title: Small Molecule-induced hiPSC-derived HLCs Day 40 [GC117501]

data_processing:
Single-end reads were generated, with an average of 4 million reads obtained per sample. Alignment was performed with Hisat2. Raw counts were log2 transformed before performing downstream analyses.
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes number of transcripts for each sample
Supplementary files format and content: comparison between different samples, includes tab-delimited text file for all samples

source_name: reprogrammed epithelial cells

extract_protocol:
RNA was extracted and quality control was performed as mentioned above.We performed RTqPCR, using progeny from 3 wells of 96 well plates for RNA extraction using the GenElute Mammalian Total RNA Miniprep Kit (Sigma-Aldrich) according to the manufacturer’s instructions with addition of DNAseI from the On-Column DNase I Digestion kit (Sigma-Aldrich).
Library preparation was performed with the LexoGen Quant Seq. Kit. Libraries were sequenced on an Illumina HiSeq4000 sequencing system.

value: reprogrammed epithelial cells

tag: cell line

value: Sigma 3X (induced pluripotent stem cells)

value: iPSC0028 (Sigma-Aldrich) genome engineered

tag: cell subtype

value: hepatic differentiation

value: Day 40


title: Serum,MCI,46

status: Public on Feb 26 2024

type: SRA

city: Maastricht

first: Qingfeng

last: Wen

state: Limburg

address: Universiteitssingel 40

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

description:
Memories_HB04500_Serum_S152_R1_001.fastq
miR.Counts_serum.csv

library_source: transcriptomic

data_processing:
We used cutadapt (version 1.8.1) to trim adapters and random bases
Data were processed with miRge2 with the latest release of miRbase
Supplementary files format and content: For miR.Counts_serum.csv, each row represents one miRNA, each column represents one serum sample.
Supplementary files format and content: For miR.Counts_plasma.csv, each row represents one miRNA, each column represents one plasma sample.

molecule: total RNA

organism: Homo sapiens

source_name: Serum

extract_protocol:
RNAs were isolated using the tRNA/YRNA Depletion Protocol.
Libraries were prepared for sequencing with the automated Gel-Free option in the NEXTFLEX® Small RNA-Seq Kit v3.

tag: tissue

value: Serum

tag: Sex

value: Male

tag: age

tag: disease state

value: MCI

tag: subject


title: MsNxCO2_077

city: Urbana

first: Matthew

middle: D.

last: Brooks

state: Illinois

address: 1201 W Gregory Drive

department: GCPRU

country: USA

institute: USDA

data_processing:
Raw reads were filtered for low quality reads using BBDuk (BBtools, Joint Genome Institute)
Reads were aligned to the chromosome-level haploid genome (Zhongmu-1) (Shen et al. 2020).
Gene-level counts were obtained using featureCounts (Liao et al. 2014)
Supplementary files format and content: tab delimited file contains raw counts for each sample

molecule: polyA RNA

organism: Medicago sativa

source_name: Agate, Ineffective, Low nitrogen, Ambient CO2, Replicate 4

growth_protocol: Seeds were germinated on plates in sterile water and at room temperature for 3 days before sowing. Plants were transferred to two inch square pots containing equal parts (by weight) of calcined clay and coarse sand. The soil substrate was mixed, washed, autoclaved, and cooled before use. To each pot, 10 mL of rhizobium was added from a 1 L bacterial culture grown in modified arabinose-gluconate media for 5 days. Plants were grown in growth chambers with 500 µmol m-2 s-2 light, 8hr/16hr day/night cycles, and 22 C. Plants were bottom-watered with an equal volume of distilled water every 2-3 days

extract_protocol: Kapa Hyper Stranded mRNA library kit (Roche)

treatment_protocol: Plants split between chambers maintained at either ambient (420 ppm) or elevated (600 ppm) CO2. Plants were fertilized with 500 mL of either 6, 10 or 16 mM KNO3 in 0.5X Hoagland solution once a week

value: Leaf

tag: cultivar

value: Agate

tag: nitrogen fixation_capability

value: ineffective

tag: kno3 treatment

value: 6 mM KNO3

tag: co2 treatment

value: 420 ppm CO2


title: MsNxCO2_083

source_name: Agate, Effective, Low nitrogen, Ambient CO2, Replicate 2

value: effective


title: dpi2_scATACseq

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

library_source: genomic

data_processing:
Qualities of de-barcoded raw sequence reads were checked by fastqc.
Reads were aligned to the danRer11 reference genome using Cell Ranger ATAC.
Assembly: danRer11 genome
Supplementary files format and content: one csv file containing raw count values for scATAC-seq peaks of all the samples

molecule: genomic DNA

organism: Danio rerio

source_name: Heart

growth_protocol: Zebrafish were raised and maintained under standard laboratory conditions.

extract_protocol:
Isolated noncardiomyocytes were used as input for nuclei preparation following the 10X Genomics Chromium single-cell ATAC-seq solution protocol
scATAC-seq libraries were prepared for sequencing as outlined in the 10X Genomics single-cell ATAC-seq solution protocol.

treatment_protocol: Zebrafish were anesthetized by immersion with 0.04% tricaine and immobilized in a dampened foam with ventral side up. A small incision was made between the gills to expose the ventricle. About 20% of ventricular apex was resected using iridectomy scissors. After apex resection, fish were returned to a recovery tank with fresh system water.

value: Heart

tag: genotype

value: wild type


title: Serum,MCI,45

description:
Memories_HB04494_Serum_S125_R1_001.fastq
miR.Counts_serum.csv


title: Small Molecule-induced hiPSC-derived HLCs Day 40 [GC117499]

city: Leuven

first: Gert

last: Vanmarcke

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

tag: cell type

tag: time point


title: dpi0_scATACseq


title: MsNxCO2_076

source_name: Agate, Ineffective, Low nitrogen, Ambient CO2, Replicate 3


title: Growth Factor-induced hiPSC-derived HLCs Day 40 [GC117497]


title: Serum,AD,27

description:
Memories_HB04479_Serum_S198_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: MsNxCO2_074

source_name: Saranac, Ineffective, Med. nitrogen, Ambient CO2, Replicate 4

value: Saranac

value: 10 mM KNO3


title: Growth Factor-induced hiPSC-derived HLCs Day 40 [GC117498]

value: reprogrammed epithelial cells

value: Sigma 3X (induced pluripotent stem cells)

value: iPSC0028 (Sigma-Aldrich) genome engineered


title: CUTLL1 KD rep3

city: Bethesda

first: Stanley

last: Adoro

state: MD

address: Center Dr

department: CCR

institute: NCI

data_processing:
Alignment STAR version=2.7.9a -sjdbOverhang 100
Read counts htseq  0.11.4
Differential Expression Analysis: DESeq2_1.38.3
Assembly: GRCh38 Gencode release 39
Supplementary files format and content: HTSeq counts file tab delimeted

growth_protocol: complete RPMI + 20% FBS

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit
NuGEN Trio RNA-seq library preparation kit

treatment_protocol: CUTLL1 cells were transduced with lentivirus containing pLKO CT/KD shRNA. After 48 hours, cells were treated with 1ug/ml puromycin for 5 days.

value: T-ALL

value: t(7;9)(q34;q34) translocation

tag: treatment

value: CHMP5 shRNA


title: CUTLL1 KD rep1


title: MsNxCO2_073

source_name: Saranac, Ineffective, Med. nitrogen, Ambient CO2, Replicate 3

value: Leaf


title: Serum,MCI,47

description:
Memories_HB04508_Serum_S175_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Male

value: MCI


title: Serum,AD,26

description:
Memories_HB04476_Serum_S12_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_075

source_name: Agate, Ineffective, Low nitrogen, Ambient CO2, Replicate 2

value: Agate

value: ineffective

value: 6 mM KNO3

value: 420 ppm CO2


title: CUTLL1 KD rep2


title: Growth Factor-induced hiPSC-derived HLCs Day 40 [GC117496]

value: hepatic differentiation

value: Day 40


title: Serum,MCI,43

description:
Memories_HB04466_Serum_S173_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: Small Molecule-induced hiPSC-derived HLCs Day 40 [GC117500]

value: reprogrammed epithelial cells


title: MsNxCO2_079

source_name: Saranac, Effective, Low nitrogen, Ambient CO2, Replicate 2

value: Saranac

value: effective


title: Small Molecule-induced hiPSC-derived HLCs Day 20 [GC117495]

value: Sigma 3X (induced pluripotent stem cells)

value: iPSC0028 (Sigma-Aldrich) genome engineered

value: Day 20


title: CUTLL1 CT rep3

value: T-ALL

value: t(7;9)(q34;q34) translocation

value: CT shRNA


title: dpi7_scATACseq

value: Heart

value: wild type


title: MsNxCO2_072

source_name: Saranac, Ineffective, Med. nitrogen, Ambient CO2, Replicate 2

value: Leaf

value: ineffective

value: 10 mM KNO3


title: Serum,MCI,42

description:
Memories_HB04464_Serum_S150_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Male

value: MCI


title: Small Molecule-induced hiPSC-derived HLCs Day 20 [GC117494]

value: reprogrammed epithelial cells

value: hepatic differentiation


title: Serum,MCI,44

description:
Memories_HB04480_Serum_S34_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_071

source_name: Saranac, Ineffective, Med. nitrogen, Ambient CO2, Replicate 1

value: Saranac

value: 420 ppm CO2


title: CUTLL1 CT rep2


title: Serum,AD,25

description:
Memories_HB04463_Serum_S32_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: Small Molecule-induced hiPSC-derived HLCs Day 20 [GC117493]

value: Sigma 3X (induced pluripotent stem cells)

value: iPSC0028 (Sigma-Aldrich) genome engineered

value: Day 20


title: MsNxCO2_070

source_name: Agate, Effective, Med. nitrogen, Ambient CO2, Replicate 4

value: Agate


title: Serum,AD,24

description:
Memories_HB04462_Serum_S104_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: CUTLL1 CT rep1

value: T-ALL

value: t(7;9)(q34;q34) translocation

value: CT shRNA


title: Growth Factor-induced hiPSC-derived HLCs Day 20 [GC117491]


title: MsNxCO2_069

source_name: Agate, Effective, Med. nitrogen, Ambient CO2, Replicate 3

value: Leaf

value: effective

value: 10 mM KNO3


title: Growth Factor-induced hiPSC-derived HLCs Day 20 [GC117492]


title: Serum,AD,22

description:
Memories_HB04458_Serum_S79_R1_001.fastq
miR.Counts_serum.csv

value: Serum


title: Growth Factor-induced hiPSC-derived HLCs Day 20 [GC117490]

value: reprogrammed epithelial cells


title: MsNxCO2_068

source_name: Agate, Effective, Med. nitrogen, Ambient CO2, Replicate 2


title: Serum,AD,23

description:
Memories_HB04461_Serum_S123_R1_001.fastq
miR.Counts_serum.csv


title: Serum,AD,21

description:
Memories_HB04450_Serum_S56_R1_001.fastq
miR.Counts_serum.csv

value: Male


title: Serum,MCI,41

description:
Memories_HB04444_Serum_S52_R1_001.fastq
miR.Counts_serum.csv

value: MCI


title: Serum,MCI,40

description:
Memories_HB04441_Serum_S147_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_065

source_name: Saranac, Effective, Med. nitrogen, Ambient CO2, Replicate 3

value: Saranac

value: 420 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T062

city: Dublin

first: John Francis

last: O'Grady

state: Leinster

address: Belfield, Dublin4

department: UCD School of Agriculture and Food Science

country: Ireland

institute: University College Dublin

data_processing:
The quality of all n = 123  (n = 63 control, n = 60 bTB-reactor) paired-end RNA-seq FASTQ files was assessed using FastQC (v. 0.11.5)
RNA sequencing reads were aligned to the ARS-UCD 1.2 bovine reference genome using STAR (v 2.7.1a) .
Read counts for each gene were quantified using using featureCounts (v. 2.0.6) by specifying the Bos taurus ARS-UCD 1.2  ensembl annotation file, excluding chimeric fragments, aligning reads in a reversely stranded manner and only considering fragements which had both ends successfully aligned.
A differential expression analysis (DEA) was conducted between the control and bovine tuberculosis reactor groups using DESeq2 (v. 1.40.2) in R (v. 4.3.2) accounting for age, sequencing batch and the top two genotype principle components of the pruned SNP set prior to imputation. Normalised counts were extracted using the DESeq2 median of ratios normalisation method
A cis-eQTL and trans-eQTL analysis was conducted on the control, the bTB reactor and a combined group consiting of all 123 animals using TensorQTL (v. 1.0.8) and QTLtools(v 1.3.1) respectively . For each group, read counts were first normalised using the TMM method in edgeR (v. 3.42.4). Read counts were then inverse normally transformed (INT) accross samples using the qnorm function in R. A cis-eQTL was defined as residing proximal (< 1Mb) to the assocated gene's transcriptional start site (TSS) whereas a trans-eQTL was defined as residing distal (> 5Mb or on a different chromosome) to the associated gene's TSS with the TSS derived from the Bos taurus ARS-UCD 1.2 ensembl annotation file.
Assembly: ARS-UCD-1.2
Supplementary files format and content: count_matrix_clean.txt - Raw expression counts for all genes included in the Bos taurus ARS-UCD 1.2 ensembl annotation file determined from the feature counts software.
Supplementary files format and content: DESeq2_normalised.txt - Expression data for all animals which was normalised using the DESeq2 median of ratios method prior to conducting a differential expression analysis. Genes with raw expression counts ≥ 6 in at least 20% of samples were retained in this data set prior to the DEA
Supplementary files format and content: ALL.expr_tmm_inv.bed.gz - Expression data for all animals which was first normalised using the TMM method in edgeR then each gene inverse normally transformed across samples for inclusion in the eQTL analysis of all animals. Genes with raw expression counts ≥ 6 and a transcript per million (TPM) normalised expression count ≥ 0.1 in at least 20% of samples were retained for the eQTL analysis
Supplementary files format and content: CONTROL.expr_tmm_inv.bed.gz - Expression data for Control (bTB-) animals which was first normalised using the TMM method in EdgeR then each gene inverse normally transformed across samples for inclusion in the eQTL analysis of bTB- animals. Genes with raw expression counts ≥ 6 and a transcript per million (TPM) normalised expression count ≥ 0.1 in at least 20% of samples were retained for the eQTL analysis.
Supplementary files format and content: INFECTED.expr_tmm_inv.bed.gz - Expression data for bTB reactor (bTB+) animals which was first normalised using the TMM method in EdgeR then each gene inverse normally transformed across samples for inclusion in the eQTL analysis of bTB+ animals. Genes with raw expression counts ≥ 6 and a transcript per million (TPM) normalised expression count ≥ 0.1 in at least 20% of samples were retained for the eQTL analysis

organism: Bos taurus

source_name: Peripheral Blood

extract_protocol:
Peripheral blood was sampled from each animal using blood collection tubes with blood harvested from the tail vein.  All tubes were inverted 4-6 times immediately after sampling and transported to the laboratory in a refrigerated cool box within three hours of collection.  Whole blood was collected in Tempus™ blood RNA stabilisation tubes (Thermo Fisher Scientific) for isolation of total RNA.  All tubes intended for RNA extraction were stored at −80°C prior to isolation and purification.
Total RNA preparation was performed for each animal (bTB+ and bTB−) using the Tempus™ Spin RNA Isolation Kit (Thermo Fisher Scientific). The Tempus™ tubes were inverted to mix the contents, which were then poured into sterile 50 ml conical tubes and total RNA was isolated and purified according to the manufacturer’s instructions. Following total RNA purification, an Agilent 2100 Bioanalyzer and the RNA 6000 Nano LabChip kit (Agilent Technologies, Inc.) were used to quality check and generate RNA integrity number (RIN) values for all samples, which were then stored at −80°C. Total RNA samples (bTB+ and bTB−) were used with the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs) to construct sequence barcode-indexed RNA-seq libraries, which were then used for 150 bp paired-end sequencing on the NovaSeq™ 6000 Sequencing System (Illumina, Inc.). RNA-seq library preparation and sequencing were performed by an external provider (Novogene).

treatment_protocol: A total of n = 60 cattle infected with M. bovis and n = 63 non-infected control animals were recruited for the purpose of this study. All animals were male and were born between 2014 and 2019. The M. bovis-infected cattle were selected from a panel of naturally infected animals maintained for on-going disease surveillance at the Department of Agriculture, Food and the Marine (DAFM) Backweston Laboratory Campus (Celbridge, Co. Kildare, Ireland). These animals had a positive single intradermal comparative tuberculin test (SICTT) result where the skin-fold thickness response to purified protein derivative (PPD)-bovine exceeded that of PPD-avian by at least 12 mm. As a confirmatory test, all animals were tested for presence of M. bovis using the whole blood IFN-γ release assay [IGRA] (BoviGAM® – Prionics AG, Switzerland) test. Non-infected control animals were selected from herds with no recent history of M. bovis infection.

value: Peripheral Blood

tag: animal id

tag: experimental group

value: Reactor

tag: age (months)

value: Positive

value: Heparin tubes

tag: ifga nil

tag: ifga avian

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result

value: Negative


title: Small Molecule-induced hiPSC-derived HLCs Day 12 [GC117488]

source_name: reprogrammed epithelial cells

tag: tissue

tag: cell line

value: Sigma 3X (induced pluripotent stem cells)

value: iPSC0028 (Sigma-Aldrich) genome engineered

tag: cell subtype

value: hepatic differentiation

value: Day 12


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T061

tag: Sex


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T064


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T063


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T060


title: Serum,AD,20

description:
Memories_HB04436_Serum_S9_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

tag: age

tag: disease state

value: AD

tag: subject


title: MsNxCO2_064

source_name: Saranac, Effective, Med. nitrogen, Ambient CO2, Replicate 2

value: Leaf

tag: cultivar

tag: nitrogen fixation_capability

value: effective

tag: kno3 treatment

value: 10 mM KNO3

tag: co2 treatment


title: Small Molecule-induced hiPSC-derived HLCs Day 12 [GC117487]

value: reprogrammed epithelial cells

tag: cell type

tag: time point


title: Small Molecule-induced hiPSC-derived HLCs Day 12 [GC117489]


title: MsNxCO2_067

source_name: Agate, Effective, Med. nitrogen, Ambient CO2, Replicate 1

value: Agate


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T059

tag: animal id

tag: experimental group

tag: age (months)

value: Male

tag: ifga nil

tag: ifga avian


title: MsNxCO2_066

source_name: Saranac, Effective, Med. nitrogen, Ambient CO2, Replicate 4

tag: tissue

value: Saranac

value: 420 ppm CO2


title: Small Molecule-induced hiPSC-derived HLCs Day 12 [GC117486]

tag: cell line

tag: cell subtype


title: MsNxCO2_063

source_name: Saranac, Effective, Med. nitrogen, Ambient CO2, Replicate 1


title: Serum,AD,19

description:
Memories_HB04435_Serum_S54_R1_001.fastq
miR.Counts_serum.csv

value: Serum

tag: Sex

tag: age


title: Growth Factor-induced hiPSC-derived HLCs Day 12 [GC117485]


title: MsNxCO2_062

source_name: Agate, Ineffective, Med. nitrogen, Ambient CO2, Replicate 4

value: ineffective


title: Growth Factor-induced hiPSC-derived HLCs Day 12 [GC117484]


title: Serum,MCI,39

description:
Memories_HB04433_Serum_S212_R1_001.fastq
miR.Counts_serum.csv

value: Female

tag: disease state

value: MCI

tag: subject


title: MsNxCO2_061

source_name: Agate, Ineffective, Med. nitrogen, Ambient CO2, Replicate 3

tag: cultivar

tag: nitrogen fixation_capability


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T056

value: Peripheral Blood

value: Reactor

value: Positive

value: Heparin tubes

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: Growth Factor-induced hiPSC-derived HLCs Day 12 [GC117483]

value: Sigma 3X (induced pluripotent stem cells)

tag: cell type

value: iPSC0028 (Sigma-Aldrich) genome engineered

value: hepatic differentiation

tag: time point

value: Day 12


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T058

tag: animal id

tag: experimental group

tag: age (months)


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T055

tag: tissue

tag: ifga nil

tag: ifga avian


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T054

tag: Sex


title: MsNxCO2_059

source_name: Saranac, Ineffective, High nitrogen, Ambient CO2, Replicate 4

value: Leaf

tag: kno3 treatment

value: 16 mM KNO3

tag: co2 treatment


title: Serum,MCI,36

description:
Memories_HB04420_Serum_S122_R1_001.fastq
miR.Counts_serum.csv

tag: age

tag: disease state

tag: subject


title: Growth Factor-induced hiPSC-derived HLCs Day 12 [GC117482]

value: reprogrammed epithelial cells

tag: cell line

tag: cell subtype


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T053

value: Male

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: MsNxCO2_057

source_name: Saranac, Ineffective, High nitrogen, Ambient CO2, Replicate 2

tag: cultivar

value: Saranac

tag: nitrogen fixation_capability

value: 420 ppm CO2


title: Small Molecule-induced hiPSC-derived HLCs Day 8 [GC117505]

tag: cell type

value: hepatoblast

tag: time point

value: Day 8


title: Small Molecule-induced hiPSC-derived HLCs Day 8 [GC117506]

tag: tissue


title: MsNxCO2_058

source_name: Saranac, Ineffective, Low nitrogen, Ambient CO2, Replicate 3

value: ineffective

value: 6 mM KNO3


title: Serum,MCI,35

description:
Memories_HB04411_Serum_S76_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Female

value: MCI


title: Growth Factor-induced hiPSC-derived HLCs Day 8 [GC117504]

value: Sigma 3X (induced pluripotent stem cells)


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T057

value: Peripheral Blood

tag: animal id

tag: experimental group

value: Reactor

tag: age (months)

value: Positive

value: Heparin tubes

tag: ifga nil

tag: ifga avian


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T052

tag: Sex


title: MsNxCO2_056

source_name: Saranac, Ineffective, High nitrogen, Ambient CO2, Replicate 1

value: Leaf

tag: kno3 treatment

value: 16 mM KNO3

tag: co2 treatment


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T051

value: Male


title: Serum,MCI,38

description:
Memories_HB04432_Serum_S172_R1_001.fastq
miR.Counts_serum.csv

tag: age

tag: disease state

tag: subject


title: Growth Factor-induced hiPSC-derived HLCs Day 8 [GC117503]

value: reprogrammed epithelial cells

tag: cell line

value: iPSC0028 (Sigma-Aldrich) genome engineered

tag: cell subtype


title: Serum,MCI,34

description:
Memories_HB04410_Serum_S101_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_060

source_name: Agate, Ineffective, Med. nitrogen, Ambient CO2, Replicate 1

tag: cultivar

value: Agate

tag: nitrogen fixation_capability

value: 10 mM KNO3

value: 420 ppm CO2


title: Serum,MCI,37

description:
Memories_HB04421_Serum_S27_R1_001.fastq
miR.Counts_serum.csv


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T050

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: Serum,MCI,33

description:
Memories_HB04409_Serum_S78_R1_001.fastq
miR.Counts_serum.csv

tag: tissue


title: MsNxCO2_054

source_name: Agate, Effective, High nitrogen, Ambient CO2, Replicate 3

value: effective


title: Serum,Control,5

description:
Memories_HB04419_Serum_S195_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Control


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T049

tag: animal id

tag: experimental group

tag: age (months)


title: Growth Factor-induced hiPSC-derived HLCs Day 8 [GC117502]

tag: cell type

value: hepatoblast

tag: time point

value: Day 8


title: Serum,Control,4

description:
Memories_HB04408_Serum_S29_R1_001.fastq
miR.Counts_serum.csv

tag: Sex


title: Small Molecule-induced hiPSC-derived HLCs Day 4 [GC117481]

value: Sigma 3X (induced pluripotent stem cells)

value: endoderm

value: Day 4


title: MsNxCO2_052

source_name: Agate, Effective, High nitrogen, Ambient CO2, Replicate 1

tag: kno3 treatment

tag: co2 treatment


title: MsNxCO2_053

source_name: Agate, Effective, High nitrogen, Ambient CO2, Replicate 2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T047

source_name: Peripheral Blood

value: Peripheral Blood

value: Reactor

value: Positive

value: Heparin tubes

tag: ifga nil

tag: ifga avian


title: MsNxCO2_051

source_name: Saranac, Effective, High nitrogen, Ambient CO2, Replicate 4

value: Leaf

value: Saranac

value: 16 mM KNO3


title: Small Molecule-induced hiPSC-derived HLCs Day 4 [GC117479]

source_name: reprogrammed epithelial cells

value: reprogrammed epithelial cells

tag: cell line

value: iPSC0028 (Sigma-Aldrich) genome engineered

tag: cell subtype


title: Serum,MCI,32

description:
Memories_HB04401_Serum_S170_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

value: Male

tag: age

tag: disease state

value: MCI

tag: subject


title: Small Molecule-induced hiPSC-derived HLCs Day 4 [GC117480]


title: Serum,AD,18

description:
Memories_HB04402_Serum_S99_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: AD


title: Serum,AD,17

description:
Memories_HB04379_Serum_S167_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: MsNxCO2_050

source_name: Saranac, Effective, High nitrogen, Ambient CO2, Replicate 3

tag: cultivar

tag: nitrogen fixation_capability

value: effective

value: 420 ppm CO2


title: Small Molecule-induced hiPSC-derived HLCs Day 4 [GC117478]

tag: tissue

value: Sigma 3X (induced pluripotent stem cells)

value: endoderm

value: Day 4


title: Growth Factor-induced hiPSC-derived HLCs Day 4 [GC117477]


title: MsNxCO2_055

source_name: Agate, Effective, High nitrogen, Ambient CO2, Replicate 4

value: Agate


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T045

value: Peripheral Blood

tag: animal id

tag: experimental group

value: Reactor

value: Positive

value: Heparin tubes

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: MsNxCO2_049

source_name: Saranac, Effective, High nitrogen, Ambient CO2, Replicate 2

value: Leaf

value: Saranac

tag: kno3 treatment

value: 16 mM KNO3


title: Serum,Control,3

description:
Memories_HB04376_Serum_S8_R1_001.fastq
miR.Counts_serum.csv

tag: Sex

value: Male

value: Control


title: Serum,AD,16

description:
Memories_HB04302_Serum_S46_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: AD


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T043

tag: age (months)

tag: ifga nil


title: Growth Factor-induced hiPSC-derived HLCs Day 4 [GC117476]

value: reprogrammed epithelial cells

tag: cell line

tag: cell type

value: iPSC0028 (Sigma-Aldrich) genome engineered

tag: time point


title: MsNxCO2_048

source_name: Saranac, Effective, High nitrogen, Ambient CO2, Replicate 1

value: effective

tag: co2 treatment

value: 420 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T044

tag: ifga avian


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T048


title: Growth Factor-induced hiPSC-derived HLCs Day 4 [GC117475]

value: Sigma 3X (induced pluripotent stem cells)

tag: cell subtype

value: endoderm

value: Day 4


title: Serum,AD,15

description:
Memories_HB03436_Serum_S6_R1_001.fastq
miR.Counts_serum.csv

tag: age

tag: disease state

tag: subject


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T042

tag: tissue

value: Peripheral Blood

tag: animal id

tag: experimental group

value: Reactor


title: Serum,Control,2

description:
Memories_HB04294_Serum_S69_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: MsNxCO2_047

source_name: Agate, Ineffective, High nitrogen, Ambient CO2, Replicate 4

value: Leaf

tag: cultivar

value: Agate

tag: nitrogen fixation_capability

value: ineffective


title: MsNxCO2_046

source_name: Agate, Ineffective, High nitrogen, Ambient CO2, Replicate 3

tag: kno3 treatment

value: 16 mM KNO3


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T041

tag: age (months)

tag: Sex

value: Male

value: Positive

value: Heparin tubes

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: Serum,MCI,30

description:
Memories_AZM06793_Serum_S57_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: MCI


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T040

tag: ifga nil


title: hiPSC control [GC117473]

value: reprogrammed epithelial cells

tag: cell line

tag: cell type

value: iPSC0028 (Sigma-Aldrich) genome engineered

value: stem cells

tag: time point

value: Day 0


title: hiPSC control [GC117472]

value: Sigma 3X (induced pluripotent stem cells)

tag: cell subtype


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T046

value: Peripheral Blood

tag: ifga avian


title: Serum,MCI,31

description:
Memories_AZM06838_Serum_S64_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

tag: age

tag: disease state

tag: subject


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T039

tag: animal id

tag: experimental group

value: Reactor


title: MsNxCO2_044

source_name: Agate, Ineffective, High nitrogen, Ambient CO2, Replicate 1

tag: cultivar

tag: nitrogen fixation_capability

tag: kno3 treatment

tag: co2 treatment

value: 420 ppm CO2


title: hiPSC control [GC117471]


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T038

tag: age (months)

tag: Sex

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: hiPSC control [GC117470]

tag: cell line

tag: cell type

tag: cell subtype

tag: time point


title: Serum,Control,1

description:
Memories_AZM06780_Serum_S81_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

value: Female

tag: age

tag: disease state

value: Control


title: MsNxCO2_042

source_name: Saranac, Ineffective, Low nitrogen, Elevated CO2, Replicate 3

value: Leaf

value: Saranac

value: ineffective

value: 6 mM KNO3

value: 600 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T037

tag: animal id

tag: experimental group

value: Male

value: Positive

value: Heparin tubes

tag: ifga nil

tag: ifga avian


title: Serum,AD,14

description:
Memories_AZM06786_Serum_S120_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: AD

tag: subject


title: Growth Factor-induced hiPSC-derived HLCs Day 4 [GC117474]

value: reprogrammed epithelial cells

value: iPSC0028 (Sigma-Aldrich) genome engineered

value: endoderm

value: Day 4


title: MsNxCO2_041

source_name: Saranac, Ineffective, Low nitrogen, Elevated CO2, Replicate 2

tag: cultivar

tag: nitrogen fixation_capability

tag: kno3 treatment

tag: co2 treatment


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T036

value: Peripheral Blood

value: Reactor

tag: age (months)

tag: Sex

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: Serum,MCI,28

description:
Memories_AZM06771_Serum_S146_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

value: Female

value: MCI


title: Serum,MCI,27

description:
Memories_AZM06765_Serum_S191_R1_001.fastq
miR.Counts_serum.csv

tag: age


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T035


title: MsNxCO2_040

source_name: Saranac, Ineffective, Low nitrogen, Elevated CO2, Replicate 1

value: Leaf

value: Saranac


title: MsNxCO2_045

source_name: Agate, Ineffective, High nitrogen, Ambient CO2, Replicate 2

value: Agate

value: ineffective

value: 16 mM KNO3

value: 420 ppm CO2


title: MsNxCO2_039

source_name: Agate, Effective, Low nitrogen, Elevated CO2, Replicate 4

value: effective

value: 6 mM KNO3

value: 600 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T034

value: Male

value: Positive

value: Heparin tubes


title: MsNxCO2_043

source_name: Saranac, Ineffective, Low nitrogen, Elevated CO2, Replicate 4


title: MsNxCO2_037

source_name: Agate, Effective, Low nitrogen, Elevated CO2, Replicate 2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T032

source_name: Peripheral Blood


title: Serum,MCI,25

description:
Memories_AZM06753_Serum_S23_R1_001.fastq
miR.Counts_serum.csv

value: Serum

tag: disease state


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T033

value: Peripheral Blood

tag: animal id


title: Serum,AD,13

description:
Memories_AZM06751_Serum_S189_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: Serum,MCI,26

description:
Memories_AZM06761_Serum_S72_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: MsNxCO2_036

source_name: Agate, Effective, Low nitrogen, Elevated CO2, Replicate 1


title: MsNxCO2_038

source_name: Agate, Effective, Low nitrogen, Elevated CO2, Replicate 3


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T031

tag: experimental group

value: Reactor


title: Serum,MCI,29

description:
Memories_AZM06773_Serum_S26_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

value: MCI


title: MsNxCO2_035

source_name: Saranac, Effective, Low nitrogen, Elevated CO2, Replicate 4

value: Leaf

value: Saranac


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T030

tag: ifga nil


title: Serum,AD,12

description:
Memories_AZM06737_Serum_S20_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_034

source_name: Saranac, Effective, Low nitrogen, Elevated CO2, Replicate 3


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T029

tag: ifga avian


title: Serum,MCI,23

description:
Memories_AZM06736_Serum_S22_R1_001.fastq
miR.Counts_serum.csv

tag: subject


title: mammary_gland_SOCS2_KI_G18_184

type: RNA

city: Jouy-en-Josas

first: Fabienne

last: Le Provost

address: INRAE, Domaine de Vilvert, bât. 440

department: GABI

country: France

institute: INRAE

description: Mammary gland gene expression in R96C SOCS2 KI mice at pregnancy day 18

hyb_protocol: cRNA (600 ng with a specific activity > 6.0 pmol Cy3/µg of cRNA) was fragmented at 60°C for 30 minutes and hybridized to the SurePrint G3 Mouse Gene Expression v2 8x60K Microarray kit (Agilent) at 65°C for 17 hours with rotation at 10 rpm, followed by washing according to the manufacturer’s instructions.

scan_protocol: Microarray slides were scanned immediately after washing with the G2505CA microarray scanner (Agilent) using a scan protocol with a resolution of 3 µm and a dynamic range of 20 bit.

data_processing: The resulting .tiff images were analyzed with Feature Extraction Software 12.0.3.2 (Agilent) using default parameters.

organism: Mus musculus

source_name: Mammary gland, pregnancy day 18 SOCS2 KI mouse 184

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 100 ng total RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer’s instructions. Labeled cRNA was purified using an RNeasy Mini kit (Qiagen) and Cy3-dye incorporation and yield of cRNA was quantified with a Nanodrop ND-2000 spectrophotometer (Thermo Fisher Scientific). The quality of synthesized cRNA was assessed using the RNA 6000 Nano kit (Agilent) and the 2100 Bioanalyzer (Agilent).

extract_protocol: Two hundred milligrams of frozen mammary tissue were placed in a tube containing 1 mL of RNA NOW and then homogenized using an Ultra-Turrax® (IKA) to lyse the cells. This solution was transferred to a different tube containing 200 µL of chloroform, mixed gently, and incubated for 5 minutes on ice. The samples were then centrifuged for 10 minutes at 15 000 g, and the liquid phases were transferred to tubes containing 1 mL of isopropanol and then mixed gently. Samples were then incubated overnight at -20 °C before a second centrifugation for 10 minutes at 15 000 g and 4 °C. The supernatant was eliminated, and 1 mL of 75% ethanol was added to wash the RNA pellet. The tubes were vortexed and centrifuged for 5 minutes at 5 000 g and 4 °C. The supernatant was removed, and the pellet was dried for 10-15 minutes at RT. The RNA pellet was dissolved in 100 µL of sterile water. The RNA concentration was measured using a NanoDrop One (Thermo Scientific).

treatment_protocol: For mammary gland tissue samples, mice were euthanized via cervical dislocation and the inguinal (#4) mammary glands were removed from adult female mice at 8 weeks of age and 18 days of pregnancy. The lymphatic ganglion was removed and the tissue was frozen in liquid nitrogen before being stored at -80°C.

value: mammary gland

tag: developmental stage

value: pregnancy day 18

tag: genotype

value: R96C SOCS2 KI


title: MsNxCO2_033

source_name: Saranac, Effective, Low nitrogen, Elevated CO2, Replicate 1

tag: cultivar

tag: nitrogen fixation_capability

value: effective

tag: kno3 treatment


title: mammary_gland_SOCS2_KI_G18_239

source_name: Mammary gland, pregnancy day 18 SOCS2 KI mouse 239


title: mammary_gland_SOCS2_KI_G18_183

source_name: Mammary gland, pregnancy day 18 SOCS2 KI mouse 183


title: mammary_gland_WT_G18_235

description: Mammary gland gene expression in WT mice at pregnancy day 18

source_name: Mammary gland, pregnancy day 18 WT mouse 235

value: WT


title: mammary_gland_SOCS2_KI_G18_211

source_name: Mammary gland, pregnancy day 18 SOCS2 KI mouse 211


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T028

tag: age (months)

tag: Sex


title: mammary_gland_WT_G18_232

source_name: Mammary gland, pregnancy day 18 WT mouse 232


title: mammary_gland_WT_G18_233

source_name: Mammary gland, pregnancy day 18 WT mouse 233


title: mammary_gland_SOCS2_KI_G18_210

source_name: Mammary gland, pregnancy day 18 SOCS2 KI mouse 210


title: Serum,MCI,24

description:
Memories_AZM06747_Serum_S187_R1_001.fastq
miR.Counts_serum.csv


title: Serum,MCI,21

description:
Memories_AZM06731_Serum_S141_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_032

source_name: Agate, Ineffective, Low nitrogen, Elevated CO2, Replicate 4

value: Agate

value: ineffective

value: 6 mM KNO3

tag: co2 treatment

value: 600 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T026

value: Male

value: Positive

value: Heparin tubes

tag: ifga bovine

tag: ifga bovine_-_ifga_avian

tag: igra test_result


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T024

tag: tissue

value: Peripheral Blood


title: MsNxCO2_030

source_name: Agate, Ineffective, Low nitrogen, Elevated CO2, Replicate 2


title: MsNxCO2_031

source_name: Agate, Ineffective, Low nitrogen, Elevated CO2, Replicate 3


title: Serum,MCI,20

description:
Memories_AZM06730_Serum_S114_R1_001.fastq
miR.Counts_serum.csv

value: Serum

value: Female

tag: age

tag: disease state


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T023

source_name: Peripheral Blood

tag: animal id

tag: experimental group

value: Reactor

tag: ifga nil


title: Serum,AD,11

description:
Memories_AZM06723_Serum_S116_R1_001.fastq
miR.Counts_serum.csv

value: AD

tag: subject


title: MsNxCO2_029

source_name: Agate, Ineffective, Low nitrogen, Elevated CO2, Replicate 1

value: Leaf


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T022

tag: ifga avian


title: Serum,MCI,22

description:
Memories_AZM06732_Serum_S211_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

value: MCI


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T020


title: MsNxCO2_027

source_name: Saranac, Ineffective, Med. nitrogen, Elevated CO2, Replicate 3

tag: cultivar

value: Saranac

value: 10 mM KNO3


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T019


title: Serum,AD,10

description:
Memories_AZM06721_Serum_S185_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_028

source_name: Saranac, Ineffective, Med. nitrogen, Elevated CO2, Replicate 4

tag: nitrogen fixation_capability


title: mammary_gland_WT_G18_234

source_name: Mammary gland, pregnancy day 18 WT mouse 234

value: mammary gland

tag: developmental stage

value: pregnancy day 18

tag: genotype

value: WT


title: Serum,MCI,18

description:
Memories_AZM06716_Serum_S165_R1_001.fastq
miR.Counts_serum.csv

tag: Sex


title: MsNxCO2_026

source_name: Saranac, Ineffective, Med. nitrogen, Elevated CO2, Replicate 2

value: ineffective

tag: kno3 treatment

tag: co2 treatment


title: mammary_gland_SOCS2_KI_V8w_313

description: Mammary gland gene expression in 8 -week-old virgin R96C SOCS2 KI mice

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 313

value: virgin 8 weeks old

value: R96C SOCS2 KI


title: mammary_gland_WT_G18_206

source_name: Mammary gland, pregnancy day 18 WT mouse 206


title: mammary_gland_SOCS2_KI_V8w_376

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 376


title: mammary_gland_SOCS2_KI_V8w_384

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 384


title: mammary_gland_SOCS2_KI_V8w_314

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 314


title: mammary_gland_SOCS2_KI_V8w_198

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 198


title: MsNxCO2_025

source_name: Agate, Effective, Med. nitrogen, Elevated CO2, Replicate 4

value: Agate

value: effective

value: 600 ppm CO2


title: Serum,MCI,17

description:
Memories_AZM06714_Serum_S94_R1_001.fastq
miR.Counts_serum.csv

value: Serum


title: MsNxCO2_024

source_name: Agate, Effective, Med. nitrogen, Elevated CO2, Replicate 3


title: mammary_gland_SOCS2_KI_V8w_251

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 251


title: Serum,MCI,19

description:
Memories_AZM06720_Serum_S47_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: MsNxCO2_023

source_name: Agate, Effective, Med. nitrogen, Elevated CO2, Replicate 2


title: Serum,MCI,16

description:
Memories_AZM06710_Serum_S194_R1_001.fastq
miR.Counts_serum.csv

value: Male


title: Serum,AD,9

description:
Memories_AZM06713_Serum_S74_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: Serum,MCI,14

description:
Memories_AZM06704_Serum_S4_R1_001.fastq
miR.Counts_serum.csv


title: MsNxCO2_022

source_name: Agate, Effective, Med. nitrogen, Elevated CO2, Replicate 1

value: Leaf


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T018

source_name: Peripheral Blood

value: Peripheral Blood

value: Reactor

tag: age (months)

value: Positive

value: Heparin tubes

tag: ifga bovine

tag: ifga bovine_-_ifga_avian


title: Serum,MCI,15

description:
Memories_AZM06708_Serum_S44_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

tag: tissue

tag: age

value: MCI


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T016

tag: animal id

tag: igra test_result


title: mammary_gland_WT_V8w_320

description: Mammary gland gene expression in 8 -week-old virgin WT mice

source_name: Mammary gland, 8-week-old virgin WT mouse 320

value: mammary gland

value: WT


title: MsNxCO2_021

source_name: Saranac, Effective, Med. nitrogen, Elevated CO2, Replicate 4

value: Saranac

value: 10 mM KNO3


title: mammary_gland_SOCS2_KI_V8w_196

source_name: Mammary gland, 8-week-old virgin SOCS2 KI mouse 196

value: virgin 8 weeks old

value: R96C SOCS2 KI


title: mammary_gland_WT_V8w_318

source_name: Mammary gland, 8-week-old virgin WT mouse 318


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T013

tag: experimental group

tag: ifga nil


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T014

tag: ifga avian


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T017


title: MsNxCO2_020

source_name: Saranac, Effective, Med. nitrogen, Elevated CO2, Replicate 3

tag: cultivar

value: effective

value: 600 ppm CO2


title: Serum,MCI,13

description:
Memories_AZM06700_Serum_S68_R1_001.fastq
miR.Counts_serum.csv

value: Serum

tag: disease state

tag: subject


title: Serum,MCI,12

description:
Memories_AZM06699_Serum_S164_R1_001.fastq
miR.Counts_serum.csv

value: Female


title: MsNxCO2_019

source_name: Saranac, Effective, Med. nitrogen, Elevated CO2, Replicate 2

tag: nitrogen fixation_capability


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T011

tag: Sex

value: Male


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T010


title: Serum,MCI,11

description:
Memories_AZM06695_Serum_S2_R1_001.fastq
miR.Counts_serum.csv


title: mammary_gland_WT_V8w_317

source_name: Mammary gland, 8-week-old virgin WT mouse 317

tag: developmental stage

tag: genotype


title: MsNxCO2_018

source_name: Saranac, Effective, Med. nitrogen, Elevated CO2, Replicate 1

value: Leaf

tag: kno3 treatment

tag: co2 treatment


title: mammary_gland_WT_V8w_369

source_name: Mammary gland, 8-week-old virgin WT mouse 369


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T009

value: Peripheral Blood

tag: age (months)

tag: ifga bovine

tag: ifga bovine_-_ifga_avian


title: Serum,MCI,10

description:
Memories_AZM06694_Serum_S162_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

tag: age


title: dpi7_CUT&Tag_H3R27ac_CTRL_replicate2 [WT_2]

data_processing:
library strategy: CUT&Tag
For the CUT&Tag paired-end sequencing reads, adaptor sequences were removed using cutadapt (version 2.7). Trimmed reads were aligned to zebrafish genome assembly (GRCz11) using Bowtie2 (version 2.2.5) with default parameters.
Unmapped reads were filtered by samtools (version 1.9), and duplicates were removed using picard MarkDuplicates (version 2.5.0).
ChIPseqSpikeFree was used to calculate the Scaling factor.
Normalized bedgraph were generated using bedtools genomecov.
Peak calling was performed using SEACR with the following parameters: 0.02 non stringent.
Assembly: GRCz11
Supplementary files format and content: bed file (genomic coordinates of peaks identified from SEACR)

source_name: Cardiac tissue

extract_protocol:
freshly isolated noncardiomyocytes nonCMs from injury area of adult zebrafish hearts were used as input to immobilize on concanavalin-coated magnetic beads (Bangs Laboratories, cat. no. BP531). Beads are incubated with primary antibody H3K27ac (Abcam, ab4729) or IgG (Abcam, ab172730) overnight at 4°C, followed by incubation with a secondary antibody (Anti-Rabbit Secondary Antibody, EpiCypher, 13-0047) for 1h at room temperature. Beads are washed using Dig-wash buffer and incubated with pA-Tn5 mix (EpiCypher, 15-1017) and then resuspended with Tagmentation buffer, gently mixed, and incubated for 1 h at 37°C for adapter tagmentation reaction. To stop tagmentation and solubilize DNA fragments by de-crosslinking, 10 μl of 0.5 M EDTA, 3 μl of 10% SDS, and 2.5 μl of Proteinase K (20 mg/mL) are added to each sample and mixed thoroughly. The reaction tubes are then incubated at 55°C for 1h. After de-crosslinking, DNA is purified by Phenol-Chloroform-Isoamyl alcohol (25:24:1) extraction and Chloroform extraction followed by ethanol precipitation. Air-dried purified DNA is dissolved in 30 μl of 10 mM Tris-HCl pH 8.0 containing 1 mM EDTA and 25 μg/ml RNase A.
DNA fragments are amplified and indexed by uniquely barcoded i5 and i7 primers with the NEBNext High-Fidelity 2× PCR Master Mix (New England Biolabs, M0541S). The CUT&Tag libraries are purified using AMPure beads and are analyzed using an Agilent 2100 Bioanalyzer Instrument and High Sensitivity DNA Chips to detect the size distribution of libraries.

value: Cardiac tissue

tag: cell type

value: non-CMs

value: CTRL

tag: treatment

value: apex resection


title: mammary_gland_WT_V8w_256

source_name: Mammary gland, 8-week-old virgin WT mouse 256

value: mammary gland


title: mammary_gland_WT_V8w_365

source_name: Mammary gland, 8-week-old virgin WT mouse 365

value: WT


title: Serum,MCI,9

description:
Memories_AZM06686_Serum_S140_R1_001.fastq
miR.Counts_serum.csv

value: MCI


title: mammary_gland_WT_V8w_188

source_name: Mammary gland, 8-week-old virgin WT mouse 188


title: Serum,AD,8

description:
Memories_AZM06679_Serum_S91_R1_001.fastq
miR.Counts_serum.csv

value: AD


title: MsNxCO2_016

source_name: Agate, Ineffective, Med. nitrogen, Elevated CO2, Replicate 3

value: Agate

value: ineffective

value: 10 mM KNO3


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T007

tag: animal id

tag: experimental group

value: Reactor

value: Positive

value: Heparin tubes

tag: ifga nil

tag: ifga avian

tag: igra test_result

value: Negative


title: MsNxCO2_015

source_name: Agate, Ineffective, Med. nitrogen, Elevated CO2, Replicate 2

value: Leaf

tag: cultivar

tag: nitrogen fixation_capability

value: 600 ppm CO2


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T006

source_name: Peripheral Blood

value: Peripheral Blood

tag: Sex

value: Male


title: MsNxCO2_017

source_name: Agate, Ineffective, Med. nitrogen, Elevated CO2, Replicate 4

tag: kno3 treatment


title: Serum,MCI,8

description:
Memories_AZM06675_Serum_S137_R1_001.fastq
miR.Counts_serum.csv

source_name: Serum

value: Serum

tag: disease state

tag: subject


title: dpi7_CUT&Tag_H3R27ac_CTRL_replicate1 [WT_1]

value: Cardiac tissue

value: non-CMs

tag: genotype

value: CTRL

value: apex resection


title: MsNxCO2_014

source_name: Agate, Ineffective, Med. nitrogen, Elevated CO2, Replicate 1

tag: co2 treatment


title: Serum,MCI,7

description:
Memories_AZM06674_Serum_S118_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

value: Female

value: MCI


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T005

tag: age (months)

tag: ifga bovine

tag: ifga bovine_-_ifga_avian


title: dpi7_CUT&Tag_H3R27ac_FB:dnAP-1_replicate1 [ROSL_T_1]

tag: cell type

tag: treatment


title: MsNxCO2_013

source_name: Saranac, Ineffective, High nitrogen, Elevated CO2, Replicate 4

value: Saranac

value: ineffective

value: 16 mM KNO3


title: dpi7_CUT&Tag_H3R27ac_FB:dnAP-1_replicate2 [ROSL_T_2]


title: Serum,MCI,6

description:
Memories_AZM06673_Serum_S96_R1_001.fastq
miR.Counts_serum.csv

tag: age


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T004

tag: animal id

tag: experimental group

value: Reactor

value: Positive

tag: ifga nil

tag: ifga avian


title: MsNxCO2_012

source_name: Saranac, Ineffective, High nitrogen, Elevated CO2, Replicate 3

tag: cultivar

tag: nitrogen fixation_capability


title: MsNxCO2_011

source_name: Saranac, Ineffective, High nitrogen, Elevated CO2, Replicate 2

tag: kno3 treatment


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T002

tag: Sex

value: Heparin tubes

tag: igra test_result


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T003


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T008


title: Serum,MCI,4

description:
Memories_AZM06669_Serum_S143_R1_001.fastq
miR.Counts_serum.csv

tag: disease state

tag: subject


title: pos_ctl+nec 1-X per treatment/timepoint group rep 17

city: San Diego

first: Richard

last: Virgen-Slane

state: CA

address: 0777 Science Center Drive, CB4-2131, Pfizer La Jolla

department: Global Computational Safety Science, DSRD

institute: Pfizer

description: nec

data_processing:
aligned sample reads to Ensembl Macaca_fascicularis_6.0 using Salmon v 14.0
Assembly: Crab-eating macaque (Macaca_fascicularis_6.0)
Supplementary files format and content: txt file

organism: Macaca fascicularis

source_name: PBMCs

growth_protocol: PBMCs from immunized monkeys were thawed and washed with CTL Anti-Aggregate WashTM Solution (ImmunoSpot/Cellular Technology Limited), resuspended in CTL-TestTM Media (ImmunoSpot/Cellular Technology Limited), counted, and evaluated for viability

extract_protocol:
RNA isolation was performed using the Qiagen RNeasy Lipid Tissue (Qiagen, #74804) protocol on the Qiacubes according to manufacturer’s instruction
25 ng RNA was used as input for the Lexogen QuantSeq 3’mRNA-Seq Library Preparation kit for Illumina (Forward ) (Lexogen, #015.96) and libraries were prepared according to the manufacturer’s protocol
3' bulk RNAseq

treatment_protocol: AAV9 peptide pool (3 mg/mL/peptide final concentration) or DMSO (negative control) or anti-CD3 (positive control) were added, and cells were cultured for approximately 24 hours at 37oC with 5% CO2

tag: tissue

value: PBMCs

tag: genotype

value: WT


title: pos_ctl+nec 1-X per treatment/timepoint group rep 16

description: nec


title: Serum,MCI,5

description:
Memories_AZM06672_Serum_S90_R1_001.fastq
miR.Counts_serum.csv


title: pos_ctl+nec 1-X per treatment/timepoint group rep 18

description: nec


title: MsNxCO2_010

source_name: Saranac, Ineffective, High nitrogen, Elevated CO2, Replicate 1

value: Leaf

tag: co2 treatment

value: 600 ppm CO2


title: pos_ctl+nec 1-X per treatment/timepoint group rep 15

description: nec


title: pos_ctl+nec 1-X per treatment/timepoint group rep 14

description: nec


title: MsNxCO2_009

source_name: Agate, Effective, High nitrogen, Elevated CO2, Replicate 4

value: Agate

value: effective


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T001

value: Peripheral Blood

tag: age (months)

value: Male

tag: ifga bovine

tag: ifga bovine_-_ifga_avian


title: Control, C064

tag: animal id

value: Control

value: Negative


title: Serum,MCI,3

description:
Memories_AZM06639_Serum_S41_R1_001.fastq
miR.Counts_serum.csv

value: Serum

tag: age

value: MCI


title: Serum,AD,7

description:
Memories_AZM06666_Serum_S66_R1_001.fastq
miR.Counts_serum.csv

value: Female

value: AD


title: MsNxCO2_008

source_name: Agate, Effective, High nitrogen, Elevated CO2, Replicate 3

value: 16 mM KNO3


title: pos_ctl+nec 1-X per treatment/timepoint group rep 13

description: nec

tag: treatment


title: Control, C063

tag: experimental group

tag: ifga nil

tag: ifga avian


title: MsNxCO2_007

source_name: Agate, Effective, High nitrogen, Elevated CO2, Replicate 1

tag: cultivar

tag: nitrogen fixation_capability

tag: kno3 treatment


title: Serum,AD,6

description:
Memories_AZM06591_Serum_S18_R1_001.fastq
miR.Counts_serum.csv

tag: Sex

tag: disease state


title: Serum,MCI,2

description:
Memories_AZM06569_Serum_S98_R1_001.fastq
miR.Counts_serum.csv

tag: tissue

tag: subject


title: pos_ctl+nec 1-X per treatment/timepoint group rep 11

description: nec

tag: genotype


title: MsNxCO2_006

source_name: Saranac, Effective, High nitrogen, Elevated CO2, Replicate 3

value: Saranac

tag: co2 treatment


title: Control, C062

tag: age (months)

value: Heparin tubes

tag: ifga bovine

tag: igra test_result


title: Serum,MCI,1

description:
Memories_AZM06542_Serum_S50_R1_001.fastq
miR.Counts_serum.csv

tag: age


title: pos_ctl+nec 1-X per treatment/timepoint group rep 10

description: nec

value: PBMCs

tag: treatment


title: Control, C061

tag: animal id

tag: experimental group

tag: ifga bovine_-_ifga_avian


title: Control, C060

tag: ifga nil

tag: ifga avian


title: Serum,AD,5

description:
AD_5_Serum
miR.Counts_serum.csv


title: MsNxCO2_005

source_name: Saranac, Effective, High nitrogen, Elevated CO2, Replicate 2

tag: cultivar

tag: nitrogen fixation_capability

tag: kno3 treatment


title: aav+nec 1-X per treatment/timepoint group rep 18

description: nec

tag: tissue

value: WT

value: aav


title: MsNxCO2_004

source_name: Saranac, Effective, High nitrogen, Elevated CO2, Replicate 1

value: Leaf

value: 600 ppm CO2


title: aav+nec 1-X per treatment/timepoint group rep 17

description: nec


title: Control, C059

tag: Sex


title: MsNxCO2_003

source_name: Agate, Ineffective, High nitrogen, Elevated CO2, Replicate 4

value: Agate

value: ineffective


title: Serum,AD,4

description:
AD_4_Serum
miR.Counts_serum.csv

value: Male

tag: disease state

tag: subject


title: Serum,AD,3

description:
AD_3_Serum
miR.Counts_serum.csv


title: aav+nec 1-X per treatment/timepoint group rep 16

description: nec

tag: genotype


title: Control, C058

value: Peripheral Blood

value: Control

tag: age (months)

tag: ifga bovine


title: Serum,AD,2

description:
AD_2_Serum
miR.Counts_serum.csv

value: Serum

tag: age


title: Control, C057

value: Negative

tag: igra test_result


title: MsNxCO2_002

source_name: Agate, Ineffective, High nitrogen, Elevated CO2, Replicate 3

tag: co2 treatment


title: aav+nec 1-X per treatment/timepoint group rep 15

description: nec

tag: treatment


title: pos_ctl+nec 1-X per treatment/timepoint group rep 12

description: nec


title: MsNxCO2_001

source_name: Agate, Ineffective, High nitrogen, Elevated CO2, Replicate 1


title: Serum,AD,1

description:
AD_1_Serum
miR.Counts_serum.csv


title: aav+nec 1-X per treatment/timepoint group rep 14

description: nec


title: Plasma,MCI,63

description:
Memories_HB04750_Plasma_S160_R1_001.fastq
miR.Counts_plasma.csv

source_name: Plasma

value: Plasma

value: Female

value: MCI


title: 3D-MDA-MB-231 cells DMT1 KO 3

city: New York

first: Jonathan

last: Barra

state: New York

address: 1468 Madison Avenue

institute: Mount Sinai

description: Sph WTKO Counts.xlsx; Sph WTKO DE.xlsx; Sph WTKO Quantification_stats.xlsx; Sph WTKO TPMs.xlsx

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed using Trim Galore (GitHub repository, https://github.com/FelixKrueger/TrimGalore).
Reads were aligned to the hg38 genome using Rsubread v1.5.3
Gene counts were quantified by Entrez Gene IDs using featureCounts and Rsubread’s built-in annotation82
Genes with count-per-million above 0.5 in at least 3 samples were kept in the analysis. Differential expression analysis was performed using limma-voom
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized expression data with pvalues and including log2foldchange values

growth_protocol: MDA-MB-231 were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was obtained using TriZol (Qiagen) according to manufacturer instruction. >2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared externally by the company Genewiz.

treatment_protocol: 3D cell culture was performed using liquid overlay technique. Spheroids were processed for RNA extraction after 4 days

tag: cell line

tag: cell type

value: triple-negative breast cancer

value: DMT1 KO

tag: culture condition


title: 3D-MDA-MB-231 cells DMT1 KO 2


title: aav+nec 1-X per treatment/timepoint group rep 13

description: nec

value: PBMCs


title: Control, C054

source_name: Peripheral Blood

tag: animal id

tag: experimental group

value: Heparin tubes

tag: ifga nil

tag: ifga avian

tag: ifga bovine_-_ifga_avian


title: Plasma,Control,21

description:
Memories_HB04749_Plasma_S111_R1_001.fastq
miR.Counts_plasma.csv

tag: tissue

tag: Sex

tag: disease state


title: Control, C053

tag: age (months)


title: Plasma,Control,20

description:
Memories_HB04690_Plasma_S136_R1_001.fastq
miR.Counts_plasma.csv

tag: subject


title: 3D-MDA-MB-231 cells DMT1 KO 1

tag: genotype


title: aav+nec 1-X per treatment/timepoint group rep 11

description: nec

value: WT

value: aav


title: Plasma,Control,19

description:
Memories_HB04686_Plasma_S39_R1_001.fastq
miR.Counts_plasma.csv

tag: age


title: 3D-MDA-MB-231 cells wild type 3


title: Control, C052

tag: ifga bovine

tag: igra test_result


title: aav+nec 1-X per treatment/timepoint group rep 10

description: nec

tag: treatment


title: 3D-MDA-MB-231 cells wild type 2

tag: cell line

tag: cell type


title: Control, C056

tag: animal id


title: Control, C051

tag: experimental group


title: Control, C050

tag: ifga nil

value: Positive


title: 2D-MDA-MB-231 cells DMT1 KO 3

description: 2D_Differential_expression_analysis_table.csv; 2D_normalized_counts.csv; 2D_raw_counts.csv; 2D_rlog_transformed_counts.csv; 2D_Significant-DEGs.csv; 2D_TPM_values.csv

tag: culture condition


title: 3D-MDA-MB-231 cells wild type 1


title: Plasma,Control,18

description:
Memories_HB04685_Plasma_S184_R1_001.fastq
miR.Counts_plasma.csv


title: dmso+nec 1-X per treatment/timepoint group rep 18

description: nec

value: dmso


title: dmso+nec 1-X per treatment/timepoint group rep 17

description: nec


title: Control, C055

tag: ifga avian

tag: ifga bovine_-_ifga_avian


title: dmso+nec 1-X per treatment/timepoint group rep 16

description: nec

tag: tissue


title: Plasma,Control,17

description:
Memories_HB04662_Plasma_S131_R1_001.fastq
miR.Counts_plasma.csv

tag: Sex

tag: disease state


title: 2D-MDA-MB-231 cells DMT1 KO 2


title: Control, C048

tag: age (months)


title: Control, C049


title: aav+nec 1-X per treatment/timepoint group rep 12

description: nec

tag: genotype


title: Control, C047


title: 2D-MDA-MB-231 cells DMT1 KO 1


title: 2D-MDA-MB-231 cells wild type 3


title: Plasma,Control,15

description:
Memories_HB04642_Plasma_S181_R1_001.fastq
miR.Counts_plasma.csv

tag: age

tag: subject


title: dmso+nec 1-X per treatment/timepoint group rep 14

description: nec


title: dmso+nec 1-X per treatment/timepoint group rep 13

description: nec


title: Plasma,AD,28

description:
Memories_HB04635_Plasma_S210_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: Plasma,MCI,62

description:
Memories_HB04671_Plasma_S133_R1_001.fastq
miR.Counts_plasma.csv


title: dmso+nec 1-X per treatment/timepoint group rep 12

description: nec


title: Plasma,Control,14

description:
Memories_HB04628_Plasma_S128_R1_001.fastq
miR.Counts_plasma.csv

value: Male


title: Control, C045

value: Peripheral Blood

tag: ifga bovine

tag: igra test_result


title: Control, C044

value: Control


title: B79

city: Guangzhou

first: Peng

last: Deng

address: Panyu

country: China

institute: SYSUCC

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by STAR instruction
RSEM were used for counting
R scripts were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT file contain counts for each sample

source_name: locally advanced rectal cancer

growth_protocol: 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy were harvested for RNA-seq.

extract_protocol:
Total RNA of patient samples were harvested using Trizol reagent (Invitrogen).
RNA libraries were prepared using standard Illumina protocols.

value: locally advanced rectal cancer


title: 2D-MDA-MB-231 cells wild type 1

tag: cell line


title: dmso+nec 1-X per treatment/timepoint group rep 11

description: nec

tag: treatment


title: Plasma,MCI,61

description:
Memories_HB04623_Plasma_S15_R1_001.fastq
miR.Counts_plasma.csv


title: B38

treatment_protocol: 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy were harvested for RNA-seq.


title: dmso+nec 1-X per treatment/timepoint group rep 10

description: nec


title: Plasma,Control,16

description:
Memories_HB04661_Plasma_S87_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C042

tag: animal id

value: Negative


title: pos_ctl+pid 1-X per treatment/timepoint group rep 15

description: pid


title: Control, C043

tag: experimental group


title: dmso+nec 1-X per treatment/timepoint group rep 15

description: nec


title: Plasma,Control,13

description:
Memories_HB04615_Plasma_S61_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma


title: Control, C041

tag: ifga nil


title: Control, C046


title: Plasma,MCI,59

description:
Memories_HB04613_Plasma_S205_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+pid 1-X per treatment/timepoint group rep 14

description: pid


title: B91


title: Control, C040


title: B2


title: pos_ctl+pid 1-X per treatment/timepoint group rep 13

description: pid


title: 2D-MDA-MB-231 cells wild type 2

tag: cell type

tag: culture condition


title: Control, C039

tag: ifga avian

tag: ifga bovine_-_ifga_avian


title: bovine tuberculosis (bTB) reactor, M. bovis infected, T015

tag: tissue

value: Reactor

tag: Sex


title: Plasma,Control,11

description:
Memories_HB04610_Plasma_S157_R1_001.fastq
miR.Counts_plasma.csv

tag: disease state


title: pos_ctl+pid 1-X per treatment/timepoint group rep 12

description: pid

tag: genotype


title: Control, C038

tag: age (months)


title: Plasma,MCI,60

description:
Memories_HB04619_Plasma_S108_R1_001.fastq
miR.Counts_plasma.csv

tag: age

value: MCI

tag: subject


title: B100


title: Control, C037

tag: ifga bovine

tag: igra test_result


title: pos_ctl+pid 1-X per treatment/timepoint group rep 11

description: pid

tag: treatment


title: B84


title: Plasma,MCI,58

description:
Memories_HB04600_Plasma_S60_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+pid 1-X per treatment/timepoint group rep 10

description: pid


title: Control, C036

tag: animal id


title: aav+pid 1-X per treatment/timepoint group rep 18

description: pid


title: ChIP-seq-H3K27ac-Comb [DLD-1]

data_processing:
Raw reads were filtered and cleaned by fastp software.
Aliments were performed followed by bowtie2 and STAR instruction
MACS2 were used for the binding profile
RSEM were used for counting
IGV and R were used for visualization
Assembly: GRCh38
Supplementary files format and content: TXT/csv file contain counts for each sample

growth_protocol: DLD-1 cellls were cultured in RPMI1640 medium supplemented with 10% FBS and 1% P/S.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. RNA was harvested using Trizol reagent (Invitrogen).
ChIP-seq libraries were prepared according to NEB ChIP-Seq Library Prep Kit (E6240). RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: DLD-1 cells were plated into 6-well plate 20 h before treatment and harvest cells for RNA extraction at 48h.

value: Colorectal adenocarcinoma cell line DLD-1

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: B17


title: Control, C035

tag: experimental group

tag: ifga nil


title: Plasma,Control,12

description:
Memories_HB04614_Plasma_S207_R1_001.fastq
miR.Counts_plasma.csv


title: Plasma,Control,9

description:
Memories_HB04596_Plasma_S154_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: aav+pid 1-X per treatment/timepoint group rep 17

description: pid

value: PBMCs


title: aav+pid 1-X per treatment/timepoint group rep 16

description: pid

value: WT


title: Plasma,MCI,56

description:
Memories_HB04592_Plasma_S14_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C033

value: Heparin tubes


title: ChIP-seq-H3K27ac-Palb [DLD-1]


title: Plasma,MCI,57

description:
Memories_HB04595_Plasma_S203_R1_001.fastq
miR.Counts_plasma.csv


title: ChIP-seq-H3K27ac-OXA [DLD-1]


title: Control, C034


title: ChIP-seq-H3K27ac-CTRL [DLD-1]


title: B99


title: Control, C031


title: Plasma,MCI,55

description:
Memories_HB04581_Plasma_S37_R1_001.fastq
miR.Counts_plasma.csv


title: aav+pid 1-X per treatment/timepoint group rep 14

description: pid

value: aav


title: aav+pid 1-X per treatment/timepoint group rep 15

description: pid


title: Plasma,Control,8

description:
Memories_HB04577_Plasma_S202_R1_001.fastq
miR.Counts_plasma.csv


title: Plasma,Control,10

description:
Memories_HB04604_Plasma_S85_R1_001.fastq
miR.Counts_plasma.csv


title: ChIP-seq-Input-Comb [DLD-1]

value: input


title: Plasma,MCI,53

description:
Memories_HB04559_Plasma_S178_R1_001.fastq
miR.Counts_plasma.csv


title: aav+pid 1-X per treatment/timepoint group rep 13

description: pid


title: Control, C029


title: Plasma,MCI,54

description:
Memories_HB04568_Plasma_S180_R1_001.fastq
miR.Counts_plasma.csv


title: aav+pid 1-X per treatment/timepoint group rep 12

description: pid


title: Control, C028


title: ChIP-seq-Input-OXA [DLD-1]


title: Plasma,Control,7

description:
Memories_HB04540_Plasma_S36_R1_001.fastq
miR.Counts_plasma.csv


title: aav+pid 1-X per treatment/timepoint group rep 11

description: pid


title: ChIP-seq-Input-Palb [DLD-1]


title: ChIP-seq-Input-CTRL [DLD-1]


title: Plasma,Control,6

description:
Memories_HB04537_Plasma_S155_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C027


title: aav+pid 1-X per treatment/timepoint group rep 10

description: pid


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep4

first: Katherine

last: McJunkin

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

data_processing:
Low quality bases and adaptors were trimmed from sequence reads using Cutadapt v2.7 with parameters “–q 20 -minimum-length 25” (122). Resulting reads were mapped to WS277 using HISAT2 v2.1.0 with default parameters (127). Aligned reads were counted using subread featureCounts v1.6.4 with default parameters, except that “-s” option was used to specify appropriate strands (128). Differential expression analysis was done with DESeq2 v1.22.1 (ref4) in v3.5.1 R version (126).
Assembly: WS277
Supplementary files format and content: feature counts for annotated transcripts

organism: Caenorhabditis elegans

source_name: alg-2(cdb155) II; alg-1(cdb153) X

growth_protocol: Nematode culture was performed on NGM plates seeded with OP50. Worms were maintained at 20°C except where otherwise noted. Embryo samples were harvested by hypochlorite treatment. For L4 and young adult samples, L1s were hatched overnight in M9 supplemented with cholesterol, then grown on NGM with OP50 for 48h at 20°C (for L4s) or for 44h at 25°C (for young adults).

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
TruSeq Stranded Total RNA Library Prep kit (Total RNA sequencing) - prepped by Psomagen

tag: cell line

tag: cell type

value: mixed embryos

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)

value: hermaphrodite

value: whole animal


title: Control, C026

value: Peripheral Blood

value: Control

value: Male

value: Negative

tag: ifga avian

tag: ifga bovine_-_ifga_avian


title: wild type mixed embryos experiment 1rep4

description: TruSeq Stranded Total RNA Library Prep kit (Total RNA sequencing) - prepped by Psomagen

source_name: wild type

tag: tissue

value: wild type


title: dmso+pid 1-X per treatment/timepoint group rep 15

description: pid

value: dmso


title: Plasma,MCI,52

description:
Memories_HB04531_Plasma_S110_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

tag: Sex

tag: disease state

value: MCI


title: dmso+pid 1-X per treatment/timepoint group rep 14

description: pid

value: PBMCs

tag: genotype

value: WT


title: Control, C030

tag: age (months)

value: Heparin tubes


title: Plasma,MCI,51

description:
Memories_HB04530_Plasma_S129_R1_001.fastq
miR.Counts_plasma.csv

value: Female

tag: age

tag: subject


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep3

value: mixed embryos


title: Control, C024

tag: ifga bovine

tag: igra test_result


title: wild type mixed embryos experiment 1rep3


title: dmso+pid 1-X per treatment/timepoint group rep 13

description: pid

tag: treatment


title: dmso+pid 1-X per treatment/timepoint group rep 12

description: pid


title: Plasma,MCI,49

description:
Memories_HB04519_Plasma_S105_R1_001.fastq
miR.Counts_plasma.csv


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep2

value: alg-2(cdb155) II; alg-1(cdb153) X


title: wild type mixed embryos experiment 1rep2


title: Control, C022

tag: animal id


title: dmso+pid 1-X per treatment/timepoint group rep 11

description: pid


title: Plasma,MCI,48

description:
Memories_HB04518_Plasma_S200_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C023

tag: experimental group


title: dmso+pid 1-X per treatment/timepoint group rep 10

description: pid


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep3

value: alg-1(AEDH); alg-2(AEDH)


title: Control, C020

tag: ifga nil


title: Plasma,MCI,47

description:
Memories_HB04508_Plasma_S176_R1_001.fastq
miR.Counts_plasma.csv


title: Plasma,MCI,46

description:
Memories_HB04500_Plasma_S151_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+nec 1-X per treatment/timepoint group rep 9

description: nec


title: Control, C025


title: wild type L4 experiment 1rep3

tag: cell line

value: hermaphrodite


title: Plasma,MCI,45

description:
Memories_HB04494_Plasma_S126_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+nec 1-X per treatment/timepoint group rep 8

description: nec


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep2

tag: cell type

value: whole animal


title: Plasma,MCI,44

description:
Memories_HB04480_Plasma_S33_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+nec 1-X per treatment/timepoint group rep 7

description: nec


title: wild type L4 experiment 1rep2


title: Plasma,AD,27

description:
Memories_HB04479_Plasma_S197_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: Plasma,MCI,50

description:
Memories_HB04524_Plasma_S83_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C021

value: Peripheral Blood

value: Control

tag: ifga avian


title: Control, C016

value: Male

value: Negative

tag: ifga bovine_-_ifga_avian


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep4

tag: tissue

value: young adult


title: wild type young adult experiment 1rep4

value: wild type


title: Plasma,MCI,43

description:
Memories_HB04466_Plasma_S174_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

tag: Sex

value: MCI


title: Plasma,AD,26

description:
Memories_HB04476_Plasma_S11_R1_001.fastq
miR.Counts_plasma.csv

tag: disease state


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep3

tag: genotype


title: pos_ctl+nec 1-X per treatment/timepoint group rep 5

description: nec

value: PBMCs

value: WT


title: pos_ctl+nec 1-X per treatment/timepoint group rep 4

description: nec


title: wild type young adult experiment 1rep3


title: pos_ctl+nec 1-X per treatment/timepoint group rep 3

description: nec


title: Control, C015

tag: age (months)

value: Heparin tubes


title: Plasma,MCI,42

description:
Memories_HB04464_Plasma_S149_R1_001.fastq
miR.Counts_plasma.csv

tag: age


title: Control, C019


title: Control, C013


title: Plasma,AD,25

description:
Memories_HB04463_Plasma_S31_R1_001.fastq
miR.Counts_plasma.csv

tag: subject


title: pos_ctl+nec 1-X per treatment/timepoint group rep 2

description: nec


title: Control, C018

tag: ifga bovine


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep2


title: pos_ctl+nec 1-X per treatment/timepoint group rep 6

description: nec


title: pos_ctl+nec 1-X per treatment/timepoint group rep 1

description: nec


title: Plasma,AD,24

description:
Memories_HB04462_Plasma_S103_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: Control, C011

tag: igra test_result


title: aav+nec 1-X per treatment/timepoint group rep 9

description: nec

tag: treatment

value: aav


title: wild type young adult experiment 1rep2


title: Control, C014

tag: animal id


title: aav+nec 1-X per treatment/timepoint group rep 8

description: nec


title: Control, C010

tag: experimental group


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep1

value: mixed embryos

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: Plasma,AD,23

description:
Memories_HB04461_Plasma_S124_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: Control, C009

value: Peripheral Blood

tag: ifga nil


title: aav+nec 1-X per treatment/timepoint group rep 7

description: nec


title: Plasma,AD,22

description:
Memories_HB04458_Plasma_S80_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C012

value: Control


title: wild type mixed embryos experiment 1rep1

description: TruSeq Stranded Total RNA Library Prep kit (Total RNA sequencing) - prepped by Psomagen

tag: cell line

value: hermaphrodite

value: whole animal


title: Control, C007

value: Male

value: Negative


title: Plasma,AD,21

description:
Memories_HB04450_Plasma_S55_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma


title: Control, C008


title: aav+nec 1-X per treatment/timepoint group rep 6

description: nec


title: aav+nec 1-X per treatment/timepoint group rep 5

description: nec


title: Plasma,MCI,41

description:
Memories_HB04444_Plasma_S51_R1_001.fastq
miR.Counts_plasma.csv

value: MCI


title: wild type young adult experiment 1rep1

tag: cell type

value: young adult

value: wild type


title: Plasma,MCI,40

description:
Memories_HB04441_Plasma_S148_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C006

value: Heparin tubes

tag: ifga avian


title: Plasma,AD,20

description:
Memories_HB04436_Plasma_S10_R1_001.fastq
miR.Counts_plasma.csv


title: Control, C017

tag: ifga bovine_-_ifga_avian


title: Control, C005

tag: tissue


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep1


title: aav+nec 1-X per treatment/timepoint group rep 4

description: nec

value: PBMCs

value: WT


title: wild type L4 experiment 1rep1


title: aav+nec 1-X per treatment/timepoint group rep 3

description: nec

value: aav


title: aav+nec 1-X per treatment/timepoint group rep 2

description: nec


title: Control, C003

tag: Sex


title: Control, C004


title: Control, replicate 1, scRNAseq

city: Boston

first: Hassan

last: Bukhari

state: MA

address: 77, Avenue Louise Pasteur

department: Pathology

institute: Brigham and Womens hospital

description: 10 X genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using Cellranger, version 6.0, 10x Genomics.(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
For Control 1, Control 3 and tauP251L KI 3  libraries were sequenced once with enough sequencing depth. For control 2, tau P251L KI 1 and tau P251L KI 2, the libraries were sequenced twice to get enough sequencing depth.
Assembly: Drosophila Melanogaster
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Brain

extract_protocol:
20 male and 20 female Drosophila brain of the appropriate geneotype were dissected were dissected on ice cold Schneider’s medium. After a brief wash with PBS, the brains were incubated with 0.05% trypsin-EDTA (Fisher scientific) for 30 minutes, with continuous pipetting every 5 minutes. The dissociated tissue were filtered through a 10um cell strainer to get a single cell suspension.
10x libraries were constructed according to the manufacter’s instructions (Chromium Next GEM Single Cell 3' Kit v3.1).

value: Brain

value: Brain cells


title: Spleen TN cells from Rapamycin-treated mice, rep3 [Spl+Rapamycin-TN-3]

city: Ichikawa

first: Takashi

last: Sekiya

state: Chiba

address: 1-7-1 Kohnodai

country: Japan

institute: National Center for Global Health and Medicine

data_processing:
Next generation sequencing were performed using Illumina Hiseq X with a standard 150-bp paired-end read protocol.
Fastq output files were aligned to mm10 reference genome with STAR.
Quantification of gene expression were calculated with RSEM.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include TPM and FPKM values for each Sample

source_name: Spleen

extract_protocol:
Total RNA was extracted with RNAiso PLUS (TAKARA). Samples were further cleaned using an NucleoSpin RNA Clean-up XS (MACHEREY-NAGEL).
RNA-seq libraries were prepared with NEBNext Ultra II Directional RNA Library Prep kit for Illumina (NEB), using Multiplex Oligos for Illumina (Dual Index Primers Set 1, NEB), following the manufacturer’s protocol.

value: Spleen

value: naive CD4+ T cells

value: in vivo treatment with Rapamycin

tag: strain


title: Plasma,MCI,37

description:
Memories_HB04421_Plasma_S28_R1_001.fastq
miR.Counts_plasma.csv

value: Female

tag: disease state


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep1

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)

value: hermaphrodite

tag: genotype

value: whole animal


title: Plasma,MCI,38

description:
Memories_HB04432_Plasma_S171_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

tag: age

value: MCI


title: Plasma,MCI,36

description:
Memories_HB04420_Plasma_S121_R1_001.fastq
miR.Counts_plasma.csv

tag: subject


title: Control, C002

value: Peripheral Blood

value: Control

tag: age (months)

value: Male

value: Negative

tag: ifga bovine


title: dmso+nec 1-X per treatment/timepoint group rep 9

description: nec

source_name: PBMCs

value: PBMCs

value: WT

tag: treatment

value: dmso


title: Spleen TN cells from Rapamycin-treated mice, rep2 [Spl+Rapamycin-TN-2]

value: Spleen


title: Control, C001

tag: animal id

value: Heparin tubes

tag: igra test_result


title: Spleen TN cells from Rapamycin-treated mice, rep1 [Spl+Rapamycin-TN-1]

value: naive CD4+ T cells

value: in vivo treatment with Rapamycin


title: Plasma,AD,19

description:
Memories_HB04435_Plasma_S53_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: Spleen TN cells from untreated mice, rep3 [Spl-non-TN-3]

value: no treatment


title: Plasma,Control,5

description:
Memories_HB04419_Plasma_S196_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: dmso+nec 1-X per treatment/timepoint group rep 8

description: nec


title: Y47(mir-243bs_del); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep2

data_processing:
Small RNA libraries were trimmed using Cutadapt 3.4 (122), then mapped using bowtie2 2.4.4 with settings “--no-unal --end-to-end –sensitive” (123). BAM files were sorted and indexed using samtools 1.13, then assigned to miRNAs using htseq 0.13.5 (124, 125). For genome mapping and miRNA assignment, custom reference files were used which included the spiked in RNA oligos. Statistical analysis was performed using DESeq2 and GraphPad Prism (126). For spike-in normalization (Figure S3), size factors for DESeq2 analysis were calculated by dividing spike-in reads in each sample by the median number of spike-in reads per sample. For all other analyses, default DESeq2 normalization was performed using all endogenous miRNA-mapping reads (spike-in reads were excluded from analysis).
Assembly: genome_c_elegans.PRJNA13758.WS280.genomic_with_spike_mut_mir35.fa
Assembly: cel_mirGeneDB_spikeins_010622.gff
Supplementary files format and content: xlsx file containing counts of reads mapped to miRNA and spike in RNA annotations

source_name: whole animal

extract_protocol:
Samples were snap frozen, then resuspended in Trizol and vortexed for 15 minutes at room temperature. Thereafter, total RNA was purified according to the Trizol manufacturer’s instructions (ThermoFisher).
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

tag: dev stage

value: young adult

tag: alias in_text_and_figures

value: hermaphrodite

value: whole animal


title: dmso+nec 1-X per treatment/timepoint group rep 7

description: nec


title: Y47(mir-243bs_del) young adult experiment 2rep2

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.


title: Spleen TN cells from untreated mice, rep2 [Spl-non-TN-2]

tag: cell type


title: Plasma,MCI,34

description:
Memories_HB04410_Plasma_S102_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: MCI


title: dmso+nec 1-X per treatment/timepoint group rep 6

description: nec


title: Spleen TN cells from untreated mice, rep1 [Spl-non-TN-1]


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep2

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: dmso+nec 1-X per treatment/timepoint group rep 5

description: nec

value: PBMCs


title: Spleen TN cells from MCC950-treated mice, rep3

value: WT

value: in vivo treatment with MCC950 for 10 consecutive days


title: aav+nec 1-X per treatment/timepoint group rep 1

description: nec

value: aav


title: Plasma,MCI,33

description:
Memories_HB04409_Plasma_S77_R1_001.fastq
miR.Counts_plasma.csv


title: wild type young adult experiment 2rep2

value: wild type


title: Plasma,Control,4

description:
Memories_HB04408_Plasma_S30_R1_001.fastq
miR.Counts_plasma.csv

value: Male

value: Control


title: Spleen TN cells from MCC950-treated mice, rep2

value: Spleen

value: naive CD4+ T cells


title: dmso+nec 1-X per treatment/timepoint group rep 4

description: nec

value: dmso


title: Spleen TN cells from MCC950-treated mice, rep1


title: dmso+nec 1-X per treatment/timepoint group rep 3

description: nec


title: Y47(mir-243bs_del); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep1

value: young adult


title: Plasma,AD,18

description:
Memories_HB04402_Plasma_S100_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: Y47(mir-243bs_del) young adult experiment 2rep1

value: hermaphrodite

value: whole animal


title: Plasma,MCI,35

description:
Memories_HB04411_Plasma_S75_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: Female

value: MCI


title: dmso+nec 1-X per treatment/timepoint group rep 2

description: nec

value: PBMCs


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep1

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: Plasma,MCI,32

description:
Memories_HB04401_Plasma_S169_R1_001.fastq
miR.Counts_plasma.csv


title: Spleen TN cells from anti-IL-1b-treated mice, rep3

value: WT

value: in vivo treatment with anti-IL-1b for 10 consecutive days


title: wild type young adult experiment 2rep1

value: wild type


title: dmso+nec 1-X per treatment/timepoint group rep 1

description: nec


title: Spleen TN cells from anti-IL-1b-treated mice, rep2


title: Plasma,AD,17

description:
Memories_HB04379_Plasma_S168_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+pid 1-X per treatment/timepoint group rep 9

description: pid


title: Plasma,Control,3

description:
Memories_HB04376_Plasma_S7_R1_001.fastq
miR.Counts_plasma.csv

value: Male

value: Control


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep4

value: mixed embryos


title: Spleen TN cells from anti-IL-1b-treated mice, rep1

value: Spleen

value: naive CD4+ T cells


title: Plasma,AD,16

description:
Memories_HB04302_Plasma_S45_R1_001.fastq
miR.Counts_plasma.csv

value: AD


title: pos_ctl+pid 1-X per treatment/timepoint group rep 8

description: pid


title: Spleen TN cells from untreated mice, rep3

value: no treatment


title: Plasma,Control,2

description:
Memories_HB04294_Plasma_S70_R1_001.fastq
miR.Counts_plasma.csv


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep3

value: hermaphrodite

value: whole animal


title: pos_ctl+pid 1-X per treatment/timepoint group rep 6

description: pid


title: pos_ctl+pid 1-X per treatment/timepoint group rep 7

description: pid


title: Plasma,AD,15

description:
Memories_HB03436_Plasma_S5_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma


title: Spleen TN cells from untreated mice, rep1


title: Spleen TN cells from untreated mice, rep2


title: wild type mixed embryos experiment 1rep3


title: pos_ctl+pid 1-X per treatment/timepoint group rep 4

description: pid


title: Plasma,MCI,31

description:
Memories_AZM06838_Plasma_S63_R1_001.fastq
miR.Counts_plasma.csv

value: MCI


title: wild type mixed embryos experiment 1rep2


title: Plasma,MCI,30

description:
Memories_AZM06793_Plasma_S58_R1_001.fastq
miR.Counts_plasma.csv


title: pos_ctl+pid 1-X per treatment/timepoint group rep 3

description: pid

value: PBMCs


title: pos_ctl+pid 1-X per treatment/timepoint group rep 5

description: pid


title: Plasma,AD,14

description:
Memories_AZM06786_Plasma_S119_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep2

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: TN cells cultured with IL-1b, rep1

source_name: lymph nodes

value: lymph nodes

value: naive CD4+ T cells, cultured in vitro for 20 h

value: WT

value: recombinant IL-1Beta (10 ng/mL) for 20 h


title: TN cells cultured with IL-1b, rep2


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep3


title: pos_ctl+pid 1-X per treatment/timepoint group rep 2

description: pid


title: wild type L4 experiment 1rep3

value: wild type


title: pos_ctl+pid 1-X per treatment/timepoint group rep 1

description: pid


title: TN cells cultured without IL-1b, rep2


title: TN cells cultured without IL-1b, rep3


title: Plasma,Control,1

description:
Memories_AZM06780_Plasma_S82_R1_001.fastq
miR.Counts_plasma.csv

value: Control


title: wild type mixed embryos experiment 1rep4

value: mixed embryos


title: Plasma,MCI,28

description:
Memories_AZM06771_Plasma_S145_R1_001.fastq
miR.Counts_plasma.csv


title: Plasma,MCI,29

description:
Memories_AZM06773_Plasma_S25_R1_001.fastq
miR.Counts_plasma.csv

value: Male


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep2

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.


title: TN cells cultured with IL-1b, rep3


title: aav+pid 1-X per treatment/timepoint group rep 9

description: pid

value: aav


title: wild type L4 experiment 1rep2

value: hermaphrodite


title: Plasma,MCI,27

description:
Memories_AZM06765_Plasma_S192_R1_001.fastq
miR.Counts_plasma.csv


title: TN cells cultured without IL-1b, rep1

value: no treatment


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep4

value: young adult

value: whole animal


title: aav+pid 1-X per treatment/timepoint group rep 8

description: pid

value: PBMCs


title: freshly prepared TN cells, rep3

value: naive CD4+ T cells


title: Plasma,MCI,26

description:
Memories_AZM06761_Plasma_S71_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: Female

value: MCI


title: aav+pid 1-X per treatment/timepoint group rep 7

description: pid


title: wild type young adult experiment 1rep4


title: freshly prepared TN cells, rep2

value: lymph nodes


title: aav+pid 1-X per treatment/timepoint group rep 6

description: pid

value: WT


title: Plasma,MCI,25

description:
Memories_AZM06753_Plasma_S24_R1_001.fastq
miR.Counts_plasma.csv


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep3

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: freshly prepared TN cells, rep1


title: aav+pid 1-X per treatment/timepoint group rep 5

description: pid


title: freshly prepared mLN TN cells, rep3

source_name: mesenteric lymph node

value: mesenteric lymph node


title: wild type young adult experiment 1rep3

value: wild type


title: Plasma,AD,13

description:
Memories_AZM06751_Plasma_S190_R1_001.fastq
miR.Counts_plasma.csv

value: Male

value: AD


title: aav+pid 1-X per treatment/timepoint group rep 4

description: pid

value: aav


title: Plasma,MCI,24

description:
Memories_AZM06747_Plasma_S188_R1_001.fastq
miR.Counts_plasma.csv


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep2

value: hermaphrodite


title: freshly prepared mLN TN cells, rep2

value: no treatment


title: Plasma,AD,12

description:
Memories_AZM06737_Plasma_S19_R1_001.fastq
miR.Counts_plasma.csv


title: wild type young adult experiment 1rep2

value: young adult

value: whole animal


title: Plasma,MCI,23

description:
Memories_AZM06736_Plasma_S21_R1_001.fastq
miR.Counts_plasma.csv


title: freshly prepared mLN TN cells, rep1

value: naive CD4+ T cells


title: freshly prepared spleen TN cells, rep3

value: Spleen


title: alg-1(AEDH); alg-2(AEDH)  mixed embryos experiment 1rep1

value: mixed embryos


title: Plasma,MCI,21

description:
Memories_AZM06731_Plasma_S142_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: MCI


title: aav+pid 1-X per treatment/timepoint group rep 2

description: pid

value: PBMCs

value: WT


title: Plasma,MCI,20

description:
Memories_AZM06730_Plasma_S113_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: wild type mixed embryos experiment 1rep1


title: dmso+pid 1-X per treatment/timepoint group rep 9

description: pid

value: dmso


title: freshly prepared spleen TN cells, rep2


title: aav+pid 1-X per treatment/timepoint group rep 1

description: pid


title: alg-1(AEDH); alg-2(AEDH)  L4 experiment 1rep1

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)


title: Plasma,AD,11

description:
Memories_AZM06723_Plasma_S115_R1_001.fastq
miR.Counts_plasma.csv

value: Male

value: AD


title: freshly prepared spleen TN cells, rep1


title: Plasma,AD,10

description:
Memories_AZM06721_Plasma_S186_R1_001.fastq
miR.Counts_plasma.csv


title: dmso+pid 1-X per treatment/timepoint group rep 8

description: pid


title: dmso+pid 1-X per treatment/timepoint group rep 7

description: pid


title: mLN CD45+ cells, freshly prepared, rep2

source_name: mLN

value: mLN

value: total hematopoietic cells

value: freshly prepared


title: wild type young adult experiment 1rep1

value: young adult

value: wild type

value: hermaphrodite

value: whole animal


title: mLN CD45+ cells, freshly prepared, rep3


title: dmso+pid 1-X per treatment/timepoint group rep 6

description: pid


title: aav+pid 1-X per treatment/timepoint group rep 3

description: pid

value: aav


title: Plasma,MCI,19

description:
Memories_AZM06720_Plasma_S48_R1_001.fastq
miR.Counts_plasma.csv

value: Plasma

value: MCI


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 1rep1


title: Plasma,MCI,18

description:
Memories_AZM06716_Plasma_S166_R1_001.fastq
miR.Counts_plasma.csv


title: mLN CD45+ cells, freshly prepared, rep1

value: WT


title: dmso+pid 1-X per treatment/timepoint group rep 5

description: pid

value: PBMCs


title: Plasma,MCI,17

description:
Memories_AZM06714_Plasma_S93_R1_001.fastq
miR.Counts_plasma.csv

value: Female


title: Plasma,MCI,16

description:
Memories_AZM06710_Plasma_S193_R1_001.fastq
miR.Counts_plasma.csv


title: Spleen CD45+ cells, freshly prepared, rep3

value: Spleen


title: dmso+pid 1-X per treatment/timepoint group rep 4

description: pid

value: dmso


title: ebax-1(null); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep4

value: ebax-1(null); alg-1(AEDH); alg-2(AEDH)


title: ebax-1(null) young adult experiment 2rep4

value: ebax-1(tm2321) IV


title: dmso+pid 1-X per treatment/timepoint group rep 2

description: pid


title: Spleen CD45+ cells, freshly prepared, rep2


title: Y47(mir-243bs_del); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep4


title: Y47(mir-243bs_del) young adult experiment 2rep4


title: Spleen CD45+ cells, freshly prepared, rep1


title: dmso+pid 1-X per treatment/timepoint group rep 1

description: pid


title: freshly prepared axillary TN cells with high TTS, biol rep1

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Generated sequencing reads in FASTQ format were mapped to mm10 reference genome using bowtie2.
Reads mapped to the "black list" regions were removed with intersectBed command, inputting the bed file which denotes the black list region (mm10-blacklist.v2.bed.gz).
Peak calling was performed with MACS14, with default parameters.
Assembly: bedGraph files were generated using MACS14. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak  files were generated using MACS14 with default settings.
Supplementary files format and content: mm10
Supplementary files format and content: bedGraph, narrowPeak

source_name: axillary lymph node

extract_protocol:
5x10^5 cells were suspended in 200 μl Hypotonic buffer (20 mM Tris pH 7.5, 10 mM NaCl, 3 mM ), and incubated for 15 min on ice. Then, 10 μl 10% NP-40 was added to the sample and vortexed for 10 sec at maximum speed. Nuclei were pelleted by centrifugation at 6,000 rpm for 5 min.
Nuclei pelets were suspended in 40 μl 1x Tagmentation buffer. Samples were added with 2 μl Tagment DNA Enzyme 1, and incubated for 30 min at 37 oC. Then, samples were cleaned up with FastGene Gel/PCR clean up kit (Nippon Genetics), and eluted with 20 μl elution buffer. 5 μl of the eluted samples were PCR amplified with index 1 (i7) and index 2 (i5) adapter primers, using PCR Primer Cocktail which was attached to Nextera DNA Library Preparation Kit.

value: axillary lymph node

value: naive CD4+ T cells

value: no treatment


title: Plasma,MCI,13

description:
Memories_AZM06700_Plasma_S67_R1_001.fastq
miR.Counts_plasma.csv

value: Male


title: wild type young adult experiment 2rep4

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

value: young adult

value: wild type


title: alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep4

value: alg-2(cdb155) II; alg-1(cdb153) X

value: alg-1(AEDH); alg-2(AEDH)

value: hermaphrodite

value: whole animal


title: ebax-1(null); alg-1(AEDH); alg-2(AEDH)  young adult experiment 2rep3


title: St35_wt1

first: Ziyan

last: Lin

state: NY

department: Applied Bioinformatics Laboratories

institute: NYU Grossman School of Medicine

data_processing:
NovaSeq 6000 System (RTA Version 3.4.4)
bcl2Fastq v2.20
Trimming, alignment and generating count matrix were all done by using the sns/rna-star pipeline (https://igordot.github.io/sns/routes/rna-star.html)
Assembly: Xentr10.0 (http://ftp.xenbase.org/pub/Genomics/JGI/Xentr10.0/XENTR_10.0_genome.fasta.gz)
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Embryos were grown in NAM until desired stage of collection

extract_protocol:
Pools of 5 embryos were used for RNA extraction via the Qiagen Rneasy Micro Kit
Automated stranded RNA-seq library prep, polyA selection

value: whole embryo

value: WT


title: St35_wt2