title: Liver_Pnpla8_KO_6W

description: Gene expression in KO livers at 6 weeks

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: KO liver at 6 weeks

value: 6 weeks


title: 110_tumor

status: Public on Nov 30 2022

type: RNA

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

hyb_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

scan_protocol: Scanning and image analysis were performed using the Agilent DNA Microarray Scanner (P/N G2565BA) equipped with extended dynamic range (XDR) software, according to the Agilent miRNA Microarray System with miRNA Complete Labeling and Hyb Kit Protocol manual. Feature Extraction Software (Version 10.5) was used for data extraction from raw microarray image files using the miRNA_105_Dec08 FE protocol

data_processing: signal intensities were extracted by Agilent Feature Extraction 10.7.3.1 software. The arrays were normalized by dividing by the mean intensity only using the 25th and 75th percentile range of the data. Intensity level of each miRNA was scaled by the median of the distribution of the miRNA for samples processed in the first chip version and by the median of the distribution of the miRNA for samples processed in the second chip version, and all values multiplied for the mean value between the two medians. Data were log2-trasformed. For the analyses we consider just miRNAs common at the two platforms and miRs that were absent across all samples were removed. miRNAs not expressed were excluded

molecule: total RNA

organism: Homo sapiens

source_name: Larynx

extract_protocol: Total RNA extraction was performed using the RNeasy kit (Qiagen) following the manufacturer's instructions.

tag: gender

value: Male

tag: g

tag: t

tag: n

value: N+

tag: hpv

value: HPV-

tag: tissue

value: Larynx


title: Liver_Pnpla7_WT_4W

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

description: Gene expression in WT livers at 4 weeks

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray  for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.0.1.1) with set to default for all parameters.

organism: Mus musculus

source_name: WT liver at 4 weeks

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

extract_protocol: Total RNA extracted from livers was purified using a RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: strain

value: Liver

tag: genotype

value: WT

tag: age

value: 4 weeks


title: WAT_Pnpla7_KO_4W

description: Gene expression in KO WATs at 4 weeks

source_name: KO WAT at 4 weeks

value: WAT


title: 109_tumor

source_name: Oral Cavity

label_protocol: For miRNA microarray, 100 ng of RNA was labeled (Cy3) and hybridized using the miRNA complete labeling and hyb kit (Agilent Technologies, CA, USA) according to manufacturer’s protocol for use with Agilent microRNA microarrays.

value: Female

value: Oral Cavity


title: Liver_Pnpla7_WT_6W

description: Gene expression in WT livers at 6 weeks

source_name: WT liver at 6 weeks


title: Liver_Pnpla7_KO_6W

description: Gene expression in KO livers at 6 weeks


title: Liver_Pnpla8_WT_6W

description: Gene expression in WT livers at 6 weeks


title: 108_tumor


title: Liver_Pnpla7_KO_4W

description: Gene expression in KO livers at 4 weeks

source_name: KO liver at 4 weeks


title: Liver_Pnpla7_KO_3W

description: Gene expression in KO livers at 3 weeks

source_name: KO liver at 3 weeks

value: 3 weeks


title: Liver_Pnpla7_WT_3W

description: Gene expression in WT livers at 3 weeks

source_name: WT liver at 3 weeks


title: 106_tumor


title: 105_tumor

source_name: Pharynx

value: Pharynx


title: 104_tumor


title: 103_tumor


title: 101_tumor


title: 100_tumor


title: 99_tumor


title: 97_tumor


title: 89_tumor


title: 87_tumor


title: 91_tumor


title: 83_tumor


title: 79_tumor


title: 107_tumor


title: 90_tumor


title: 95_tumor


title: 116_tumor


title: 77_tumor

value: HPV+


title: 66_tumor


title: 72_tumor


title: 102_tumor


title: 7_peritumor


title: 64_tumor


title: 63_tumor


title: 50_tumor


title: 61_tumor


title: 93_tumor


title: 43_tumor


title: 94_tumor


title: 88_tumor


title: 2_tumor


title: 38_tumor


title: 3_tumor


title: 60_tumor


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R1

type: SRA

city: Beijing

first: Changchang

last: Xin

state: Beijing

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

country: China

institute: Peking University

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA2 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.

library_source: genomic

data_processing:
Followed the PEM-Q pipeline described in Liu et al., 2021
Assembly: mm10
Supplementary files format and content: tab file
Library strategy: PEM-Seq

molecule: genomic DNA

source_name: eye

extract_protocol: Followed the PEM-seq protocol that described in Yin et al., 2019.

value: eye

value: C57BL/6J mice

value: 6-8 weeks old

tag: treatment

value: AAV injection


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R2


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R3


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R10

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R4


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R5


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg2_2week_R6


title: 9_normal

value: Male


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R9


title: PEM-seq_mouse_eye_PBS_control_R6

description: PBS were injected into mouse retina. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis after the PBS were administered into the mouse eyes via subretinal injection.

value: PBS injection


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R7


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R6


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R8


title: PEM-seq_mouse_eye_PBS_control_R2


title: PEM-seq_mouse_eye_PBS_control_R4


title: PEM-seq_mouse_eye_PBS_control_R1


title: PEM-seq_mouse_eye_control_R8

description: No treatment

value: No treatment


title: PEM-seq_mouse_eye_control_R9

description: No treatment


title: PEM-seq_mouse_eye_control_R10

description: No treatment


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R11


title: PEM-seq_mouse_eye_control_R7

description: No treatment


title: PEM-seq_mouse_eye_control_R6

description: No treatment


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R4

description: 1 μL of dual AAVs with split Cas9TX and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 12-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R6


title: PEM-seq_mouse_eye_control_R2

description: No treatment


title: PEM-seq_mouse_eye_control_R3

description: No treatment


title: PEM-seq_mouse_eye_control_R5

description: No treatment


title: PEM-seq_mouse_eye_control_R4

description: No treatment


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_4week_R4

description: 1 μL of dual AAVs with split Cas9TX and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 4-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_PBS_control_R3


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R2


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R3


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R5


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_4week_R2


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_4week_R1


title: PEM-seq_mouse_eye_control_R1

description: No treatment


title: 4_normal

value: HPV-


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_12week_R1


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R6

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 12-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R4


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R3


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R5


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R2


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_12week_R1


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_4week_R4

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 4-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R6

description: PBS were injected into mouse retina. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 4-weeks after the PBS were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R5

description: PBS were injected into mouse retina. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 12-weeks after the PBS were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_4week_R3


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_4week_R1


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R5


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R6


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R2


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R3


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R4


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R1


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R2


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R1


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R6

description: 1 μL of single AAV with Cas9TX-Cter and Vegfa-sgRNA1 were injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_4week_R3


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R5


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R4


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R3


title: 6_tumor

value: Larynx


title: 96_tumor

value: N+


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R2

value: WT


title: PEM-seq_mouse_eye_Cas9TX-Cter_VEGFA-sg1_2week_R1


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_4week_R2


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R8

description: 1 μL of single AAV with Cas9-Cter and Vegfa-sgRNA1 were injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R7


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_2week_R5

description: 1 μL of dual AAVs with split Cas9TX and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R1


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R3


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R2


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_2week_R4


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R5


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R6


title: PEM-seq_mouse_eye_Cas9-Cter_VEGFA-sg1_2week_R4


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_2week_R2


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_2week_R1


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R5


title: Cn_D_14

city: Klong-luang

first: Pornpimon

last: Angkasekwinai

state: Patumthani

country: Thailand

institute: Thammasat University

library_source: transcriptomic

data_processing:
All high-quality paired-end reads were aligned to the Mus musculus reference genome GRCm38/mm10 using TopHat2 v2.0.12/Bowtie v2.2.3.
NCBI BLAST v2.2.28 was used to annotate the reads based on known mouse genes with the expected value (e-value) of 1.0 x 10-10.
To estimate the abundance of the gene expression, the read numbers mapped of each gene from each transcript were counted and then normalized by fragment per kilobases per million mapped reads (FPKM) approach using HTSeq v0.6.1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Alveolar macrophage

extract_protocol:
The alveolar macrophages isolated from mice (6-10 mice per group) were pooled and extracted for total RNA by using RNeasy® Plus Mini kit (Qiagen). 600 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA library prep kit for Illumina® following the manufacturer's protocols.

treatment_protocol: BALB/c mice were anesthetized and treated with PBS or C. neoformans H99 cell suspension at 5 × 104 cells/mouse by the intranasal route. At indicated time points, mice were euthanized by inhalation of CO2, and lungs were aseptically collected to isolate alveolar macrophage by FACS.

value: BALB/c

tag: cell type

value: Alveolar macrophage

tag: agent

value: Cryptococcus neoformans

tag: time

value: Day 14


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R3


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R2


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R1


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R6

description: 1 μL of single AAV with Cas9-Nter and Vegfa-sgRNA1 were injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R5


title: Unlicensed 3D-N Donor 4

city: Toronto

first: Kevin

middle: P

last: Robb

state: Ontario

address: Krembil Research Institute 60 Leonard Avenue, Office 5KD416-K1 / Lab 5KD424-C1

country: Canada

institute: University Health Network

hyb_protocol: Done according to manufacturer's instructions

scan_protocol: nCounter Digital Analyzer, nCounter MAX Analysis System

data_processing:
RCC (Reporter Code Count) files were imported into the nSolverTM Analysis Software (version 4.0) for QC and analysis. RCC value normalization was performed using the geometric mean of the internal Positive Control probe counts and with selected reference genes according to the manufacturer's instructions to obtain mRNA counts. The following were measured as potential reference genes: ABCF1, GAPDH, GUSB, HPRT1, LDHA, RPL19, RPLP0, TUBB, POLR1B, and TBP. Reference gene stability was evaluated using geNorm analysis in the nSolver software; POLR1B and TBP were subsequently discarded as reference genes and not used for normalization. Normalized mRNA counts below 20 were assigned values of 1 if >33% of samples were within range.
mRNA counts obtained from RCC values normalized to synthetic positive control probes and reference genes

label: Not applicable

source_name: Adipose-derived mesenchymal stromal cells (MSC(AT)

growth_protocol: At approximately 70-80% confluence, MSC(AT) were transiently (16-20 h) cultured under varied CPP conditions, including 3D normoxic (3D-N), 2D hypoxic (2D-H), or 2D normoxic (2D-N) conditions. These culture steps were performed on separate flasks cultured in parallel using MesenCult™-ACF Plus medium supplemented with 1% (v/v) human serum album (HSA; Canadian Blood Services, Ottawa, Canada). 3D-N culture was performed by harvesting MSC(AT) from adherent flasks and plating cells on ultra-low attachment surfaces (Corning, Corning, USA) at 26,700 cells/cm2 in medium supplemented with IL-6  (Peprotech, Cranbury, USA), based on previously reported methods. Flasks from the same batch of cells were cultured in parallel under 2D-N (maintained in standard tissue culture incubator) or 2D-H conditions (38 mmHg O2, i.e., 5% O2 under standard atmospheric pressure) using a HypoxyLab workstation (Oxford Optronix, Milton, UK) for the same duration as 3D culture.

extract_protocol: RNA was extracted using a RNeasy Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentration and purity was measured using a DS-11 Spectrophotometer (DeNovix, Wilmington, USA). Samples containing 200 ng of RNA were run using the NanoString platform.

treatment_protocol: After harvesting mesenchymal stromal cells (MSCs) from 2D-N, 2D-H, and 3D-N conditions, cells were added to 24-well plates at 60,000 cells/well in MesenCult™-ACF Plus medium supplemented with 1% HSA (v/v) with or without addition of pro-inflammatory licensing cytokines. The licensing cytokines (all purchased from Peprotech) consisted of IFNγ (30 ng/mL), TNFα (10 ng/mL), and IL-1β (5 ng/mL). Cells harvested from 2D-N or 2D-H conditions were maintained under normoxic or hypoxic (38 mmHg O2) conditions for 24 h, respectively, while cell aggregates from the 3D-N condition were plated on ultra-low attachment 24-well plates (Corning) without dissociation. After the culture period, cells were washed in PBS prior to RNA extraction.

tag: individual

value: donor 4

tag: donor sex

value: F

tag: donor age

tag: donor bmi

tag: adipose depot

value: Knee

value: MSC(AT)

tag: growth protocol

value: Unlicensed


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R3

value: eye

value: C57BL/6J mice

value: 6-8 weeks old

value: AAV injection


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_2week_R3


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R4


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R1


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R7

description: PBS were injected into mouse retina. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 2-weeks after the PBS were administered into the mouse eyes via subretinal injection.

value: PBS injection


title: PEM-seq_mouse_eye_Cas9-Nter_VEGFA-sg1_2week_R2


title: Unlicensed 3D-N Donor 2

value: donor 2


title: Unlicensed 3D-N Donor 3

value: donor 3

value: M


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R6

value: WT


title: PEM-seq_mouse_eye_Cas9_VEGFA-sg1_2week_R4


title: Unlicensed 3D-N Donor 1

value: donor 1


title: Unlicensed 2D-H Donor 1


title: Unlicensed 2D-H Donor 5

value: donor 5

value: Abdomen


title: Unlicensed 2D-H Donor 2


title: Unlicensed 3D-N Donor 5


title: Unlicensed 2D-H Donor 4

value: donor 4


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R4


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R3


title: 112_tumor

tag: gender

value: Male

tag: g

tag: t

value: N+

value: HPV-

value: Oral Cavity


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R2

tag: tissue

value: eye


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg2_R5

description: 1 μL of dual AAVs with split Cas9TX and Vegfa-sgRNA2 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.

tag: strain

value: C57BL/6J mice


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R5

value: 6-8 weeks old

tag: genotype


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R1

tag: age


title: Unlicensed 2D-H Donor 3

value: Knee

value: MSC(AT)

tag: treatment

value: Unlicensed


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg2_R3

value: AAV injection


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg2_R4


title: Unlicensed 2D-N Donor 1

value: M

tag: cell type


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg2_R5

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA2 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.

value: WT


title: Licensed 3D-N Donor 4

value: F

value: Licensed


title: Unlicensed 2D-N Donor 2

value: donor 2


title: Unlicensed 2D-N Donor 3

value: donor 3


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg2_R4


title: Unlicensed 2D-N Donor 4

value: donor 4


title: Licensed 3D-N Donor 3


title: Unlicensed 2D-N Donor 5

value: donor 5

value: Abdomen


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg2_R3


title: Licensed 3D-N Donor 1

value: donor 1


title: Licensed 3D-N Donor 2


title: 1_tumor

value: Male

tag: n

value: N+

tag: hpv

value: HPV-

value: Oral Cavity


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_R4

description: 1 μL of dual AAVs with split Cas9TX and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.

value: eye

value: C57BL/6J mice

value: 6-8 weeks old


title: Licensed 2D-H Donor 5

tag: individual

value: M

value: MSC(AT)


title: Licensed 2D-H Donor 4

tag: donor sex

value: F

value: Knee


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_R3

value: WT

value: AAV injection


title: Licensed 3D-N Donor 5

tag: donor age

value: Licensed


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg1_R5

description: 1 μL of dual AAVs with split SpCas9 and Vegfa-sgRNA1 were co-injected into mouse retina at a dose of 3E9 vector genomes (vg)/eye. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis after the resulting dual AAVs were administered into the mouse eyes via subretinal injection.


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg1_R3


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg1_R4


title: Licensed 2D-H Donor 3

value: donor 3

tag: donor bmi


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg2_R2


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg2_R2


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg2_R1


title: Licensed 2D-N Donor 2

value: donor 2

tag: adipose depot


title: (Bulk RNA-Seq) 2dpf rpgrip1l wild-type Replicate #2

city: Birmingham

first: John

middle: M

last: Parant

state: AL

address: 1670 University Blvd

country: USA

institute: University of Alabama at Birmingham

data_processing:
RNA-seq raw reads were trimmed with TrimGalore 0.4.4
Trimmed reads were aligned to Danio rerio GRCz11 with Star 2.7.3a with default setting
Expression counts were calculated with HTSeq-count 0.12.3 with default setting
Assembly: GRCz11
Supplementary files format and content: tab-delimited text files include raw counts for each sample

organism: Danio rerio

source_name: whole embryos

extract_protocol:
30-35 2-dpf or 5-dpf zebrafish embryos were pooled to extract RNA with Qiagen Rneasy Plus Mini Kit
The library was prepared with Illumina RNA with PolyA selection package and sequenced with Illumina HiSeq 2x150bp, single index

value: whole embryos

value: Control

tag: time point

value: Day 2


title: (Bulk RNA-Seq) 2dpf rpgrip1l wild-type Replicate #1


title: Licensed 2D-H Donor 1

value: donor 1

tag: growth protocol


title: Licensed 2D-N Donor 4

value: donor 4


title: Licensed 2D-N Donor 1


title: (Bulk RNA-Seq) 2dpf rpgrip1l KO with normal phenotype Replicate #1

value: rpgrip1l KO


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg2_R1

value: eye

value: C57BL/6J mice


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_R2

value: 6-8 weeks old


title: (Bulk RNA-Seq) 2dpf rpgrip1l KO with CDT phenotype Replicate #2


title: Licensed 2D-H Donor 2

value: MSC(AT)


title: (Bulk RNA-Seq) 2dpf rpgrip1l KO with CDT phenotype Replicate #1


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_R1


title: (Bulk RNA-Seq) 5dpf wild-type Replicate #2

value: Day 5


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg1_R1


title: SV 385 3m Sal eWAT Cy3

city: Alcorcon

first: Gema

last: Medina-Gomez

state: Madrid

address: Avda de Atena s/n

department: Ciencias Básicas de la Salud

country: Spain

institute: Universidad Rey Juan Carlos

description: microRNA expression in 3m eWAT

hyb_protocol: RNA was hybridized on the SurePrint Mouse miRNA Microarrays 8x60K microarray (AMADID number 070155) for 20 h at 55° C, containing a total of 2164 control and 62976 mouse-19 specific probes.

scan_protocol: Agilent G2565C Microarray Scanner was used for scanning the samples

data_processing: Data were extracted with Feature Extraction Software 11.5.11 following the protocol developed by Agilent in Agilent miR_1105_Oct12 in conjunction with the miRNA_QCMT_Oct12 metrics and using 070155_D_F_20141006 as Grid.

source_name: 3m eWAT

label_protocol: RNA was labeled with Cyanine 3-pCp

growth_protocol: subcutaneous and visceral white adipose tissue samples from 3 groups of animals (SV129 mouse strain) were studied: 3 month-old animals, 12 month-old animals fed adlibitum and 12 month-old animals fed with a 20% caloric restricted diet from 3 months of age.

extract_protocol: total RNA and miRNA fraction was isolated by using TaqMan® Advanced miRNA Assays (Applied Biosystems) following the manufacturer’s protocol. RNA integrity determined by RIN (RNA integrity number) value was assessed with the Agilent 2100 Bioanalyzer using the RNA 6000 nano Bioanalyzer (Agilent Technologies). RIN value lower than 8 was considered as an exclusion criteria for the samples.

treatment_protocol: 3m and 12m animals fed ad libitum; another third group of 12m fed under a 20% of caloric restriction

value: epidydimal white adipose tissue

value: 129S2/SvPasCrl mice

tag: gender

value: Male

tag: diet

value: Ad libitum


title: Licensed 2D-N Donor 3

value: donor 3

value: M

value: Knee

value: Licensed


title: (Bulk RNA-Seq) 2dpf rpgrip1l KO with normal phenotyep Replicate #2

tag: tissue

value: whole embryos

value: Day 2


title: SV 400 12m CR Sal scWAT Cy3

description: microRNA expression in 12mCR scWAT

source_name: 12mCR scWAT

value: subcutaneous white adipose tissue

tag: strain

value: 20% Caloric restriction


title: (Bulk RNA-Seq) 5dpf wild-type Replicate #1

tag: genotype

value: Control


title: (Bulk RNA-Seq) 5dpf rpgrip1l KO Replicate #2

value: rpgrip1l KO


title: (Bulk RNA-Seq) 5dpf tmem67 KO Replicate #2

value: tmem67 KO


title: SV 34 3m Sal scWAT Cy3

description: microRNA expression in 3m scWAT

source_name: 3m scWAT

tag: age


title: (Bulk RNA-Seq) 5dpf cep290 KO Replicate #2

value: cep290 KO


title: (Bulk RNA-Seq) 5dpf tmem67 KO Replicate #1

value: Day 5


title: PEM-seq_mouse_eye_SpCas9_VEGFA-sg1_R2

value: eye

value: C57BL/6J mice

value: 6-8 weeks old

value: WT

tag: treatment

value: AAV injection


title: (Bulk RNA-Seq) 5dpf cep290 KO Replicate #1


title: 122_tumor

value: Male

tag: g

tag: t

value: N+

value: HPV-

value: Oral Cavity


title: SV 247 12m Sal scWAT Cy3

description: microRNA expression in 12m scWAT

source_name: 12m scWAT

value: 129S2/SvPasCrl mice

value: Ad libitum


title: SV 325 12R Sal eWAT Cy3

description: microRNA expression in 12CR eWAT

source_name: 12CR eWAT

value: epidydimal white adipose tissue

value: 20% Caloric restriction


title: SV 330 12R Sal scWAT Cy3

description: microRNA expression in 12CR scWAT

source_name: 12CR scWAT

value: subcutaneous white adipose tissue


title: (Bulk RNA-Seq) 5dpf tmeme216 KO Replicate #2

value: whole embryos

value: tmem216 KO


title: (Bulk RNA-Seq) 5dpf tmem216 KO Replicate #1

value: Day 5


title: SV 34 3m Sal eWAT Cy3

description: microRNA expression in 3m eWAT


title: SV 389 3m Sal eWAT Cy3

description: microRNA expression in 3m eWAT


title: SV 330 12R Sal eWAT Cy3

description: microRNA expression in 12CR eWAT


title: SV 241 12m Sal eWAT Cy3

description: microRNA expression in 12m eWAT

source_name: 12m eWAT


title: PEM-seq_mouse_eye_PBS_control_R5

value: eye

value: PBS injection


title: (Bulk RNA-Seq) 5dpf rpgrip1l KO Replicate #1

value: rpgrip1l KO


title: (Bulk RNA-Seq) 5dpf cc2d2a KO Replicate #2

value: cc2d2a KO


title: (Bulk RNA-Seq) 5dpf mks1 KO Replicate #2

value: mks1 KO


title: (Bulk RNA-Seq) 5dpf mks1 KO Replicate #1


title: SV 325 12R Sal scWAT Cy3

description: microRNA expression in 12CR scWAT

value: Male


title: SV 385 3m Sal scWAT Cy3

description: microRNA expression in 3m scWAT


title: (Bulk RNA-Seq) 5dpf b9d2 KO Replicate #2

value: b9d2 KO


title: SV 400 12m CR Sal eWAT Cy3

description: microRNA expression in 12mCR eWAT

source_name: 12mCR eWAT


title: (Bulk RNA-Seq) 5dpf cc2d2a KO Replicate #1


title: (Bulk RNA-Seq) 5dpf b9d2 KO Replicate #1


title: (Bulk RNA-Seq) 5dpf Ift88 KO Replicate #2

value: Ift88 KO


title: (Bulk RNA-Seq) 5dpf Ift88 KO Replicate #1


title: (Bulk RNA-Seq) 5dpf Ift172 KO Replicate #2

value: Ift172 KO


title: SV 435 3M Sal scWAT Cy3

description: microRNA expression in 3M scWAT

source_name: 3M scWAT

value: 129S2/SvPasCrl mice


title: SV 32 3m Sal scWAT Cy3

description: microRNA expression in 3m scWAT

value: Ad libitum


title: SV 30 3m Sal eWAT Cy3

description: microRNA expression in 3m eWAT

value: epidydimal white adipose tissue


title: SV 247 12m Sal eWAT Cy3

description: microRNA expression in 12m eWAT


title: (Bulk RNA-Seq) 5dpf Ift172 KO Replicate #1


title: Tumor Cell Enriched MPE - Patient BCB66

city: Heidelberg

first: Delphine

last: Merino

state: Victoria

address: Level 5, ONJ Centre, 145 Studley Rd, Heidelberg

department: Translational Breast Cancer Program

country: Australia

institute: Olivia Newton-John Cancer Research Institute

library_source: transcriptomic single cell

data_processing:
Base calling used Real-Time Analysis on board software v2.4.6
Demultiplexed into fastq files using cellranger software v3.0.2
Reads were mapped and quantified using cellranger software v3.0.2
Empty droplets were removed from the raw matrix using the DropletUtils package in R
Low-quality cells were removed from the raw matrix using the scater package in R
Assembly: GRCh38
Supplementary files format and content: Standard cellranger output file format: MatrixMarket sparse matrices (per sample) that contain raw gene counts for every gene in each cell. Feature and barcode files correspond to row and column indices, respectively.

source_name: Malignant pleural effusion

extract_protocol:
Chromium Single Cell 3' V3 kit (#1000078; 10X-Genomics) for samples BCB-0066, BCB-0112, BCB-0139, BCB-0020, BCB-0021, BCB-0114, BCB-0090. Chromium Single Cell 3’ V2 kit (#120237; 10X-Genomics) for samples BCB-0066_E, BCB-0020_E, BCB-0021_E.
Single Cell RNA sequencing

tag: disease state

value: metastatic breast cancer

tag: breast tumor subtype

value: TNBC (BRCA1)

value: Tumor Cell Enriched MPE


title: Tumor Cell Enriched MPE - Patient BCB21

tag: individual

value: Luminal B


title: human, 5-ALA+, sample 0714

city: New York

first: Peter

last: Sims

state: NY

address: 3960 Broadway

institute: Columbia University

data_processing:
Read 1 and read 2 fastq files were generated on basespace. 16-nt cell barcodes (CBs) were extracted from position 3-10 and 13-20, and 8-nt unique molecular identifiers (UMIs) were extracted from position 1-2, 11-12 and 21-24 of Read 1. Read 2 were trimmed to remove poly(A) tails (> dA(7)) from the 3'-ends of each read. Trimmed reads were then aligned to the reference human or(and) mouse genome using STAR v.2.7.0 with parameters "-- sjdbOverhang 65 --twopassMode Basic --outSAMtype BAM Unsorted". Only reads with unique, strand-specific alignments to exons were kept for further analysis. All reads with the same CB, UMI, and gene mapping were collapsed to represent a single molecule. To correct for sequencing errors in UMIs, we further collapsed UMIs that were within Hamming distance 1 of another UMI with the same barcode and gene. A digital gene expression matrix was then generated from the corrected barcode-UMI-gene triplets.
Assembly: GRCh38
Supplementary files format and content: Tab-separated count matrix files

source_name: GBM

extract_protocol:
Collected tissue samples were dissociated using the Adult Brain Dissociation kit (Miltenyi Biotec) on gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec) according to the manufacturer’s instructions. mRNA molecues were captured using bead-bound oligo dT(30). Captured mRNA molecues were reverse transcriped to obtain cDNA which is then amplified by PCR reactions. The cDNA PCR reaction product was then purified with AMPure XP beads. The purified cDNA PCR product was used as the input for Nextera XT reactions to generate sequencing library.
scRNA-seq libraries were prepared using Nextera XT DNALibrary Prep Kit following manufacturer's protocols.

value: GBM


title: human, 5-ALA+, sample 0519

source_name: high grade glioma

value: high grade glioma


title: human, 5-ALA+, sample 0409


title: Tumor Cell Enriched MPE - Patient BCB20

value: Luminal B (Inflammatory breast cancer)


title: MPE - Patient BCB66

value: MPE


title: SV 30 3m Sal scWAT Cy3

description: microRNA expression in 3m scWAT

value: subcutaneous white adipose tissue


title: MPE - Patient BCB21


title: siNeg-H3K27Me3-2

city: Philadelphia

first: Christian

last: Sell

state: Pennsylvania

address: 245 N 15th St, Room

department: Biochemistry

institute: Drexel University

data_processing:
Fasq files were transferred to Basepair bioinformatic platform and analyzed using the Cut and Tag pipeline developed by Basepair
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&TAG

source_name: HCF

growth_protocol: MEM, 10% fetal bovine serum, 2mM glutamine, no antibiotics. Cells were cultured at 37C at 5% CO2, 5% O2.

extract_protocol:
Wjole cells were utilized according to the Active Motif Cut and Tag protocol.
libraries were prepared using Illumina i5 and i7 primers. Quality control was perfomed using bioanalyzer chips performed by GeneWiz, sequencing was performed by GeneWiz

treatment_protocol: Cells were used at early passage (20-30population doublings), late passage (>50 population doublings), or late passage cultured in the continous presence of 1nM rapamycin

tag: cell line

value: HCF

tag: cell type

value: Human cardiac fibroblast

tag: cut and_tag_antibody

value: H2K27me3 (Millipore 07-449)


title: siNeg-H3K27Me3-1


title: SV 361 12m Sal scWAT Cy3

description: microRNA expression in 12m scWAT

value: Male


title: SV 327 12R Sal eWAT Cy3

description: microRNA expression in  12CR eWAT

value: 20% Caloric restriction


title: SV 361 12m Sal eWAT Cy3

description: microRNA expression in 12m eWAT

value: 129S2/SvPasCrl mice


title: siH19-H3K27Me3-3


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_2week_R8

source_name: eye

value: eye

value: C57BL/6J mice

value: 6-8 weeks old

value: WT

value: PBS injection


title: SV 340 12m Sal eWAT Cy3

description: microRNA expression in 12m eWAT

value: epidydimal white adipose tissue

value: Ad libitum


title: 98_tumor

source_name: Oral Cavity

tag: n

tag: hpv

value: HPV-

value: Oral Cavity


title: SV 241 12m Sal scWAT Cy3

description: microRNA expression in 12m scWAT

tag: gender


title: MPE - Patient BCB139

value: metastatic breast cancer

value: Luminal B

value: MPE


title: siH19-H3K27Me3-2

value: HCF

value: Human cardiac fibroblast


title: siH19-H3K27Me3-1

value: H2K27me3 (Millipore 07-449)


title: PEM-seq_mouse_eye_Cas9TX_VEGFA-sg1_4week_R3

value: AAV injection


title: MPE - Patient BCB112

value: TNBC


title: SV 340 12m Sal scWAT Cy3

description: microRNA expression in 12m scWAT

value: subcutaneous white adipose tissue

value: 129S2/SvPasCrl mice

value: Male

tag: diet


title: SV 32 3m Sal eWAT Cy3

description: microRNA expression in 3m eWAT

tag: tissue


title: MPE - Patient BCB114

value: Luminal A


title: Late Pass p53


title: MPE - Patient BCB90


title: Early Pass p53


title: Rapa Treated CTCF-3

value: CTCF Active Motif


title: Rapa Treated CTCF-1


title: Rapa Treated CTCF-2


title: Late Pass CTCF-3


title: Late Pass CTCF-2


title: Late Pass CTCF-1


title: MPE - Patient BCB20

value: Luminal B (Inflammatory breast cancer)


title: Early Pass CTCF-2


title: brain 3

type: genomic

city: Erlangen

first: Samir

last: Jabari

state: Bavaria

address: Schwabachanlage 6

department: Department of Neuropathology

country: Germany

institute: Universitätsklinikum Erlangen, Friedrich-Alexander University Erlangen-Nürnberg (FAU)

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200705420040_R06C01
SAMPLE 3

hyb_protocol: Following FFPE restoration bisulphite converted DNA was hybridised to Illumina Infinium Human Methylation 450k and 850K Beadchip using standard Illumina protocol

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

data_processing:
Differential DNA methylation analysis was performed with a self-customized Python wrapped cross R package pipeline, utilizing 'Champ,' 'watermelon,' 'DNAMarray,' and 'minfi' as R packages. Additional own implementations of lacking functionality were used where needed. All these packages were wrapped by using 'rpy2', an interface to R running embedded in a Python process.
Data was stratified quantile normalized using the ‘minfi‘ ‘preprocessQuantile‘ function
We used the combineArray method from minfi to process 450K and 850K data together. Due to that fact and to quality control and postprocessing, the resulting matrix only contains 128K rows of datapoints per sample. The included idats contain the full raw information though.
Matrix_processed.txt represents ‘minfi‘ beta values
Matrix_signal.txt represents unmethylated and methylated signal intensities

label: Cy5 and Cy3

source_name: Cortex

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified from FFPE tissue punches using Maxwell 16 FFPE Plus LEV DNA Kit according to standard instructions

value: Cortex

tag: condition

value: epilepsy associated brain tumor

tag: diagnosis

value: GG

tag: cns who grade

tag: methylation class

value: LGG, PXA


title: H37Rv in AIOF #1 vs 7H9 replicate 2 (dye flip)

first: Michelle

middle: Beth

last: Ryndak

address: 550 First Avenue

department: Pathology

institute: NYU Langone

hyb_protocol: For hybridization, labeled cDNA probes generated from aRNA obtained from M. tb grown in AIOF for 6 days was mixed with the labeled reference cDNA (obtained from M. tb grown to log phase in 7H9) probe prior to purification with Microcon YM10 filter (Millipore). For each AIOF grown M. tb sample (three biological replicates), the M. tb arrays were hybridized overnight with the mixed labeled cDNA probes in duplicate including a Cy3/Cy5 dye swap (Fontan et al, 2008).

scan_protocol: The microarrays were scanned at sub-saturating PMT gains with 10 µm resolution under two color wavelengths (green-532 nm and red-635 nm) and processed with a GenePix 4000B scanner and images saved as TIFF files for analysis using GenePix Pro 7 software.

data_processing: Normalized by the WinPrint-Tip Lowess method; Cy5/Cy3 intensity ratio data obtained used to perform Significance Analysis of Microarrays (SAM) with Multiarray Viewer Software on the TMEV website for determination of differentially expressed genes; ≥ 2 fold change at a false discovery rate of < 1% were considered significantly differentially expressed.

organism: Mycobacterium tuberculosis

source_name: 7H9 broth grown M. tb

label_protocol: The synthesis and fluorescent labeling of cDNA with Cy3 or Cy5 from amplified RNA (aRNA) was accomplished by first performing reverse transcriptase (RT) reaction with Superscript II RT followed by labeling with Klenow fragment using Bioprime Kit (Invitrogen) following a published method (Schlingemann 2005).

growth_protocol: AIOF was prepared as previously described (Macri A, et al., 2015). Essentially, it contains NaCl, KCl, CaCl2, NaHCO3, Na-lactate, Na-ascorbate, glucose, urea, and albumin. Frozen stocks of M. tb H37Rv (1 ml), collected at log phase, were used to inoculate 10 ml of Middlebrook 7H9 broth media (optical density [OD] 600 ~0.05) and grown to log phase (~5–7 days; OD600 ~0.5–0.7; CFU/ml = ~9 x 107). This culture was used to inoculate 10 ml 7H9 and AIOF in parallel and in triplicate to OD600 ~0.05; CFU/ml ~2–3 x 105. These were grown for 6 days at 37 °C with shaking. The log phase 7H9 inoculum culture was used as the reference.

extract_protocol: RNA was isolated from M tb  as described previously (Dubnau et al., 2002; Ryndak et al., 2014). DNAse I (Invitrogen) treatment removed contaminating DNA which was verified by real time by PCR using 16s rRNA M. tb specific primers (forward primer: 5’GTGGCGAACGGGTGAGTAAC3’ reverse primer: 5’ATGCATCCCGTGGTCCTATC3’). The RNA was then purified using RNeasy Cleanup kit (Qiagen), and both quality and quantity were determined with an Agilent 2100 Bioanalyzer.

tag: strain

source_name: M. tb 6 days in AIOF Expt #1


title: H37Rv in AIOF #2 vs 7H9 replicate 3

source_name: M. tb 6 days in AIOF Expt #2


title: H37Rv in AIOF #3 vs 7H9 replicate 2 (dye flip)

source_name: M. tb 6 days in AIOF Expt #3


title: H37Rv in AIOF #3 vs 7H9 replicate 1


title: H37Rv in AIOF #1 vs 7H9 replicate 1


title: H37Rv in AIOF #2 vs 7H9 replicate 4 (dye flip)


title: brain 72

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200394970064_R06C02
SAMPLE 116


title: brain 81

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200394970064_R05C02
SAMPLE 125

value: PXA/GG


title: brain 59

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203273200106_R05C01
SAMPLE 103


title: brain 74

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640034_R06C02
SAMPLE 118

value: DNT

value: LGG, DNT


title: brain 75

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R02C01
SAMPLE 119


title: brain 71

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640049_R06C01
SAMPLE 115

value: LGG, GG


title: brain 69

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R05C01
SAMPLE 113


title: brain 80

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200394870007_R02C01
SAMPLE 124


title: brain 68

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R04C01
SAMPLE 112


title: brain 73

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640034_R05C02
SAMPLE 117


title: brain 76

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R03C01
SAMPLE 120


title: brain 26

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
101178130129_R06C02
SAMPLE 58


title: brain 70

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
101178130129_R05C02
SAMPLE 114


title: brain 67

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R01C01
SAMPLE 111


title: brain 85

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
101178130129_R05C01
SAMPLE 129

value: isomorphic astro.

value: LGG, MYB


title: brain 84

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
101178130129_R04C01
SAMPLE 128


title: brain 48

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R07C01
SAMPLE 92


title: brain 78

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640049_R01C02
SAMPLE 122


title: brain 79

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640035_R01C02
SAMPLE 123


title: brain 77

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200091640049_R02C01
SAMPLE 121


title: brain 55

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203273200108_R08C01
SAMPLE 99

value: GG, PTPN11


title: brain 51

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200925700143_R05C01
SAMPLE 95


title: brain 53

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R01C01
SAMPLE 97


title: brain 52

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480071_R03C01
SAMPLE 96


title: brain 50

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R08C01
SAMPLE 94


title: brain 47

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480074_R08C01
SAMPLE 91


title: brain 49

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480071_R04C01
SAMPLE 93


title: PEM-seq_mouse_eye_PBS_VEGFA-sg1_12week_R4

description: PBS were injected into mouse retina. The editing efficiency and chromatin structural variations were monitored by PEM-seq analysis at 12-weeks after the PBS were administered into the mouse eyes via subretinal injection.

value: eye

value: C57BL/6J mice

tag: age

value: 6-8 weeks old

tag: genotype

value: WT

tag: treatment

value: PBS injection


title: brain 46

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203197470213_R07C01
SAMPLE 90

value: PXA


title: brain 40

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R03C01
SAMPLE 84

value: Cortex


title: brain 45

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203197470213_R06C01
SAMPLE 89

value: epilepsy associated brain tumor


title: brain 38

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480074_R07C01
SAMPLE 82

value: GG


title: brain 39

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200925700143_R06C01
SAMPLE 83


title: brain 37

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R05C01
SAMPLE 81


title: brain 44

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203197470213_R05C01
SAMPLE 88


title: brain 41

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203259190053_R03C01
SAMPLE 85


title: brain 42

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203273200103_R01C01
SAMPLE 86


title: brain 36

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R04C01
SAMPLE 80


title: brain 35

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200783410061_R06C01
SAMPLE 79


title: brain 43

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203197470213_R04C01
SAMPLE 87


title: brain 34

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R01C01
SAMPLE 78


title: brain 8

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205555380065_R05C01
SAMPLE 8


title: brain 32

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R06C01
SAMPLE 76


title: brain 33

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480017_R02C01
SAMPLE 77


title: brain 31

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R04C01
SAMPLE 75


title: brain 30

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480071_R02C01
SAMPLE 74


title: brain 54

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R02C01
SAMPLE 98


title: brain 29

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R02C01
SAMPLE 73


title: brain 28

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R06C01
SAMPLE 72


title: brain 7

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R02C01
SAMPLE 7


title: brain 27

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203179340057_R01C01
SAMPLE 67


title: brain 6

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205555380065_R03C01
SAMPLE 6


title: brain 25

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480017_R01C01
SAMPLE 56


title: brain 24

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R05C01
SAMPLE 50


title: brain 5

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R05C01
SAMPLE 5


title: brain 22

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R03C01
SAMPLE 48


title: Early Pass CTCF-3

value: HCF

value: Human cardiac fibroblast

value: CTCF Active Motif


title: Early Pass CTCF-1


title: brain 21

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R07C01
SAMPLE 47


title: brain 20

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R01C01
SAMPLE 46


title: brain 16

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203049640108_R05C01
SAMPLE 38


title: brain 19

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205555380065_R04C01
SAMPLE 43


title: brain 15

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100108_R03C01
SAMPLE 37


title: brain 14

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203175700022_R01C01
SAMPLE 36


title: brain 17

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840015_R05C01
SAMPLE 39


title: brain 23

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R04C01
SAMPLE 49


title: brain 2

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R06C01
SAMPLE 2


title: brain 4

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R03C01
SAMPLE 4


title: brain 86

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
201904660142_R01C01
SAMPLE 130


title: brain 18

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205555380065_R06C01
SAMPLE 41


title: brain 12

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205705530157_R06C01
SAMPLE 19


title: brain 13

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203048410053_R02C01
SAMPLE 31


title: brain 11

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100108_R01C01
SAMPLE 13


title: brain 82

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200772300041_R05C01
SAMPLE 126


title: brain 62

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R02C01
SAMPLE 106


title: brain 66

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R08C01
SAMPLE 110


title: brain 10

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
205705530147_R08C01
SAMPLE 11


title: brain 64

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R08C01
SAMPLE 108


title: brain 63

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100108_R02C01
SAMPLE 107


title: brain 83

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
200784530003_R08C01
SAMPLE 127


title: brain 65

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206467100153_R07C01
SAMPLE 109


title: brain 61

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203175830093_R06C01
SAMPLE 105


title: brain 60

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
202292310025_R04C01
SAMPLE 104


title: brain 58

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203259190053_R04C01
SAMPLE 102


title: brain 9

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R07C01
SAMPLE 10


title: brain 57

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203257030151_R03C01
SAMPLE 101


title: brain 56

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
203189480060_R05C01
SAMPLE 100


title: brain 1

description:
GPL13534 (450K) and GPL23976 (850K)
epilepsy asscociated brain tumor
206439840009_R04C01
SAMPLE 1


title: N2 krill day 3, replicate 3

city: Lørenskog

first: Hilde

last: Loge Nilsen

address: Sykehusveien 25

country: Norway

institute: Akershus University Hospital

data_processing:
Demultiplexed using BCL Convert (Illumina).Sequencing data preprocess starts right after being demultiplexed. Sequences were aligned to C.elegans WBcel235 dna reference (release-96)26 using annotations, general transfer format (.gtf) file from the same release, and with STAR  aligner (version 2.7.10a)27. First, an index was created using parameters --runMode genomeGenerate, --runThreadN 8 --genomeSAindexNbases 12, --sjdOverhang 69, and for any other parameter the default, in the specified version, was used. Second, reads were aligned using parameters --runThreadN 8, --outSAMtype BAM SortedByCoordinate --sjdbOverhang 69 and the ones suggested by STAR manual in ENCODE options section --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverReadLmax 0.04, --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000. From the BAM file obtained we created an index using samtools version 1.15.128 so we could remove UMI-duplicates using umi-tools version 1.1.229 , with parameters --log2stderr, --paired, --umi-separator=”:”. We then sorted the deduplicated BAM file by name and created new fastq files with the same parameters -@ 4, -n.
New fastq files were processed with fastp (version 0.23.2) with parameters -g -x -q 30 -e 30 -w 8. Then, reads were aligned with STAR aligner and parameters --quantMode GeneCounts --runThreadN 8, --outSAMtype BAM Unsorted --sjdbOverhang 69 and parameters suggested by STAR manual in ENCODE options to obtain the raw counts.
Differential gene expression was performed using the DESeq2 R package 30, version 1.32.0. Count files were split into their respective groups and attributed defining conditions, such as ‘control’ and ‘experiment’. The counts for the respective conditions are merged into one dataframe, from this dataframe, genes which have no counts for every sample are removed. A sample defining file containing the sample names along with their associated condition is also created, this file contains the relevant information for the samples within the merged count file. The values are then normalized using the DESeq2 normalization method. The standard DESeq2 pipeline was used to obtain the differential gene expression results. It starts by creating the DESeqDataSet-class by calling the DESeqDataSetFromMatrix function, using the merged count file, and the sample defining file are used as inputs, while the condition is used as the design. The design always uses the ‘experiment’ and compares it with the ‘control’. Using the estimateSizeFactors function, the median ratio method is utilized to estimate the size factors of the DESeqDataSet object. The DESeq2 function is called, which performs an estimate of dispersion followed by a negative binomial generalized linear model fitting and wal statistics in order to obtain the differential gene expression results. Selection of significant differentially expressed genes was made based on an adjusted p value (false discovery rate) below 0.05 and a log 2-fold change value greater than 1 or smaller than -1.
The timeseries analysis was performed using a package develop in our lab (Lefol et al., manuscript in preparation). The package takes in raw RNAseq files and creates a matrix of raw counts, these counts are then normalized using the DESeq2 method. (REF DESeq2 processing and normalization seen above) It then performs differential gene expression analyses for both the conditional and temporal elements of the timeseries analysis. Where conditional elements are the comparison of the experiment versus the control at every time point. Temporal elements are the comparison of subsequent timepoints, where the later time point is used as the experiment and the earlier time point is used as the control. The significant genes from all differential gene experiments are pooled together and clustered using the clusterGenomics (Identifying clusters in genomics data by recursive partitioning package, version 1.0.). A functional enrichment of each cluster is obtained using gprofiler (g:Profiler: a web server for functional enrichment analysis and conversions of gene lists (2019 update)).
The WGCNA package 31, version 1.70-3 was used to obtain a weighted correlation association between gene modules and behavioral parameters. WGCNA takes in RNAseq count data. A sample file was manually prepared for the WGCNA package, the sample file details which behavioral values are associated with the samples inputted. The pipeline first removes any samples with too many missing values in proportion with the amount of samples and values inputted. The samples are then clustered and their power is evaluated. Based on the indications of 31, the power value used is the first value above the 0.8 threshold which was a value of 4. The blockwise Modules function is used to calculate the gene modules and obtains the correlation values with the clinical parameters. Each gene module is run through gprofiler 32 in order to extract potential biological relevance of each gene module.
Biological age predictions were performed using the fastq files as raw data as input in the preprocessing specified in the Bit age pipeline33. First, the data were processed with fastp version 0.23.234 with parameters -g -x -q 30 -e 30 -w 8. And second, reads were aligned with STAR aligner and parameters --quantMode GeneCounts --runThreadN 8, --outSAMtype BAM Unsorted --sjdbOverhang 69 and again the ones suggested by STAR manual in ENCODE options, as above. For predicting biological age we took raw counts from the STAR aligner output and computed count per million(CPM), as required by bit age method, with edgeR library version 3.38.135. We then computed predicted biological age using elastic net coefficients and code provided in the bit age material33.
Assembly: C.elegans WBcel235 dna reference (release-96)
Supplementary files format and content: tab-delimited text files containing raw counts for each sample.

organism: Caenorhabditis elegans

source_name: whole worm

extract_protocol:
Total RNA was isolated with RNeasy mini kit (Qiagen) following the manufacturer’s instructions. Reverse transcription was performed using High-Capacity cDNA Reverse Transcription kit (Applied Biosystems). Quantitative PCR was carried out on a QuantStudio 7 Flex detection system (Applied Biosystems) with the Power SYBR green PCR master mix (Applied Biosystems). Each sample was analysed in triplicate. Primer sequences are provided in Supplementary Table. 2.
Sequencing libraries were prepared from 200 ng total RNA using Nugen Universal Plus Total RNA-Seq library preparation kit (Tecan) with custom AnyDeplete design for C. elegans. Final libraries were pooled (10 samples/run) and paired-end sequencing (2 x 71 bp) performed using NextSeq High Output kits on the NextSeq 550 sequencer. The raw sequencing data were demultiplexed using BCL Convert (Illumina). Sequencing data preprocess starts right after being demultiplexed. Sequences were aligned to C.elegans WBcel235 dna reference (release-96)26 using annotations, general transfer format (.gtf) file from the same release, and with STAR aligner (version 2.7.10a)27.

treatment_protocol: Animals were cultured on nematode growth medium (NGM) plates with the Escherichia coli strain OP50 at 20°C using standard procedure (Brenner, 1974). The adult animals were bleached to obtain synchronized populations. For all aging associated studies, L4 hermaphrodites were grown in NGM plates containing 0,5µl/ml krill oil (provided by Aker BioMarine) from day 1 to day 6. The aging population of worms were maintained in NGM plates without FdUrd. Instead, animals were washed with M9 buffer and filtered through Nylon Net Filter (catalog #NY4104700) everyday post adult day 2 stage, till the desired age. The adult Day 1 was defined as 24 hours post L4 stage. The following nematode strains were used in this study: N2: wild type; BY273 Is[pdat-1GFP; pdat-1 a-syn] to monitor dopaminergic neurons.

value: whole worm

value: Wildtype

value: Krill

tag: time

value: day 3 adult


title: N2 krill day 6, replicate 1

value: day 6 adult


title: N2 krill day 6, replicate 3


title: Control RNA-seq rep2

city: San Diego

first: Lingling

last: Wang

state: California

address: 9500 Gilman Dr

institute: University of California San Diego

description: RNA-seq of human lung cancer

data_processing:
Paired-end sequencing data were trimmed by paired-end model of cutadapt software. Reads longer than 15bp were retained for mapping.
Trimmed reads were aligned to hg38 genome assembly by hisat2 software using the default parameter for single or pair-end model
For RNA-seq, reads were counted by htseq, then gene expression was quantified by DESeq2. Read counts were saved as control.rep.counts.csv or PCIF1_KO.rep.counts.csv
For m6A-exo-seq, reads were counted by featureCount, then differential methylation sites at cap-region was detected by hypergeometric test through in-house scripts. The m6A marked genes are listed in m6Am.genes.rep.csv, with the gene names at first column, differential methylation FDR and p-value at second and third columns, change of enrichment fold in KO PCIF1 compared to KO control samples at the fourth column.
Assembly: hg38
Supplementary files format and content: m6Am.genes.rep.csv for m6Am marked genes in m6A-exo-seq
Supplementary files format and content: control.rep.counts.csv or PCIF1_KO.rep.counts.csv for raw gene counts in RNA-seq,

source_name: lung

extract_protocol:
After the extraction of total RNA, for RNA-seq, RNA was extracted from PCIF1-KO and control Calu-3 cells (three biological replicates for each) using a Quick-RNA Miniprep Kit. For m6A-exo-seq, mRNA was purified using Magnetic mRNA Isolation Kit (New England Biolabs, S1550S)
For m6A-exo-seq,  aliquots (100 μg) of mRNA were fragmented using a Fragmentation Reagents Kit (Invitrogen, AM8740) according to the manufacturer’s protocol. Fragmented mRNAs were phosphorylated with T4 PNK (NEB, M0201S) and then dephosphorylated with Terminator 5′-Phosphate-Dependent Exonuclease (Lucigen). Finally, Cap-Clip (CellScript) was added to remove capped transcripts. Of the final uncapped fragmented mRNA preparation, 10% was reserved as input material and the remaining 90% was subjected to immunoprecipitation with anti-m6A antibody (Abcam, ab151230). Immunoprecipitated RNA was eluted with RLT buffer (QIAGEN, 160051456), purified by ethanol precipitation, and prepared for library generation using a TruSeq mRNA library preparation kit (Illumina).
RNA-seq and m6A-exo-seq were sequenced at  Illumina NovaSeq 6000 platform with paired-end model

value: lung

tag: cell line

value: lung cancer cell

value: Control


title: PCIF1 KO RNA-seq rep1

description: RNA-seq of human lung cancer

tag: cell type

value: PCIF1 knockout


title: Control RNA-seq rep3

description: RNA-seq of human lung cancer


title: Control RNA-seq rep1

description: RNA-seq of human lung cancer


title: PCIF1 KO RNA-seq rep3

description: RNA-seq of human lung cancer


title: N2 krill day 6, replicate 2


title: PCIF1 KO RNA-seq rep2

description: RNA-seq of human lung cancer


title: N2 krill day 3, replicate 1


title: N2 krill day 1, replicate 3

value: day 1 adult


title: N2 control day 6, replicate 3


title: N2 krill day 1, replicate 2


title: N2 krill day 1, replicate 1


title: N2 control day 6, replicate 2


title: N2 control day 6, replicate 1


title: N2control day 3, replicate 3


title: N2 control day 3, replicate 2


title: N2 control day 3, replicate 1


title: N2 control day 1, replicate 3


title: N2 control day 1, replicate 2


title: N2 control day 1, replicate 1


title: 6_DH

city: St Louis

first: Maud

last: Gratuze

state: Missouri

address: 660 S. Euclid Avenue

department: Neurology

institute: Washington University in St. Louis

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

source_name: Brain, Hippocampus

extract_protocol:
Hippocampi from 3 mice per experimental group were pooled for single nuclei RNA-seq. Dissected hippocampi were homogenized in lysis buffer (10% Triton X-100, 0.1M DTT, 40U/μL RNasin Promega, protease inhibitor complex, and 2% BSA in PBS) using a Dounce homogenizer for 10 strokes. Samples were incubated for 5 minutes on ice and then centrifuged at 500 x g for 5 minutes at 4μ°C in a tabletop centrifuge. The pellet was resuspended in sort buffer (0.5M EDTA, 40U/μL RNasin Promega, 2% BSA in PBS), transferred to FACS tube, filtered through a 70-μm mesh strainer, and centrifuged at 800 x g for 5 minutes at 4°C in a swinging bucket centrifuge. We resuspended the pellet in sort buffer and stained with the following antibodies: mouse anti-NeuN-Alexa Fluor 488 (1:500; MilliporeSigma; MAB377X [clone A60] and rat anti-SPI1 (PU.1) - PE (1:100; Biolegend 681308 [clone 7C2C34]) for neurons and microglia, respectively. DAPI (1:1,000; BioLegend 422801) was used to label nuclei. After immunolabeling, samples were strained through a 70-μm mesh strainer, washed 1 more time, resuspended in sort buffer, and kept on ice until FANS. PU.1+ nuclei were purified by FANS using a Beckman Coulter Mo-Flo Astrios EQ sorter. After selection of DAPI+ nuclei and exclusion of doublets, we gated on PU.1+ nuclei
The resulting purified nuclei were centrifuged at 800 x g for 5 minutes at 4°C and then resuspended in PBS supplemented with 400 mg/mL bovine serum albumin (Sigma Aldrich, B6917). Individual nuclei were then coupled to beads using the 10X Genomics Chromium controller. Single nuclei sequencing libraries were prepared following the 10X Genomics Protocol using v3.1 chemistry and sequenced to a median depth of approximately 50,000 reads per nucleus using an Illumina NovaSeq 6000 on a rapid run. Data was mapped using Cell Ranger (10X Genomics) to mm10 and analyzed using the Seurat R toolkit for single-cell genomics (Satija et al., 2015). We obtained a median of ~500 genes per nucleus. Nuclei with more than 5% of mitochondrial genes and clusters enriched for mitochondrial genes were removed. We also filtered out 1 non-myeloid nuclei cluster based on predominantly neuronal marker expression.

value: Microglia

value: Brain, Hippocampus

value: 9.5 months old


title: BY273 krill day 6, replicate 3


title: 5_DH

description: 10x Genomics


title: BY273 krill day 6, replicate 2


title: 4_DH

description: 10x Genomics


title: BY273 krill day 6, replicate 1


title: BY273 krill day 3, replicate 3


title: human, 5-ALA+, sample 0826

value: GBM


title: BY273 krill day 3, replicate 2


title: N2 krill day 3, replicate 2


title: BY273 krill day 3, replicate 1


title: 3_DH

description: 10x Genomics


title: BY273 krill day 1, replicate 3


title: BY273 krill day 1, replicate 2


title: BY273 krill day 1, replicate 1


title: BY273 control day 3, replicate 3


title: BY273 control day 6, replicate 2


title: BY273 control day 6, replicate 1


title: BY273 control day 6, replicate 3


title: BY273 control day 1, replicate 2


title: CD, replicate 1, scRNAseq

city: Nanjing

first: Hemin

last: Jiang

address: Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: pancreatic islet

extract_protocol:
The mice were anesthetized and the bile duct was injected with 0.5 mg/ml collagenase P dissolved in cold Hanks’ balanced salt solution. The expanded pancreatic tissue was digested at 37°C for 11 min and then stopped using cold Hank's Balanced Salt Solution (HBSS) with 10% fetal bovine serum (FBS). The islets were separated using a density gradient composed of layers of HBSS and Histopaque (11191; Sigma Aldrich). After two rounds of manual selection, the islets were dispersed into single cells with TrypLE (Thermo Scientific) for 15 min in a 37°C water bath and then resuspended in Dulbecco phosphate-buffered saline (containing 2% FBS). Islet cells were confirmed to have >80% viability using Trypan blue staining.
Single cells were processed to produce gel bead-in-emulsion (GEM) using a Chromium™ Single Cell Platform (10x Genomics) with a Chromium™ Single Cell 3' GEM, Library & Gel Bead Kit v3 and a Chromium™ Chip B Single Cell Kit, following the manufacturer’s protocol. Thereafter, the beads were retrieved into a single tube for reverse transcription, and the cDNAs were tagged at the 5’ ends (that is, the 3’ ends of mRNAs were tagged) with a unique molecular identifier (UMI) and a label indicating each molecule’s cell of origin (CG000206 Rev D). The libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a 2100 Bioanalyzer system (Agilent) with a Qubit High Sensitivity DNA Assay Kit (Thermo Fisher Scientific). The libraries were sequenced (2x150 bp) on a NovaSeq 6000 system (Illumina).

value: islet

value: pancreatic islet

value: 13 weeks old

value: CD


title: BY273 control day 1, replicate 3

value: whole worm

value: Wildtype


title: SEPSIS patient_P29

status: Public on Nov 29 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

institute: Osaka univ.

description: PBMCs derived from sepsis patient_P29

data_processing:
Sequencing was performed on a DNBSEQ-G400RS platform in 2 x 100 bp paired-end mode.
The sequenced reads were mapped to the human reference genome sequences (hg19) using TopHat, version 2.0.13, in combination with Bowtie2, version 2.2.3, and SAMtools, version 0.1.19.
The fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using Cufflinks version 2.2.1.
Assembly: hg19 (GRCh37)
Supplementary files format and content: *FPKM.txt: Tab-delimited text files include FPKM values for each sample.

source_name: SEPSIS patient_P29

extract_protocol:
Total RNA isolation of leukocytes from 9 COVID-19 patients on day1 and 18 sepsis patients in the Osaka Covid-19 Cohort was performed using the PAXgene™ Blood RNA System (BD Bioscience, San Jose, CA, USA). The collection tubes were stored after blood collection until further analysis at -30°C.
Full-length cDNA was generated using a SMART-Seq HT Kit (Takara Bio, Mountain View, CA) according to the manufacturer’s instructions. An Illumina library was prepared using a Nextera DNA Library Preparation Kit (Illumina, San Diego, CA) according to SMARTer kit instructions. DNA libraries were converted to libraries for DNBSEQ using MGIEasy Universal Library Conversion Kit (App-A).

value: peripheral blood mononuclear cells

value: sepsis


title: BY273 control day 1, replicate 1


title: SEPSIS patient_P27

description: PBMCs derived from sepsis patient_P27

source_name: SEPSIS patient_P27


title: SEPSIS patient_P25

description: PBMCs derived from sepsis patient_P25

source_name: SEPSIS patient_P25


title: SEPSIS patient_P28

description: PBMCs derived from sepsis patient_P28

source_name: SEPSIS patient_P28


title: SEPSIS patient_P24

description: PBMCs derived from sepsis patient_P24

source_name: SEPSIS patient_P24


title: SEPSIS patient_P26

description: PBMCs derived from sepsis patient_P26

source_name: SEPSIS patient_P26


title: 1_DH

description: 10x Genomics


title: SEPSIS patient_P23

description: PBMCs derived from sepsis patient_P23

source_name: SEPSIS patient_P23


title: SEPSIS patient_P12

description: PBMCs derived from sepsis patient_P12

source_name: SEPSIS patient_P12


title: HFD, replicate 1, scRNAseq

institute: Department of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China

description: 10x Genomics

value: HFD


title: SEPSIS patient_P17

description: PBMCs derived from sepsis patient_P17

source_name: SEPSIS patient_P17


title: SEPSIS patient_P14

description: PBMCs derived from sepsis patient_P14

source_name: SEPSIS patient_P14


title: SEPSIS patient_P19

description: PBMCs derived from sepsis patient_P19

source_name: SEPSIS patient_P19


title: SEPSIS patient_P15

description: PBMCs derived from sepsis patient_P15

source_name: SEPSIS patient_P15


title: 2_DH

description: 10x Genomics


title: SEPSIS patient_P11

description: PBMCs derived from sepsis patient_P11

source_name: SEPSIS patient_P11


title: SEPSIS patient_P20

description: PBMCs derived from sepsis patient_P20

source_name: SEPSIS patient_P20


title: BY273 control day 3, replicate 2

source_name: whole worm

value: day 3 adult


title: BY273 control day 3, replicate 1


title: SEPSIS patient_P9

description: PBMCs derived from sepsis patient_P9

source_name: SEPSIS patient_P9


title: SEPSIS patient_P16

description: PBMCs derived from sepsis patient_P16

source_name: SEPSIS patient_P16


title: SEPSIS patient_P7

description: PBMCs derived from sepsis patient_P7

source_name: SEPSIS patient_P7


title: COVID-19 patient_COV111

description: PBMCs derived from COVID-19 patient_COV111

source_name: COVID-19 patient_COV111


title: COVID-19 patient_COV109

description: PBMCs derived from COVID-19 patient_COV109

source_name: COVID-19 patient_COV109


title: COVID-19 patient_COV96

description: PBMCs derived from COVID-19 patient_COV96

source_name: COVID-19 patient_COV96


title: COVID-19 patient_COV84

description: PBMCs derived from COVID-19 patient_COV84

source_name: COVID-19 patient_COV84


title: COVID-19 patient_COV30

description: PBMCs derived from COVID-19 patient_COV30

source_name: COVID-19 patient_COV30


title: COVID-19 patient_COV48

description: PBMCs derived from COVID-19 patient_COV48

source_name: COVID-19 patient_COV48


title: COVID-19 patient_COV13

description: PBMCs derived from COVID-19 patient_COV13

source_name: COVID-19 patient_COV13


title: SEPSIS patient_P21

description: PBMCs derived from sepsis patient_P21

source_name: SEPSIS patient_P21


title: scRNAseq_CD44+CD4+_CD4depl2

city: Chicago

first: Weiguo

last: Cui

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Matrix files were generated using Cell Ranger (10x Genomics).

source_name: Spleen

extract_protocol:
10x Genomics
10x Genomics

treatment_protocol: CD44+ CD4+ T cells were FACS-sorted from control or CD4+ T cell-depleted mice on day 21 post-LCMV Cl13 infection (2 mice per condition) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Next GEM Single Cell 5’ Reagent Kits v2 (Dual Index) according to manufacturer’s protocol.

value: Spleen

value: C57BL/6 mice

value: Splenic CD44+ CD4+ T cells

tag: infection

value: LCMV Cl13 infection

value: CD4 Depleted


title: scRNAseq_CD44+CD4+_CD4depl1


title: scRNAseq_GP33+CD8+_M2

data_processing:
Reads were aligned to mouse reference genome mm10
Matrix files were generated using Cell Ranger (10x Genomics).
Assembly: mm10
Supplementary files format and content: Matrix files  generated using Cell Ranger

extract_protocol: 10x Genomics

treatment_protocol: GP33+ CD8+ T cells were FACS-sorted from LCMV Cl13-infected mice on day 33 post- infection (2 mice) and were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were loaded on the Chromium Controller (10x Genomics). Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 5’ v2 Reagent Kit (10x Genomics) according to manufacturer’s protocol

value: Splenic GP33+ CD8+ T cells


title: scRNAseq_CD44+CD4+_Control2

value: Control


title: scRNAseq_CD44+CD4+_Control1


title: Visium_Day21_Control_2

data_processing:
Reads were aligned to mouse reference genome mm10
Assembly: mm10
Supplementary files format and content: Loupe Browser (v5.0, 10x Genomics) was used to identify which spatial sequencing capture area spots were in contact with tissue. Demultiplexing and alignment was performed with Space Ranger (v2.1, 10x Genomics) and the mm10 2020-A reference transcriptome (10x Genomics).

extract_protocol:
10x Genomics
10x Genomics
Visium spatial RNA sequencing

treatment_protocol: Spleens from Control or CD4+ T cell-depleted mice on Day 7 and Day 21 post-LCMV Cl13 infection (2 mice per condition total, conducted in two separate rounds of experiments) and were frozen fresh, stored, and processed as instructed by the Visium kit (10x Genomics). 10 μm sections were generated from frozen spleens and placed on barcoded slides (10x Genomics). The Visium Spatial Gene Expression Slide & Reagent Kit (10x Genomics) was used to generate barcoded cDNA libraries. H&E stained tissues on Visium slides were imaged using a Nikon Eclipse Ti2 inverted microscope. Spleen tissue on Visium slides was permeabilized for 18 minutes to extract mRNA and downstream library preparation and sequencing were conducted according to manufacturer’s protocol.

tag: timepoint

value: Day 21


title: 24_AMIO_4

city: Leiden

first: Ralf

last: Boland

address: Einsteinweg 55

department: IBL-ASH-CO

country: Netherlands

institute: Leiden University

data_processing:
Filtered reads were mapped to the zebrafish version GRzv11 using Salmon v.0.14.1
Data were analyzed in DESeq2 (86) following a linear model taking into account possible gene expression differences from the embryo parents, drug treatments, infections, and its interaction (design: ~genotype + treatment + infection + treatment:infection). Statistical significance was defined by s-value ≤ 0.005 using apeglm. S-values are aggregate statistics that have been recently proposed as an alternative to adjusted p-value and false discovery rate (FDR), calculating the probability of getting the sign of an effect wrong in biological contexts.
Supplementary_files_format_and_content: tab-delimited text files include read values for each gene in each Sample

source_name: zebrafish embryo with Amidarone treatment, 2 dpi

growth_protocol: Zebrafish were handled in compliance with the local animal welfare regulations and maintained according to standard protocols (http://ZFIN.org). Embryos were kept in egg water (60µg/ml Instant Ocean sea salts) at 28.5°C.

extract_protocol:
Pools of embryos for RNA isolation were snap frozen in liquid nitrogen and subsequently stored at -80°C. Embryos were homogenized in 0,7 ml of QIAzol® Reagent (Qiagen) and subsequently total RNA was extracted and on-column DNase digestion was performed with a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions. The integrity of the RNA was confirmed by Lab-on-chip analysis using the 2100 Bioanalyzer (Agilent Technologies).
3µg was used to create RNAseq libraries using the Illumina TruSeq strand-specific mRNA polyA preparation kit (Illumina, San Diego, US). The resulting RNAseq library was sequenced for at least 10 million reads per sample using an Illumina HiSeq2500 with a read length of 1 × 50 nucleotides (Baseclear, Leiden, The Netherlands).

treatment_protocol: Zebrafish embryos from four independent crosses were manually dechorionated at 24 hpf and at 30 hpf they were micro-injected into the blood island with 200  CFU of M. marinum strain M bacteria suspended in PBS/2%PVP or mock-injected with PBS/2%PVP as a control. Embryos were treated with 0.02% ethyl 3-aminobenzoate methanesulfonate (Tricaine, SIGMA-ALDRICH) for anesthesia before bacterial injections and RNA extraction. Embryos were incubated with the specified drug treatment (10uM Tamoxifen, 10uM Amiodarone, or same v/v DMSO). At 4 days post fertilization (2 days post infection), total RNA from pools of 10 embryos for treatment group was isolated using QIAzol® Reagent (Qiagen).

tag: blood island injection

tag: developmental stage rna isolation

value: 2 dpi

tag: parental strain

value: D

tag: description


title: Visium_Day21_Control_1

tag: tissue

tag: condition


title: Visium_Day21_CD4depl_1


title: 23_TAM_4

source_name: zebrafish embryo with Tamoxifen treatment, 2 dpi


title: Visium_Day21_CD4depl_2


title: 21_AMIO_Mm_4

source_name: zebrafish embryo infected with 200CFU of M. marinum with Amiodarone treatment, 2 dpi

value: M. marinum, M strain 200 cfu


title: 22_DMSO_4

source_name: zebrafish embryo with control treatment, 2 dpi


title: Visium_Day7_CD4depl_1

value: Day 7


title: 19_DMSO_Mm_4

source_name: zebrafish embryo infected with 200CFU of M. marinum with control treatment, 2 dpi


title: 20_TAM_Mm_4

source_name: zebrafish embryo infected with 200CFU of M. marinum with Tamoxifen treatment, 2 dpi


title: COVID-19 patient_COV20

description: PBMCs derived from COVID-19 patient_COV20

source_name: COVID-19 patient_COV20

tag: diagnosis


title: 16_DMSO_3

value: C

value: zebrafish embryo with control treatment, 2 dpi


title: COVID-19 patient_COV16

description: PBMCs derived from COVID-19 patient_COV16

source_name: COVID-19 patient_COV16

value: peripheral blood mononuclear cells


title: 18_AMIO_3

value: zebrafish embryo with Amidarone treatment, 2 dpi


title: 17_TAM_3

value: zebrafish embryo with Tamoxifen treatment, 2 dpi


title: 15_AMIO_Mm_3

value: zebrafish embryo infected with 200CFU of M. marinum with Amiodarone treatment, 2 dpi


title: 14_TAM_Mm_3

value: zebrafish embryo infected with 200CFU of M. marinum with Tamoxifen treatment, 2 dpi


title: Visium_Day7_CD4depl_2

value: Spleen

value: C57BL/6 mice


title: scRNAseq_GP33+CD8+_M1

value: LCMV Cl13 infection


title: 12_AMIO_2

value: B


title: G1s-C1-26_CUTRUN_H3K4me1

city: Hirosaki

first: Rika

last: Kanezaki

address: 5 Zaifucho

institute: Hirosaki University Graduate School of Medicine

data_processing:
library strategy: CUT&RUN
For ChIP-seq data,sequence reads were aligned to genome by Bowtie2 (ver 2.2.2) with option -N1. For CUT&RUN-seq data, reads were aligned according to the method by Skene and Heinikoff (Nature Protocols 2018 13, 1006-1019). For RNA-seq data, sequence reads were aligned to genome using STAR (ver 2.6.1d). Aligned reads were counted by RSEM (ver 1.3.1). The count data normalized using the DESeq2 package (ver 1.32.0).
Duplicated reads of ChIP-seq and CUT&RUN-seq were removed by Picard (ver. 2.18).
The BAM files of ChIP-seq and CUT&RUN data were converted to bigWig coverage files using bamCoverage command of deepTools (ver 3.1.3). Read coverages were normalized to Read per genomic content (RPGC). For the GATA1 and GATA2 ChIP-seq data, peak call was performed using HOMER (ver 4.11)  with default settings.
Genome_build: hg19 (ChIP-seq, CUT&RUN-seq), hg38 (RNA-seq)
Supplementary_files_format_and_content: bigWig files normalized in reads per genomic content (RPGC) and bed files.

growth_protocol: K562 cells were cultured with RPMI1640 (Sigma-Aldrich) containing 10% heat inactivated fetal bovine serum (FBS) at 37°C in 5% CO2 atmosphere.

extract_protocol:
Chromatin samples were extracted using SimpleChIP Enzymatic Chromatin IP Kit (CST) according to the protocol. For ChIP reactions, Dynabeads anti-rabbit IgG (Thermo Fisher Scientific) was used to reduce noise instead of the Protein G magnetic beads included in the kit. CUT&RUN assay was performed using CUT&RUN Assay Kit (CST), and samples were purified using Monarch PCR & DNA Cleanup Kit (NEB). total RNA was extracted using the RNeasy plus mini kit (Qiagen).
ChIP-seq and CUT&RUN libraries were prepared using KAPA HyperPrep Kit (KAPA Biosystems). Total RNA was purified by NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB), and RNA-seq library was prepared by KAPA RNA Hyper prep kit (KAPA Biosystems).

value: mutant

tag: chip and cut&run antibody

value: H3K4me1 (Active motif, 39298)


title: G1s-C1-26_CUTRUN_H3K4me3


title: G1s-C1-26_CUTRUN_IgG

value: normal IgG (CST, 66362)


title: WT_CUTRUN_H3K4me3

source_name: K562, wild type

value: wild


title: 10_DMSO_2

value: 2 dpi


title: Visium_Day7_Control_2

tag: strain

value: Day 7

value: Control


title: Visium_Day7_Control_1


title: 9_AMIO_Mm_2

value: M. marinum, M strain 200 cfu


title: WT_CUTRUN_H3K4me1


title: 7_DMSO_Mm_2

value: zebrafish embryo infected with 200CFU of M. marinum with control treatment, 2 dpi


title: 6_AMIO_1

value: A

value: zebrafish embryo with Amidarone treatment, 2 dpi


title: 5_TAM_1

value: zebrafish embryo with Tamoxifen treatment, 2 dpi


title: 4_DMSO_1

value: zebrafish embryo with control treatment, 2 dpi


title: 3_AMIO_Mm_1

value: zebrafish embryo infected with 200CFU of M. marinum with Amiodarone treatment, 2 dpi


title: 2_TAM_Mm_1

value: zebrafish embryo infected with 200CFU of M. marinum with Tamoxifen treatment, 2 dpi


title: 1_DMSO_Mm_1


title: 13_DMSO_Mm_3

value: C


title: Brain microglia: Old  (4posI)

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

institute: CIBEREHD

description: Brain microglia: Old  (4posI)

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCm38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.vM15 database .
We use TMM method and limma-voom transformation from rounded expected counts to normalize the non biological variability
Assembly: Mus musculus (GRCm38)
Supplementary files format and content: RSEM expected counts

molecule: polyA RNA

source_name: Brain microglia

growth_protocol: Mice were anesthetized with isoflurane and euthanized by cervical dislocation. The brain was carefully collected, in order not to damage the tissue, and immersed in Hanks’ Balanced Salt solution w/o ions (HBSS w/o Ca2+ and Mg2+; #14175-053, Thermo Fisher Scientific) on ice. The forebrain was dissected with a scalpel, discarding the cerebellum and the olfactory bulbs, and minced in small pieces. The Neural Tissue Dissociation Kit - P (NTDK, #130-092-628, Miltenyi Biotec) based on the enzymatic dissociation with papain was used to homogenize the tissue. Mechanical dissociation was performed with the gentleMACS™ Octo Dissociator (#130-096-427, Miltenyi Biotec: 1x m_Brain_1 program and 1x ABDK_37C program by Miltenyi) with the tissue immersed in the buffers and enzymes from the NTDK kit, according to manufacturer instructions. The tissue was then filtered through a 70 mm cell strainer (#352350, Falcon) previously humidified with HBSS with Ca2+ and Mg2+ (#14025-092, Thermo Fisher Scientific). Then, cells were separated from myelin by an immunomagnetic separation method. Brain cells were incubated with Myelin Removal Beads II (#130-096-733, Miltenyi Biotec) and then passed through LS Columns (#130-042-401, Miltenyi Biotec) held onto the OctoMACS Separator (#130-091-051, Miltenyi Biotec) and to the MACS® MultiStand (#130-042-303, Miltenyi Biotec). Unspecific binding of antibodies was blocked by previous incubation for 10 min with anti CD16/CD32 (Fc block, clone 2.4G2; #55314, BD Pharmingen) in Fluorescence Activated Cell Sorting (FACS) buffer at 4 °C. LViakrome 405 Fixable Viability Dye (#C36614, Beckman Coulter) was used to determine the viability of cells. Cells were incubated during 30 minutes at 4°C with the following primary antibodies: CD11b (clone M1/70, AF647, #557686, BD Pharmingen), CD45 (clone 30-F11, Brilliant Violet 786, #564225, BD Horizon). After washing once with phosphate buffered saline (PBS), cells were stained with BODIPY (4,4-difluoro-3a,4adiaza-s-indacene, Molecular Probes BODIPY 493/503, #D3922, Life Technologies) diluted 1:1,000 during 15min at RT. After washing with FACS Stain Buffer (#554656, BD Biosciences), the cells were sorted in a FACSAriaII SORP sorter (BD Biosciences). Microglial cells were collected in sterile DPBS (#14190-094, Thermo Fisher Scientific), centrifuged, and resuspended in lysis buffer (from PureLink™ RNA Micro Kit #12183016, Invitrogen) supplemented with 10% β-mercaptoethanol and finally snap-frozen in dry ice.

extract_protocol:
RNA was extracted from samples of FACS-sorted microglia with PureLink™ RNA Micro Kit (#12183016, Invitrogen) following manufacturer indications with minor modifications. RNA was precipitated with 70% ethanol overnight at -20°C. To avoid genomic DNA contamination a DNAse step was performed. RNA quantity and purity were assessed with the High Sensitivity RNA ScreenTape® (Agilent 2200 TapeStation system).
Library Preparation - custom SMARTseq2 (NEBnext) (low input/non-stranded),

treatment_protocol: No drug treatment. We compared microglia of adult young (3-4 month) male mice with microglia of  old (21-22 month) male mice in the C57BL/6 background obtained from Janvier (Lyon, France)

tag: group

value: Old


title: Brain microglia: Old (3posI)

description: Brain microglia: Old (3posI)


title: 11_TAM_2

value: B


title: Sp_DFxDF_+y_1

city: Munich

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

institute: Technical University Munich

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.5.0c). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
Assembly: mm10

source_name: adult spleen

extract_protocol:
RNA was extracted from TRIzol using standard protocols.
The Illumina TruSeq kit was used to create polyA+ libraries from total RNA. We generated strand-specific libraries for tissues collected form the F1 crosses (TruSeq stranded Illumina) and non-strand-specific TruSeq libraries for the adult organs. All the libraries were run on a Bioanalyzer to assess purity, fragment size, and concentration and sequenced on a HiSeq 2500 at Harvard University’s Bauer Sequencing Core (75 bp paired end).

value: adult spleen

tag: age

value: 6 weeks

tag: brackground

tag: genotype

value: +y

tag: Sex

value: M


title: Sp_DFxDF_-y_1

value: -y


title: Sp_DFxDF_+y_2


title: Brain microglia: Old (2posI)

description: Brain microglia: Old (2posI)


title: Sp_DFxDF_-y_2


title: Brain microglia: Young (29C)

description: Brain microglia: Young (29C)

value: Young


title: Brain microglia: Young (23C)

description: Brain microglia: Young (23C)


title: WT_Maternal

first: Miklos

last: Toth

address: 525 E. 68th St Whitney Pavilion Floor 5

institute: Weill Cornell Medicine

description: 10X Genomics

data_processing:
Blood: Raw sequencing data was processed using the CellRanger v5.0.0 pipeline.
Placenta: Raw sequencing data was processed using the CellRanger v6.0.0 pipeline.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Placenta

extract_protocol:
Placenta
Blood: N=4 non-sister female mice at GD10.5 were processed per group (WT and Het). After terminal anesthesia by pentobarbital, maximum peripheral whole blood (~2 mL) was collected via cardiac puncture. Biological replicates from each group were then pooled together and an equal volume of 1X DPBS without magnesium or calcium was added to the whole blood. The diluted whole blood was layered onto Ficoll-Paque PREMIUM 1.084 (2 parts blood to 3 parts Ficoll in volume). The gradient was spun at 400 x g for 30 min with the brakes off at room temperature (RT). Plasma was removed and the layer containing peripheral blood mononuclear cell (PBMC) was collected and transferred to a new tube. The remaining Ficoll layer was removed, and the RBC/granulocyte pellet was suspended in 1X RBC Lysis Buffer in a 1:10 ratio. The solution was gently inverted a few times, incubated at RT for 15 minutes, then spun at 300 x g for 5 minutes with brakes on low at RT. The supernatant with lysed RBC fragments was removed. The pellet was washed with a volume of DPBS equal to the amount of RBC Lysis Buffer used and spun at 350 x g with brakes on low for 5 minutes at RT. Wash was repeated, the supernatant was removed, and the resulting pellet of granulocytes was resuspended in 1 mL DPBS with 2% FBS and set on ice. Separately, the volume of collected PBMC was estimated and 4X that volume of DPBS was added to the PBMC fraction. The sample was gently triturated with a serological pipet, then spun at 400 x g for 10 minutes with brakes on low at RT. RBC lysis buffer was added to the pellet as above and the resulting pellet was washed twice with DPBS. Final PBMC pellet was resuspended in 1 mL DPBS with 2% FBS, combined with granulocyte suspension, and visually inspected with a hemocytometer under a microscope for cell counting.
Placenta: After dissection of the maternal decidua, N=3 decidua from non-sibling placenta at GD10.5 were processed per group (WT and Het decidua from WT and F1 placenta). Single nuclei suspension was prepared from frozen tissue with slight modifications to the method described by Marsh and Blelloch 2020 (Marsh and Blelloch 2020). In brief, 1 mL prechilled Nuclei EZ lysis buffer was added to each flash-frozen decidua sample, which was then minced finely with dissection scissors. A wide bore pipet was used to transfer pooled minced tissue into a glass dounce homogenizer. Tissue was lysed with 20 strokes of the loose pestle followed by 20 strokes of the tight pestle. The homogenate was transferred to a new tube and an additional 3 mL of prechilled Nuclei EZ Lysis Buffer was added. The sample was incubated on ice for 5 min and was resuspended a few times throughout. The lysate was filtered through a 70 µM filter and spun at 500 x g for 5 min at 4°C in a centrifuge with a swinging bucket rotor. The supernatant was removed, and the pellet was resuspended with 2 mL Nuclei EZ Lysis Buffer and incubated for an additional 5 min on ice. The sample was spun at 500 x g for 5 min at 4°C and the supernatant was removed. 1 mL Nuclei Wash Buffer (DPBS without magnesium and calcium, 2% BSA, and 0.2U Protector RNase inhibitor was layered onto the pellet and the sample was incubated on ice for 5 min without mixing or resuspending in order to promote buffer exchange. An additional 2 mL Nuclei Wash Buffer was used to resuspend, and the sample was spun at 500 x g for 5 min at 4°C. The lysate was removed, and this wash step was repeated. Finally, the pellet was resuspended in 1.5 mL Nuclei Wash Buffer, filtered through a 70 µM filter, and visually inspected with a hemocytometer under a microscope for cell counting.
Libraries were constructed according to manufacterer protocols by the Weill Cornell Epigenomics Core using the Chromium Single Cell 3' Reagent V3 kit.

value: Placenta

tag: cell type

value: Decidual cells; immune cells

value: Swiss Webster wild type

value: Female

tag: gestational day


title: Brain microglia: Young (18C)

description: Brain microglia: Young (18C)