title: CRISPRi_target_chr17-45873822_rep3

description:
column name: CRISPRi_target_chr17-45873822_rep3
7136.NC.0005_5


title: Cpa3Cre/+ day 7 AS-935775-LR-66850

status: Public on Apr 11 2023

type: SRA

city: Heidelberg

first: Robin

last: Thiele

address: Im Neuenheimer Feld 280

department: Immunology

country: Germany

institute: German Cancer Research Center

library_source: transcriptomic

data_processing:
reads were aligned via STAR aligner (default settings, v.2.5.2b)
and counted via FeatureCount (default settings, stranded library, subread/1.5.1)
Assembly: mm10 (Mus_musculus_GRCm38_102)
Supplementary files format and content: text delimeted file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: stomach

extract_protocol:
Total RNA was extracted from whole stomach (fat removed) according to the instructions of the PureLink RNA Mini kit (Invitrogen).
RNA libraries for RNA-seq were prepared using TruSeq Stranded RNA Kit (Illumina) following manufacturer's protocols.

tag: genotype

tag: tissue

value: stomach

tag: Sex

value: male

tag: treatment

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-28

tag: time

value: day 7

tag: ova(ag) delivery

value: 2-bottle test


title: Cpa3Cre/+ day 0 AS-935771-LR-66850

value: 2 mg alum + 25 ug ovalbumin i.p. on day 0 and 14

value: day 0

value: non


title: Cpa3Cre/+ day11 AS-935785-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25, 27, 29 and 32

value: oral gavage


title: Cpa3Cre/+ day 0 AS-935821-LR-66850

value: female


title: CRISPRi_target_chr17-45309260_rep8

city: Huntsville

first: J.

middle: Nicholas

last: Cochran

state: AL

address: 601 Genome Way

country: USA

institute: HudsonAlpha Institute for Biotechnology

description:
column name: CRISPRi_target_chr17-45309260_rep8
7136.NC.0005_4

data_processing:
UMIs extracted with UMI-tools extract with the regex extraction method.
Reads were trimmed with bbduk and aligned to hg38 with STAR using the Lexogen recommended parameters.
Bams were deduplicated by UMI and mapping coordinate using UMI-tools dedup.
Counts were generated with htseq-count using the intersection-nonempty method. The count matrix was normalized to counts per million (CPM).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: For iCell Glutas, cells were maintained according to FujiFilm Cellular Dynamics recommendations. For XCL4 and BC1, NPCs were maintained in 2:1 DMEM:Ham's F12 supplemented with hFGF, hEGF, and heparin. NPCs were differentiated following the BrainPhys protocol from Bardy, et al. (doi:10.1073/pnas.1504393112)

extract_protocol:
RNA isolation was performed using the Norgen Total RNA isolation and RNase-Free DNase I kits (Norgen 17250 and 25720, respectively) and quantified using the Qubit RNA HS Assay Kit (Thermo Q32855).
Libraries were prepared using the QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina and UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1) from Lexogen (015.96 and 081.96, respectively). Libraries were quantified using the Qubit DNA HS Assay Kit (Thermo Q32854) and visualized with the BioAnalyzer High Sensitivity DNA Analysis kit (Agilent 5067-4626) and 2100 BioAnalyzer Instrument (Agilent).

tag: cell line

tag: cell type

value: Neurons


title: CRISPRi_target_chr17-45309260_rep7

description:
column name: CRISPRi_target_chr17-45309260_rep7
7136.NC.0005_3


title: Cpa3Cre/+ naive AS-935851-LR-66850

value: untreated

value: naive


title: CRISPRi_target_chr17-44988418_rep8

description:
column name: CRISPRi_target_chr17-44988418_rep8
7136.NC.0005_14


title: Cpa3Cre/+ naive AS-935795-LR-66850


title: Cpa3Cre/+ naive AS-935769-LR-66850


title: WT (Cpa3+/+) day16 AS-935863-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 26, 28, 30, 32, 34 and 37


title: CRISPRi_target_chr17-45787210_rep4

description:
column name: CRISPRi_target_chr17-45787210_rep4
7136.NC.0004_48


title: CRISPRi_target-GFP_rep8

description:
column name: CRISPRi_target-GFP_rep8
7136.NC.0004_46


title: WT (Cpa3+/+) day16 AS-935789-LR-66850


title: WT (Cpa3+/+) day16 AS-935815-LR-66850


title: CRISPRi_target_chr17-44988418_rep7

description:
column name: CRISPRi_target_chr17-44988418_rep7
7136.NC.0004_41


title: CRISPRi_target_chr17-45326805_rep3

description:
column name: CRISPRi_target_chr17-45326805_rep3
7136.NC.0004_47


title: CRISPRi_target_chr17-45309544_rep2

description:
column name: CRISPRi_target_chr17-45309544_rep2
7136.NC.0004_45


title: WT (Cpa3+/+) day11 AS-935809-LR-66850


title: CRISPRi_target_chr17-45949229_rep3

description:
column name: CRISPRi_target_chr17-45949229_rep3
7136.NC.0004_87


title: CRISPRi_target_chr17-45977337_rep2

description:
column name: CRISPRi_target_chr17-45977337_rep2
7136.NC.0005_1


title: CRISPRi_target_chr17-45942497_rep3

description:
column name: CRISPRi_target_chr17-45942497_rep3
7136.NC.0004_96


title: WT (Cpa3+/+) day 7 AS-935825-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25 and 28


title: WT (Cpa3+/+) day 7 AS-935835-LR-66850


title: CRISPRi_target_chr17-45787210_rep3

description:
column name: CRISPRi_target_chr17-45787210_rep3
7136.NC.0004_85


title: CRISPRi_target_chr17-44988418_rep6

description:
column name: CRISPRi_target_chr17-44988418_rep6
7136.NC.0004_32


title: WT (Cpa3+/+) day16 AS-935831-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-37


title: WT (Cpa3+/+) day16 AS-935813-LR-66850

value: stomach


title: WT (Cpa3+/+) day16 AS-935861-LR-66850


title: CRISPRi_target_chr17-45787210_rep2

description:
column name: CRISPRi_target_chr17-45787210_rep2
7136.NC.0004_39


title: CRISPRi_target_chr17-45321056_rep3

description:
column name: CRISPRi_target_chr17-45321056_rep3
7136.NC.0004_29


title: CRISPRi_target_chr17-45219542_rep4

description:
column name: CRISPRi_target_chr17-45219542_rep4
7136.NC.0005_2


title: WT (Cpa3+/+) day16 AS-935787-LR-66850

value: male


title: WT (Cpa3+/+) day11 AS-935857-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-32


title: CRISPRi_target_chr17-44988418_rep5

description:
column name: CRISPRi_target_chr17-44988418_rep5
7136.NC.0004_28


title: CRISPRi_target_chr17-45873822_rep2

description:
column name: CRISPRi_target_chr17-45873822_rep2
7136.NC.0004_84


title: CRISPRi_target_chr17-45309260_rep6

description:
column name: CRISPRi_target_chr17-45309260_rep6
7136.NC.0004_66


title: WT (Cpa3+/+) day11 AS-935837-LR-66850


title: WT (Cpa3+/+) day11 AS-935781-LR-66850


title: WT (Cpa3+/+) day11 AS-935807-LR-66850


title: WT (Cpa3+/+) day 7 AS-935855-LR-66850

value: 2mg alum + 25 ug ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-28

value: day 7


title: CRISPRi_target_chr17-45813425_rep2

description:
column name: CRISPRi_target_chr17-45813425_rep2
7136.NC.0004_86


title: CRISPRi_target-GFP_rep7

description:
column name: CRISPRi_target-GFP_rep7
7136.NC.0004_82


title: CRISPRi_target_chr17-45309260_rep5

description:
column name: CRISPRi_target_chr17-45309260_rep5
7136.NC.0004_65


title: WT (Cpa3+/+) day11 AS-935779-LR-66850

value: 2-bottle test


title: CRISPRi_target_chr17-45977337_rep1

description:
column name: CRISPRi_target_chr17-45977337_rep1
7136.NC.0004_81


title: CRISPRi_target_chr17-45219542_rep3

description:
column name: CRISPRi_target_chr17-45219542_rep3
7136.NC.0004_83


title: WT (Cpa3+/+) day 7 AS-935823-LR-66850


title: CRISPRi_target_chr17-45309544_rep1

description:
column name: CRISPRi_target_chr17-45309544_rep1
7136.NC.0004_38


title: WT (Cpa3+/+) day 7 AS-935773-LR-66850


title: WT (Cpa3+/+) day 7 AS-935799-LR-66850


title: CRISPRi_target_chr17-45949229_rep2

description:
column name: CRISPRi_target_chr17-45949229_rep2
7136.NC.0004_80


title: WT (Cpa3+/+) day 0 AS-935853-LR-66850

value: 2 mg alum + 25 ug ovalbumin i.p. on day 0 and 14

value: day 0


title: WT (Cpa3+/+) day 7 AS-935801-LR-66850


title: CRISPRi_target_chr17-45949229_rep1

description:
column name: CRISPRi_target_chr17-45949229_rep1
7136.NC.0004_44


title: CRISPRi_target_chr17-45942497_rep1

description:
column name: CRISPRi_target_chr17-45942497_rep1
7136.NC.0004_40


title: CRISPRi_target_chr17-45813425_rep1

description:
column name: CRISPRi_target_chr17-45813425_rep1
7136.NC.0004_31


title: CRISPRi_target_chr17-45942497_rep2

description:
column name: CRISPRi_target_chr17-45942497_rep2
7136.NC.0004_64


title: WT (Cpa3+/+) day 0 AS-935797-LR-66850

value: non


title: WT (Cpa3+/+) day 0 AS-935819-LR-66850


title: WT (Cpa3+/+) naive AS-935849-LR-66850


title: CRISPRi_target_chr17-45787210_rep1

description:
column name: CRISPRi_target_chr17-45787210_rep1
7136.NC.0004_30


title: WT (Cpa3+/+) naive AS-935793-LR-66850


title: CRISPRi_target_chr17-44988418_rep3

description:
column name: CRISPRi_target_chr17-44988418_rep3
7136.NC.0004_77


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 16, rep2 [AS-929298]

source_name: intestine

extract_protocol:
Total RNA was isolated from whole Jejunum (fat and Peyer's plaques removed) according to the instructions of the PureLink RNA Mini kit (Invitrogen)
RNA libraries for RNA-seq were prepared using TruSew Stranded RNA Kit (Illumina) following manufacturer's protocols.

value: intestine

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 26, 28, 30, 32, 34 and 37

tag: ova(ag) dlivery

value: oral gavage


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 16, rep3 [AS-929330]


title: CRISPRi_target_chr17-44987687_rep3

description:
column name: CRISPRi_target_chr17-44987687_rep3
7136.NC.0004_94

value: Neurons


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 11, rep3 [AS-929322]

value: female

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25, 27, 29 and 32


title: CRISPRi_target_chr17-45321056_rep2

description:
column name: CRISPRi_target_chr17-45321056_rep2
7136.NC.0004_79


title: CRISPRi_target_chr17-45326805_rep2

description:
column name: CRISPRi_target_chr17-45326805_rep2
7136.NC.0004_78


title: CRISPRi_target-GFP_rep6

description:
column name: CRISPRi_target-GFP_rep6
7136.NC.0004_42


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 11, rep2 [AS-929292]


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 7, rep3 [AS-929314]

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + oral gavage (50 mg ovalbumin in PBS) on days 21, 23, 25 and 28


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 11, rep1 [AS-929264]


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 7, rep1 [AS-929256]


title: CRISPRi_target_chr17-44988418_rep1

description:
column name: CRISPRi_target_chr17-44988418_rep1
7136.NC.0004_95


title: CRISPRi_target_chr17-45894000_rep6

description:
column name: CRISPRi_target_chr17-45894000_rep6
7136.NC.0004_76


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 7, rep2 [AS-929282]


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 16, rep2 [AS-929328]

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-37


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 16, rep1 [AS-929268]


title: CRISPRi_target_chr17-44987687_rep2

description:
column name: CRISPRi_target_chr17-44987687_rep2
7136.NC.0004_43


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 11, rep3 [AS-929320]

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-32


title: CRISPRi_target-GFP_rep5

description:
column name: CRISPRi_target-GFP_rep5
7136.NC.0004_93


title: CRISPRi_target_chr17-44988418_rep4

description:
column name: CRISPRi_target_chr17-44988418_rep4
7136.NC.0004_27


title: CRISPRi_target-GFP_rep4

description:
column name: CRISPRi_target-GFP_rep4
7136.NC.0004_92


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 11, rep1 [AS-929262]


title: CRISPRi_target_chr17-45326805_rep1

description:
column name: CRISPRi_target_chr17-45326805_rep1
7136.NC.0004_26


title: CRISPRi_target_chr17-45321056_rep1

description:
column name: CRISPRi_target_chr17-45321056_rep1
7136.NC.0004_37


title: CRISPRi_target_chr17-44987687_rep1

description:
column name: CRISPRi_target_chr17-44987687_rep1
7136.NC.0004_36


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 11, rep2 [AS-929290]

value: male


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 7, rep2 [AS-929284]

value: 2mg alum + 25 µg ovalbumin i.p. on day 0 and 14 + 2 bottle test (water vs. water + 20% egg white + 8% sugar) on days 21-28


title: Cpa3Cre/+, immunized, oral gavage (forced AG intake) day 16, rep1 [AS-929270]


title: CRISPRi_target-GFP_rep3

description:
column name: CRISPRi_target-GFP_rep3
7136.NC.0004_34


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 7, rep1 [AS-929254]


title: CRISPRi_target_chr17-45583947_rep4

description:
column name: CRISPRi_target_chr17-45583947_rep4
7136.NC.0004_71


title: CRISPRi_target_chr17-44988418_rep2

description:
column name: CRISPRi_target_chr17-44988418_rep2
7136.NC.0004_35


title: Cpa3Cre/+, immunized, rep3 [AS-929306]

value: 2 mg alum + 25 µg ovalbumin i.p. on day 0 and 14


title: Cpa3Cre/+, immunized, rep2 [AS-929278]


title: Cpa3Cre/+, immunized, rep1 [AS-929248]


title: CRISPRi_target_chr17-45309260_rep4

description:
column name: CRISPRi_target_chr17-45309260_rep4
7136.NC.0004_70


title: CRISPRi_target_chr17-45903110_rep4

description:
column name: CRISPRi_target_chr17-45903110_rep4
7136.NC.0004_22


title: Cpa3Cre/+, naive, rep2 [AS-929274]

value: untreated

value: naive


title: CRISPRi_target_chr17-45894000_rep5

description:
column name: CRISPRi_target_chr17-45894000_rep5
7136.NC.0004_14


title: CRISPRi_target_chr17-45784528_rep6

description:
column name: CRISPRi_target_chr17-45784528_rep6
7136.NC.0004_53


title: CRISPRi_target_chr17-45907842_rep6

description:
column name: CRISPRi_target_chr17-45907842_rep6
7136.NC.0004_13


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 16, rep2 [AS-929326]


title: CRISPRi_target_chr17-46264873_rep6

description:
column name: CRISPRi_target_chr17-46264873_rep6
7136.NC.0004_91


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 11, rep2 [AS-929318]


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 16, rep1 [AS-929296]


title: Cpa3Cre/+, immunized, 2-bottle test (natural avoidance) day 7, rep3 [AS-929312]

value: 2-bottle test


title: Cpa3Cre/+, naive, rep1 [AS-929244]


title: CRISPRi_target_chr17-45861418_rep2

description:
column name: CRISPRi_target_chr17-45861418_rep2
7136.NC.0004_10


title: CRISPRi_target_chr17-46004171_rep2

description:
column name: CRISPRi_target_chr17-46004171_rep2
7136.NC.0004_12


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 7, rep3 [AS-929310]


title: CRISPRi_target_chr17-45907842_rep5

description:
column name: CRISPRi_target_chr17-45907842_rep5
7136.NC.0004_9


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 7, rep1 [AS-929252]


title: CRISPRi_target_chr17-45948622_rep2

description:
column name: CRISPRi_target_chr17-45948622_rep2
7136.NC.0004_11


title: CRISPRi_target_chr17-45784528_rep5

description:
column name: CRISPRi_target_chr17-45784528_rep5
7136.NC.0004_72


title: CRISPRi_target_chr17-45840618_rep4

description:
column name: CRISPRi_target_chr17-45840618_rep4
7136.NC.0004_73


title: CRISPRi_target-GFP_rep2

description:
column name: CRISPRi_target-GFP_rep2
7136.NC.0004_90


title: Cpa3Cre/+, naive, rep3 [AS-929302]


title: CRISPRi_target_chr17-45894000_rep4

description:
column name: CRISPRi_target_chr17-45894000_rep4
7136.NC.0004_69


title: CRISPRi_target_chr17-46267785_rep2

description:
column name: CRISPRi_target_chr17-46267785_rep2
7136.NC.0004_54


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 16, rep1 [AS-929294]


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 16, rep2 [AS-929324]


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 11, rep2 [AS-929316]


title: CRISPRi_target_chr17-45583947_rep3

description:
column name: CRISPRi_target_chr17-45583947_rep3
7136.NC.0004_52


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 7, rep3 [AS-929308]


title: CRISPRi_target_chr17-45903110_rep3

description:
column name: CRISPRi_target_chr17-45903110_rep3
7136.NC.0004_17


title: CRISPRi_target_chr17-45309260_rep3

description:
column name: CRISPRi_target_chr17-45309260_rep3
7136.NC.0004_68


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 7, rep2 [AS-929280]


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 11, rep1 [AS-929288]


title: Cpa3+/+, immunized, oral gavage (forced AG intake) day 7, rep2 [AS-929286]


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 7, rep1 [AS-929250]


title: Cpa3+/+, immunized, rep3 [AS-929304]

value: day 0


title: CRISPRi_target_chr17-46267785_rep1

description:
column name: CRISPRi_target_chr17-46267785_rep1
7136.NC.0004_50


title: CRISPRi_target_chr17-45784528_rep4

description:
column name: CRISPRi_target_chr17-45784528_rep4
7136.NC.0004_15


title: Cpa3+/+, immunized, rep2 [AS-929276]

value: non


title: CRISPRi_target_chr17-45894000_rep3

description:
column name: CRISPRi_target_chr17-45894000_rep3
7136.NC.0004_7


title: Cpa3+/+, immunized, rep1 [AS-929246]

value: intestine


title: Cpa3+/+, naive, rep3 [AS-929300]


title: CRISPRi_target_chr17-46004171_rep1

description:
column name: CRISPRi_target_chr17-46004171_rep1
7136.NC.0004_5


title: Cpa3+/+, naive, rep2 [AS-929272]


title: CRISPRi_target_chr17-46264873_rep5

description:
column name: CRISPRi_target_chr17-46264873_rep5
7136.NC.0004_67


title: Cpa3+/+, naive, rep1 [AS-929242]


title: Cpa3+/+, immunized, 2-bottle test (natural avoidance) day 11, rep1 [AS-929258]


title: CRISPRi_target_chr17-45948622_rep1

description:
column name: CRISPRi_target_chr17-45948622_rep1
7136.NC.0004_4


title: CRISPRi_target_chr17-45907842_rep3

description:
column name: CRISPRi_target_chr17-45907842_rep3
7136.NC.0004_2


title: CRISPRi_target_chr17-45861418_rep1

description:
column name: CRISPRi_target_chr17-45861418_rep1
7136.NC.0004_3


title: cKO_3

city: Beijing

first: Yang

last: Xu

address: Beijing HaiDian District, Mingyuanxilu No.2

country: China

institute: China Agricultural University

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were masked for sequences containing adapter or undetermined base , and  masked for low-complexity or low-quality sequence
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Supplementary files format and content: Table with differentially expressed genes for every gene and every sample

source_name: Intestine

extract_protocol:
Intestinal crypt cells were isolated from the intestines of four cKO mice and four littermate controls by incubation with 10 mM EDTA, 10 mM HEPES and 2% FBS in HBSS for 25 min at 37°C. The crypt fractions were collected by vigorous shaking and filtered through a 100 μm cell strainer. The gathered crypt cells were centrifuged at 1200 rpm for 5 min. Total RNA was isolated from the collected crypt cells using TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Intestine

value: Intestinal epithelium

value: cKO


title: CRISPRi_target_chr17-45840618_rep3

description:
column name: CRISPRi_target_chr17-45840618_rep3
7136.NC.0004_1

value: Neurons


title: cKO_2


title: CRISPRi_target_chr17-45873822_rep1

description:
column name: CRISPRi_target_chr17-45873822_rep1
7136.NC.0004_89


title: CRISPRi_target_chr17-45784528_rep3

description:
column name: CRISPRi_target_chr17-45784528_rep3
7136.NC.0004_8


title: CRISPRi_target_chr17-45894500_rep1

description:
column name: CRISPRi_target_chr17-45894500_rep1
7136.NC.0004_49


title: CRISPRi_target_chr17-45903110_rep2

description:
column name: CRISPRi_target_chr17-45903110_rep2
7136.NC.0004_55


title: CRISPRi_target_chr17-45907842_rep4

description:
column name: CRISPRi_target_chr17-45907842_rep4
7136.NC.0004_6


title: Ctrl_2

value: WT


title: Ctrl_1


title: Ctrl_4


title: CRISPRi_target_chr17-46264873_rep4

description:
column name: CRISPRi_target_chr17-46264873_rep4
7136.NC.0004_21


title: CON3

city: Guangzhou

first: Ren-Wei

last: Su

state: Guangdong

address: 483 Wushan Road

department: Histology and Embryology

institute: South China Agricultural University

data_processing:
featureCounts v 1.5.0-p3 and stringtie v 1.3.3b
Initial quantification was performed using Qubit2.0 Fluorometer, followed by Agilent 2100 BioAnalyzer testing the insert size of the library. When the insert size met expectations, Qrt-pcr accurately quantified effective library concentration (effective library concentration is higher than 2nM) to ensure library quality.
The image data measured by the high-throughput sequencer were converted into sequence data (reads) by CASAVA base recognition.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: HISAT2
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: prostate

extract_protocol:
Anterior prostates from 20-week-old male mice for RNA-Seq analysis (the prostatic secretions must be cleaned otherwise RNA quality was poor）. Using the Trizol RNA Reagent (Takara, Dalian, China) to extract total RNA from the tissues and measured the concentration and integrity of the RNA with the ND-1000 Nanodrop, as well as the Agilent 2100 TapeStation (Novogene Bioinformatic Technology, Beijing, China). The quality control parameters used in this study were: A260/A280 ratio ≥1.8, A260/A230 ratio ≥2.0, and RNA integrity number ≥8.0.
The TruSeq RNA sample preparation kit (Illumina, San Diego, CA, USA) was used to generate cDNA libraries. High-throughput sequencing was run on an Illumina HiSeq 2500 system. Raw RNA-seq data were processed with an in-house computational pipeline.

value: prostate

value: mouse anterior prostatic cells

value: Wild type

tag: age

value: 20 weeks


title: CON2

value: male


title: CRISPRi_target_chr17-45583947_rep2

description:
column name: CRISPRi_target_chr17-45583947_rep2
7136.NC.0004_63


title: CRISPRi_target-GFP_rep1

description:
column name: CRISPRi_target-GFP_rep1
7136.NC.0004_33


title: CRISPRi_target_chr17-45894000_rep2

description:
column name: CRISPRi_target_chr17-45894000_rep2
7136.NC.0004_62


title: CON1


title: cKO_4


title: OEX3


title: OEX2


title: cKO_1


title: OEX1


title: B97A3

city: Vienna

first: Monika

last: Schmoll

address: Djerassiplatz 1

department: Centre of Microbiology and Environmental Systems Science

country: Austria

institute: University of Vienna

data_processing:
The mapping of reads was performed using bowtie2 with standard parameter setting
The resulting files were further processed using samtools
The comparison to the annotation was performed using bedtools
Values were calculated for each annotated transcript based on the results of the mapping (RSEM)
Assembly: https://mycocosm.jgi.doe.gov/Triha1/Triha1.home.html;   Compant et al., 2017 (PMID 28360171)
Supplementary files format and content: The .csv file contains FPKM values (log) of normalized samples (values for all samples in this file).

organism: Trichoderma harzianum

source_name: fungal mycelium

extract_protocol:
Mycelia were harvested and frozen in liquid nitrogen. Total RNA was isolated essentially as described previously (Tisch et al., 2011 PMID  21220037) using the QIAGEN plant RNA kit (QIAGEN, Hilden, Germany) according to manufacturers instructions. Quality control of total RNA was performed using Bioanalyzer 2100 (Agilent) and only high quality RNA was used for further analysis.
Next generation sequencing was performed at VBCF (Vienna, Austria) on a HiSeq2000/SR50 machine.

treatment_protocol: Precultures for cultivation on cellulose were performed on plates with malt extract agar (3 % w/v) in constant darkness for 14 days in order to avoid interference of light pulses or circadian rhythms with transcriptome analysis. An inoculum of 109 conidia/L was applied to  Mandels Andreotti minimal medium plates with 0.1 % (w/v) glucose. After incubation for 34 hours, roots of a soybean plant were placed on the plate and interaction with T. harzianum was allowed for 13 hours prior to harvesting.

tag: strain

tag: property

value: wildtype

value: axenic growth (control)


title: 133G2-shLAP-3

city: Fuzhou

first: Jianping

last: Liao

state: Fujian

address: 88 Jiaotong Road, Fuzhou, Fujian

institute: Fujian medical university

data_processing:
The sequencing reads were automatically uploaded and evaluated for quality using Illumina BaseSpace Onsite Computing platform.
Fastq sequence files were generated and analysis was performed using applications available on BaseSpace Onsite Computing platform
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated.
Clustering and correlation analysis were carried out using Metaboanalyst 3.0 software analysis package (http://www.metaboanalyst.ca).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Liver

extract_protocol:
The total RNA of HPC  was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-2501) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Liver

value: hepatoma cells

value: LAPTM4B knockdown


title: 133G2-shLAP-2


title: 133G2-shLAP-1


title: B97A2


title: 133G2-NC-3


title: Ctrl_3


title: CRISPRi_target_chr17-45784528_rep2

description:
column name: CRISPRi_target_chr17-45784528_rep2
7136.NC.0004_75


title: CRISPRi_target_chr17-45219542_rep2

description:
column name: CRISPRi_target_chr17-45219542_rep2
7136.NC.0004_24


title: 133G2-NC-2


title: DCH24_DOX_IFNg_biol rep 3_total_mRNA

city: Seattle

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

data_processing:
Polysome RNA-Seq reads were quality checked with FastQC, trimmed using Trim Galore!, and aligned to the human reference genome GRCh38 p13 as well as the DM6 Drosophila reference genome using Rsubread.
Reads were mapped to the Gencode v35 reference annotation using FeatureCounts.
The human counts were normalized using both the DM6 and GRCh38 library sizes, log transformed, and analyzed for differential gene expression using DESeq2.
Assembly: GRCh38.p13
Supplementary files format and content: R compressed format (.rData) and CSV format,  non-normalized gene counts

growth_protocol: MB135iDUX4 myoblasts were grown in Ham’s F-10 (Gibco) supplemented with 10% FBS (HyClone), 1% penicillin/streptomycin (Thermo Fisher Scientific), 10ng/mL rhFGF (Promega), 1uM dexamethasone (Sigma), and 3ug/mL puromycin (Sigma)

extract_protocol:
Gradients were fractionated using a Biocomp Piston Gradient Fractionator. Samples were resuspended in Trizol and Drosophila S2 cells were added as an internal spike-in control. RNA was harvested using the Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer's protocols.
RNA-seq libraries were prepared using the Illumina TruSeq RNA Sample Prep v2 Kit following manufacturer's protocols.

treatment_protocol:
MB135iDUX4 myoblasts were pulsed with or without 1ug/mL doxycycline for 4 hours, incubated for 48 hours, supplemented with 50ng/mL IFNg for 16 hours, and harvested at a terminal time point of 68 hours.
Culture medium was supplemented with 100µg/mL cycloheximide (CHX; Sigma) and cells were incubated at 37oC for 10 minutes prior to harvest.

value: myoblasts

value: DOX+IFNg


title: CRISPRi_target_chr17-45907842_rep2

description:
column name: CRISPRi_target_chr17-45907842_rep2
7136.NC.0004_23


title: CRISPRi_target_chr17-45309260_rep2

description:
column name: CRISPRi_target_chr17-45309260_rep2
7136.NC.0004_60


title: B97P3

value: strain grown in the presence of soybean roots


title: 133G2-NC-1


title: B97P2


title: DCH23_DOX_IFNg_biol rep 3_high_polysomes


title: B97P1


title: DCH22_DOX_IFNg_biol rep 3_low_polysomes


title: CRISPRi_target_chr17-45784528_rep1

description:
column name: CRISPRi_target_chr17-45784528_rep1
7136.NC.0004_74


title: CRISPRi_target_chr17-45903110_rep1

description:
column name: CRISPRi_target_chr17-45903110_rep1
7136.NC.0004_51


title: CRISPRi_target_chr17-46264873_rep2

description:
column name: CRISPRi_target_chr17-46264873_rep2
7136.NC.0004_16


title: DCH21_DOX_IFNg_biol rep 3_40-60-80S


title: CRISPRi_target_chr17-46264873_rep3

description:
column name: CRISPRi_target_chr17-46264873_rep3
7136.NC.0004_25


title: DCH19_DOX_IFNg_biol rep 2_high_polysomes


title: DCH20_DOX_IFNg_biol rep 2_total_mRNA


title: DCH18_DOX_IFNg_biol rep 2_low_polysomes


title: CRISPRi_target_chr17-45583947_rep1

description:
column name: CRISPRi_target_chr17-45583947_rep1
7136.NC.0004_59


title: B97A1


title: WT3 time-point 50

city: Aurora

first: Olivia

last: Rissland

state: CO

address: 12801 East 17th Ave

department: BMG

institute: University of Colorado Denver

data_processing:
Reads were trimmed and clipped for Illumina adaptors using Trimmomatic v0.36
Reads were aligned to the S. pombe genome using STAR version 2.5.2a
HTSeq 0.6.1p2 was used to calculate coverage per gene
DRUID pipeline (Lugowski et al., Methods, 2018) was used to calculate half-lives and downstream analyses were completed using R
Downstream analyses were performed with R version 3.5.2, using in-house scripts.
Assembly: S. pombe genome acquired from https://www.pombase.org/data/
Supplementary files format and content: Tab separated values files contain read counts per gene for each sample

organism: Schizosaccharomyces pombe

source_name: WT cells

growth_protocol: S. pombe strains were streaked on YES plates and incubated at 32C. For biological replicates, single colonies were used to inoculate 10mL of liquid media

extract_protocol:
4tU containing RNA was purified by biotin-streptavidin pull down and purified RNA was prepared for seqeucnign using the Illumina TruSeq Stranded mRNA Sample Preparation Kit
RNA was extracted from cells with acid phenol
Illumina TruSeq Stranded mRNA Sample Preparation

treatment_protocol: 5mM 4tU was added to cultures and a portion of cells were removed at various time points. Cells were washed and flash frozen until extraction


title: CRISPRi_target_chr17-45894000_rep1

description:
column name: CRISPRi_target_chr17-45894000_rep1
7136.NC.0004_58


title: DCH17_DOX_IFNg_biol rep 2_40-60-80S


title: DCH16_DOX_IFNg_biol rep 1_total_mRNA


title: WT3 time-point 5


title: WT3 time-point 20


title: Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 4

city: Chicago

first: Yoav

last: Gilad

state: IL

department: Genetic Medicine

institute: University of Chicago

library_source: transcriptomic single cell

data_processing:
Samples were aligned to the human or chimpanzee orthologous exons using cellranger. Samples were also aligned to a joint human/chimpanzee geneome in order to assign each barcode to a species. Inividuals were assigned using demuxlet
Aligned UMI count matrices were loaded in R using the Seurat package. Samples were normalized using the SCTransform pipeline and aligned to an external reference using Harmony.Cells types were assigned by proximity to reference cell types in harmony-corrected PCA space
We generated pseudobulk for each species/individual/replicate/cell type by taking the sum of UMI counts for every cell in each group.
We assessed differential expression in each cell type using DREAM from the VariancePartition package. We treated species as a fixed effect and included random effects for individual and replicate
We used Cormotif to assess sharing of differetial expression across cell types
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: the mtx file contains UMI counts for every gene and cell
Supplementary files format and content: The features tsv contains the row names (genes) while the barcodes tsv contains the colun names (cell barcodes) for the counts matrix. The metadata tsv contains individual and species calls.
Supplementary files format and content: The VCFs contain the genotypes used for assigning individuals
Supplementary files format and content: The GTFs contain the orthologous exons used for mapping to human or chimpanzee genomes
Supplementary files format and content: DataS1 contains the results of differential expression analysis

organism:
Pan troglodytes
Homo sapiens

source_name: iPS-derived Embryoid Body cells

growth_protocol: iPSCs were dissociated and EBs were generated at 1000 cells per EB using Aggrewell micropatterned plates. EBs were formed in Aggrewell EB formation medium. They were half-fed with 1mL Aggrewell EB formation medium at 24 hours. After 48 hours they were transferred to Corning ultra-low adherence plates in E6 media. Media was replaced every other day until 21 days were met.

extract_protocol:
EBs were dissocated in Accumax, pooled, and collected on a 10x Chromium controller.
Libraries were constructed using 10x 3' scRNA-seq v3.1 according to manufacturer directions.

value: iPS-derived Embryoid Body cells

tag: individuals


title: CRISPRi_target_chr17-45840618_rep2

description:
column name: CRISPRi_target_chr17-45840618_rep2
7136.NC.0004_61


title: CRISPRi_target_chr17-45840618_rep1

description:
column name: CRISPRi_target_chr17-45840618_rep1
7136.NC.0004_57


title: DCH15_DOX_IFNg_biol rep 1_high_polysomes


title: DCH14_DOX_IFNg_biol rep 1_low_polysomes


title: WT3 steady-state


title: CRISPRi_target_chr17-46264873_rep1

description:
column name: CRISPRi_target_chr17-46264873_rep1
7136.NC.0004_20


title: Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 3


title: Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 2


title: Human and chimpanzee 21 day embryoid bodies - replicate 3, lane 1


title: CRISPRi_target_chr17-45219542_rep1

description:
column name: CRISPRi_target_chr17-45219542_rep1
7136.NC.0004_19


title: WT2 time-point 125


title: DCH13_DOX_IFNg_biol rep 1_40-60-80S


title: CRISPRi_target_chr17-45907842_rep1

description:
column name: CRISPRi_target_chr17-45907842_rep1
7136.NC.0004_18


title: DCH12_IFNg_biol rep 3_total_mRNA

value: IFNg


title: Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 4


title: DCH11_IFNg_biol rep 3_high_polysomes


title: CRISPRi_target_chr17-45309260_rep1

description:
column name: CRISPRi_target_chr17-45309260_rep1
7136.NC.0004_56

value: Neurons


title: Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 3


title: WT2 time-point 50


title: DCH10_IFNg_biol rep 3_low_polysomes

value: WT


title: Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 2


title: WT2 time-point 5


title: DCH09_IFNg_biol rep 3_40-60-80S


title: Human and chimpanzee 21 day embryoid bodies - replicate 2, lane 1


title: WT2 time-point 20


title: R16-1

city: Oklahoma City

first: Jie

last: Wu

state: OK

address: 975 NE 10th Street

department: Stephenson Cancer Center

institute: University of Oklahoma Health Sciences Center

description: FPKM

data_processing:
Illumina platforms
Basecalls performed using CASAVA base recognition (Base Calling), Raw data are stored in FASTQ format files
Data QC: Error rate distribution, GC content distribution, data filering
Filtering sequenced reads/raw reads of low quality to get clean reads: (1) Remove reads with adaptor contamination; (2) Remove reads when uncertain nucleotides constitute more than 10 percent of either read (N > 10%); (3) Remove reads when low quality nucleotides (Base Quality less than 20) constitute more than 50 percent of the read). The Qscore of over 50% bases of these read is <= 5.
Mapping clean reads to Human GRCh38/hg38 using STAR v2.5 (mismatch = 2)
Quantificating gene expression using  HTSeq  v0.6.1
Differential Analysis using DESeq2 v2_1.6.3 (adjust p value < 0.05, |log2(Fold Change)| >1)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: thyroid

extract_protocol:
Total RNA was isolated from TPC-1 cells using a modified protocol with the Direct-zol RNA MiniPrep kit (Catalog No. R2050, Zymol Research) and TRI reagent (Catalog No. T9424, Sigma).
GlobinClear kit and NEB non-directional library

value: thyroid

value: papillary thyroid carcinoma

value: CCDC6-RET fusion

value: 5uM BLU667  (>50 days)


title: R16-2

description: FPKM


title: WT2 steady-state


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 9


title: WT1 time-point 125


title: DCH07_IFNg_biol rep 2_high_polysomes


title: WT2 time-point 105


title: DCH06_IFNg_biol rep 2_low_polysomes


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 8


title: R10-2

description: FPKM


title: R8_2

description: FPKM


title: DCH05_IFNg_biol rep 2_40-60-80S


title: WT1 time-point 105


title: WT1 time-point 50


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 6


title: R8_1

description: FPKM


title: DCH04_IFNg_biol rep 1_total_mRNA


title: B_2

description: FPKM


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 5


title: WT1 time-point 20


title: DCH08_IFNg_biol rep 2_total_mRNA


title: DCH03_IFNg_biol rep 1_high_polysomes


title: B_1

description: FPKM


title: WT1 steady-state


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 3


title: DCH01_IFNg_biol rep 1_40-60-80S


title: P_2

description: FPKM

value: DMSO (24h)


title: DCH02_IFNg_biol rep 1_low_polysomes


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 4


title: R10-1

description: FPKM


title: duf89∆ biol rep 3

city: New York

first: Angad

last: Garg

state: New York

department: Molecular Biology

institute: Memorial Sloan Kettering Cancer Center

data_processing:
Base calls from Illumina NovaSeq 6000 or HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
Supplementary files format and content: DESeq output file

growth_protocol: log phase cultures, 30ºC, YES medium

extract_protocol:
hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 or Illumina HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).

tag: growth phase

value: log phase growth

tag: growth medium

value: Yeast Extract Supplemented

value: h- duf89delta::hygR


title: P_1

description: FPKM


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 1


title: duf89∆ biol rep 2


title: Human and chimpanzee 21 day embryoid bodies - replicate 1, lane 7


title: duf89∆ biol rep 1


title: Primary patient-derived T1CAF, patient 5 (FBB021) [S103710-001-041]

city: Leiden

first: Hailiang

last: Mei

address: Einthovenweg 20

department: Sequencing Analysis Support Core

country: Netherlands

institute: Leiden University Medical Center

description: Fibroblasts isolated from endoscopic biopsies of T1CRC tissue. Clinical characteristics of the T1CRC can be found in the Supplementary file of the manuscript

data_processing:
RNA-Seq files were processed using the opensource BIOWDL RNAseq pipeline developed at the LUMC.
This pipeline performs FASTQ preprocessing (including quality control, quality trimming, and adapter clipping), RNA-Seq alignment, read quantification, and optionally transcript assembly.
FastQC was used for checking raw read QC. Adapter clipping was performed using Cutadapt (v2.4) with default settings.
RNA-Seq reads’ alignment was performed using STAR (v2.6.0c) on GRCh38 human reference genome.
The gene read quantification was performed using HTSeq-count (v0.9.1) with setting “–stranded=reverse”. The gene annotation used for quantification was Ensembl version 94.
Assembly: GRCh38
Supplementary files format and content: raw read count in TSV format

source_name: T1CRC tissue, ascending colon

growth_protocol: Primary patient-matched T1CAFs and NFs were isolated from fresh endoscopic biopsies of T1 colorectal cancer (T1CRC) and normal tissue, respectively. During colonoscopy, 2-6 targeted biopsies were taken from tumor regions with optical features of submucosal invasion (e.g. Kudo Vi pit pattern, Sano IIIa vessel pattern), and from normal adjacent mucosa 5-10 centimeters away from the tumor. Patient-matched biopsies were taken during the same procedure and within the same intestinal segment to maximize comparability of the samples. All included T1CRC cases had to be histologically confirmed by an expert gastrointestinal pathologist. T1CRC was defined as histological tumor invasion through the muscularis mucosa and into, but not beyond, the submucosa. Biopsies were collected in fibroblast medium (Dulbecco’s 123 Modified Eagle’s medium (DMEM)/F12 GlutaMAX™ supplemented with 10% fetal calf serum (FCS), 50 μg/mL gentamycin, 2.5 μg/mL fungizone, 100 IU/mL penicillin and 100 μg/mL streptomycin (all from Thermo Fisher Scientific, Waltham, MA, USA)) and digested with a 3:1 mix of collagenase type II (Thermo Fisher Scientific) and dispase II (Roche, Basel, Switzerland) for 2 hours at 37°C. After digestion, single-cell suspensions were plated in cell culture dishes (Greiner Bio-One, Kremsmünster, Austria) and cultured in fibroblast medium at 37°C and 5% CO2. Outgrowth of fibroblast-like cells was observed after 2-7 days. Media were changed weekly. Cells were cultured up to 4 passages for mRNA sequencing. All cells were routinely tested for mycoplasma contamination using polymerase chain reaction analysis.

extract_protocol:
RNA isolation of the harvested cell pellets was performed using the Nucleospin® RNA kit or RNA XS kit (both from Macherey-Nagel, Düren, Germany) according to manufacturer’s protocol. The concentration and integrity of the extracted RNA was measured using a BioAnalyzer (Agilent Technologies, Wilmington, DE, USA). Samples with a RNA integrity number (RIN) ≥ 8 were subjected to mRNA sequencing (RIN range of the analyzed samples: 9.6-10).
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples. The sample preparation was performed according to the protocol "NEBNext Ultra II Directional RNA Library Prep  Kit for Illumina" (NEB #E7760S/L). Briefly, mRNA was isolated from total RNA using the oligo-dT magnetic beads. After fragmentation of the mRNA, a cDNA synthesis was performed. This was used for ligation with the sequencing adapters and PCR amplicification of the resulting product. The quality and yield after sample preparation was measured with the Fragment Analyzer. The size of the resulting products was consistent with the expected size distribution (a broad peak between 300-500 bp).

treatment_protocol: Not applicable

tag: tissue type

value: T1CRC tissue

value: ascending colon

tag: subject id

value: patient 5 (FBB021)

value: Fibroblast


title: Primary patient-derived T1CAF, patient 8 (FBB031) [S103710-001-049]

source_name: T1CRC tissue, rectum

value: rectum

value: patient 8 (FBB031)


title: Day180_2, Spleen, Meishan pig

city: Yangzhou

first: Chao

state: Jiangsu

address: Hanjiang

institute: Yangzhou University

data_processing:
Raw data quality control:fastqc
Adapter and quality trimming:Cutadapt
Read mapping:TopHat2
De novo circRNA identification: CIRI
CircRNA quantification: CIRIquant
Assembly: Sus scrofa 11.1
Supplementary files format and content: tab-delimited text file includes raw count values for each Sample

organism: Sus scrofa

source_name: Spleen

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA was harvested using TruSeq Stranded Total RNA with Ribo-Zero Gold. 1.3 ug of total RNA was used for the construction of sequencing libraries.

value: Spleen

tag: breed

value: Meishan


title: Day180_3, Spleen, Meishan pig

tag: tissue


title: Day180_1, Spleen, Meishan pig


title: SLR3 time-point 125

source_name: slr1- knockout cells


title: Primary patient-derived T1CAF, patient 4 (FBB019) [S103710-001-040]

source_name: T1CRC tissue, transverse colon

value: transverse colon

value: patient 4 (FBB019)


title: WT1 time-point 5


title: RNAseq_LN_TEM_rep2

city: Bethesda

first: Verena

last: Link

address: 4 Memorial Drive

department: NIAID

institute: NIH

data_processing:
RNA-seq samples were mapped to the mm10 mouse genome with STAR. Gene expression was assessed using HOMER’s analyze Repeats with parameters rna, mm10, -count exons, -condenseGenes. Raw data are shown as transcripts per million (TPM). Differential expression was calculated using DESeq2. Genes were considered differentially expressed with FDR < 0.05 and FC > 2. Gene ontology analysis was done with Metascape or IPA (Qiagen).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include TPM values for each RNA-seq sample

source_name: memory T cells from lymph node

extract_protocol: For S. aureus RNA-seq: Ear pinna skin was split into the dorsal and the ventral sheets and placed in RPMI 1640 media supplemented with 2 mM L-glutamine, 1 mM sodium pyruvate, 1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 20 mM HEPES, 100 U/ml of penicillin, 100 mg/ml of streptomycin, 0.5 mg/ml of DNAse I (Sigma-Aldrich) and 0.25 mg/ml of Liberase TL purified enzyme blend (Roche) for 90 minutes at 37C and 5% CO2. Digested ear skin sheets were homogenized using the Medicon/Medimachine tissue homogenizer system. T cells were FACsorted (BD FACS Aria, Becton Dickinson) from Foxp3-GFP reporter mice. The RNA from the sorted T cells was extracted using the RNeasy Plus Micro Kit (Qiagen) as per manufacturer instructions. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.  For DRG RNA-seq: Supernatant was removed from cells, cells were lysed with RLT Plus buffer (Qiagen) and the RNA was extracted to perform bulk RNA sequencing. Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.  Libraries were prepared using the Clontech SMARTer Ultra low input mRNA-Seq sequence kit and samples were sequenced paired end on one lane of NextSeq 550.

treatment_protocol: For S. aureus treatment: Staphyloccocus aureus (42F02) was cultured in tryptic soy broth for 4 hours at 37oC with shaking at 200 rpm. For commensal colonization, each mouse was topically associated by applying up to 5 mL of a culture of S. aureus (approximately 10^9 CFU/mL) across the entire skin surface, or by applying 1 mL in each ear skin, using a sterile cotton swab. Unless otherwise noted, associations were repeated every other day for a total of 4 times. For infections, mice were intradermally injected in the ear pinnae with 2x10^7 CFU of S. aureus (42F02).  For dorsal ganglion neuron treatment: 5000 cells were seeded into flat-bottom 96-well plates coated with laminin (Thermo Fisher) and allowed to attach to the bottom of the wells for 2 hours, then the medium was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor (Thermo Fisher). Following an overnight incubation, the supernatant was removed and replaced with neurobasal medium containing 50 ng/ul nerve growth factor, 10 uM cytosine arabinoside (Sigma), and 100 ng/ml IL17-A. Culture medium was replaced daily for the duration of the experiment.

tag: organ

value: lymph node


title: Day120_3, Spleen, Meishan pig


title: RNAseq_LN_TEM_rep1


title: T47D.15.DOX.3

city: Urbana

first: Michael

last: Spinella

address: 2001 S Lincoln Ave

department: Comparative Biosciences

institute: University of Illinois at Urbana-Champaign

data_processing:
fastq files were aligned to human genome assembly NCBI GRCh38.p13 using STAR aligner .
BAM files resulting from the alignments were summarized to genes using the featureCounts algorithm
Expression data was TMM normalized using the calcNormFactors function in R
Differentially expressed genes (³|2.0|-fold and £1% false discovery rate) were identified by linear modeling and Bayesian statistics using the Limma trend package.
Assembly: human genome assembly NCBI GRCh38.p13
Supplementary files format and content: tab-delimited text files includeTMM normalized log counts per million (log CPM) values for each Sample …

source_name: T47D ER+ breast cancer cell line

growth_protocol: Cells were treated with 0.5 ug/ml doxycycline for 15 days and then assessed for cell  proliferation by CellTiter-Glo (Promega).

extract_protocol:
RNA was isolated using the RNeasy Mini Kit (Qiagen) and processed as per manufacturer’s instructions.
The libraries were sequenced on a HiSeq 4000 using HiSeq 4000 sequencing kit version 1. according to the manufacturer’s instructions.

value: ER+ breast cancer

tag: tissue origin

value: breast

tag: g0s2 overexpression

value: 15 day G0S2


title: Primary patient-derived T1CAF, patient 6 (FBB025) [S103710-001-039]

value: patient 6 (FBB025)


title: T47D.15.DOX.1


title: SLR3 time-point 50


title: Day120_2, Spleen, Meishan pig


title: Day120_1, Spleen, Meishan pig


title: Primary patient-derived T1CAF, patient 9 (FBB035) [S103710-001-036]

value: patient 9 (FBB035)


title: Primary patient-derived NF, patient 3 (FBB018) [S103710-001-032]

description: Fibroblasts isolated from endoscopic biopsies of normal mucosa

source_name: Normal mucosa, rectosigmoid

value: Normal mucosa

value: rectosigmoid

value: patient 3 (FBB018)


title: Primary patient-derived NF, patient 7 (FBB028) [S103710-001-029]

source_name: Normal mucosa, rectum

value: patient 7 (FBB028)


title: Day35_3, Spleen, Meishan pig


title: SLR3 time-point 20


title: SLR3 time-point 5


title: T47D.3.DOX.2

value: 3 day G0S2


title: T47D.15.DOX.2


title: Day35_2, Spleen, Meishan pig


title: T47D.3.DOX.1


title: Primary patient-derived T1CAF, patient 7 (FBB028) [S103710-001-028]

value: T1CRC tissue

value: rectum

value: Fibroblast


title: SLR2 time-point 125


title: SLR3 time-point 105


title: Primary patient-derived NF, patient 1 (FBB007) [S103710-001-027]

source_name: Normal mucosa, sigmoid

value: sigmoid

value: patient 1 (FBB007)


title: T47D.0.DOX.3

value: control


title: Primary patient-derived T1CAF, patient 1 (FBB007) [S103710-001-024]

source_name: T1CRC tissue, sigmoid


title: SLR2 time-point 105


title: Day28_3, Spleen, Meishan pig

value: Spleen

value: Meishan


title: T47D.0.DOX.2

value: ER+ breast cancer

value: breast


title: T47D.3.DOX.3


title: Day28_2, Spleen, Meishan pig


title: T47D.0.DOX.1


title: SLR2 time-point 50


title: Primary patient-derived NF, patient 10 (FBB041) [S103710-001-023]

value: patient 10 (FBB041)


title: SLR2 time-point 20


title: Day21_3, Spleen, Meishan pig


title: Day28_1, Spleen, Meishan pig


title: Primary patient-derived T1CAF, patient 3 (FBB018) [S103710-001-021]

source_name: T1CRC tissue, rectosigmoid


title: Primary patient-derived NF, patient 4 (FBB019) [S103710-001-018]

source_name: Normal mucosa, transverse colon

value: transverse colon

value: patient 4 (FBB019)


title: MDA.15.DOX.2

source_name: MDA-MB-231 ER-breast cancer cell line

value: ER- breast cancer

value: 15 day G0S2


title: SLR2 steady-state


title: Day21_2, Spleen, Meishan pig


title: MDA.15.DOX.3


title: Primary patient-derived T1CAF, patient 10 (FBB041) [S103710-001-017]

value: rectosigmoid


title: Day35_1, Spleen, Meishan pig


title: SLR1 time-point 125


title: Day21_1, Spleen, Meishan pig


title: Primary patient-derived T1CAF, patient 2 (FBB015) [S103710-001-014]

source_name: T1CRC tissue, cecum

value: cecum

value: patient 2 (FBB015)


title: Day14_3, Spleen, Meishan pig


title: SLR1 time-point 105


title: MDA.3.DOX.3

value: 3 day G0S2


title: MDA.15.DOX.1


title: SLR1 time-point 50


title: MDA.3.DOX.2


title: MDA.3.DOX.1


title: Day14_2, Spleen, Meishan pig


title: Primary patient-derived NF, patient 6 (FBB025) [S103710-001-011]

value: Normal mucosa

value: rectum

value: patient 6 (FBB025)

value: Fibroblast


title: Day14_1, Spleen, Meishan pig

value: Spleen


title: SLR1 time-point 20


title: SLR3 steady-state


title: Primary patient-derived NF, patient 5 (FBB021) [S103710-001-010]

source_name: Normal mucosa, ascending colon

value: ascending colon

value: patient 5 (FBB021)


title: SLR2 time-point 5


title: MDA.0.DOX.3

value: breast

value: control


title: Day7_3, Spleen, Meishan pig

value: Meishan


title: SLR1 time-point 5


title: Primary patient-derived NF, patient 8 (FBB031) [S103710-001-005]

value: patient 8 (FBB031)


title: MDA.0.DOX.2

value: ER- breast cancer


title: Day7_2, Spleen, Meishan pig


title: SLR1 steady-state


title: WT3 time-point 125

source_name: WT cells


title: Day7_1, Spleen, Meishan pig


title: MDA.0.DOX.1


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 3, 10x lane 2

description:
Hybrid.human.counts.mtx.gz
Hybrid.human.features.tsv.gz
Hybrid.human.barcodes.tsv.gz
Hybrid.human.metadata.tsv.gz
Hybrid.combined.counts.mtx.gz
Hybrid.combined.features.tsv.gz
Hybrid.combined.barcodes.tsv.gz
Hybrid.combined.metadata.tsv.gz
DataS1.tsv.gz

data_processing:
Samples were aligned to the human genome using cellranger from 10x genomics.
Aligned UMI count matrices were loaded in R using the Seurat package. Samples were normalized using the SCTransform pipeline and aligned to an external reference using Harmony.Cells types were assigned by proximity to reference cell types in harmony-corrected PCA space
Samples were aligned to a set of orthologous exons in the combined human/chimpanzee genome using cellranger. We only kept reads that uniquely aligned to either the human or chimpanzee genome.
We used cell-type assignmnts from the human-aligned data to annotate the allele specific reads from the combined species alignment.
We assessed differential expression in each cell type using the paired Wilcoxon signed-ranks test.
We computed the percent of DE due to allele-secific changes between species for each gene in each cell type
Assembly: hg38
Assembly: panTro6
Supplementary files format and content: the mtx file contains UMI counts for every gene and cell
Supplementary files format and content: The features tsv contains the row names (genes) while the barcodes tsv contains the colun names (cell barcodes) for the counts matrix. The metadata tsv contains individual and species calls.
Supplementary files format and content: The GTFs contain the orthologous exons used for mapping to human or chimpanzee genomes
Supplementary files format and content: DataS1 contains the results of differential expression analysis
Supplementary files format and content: DataS2 contains a list of tissue-specific differentially expressed genes

source_name: human/chimpanzee tetraploid hybrid

value: iPS-derived Embryoid Body cells


title: Primary patient-derived NF, patient 9 (FBB035) [S103710-001-013]

value: patient 9 (FBB035)


title: Day1_3, Spleen, Meishan pig


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 3, 10x lane 1


title: WT3 time-point 105


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 2, 10x lane 2


title: Day1_2, Spleen, Meishan pig


title: Day1_1, Spleen, Meishan pig


title: CD34+ HSPCs, day 4 under cytokine treatment, ADT-derived cDNA

first: Tiphaine

middle: Christiane

last: Martin

address: 1470 Madison Ave

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
V-control-day4-ADT_ADT_Ava_093.citeseq

library_source: other

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression and ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline where ADT were concatenated and treated as Custom library with default settings (v3.0.2) and aligning to the hg19 genome build and Ensembl 105 annotations.
Further processing was done with Seurat v4.1.1 (cell and gene filtering, hashtag identification, clustering, cell cycle analysis).
Assembly: hg19
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

molecule: protein

source_name: Umbilical cord blood

growth_protocol: Highly purified (90%–98%) CD34+ cells were seeded at a density of 3.3×10^4 cells/mL in StemSpan SFEM II (StemCell Technologies) culture medium containing 1% penicillin-streptomycin (Life Technologies) supplemented with 150 ng/mL human stem cell factor (SCF), 100 ng/mL human fms-like tyrosine kinase receptor 3 (FLT3 ligand), 100 ng/mL human thrombopoietin (TPO), and 50 ng/mL human interleukin 3 (IL-3) (R&D Systems)

extract_protocol:
Mononuclear cells were isolated by Ficoll-Hypaque (GE Healthcare) density centrifugation, and CD34+ cells were purified by immunomagnetic sorting using the CD34 Microbead kit (Miltenyi) and the AutoMACS Pro Separator (Miltenyi).
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE-seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library and 20% ADT library before sequencing.

treatment_protocol: Following priming for 16 hours with cytokines, cells were exposed to 1mM VPA (Sigma-Aldrich).

value: Umbilical cord blood

value: CD34+ Hematopoietic Stem and Progenitor Cells (HSPCs)

tag: treatment

value: day 4 under cytokine treatment

tag: library type

value: ADT

tag: antibodies/tags


title: CD34+ HSPCs, day 4 under cytokine treatment, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TD005069-V-control-day4-GEX

tag: cell type

value: RNA


title: CD34+ HSPCs, day 1 under cytokine treatment, ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)
TD005137-V-control-day1-ADT_ADT_citeseq

value: day 1 under cytokine treatment


title: CD34+ HSPCs, day 1 under cytokine treatment, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA
TD005069-V-control-day1-GEX


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 2, 10x lane 1


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 1, 10x lane 2


title: cells isolated from peritumoral tissue of lung metastasis, scRNAseq

city: Jiaxing

first: Wu

last: Zhou

address: No 118, Rd Jiahang Avenue

institute: Jiaxing University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: not provided
Supplementary files format and content: clustering, rds format

extract_protocol:
The lung metastatic tumors from 16 weeks MPG mice were separately collected and digested as single cells for FACS sorting by the green laser (561 nm, 100 mV). The positive fluorescent cells were discarded, and non-fluorescent cell suspension were FACS sorted out CD3 positive cells. The remaining cells after two round FACS sorting (infil) or single cells from one peritumoral lung tissue of 16 weeks MPG mice (peri) were respectively loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: MPG mice

tag: age

value: 16 weeks old


title: lung metastasis infiltrating cells, scRNAseq

description: 10x Genomics

source_name: lung metastasis infiltrating cells

value: lung metastasis infiltrating cells

tag: strain


title: Human/chimpanzee tetraploid hybrid 21 day embrypoid bodies - replicate 1, 10x lane 1


title: Primary patient-derived NF, patient 2 (FBB015) [S103710-001-004]

source_name: Normal mucosa, cecum

value: Normal mucosa

value: cecum

value: patient 2 (FBB015)

value: Fibroblast


title: eWAT, FANKO, ZT6, rep4

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
Reads were aligned using STAR v. 2.5.3a, against the GRCm38.p5 primary assembly and GENCODE Comprehensive gene annotations version 15 with the flags --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonicalUnannotated set
Read summation onto genes was performed onto the same gene annotations as during mapping, by featureCounts v. 1.5.3 with the -p -B -C -t exon -g gene_id flags set
Quality was tested using fastqc v 0.11.5 and multiqc v 1.2
Assembly: GRCm38.p5
Supplementary files format and content: csv file with read counts for each sample

source_name: epididymal white adipose tissue

extract_protocol:
Total RNA was extracted from tissues using TRI reagent (T9424, Sigma-Aldrich) and isolated using RNeasy Mini Kit (74106, Qiagen). From this, 500-1000 ng RNA was used for reverse transcription with the High Capacity cDNA Reverse Transcription kit (4368814, Applied Biosystems).
RNA sequencing libraries were prepared using the Illumina TruSeq Stranded Total RNA with Ribo-Zero Gold protocol (Illumina)

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)

value: epididymal white adipose tissue

tag: Sex

value: male

tag: genotype

value: fat-specific Nampt knockout

tag: timepoint

tag: replicate


title: eWAT, FANKO, ZT6, rep3


title: CD34+ HSPCs, day 4 under VPA treatment,  ADT-derived cDNA

description:
Antibody-derived oligonucleotide library: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads
Antibody-derived oligonucleotide (ADT)

growth_protocol: Highly purified (90%–98%) CD34+ cells were seeded at a density of 3.3×104 cells/mL in StemSpan SFEM II (StemCell Technologies) culture medium containing 1% penicillin-streptomycin (Life Technologies) supplemented with 150 ng/mL human stem cell factor (SCF), 100 ng/mL human fms-like tyrosine kinase receptor 3 (FLT3 ligand), 100 ng/mL human thrombopoietin (TPO), and 50 ng/mL human interleukin 3 (IL-3) (R&D Systems)

value: Umbilical cord blood


title: CD34+ HSPCs, day 4  under VPA treatment, mRNA-derived cDNA

description:
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: CD34+ Hematopoietic Stem and Progenitor Cells (HSPCs)


title: CD34+ HSPCs, day 1  under VPA treatment, mRNA-derived cDNA


title: CD34+ HSPCs, day 1 under VPA treatment,  ADT-derived cDNA


title: eWAT, FANKO, ZT6, rep2


title: J774 KO2 UT rep3

city: Boulder

first: Edward

last: Chuong

state: Colorado

address: 3415 Colorado Ave. JSC Biotech Bldg

department: Molecular, Cellular and Developmental Biology

institute: BioFrontiers Institute at University of Colorado Boulder

data_processing:
Real-Time Analysis v3.4.4 was used for basecalling.
Adapters and low quality reads were trimmed using BBDuk v38.05 with arguments 'ktrim=r k=31 mink=11 hdist=1 qtrim=r trimq=10 tpe tbo' and mapped to mm10 using hisat2 v2.1.0 with options '--rna-strandness RF --no-softclip'. Aligned fragments with an alignment score less than 10 were removed with samtools v1.10. Alignment files corresponding to technical replicates (designated as "S1" and "S2") were merged, and all samples were mapped to genes in the complete refseq annotation using featureCounts v1.6.2 with options '-s 2 -t exon -g gene_id -0 -p'. For visualization aligned fragments were converted to stranded, CPM normalized bigwigs using deepTools bamCoverage v3.0.1.
Differentially expressed genes were called using DESeq2 v1.26.0 with design '~ treatment'. For the knockout differential expression analysis, normalized count data is derived from DESeq2 comparisons between KO IFNG vs WT IFNG.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files with raw fragment counts for each gene
Supplementary files format and content: CPM normalized signal tracks in UCSC bigwig format

growth_protocol: J774 cells were routinely grown at 37C in 5% CO2 on coated plastic (Corning #430591, typically 1,000,000-2,000,000 cells in 10cm dishes) in DMEM (Gibco#10566-016) supplemented with 1X penicillin-streptomycin (Gibco #15140122) and 10% fetal bovine serum (Gibco #10437010).

extract_protocol:
RNA from J774 was harvested using Zymo Quick-RNA Miniprep Plus Kit (Zymo #R1504)). All lysates were frozen at -80°C prior to extraction, and all extracted RNA were stored at -80°C as single-use aliquots.
Libraries were generated with 200ng or 500ng RNA using KAPA mRNA HyperPrep Kit (Kapa Biosystems #08098123702) according to the manufacturer's instructions. Briefly, single-indexed adapters (Kapa Biosystems #08005699001) or unique dual-indexed adapters (Kapa Biosystems #KK8727) were added to each sample at a final concentration of ? nM. Excess adapter was removed using sequential 0.63X and 0.70X KAPA Pure Bead (KAPA #KK8002) cleanups.

treatment_protocol: Cells were either untreated or stimulated with 100 ng/mL mouse IFNG (R&D Systems #485-MI-100) for 4h.

value: B2_Mm2 knockout

value: untreated


title: J774 KO2 IFNG 4h rep1

value: IFNG


title: J774 KO2 IFNG 4h rep2


title: J774 KO2 IFNG 4h rep3


title: CD34+ HSPCs, day 0, mRNA-derived cDNA

value: RNA


title: CD34+ HSPCs, day 0,  ADT-derived cDNA

value: ADT


title: J774 KO2 UT rep2


title: eWAT, FANKO, ZT22, rep4


title: 11-cb1rko-bleo

city: Gothenburg

first: Muhammad

last: Arif

state: Västra Götaland

address: Blå Straket 5/WLAB

department: Department of Molecular and Clinical Medicine

country: Sweden

institute: University of Gothenburg

data_processing:
Kallisto with index generated from GRCm39
Protein_coding transcripts were summed to get the gene expression levels
Assembly: GRCm39
Supplementary files format and content: Estimated counts and TPM

source_name: Lung

extract_protocol:
Lower right lobe of the lung tissues was immediately placed in RNAlater solution, then held on ice for 4–5 hours, and then stored at -80ºC until the RNA extraction procedure. RNA extraction was performed using RNeasy Mini Kits from Qiagen (Valencia, CA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on flowcells. After clustering, the flowcells were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.

value: Lung

value: CB1R KO + Bleomycin


title: J774 KO2 UT rep1


title: PA14_EV_42I

city: Hanover

first: Thomas

middle: H.

last: Hampton

state: NH

address: Dewey Field Road, HB 7550

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth

data_processing:
Raw reads were trimmed using CLC Genomics Workbench software (Qiagen).
Trimmed reads were aligned to the Pseudomonas earuginosa PA14 reference genome using CLC Genomics Workbench.
Assembly: UCBPP-PA14 NC_008463
Supplementary files format and content: csv file with counts for reads that aligned with the PA14 reference

organism:
Pseudomonas aeruginosa
Homo sapiens

source_name: Pseudomonas aeruginosa

growth_protocol: P. aeruginosa strain PA14 were grown in Luria broth. Primary human airway epithelial cells from 3 donors were obtained from Dr. Scott Randell (University of North Carolina, Chapel Hill, NC) and cultured in BronchiaLife basal medium (Lifeline Cell Technology, Frederick, MD, Cat. # LM-0007) supplemented with the BronchiaLife B/T LifeFactors Kit (Lifeline Cell Technology, Cat. # LS-1047) as well as 10,000 U/ml Penicillin and 10,000 μg/ml Streptomycin (Sigma-Aldrich, Cat. # P4333). EVs were purified from cell culture supernatants (passages 4-8) using the ExoQuick-TC EV isolation kit (System Biosciences, Palo Alto, CA, Cat. # EXOTC50A-1).

extract_protocol:
Total RNA was isolated with the miRNeasy Mini Kit (Qiagen, Germantown, MD, Cat. # 217004), including the on-column DNA digestion. RNA was ribosome-depleted prior to library prep.
Sequencing libraries were prepared with an Illumina Stranded mRNA Prep kit (Illumina).
150-bp single-end reads were generated using an Illumina MiniSeq.

treatment_protocol: P. aeruginosa (1.5E+07 CFU) were exposed to PBS vehicle control or EVs (5E+09 EV/ml) for 6 h. To avoid possible carry-over of EVs (and miRNA) attached to the outside of the bacteria, the bacteria were washed with PBS and the bacterial outer membrane was lysed with EDTA to release periplasmic contents and factors associated with the bacterial outer membrane and periplasm (77-79). The cells were then washed again in PBS, and cytoplasmic RNA was harvested after lysis of bacterial cell wall and inner membrane.

value: airway epithelial cell EVs donor 42I

value: bacterial cell


title: PA14_EV_55J

value: airway epithelial cell EVs donor 55J


title: 10-cb1rko-bleo


title: PA14_EV_25J

value: airway epithelial cell EVs donor 25J


title: eWAT, FANKO, ZT22, rep3

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)


title: J774 KO1 IFNG 4h rep3


title: eWAT, FANKO, ZT22, rep2

value: epididymal white adipose tissue


title: 9-cb1rko-bleo


title: eWAT, FANKO, ZT22, rep1

value: male


title: eWAT, FANKO, ZT6, rep1

value: fat-specific Nampt knockout


title: d83_IM_5

type: protein

city: Irvine

first: Sharon

last: Jan

state: CA

address: 812 Medical Plaza Dr Rm 387 Med Surge II

department: Physiology & Biophysics

institute: UC Irvine

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

scan_protocol: Slides were imaged using the ArrayCam system (https://gracebio.com/) for 200ms and images processed using ScanArray Express.

data_processing: Raw data was normalized by subtracting the signals from plasma collected at day 0

label: biotin anti-mouse IgG, streptavidin Qdot 800

source_name: Plasma

label_protocol: No labeling

extract_protocol: Sera samples were extracted from cheek bleeds with a needle and collected by capilary. Plasma was then separated from the blood cells by centrifugation.

value: separated whole blood


title: d83_IM_4


title: C. elegans mdt-15(tm2182) 4

type: RNA

city: Vancouver

first: Stefan

last: Taubert

state: BC

address: 950 W 28th Ave, CMMT Room 2024

department: Medical Genetics

country: Canada

institute: UBC

description: Gene expression in 4th larval stage

hyb_protocol: Hybridizations were performed for 14 hrs, according to the manufacturers protocol.

scan_protocol: Arrays were scanned using the Agilent microarray scanner and raw signal intensities were extracted with Feature Extraction v9.1 software (Agilent).

data_processing: This dataset was normalized using the quantile normalization method (Bolstad et al., 2003). No background subtraction was performed, and the median feature pixel intensity was used as the raw signal before normalization. A small number of probes (245) have replicate spots, and these were summarized by taking the median intensity. All arrays were of good quality and had similar foreground and background signal distributions for both mRNA and control probes. This suggests that quantile normalization is appropriate. To identify differentially expressed genes, a linear model was fit to the comparison to estimate the mean M values and calculate moderated t-statistic, B statistic, false discovery rate and p-value for each gene for the comparison of interest. Adjusted p-values (AdjP) were produced as described (Holm, 1979). All procedures were carried out using functions in the R package limma in Bioconductor (Gentleman et al., 2004; Smyth, 2004)

organism: Caenorhabditis elegans

source_name: mdt-15(tm2182) mutant

label_protocol: RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent). Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to the microarrays (Agilent GPL10094: Agilent-020186 C. elegans (V2) Gene Expression Microarray (Feature Number version)).

growth_protocol: We grew synchronized mid-L4 stage worms (wild-type N2 worms and mdt-15(tm2182) mutants that had been outcrossed 6 times to corresponding WT) that were grown on nematode growth medium (NGM)-lite agar plates seeded with Escherichia coli strain OP50, incubated at 20°C. 4 independent biological repeats (individual worms growths) were collected per strain. ~4000 worms/sample were harvested in M9, washed 3x15ml M9, flash-frozen in liquid N2 and then stored in a -80oC freezer until RNA processing

extract_protocol: Total RNA was extracted by the Trizol extraction method as described in Taubert S et al., PLoS Genetics 2008 (PMID: 18454197). RNA quality was assessed on an Agilent 2100 Bioanalyzer using a Pico Chip (Agilent Technologies, Palo Alto, CA).

treatment_protocol: No treatment. WT vs mutant comparison

value: whole worm

value: mdt-15(tm2182) mutant

tag: developmental stage

value: L4 stage (synchronized)

value: hermaphrodite


title: C. elegans mdt-15(tm2182) 3

description: Gene expression in 4th larval stage


title: J774 KO1 IFNG 4h rep2

value: B2_Mm2 knockout

value: IFNG


title: C. elegans mdt-15(tm2182) 1

description: Gene expression in 4th larval stage


title: C. elegans mdt-15(tm2182) 2

description: Gene expression in 4th larval stage


title: J774 KO1 IFNG 4h rep1


title: d83_IM_2


title: J774 KO1 UT rep3

value: untreated


title: eWAT, FANKO, ZT18, rep3


title: eWAT, FANKO, ZT18, rep4


title: 7-Wt-Bleo

value: Lung

value: wild-type+ Bleomycin


title: eWAT, FANKO, ZT18, rep2


title: 5-wt-bleo


title: J774 KO1 UT rep2


title: eWAT, FANKO, ZT18, rep1


title: 8-cb1rko-bleo

value: CB1R KO + Bleomycin


title: 4-Wt-Bleo-B2


title: d83_IM_1


title: d83_IM_3


title: eWAT, FANKO, ZT10, rep4


title: 2-wt-bleo


title: 4-wt-bleo


title: d83_SC_3


title: d83_SC_5


title: d83_SC_4


title: eWAT, FANKO, ZT10, rep3


title: 26-Wt-C

value: Control


title: J774 WT3 IFNG 4h rep2

value: wildtype


title: eWAT, FANKO, ZT10, rep2

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)


title: J774 WT3 IFNG 4h rep1


title: 24-wt-c


title: J774 KO1 UT rep1


title: eWAT, FANKO, ZT10, rep1

value: epididymal white adipose tissue


title: 21-wt-c


title: J774 WT3 UT rep2


title: d67_IM_5


title: J774 WT3 IFNG 4h rep3


title: eWAT, wildtype, ZT6, rep4

value: male


title: d83_SC_2


title: 3-wt-c


title: d83_SC_1


title: J774 WT3 UT rep1


title: eWAT, wildtype, ZT6, rep3


title: 8-Bleo7D-6

extract_protocol:
RNA extraction was performed using RNeasy Mini Kits from Qiagen (Valencia, CA). One microgram of total RNA was reverse transcribed to cDNA using Bio-Rad iScript cDNA synthesis kit (Hercules, CA).
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using manufacturer’s instructions (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads.  Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. cDNA fragments were end repaired and adenylated at 3’ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The sequencing libraries were validated on the Agilent TapeStation (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) as well as by quantitative PCR (KAPA Biosystems, Wilmington, MA, USA).
The sequencing libraries were clustered on flowcells. After clustering, the flowcells were loaded on to the Illumina HiSeq instrument (4000 or equivalent) according to manufacturer’s instructions.  The samples were sequenced using a 2x150bp Paired End (PE) configuration. Image analysis and base calling were conducted by the HiSeq Control Software (HCS). Raw sequence data (.bcl files) generated from Illumina HiSeq was converted into fastq files and de-multiplexed using Illumina's bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.


title: eWAT, wildtype, ZT6, rep2


title: J774 WT2 IFNG 4h rep2


title: 6-Bleo7D-4


title: eWAT, wildtype, ZT6, rep1


title: J774 WT3 UT rep3


title: d67_IM_3


title: d67_IM_4


title: 5-Bleo7D-3


title: J774 WT2 UT rep3


title: eWAT, wildtype, ZT22, rep4


title: eWAT, wildtype, ZT22, rep3


title: d67_IM_1


title: J774 WT2 IFNG 4h rep1


title: d67_IM_2


title: d67_SC_5


title: 39-Bleo28D-7


title: eWAT, wildtype, ZT22, rep2


title: 37-Bleo28D-5


title: d67_SC_4


title: eWAT, wildtype, ZT22, rep1


title: J774 WT2 UT rep2


title: d67_SC_3


title: 7-Bleo7D-5


title: J774 WT1 IFNG 4h rep3


title: d67_SC_2


title: J774 WT2 IFNG 4h rep3


title: d67_SC_1


title: d49_IM_5


title: eWAT, wildtype, ZT18, rep4


title: 34-Bleo28D-2


title: eWAT, wildtype, ZT18, rep3


title: 33-Bleo28D-1


title: d49_IM_4


title: eWAT, wildtype, ZT18, rep2


title: J774 WT1 UT rep3


title: 30-Bleo21D-8


title: 32-Control28D-8


title: J774 WT2 UT rep1


title: eWAT, wildtype, ZT10, rep4


title: J774 WT1 IFNG 4h rep1


title: 36-Bleo28D-4


title: d49_IM_3


title: J774 WT1 UT rep2


title: 3-Bleo7D-1


title: d49_SC_5


title: J774 WT1 UT rep1


title: 29-Bleo21D-7


title: d49_IM_1


title: J774 WT1 IFNG 4h rep2


title: eWAT, wildtype, ZT10, rep2


title: 26-Bleo21D-4


title: eWAT, wildtype, ZT10, rep3


title: eWAT, wildtype, ZT10, rep1


title: eWAT, wildtype, ZT18, rep1


title: 25-Bleo21D-3


title: ILCs (cartridge 1+2)

city: Newcastle Upon Tyne

first: Jing Xuan

last: Lim

address: Framlington Place

department: Bioscience Institute

country: United Kingdom

institute: Newcastle University

description: BD Rhapsody

data_processing:
Fastq files were transferred to seven brdiges platform and files were checked for quality control and DBEC files were obtained through the BD Rhapsody Targeted Analysis Pipeline run.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Melanoma tumours

extract_protocol: As per manufacturer's instruction

treatment_protocol:
None
None

value: Immune cells

value: Melanoma tumours

value: C57BL6 WT and PD1Ko

value: 6-8 weeks old


title: d49_SC_3

value: separated whole blood


title: d49_SC_4


title: d49_IM_2


title: Cochlea, miR_29aKO3

city: Yantai

first: peng

last: ma

address: Marina Road Street

institute: Binzhou Medical University

data_processing:
After the initial quantification by Qubit, the library was diluted to 1 ng/ul, and the insert size was measured by Agilent 2100 bioanalyzer, and the insert size was approximately 250-300 bp. The effective concentration of the library was >2nM, which ensured the quality of the sample library.
After passing the library check, the libraries are pooled according to their effective concentration and data yield requirements and then sequenced with Illumina PE150 (Pair end 150 bp), which refers to high-throughput double-end sequencing of 150 bp at each end.
Sequencing data quality assessment: mainly through the sequencing error rate, data volume, comparison rate and other statistics, to assess whether the library sequencing standards, meet the standards for subsequent analysis, otherwise need to re-construction or additional testing
Information mining and analysis: The RNA-seq standard analysis process includes quality control, comparison, splicing, screening, quantification, differential significance analysis and functional enrichment, as well as analysis of variable shear and variant sites associated with structural variation of transcripts.
Assembly: mm9
Supplementary files format and content: Resulting data table files; files are tab-delimited

source_name: Cochlear

extract_protocol:
Cochlear were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent
A strand-specific library was constructed using a ribosomal RNA removal method (circRNA library building adding a de-linearization RNA process). First, ribosomal RNA was removed from total RNA, followed by breaking the RNA into short fragments of 250-300 bp using RNase R enzyme. The fragmented RNA was used as a template and random oligonucleotides were used as primers to synthesise the first strand of cDNA, followed by degradation of the RNA strand with RNase H and synthesis of cDNA under a DNA polymerase I system with dNTPs (dUTP, dATP, dGTP and dCTP) as raw material for the synthesis of the second strand of cDNA. The purified double-stranded cDNA was end-repaired, A-tailed and ligated to sequencing junctions. cDNAs of around 350-400 bp were screened using AMPure XP beads. The second strand of cDNA containing U was degraded using USER enzymes and finally PCR was performed to amplify and obtain libraries.

value: Cochlear


title: Cochlea, miR_29aKO4


title: 23-Bleo21D-1


title: BAT, FANKO, ZT6, rep3

source_name: brown adipose tissue

value: brown adipose tissue

value: fat-specific Nampt knockout


title: d49_SC_2


title: Cochlea, miR_29aKO2


title: d28_IM_5


title: 22-Control21D-6


title: Cochlea, miR_29aKO1


title: BAT, FANKO, ZT6, rep2


title: d49_SC_1


title: Cochlea, WT4

value: WT


title: 17-Bleo14D-5

value: Lung


title: 18-Bleo14D-6


title: 16-Bleo14D-4


title: Cochlea, WT2


title: d28_IM_3


title: BAT, FANKO, ZT22, rep3


title: 15-Bleo14D-3


title: BAT, FANKO, ZT6, rep4


title: BAT, FANKO, ZT22, rep2


title: 13-Bleo14D-1


title: BAT, FANKO, ZT22, rep1


title: BAT, FANKO, ZT22, rep4


title: d28_IM_2


title: 14 month old

city: Pittsburgh

first: Giuseppe

last: Intini

state: Pennsylvania

address: 335 Sutherland Drive, 508 Salk Pavilion

department: Periodontics and Preventive Dentistry

institute: University of Pittsburgh

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0
Single cell counts were filtered to remove potential cell duplets and dead cell by excluding cells with <200 and >6000 genes and cells with a mitochondrial gene percentage of >10% using Partek®Flow®software, v10.0.
Normalized counts on a per-cell basis were expressed in count per million (CPM). Graph-based analysis and successive evaluation with uniform manifold approximation and projection (UMAP) were executed over the first 11 principal components, with resolution parameters of 0.5 for all using Partek®Flow®software, v10.0.
Assembly: mm10
Supplementary files format and content: h5 format

source_name: Calvarial sutures

extract_protocol:
Mice were euthanized following the IACUC guidelines and sagittal, coronal, and lambdoid sutures were manually dissected using a dissecting microscope. Upon dissection, and consistently for all samples, no more than 1/4 mm of bone tissue surrounding the sutures was collected. Samples were incubated in 4 mL of collagenase solution (3.2mg Collagenase Type 2, Worthington-Biochem, catalog#LS004176, 1 mL of Trypsin-EDTA, GIBCO, catalog#25200-056 and 3mL of DPBS, GIBCO catalog#14190-144) for 20 minutes at 37°C, for 4 consecutive times. Cell suspensions derived from each incubation were pulled and centrifuged, and the obtained cell pellet was resuspended in 10mL of media.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. cDNA library QC and quantification were performed using Agilent 4150 TapeStation with High Sensitivity D1000 ScreenTape® Page.

treatment_protocol: Mice were anesthetized by intraperitoneal injection of ketamine (100 mg/Kg) and xylazine (10 mg/Kg), and a longitudinal incision was made with a #15 scalpel blade over the midline of the calvarial skin to expose the parietal bones. Two equidistant holes, one in each parietal bone, were manually created 2 mm from the sagittal suture using a 0.25 mm round dental bur. Next, the expansion apparatus, made by bending a 0.3 mm (diameter) orthodontic nickel-titanium wire was inserted in the holes. Using a dial tension gauge, (Teclock, Nagano, Japan) the wire was calibrated to exert an initial tensile force of 0.2N. Then, using absorbable 5-0 Vicryl sutures (Hu-Friedy, Chicago, IL, United States), the incision was closed, fully covering the expansion devise. Control mock surgery (NON EXPANDED group) consisted in the creation of the 2 equidistant holes in the parietal bones without the insertion of the expansion apparatus. Immediately after surgery, and every 12 h for the following 48 h, animals were injected with Buprenorphine (subcutaneous injection, 0.05 mg/kg) for pain control.

value: Calvarial sutures

value: Male

value: Wild type

value: 14 months old


title: 4 month old

description: 10X Genomics

value: 4 months old


title: BAT, FANKO, ZT6, rep1

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)


title: BAT, FANKO, ZT18, rep4

value: male


title: Cochlea, WT1


title: 2 month old EXPANDED

description: 10X Genomics

value: 2 months old

value: surgery with expansion device


title: d28_IM_4


title: d28_IM_1


title: d28_SC_5


title: 11-Control14D-3


title: Cochlea, WT3


title: 1-Control7D-1


title: 12-Control14D-4


title: BAT, FANKO, ZT18, rep3


title: d28_SC_4


title: BAT, FANKO, ZT18, rep2


title: 2 month old NON EXPANDED

description: 10X Genomics

value: surgery without expansion device


title: 2 month old

description: 10X Genomics


title: BAT, FANKO, ZT18, rep1


title: 4 day old

description: 10X Genomics

value: 4 days old


title: d28_SC_1

value: separated whole blood


title: d28_SC_3


title: C57BL/6N mice,Dilated cardiomyopathy,M-3

city: Shijiazhuang

first: Zhimin

address: Zhongshan East Road

department: Department of phamarcy

institute: Hebei Medical University

data_processing:
Raw data (or Raw reads) of fastq format were firstly processed through in-house perl scripts. Int his step, remove the adapter sequence and filter out low quality (low quality, the number of lines with astring quality value less than or equal to 25 accounts for more than 60% of the entire reading) and N (N means that the base information cannot be determined) ratio is greater than 5% reads to obtain clean reads that can be used for subsequent analysis.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software (http://daehwankimlab.github.io/hisat2/) to obtain mapped reads.
FeatureCounts (http://subread.sourceforge.net/) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Left ventricle

extract_protocol:
Total RNA was extracted from the heart tissue using TRIzol® Reagent according to the manufacturer’s instructions (Magen).
Paired-end libraries were prepared using an ABclonal mRNA-seq Lib Prep Kit (ABclonal, China) following the manufacturer’s instructions.

value: Left ventricle

tag: disease state

value: Dilated cardiomyopathy

value: Intraperitoneal injection of doxorubicin


title: BAT, FANKO, ZT10, rep4

value: brown adipose tissue

value: fat-specific Nampt knockout


title: C57BL/6N mice,Dilated cardiomyopathy,M-2


title: BAT, FANKO, ZT10, rep3


title: H14_2nd_assay

type: genomic

city: São Paulo

first: José

middle: Franco

last: Da Silveira

state: São Paulo

address: Rua Botucatu, 862

department: Departamento de Microbiologia, Imunologia e Parasitologia

country: Brazil

institute: Universidade Federal de São Paulo

hyb_protocol: After assembling the chamber the Hybridization was performed into the oven rotator rack at 67 ºC, 20 rpm for 24 hours, according to the manufacturer's instructions.

scan_protocol: The Scanning of the microarray slides was performed in a Agilent G2565CA Microarray Scanning System following the manufacturer's steps described in Oligonucleotide Array-Based CGH for Genomic DNA Analysis - Enzymatic Labeling (Agilent).

data_processing:
Raw data was first normalized using Feature Extraction software (Agilent).
Agilent Genomic Workbench Standard Edition 6.5 was then used to perform CNV interval detection. The QC metrics motif of Workbench 6.5 ensured adequate quality control of the hybridization data. In our study, an array signal which met the requirements if intensity value >50 and signal-to-noise ratio >25 was included in the analysis. The Aberration Detection Method 2 algorithm was used with a threshold of 6 and bin size of 10 to identify genomic variation. Additionally, we applied a relatively stringent post-analysis filter (4 probes, 0.5 log ratio) to ignore small, spurious or low-quality
Logratio.xlsx: represents final processed data, contains the probes, gene name, genomic location, and log2 of (Cy5/Cy3)ratios.

molecule: genomic DNA

organism: Trypanosoma rangeli

source_name: Epimastigotes (test)

label_protocol: Fluorescent labeling of gDNA was performed with SureTag DNA Labeling kit (Agilent) following the manufacturer's instructions.

growth_protocol: Axenic cultures at 28 °C in liver-infusion tryptose medium (LIT) containing 10% fetal calf serum.

extract_protocol: Genomic DNA extraction was performed with the Dneasy Blood & Tissue kit (Qiagen) using 5x107 cells/mL according to the manufacturer's instructions.

tag: Stage

value: Epimastigotes

value: Axenic culture

tag: assay

value: H14 Second Assay

organism: Trypanosoma cruzi

source_name: Epimastigotes (control)

value: CL brener

value: CLB Second Assay


title: R1625_2nd_assay

value: R1625 Second Assay


title: d28_SC_2

tag: tissue


title: C23_2nd_assay

value: C23 Second Assay


title: C57BL/6N mice,Dilated cardiomyopathy,M-1

last: Wu

value: male


title: BAT, FANKO, ZT10, rep1

value: NamptTM1Jtree line crossed with the Adiponectin-Cre mice (010803, Jackson Labs)


title: C57BL/6N mice,Control,C-3

value: health

value: Intraperitoneal injection of saline


title: C57BL/6N mice,Control,C-2


title: BAT, FANKO, ZT10, rep2


title: BAT, wildtype, ZT6, rep4

value: wildtype


title: WT_3_Non

city: Aurora

first: Kristen

last: Wells

address: 1775 Aurora Ct,

department: Barbara Davis Center

institute: University of Colorado Anschutz

description: ZNT8 +/+ Rep 2 not treated

data_processing:
Fastqc (version 0.11.7) was run on the raw fastq files to check quality
Cutadapt (version 1.16) was used to trim illumina sequencing adaptors from the raw fastq files. Cutadapt was run using the following parameters -m 20 -a 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
STAR (version 2.5.2a) was used to align reads to the mouse GRCm38 genome post adaptor trimming. Star was run using the following parameters --outFilterMultimapNmax 10 --outFilterMismatchNmax 10 --outFilterMismatchNoverReadLmax 0.04 --tSAMmultNmax 1 --outMultimapperOrder Random --outSAMattrIHstart 0 --outSAMstrandField intronMotif
Reads were counted using featureCounts (version 1.6.2) from the subread package. FeatureCOunts was run with the following parameters --extraAttributes 'gene_name,gene_biotype' -s 1
rRNAs, snoRNAs, and snRNAs were filtered out of the count matrix and raw reads were loaded into the DESeq2 package (version 1.30.0). DESeq analysis was performed using the following design ~group + treatment + group:treatment to allow for interaction between the genotype and treatment.
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab delimited text file of counts output by feature counts and tab delimited meta data file with sample information

source_name: Pancreatic islet

extract_protocol:
Islets were isolated from 17-week-old male mice (n=3) and digested by Cizyme RI (Vitacyte), followed by Lympholyte 1.1 (Cedarlane) gradient centrifugation. Islets were cultured in RPMI1640 media (10 % FBS, 1 % P/S) for overnight for stabilization. After stabilization, Islets were cultured RPMI 1640 or RPMI 1640 with cytokines (100 pg/ml TNF-alpha, 150 pg/ml IL-1beta, 10 pg/ml IFN-gamma) for 24 hours. After cytokine treatment, wash with PBS and extract RNA.
RNA was isolated with the RNeasy Micro kit (QIAGEN). Sequencing was performed using Illumina NovaSEQ6000.

treatment_protocol: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g

value: Pancreatic islet

value: 17 weeks

value: islet cultured RPMI1640 media (no cytokines) 24 hours


title: WT_2_Non

description: ZNT8 +/+ Rep 1 not treated

growth_protocol: Islets were cultured in RPMI1640 media (10 % FBS, 1 % P/S) for overnight for stabilization.


title: WT_4_Cyto

description: ZNT8 +/+ Rep 3 cytokine treated

value: 100 pg/ml TNF-a, 150 pg/ml IL-1b, 10 pg/ml IFN-g, 24 hours


title: BAT, wildtype, ZT6, rep3

value: brown adipose tissue