title: Rattus norvegicus_male_gastrocnemius_21 months_rep3

tag: tissue

value: gastrocnemius

value: Sprague Dawley

value: 21 months


title: 13N023 high dose IV BCG wk2

status: Public on Jun 19 2023

type: SRA

city: Stanford

first: Yiran

middle: E

last: Liu

state: CA

address: 291 Campus Drive

country: USA

institute: Stanford University

library_source: transcriptomic

data_processing:
We trimmed reads with Cutadapt and performed quality control checks with FastQC before aligning to the Macaca mulatta genome (mmul_10) using kallisto. We removed genes in the globin family, genes that were unannotated, and genes with fewer than 5 reads in over two-thirds of all samples. We applied DESeq2’s variance stabilizing transformation to generate normalized expression values.
Assembly: mmul10
Supplementary files format and content: Tab-delimited text file containing a matrix with normalized expression values for all samples

molecule: total RNA

organism: Macaca mulatta

source_name: Whole Blood

extract_protocol:
Whole blood was collected in PAXgene blood RNA tubes (Qiagen) and stored at -80C for batch processing at end of study. RNA was extracted using the PAXgene Blood RNA Tube kit (PreAnalytiX) as instructed. Globin mRNA was removed using GLOBINclear Kit (Life Technologies) and remaining mRNA concentration and quality was measured on an Agilent Bioanalyzer using an Agilent nano 6000 kit.
Illumina-ready libraries were generated using NEBNext Ultra II RNA Preparation reagents (New England BioLabs).

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: Rattus norvegicus_male_gastrocnemius_21 months_rep2

city: Tarrytown

first: Kun

last: Xiong

state: NY

address: 777 Old Saw Mill River Road

department: Molecular Profiling and Data Science

institute: Regeneron Pharmaceuticals

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: B6.0
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Rattus norvegicus

source_name: gastrocnemius

growth_protocol: Male and female C57BL/6J mice were purchased from Jackson Laboratory (USA) at various ages and maintained at Regeneron animal holding facilities for ~12 weeks prior to tissue collection under specific pathogen free (SPF) conditions. Mice were housed in groups of 5 per cage with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (PicoLab Rodent Diet 20, Lab Supply) and water. Male Sprague Dawley (SD) rats were purchased at 3-4 weeks of age from Envigo (Indianapolis, USA) and aged at Envigo under specific pathogen free (SPF) conditions. Rats were imported to New York Medical College animal holding facilities 8-12 weeks prior to tissue collection. Once imported, rats were housed two per cage at the SPF facility with controlled temperature and light (22℃, 12-h light/12-h dark cycle: lights on at 0600h/lights off at 1800h) and with ad libitum access to food (2014 Teklad Global 14% Protein diet, Envigo) and water.

extract_protocol:
Tissue collection occurred over several months and tissues from the same age group (n = 8-12 per group) were collected on the same day between 9am and 1pm. Prior to tissue collection, mice were killed by CO2 asphyxiation. Diaphragm, gastrocnemius, soleus, and tibialis anterior muscles were preserved in RNA later and stored at -80℃. RNA was extracted from tissues preserved in RNA later using MagMax-96 Total RNA isolation kit (Thermo Fisher). The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent).
The RNA concentration was quantified using NanoDrop Spectrophotometer (NanoDrop Technologies) and the integrity assessed using Fragment Analyzer (Agilent). Strand specific total RNA-seq libraries were prepared using Kapa RNA HyperPrep kit (Roche) with Fastselect rRNA HMR ribosome RNA removal kit (Qiagen).

tag: strain

tag: Sex

value: male

tag: time


title: S43.SLE.BM4.X14

city: Melbourne

first: Katherine

last: Monaghan

state: Victoria

address: 30 Flemington Rd, Parkville

department: Research and Development

country: Australia

institute: CSL Limited

data_processing:
Image analysis was performed in real time by the HiSeq Control Software (HCS) v2.2.68 and Real Time Analysis (RTA) v1.18.66.3, running on the instrument computer. RTA performs real-time base calling on the HiSeq instrument computer. Then the Illumina bcl2fastq 2.17.1.14 pipeline was used to generate the sequence data.
Sequenced reads were mapped to human reference genome GRCh38.p12 using star (v2.6.1)13 with default parameters except for the --quantMode TranscriptomeSAM setting.
Reads were summarized at the gene level using featureCounts tool from the Subread package (v1.6.4)14, in a strand-specific manner.

organism: Homo sapiens

source_name: Blood

extract_protocol:
RNA extraction was done with Qiagen RNeasy plus mini kit (Cat#74134/74136)
-RNA was extracted in batched as cell pellets from each group of donors were frozen together in 96 well plates
-The plates were removed from the freezer at thawed at 4°C (approx. 1 hour) and stored at 4°C for the day while different wells had RNA extracted
-The cell pellets in 125 μl RNAprotect were mixed up and down and moved into 1.5 ml microfuge tube (eppendorf). -Cells were pelleted by centrifuging for 5 mins at 5000 x g.
-The SN was then aspirated
-RNA was then extracted using the manufacturer’s instructions from step 2, Briefly-
-The pellets were loosened by flicking
-Cells were then disrupted with RLT plus buffer by adding 350 μl RLT plus buffer and vortexing to mix.
-Cells were then homogenised by pipetting sample on a QIAshredder column and centrifuging 2 mins at full speed -The lysate was transferred to a gDNA eliminator spin column and centrifuge for 30s at 10,000 x g, collect flow through (can repeat spin if membrane has any remaining liquid)
-350 μl 70% ethanol was added and mixed well by pipetting (adjust volume if ethanol if some lysate lost in previous steps)
-Sample and any precipitate was transferred to a RNeasy spin column, close the lid gently and centrifuge for 15 sec at 10,000 x g, discard flow through
-700 μl buffer RW1 was added to the column, close the lid gently and centrifuge for 15 sec at 10,000 x g, flow through discarded
-500 μl buffer RPE was added to the column, close the lid gently and centrifuge for 15 sec at 10,000 x g, flow through discarded
-500 μl buffer RPE was added to the column, close the lid gently and centrifuge for 2 mins at 10,000 x g, collection tube and flow through discarded
-Column placed in new 2 ml collection tube, lid of spin column opened, spin at full speed for 5 mins, collection tube and flow through discarded
-RNeasy spin column placed in a new 1.5 ml collection tube, 30 μl RNase free water (warmed to 55°C) was added directly to the centre of the spin column and incubated for 10 mins, then centrifuged for 1 min at 16,000 x g
-An additional 10 μl RNase free water was added, then centrifuged for 1 min at 16,000 x g – approx. 35 μl will be eluted for potential RNAseq
-Eluted RNA was immediately stored at -80°C and shipped for sequencing for RNAseq frozen on dry ice
RNA libraries were prepared for sequencing using standard Illumina protocols for polyA extraction for samples from stimulated cells.

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

tag: drug

tag: stimulus

tag: stimdescription

value: 10 ug/ml POLY I:C


title: Rattus norvegicus_male_gastrocnemius_21 months_rep1

tag: tissue


title: Mus musculus_female_soleus_24 months_rep3

data_processing:
Sequencing reads were processed with ArrayStudio RNA-seq pipeline to quantify gene expression levels
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

organism: Mus musculus

source_name: soleus

value: soleus

value: female

value: 24 months


title: 13N023 high dose IV BCG d2

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome


title: 13N025 high dose IV BCG d2


title: Mus musculus_female_soleus_24 months_rep2

tag: strain

tag: Sex

tag: time


title: Mus musculus_female_soleus_24 months_rep8


title: 13N023 high dose IV BCG pre

value: pre


title: S43.SLE.BM4.X12

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_18 months_rep9

tag: tissue

value: gastrocnemius

value: Sprague Dawley

value: 18 months


title: Rattus norvegicus_male_gastrocnemius_21 months_rep4

value: 21 months


title: S43.SLE.BM4.X11

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: 13N022 high dose IV BCG wk12

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_female_soleus_24 months_rep0

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_gastrocnemius_18 months_rep8

value: male


title: Mus musculus_female_soleus_24 months_rep1


title: S43.SLE.BM4.X10

value: Blood

tag: donorid

tag: group

tag: diseasenormal

value: Disease

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_24 months_rep5

tag: tissue

value: soleus

value: female

value: 24 months


title: 13N022 high dose IV BCG wk4

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: 13N022 high dose IV BCG wk2

tag: log grans_nx

tag: protect outcome


title: Mus musculus_female_soleus_21 months_rep7

tag: strain

tag: Sex

tag: time


title: Rattus norvegicus_male_gastrocnemius_18 months_rep7

value: gastrocnemius


title: Mus musculus_female_soleus_24 months_rep4


title: S43.SLE.362.X9

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

tag: stimulus

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_21 months_rep6

tag: tissue

value: 21 months


title: Rattus norvegicus_male_gastrocnemius_18 months_rep6

value: Sprague Dawley

value: 18 months


title: 13N022 high dose IV BCG d2

value: Whole Blood

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

value: high

tag: timeafterbcg

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx


title: S43.SLE.BM4.X13

tag: donorid

tag: group

tag: diseasenormal

tag: sledai

tag: drug

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_21 months_rep0

tag: strain

tag: Sex

value: male

tag: time


title: S43.SLE.362.X8

tag: tissue

value: Blood

value: Disease

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: stimulus

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: 13N022 high dose IV BCG pre

tag: animal id

tag: pitt id

tag: bcg dose_log10

tag: dose group

tag: timeafterbcg

value: pre

tag: total mtb_cfu

tag: log mtb_cfu

tag: grans nx

tag: log grans_nx

tag: protect outcome

value: protected


title: Mus musculus_female_soleus_21 months_rep5

tag: tissue

value: soleus

tag: strain

tag: Sex

value: female

tag: time


title: S43.SLE.362.X7

tag: donorid

tag: group

tag: diseasenormal

tag: diseasegroup

value: SLE

tag: gender

value: F

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

tag: drug

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_18 months_rep5

value: gastrocnemius


title: S43.SLE.362.X6

value: Caucasian

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_18 months_rep4

value: Sprague Dawley

value: 18 months


title: Mus musculus_female_soleus_21 months_rep4

value: 21 months


title: Rattus norvegicus_male_gastrocnemius_18 months_rep3

value: male


title: Mus musculus_female_soleus_21 months_rep3


title: OTM ID wk2

value: Whole Blood

value: OTM

value: ID

value: low

tag: time after bcg


title: OTM ID d2

tag: tissue


title: S43.SLE.362.X5

value: Blood

value: Disease

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_18 months_rep2

tag: strain


title: Mus musculus_female_soleus_21 months_rep1

value: soleus

tag: Sex

value: female


title: S43.SLE.362.X4

value: SLE

value: F

value: 10 ug/ml LPS


title: Mus musculus_female_soleus_21 months_rep0

tag: time


title: Mus musculus_female_soleus_21 months_rep2


title: OTM ID wk12


title: Rattus norvegicus_male_gastrocnemius_18 months_rep1

value: gastrocnemius


title: Rattus norvegicus_male_gastrocnemius_18 months_rep10

value: Sprague Dawley


title: OTM ID pre

value: pre


title: S43.SLE.362.X3

tag: donorid

value: Caucasian

value: 10% SLE patient #4 sera


title: ONF ID/AE wk12

value: Whole Blood

value: ONF

value: ID/AE

value: high


title: S43.SLE.362.X2

value: Blood

tag: group

value: 0.25 uM CpGc


title: Mus musculus_female_soleus_18 months_rep7

value: 18 months


title: Rattus norvegicus_male_gastrocnemius_18 months_rep0

value: male


title: S43.SLE.362.X1

tag: diseasenormal

value: Disease

value: Untreated and Unstimulated


title: Rattus norvegicus_male_gastrocnemius_12 months_rep9

value: 12 months


title: S43.SLE.362.X14

tag: diseasegroup

value: SLE

value: F

value: 10 ug/ml POLY I:C


title: ONF ID/AE d2


title: Rattus norvegicus_male_gastrocnemius_12 months_rep8

value: gastrocnemius

value: Sprague Dawley


title: Mus musculus_female_soleus_18 months_rep5

value: soleus

value: female


title: Mus musculus_female_soleus_18 months_rep6


title: ONF ID/AE pre

value: Whole Blood

value: ONF

value: pre


title: Mus musculus_female_soleus_18 months_rep4


title: Rattus norvegicus_male_gastrocnemius_12 months_rep7


title: S43.SLE.362.X13

value: Blood

tag: gender

value: Caucasian

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: S43.SLE.362.X12

tag: diagnosis

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_18 months_rep3

value: 18 months


title: OMI HD-ID wk12

value: OMI

value: HD-ID

value: high


title: S43.SLE.362.X11

value: Disease

value: SLE

value: F

tag: age

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: S43.SLE.362.X10

tag: ethnicity

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_12 months_rep6

value: gastrocnemius

value: Sprague Dawley

value: male

value: 12 months


title: Rattus norvegicus_male_gastrocnemius_12 months_rep5


title: Mus musculus_female_soleus_18 months_rep2

value: soleus

value: female


title: S42.SLE.BM4.X9

value: Blood

value: M

value: Asian

tag: sledai

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_soleus_18 months_rep0

value: 18 months


title: ONF ID/AE wk2

value: Whole Blood

value: ONF

value: ID/AE

value: high


title: Mus musculus_female_soleus_18 months_rep1


title: Rattus norvegicus_male_gastrocnemius_12 months_rep4


title: Rattus norvegicus_male_gastrocnemius_12 months_rep3


title: S42.SLE.BM4.X6

value: Disease

value: SLE

tag: drug

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_gastrocnemius_12 months_rep2

value: gastrocnemius

value: Sprague Dawley


title: Mus musculus_female_soleus_12 months_rep7

value: 12 months


title: Mus musculus_female_soleus_12 months_rep5

value: soleus


title: OHJ AE wk2

value: OHJ

value: AE


title: OHJ AE d2


title: OHJ AE wk12


title: OMI HD-ID pre

value: OMI

value: HD-ID

value: pre


title: OMI HD-ID wk2


title: OMI HD-ID d2


title: S42.SLE.BM4.X4

value: Blood

value: M

value: Asian

tag: stimulus

value: 10 ug/ml LPS


title: Rattus norvegicus_male_gastrocnemius_12 months_rep1

value: male


title: O96 ID wk12

value: Whole Blood

value: ID

value: low


title: Rattus norvegicus_male_diaphragm_9 months_rep9

source_name: diaphragm

value: diaphragm

value: 9 months


title: Rattus norvegicus_male_gastrocnemius_12 months_rep0

value: gastrocnemius

value: Sprague Dawley

value: 12 months


title: S42.SLE.BM4.X3

value: Disease

value: SLE

tag: stimdescription

value: 10% SLE patient #4 sera


title: O96 ID wk2

tag: time after bcg


title: Mus musculus_female_soleus_12 months_rep3

tag: tissue

value: soleus

value: female


title: S42.SLE.BM4.X2

value: Blood

value: M

value: 0.25 uM CpGc


title: S42.SLE.BM4.X8

value: Asian

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: O96 ID d2

value: Whole Blood

value: ID


title: S42.SLE.BM4.X1

value: Untreated and Unstimulated


title: Mus musculus_female_soleus_12 months_rep2

tag: strain


title: Mus musculus_female_soleus_12 months_rep1

tag: Sex


title: Rattus norvegicus_male_diaphragm_9 months_rep8

value: diaphragm

value: male

tag: time

value: 9 months


title: Mus musculus_female_soleus_12 months_rep6

value: 12 months


title: S42.SLE.BM4.X5

tag: donorid

value: Disease

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: OHJ AE pre

value: OHJ

value: AE

value: high

value: pre


title: Rattus norvegicus_male_diaphragm_9 months_rep6

value: Sprague Dawley


title: S42.SLE.BM4.X14

value: Blood

tag: group

value: SLE

value: M

value: 10 ug/ml POLY I:C


title: Mus musculus_female_gastrocnemius_6 months_rep7

value: gastrocnemius

value: female

value: 6 months


title: S42.SLE.BM4.X13

tag: diseasenormal

value: Asian

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_9 months_rep5

value: diaphragm

value: male

value: 9 months


title: Mus musculus_female_soleus_12 months_rep0

value: soleus

value: 12 months


title: O96 ID pre

value: Whole Blood

value: ID

value: low


title: O5G HD-ID wk12

value: HD-ID

value: high

value: protected


title: Mus musculus_female_gastrocnemius_6 months_rep6


title: O5G HD-ID wk2


title: Mus musculus_female_gastrocnemius_6 months_rep5


title: Mus musculus_female_soleus_12 months_rep4


title: Rattus norvegicus_male_diaphragm_9 months_rep4

value: Sprague Dawley


title: Rattus norvegicus_male_diaphragm_9 months_rep3


title: S42.SLE.BM4.X12

value: Blood

value: Disease

tag: diseasegroup

value: SLE

value: M

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: S42.SLE.BM4.X10

tag: gender

value: Asian

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: O5G HD-ID d2


title: Mus musculus_female_gastrocnemius_6 months_rep4

value: gastrocnemius

value: female

value: 6 months


title: Rattus norvegicus_male_diaphragm_9 months_rep2

value: diaphragm

value: male

value: 9 months


title: S42.SLE.362.X9

tag: diagnosis

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: S42.SLE.362.X8

tag: age

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: HCL IV wk12

value: Whole Blood

value: HCL

value: IV

value: high

value: protected


title: Mus musculus_female_gastrocnemius_6 months_rep3


title: Rattus norvegicus_male_diaphragm_9 months_rep10

value: Sprague Dawley


title: O5G HD-ID pre

value: HD-ID

value: pre


title: S42.SLE.362.X6

value: Blood

value: Disease

value: SLE

value: M

tag: ethnicity

value: Asian

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_9 months_rep7

value: diaphragm

value: male

value: 9 months


title: HCL IV wk2

value: Whole Blood


title: Mus musculus_female_gastrocnemius_6 months_rep2

value: gastrocnemius

value: female

value: 6 months


title: Rattus norvegicus_male_diaphragm_9 months_rep1


title: HCL IV d2

value: HCL

value: IV

value: high

value: protected


title: S42.SLE.362.X5

value: Blood

tag: sledai

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_6 months_rep1


title: Rattus norvegicus_male_diaphragm_9 months_rep0

value: Sprague Dawley


title: S42.SLE.362.X4

value: Disease

value: SLE

value: M

tag: drug

value: 10 ug/ml LPS


title: HCL IV pre

value: pre


title: Mus musculus_female_gastrocnemius_6 months_rep0


title: S42.SLE.362.X3

value: Asian

tag: stimulus

value: 10% SLE patient #4 sera


title: Mus musculus_female_gastrocnemius_27 months_rep9

value: gastrocnemius

value: 27 months


title: Rattus norvegicus_male_diaphragm_6 months_rep9

value: diaphragm

value: male

value: 6 months


title: Rattus norvegicus_male_diaphragm_6 months_rep7


title: HCE HD-ID wk12

value: Whole Blood

value: HCE

value: HD-ID

value: high


title: HCE HD-ID d2


title: S42.SLE.362.X1

value: Blood

tag: stimdescription

value: Untreated and Unstimulated


title: Mus musculus_female_gastrocnemius_27 months_rep7

value: female


title: Mus musculus_female_gastrocnemius_27 months_rep8


title: S42.SLE.362.X2

value: Disease

value: SLE

value: M

value: 0.25 uM CpGc


title: HCE HD-ID pre

tag: time after bcg

value: pre


title: HCE HD-ID wk2

tag: tissue


title: Mus musculus_female_gastrocnemius_27 months_rep6

value: gastrocnemius

tag: strain


title: HCA AE wk12

value: HCA

value: AE


title: S42.SLE.362.X14

value: Asian

value: 10 ug/ml POLY I:C


title: Rattus norvegicus_male_diaphragm_6 months_rep6

value: diaphragm

value: Sprague Dawley

tag: Sex

value: male

value: 6 months


title: S42.SLE.362.X13

value: Blood

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_27 months_rep5

value: female

tag: time

value: 27 months


title: Rattus norvegicus_male_diaphragm_6 months_rep4


title: HCA AE wk2

value: Whole Blood

value: high


title: Mus musculus_female_gastrocnemius_27 months_rep4


title: Rattus norvegicus_male_diaphragm_6 months_rep3


title: S42.SLE.362.X12

tag: donorid

value: Disease

value: SLE

value: M

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: HCA AE d2

value: HCA

value: AE


title: Mus musculus_female_gastrocnemius_27 months_rep3

value: gastrocnemius


title: Rattus norvegicus_male_diaphragm_6 months_rep8

value: diaphragm


title: Rattus norvegicus_male_diaphragm_6 months_rep2

value: Sprague Dawley


title: Mus musculus_female_gastrocnemius_27 months_rep2


title: Rattus norvegicus_male_diaphragm_6 months_rep5

value: male


title: Rattus norvegicus_male_diaphragm_6 months_rep11

value: 6 months


title: HCA AE pre

value: pre


title: HBN ID/AE wk12

value: HBN

value: ID/AE


title: HBN ID/AE wk2


title: Mus musculus_female_gastrocnemius_27 months_rep1

value: female

value: 27 months


title: Mus musculus_female_gastrocnemius_27 months_rep0


title: S41.SLE.BM4.X7

value: Blood

tag: group

value: F

value: Caucasian

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: HBN ID/AE d2

value: Whole Blood

value: high


title: S41.SLE.BM4.X8

tag: diseasenormal

value: Disease

value: SLE

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: S41.SLE.BM4.X9

tag: diseasegroup

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_24 months_rep9

value: gastrocnemius

value: 24 months


title: Rattus norvegicus_male_diaphragm_6 months_rep1

value: diaphragm

value: Sprague Dawley

value: male

value: 6 months


title: Rattus norvegicus_male_diaphragm_6 months_rep10


title: S41.SLE.BM4.X5

tag: gender

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: S41.SLE.BM4.X6

value: Blood

tag: diagnosis

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_6 months_rep0


title: Mus musculus_female_gastrocnemius_24 months_rep8

value: female


title: S42.SLE.362.X10

value: M

tag: age

value: Asian

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: S41.SLE.BM4.X4

value: Disease

value: F

tag: ethnicity

value: Caucasian

value: 10 ug/ml LPS


title: DJF9 IV wk12

value: Whole Blood

value: IV

value: high

value: protected


title: HBN ID/AE pre

value: HBN

value: ID/AE

value: pre


title: Mus musculus_female_gastrocnemius_24 months_rep7

value: gastrocnemius

value: 24 months


title: Rattus norvegicus_male_diaphragm_27 months_rep8

value: diaphragm

value: Sprague Dawley

value: male

value: 27 months


title: DJF9 IV wk2


title: S41.SLE.BM4.X3

value: Blood

value: Disease

value: SLE

tag: sledai

value: 10% SLE patient #4 sera


title: Mus musculus_female_gastrocnemius_24 months_rep6

value: female


title: Rattus norvegicus_male_gastrocnemius_12 months_rep10

value: 12 months


title: DJF9 IV d2

value: Whole Blood

value: IV

value: high


title: Mus musculus_female_gastrocnemius_24 months_rep5


title: Rattus norvegicus_male_diaphragm_27 months_rep6


title: S41.SLE.BM4.X1

value: F

value: Caucasian

tag: drug

value: Untreated and Unstimulated


title: Rattus norvegicus_male_diaphragm_27 months_rep7


title: Rattus norvegicus_male_diaphragm_27 months_rep5


title: DG82 ID/AE wk12

value: ID/AE


title: S41.SLE.BM4.X14

tag: stimulus

value: 10 ug/ml POLY I:C


title: Mus musculus_female_gastrocnemius_24 months_rep4

value: gastrocnemius

value: 24 months


title: DG82 ID/AE wk2


title: S41.SLE.BM4.X13

tag: stimdescription

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_27 months_rep9

value: diaphragm

value: Sprague Dawley

value: male

value: 27 months


title: Mus musculus_female_gastrocnemius_24 months_rep2

value: female


title: DG82 ID/AE d2

tag: time after bcg


title: Mus musculus_female_gastrocnemius_24 months_rep1

tag: tissue


title: S41.SLE.BM4.X12

value: Blood

value: Disease

value: SLE

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_24 months_rep0

tag: strain


title: S41.SLE.BM4.X11

value: F

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: DG75 IV wk12

value: Whole Blood

value: IV

value: high

value: protected


title: Mus musculus_female_gastrocnemius_21 months_rep7

value: gastrocnemius

tag: Sex

value: 21 months


title: S41.SLE.BM4.X10

value: Caucasian

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_27 months_rep11

value: diaphragm

value: Sprague Dawley

value: male

tag: time


title: DJF9 IV pre

value: pre


title: Rattus norvegicus_male_diaphragm_27 months_rep10

value: 27 months


title: DG75 IV wk2


title: S41.SLE.362.X8

value: Blood

tag: donorid

value: Disease

value: SLE

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: S41.SLE.362.X9

tag: group

value: F

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DG75 IV d2

value: Whole Blood

value: IV

value: high


title: DG75 IV pre

value: protected


title: Rattus norvegicus_male_diaphragm_27 months_rep1


title: Mus musculus_female_gastrocnemius_21 months_rep5

value: gastrocnemius

value: female

value: 21 months


title: Mus musculus_female_gastrocnemius_21 months_rep6


title: Mus musculus_female_gastrocnemius_21 months_rep4


title: S41.SLE.362.X7

tag: diseasenormal

value: Caucasian

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_27 months_rep0

value: diaphragm

value: Sprague Dawley

value: male


title: Rattus norvegicus_male_diaphragm_24 months_rep9

value: 24 months


title: DG49 HD-ID wk12

value: HD-ID


title: Rattus norvegicus_male_diaphragm_27 months_rep2

value: 27 months


title: DG82 ID/AE pre

value: ID/AE

value: pre


title: S41.SLE.362.X6

value: Blood

value: Disease

tag: diseasegroup

value: SLE

value: F

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_21 months_rep3

value: gastrocnemius

value: female


title: Rattus norvegicus_male_diaphragm_24 months_rep8


title: DG49 HD-ID wk2

value: Whole Blood

value: high


title: S41.SLE.362.X5

tag: gender

value: Caucasian

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_21 months_rep2

value: 21 months


title: S41.SLE.362.X4

tag: diagnosis

value: 10 ug/ml LPS


title: DG49 HD-ID d2

value: HD-ID


title: Mus musculus_female_gastrocnemius_21 months_rep1


title: Rattus norvegicus_male_diaphragm_24 months_rep7

value: diaphragm

value: Sprague Dawley

value: male

value: 24 months


title: DG49 HD-ID pre

value: pre


title: DG05 ID/AE wk12

value: ID/AE


title: Mus musculus_female_gastrocnemius_21 months_rep0


title: Rattus norvegicus_male_diaphragm_24 months_rep4


title: Mus musculus_female_gastrocnemius_18 months_rep7

value: 18 months


title: S41.SLE.362.X3

value: Blood

value: Disease

value: SLE

value: F

tag: age

value: 10% SLE patient #4 sera


title: Mus musculus_female_gastrocnemius_18 months_rep6

value: gastrocnemius

value: female


title: DG05 ID/AE d2

value: Whole Blood

value: high


title: Rattus norvegicus_male_diaphragm_24 months_rep3


title: S41.SLE.362.X14

tag: ethnicity

value: Caucasian

value: 10 ug/ml POLY I:C


title: Mus musculus_female_gastrocnemius_18 months_rep5


title: Rattus norvegicus_male_diaphragm_24 months_rep2

value: diaphragm

value: Sprague Dawley


title: S41.SLE.362.X13

tag: sledai

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_18 months_rep4


title: DG05 ID/AE pre

value: pre


title: DG02 HD-ID wk12

value: HD-ID


title: Rattus norvegicus_male_diaphragm_24 months_rep11

value: male

value: 24 months


title: Rattus norvegicus_male_diaphragm_24 months_rep6


title: S41.SLE.362.X12

value: Blood

value: Disease

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_18 months_rep3

value: 18 months


title: Rattus norvegicus_male_diaphragm_24 months_rep10


title: DG02 HD-ID wk2


title: S41.SLE.362.X2

value: SLE

value: F

tag: stimulus

value: 0.25 uM CpGc


title: Rattus norvegicus_male_diaphragm_24 months_rep5


title: DG05 ID/AE wk2

value: Whole Blood

value: ID/AE

value: high


title: S41.SLE.362.X11

value: Caucasian

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: S41.SLE.362.X1

value: Untreated and Unstimulated


title: Mus musculus_female_gastrocnemius_18 months_rep2

value: gastrocnemius

value: female


title: Rattus norvegicus_male_diaphragm_24 months_rep1

value: diaphragm

value: Sprague Dawley

value: male


title: S41.SLE.362.X10

value: Blood

value: Disease

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_18 months_rep1

value: 18 months


title: DG02 HD-ID pre

value: HD-ID

tag: time after bcg

value: pre


title: Rattus norvegicus_male_diaphragm_24 months_rep0

tag: tissue

value: 24 months


title: N37.Healthy.BM4.X9

value: Normal

value: Healthy

value: F

value: Asian

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_21 months_rep9

tag: strain

value: 21 months


title: Mus musculus_female_gastrocnemius_18 months_rep0

value: gastrocnemius

tag: Sex

value: female


title: DFZ4 ID wk12

value: Whole Blood

value: ID

value: low


title: N37.Healthy.BM4.X8

value: Blood

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_12 months_rep7

tag: time

value: 12 months


title: Rattus norvegicus_male_diaphragm_21 months_rep8

value: diaphragm

value: Sprague Dawley

value: male


title: N37.Healthy.BM4.X7

tag: donorid

value: Normal

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_gastrocnemius_12 months_rep6


title: N37.Healthy.BM4.X6

tag: group

value: Healthy

value: F

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_21 months_rep7

value: 21 months


title: Mus musculus_female_gastrocnemius_12 months_rep5

value: gastrocnemius


title: DFZ4 ID d2


title: Rattus norvegicus_male_diaphragm_21 months_rep6


title: DFZ4 ID pre

value: pre


title: N37.Healthy.BM4.X5

tag: diseasenormal

value: Asian

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: DG02 HD-ID d2

value: Whole Blood

value: HD-ID

value: high


title: Rattus norvegicus_male_diaphragm_21 months_rep5


title: Mus musculus_female_gastrocnemius_12 months_rep4

value: female

value: 12 months


title: Mus musculus_female_gastrocnemius_12 months_rep3


title: N37.Healthy.BM4.X3

value: Blood

tag: diseasegroup

value: 10% SLE patient #4 sera


title: Mus musculus_female_gastrocnemius_12 months_rep2


title: Rattus norvegicus_male_diaphragm_21 months_rep3

value: diaphragm

value: Sprague Dawley

value: male


title: DFXL ID wk2

value: DFXL

value: ID

value: low


title: DFXL ID d2


title: DFZ4 ID wk2


title: Mus musculus_female_gastrocnemius_12 months_rep1

value: gastrocnemius


title: DFXL ID pre

value: pre


title: N37.Healthy.BM4.X1

value: Normal

value: Healthy

tag: gender

value: F

value: Asian

value: Untreated and Unstimulated


title: Mus musculus_female_gastrocnemius_12 months_rep0

value: female


title: DFXH ID/AE wk12

value: Whole Blood

value: DFXH

value: ID/AE

value: high


title: Rattus norvegicus_male_diaphragm_21 months_rep11

value: diaphragm

value: Sprague Dawley

value: 21 months


title: Rattus norvegicus_male_diaphragm_21 months_rep10

value: male


title: Mus musculus_female_diaphragm_6 months_rep7

value: 6 months


title: DFXH ID/AE wk2


title: DFXL ID wk12

value: DFXL

value: ID

value: low


title: Mus musculus_female_diaphragm_6 months_rep6


title: N37.Healthy.BM4.X4

value: Blood

value: Normal

value: Healthy

tag: diagnosis

value: 10 ug/ml LPS


title: S41.SLE.BM4.X2

value: Disease

value: SLE

value: F

tag: age

value: Caucasian

value: 0.25 uM CpGc


title: Rattus norvegicus_male_diaphragm_21 months_rep1

value: diaphragm


title: Rattus norvegicus_male_diaphragm_21 months_rep4

value: Sprague Dawley


title: N37.Healthy.BM4.X12

tag: ethnicity

value: Asian

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: DFXH ID/AE d2

value: Whole Blood

value: DFXH

value: ID/AE

value: high


title: N37.Healthy.BM4.X11

value: Blood

tag: sledai

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_6 months_rep5

value: female

value: 6 months


title: Rattus norvegicus_male_diaphragm_21 months_rep0

value: male

value: 21 months


title: DFXH ID/AE pre

value: pre


title: Rattus norvegicus_male_diaphragm_21 months_rep2


title: Mus musculus_female_diaphragm_6 months_rep4


title: Rattus norvegicus_male_diaphragm_18 months_rep9

value: 18 months


title: N37.Healthy.BM4.X10

value: Normal

value: Healthy

value: F

tag: drug

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: N37.Healthy.BM4.X2

value: Asian

tag: stimulus

value: 0.25 uM CpGc


title: N37.Healthy.362.X9

tag: stimdescription

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DFX6 AE wk12

value: Whole Blood

value: AE

tag: time after bcg


title: N37.Healthy.BM4.X13

tag: tissue

value: Blood

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_18 months_rep8

value: diaphragm

tag: strain

value: Sprague Dawley


title: Mus musculus_female_diaphragm_6 months_rep3

tag: Sex

value: female

value: 6 months


title: DFX6 AE wk2

value: high


title: Mus musculus_female_diaphragm_6 months_rep2

tag: time


title: DFX6 AE d2


title: N37.Healthy.362.X8

tag: donorid

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: N37.Healthy.362.X7

tag: group

value: Normal

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_18 months_rep7

value: male

value: 18 months


title: Mus musculus_female_diaphragm_6 months_rep1


title: Rattus norvegicus_male_diaphragm_18 months_rep6


title: Mus musculus_female_diaphragm_6 months_rep0


title: Rattus norvegicus_male_diaphragm_18 months_rep5


title: DFWG ID/AE wk12

value: DFWG

value: ID/AE


title: DFX6 AE pre

value: pre


title: N37.Healthy.362.X6

tag: diseasenormal

value: Healthy

value: F

value: Asian

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_27 months_rep9

value: diaphragm

value: 27 months


title: DFWG ID/AE wk2

value: Whole Blood


title: Rattus norvegicus_male_diaphragm_18 months_rep4

value: Sprague Dawley


title: N37.Healthy.362.X4

value: Blood

tag: diseasegroup

value: 10 ug/ml LPS


title: DFWG ID/AE d2

value: high


title: N37.Healthy.362.X3

value: Normal

tag: gender

value: 10% SLE patient #4 sera


title: Mus musculus_female_diaphragm_27 months_rep8

value: female


title: Rattus norvegicus_male_diaphragm_18 months_rep3

value: male

value: 18 months


title: Mus musculus_female_diaphragm_27 months_rep7


title: Rattus norvegicus_male_diaphragm_18 months_rep2


title: DFWG ID/AE pre

value: DFWG

value: ID/AE

value: pre


title: N37.Healthy.362.X2

value: Healthy

value: F

tag: diagnosis

value: Asian

value: 0.25 uM CpGc


title: Mus musculus_female_diaphragm_27 months_rep6

value: diaphragm

value: 27 months


title: N37.Healthy.362.X1

value: Blood

tag: age

value: Untreated and Unstimulated


title: DFVJ ID wk12

value: Whole Blood

value: DFVJ

value: ID

value: low


title: DFVJ ID wk2


title: Rattus norvegicus_male_diaphragm_18 months_rep10

value: Sprague Dawley

value: male


title: N37.Healthy.362.X13

value: Normal

tag: ethnicity

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_27 months_rep4

value: female


title: DFVJ ID d2


title: N37.Healthy.362.X5

value: Healthy

tag: sledai

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_18 months_rep1

value: 18 months


title: Mus musculus_female_diaphragm_27 months_rep5


title: N37.Healthy.362.X12

value: F

value: Asian

tag: drug

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: N37.Healthy.362.X11

value: Blood

tag: stimulus

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_27 months_rep2

value: diaphragm

value: 27 months


title: N37.Healthy.362.X10

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_27 months_rep1


title: Rattus norvegicus_male_diaphragm_12 months_rep9

value: 12 months


title: Rattus norvegicus_male_diaphragm_12 months_rep8

value: Sprague Dawley


title: Rattus norvegicus_male_diaphragm_18 months_rep0

value: male


title: DFTA IV wk2

value: Whole Blood

value: DFTA

value: IV

value: high

tag: time after bcg

value: protected


title: Mus musculus_female_diaphragm_27 months_rep0

tag: tissue

value: female


title: Mus musculus_female_gastrocnemius_24 months_rep3

value: gastrocnemius

tag: strain

value: 24 months


title: DFTA IV d2


title: N36.Healthy.BM4.X8

value: Normal

value: Healthy

value: F

value: Caucasian

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_12 months_rep7

value: diaphragm

tag: Sex


title: Rattus norvegicus_male_diaphragm_27 months_rep3

tag: time

value: 27 months


title: Rattus norvegicus_male_diaphragm_27 months_rep4

value: Sprague Dawley


title: DFTA IV pre

value: pre


title: Rattus norvegicus_male_diaphragm_18 months_rep11

value: male

value: 18 months


title: N36.Healthy.BM4.X7

value: Blood

tag: donorid

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_27 months_rep3


title: Rattus norvegicus_male_diaphragm_12 months_rep6

value: 12 months


title: DFL6 ID/AE wk12

value: Whole Blood

value: ID/AE

value: high


title: DFVJ ID pre

value: DFVJ

value: ID

value: low


title: Mus musculus_female_diaphragm_24 months_rep9

value: female

value: 24 months


title: Mus musculus_female_diaphragm_24 months_rep8

value: diaphragm


title: Mus musculus_female_diaphragm_24 months_rep7


title: DFTA IV wk12

value: DFTA

value: IV

value: protected


title: N36.Healthy.BM4.X6

tag: group

value: Normal

value: Healthy

value: F

value: Caucasian

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: N36.Healthy.BM4.X5

value: Blood

tag: diseasenormal

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Rattus norvegicus_male_diaphragm_12 months_rep4

value: Sprague Dawley

value: male

value: 12 months


title: Rattus norvegicus_male_diaphragm_12 months_rep3


title: DFL6 ID/AE d2

value: Whole Blood

value: ID/AE

value: high


title: N36.Healthy.BM4.X9

tag: diseasegroup

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: N36.Healthy.BM4.X4

tag: gender

value: 10 ug/ml LPS


title: Rattus norvegicus_male_diaphragm_12 months_rep2

value: diaphragm


title: DFL6 ID/AE pre

value: pre


title: N36.Healthy.BM4.X3

value: Normal

tag: diagnosis

value: 10% SLE patient #4 sera


title: Rattus norvegicus_male_diaphragm_12 months_rep5


title: Mus musculus_female_diaphragm_24 months_rep5

value: female

value: 24 months


title: Mus musculus_female_diaphragm_24 months_rep6


title: Rattus norvegicus_male_diaphragm_12 months_rep11


title: DFL6 ID/AE wk2


title: DFJ3 AE wk12

value: AE


title: N36.Healthy.BM4.X2

value: Blood

value: Healthy

value: F

tag: age

value: Caucasian

value: 0.25 uM CpGc


title: Rattus norvegicus_male_diaphragm_12 months_rep10

value: Sprague Dawley

value: male

value: 12 months


title: DFJ3 AE d2

value: Whole Blood

value: high


title: Rattus norvegicus_male_diaphragm_12 months_rep1

value: diaphragm


title: DFJ3 AE wk2


title: N36.Healthy.BM4.X13

tag: ethnicity

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: N36.Healthy.BM4.X12

value: Normal

tag: sledai

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_24 months_rep2

value: female


title: N36.Healthy.BM4.X1

tag: drug

value: Untreated and Unstimulated


title: Mus musculus_female_diaphragm_24 months_rep1

value: 24 months


title: DFJ3 AE pre

value: AE

value: pre


title: Mus musculus_female_diaphragm_24 months_rep0


title: Rattus norvegicus_male_diaphragm_12 months_rep0


title: spermatozoa 4

city: Laval

first: Geraldine

last: Delbes

state: Quebec

address: 531 Boul des Prairies

department: Biology

country: Canada

institute: INRS Centre Armand-Frappier Santé Biotechnologie

library_source: genomic

data_processing:
Raw reads were cleaned from remaining adaptor sequences and low-quality nucleotides using Trimmomatics 0.36 and a minimum sequencing quality of 30.
Reads longer than 30 bp were then aligned to the converted and unconverted reference genome  (ensembl/release99/fasta/rattus_norvegicus/) using Bowtie2   as implemented in the Bismark 0.19.0 program.
Based on read alignments with converted and unconverted genomes,DNA methylation was extracted by Bismark 0.19.0 program,
Assembly: ensembl/release99/fasta/rattus_norvegicus/
Supplementary files format and content: tab-delimited text files include DNA methylation values and count for each Sample

molecule: genomic DNA

source_name: Germ cell

growth_protocol: Transgenic Sprague-Dawley rats expressing germ cell-specific GFP (GCS-EGFP) were housed on a 12L:12D cycle and were fed with commercial food (Teklad global 18% protein, Envigo, Madison, WI) and tap water ad libitum.

extract_protocol:
Genomic DNA  were extracted from FACS-sorted germ cells using QIAamp DNA micro kit (QIAgen, Toronto, Ontario, Canada) and  the DNeasy Blood & Tissue kit (QIAgen) for spermatozoa (Purification of DNA from sperm using the DNeasy Blood and Tissue kit; protocol 2, DY03 Aug-06,available on QIAgen website).
Methyl-Seq capture libraries were prepared using the Rat SureSelectXT Methyl-Seq Target Enrichment Panels kit (Agilent) as described in the SureSelectXT Methyl-Seq target Enrichment System for Illumina Multiplexed Sequencing protocol (Agilent, Version E0, April 2018).

treatment_protocol: No treatment

value: Germ cell

tag: developmental stage

value: spermatozoa

value: Sprague-Dawley

tag: genotype

value: GFP-GCS


title: DFI0 AE wk12

tag: time after bcg


title: N36.Healthy.BM4.X11

tag: tissue

value: Blood

value: Healthy

value: F

value: Caucasian

tag: stimulus

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: spermatozoa 3

tag: strain


title: Mus musculus_female_diaphragm_24 months_rep3

value: diaphragm

tag: Sex

tag: time


title: DFI0 AE wk2

value: Whole Blood

value: high


title: N36.Healthy.362.X9

tag: donorid

tag: group

tag: diseasenormal

value: Normal

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_21 months_rep6

value: female

value: 21 months


title: DFI0 AE d2

value: AE


title: Mus musculus_female_diaphragm_21 months_rep5


title: Mus musculus_female_diaphragm_21 months_rep7


title: Mus musculus_female_diaphragm_24 months_rep4

value: 24 months


title: DFI0 AE pre

value: pre


title: N36.Healthy.BM4.X10

tag: diseasegroup

tag: gender

tag: diagnosis

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: spermatozoa 2

value: Germ cell

value: spermatozoa

value: Sprague-Dawley

value: GFP-GCS


title: N36.Healthy.362.X8

value: Blood

value: Healthy

value: F

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_21 months_rep4

value: diaphragm


title: Mus musculus_female_diaphragm_21 months_rep3


title: DFG1 IV wk12

value: Whole Blood

value: IV

value: high


title: Spermatids R15-17 4

tag: developmental stage

value: Spermatids R15-17

tag: genotype


title: spermatozoa 1

tag: tissue


title: Spermatids R15-17 3


title: DFG1 IV wk2

tag: time after bcg


title: N36.Healthy.362.X6

value: Normal

tag: drug

tag: stimulus

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_21 months_rep2

tag: strain

tag: Sex

value: female

tag: time

value: 21 months


title: DFG1 IV d2


title: Spermatids R15-17 2

value: Germ cell


title: N36.Healthy.362.X5

tag: donorid

tag: group

tag: diseasenormal

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Spermatids R15-17 1

value: Sprague-Dawley

value: GFP-GCS


title: Mus musculus_female_diaphragm_21 months_rep1


title: N36.Healthy.362.X4

value: Blood

tag: diseasegroup

value: Healthy

tag: gender

tag: diagnosis

value: 10 ug/ml LPS


title: Mus musculus_female_diaphragm_21 months_rep0


title: DFB3 AE wk12

value: AE


title: N36.Healthy.362.X3

value: F

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

value: 10% SLE patient #4 sera


title: Spermatids R13-14 3

tag: tissue

tag: developmental stage

value: Spermatids R13-14

tag: genotype


title: Spermatids R13-14 4


title: N36.Healthy.362.X2

tag: drug

tag: stimulus

value: 0.25 uM CpGc


title: Mus musculus_female_diaphragm_18 months_rep6

value: diaphragm

tag: strain

value: 18 months


title: DFB3 AE wk2

value: Whole Blood

value: high

tag: time after bcg


title: Mus musculus_female_diaphragm_18 months_rep5

tag: Sex

value: female

tag: time


title: N36.Healthy.362.X7

tag: donorid

tag: group

value: Normal

tag: stimdescription

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: N36.Healthy.362.X1

tag: diseasenormal

tag: diseasegroup

tag: gender

value: Untreated and Unstimulated


title: Mus musculus_female_diaphragm_18 months_rep4


title: Spermatids R13-14 2

value: Germ cell

value: Sprague-Dawley

value: GFP-GCS


title: N36.Healthy.362.X13

value: Blood

value: Healthy

tag: diagnosis

tag: age

tag: ethnicity

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: Spermatids R13-14 1

tag: tissue

tag: developmental stage


title: DFB3 AE pre

value: AE

value: pre


title: Spermatids R9-12 4

value: Spermatids R9-12

tag: genotype


title: Mus musculus_female_diaphragm_18 months_rep3

value: diaphragm


title: N36.Healthy.362.X12

value: F

value: Caucasian

tag: sledai

tag: drug

tag: stimulus

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: Mus musculus_female_diaphragm_18 months_rep2

tag: strain

tag: Sex

value: female

value: 18 months


title: DF9I ID wk12

value: Whole Blood

value: ID

value: low

tag: time after bcg


title: DF9I ID wk2


title: Mus musculus_female_diaphragm_18 months_rep1

tag: time


title: Spermatids R9-12 3

value: Germ cell

value: Sprague-Dawley


title: DFG1 IV pre

value: IV

value: high


title: N36.Healthy.362.X11

value: Blood

tag: donorid

tag: group

value: Normal

value: Healthy

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: DF9I ID d2


title: N36.Healthy.362.X10

tag: diseasenormal

tag: diseasegroup

tag: gender

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: DFB3 AE d2

value: AE


title: Spermatids R9-12 1

value: Spermatids R9-12

value: GFP-GCS


title: N35.Healthy.BM4.X9

value: F

tag: diagnosis

tag: age

tag: ethnicity

value: Caucasian

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DF9I ID pre

tag: tissue

value: Whole Blood

value: ID

value: pre


title: N35.Healthy.BM4.X8

tag: sledai

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: Spermatids R1-8 4

value: Germ cell

tag: developmental stage

value: Spermatids R1-8

value: Sprague-Dawley

tag: genotype


title: Mus musculus_female_diaphragm_18 months_rep0

value: diaphragm

tag: strain

value: female

value: 18 months


title: Mus musculus_female_diaphragm_12 months_rep6

tag: Sex

value: 12 months


title: DF9F HD-ID wk12

value: HD-ID

value: high

tag: time after bcg


title: Spermatids R1-8 3

value: GFP-GCS


title: DF9F HD-ID wk2


title: Mus musculus_female_diaphragm_12 months_rep5

tag: time


title: N35.Healthy.BM4.X7

value: Blood

tag: donorid

value: Normal

value: Healthy

value: F

tag: drug

tag: stimulus

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: DF9F HD-ID d2

value: Whole Blood


title: Mus musculus_female_diaphragm_12 months_rep4


title: N35.Healthy.BM4.X6

tag: group

tag: diseasenormal

value: Caucasian

tag: stimdescription

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: Spermatids R1-8 2

value: Germ cell

value: Spermatids R1-8


title: Mus musculus_female_diaphragm_12 months_rep3

value: diaphragm


title: N35.Healthy.BM4.X5

tag: diseasegroup

tag: gender

tag: diagnosis

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: Spermatids R1-8 1

tag: tissue

value: Sprague-Dawley


title: DF9F HD-ID pre

value: pre


title: DF8J HD-ID wk12

value: HD-ID


title: N35.Healthy.BM4.X4

tag: age

tag: ethnicity

tag: sledai

value: 10 ug/ml LPS


title: Mus musculus_female_diaphragm_12 months_rep1

tag: strain

value: female

value: 12 months


title: Mus musculus_female_diaphragm_12 months_rep2

tag: Sex


title: PND5 spermatogonia 3

tag: developmental stage

value: PND5 spermatogonia

tag: genotype

value: GFP-GCS


title: DF8J HD-ID d2

value: high

tag: time after bcg


title: Mus musculus_female_diaphragm_12 months_rep0

tag: time


title: N35.Healthy.BM4.X2

value: Blood

tag: donorid

value: Normal

value: Healthy

value: F

tag: drug

tag: stimulus

value: 0.25 uM CpGc


title: N35.Healthy.BM4.X1

tag: group

tag: diseasenormal

value: Caucasian

tag: stimdescription

value: Untreated and Unstimulated


title: BVMA01R tumor, ADI-PEG20+CQ, rep2

city: St. Louis

first: Brian

last: Van Tine

state: Missouri

address: 4515 McKinley Ave

institute: Washington University in St. Louis

data_processing:
Samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000.  Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a.  Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p5. Isoform expression of known Ensembl transcripts were estimated with Salmon version 0.8.2.  Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 2.6.2.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.  Ribosomal genes and genes not expressed in the smallest group size minus one samples greater than one count-per-million were excluded from further analysis.  The TMM size factors and the matrix of counts were then imported into the R/Bioconductor package Limma. Weighted likelihoods based on the observed mean-variance relationship of every gene and sample were then calculated for all samples and the count matrix was transformed to moderated log 2 counts-per-million with Limma’s voomWithQualityWeights.  The performance of all genes was assessed with plots of the residual standard deviation of every gene to their average log-count with a robustly fitted trend line of the residuals. Differential expression analysis was then performed to analyze for differences between conditions and the results were filtered for only those genes with Benjamini-Hochberg false-discovery rate adjusted p-values less than or equal to 0.05.
For each contrast extracted with Limma, global perturbations in known Gene Ontology (GO) terms, MSigDb, and KEGG pathways were detected using the R/Bioconductor package GAGE to test for changes in expression of the reported log 2 fold-changes reported by Limma in each term versus the background log 2 fold-changes of all genes found outside the respective term.  The R/Bioconductor package heatmap3 was used to display heatmaps across groups of samples for each GO or MSigDb term with a Benjamini-Hochberg false-discovery rate adjusted p-value less than or equal to 0.05.  Perturbed KEGG pathways where the observed log 2 fold-changes of genes within the term were significantly perturbed in a single-direction versus background or in any direction compared to other genes within a given term with p-values less than or equal to 0.05 were rendered as annotated KEGG graphs with the R/Bioconductor package Pathview.
To find the most critical genes, the Limma voomWithQualityWeights transformed log 2 counts-per-million expression data was then analyzed via weighted gene correlation network analysis with the R/Bioconductor package WGCNA.  Briefly, all genes were correlated across each other by Pearson correlations and clustered by expression similarity into unsigned modules using a power threshold empirically determined from the data.  An eigengene was then created for each de novo cluster and its expression profile was then correlated across all coefficients of the model matrix.  Because these clusters of genes were created by expression profile rather than known functional similarity, the clustered modules were given the names of random colors where grey is the only module that has any pre-existing definition of containing genes that do not cluster well with others. These de-novo clustered genes were then tested for functional enrichment of known GO terms with hypergeometric tests available in the R/Bioconductor package clusterProfiler.  Significant terms with Benjamini-Hochberg adjusted p-values less than 0.05 were then collapsed by similarity into clusterProfiler category network plots to display the most significant terms for each module of hub genes in order to interpolate the function of each significant module.  The information for all clustered genes for each module were then combined with their respective statistical significance results from Limma to determine whether or not those features were also found to be significantly differentially expressed.
Assembly: mm10
Supplementary files format and content: Merged_differential_expression_results is a tab-separated values file showing moderated log 2 counts-per-million of the transcripts of each gene for each sample.
Supplementary files format and content: The other processed data files are tab-separated values files showing the mean log 2 fold-changes of genes within KEGG signaling and metabolism pathway gene sets in a single-direction for the indicated treatment groups in the file titles versus untreated tumors.

source_name: tumor

extract_protocol:
RNA was isolated from frozen tumor samples with the Direct-zol RNA Miniprep Plus kit (Zymo Research, Irvine, CA).
RNA libraries for RNA-seq were prepared using KAPA RiboErase Kit following manufacturer's protocols.

value: tumor

tag: cell line

tag: cell type

value: murine sarcoma cell line

tag: treatment

value: ADI-PEG20 + chloroquine


title: PND5 spermatogonia 1

tag: tissue

value: Germ cell

value: Sprague-Dawley


title: PND5 spermatogonia 2


title: DF8J HD-ID wk2

value: Whole Blood

value: HD-ID


title: N35.Healthy.BM4.X13

tag: diseasegroup

tag: gender

tag: diagnosis

tag: age

tag: ethnicity

tag: sledai

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: GD20 Gonocytes 4

tag: developmental stage

value: GD20 Gonocytes

tag: strain

tag: genotype

value: GFP-GCS


title: BVMA01R tumor, ADI-PEG20+CQ, rep3

tag: Sex

value: female


title: BVMA01R tumor, ADI-PEG20, rep3


title: N35.Healthy.BM4.X12

value: Blood

tag: donorid

tag: group

value: Normal

tag: drug

tag: stimulus

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: GD20 Gonocytes 3


title: GD20 Gonocytes 2


title: DF8J HD-ID pre

value: high

tag: time after bcg

value: pre


title: BVMA01R tumor, ADI-PEG20+CQ, rep1

tag: cell line

tag: cell type

tag: treatment


title: PND5 spermatogonia 4

tag: tissue

value: PND5 spermatogonia


title: DF7X ID wk12

value: ID

value: low


title: DF7X ID d2


title: N35.Healthy.BM4.X11

tag: diseasenormal

tag: diseasegroup

value: Healthy

tag: gender

value: F

tag: diagnosis

value: Caucasian

tag: stimdescription

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: N35.Healthy.BM4.X3

tag: age

tag: ethnicity

tag: sledai

value: 10% SLE patient #4 sera


title: DF7X ID pre

value: Whole Blood


title: N35.Healthy.BM4.X10

tag: donorid

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: BVMA01R tumor, ADI-PEG20, rep2

tag: Sex

tag: strain

value: tumor

value: murine sarcoma cell line

tag: genotype


title: BVMA01R tumor, ADI-PEG20, rep1

value: female


title: GD20 Gonocytes 1

value: Germ cell

tag: developmental stage

value: GD20 Gonocytes

value: Sprague-Dawley

value: GFP-GCS


title: GD18 Gonocytes 4

value: GD18 Gonocytes


title: N35.Healthy.362.X9

value: Blood

tag: group

value: Normal

tag: drug

tag: stimulus

value: 20% SLE patient  #22 sera + 0.1 mg/ml necrotic cell lysates


title: DF2A IV wk12

tag: tissue

value: IV

value: high

tag: time after bcg

value: protected


title: BVMA01R tumor, CQ, rep3

tag: cell line

tag: cell type

tag: treatment

value: Chloroquine


title: DF7X ID wk2

value: Whole Blood

value: ID

value: low


title: GD18 Gonocytes 3


title: N35.Healthy.362.X8

tag: diseasenormal

tag: diseasegroup

value: Healthy

tag: gender

value: F

tag: diagnosis

value: Caucasian

tag: stimdescription

value: 20% SLE patient #06 sera + 0.1 mg/ml necrotic cell lysates


title: GD18 Gonocytes 2

value: Germ cell

value: Sprague-Dawley


title: DF2A IV d2


title: DF2A IV wk2


title: BVMA01R tumor, CQ, rep1

tag: Sex

value: female

value: tumor

value: murine sarcoma cell line


title: BVMA01R tumor, CQ, rep2

tag: strain


title: GD18 Gonocytes 1

value: GD18 Gonocytes

tag: genotype

value: GFP-GCS


title: DF2A IV pre

value: IV

value: high

value: pre


title: N35.Healthy.362.X6

value: Blood

tag: donorid

value: Normal

tag: age

tag: ethnicity

tag: sledai

value: 0.05 mg/ml SLE patient #92 Ig + 0.1 mg/ml necrotic cell lysates


title: N35.Healthy.362.X7

tag: tissue

tag: group

value: Healthy

tag: drug

tag: stimulus

value: 0.1 mg/ml SLE patient #109 Ig + 0.1 mg/ml necrotic cell lysates


title: N35.Healthy.362.X5

value: F

value: Caucasian

value: 0.1 mg/ml Healthy Ig + 0.1 mg/ml necrotic cell lysates


title: BVMA01R tumor, NT, rep2

tag: cell line

tag: cell type

tag: treatment

value: No treatment


title: GD16 Gonocytes 4

value: Germ cell

tag: developmental stage

value: GD16 Gonocytes

value: Sprague-Dawley


title: CZRJR AE wk2

value: Whole Blood

value: CZRJR

value: AE

tag: time after bcg


title: GD16 Gonocytes 3

value: GFP-GCS


title: N35.Healthy.362.X4

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimdescription

value: 10 ug/ml LPS


title: BVMA01R tumor, NT, rep1

tag: Sex

value: female

tag: strain

value: tumor

value: murine sarcoma cell line

tag: genotype


title: CZRJR AE d2

tag: tissue

value: high


title: GD16 Gonocytes 2


title: N35.Healthy.362.X3

value: Blood

tag: donorid

tag: group

value: Normal

value: Healthy

tag: age

tag: ethnicity

tag: sledai

value: 10% SLE patient #4 sera


title: p57WT-5

city: Toulouse

first: Arnaud

last: Besson

address: 118 route de Narbonne

department: MCD UMR5077

country: France

institute: Centre de Biologie Integrative - CNRS

data_processing:
Ten RNA-seq samples were sequenced using Illumina HiSeq (paired-end, 2x150 bp reads) at Genewiz. The quality of each raw sequencing file (fastq) was verified with FastQC.
For all files adapters were trimmed with Trim Galore (v-0.6.5) and clean fastq were aligned to the reference mouse genome (mm10) using STAR aligner (STAR_2.6.1d) (Dobin et al., 2013). FPKM were computed using cufflinks (v2.2.1) (Trapnell et al., 2012) with the annotation from Ensembl database (gtf GRCm38.91). Raw read count per sample was computed using HT-seq count (V1.0) (Anders and Huber, 2010) on that same annotation database. Then the raw count table was cleaned, with only genes with a total higher than 50 reads aligned over all samples were kept. The remaining raw read count were normalized using the RLE methods and differential analysis was applied per pairs of conditions using DESeq2 (DESeq2 package version: 1.22.2) (Love et al., 2014), available as an R package in bioconductor (www.biocondutor.org), to generate the log fold change (log2FC) values and adjusted p-values (Benjamini and Hochberg method).
Genome_build: mm10

source_name: Hopx+ intestinal stem cells

growth_protocol: Cells were isolated from E18.5 embryos

extract_protocol:
Cells were sorted directly in trizol
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina HiSeq 2x150 bp

treatment_protocol: Intestinal crypts were mechanically dissociated and a single cell suspension was prepared and Hopx+ cells were isolated by FACS sorting based on GFP expression under the Hopx promoter

value: Intestine

tag: cell type

value: Hopx+ intestinal stem cells


title: CZRJR AE pre

value: pre


title: dbdb-ImeMet3

city: Maebashi

first: Jun

last: Shirakawa

address: 3-39-15 Showa-machi

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

data_processing:
After removing adapter sequences with cutadapt (ver. 1.9.1), sickle (ver. 1.3.3) was used to remove bases with quality scores less than 20 and paired reads with quality scores less than 40 bases.
Trimmed sequence reads were mapped to GRCm39 using hisat2 (ver. 2.2.1).
Read count extraction was performed using featureCounts ( ver. 2.0.0)
Assembly: GRCm39
Supplementary files format and content: excel file includes raw count

source_name: pancreatic islets

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set following manufacturer's protocols.

value: pancreatic islets

value: db/db

tag: treatment

value: imeglimin and metformin


title: 0TL HD-ID wk12

value: Whole Blood

value: HD-ID

tag: time after bcg


title: N35.Healthy.362.X1

tag: diseasenormal

value: F

value: Caucasian

tag: drug

tag: stimulus

value: Untreated and Unstimulated


title: p57WT-3

tag: developmental stage


title: 0TL HD-ID wk2


title: N35.Healthy.362.X13

tag: diseasegroup

tag: gender

tag: diagnosis

tag: stimdescription

value: 20% Healthy donor #07 sera + 0.1 mg/ml necrotic cell lysates


title: dbdb-ImeMet2

tag: tissue

tag: genotype


title: BVMA01R tumor, NT, rep3

tag: Sex

value: female

tag: strain

value: tumor

tag: cell line

value: murine sarcoma cell line

value: No treatment


title: CZRJR AE wk12

value: CZRJR

value: AE

value: high


title: p57WT-2

value: Intestine

value: Hopx+ intestinal stem cells


title: dbdb-ImeMet1

value: pancreatic islets

value: db/db


title: 0TL HD-ID d2

value: Whole Blood


title: 0TL HD-ID pre

value: HD-ID

value: pre


title: dbdb-Ctrl2

value: no treatment


title: p57KO-4


title: N35.Healthy.362.X11

value: Blood

tag: donorid

tag: group

value: Normal

value: Healthy

value: F

tag: age

tag: ethnicity

value: Caucasian

tag: sledai

value: 20% SLE patient #33 sera+ 0.1 mg/ml necrotic cell lysates


title: p57KO-5

tag: cell type


title: dbdb-Ctrl3

tag: treatment


title: 0NR IV wk2

value: IV

tag: time after bcg

value: protected


title: 0NR IV wk12

value: high


title: p57KO-3

value: Intestine

tag: developmental stage


title: dbdb-Ctrl1


title: p57WT-4

value: Hopx+ intestinal stem cells


title: GD16 Gonocytes 1

value: Germ cell

value: GD16 Gonocytes

value: Sprague-Dawley

value: GFP-GCS


title: N35.Healthy.362.X2

tag: diseasenormal

tag: diseasegroup

tag: gender

tag: drug

tag: stimulus

value: 0.25 uM CpGc


title: db-3

tag: tissue

value: pancreatic islets

tag: genotype

value: db/+

value: no treatment


title: p57KO-1

tag: strain


title: GSU_trametinib_DAY14

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

country: China

institute: Shanghai Institutes for Biological Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were mapped to GeCKO V2 Human library A sgRNA sequences using MAGeCK with parameters mageck count --fastq -l -n
Normalization measurements were generated using MAGeCK with parameters mageck count -k --norm-method median -n
Differential analysis between two groups was proceeded by MAGeCK with parameters mageck mle
Genome_build: Ensemble
Supplementary_files_format_and_content: tab-delimited text files include the normalized counts of sgRNAs.

source_name: GSU

growth_protocol: Cells were maintained in RPMI 1640 with 10% FBS and 1% penicillin & streptomycin. Cell were passaged every 2 days. After ininfection with the lentivirus containing human GeCKOv2 library, cells were selected with puromycin for 7 days.

extract_protocol:
Genome DNA in per group was extracted using Wizard ® Genomic DNA Purification Kit (Promega).
Genome DNA in per group was amplified using two-step PCR.
GeCKO library  screen

treatment_protocol: After puromycin selection, cells were divided into three groups, 2*10^7 cells without further treatment were harvested as GSU_DMSO_DAY0 group, 2*10^7 cells receiving 0.015% DMSO for 14 days as GSU_DMSO_DAY14 group, 2*10^7 cells treated with 15 nM tametinib for14 days as GSU_MMC_DAY14 group.

value: gastric cancer cell line

value: treated with trametinib for 14 days after puromycin selection

value: human stomach


title: p57KO-2


title: 0NR IV d2

value: Whole Blood


title: GSU_DMSO_DAY0

value: no furhter treatment after puromycin selection


title: db-2


title: 0NR IV pre

value: IV

value: pre

value: protected


title: p57WT-1

value: Intestine

value: Hopx+ intestinal stem cells


title: N35.Healthy.362.X10

value: Blood

tag: donorid

value: Normal

value: Healthy

value: F

tag: diagnosis

value: Caucasian

tag: stimdescription

value: 20% SLE patient #23 sera+ 0.1 mg/ml necrotic cell lysates


title: db-1

value: pancreatic islets

value: db/+

value: no treatment


title: U87_NFAT5_2

status: Public on Jun 18 2023

city: Tianjin

first: zhenyue

last: gao

address: Qixiangtai road 22

department: School of Basic Medical Sciences

institute: Tianjin Medical University

data_processing:
A propriety Sub-pixel Registration algorithm developed by MGI was used for base call.
This project uses the filtering software SOAPnuke developed by BGI independently for filtering. The specific steps are as follows:  1) Remove the reads containing the adaptor(adaptor pollution);  2) Remove reads whose N content is greater than 5%;  3) Remove low-quality reads (we define reads with bases with a quality score less than 10 as the proportion of total bases in the reads that are greater than 20% as low-quality reads).  The filtered "Clean Reads" are saved in FASTQ format.
Bowtie2 was used to map the clean reads to the reference gene sequence (transcriptome), and then RSEM was used to calculate the gene expression level of each sample.
The DEseq2 was used to perform differential expression analysis.DESeq2: Qvalue (Adjusted Pvalue) <= 0.05

growth_protocol: U87 and U251 cells were cultured with Dulbecco's modified Eagle medium. The culture medium was supplemented with 100 U/mL penicillin, 100 μg/mL streptomycin, and 10% fetal bovine serum. The cells were cultured at 5% CO2 and 37°C.

extract_protocol:
106 cells were lysed by trizol, and mRNA sequencing was performed.
RNA libraries were prepared for sequencing using oligo-dT beads

treatment_protocol: NFAT5-overexpressing U251 and U87 cell lines were constructed.

tag: cell line

value: Glioblastoma


title: U251_NFAT5_1


title: U87_2

value: NC


title: U251_2


title: GSU_DMSO_DAY14

value: gastric cancer cell line

value: treated with vehicle for 14 days after puromycin selection

value: human stomach


title: U87_1


title: N35.Healthy.362.X12

tag: group

tag: age

tag: ethnicity

tag: sledai

value: 20% Healthy donor #02 sera + 0.1 mg/ml necrotic cell lysates


title: splenic CD4+T cells-KD_rep2

first: Junwei

last: Hao

address: 154 Anshan Road, Heping District

institute: Tianjin Medical University General Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads Vontaining adapter, reads containing ploy-N and low quality reads from raw data. All the downstream analyses were based on the clean data with high quality.
Index  of  the  reference  genome  was  built  using  Bowtie  v2.0.6  and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
RPKM of each gene was calculated based on the length of the gene and reads count mapped to  this  gene, considering the effect of sequencing depth and gene length for the reads count at the same time(Mortazavi et al., 2008)
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text file includes counts and FPKM values for each Sample

source_name: primary splenic CD4+T cells

extract_protocol:
CD4+ T cells were isolated, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 3 ug of total RNA for the Vonstruction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Ogtfl/wt CD4-Cre

value: spleen

tag: cell type

value: primary splenic CD4+T cells


title: WT-NT

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

data_processing:
All high-quality paired-end reads were aligned to the Mus musculus reference genome GRCm39.104 using Hisat2 (v2.0.1).
NCBI BLAST v2.2.28 was used to annotate the reads based on known mouse genes with the expected value (e-value) of 1.0 x 10-10.
To estimate the abundance of the gene expression, the read numbers mapped of each gene from each transcript were counted and then normalized by fragment per kilobases per million mapped reads (FPKM) approach using HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Effector CD4+ T helper cell isolated from day-14 C. neoformans-infected BALB/c mice

extract_protocol:
The IL-25/IL-33 stimulated effector CD4+ T cells of BALB/c and Il17rb-/- mice (pooled from 3 independent experiments) were extracted for total RNA by using RNeasy® Plus Mini kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA library prep kit for Illumina® following the manufacturer's protocols.

treatment_protocol: BALB/c and Il17rb-/- mice were anesthetized and treated with PBS or C. neoformans H99 cell suspension at 5 × 104 cells/mouse by the intranasal route. At 14 days postinfection, mice were euthanized by inhalation of CO2, and lungs were aseptically collected to isolate effector CD4+ T helper cells by FACS which were then stimulated with IL-25 and IL-33 cytokines at 10 ng/mL for 36 hours.

value: Effector CD4+ T helper cell

value: WT

tag: background strain

value: BALB/c

tag: treatment

value: Untreated

tag: time

value: 36 hours


title: WT-CN

source_name: Effector CD4+ T helper cell isolated from day-14 C. neoformans-infected BALB/c mice treated with IL-25 and IL-33 combination


title: KO-NT

source_name: Effector CD4+ T helper cell isolated from day-14 C. neoformans-infected Il17rb-/- mice

value: IL-17RB knockout


title: KO-CN

source_name: Effector CD4+ T helper cell isolated from day-14 C. neoformans-infected Il17rb-/- mice treated with IL-25 and IL-33 combination


title: splenic CD4+T cells-KD_rep3


title: splenic CD4+T cells-KD_rep1


title: U251_NFAT5_2


title: splenic CD4+T cells-control_rep3

value: wild type


title: splenic CD4+T cells-control_rep2


title: splenic CD4+T cells-control_rep1


title: A4

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

country: Israel

institute: Tel Aviv University

data_processing:
Partek® Flow® (build version 9.0.20.0804)
Bases were trimmied on quality score=20. Adaptors were also trimmed.
Filter BAM files with minimal mapping quality=20.
Alignment usign STAR - 2.7.3a to B. cinerea reference genome (assembly ASM14353v4)
Quantification to transcriptome performed using Partek E/M algorithm.
Assembly: B. cinerea reference genome (assembly ASM14353v4)

organism: Botrytis cinerea

source_name: Botrytis cinerea (strain B05.10)

growth_protocol: B. cinerea strain B05.10 and derived transgenic strains were routinely cultured on potato dextrose agar (PDA, Acumedia) or suspended in potato dextrose broth (PDB) at 22°C under continuous fluorescent light supplemented with near UV light. Additional media that were used for specific experiments included malt medium (5 g glucose, 15 g malt extract, 1 g peptone, 1 g casamino acids) and GB5-Glc medium (Gamborg B5 with vitamins and 2% glucose, Duchefa Biochemie). B. cinerea cultures were produced by spreading 500 μl of spore suspension (107/ml) on a cellophane-covered PDA plate.

extract_protocol:
Total RNA was extracted with TRIzol reagent (Sigma-Aldrich) according to the manufacturer’s instructions.
cDNA libraries were prepared using a NEBNext Ultra II RNA Library Prep Kit (NEB). RNA and cDNA quality and quantity were evaluated by performing a Qubit assay with the TapeStation 4200 system (Agilent Technologies). Sequencing libraries were constructed with barcodes using NEBNext multiplex oligos for Illumina (NEB).

treatment_protocol: Treatments included incubation at 22°C or 29°C for 10 h (OT and MHT, respectively), followed by 22°C or 29°C for 8 h and 37°C for 2 h (SHT and SHT-P, respectively). GTs were collected from the plates by washing with water, centrifuged, separated into two 1.5-ml Eppendorf tubes, flash-frozen in liquid nitrogen and stored at –80°C.

tag: sample type

value: Control 22C 10h


title: C4

value: Moderate 29C 10h


title: B4

value: Severe 22C 8h + 37C 2h


title: A3


title: D2

value: High 29C 8h + 37C 2h


title: A2


title: B2


title: C2


title: A1


title: D1


title: B1


title: U87_NFAT5_1

value: Glioblastoma


title: U251_1

value: NC


title: D3


title: C3


title: D4


title: B3


title: 25_Negative_nonpregnant

first: Adam

last: Kirosingh

address: 1265 Welch Rd

department: Microbiology & Immunology

description: Sample 25

data_processing:
The sequencing data were uploaded to the Galaxy web platform (usegalaxy.org), where we performed quality control, groomed with FASTQ groomer, aligned to hg38 with bowtie2, filtered using SAM Tools and calculated gene expression using featureCounts
Assembly: hg38
Supplementary files format and content: comma-separated values with combined counts for genes

source_name: whole blood

extract_protocol:
RNA extraction was performed using Quick-RNA MagBead Kit (R2132) on KingFisher followed by sample quality control checks using a Qubit and Bioanalyzer 2100
Libraries were prepared using ZymoSeq RiboFree Total RNA Library Kit (R3000).

value: whole blood

tag: parasitemia

value: Negative

tag: pregnancy status

value: nonpregnant


title: 28_Negative_nonpregnant

description: Sample 28

tag: tissue


title: 26_Positive_pregnant

description: Sample 26

value: Positive

value: pregnant


title: 30_Negative_nonpregnant

description: Sample 30


title: 24_Negative_pregnant

description: Sample 24


title: 32_Negative_pregnant

description: Sample 32


title: 29_Negative_nonpregnant

description: Sample 29


title: 33_Negative_pregnant

description: Sample 33


title: 27_Positive_pregnant

description: Sample 27


title: 23_Positive_pregnant

description: Sample 23


title: 31_Negative_pregnant

description: Sample 31


title: 21_Positive_pregnant

description: Sample 21


title: 22_Negative_pregnant

description: Sample 22


title: C1


title: 20_Positive_pregnant

description: Sample 20


title: 18_Positive_pregnant

description: Sample 18


title: 17_Positive_pregnant

description: Sample 17


title: 16_Positive_pregnant

description: Sample 16


title: 104266-001-038

city: Leiden

first: Martine

middle: C

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: hippocampus

growth_protocol: The studies were approved by an independent Animal Welfare Body (IVD TNO; approval numbers TNO-451 and TNO-499) under project licenses granted by the Netherlands Central Authority for Scientific Procedures on Animals (CCD; project license numbers AVD5010020172064 and AVD5010020172931). All animal experiments were performed in compliance with the European Union directive 2010/63/EU regarding the use of laboratory animals. Male C57BL/6J and Ldlr-/-.Leiden mice obtained from the breeding stock at TNO Metabolic Health Research (Leiden, the Netherlands) were group-housed (two to six animals per cage) in a conventional animal room (temperature ~21 ◦C, relative humidity 50–60%, light cycle 07:00 to 19:00) and received food and water ad libitum. Until the start of the studies, the animals were fed a standardized chow diet (Sniff R/M V1530, Uden, the Netherlands). Randomization, blinding methods and power calculations were used as previously described (Seidel et al., 2022; doi: 10.3390/ijms231810736)

extract_protocol:
Hippocampus gene expression and pathway analysis.   The left hemispheres of the brains were snap frozen in liquid nitrogen. The hippocampi were isolated and used to prepare homogenates using glass beads and ribonucleic nucleic acid (RNA) was extracted as described (Salic et al., 2019, doi: 10.3390/ijms20184359). RNA integrity and concentration were examined for each sample using the RNA 6000 Nano LabChip kit and a bioanalyzer 2100 (both Agilent Technologies, Amstelveen, the Netherlands) and the samples were sequenced by GenomeScan BV (Leiden, the Netherlands). RNA sequencing and RNA counts processing were performed as reported previously (Gart et al., 2021; Seidel et al., 2022). Differentially expressed genes were determined using the Deseq2-pipeline (Love et al., 2014, doi: 10.1186/s13059-014-0550-8) with a statistical cut-off of p-value (p) < 0.05 and used for gene enrichment analysis across pathways and biological processes using the Ingenuity Pathway Analysis suite (IPA; www.ingenuity.com, accessed on 15 September 2022).  The upstream regulator analysis tool of IPA was used to assess the activity of upstream regulators as detailed in (Salic et al., 2019).
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from total-RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra II Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 v1.5 system (Illumina, New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 150 bp sequencing protocol, 29-60 million reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.8 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: Effect of genetic background.   To investigate the effect of genetic background on the development of neuropathology in Ldlr-/-.Leiden mouse model, two groups of Ldlr-/-.Leiden mice were terminated at 18 or 50 weeks of age (Figure 1A). For comparison, two groups of C57BL/6J mice were terminated at the same age. All groups were kept on chow diet. The mice were terminated by isoflurane inhalation (4%) and heart puncture followed by perfusion with phosphate-buffered saline (PBS) for 10 min (1 ml/min).      Effect of HFD feeding and anti-complement C5 treatment.   To investigate the effect of HFD feeding and treatment with an established antibody (BB5.1) targeting complement C5 on neuropathology in Ldlr-/-.Leiden  mice, 17–18 week-old Ldlr-/-.Leiden mice were matched into two groups based on body weight, blood glucose, plasma cholesterol and plasma triglyceride levels (Figure 1B). These two groups were fed an energy-dense HFD (45 kcal% fat with 39 kcal% fat from lard and 6 kcal% fat from soybean oil, 20 kcal% protein and 35 kcal% carbohydrates, D12451, Research Diets, New Brunswick, NJ, USA, (Gart et al., 2021, doi: 10.3390/nu13082836) for 32 weeks. During the last 12 weeks of HFD feeding, mice received intraperitoneal injections of either a vehicle (sterile PBS) or the established anti-C5 antibody (BB5.1, 5 mg/mL in PBS, 1 mg/mouse, (Zelek et al., 2020, doi: 10.1111/imm.13228) twice a week until the end of the study as we detailed previously (Seidel et al., 2022). The BB5.1 antibody was produced as reported (Seidel et al., 2022). Mice were euthanized at 50 weeks old using the aforementioned method. A separate group of chow-fed Ldlr-/-.Leiden mice was sacrificed at 50 weeks of age and used as a non-obese reference.

tag: organism strain

tag: diet+treatment

tag: mousenr

value: hypo 38

tag: Sex

value: Male


title: 104266-001-042

value: hypo 42


title: 104266-001-040

value: hypo 40


title: 104266-001-041

value: hypo 41


title: 104266-001-037

value: hypo 37


title: 104266-001-035

value: hypo 35


title: 104266-001-039

value: hypo 39


title: 104266-001-033

value: hypo 33


title: 14_Positive_nonpregnant

description: Sample 14


title: 104266-001-032

value: hypo 32


title: 15_Negative_pregnant

description: Sample 15


title: 13_Positive_pregnant

description: Sample 13


title: 104266-001-031

value: hypo 31


title: 10_Negative_pregnant

description: Sample 10


title: 19_Negative_pregnant

description: Sample 19


title: 7_Positive_nonpregnant

description: Sample 7


title: 12_Negative_nonpregnant

description: Sample 12


title: 11_Positive_pregnant

description: Sample 11


title: 104266-001-026

value: hypo 26


title: 104266-001-024

value: hypo 24


title: 8_Positive_pregnant

description: Sample 8

value: whole blood


title: 9_Negative_pregnant

description: Sample 9

value: Negative


title: 6_Positive_pregnant

description: Sample 6

value: Positive


title: 104266-001-030

value: hypo 30


title: 104266-001-025

value: hypo 25


title: 104266-001-027

value: hypo 27

value: Male


title: 104266-001-028

value: hypo 28


title: 5_Negative_pregnant

description: Sample 5

value: pregnant


title: 2_Positive_nonpregnant

description: Sample 2

value: nonpregnant


title: 4_Positive_nonpregnant

description: Sample 4


title: 1_Positive_pregnant

description: Sample 1


title: 3_Positive_nonpregnant

description: Sample 3


title: 104266-001-022

value: hypo 22


title: 104266-001-021

value: hypo 21


title: 104266-001-019

value: hypo 19


title: 104266-001-018

value: hypo 18


title: 104266-001-017

value: hypo 17


title: 104266-001-015

value: hypo 15


title: 104266-001-016

value: hypo 16


title: 104266-001-014

value: hypo 14


title: HS8 Week 4

type: protein

city: Liverpool

first: John

last: Frew

address: Elizabeth St

department: Dermatology

institute: Liverpool Hospital

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS8W4

data_processing:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay. (Assarsson et al., 2014). All of the samples met the quality control (QC) for the Olink panels. Gene set enrichment (pathway) analysis was performed using Reactome (Croft et al., 2014), False discovery rate cutoff at 0.05 was used to identify significant enrichment.
IPC normalized

label: OLINK PEA

molecule: protein

source_name: Serum

extract_protocol: 5mL of serum was drawn from patients at baseline and after 4 weeks of therapy with Upadacitinib 15mg daily. Samples were centrifuged after collection, and serum was stored at -80 C.

tag: disease

value: Hidradenitis Suppurativa

tag: time point

value: Week 4


title: HS17 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS17W4


title: HS19 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS19W4


title: HS20 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS20W4


title: HS4 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS4W4


title: 104266-001-013

value: hypo 13

tag: age


title: HS14 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS14W4


title: HS16 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS16W4


title: HS3 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS3W4


title: HS18 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS18W4


title: 104266-001-023

value: hypo 23


title: 104266-001-011

value: hypo 11


title: 104266-001-012

value: hypo 12

value: Male


title: 104266-001-020

value: hypo 20


title: HS13 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS13W4


title: HS12 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS12W4


title: HS10 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS10W4


title: HS9 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS9W4


title: HS11 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS11W4


title: HS5 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS5W4


title: HS2 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS2W4


title: Spermatids R9-12 2

value: Germ cell

tag: developmental stage

value: Spermatids R9-12

tag: strain

value: Sprague-Dawley

tag: genotype

value: GFP-GCS


title: 104266-001-010

value: hypo 10


title: 104266-001-007

value: Chow(weaned-50wk), vehicle(30-50wk)

value: hypo 07


title: 104266-001-008

value: hypo 08


title: 104266-001-009

value: hypo 09


title: HS1 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS1W4

value: Hidradenitis Suppurativa


title: 104266-001-002

value: hypo 02


title: 104266-001-001

value: hypo 01


title: 104266-001-003

value: hypo 03


title: 104266-001-005

value: hypo 05


title: HS6 Week 4

description:
Analysis was performed using the Olink Inflammation panel (92 analytes) proseek multiplex assay.
HS6W4

value: Week 4


title: 105150-001-004R

value: Male


title: 105150-001-005R


title: abortive tubal ectopic pregnancy 01 [AEP1]

first: Xiaoya

last: Zhao

state: -- None selected --

address: No. 910, Hengshan Rd

institute: School of Medicine, Shanghai Jiaotong University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fallopian tube and placenta

extract_protocol:
The tissues of maternal-fetal interface were isolated and obtained for single cell sequence, with a proportion of 1 to 2 (maternal to fetus). Freshly collected tissues were flushed with ice-cold PBS. In details, for decidua and fallopian tube were digested with 20ml type I collagenase at 1.0 mg/ml in RPIM 1640 medium/10% fetal bovine serum (FBS) with gentle shaking at 37 °C for 1h and 20ml type I DNase at 0.1mg/ml for 5 mins in a shaking incubator. For placenta were digested twice for 30 min each at 37 °C with 30 ml mix digestive enzyme (15ml TrypLE and 15ml ACCUMAX) with gentle shaking. The digested suspension was filtered through a 100-µm cell strainer and 40-µm cell strainer, then the enzymatic reaction was stopped by adding 10% FBS. If the red cells were visualized, the RBC lysis step was performed: 1-2ml of RBC lysis buffer were added and triturated several times, then incubated for 1-2 minutes on ice. Cells were analyzed with a hemocytometer using trypan blue, and which survival rate is generally above 90%.
This process was performed by Genergy Bio-Technology Corporation and in accordance with the manufacturer's protocol. Cells were counted and loaded onto the Chromium Controller (10X Genomics) for a target recovery of 8000 single cells. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were performed. Qubit was used for library quantification before pooling. The final library pool was sequenced on an Illumina Nova6000 platform using 150-base-pair paired-end reads.

value: fallopian tube and placenta

tag: geatational days

tag: sample group

value: abortive tubal ectopic pregnancy


title: ruptured tubal ectopic pregnancy 03 [REP3]

description: 10x Genomics

value: ruptured tubal ectopic pregnancy


title: abortive tubal ectopic pregnancy 02 [AEP2]

description: 10x Genomics


title: ruptured tubal ectopic pregnancy 02 [REP2]

description: 10x Genomics


title: 105150-001-006R


title: HEK293T_GLORI+_rep2

city: Beijing

first: Cong

address: No.5 Yiheyuan Road Haidian District, Beijing 100871 P.R. China

department: School of Life Sciences

institute: Peking university

description: wildtype HEK293T cells with GLORI treatment

data_processing:
Adapters and low-quality bases were trimmed with trim_galore (version 0.6.6).
PCR duplications was removed with Seqkit. UMI were removed with FASTX-Toolkit (version 0.0.13).
Clean reads were firstly mapped to the genome with STAR and then transcriptome with bowtie. Pileup was performed using samtools API pysam. Customized scripts were used to call m6A sites from samples.
To make the analysis pipeline easy to implement, we developed GLORI-tools, a computational pipeline that quantifies the A rate of each A site and follows multiple filters for false positives.
The code of the GLORI-tools is available in the following GitHub repositories: https://github.com/liucongcas/GLORI-tools.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include non-A-to-G conversion rate
Supplementary files format and content: tab-delimited text files include m6A sites with quantified modification levels

molecule: polyA RNA

growth_protocol: HEK293Tcells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
mRNA was purified by oligo (dT) beads. 100-200 ng of mRNA was used for GLORI treatment and construction of sequencing libraries.
RNA libraries were prepared using modified eCLIP library construction.

tag: cell line

tag: cell type

value: human embryonic kidney 293 cells

value: WT

tag: treatment

value: GLORI+

tag: time

value: Day 0


title: ruptured tubal ectopic pregnancy 01 [REP1]

description: 10x Genomics

tag: tissue


title: 105150-001-003R

tag: organism strain


title: HEK293T_GLORI+_rep1


title: 10098, IFNgIL10

data_processing:
FASTQ files were generated using the bcl2fastq2 Conversion v2.19 tool. Each set of samples seq data was aligned and normalized using STAR aligner to assemble the mapped reads into homo sapiens transcriptome hg10 Refseq
Assembly: hg10
Supplementary files format and content: comma-separated values with combined counts for genes

source_name: PBMCs

growth_protocol: Thawed PBMCs were rested overnight at 37°C in a CO2 incubator at 1x10^6 cells per well in a U-shaped 96-well plate in complete RPMI

extract_protocol:
First-strand cDNA was primed by the 3’ SMART-Seq CDS Primer II A and used the SMART-Seq v4 Oligonucleotide for template switching at the 5’ end of the transcript. Full length of cDNA was synthesized and amplified by LD PCR for 14 cycles using a SMARTseq v4 Ultra Low Input RNA kit (Cat#634888)
Illumina Nextera XT library preparation kit per the manufacturer’s protocol

treatment_protocol: PBMCs were then stimulated with iRBC E:T ratio of 2:1 for 12 hours at 37°C. IFN-γ+IL-10+TNFα- and IFN-γ-IL-10-TNFα+ cells were isolated using IFN- γ Secretion Assay - Detection Kit (FITC), human (Cat# 130-090-433) TNF-α Secretion Assay - Detection Kit (PE), human (Cat# 130-091-268), and IL-10 Secretion Assay - Detection Kit (APC), human (Cat# 130-090-761), according to the manufacturer’s instructions

value: PBMCs

tag: cytokine expression

value: CD4+ T cells

value: female

value: iRBC


title: 10098, TNF

value: TNF


title: 104266-001-006

tag: diet+treatment

value: Chow(weaned-50wk), vehicle(30-50wk)

tag: mousenr

value: hypo 06


title: 10036, TNF

tag: Sex


title: 105150-001-002R


title: 105150-001-008R


title: intrauterine pregnancy 02 [IP2]

description: 10x Genomics

source_name: decidua and placenta

value: decidua and placenta

value: intrauterine pregnancy


title: 10036, IFNgIL10


title: 10282, IFNgIL10


title: 105150-001-001R

value: Male


title: 10282, TNF


title: intrauterine pregnancy 01 [IP1]

description: 10x Genomics