IP rep2

city: Shenyang

first: li

last: bingwu

address: shenhe

institute: Shenyang Pharmaceutical University

data_processing:
The trim galore tool was used to remove splice and quality control reads, the bbduk tool was used to remove rRNA-derived reads, and the hisat2 tool was used to align the filtered reads to the mouse GRCm39 genome. PCR replicates were removed using the samtools tool. For the sequenced files after alignment, exomepeak2 was used for the callpeak of the m6A peak.
Assembly: GRCm39
Supplementary files format and content: bed format file, the callpeak result of the exomepeak2 tool
Library strategy: MeRIP-seq

source_name: cerebral cortical

extract_protocol:
Total RNA was isolated from cerebral cortical peri-infarct tissue of sham, MCAO/R-0h, MCAO/R-6h and MCAO/R-24h mice and extracted with TRIzol reagent (TaKaRa) according to the manufacturer's instructions. 10μg total RNA was incubated with 5μl DNase I at 37°C for 20 minutes to remove DNA contamination. 5 µg of total RNA was used for digestion and the total RNA was chemically digested into fragments of approximately 200nt length. Approximately 1/10 of the fragmented RNA was isolated as an input control for further RNA-Seq. The remaining fragmented RNA was mixed with 3.5 µg of m6A antibody (Millipore) magnetic beads pre-mixed in IP buffer [50mM NaCl, 10mM Tris-HCl, pH7.5, 0.1%IGEPAL CA-630] at 4°C overnight. The eluted RNA was precipitated with 75% ethanol.
PCR primers HT (Indexing Primer Set HT for illumina® V2-96-Takara) were used to transform the eluted fragment containing m6A (IP) and the untreated input control fragment into the final cDNA library according to the stark-specific library preparation. Average insert size of paired-end libraries was ∼150 bp.

value: cerebral cortical

tag: time point

value: ischemia-reperfusion


title: MMRF_1424


title: MMRF_1454


title: Re_24h input rep2


title: Re_24h IP rep1


title: THP-1, WT, LPS&IFNg Stimulated, 12Hr, rep3


title: Re_24h input rep1


title: MMRF_1407


title: DMBA/TPA-induced skin tumor Visium Spatial Transcriptomics, replicate 4 (C1_231204)


title: MMRF_1383


title: WT,treated,48h,2

city: Nanchang

first: shaochun

last: Liu

address: Jiaoqiao town

institute: Jiangxi Agricultural University

data_processing:
Fastp( version 0.19.7 ) was used to quality control the raw data to obtain clean reads
Assembly: the indica reference genome (Oryza_indica.ASM465v1.dna.toplevel. fa),the  Japonica reference genome(Oryza sativa Japonica IRGSP-1.0)
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: leaf

extract_protocol:
Total RNA was isolated according to the protocol of Trizol Reagent kit and purification (Invitrogen)
The experimental samples were constructed and sequenced by cDNA library of Beijing Novogene using Novaseq 6000 platform.

value: leaf

value: MESOPHYLL cell

value: Non knockdown

value: 48h with Guy11


title: WT,treated,48h,3


title: THP-1, WT, Vehicle, 12Hr, rep3


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 6Hr, rep3


title: MMRF_1352


title: Re_6h IP rep1


title: Re_6h IP rep2


title: DMBA/TPA-induced skin tumor Visium Spatial Transcriptomics, replicate 3 (B1_231204)

value: mouse epidermis

value: JAX #026179, CD1 wildtype x Tg(B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J


title: MMRF_1304


title: THP-1, IRG1 KO, Vehicle, 6Hr, rep3


title: WT,treated,48h,1


title: WT,treated,36h,3

value: 36h with Guy11


title: Re_6h input rep2


title: MMRF_1274


title: THP-1, IRG1 KO, Vehicle, 12Hr, rep3

value: IRG1 KO


title: THP-1, WT, LPS&IFNg Stimulated, 6Hr, rep3

value: LPS + IFNg


title: WT,treated,36h,2


title: Re_6h input rep1


title: MMRF_1269


title: MG_rep2_RNAseq

value: fruit

value: wild type

value: no

value: 42 days after anthesis


title: THP-1, WT, Vehicle, 6Hr, rep3

value: WT

value: Vehicle


title: MMRF_1251

value: Bone marrow aspirates

value: Responders


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 24Hr, rep2


title: WT,treated,36h,1

value: leaf


title: Re_0h IP rep1

value: cerebral cortical

value: ischemia-reperfusion


title: WT,treated,24h,3

value: MESOPHYLL cell

value: Non knockdown

value: 24h with Guy11


title: MMRF_1185


title: MMRF_1153


title: THP-1, WT, LPS&IFNg Stimulated, 24Hr, rep2


title: THP-1, IRG1 KO, Vehicle, 24Hr, rep2


title: WT,treated,24h,2


title: WT,treated,12h,3

value: 12h with Guy11


title: Re_0h input rep1


title: MMRF_1086


title: THP-1, WT, Vehicle, 24Hr, rep2


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 12Hr, rep2

value: IRG1 KO


title: MMRF_1077


title: sham IP rep1

value: sham


title: MMRF_1048


title: Re_0h IP rep2


title: THP-1, IRG1 KO, Vehicle, 12Hr, rep2


title: shami input rep2


title: WT,treated,12h,1


title: THP-1, WT, LPS&IFNg Stimulated, 12Hr, rep2

value: LPS + IFNg


title: sham input rep1


title: WT,untreated,0h,3

value: 0h with Guy11


title: WT,treated,24h,1


title: sham IP rep2


title: MMRF_2541

value: Non - Responders


title: MMRF_2548


title: KO P14 run 2 mouse 3

city: Grand Rapids

first: Russell

last: Jones

state: MI

address: 333 Bostwick Ave NE

department: Department of Metabolism and Nutritional Programming

institute: Van Andel Insitute

description:
KO8880
raw_counts.txt

data_processing:
Adaptor sequences and low-quality reads were trimmed using Trim Galore (v0.6.0; Martin, 2011). Trimmed reads were aligned to the mm10 reference genome using STAR (v2.7.8; Dobin et al., 2013) with --quantMode GeneCounts.
Assembly: mm10
Supplementary files format and content: Counts per million (CPM) of each sample processed using edgeR (with low expressed genes removed)

molecule: nuclear RNA

source_name: Spleen

extract_protocol:
Total RNA was isolated from the cells
mRNA was captured using polyA, and stranded libraries were constructed.

treatment_protocol: mice were infected with 2E5 pfu LCMV Armstrong and adoptively transferred antigen specific cells were isolated by flow cytometry 7 days later

value: Spleen

value: KEAP1 KO

tag: infection

value: LCMV Armstrong

value: day 7 post infection


title: MMRF_2531

value: Bone marrow aspirates


title: WT,treated,12h,2

value: leaf

tag: cell type


title: WT,untreated,0h,1

tag: genotype


title: THP-1, IRG1 KO, Vehicle, 6Hr, rep2

value: Vehicle


title: KO P14 run 2 mouse 1

description:
KO8878
raw_counts.txt

tag: tissue


title: KO P14 run 2 mouse 2

description:
KO8879
raw_counts.txt


title: THP-1, WT, LPS&IFNg Stimulated, 6Hr, rep2

value: WT

tag: treatment


title: KO P14 run 1 mouse 2

description:
KO3
raw_counts.txt


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 6Hr, rep2


title: THP-1, WT, Vehicle, 12Hr, rep2


title: MMRF_2313


title: MMRF_2595


title: KO P14 run 1 mouse 1

description:
KO1
raw_counts.txt


title: wd-1,treated,48h,1

value: MESOPHYLL cell

value: knockdown

value: 48h with Guy11


title: THP-1, WT, Vehicle, 6Hr, rep2


title: wd-1,treated,48h,2


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 24Hr, rep1


title: MMRF_2286


title: WT P14 run 2 mouse 3

description:
WT9035
raw_counts.txt


title: MMRF_2253


title: wd-1,treated,36h,3

value: 36h with Guy11


title: WT,untreated,0h,2

value: Non knockdown


title: THP-1, IRG1 KO, Vehicle, 24Hr, rep1

value: IRG1 KO


title: MMRF_2438


title: WT P14 run 2 mouse 2

description:
WT9034
raw_counts.txt


title: wd-1,treated,36h,2


title: MMRF_2093


title: THP-1, WT, LPS&IFNg Stimulated, 24Hr, rep1

value: LPS + IFNg


title: WT P14 run 2 mouse 1

description:
WT9024
raw_counts.txt


title: wd-1,treated,36h,1


title: MMRF_2054


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 12Hr, rep1


title: WT P14 run 1 mouse 2

description:
WT2
raw_counts.txt


title: WT P14 run 1 mouse 1

description:
WT1
raw_counts.txt


title: wd-1,treated,24h,2

value: 24h with Guy11


title: THP-1, IRG1 KO, Vehicle, 12Hr, rep1


title: MMRF_1965

value: Non - Responders


title: EAE CNS WT

city: INDIANAPOLIS

first: Nada

middle: S

last: Alakhras

state: Indiana

address: 635 Barnhill Dr. Bldg MS218 VanNuys Med Sci

department: Immunology & Microbiology

institute: Indiana university school of medicine

description: 10x Genomics

data_processing:
CellRanger 7.0.0 (http://support.10xgenomics.com/) was utilized to process the raw sequence data generated. Briefly, CellRanger used bcl2fastq (https://support.illumina.com/) to demultiplex raw base sequence calls generated from the sequencer into sample-specific FASTQ files. The FASTQ files were then aligned to the mouse reference genome mm10 with RNAseq aligner STAR. The aligned reads were traced back to individual cells and the gene expression level of individual genes were quantified based on the number of UMIs (unique molecular indices) detected in each cell. The filtered feature-cell barcode matrices generated by CellRanger were used for further analysis.
Quality control (QC) process, graph-based clustering, and differentially expressed gene analyses of the scRNA-seq were performed using Seurat packages in R (version 4.3.0). QC criteria was applied, only gene expressed in 3 or more cells were preserved, doublet cells with less than 200 unique genes and more than 4000 genes were discarded, and cells > 10 % mitochondrial counts were filtered.
Data were normalized by using Seurat “LogNormalize” function, which applies global-scaling normalization method by dividing genes expression for each cell by total number of transcripts multiplied by median of unique molecular identifier (UMI) counts
Assembly: mm10

source_name: CNS

extract_protocol:
mononuclear cells were extracted by Percoll gradient and FACS sorted for MHCII+CD11c+ cells
Chromium™ Single Cell 3’ Library & Gel Bead Kit V3, 4 rxns PN-120267, Chromium™ Single Cell A Chip Kit, 16 rxns PN-1000009, Chromium™ i7 Multiplex Kit, 96 rxns PN-120262
28 bp of cell barcode and UMI sequences and 91 bp RNA reads were generated with Illumina NovaSeq 6000 at CMG of Indiana University School of Medicine.

treatment_protocol: dose of MOG peptide+CFA and PTX

value: CNS

value: lekocytes

tag: strain

value: EAE immunized


title: MMRF_1949


title: wd-1,treated,24h,1


title: THP-1, WT, LPS&IFNg Stimulated, 12Hr, rep1


title: THP-1, WT, Vehicle, 24Hr, rep1


title: wd-1,treated,24h,3


title: EAE CNS CKO

description: 10x Genomics


title: wd-1,treated,12h,3

value: 12h with Guy11


title: THP-1, WT, Vehicle, 12Hr, rep1


title: MMRF_1935

value: Bone marrow aspirates


title: MMRF_1928


title: THP-1, IRG1 KO, LPS&IFNg Stimulated, 6Hr, rep1


title: wd-1,treated,12h,2

value: leaf


title: MMRF_1974


title: wd-1,treated,12h,1


title: 4Cseq_mG900_WT_Th2

city: Chiba-shi

first: Arifumi

last: Iwata

state: Chiba

address: 1-8-1 Inohana, Chuou-ku

department: Department of Allergy and Clinical Immunology

country: Japan

institute: Chiba University

data_processing:
library strategy: 4C-seq
4C-seq data were analyzed and visualized using w4Cseq.
Significant interacting regions were detected with the following parameters, size_inter: 400, size_intra: 50, window_intra:3000, and false discovery rate: 0.05
Assembly: mm10
Supplementary files format and content: bedfile, significant interacting regions

source_name: T cell

growth_protocol: Naïve CD4+ T cells were isolated from lymph nodes and spleen using an EasySep Mouse Naïve CD4+ T Cell Isolation Kit. Naïve CD4+ T cells were stimulated with plate-bound anti-CD3ε and soluble anti-CD28 under Th0 conditions (no antibody, no cytokine), Th1 conditions (IL-12, anti-IL-4), and Th2 conditions (IL-4, anti-IFN-γ) for 3 days.

extract_protocol:
Cells were crosslinked with 1% formaldehyde at room temperature for 10 min.
Cross-linked DNA was digested with NlaIII then ligated using T4 DNA ligase followed by de-crosslink. DNA fragments were subjected to a second digestion by DpnII and circular ligation with T4 DNA ligase. Circular DNA were subjected to PCR reaction using inverse primers containing adaptors and indexes. 4C-seq libraries were sequenced on a NextSeq.

value: T cell

value: Th2 cells

value: Wild type

value: no treatment

tag: bait


title: wd-1,untreated,0h,3

value: MESOPHYLL cell

value: knockdown

value: 0h with Guy11


title: MMRF_1891


title: THP-1, IRG1 KO, Vehicle, 6Hr, rep1

value: IRG1 KO

value: Vehicle


title: 4Cseq_mG900_WT_Naive

value: Naive CD4 T cells


title: MMRF_1889

value: Non - Responders


title: THP-1, WT, LPS&IFNg Stimulated, 6Hr, rep1

value: WT

value: LPS + IFNg


title: 4Cseq_mG900_WT_Th0

value: Th0 cells


title: Re_0h input rep2

value: cerebral cortical

value: ischemia-reperfusion


title: wd-1,untreated,0h,2

value: leaf


title: 4Cseq_Gata3-TSS_mG900KO_Th2

value: T cell


title: THP-1, WT, Vehicle, 6Hr, rep1


title: MMRF_1876

value: Bone marrow aspirates


title: 4Cseq_Gata3-TSS_WT_Th2

value: Th2 cells

value: Wild type


title: wd-1,untreated,0h,1

value: MESOPHYLL cell


title: iPSC-NSCs-Exosome, Rep3

city: nanjing

first: Jie

state: Jiang Su

address: 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

data_processing:
first of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice.
Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated.
The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries.
At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RPM amd Count values  for each sample

source_name: Induced pluripotent stem cells-derived neural stem cells

growth_protocol: iPSC-NSCs were cultured in NeuroEasy recovery and maintaining medium (Cellapy Biotechnology Co. Beijing, China) under 5% CO2 at 37°C

extract_protocol:
A total amount of 2.5 ng RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNextR UltraTM small RNA Sample Library Prep Kit for Illumina R(NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
first of all, ligated the 3′ SR Adaptor. Mixed 3′ SR Adaptor for Illumina, RNA and Nuclease-Free Water, mixture system after incubation for 2 minutes at 70 degrees in a preheated thermal cycler. Tube was transfer to ice.
Then, add 3′ Ligation Reaction Buffer (2X) and 3′ Ligation Enzyme Mix ligate the 3′ SR Adaptor. Incubated for 1 hour at 25°C in a thermal cycler. To prevent adaptor-dimer formation, the SR RT Primer hybridizes to the excess of 3′ SR Adaptor (that remains free after the 3′ ligation reaction) and transforms the single stranded DNA adaptor into a double-stranded DNA molecule. dsDNAs are not substrates for ligation mediated.
The second, ligated the 5′ SR Adaptor. Then, reverse transcription synthetic first chain. Last, PCR amplification and Size Selection. PAGE gel was used to electrophoresis fragment screening purposes, rubber cutting recycling as the pieces get small RNA libraries.
At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: iPSC-NSCs-Exosome


title: MMRF_1842


title: 4Cseq_Gata3-TSS_WT_Th0

value: no treatment


title: primary cortical neurons, WT, H3K27ac

data_processing:
Fastq files were aligned by Bowtie2
bam files were generated using SAMtools
NGSplot was used to generate metaplots
tdf files were generated using IGVtools
Assembly: mm10
Supplementary files format and content: tdf files generated by IGVtools from bam files aligned to bowtie2
Library strategy: CUT&TAG

extract_protocol:
At 12DIV, primary cortical neurons were collected in wash buffer (Kaya-Okur et al. 2019) and CUT&Tag was performed with anti-H2BE antibody (Millipore ABE1384)
Transposition reaction mix from Nextera Library Prep kit was used (Tagment DNA Enzyme 1 and Tagment DNA Buffer)
Nextera primer sets with NEBNext Master Mix was used to generate libraries with AMPure beads used for cleanup

tag: age

value: primary cortical neurons


title: MMRF_1393

value: Responders


title: primary cortical neurons, H2BE-KO


title: MMRF_1823


title: iPSC-NSCs cells, Rep3

value: Induced pluripotent stem cells-derived neural stem cells

value: iPSC-NSCs cells


title: iPSC-NSCs-Exosome, Rep1

value: WT


title: Adipose tissue,replicate2, scRNA_seq

city: chengdu

first: lu

last: lu

state: sichuan

address: 211 Huimin Road, Wenjiang District

department: animal science and technology

institute: Sichuan Agricultural University

description: 10x Genomics

data_processing:
We used the Singleron GEXSCOPE® Single Nucleus RNA Library Kit for sequencing the obtained samples, and all experimental protocols were strictly carried out in accordance with the GEXSCOPE庐 Single Nucleus Transcriptome Library Kit manual provided by Singleron.
Assembly: GEXSCOPE® Single Nucleus RNA Library Kit
Supplementary files format and content: Tab-separated values files and matrix files

source_name: VAT

extract_protocol: The single-nucleus suspension was adjusted to a concentration of 3-4 × 105 nuclei/mL in PBS. This suspension was loaded onto a microfluidic chip, utilizing the GEXSCOPE® Single NucleusRNA-seq Kit (Singleron Biotechnologies). Following the manufacturer’s guidelines (Singleron Biotechnologies), we proceeded to construct the snRNA-seq libraries. These libraries were sequenced on an Illumina HiSeq X10 platform, using 150 bp paired-end reads.

value: VAT

value: 2 months

value: Adipocytes


title: MMRF_1797

value: Non - Responders


title: MMRF_1808


title: primary cortical neurons, WT

first: Emily

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

source_name: primary cortical neurons


title: MMRF_1771


title: primary cortical neurons, KO+I39V biol rep 2

data_processing:
Fastq files were aligned by Bowtie2
bam files from the three sequencing runs were merged for each biological replicate, all biological replicates from the same group were merged, and 80 million reads were subset for each group SAMTools for downstream analysis
NGSplot was used to generate metaplots
deepTools was used to generate bigwig files
Assembly: mm10
Supplementary files format and content: bigwig files generated by deepTools from bam files aligned to bowtie2

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


title: MMRF_1810


title: iPSC-NSCs cells, Rep1


title: 4Cseq_Gata3-TSS_WT_Naive

value: Naive CD4 T cells


title: SUM159_attached_doxorubicin_rep2

first: Spyros

last: Foutadakis

address: Soranou

country: Greece

institute: Biomedical Research Foundation Academy of Athens

data_processing:
The quality of the sequencing reads was assessed with FastQC
Reads were mapped to the human genome with HISAT2
Gene counts were calculated with HTSeq count
Bigwig files were prepared with the bamcoverage command from Deeptools
Assembly: hg19
Supplementary files format and content: bigwig files
Supplementary files format and content: text files containg gene counts for each replicate

growth_protocol: SUM159 cells were cultured in Ham's medium  supplemented with 5% fetal bovine serum, 1% penicillin/streptomycin, 5 μg/mL insulin and 1 μg/mL hydrocortisone in a humidified atmosphere of 5% CO2 at 37 °C.

extract_protocol:
Cells were collected and lysed with TRI reagent to isolate total RNA
The NEBNext Ultra II Directional RNA Library Prep Kit was used to prepare libraries following the manual

treatment_protocol: SUM159 attached cells were made resistant to doxorubicin by long term treatment with escalating doses

value: Wt

value: doxorubicin


title: Adipose tissue,replicate1,scRNA_seq

description: 10x Genomics


title: iPSC-NSCs-Exosome, Rep2