title: comrhy29, SM, adult

status: Public on Aug 31 2023

type: SRA

city: Potsdam

first: Feng

last: Cheng

address: Meistersingerstr., 5

country: Germany

institute: University of Potsdam

library_source: transcriptomic

data_processing:
We trimmed the adapter sequences and low quality reads using a 4 bp sliding window with a mean quality threshold of 25, and a minimum read length of 36 bp by Trimmomatic v0.39
The quality-filtered reads were mapped to the C. compressirostris genome using RSEM for gene level-quantification estimation. The estimated counts were imported into R/Bioconductor with the tximport package, which produced count matrices from gene-level quantification by taking the effective gene length into account
Supplementary files format and content: Tab-delimited text file includes length, effective_length, expected_count, TPM and FPKM on gene level

molecule: total RNA

organism: Campylomormyrus compressirostris x Campylomormyrus rhynchophorus

source_name: skeletal muscle

extract_protocol:
The RNA isolation was performed in all the electric organ and skeletal muscle samples using QIAGEN RNeasy Fibrous Tissue Mini Kit.
mRNA enrichment was performed by poly (A) capture from isolated RNA using NEXTflex Poly (A) Beads. Strand-specific transcriptomic libraries were built using NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific, USA) based on the manufacturer’s instructions.

tag: tissue

value: skeletal muscle

tag: hybrid

value: Hybrid Campylomormyrus compressirostris (M) x Campylomormyrus rhynchophorus (F)


title: comrhy111, EO, adult

source_name: electric organ

value: electric organ


title: comrhy62, EO, 6cm

extract_protocol:
The RNA isolation was performed in all the electric organ samples using QIAGEN RNeasy Fibrous Tissue Mini Kit.
mRNA enrichment was performed by poly (A) capture from isolated RNA using NEXTflex Poly (A) Beads. Strand-specific transcriptomic libraries were built using NEXTflex Rapid Directional RNA-Seq Kit (Bioo Scientific, USA) based on the manufacturer’s instructions.


title: comrhy28, SM, adult


title: comrhy60, EO, 6cm


title: comrhy113, EO, adult


title: comrhy63, EO, 6cm


title: comtsh37, SM, adult

organism: Campylomormyrus compressirostris x Campylomormyrus tshokwe

value: Hybrid Campylomormyrus compressirostris (M) x Campylomormyrus tshokwe (F)


title: comrhy61, EO, 6cm


title: comrhy112, EO, adult


title: comrhy31, SM, adult


title: comrhy32, SM, adult


title: comtsh38, SM, adult


title: comtsh36, SM, adult


title: comrhy30, SM, adult


title: comrhy59, EO, 6cm


title: comrhy110, EO, adult


title: comrhy114, EO, adult


title: comtsh35, SM, adult


title: comtsh34, SM, adult


title: comtsh130, EO, adult


title: comtsh129, EO, adult


title: rhy53, EO, 6cm

organism: Campylomormyrus rhynchophorus


title: rhy52, EO, 6cm


title: rhy51, EO, 6cm


title: comtsh126, EO, adult


title: comtsh128, EO, adult


title: comtsh127, EO, adult


title: rhy50, EO, 6cm


title: rhy21, SM, adult


title: tshBr_c26, SM, adult

organism: Campylomormyrus tshokwe


title: rhy18, SM, adult


title: bruli(RNAi) biol rep 3

city: Evanston

first: Christian

middle: Paul

last: Petersen

state: IL

address: 2205 Tech Drive, Hogan 2-100

department: Molecular Biosciences

country: USA

institute: Northwestern University

data_processing:
Sequences were mapped to the ddv4 transcriptome using Bowtie v1.2 with parameter --best.
Raw read counts were generated with Samtools v1.6 idxstats and transcripts from different isoforms were summed (sum of counts for dd_v4_Smed_XXX_Y_Z for all Z)
Differential expression was determined with DESeq
Assembly: Genome_build: Dresden S. mediterranea Transcriptome Assembly (ddv6, Rozanski et al, Nucleic Acids Research 2019)
Supplementary files format and content: Supplementary_files_format_and_content: Tab-separated text and Excel spreadsheet files

organism: Schmidtea mediterranea

source_name: whole-animal

growth_protocol: Standard planarian culture conditions

extract_protocol:
4 animals per replicate were homogenized in 200 ul TEN buffer (0.1 M Tris-Cl pH 8.0, 0.01 M EDTA pH 8.0, 1 M NaCl) supplemented with SDS (0.4%), proteinase K (0.48 mg/ml) and beta-mercaptoethanol (0.14%) and pipetted gently with a multichannel pipette every 2-3 minutes at room temperature until homogenized (~10 minutes), then RNA extracted using 600 ul Trizol-LS reagent.
Kapa stranded mRNA seq, 96-well format

treatment_protocol: Animals fed liver mixed with dsRNA 2-3 times twice per week for 14 days followed by RNA extraction 7 days after the final feeding.

value: whole-animal

tag: genotype

value: CIW4 asexual

tag: treatment

value: bruli(RNAi)


title: rhy115, EO, adult


title: rhy19, SM, adult


title: rhy107, EO, adult


title: rhy20, SM, adult


title: rhy109, EO, adult


title: tsh120, EO, adult


title: rhy106, EO, adult


title: rhy116, EO, adult


title: tshBr_c39, SM, adult


title: tshBr_c48, SM, adult


title: tsh117, EO, adult


title: Ppluc(RNAi) biol rep 3

value: Ppluc(RNAi)


title: Ppluc(RNAi) biol rep 1


title: bruli(RNAi) biol rep 2


title: Ppluc(RNAi) biol rep 2


title: rhy17, SM, adult


title: zfp-1(RNAi) biol rep 2


title: bruli(RNAi) biol rep 1


title: rhy49, EO, 6cm


title: tsh118, EO, adult


title: zfp-1(RNAi) biol rep 1


title: repA1(RNAi) biol rep 2


title: zfp-1(RNAi) biol rep 3


title: repA1(RNAi) biol rep 3


title: repA1(RNAi) biol rep 1


title: MARK2(RNAi) biol rep 3


title: MARK2(RNAi) biol rep 2


title: AKT(RNAi) biol rep 3

value: AKT(RNAi)


title: MARK2(RNAi) biol rep 1


title: PKN2(RNAi) biol rep 3


title: PKN2(RNAi) biol rep 2


title: AKT(RNAi) biol rep 2


title: LAMTOR(RNAi) biol rep 1

value: LAMTOR(RNAi)


title: LAMTOR(RNAi) biol rep 2


title: LAMTOR(RNAi) biol rep 3


title: AKT(RNAi) biol rep 1


title: PKN2(RNAi) biol rep 1


title: TRRAP(RNAi) biol rep 3

value: TRRAP(RNAi)


title: TRRAP(RNAi) biol rep 2


title: PLK1(RNAi) biol rep 3


title: STK39(RNAi) biol rep 3


title: PLK1(RNAi) biol rep 1


title: PLK1(RNAi) biol rep 2


title: STK39(RNAi) biol rep 2


title: TRRAP(RNAi) biol rep 1


title: STK39(RNAi) biol rep 1


title: ANAPC(RNAi) biol rep 2

value: ANAPC(RNAi)


title: AK2(RNAi) biol rep 2


title: AK2(RNAi) biol rep 3


title: ANAPC(RNAi) biol rep 3


title: ANAPC(RNAi) biol rep 1


title: CDK7(RNAi) biol rep 1


title: AK2(RNAi) biol rep 1


title: CDK7(RNAi) biol rep 3


title: CDK7(RNAi) biol rep 2


title: nat10(RNAi) biol rep 3


title: nat10(RNAi) biol rep 2


title: Rb(RNAi) biol rep 3

value: Rb(RNAi)


title: nat10(RNAi) biol rep 1


title: Rb(RNAi) biol rep 2


title: Rb(RNAi) biol rep 1


title: MNAT1(RNAi) biol rep 2


title: LPT(RNAi) biol rep 2

value: LPT(RNAi)


title: MNAT1(RNAi) biol rep 1


title: MNAT1(RNAi) biol rep 3


title: LPT(RNAi) biol rep 1


title: LPT(RNAi) biol rep 3


title: PANK3(RNAi) biol rep 3


title: PANK3(RNAi) biol rep 1


title: piwi-2(RNAi) biol rep 3


title: piwi-2(RNAi) biol rep 2


title: PANK3(RNAi) biol rep 2


title: piwi-2(RNAi) biol rep 1


title: PRPF4B(RNAi) biol rep 2


title: PRPF4B(RNAi) biol rep 3


title: MINK1(RNAi) biol rep 3


title: MINK1(RNAi) biol rep 2


title: PRPF4B(RNAi) biol rep 1


title: MINK1(RNAi) biol rep 1


title: ANK1(RNAi) biol rep 3


title: ANK1(RNAi) biol rep 1


title: CSNK1A1(RNAi) biol rep 2


title: ANK1(RNAi) biol rep 2


title: CSNK1A1(RNAi) biol rep 1


title: CSNK1A1(RNAi) biol rep 3


title: PAPSS2(RNAi) biol rep 3


title: PAPSS2(RNAi) biol rep 2


title: PAPSS2(RNAi) biol rep 1


title: Donor3_100ng_IL10

type: RNA

city: Hanover

first: Anton

last: Selich

address: Carl-Neuberg-Str. 1

institute: Hannover Medical School

description: Activation of MSCs from donor 3 with 100 ng/mL IL10

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘One-Color Microarray-Based Gene Expression Analysis Protocol V5.7’, except that 700 ng of each fluorescently labelled cRNA population was used for hybridization.

scan_protocol: Slides were scanned using the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction was performed with the ‘Feature Extraction Software V10.7.3.1’ by use of the extraction protocol file ‘GE1_107_Sep09.xml’.

organism: Homo sapiens

source_name: Donor 3, 100 ng/mL IL10

label_protocol: 100 ng of total RNA were used to prepare aminoallyl-UTP-modified (aaUTP) cRNA (Amino Allyl MessageAmp™ II Kit; #AM1753; Thermo Fisher Scientific) applying one-round of amplification as directed by the company, except for a twofold downscaling of all reaction volumes. Prior to the reverse transcription reaction, 1 µl of a 1:5000 dilution of Agilent’s One-Color spike-in Kit stock solution (#5188-5282, Agilent Technologies) was added to 100 ng

extract_protocol: Cells were harvested by 400xg, resuspended in 700 µl of RNAzol B reagent (WAK-Chemie Medical) and frozen at -80°C. Total RNA was isolated with the Direct-Zol RNA MiniPrep Kit (Zymo Research) and on-column DNAse treatment.

tag: donor

tag: cell type

value: Umbilical cord mesenchymal stromal cells (UC-MSCs)

value: 100 ng/mL IL10


title: Donor2_1ng_IL10

description: Activation of MSCs from donor 2 with 1 ng/mL IL10

source_name: Donor 2, 1 ng/mL IL10

value: 1 ng/mL IL10


title: Donor2_10ng_IL10

description: Activation of MSCs from donor 2 with 10 ng/mL IL10

source_name: Donor 2, 10 ng/mL IL10

value: 10 ng/mL IL10


title: Donor3_1ng_IL10

description: Activation of MSCs from donor 3 with 1 ng/mL IL10

source_name: Donor 3, 1 ng/mL IL10


title: Donor3_0ng_IL10

description: Activation of MSCs from donor 3 with 0 ng/mL IL10

source_name: Donor 3, 0 ng/mL IL10

value: 0 ng/mL IL10


title: Donor3_10ng_IL10

description: Activation of MSCs from donor 3 with 10 ng/mL IL10

source_name: Donor 3, 10 ng/mL IL10


title: Donor2_0ng_IL10

description: Activation of MSCs from donor 2 with 0 ng/mL IL10

source_name: Donor 2, 0 ng/mL IL10


title: Donor2_100ng_IL10

description: Activation of MSCs from donor 2 with 100 ng/mL IL10

source_name: Donor 2, 100 ng/mL IL10


title: Donor1_100ng_IL10

description: Activation of MSCs from donor 1 with 100 ng/mL IL10

source_name: Donor 1, 100 ng/mL IL10


title: Donor1_1ng_IL10

description: Activation of MSCs from donor 1 with 1 ng/mL IL10

source_name: Donor 1, 1 ng/mL IL10


title: Donor1_0ng_IL10

description: Activation of MSCs from donor 1 with 0 ng/mL IL10

source_name: Donor 1, 0 ng/mL IL10


title: TS-R-3

city: Nanjing

first: Tai

last: Guangjie

state: Jiangsu

address: Longmiandadao 639

department: Clinical pharmacy

country: China

institute: China pharmaceutical university

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads.
FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: NOT PROVIDED
Supplementary files format and content: Raw_counts.txt

organism: Mus musculus

source_name: Perivascular adipose tissue

extract_protocol:
Total RNA was extracted from the PVAT using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit following the manufacturer’s instructions..The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system.

value: Perivascular adipose tissue

value: WT

tag: strain background


title: NTS-R-3

value: Nlrp3 KO


title: NS-R-3


title: NTS-R-2


title: TS-R-1


title: NS-R-2


title: NS-R-1


title: WTS-R-3


title: WTS-R-2


title: TS-R-4


title: CircRNA_in_subpolysome_of_Control_siRNA_transfected_set_1

city: Daejeon

first: Jeeyoon

last: Chang

address: 291 Daehak-ro, Yuseong-gu, Daejeon

department: Life Science

country: South Korea

institute: Korea Advanced Institute of Science & Technology

description:
circRNA
Biological replicate 1 of 2

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven. The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

scan_protocol: The signals were scanned using the Agilent Scanner G2505C.

data_processing: Quantification was performed by Feature Extraction Software (Agilent Technology, Palo Alto, CA), and analysis were performed using GeneSpringGX 7.3 (Agilent Technology, USA).

source_name: Subpolysome of Control siRNA-transfected HeLa cells, set 1

label_protocol: The enriched circular RNAs were amplified and transcribed into Cy3-labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).

growth_protocol: HeLa cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% (v/v) fetal bovine serum and 1% (v/v) of a penicillin/streptomycin solution at 37°C and 5% CO2.

extract_protocol: Polysomal and subpolysomal fractions were pooled according to the absorbance at 254 nm, and RNAs were purified using TRIzol reagent. Before labeling, RNAs were treated with RNase R to remove linear RNAs.

treatment_protocol: HeLa cells were transfected with either Control siRNA or eIF4A3 siRNA for three days. Then, the cytoplasmic extracts were subjected to polysome fractionation experiment.

tag: cell line

value: HeLa

tag: transfection

value: control siRNA

tag: fraction

value: subpolysome


title: NTS-R-1


title: CircRNA_in_polysome_of_eIF4A3_siRNA_transfected_set_2

description:
circRNA
Biological replicate 2 of 2

source_name: Polysome of eIF4A3 siRNA-transfected HeLa cells, set 2

value: eIF4A3 siRNA

value: polysome


title: CircRNA_in_subpolysome_of_eIF4A3_siRNA_transfected_set_2

description:
circRNA
Biological replicate 2 of 2

source_name: Subpolysome of eIF4A3 siRNA-transfected HeLa cells, set 2


title: WTS-R-1


title: CircRNA_in_subpolysome_of_Control_siRNA_transfected_set_2

description:
circRNA
Biological replicate 2 of 2

source_name: Subpolysome of Control siRNA-transfected HeLa cells, set 2


title: CircRNA_in_polysome_of_eIF4A3_siRNA_transfected_set_1

description:
circRNA
Biological replicate 1 of 2

source_name: Polysome of eIF4A3 siRNA-transfected HeLa cells, set 1


title: CircRNA_in_polysome_of_Control_siRNA_transfected_set_2

description:
circRNA
Biological replicate 2 of 2

source_name: Polysome of Control siRNA-transfected HeLa cells, set 2


title: TS-R-2


title: CircRNA_in_subpolysome_of_eIF4A3_siRNA_transfected_set_1

description:
circRNA
Biological replicate 1 of 2

source_name: Subpolysome of eIF4A3 siRNA-transfected HeLa cells, set 1


title: CircRNA_in_polysome_of_Control_siRNA_transfected_set_1

description:
circRNA
Biological replicate 1 of 2

source_name: Polysome of Control siRNA-transfected HeLa cells, set 1


title: Donor1_10ng_IL10

description: Activation of MSCs from donor 1 with 10 ng/mL IL10

source_name: Donor 1, 10 ng/mL IL10


title: Whole blood, B1, No Arthritis,Day2, replicate 2 [D2_S42_R2]

city: Jammu

first: Santhilal

last: Subhash

state: Jammu and Kashmir

address: Jagti, NH-44, PO Nagrota

department: Biosciences and Bioengineering

country: India

institute: Indian Institite of Technology Jammu

data_processing:
The paired-end reads with strand-specific library (fr-firststrand) preparation of samples were aligned using HISAT2 (v2.2.1) against reference ensemble mouse genome GRCm39.
Alignment (BAM) files were further used for gene quantification using GENCODE gene annotation corresponds to GRCm39 genome. featureCounts from subread (v2.0.0) package is used for assigning high quality uniquely mapped reads to the gene features with paired-end and strand-specific parameters (-p -s 2 -B --minOverlap 10 -Q 30 --ignoreDup).
Assembly: mm39
Supplementary files format and content: tab-delimited text files include RAW count values for each Sample

source_name: Whole blood

extract_protocol:
RNA was harvested using miRneasy mini kit (Qiagen). 0.5 - 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq was performed with TruSeq Stranded Total RNA Sample Preparation Kit with Ribo-Zero Gold (Illumina, San Diego, USA), following the manufacturer’s instructions.

value: Whole blood

value: NMRI WT

tag: disease state

value: No Arthritis

tag: time

value: Day 2


title: Whole blood, B1, No Arthritis,Day2, replicate 1 [D2_S42_R1]


title: Whole blood, A2, No Arthritis,Day2, replicate 2 [D2_S41_R2]


title: Whole blood, A2, No Arthritis,Day2, replicate 1 [D2_S41_R1]


title: Whole blood, A6, No Arthritis,Day2, replicate 2 [D2_S27_R2]


title: Whole blood, B7, No Arthritis,Day2, replicate 1 [D2_S28_R1]


title: Whole blood, A6, No Arthritis,Day2, replicate 1 [D2_S27_R1]


title: Whole blood, B7, No Arthritis,Day2, replicate 2 [D2_S28_R2]


title: T2DM-PBMC1

data_processing:
Raw data of fastq format were firstly processed through in-house perl scripts.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2 software to obtain mapped reads.
FeatureCounts was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: Raw_counts.txt

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was extracted from the PBMCs using TRIzol® Reagent according the manufacturer’s instructions (Magen). RNA samples were detected based on the A260/A280 absorbance ratio with a Nanodrop ND-2000 system (Thermo Scientific, USA), and the RIN of RNA was determined by an Agilent Bioanalyzer 4150 system (Agilent Technologies, CA, USA). Only qualified samples will be used for library construction.
Paired-end libraries were prepared using a ABclonal mRNA-seq Lib Prep Kit following the manufacturer’s instructions..The synthesized double stranded cDNA fragments were then adapter-ligated for preparation of the paired-end library. Adaptor-ligated cDNA were used for PCR amplification. PCR products were purified (AMPure XP system) and library quality was assessed on an Agilent Bioanalyzer 4150 system.

value: Peripheral Blood Mononuclear Cells

tag: group

value: type 2 diabetic mice


title: WT-PBMC3

value: age-matched control mice


title: T2DM-PBMC3


title: WT-PBMC1


title: T2DM-PBMC2


title: T2DM-PBMC4


title: DM_H3K27ac

city: Beijing

first: Baoling

last: Bai

state: Beijing

address: Yabao Road2, Chaoyang District

institute: Capital institute of pediatrics

library_source: genomic

data_processing:
BclTofastq v1.8.4 software was uesd to process Illumina output data.
ChIP-seq reads were aligned to the Mus musculus reference genome (UCSC, mm9) using Bowtie 2.
Peak callings were further analyzed by MACS (Model–based Analysis for ChIP-Seq; https://github.com/taoliu/MACS), with the significance cut-off q-value ＜=0.01.
Assembly: mm9
Supplementary files format and content: excel files include FPKM values for each samples

molecule: genomic DNA

source_name: brain

extract_protocol:
Brain tissue sample were fixed in 1% formaldehyde for 10 minutes at room temperature. After quenching and cell lysis, chromatin was sonicated by Bioruptor Pico (Diagenode, Germany) ultrasonicator.
NEBNext Ultra DNA Library Prep Kit was uesed for ChIP-seq library construction.10ng of DNA was ussed as starting material for Input and IP samples. Libraries were validated by the 2100 Bioanalyzer High Sensitivity DNA chip.

value: brain

value: Neural cells

tag: chip antibody

value: H3K27ac (ab4729, Abcam)


title: DM_1

data_processing:
Illumina Casava1.7 software uesd for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity and low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.2 parameters
Reads per FPKM were caculated using a protocol from Chepelev et al. Nucleic Acids Reasearch,2009.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each samples

extract_protocol:
Total RNA was extracted from frozen tissue samples at -80°C using TRIzol® (15596–026, Invitrogen).
NEBNext® Ultra™ RNA Library Prep Kit was uesed for RNA-seq library construction.

value: DM induced NTDs


title: DM_3


title: DM_2


title: control_H3K27ac


title: Fob from infected FoxP3-Cre-BCL6fl/fl [F-3]

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

data_processing:
FastQC and MultiQC were used for raw reads quality control, and fastp was used to remove adapter sequences and quality trim reads
Trimmed reads were aligned to the mouse genome assembly (mm39, annotation V109).
gene read count was quantified using STAR, The gene counts for each sample were transformed and normalized using the variance-stabilizing transformation method implemented in the Bioconductor package DESeq2
Linear regression models within DESeq2 were used to identify differentially expressed genes between case vs. control sample sets. Final values for differential expression are log2 fold change ≥ 1 or ≤ -1 with false discovery rate < 0.05 (FDR, Benjamini-Hochberg) as significant.
Assembly: mm39, annotation, V109
Supplementary files format and content: tab-delimited excel file include base mean values for each sample

source_name: Fob from infected FoxP3-Cre-BCL6fl/fl

extract_protocol:
RNA was isolated via Rneasy kit.
Stranded mRNA libaries were constructed by the University of Missouri Genomics Core facility using a poly A enrichment method

value: FoB

value: B. melitensis

value: Day 14


title: control_3

value: WT


title: control_1


title: control_2


title: Fob from infected FoxP3-Cre-BCL6fl/fl [F-2]


title: Embryonic stem cell, 5fC mapping by CLED-seq, rep2

city: 北京

first: li

middle: gao

last: jie

state: Alabama

address: Building 104, Yard 1, Beichen West Road, Chaoyang District, Beijing

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: Sequencing data for 5fC from embryonic stem cells by CLED-seq

data_processing:
cutadapt v4.1, -e 0.3 , FastQC v0.11.9
bismark v0.23.1, bowtie2 v2.4.5, -N 1 -p 12
samtools sort -n v1.7
deduplicate_bismark --paired --bam  v0.24.0
bismark_methylation_extractor -P --CX --comprehensive --no_overlap --bedGraph --counts --buffer_size 30G --report --gzip --cytosine_report --genome_folder v0.24.0
Assembly: mm10
Supplementary files format and content: Methylation information file containing methylation content for each unit point

source_name: embryonic

extract_protocol:
The genomic DNA of mESCs was extracted using E.Z.N.A tissue DNA kit (Omega Bio-Tek Inc., Norcross, GA, USA) according to the manufacturer’s recommended procedure. 10 μg of genomic DNA was used for the construction of sequencing library
10 μg of genomic DNA from mESCs was fragmented with a JY92-II N Ultrasonic Homogenizer to obtain 300–500 bp DNA fragments. The fragmented DNA was reacted with 5 μM biotin-ONH2 and 100 mM MES buffer (pH 5.0) at 37°C for 4 h. The resulting DNA was purified by ethanol precipitation to remove excess biotin-ONH2. The biotin-labeled DNA fragments was isolated by using PuriMag G-streptavidin magnetic beads  according to the manufacturer’s recommended procedure. The mixture (50 μL) of enriched 5fC-containing DNA fragments and spike-ins were end-repaired and dA-tailed using Hieff NGS Fast-Pace End Repair/dA-Tailing Module kit according to the manufacturer’s recommended protocol. As for the adapter ligation, 60 μL of end-repaired DNA and 5 μL of phosphorylated adapter (10 μM) were ligated using Hieff NGS Ultima DNA Ligation Module kit at 20°C for 6 h. The DNA was washed three times with water to remove the excess adaptor. Then 2 μL of proteinase K was added and incubated at 55°C for 30 min to release 5fC-containing DNA fragments. The resulting DNA was denatured by heating at 95°C for 10 min in 10% DMSO (v/v) solution and chilling in ice water. The deamination reaction was conducted in a 20-µL reaction mixture containing 20 ng DNA, 20 mM MES (pH 7.5), and 20 µM of A3A. The resulting DNA was subjected to PCR amplification by Q5U Hot Start High-Fidelity DNA polymerase. The PCR reaction (50 μL) included 10 µL of deaminated DNA, 10 μL of 5× Q5U reaction buffer, 1 µL of 10 mM dNTPs, 1 µL of Q5U Hot Start High-Fidelity DNA polymerase, 2.5 μL of pre-i7 primer (10 μM), 2.5 μL of pre-i5 primer (10 μM), and 23 μL of H2O. The amplification program started at 98°C for 30 s, followed by 10 cycles of 98°C for 10 s, 63°C for 1 min, 68°C for 1 min, and ended with 72°C for 10 min. PCR products were sequentially purified using 0.8× KAPA Pure beads followed by the second round of PCR amplification. The PCR reaction (50 µL) included 20 µL of purified DNA, 10 µL of 5× Q5 reaction buffer, 1 µL of 10 mM dNTPs, 1 µL of Q5 High-Fidelity DNA polymerase, 2.5 μL of i7 primer (10 μM), 2.5 μL of i5 primer (10 μM), and 13 μL of H2O. The amplification program started at 98°C for 30 s, followed by 8 cycles at 98°C for 30 s, 65°C for 1 min, 72°C for 2 min, and ended with 1 cycle at 72°C for 10 min. The PCR products were purified using 0.7× KAPA Pure beads. Library quality was assessed on the Agilent Bioanalyzer 2100 system. The library was sequenced on an Illumina platform and 150-bp paired-end reads were generated.

value: embryonic

value: embryonic stem cells


title: Fob from infected BCL6fl/fl [W-5]

source_name: Fob from infected BCL6fl/fl


title: Fob from infected BCL6fl/fl [W-3]


title: Fob from infected BCL6fl/fl [W-4]


title: Fob from infected BCL6fl/fl [W-2]


title: Fob from infected BCL6fl/fl [W-1]


title: WT-PBMC4


title: Embryonic stem cell, 5fC mapping by CLED-seq, rep1


title: Fob from infected FoxP3-Cre-BCL6fl/fl [F-4]


title: Fob from naïve FoxP3-Cre-BCL6fl/fl [FU-3]

source_name: Fob from naïve FoxP3-Cre-BCL6fl/fl

value: Naïve

value: Day 0


title: Input


title: Fob from infected FoxP3-Cre-BCL6fl/fl [F-1]


title: WT-PBMC2


title: Fob from Naïve BCL6fl/fl [WU-3]

source_name: Fob from Naïve BCL6fl/fl


title: BV2, LPS, rep3

city: Singapore

first: Jessica

middle: R

last: Gaunt

address: 11 Mandalay Road

department: LKC Medicine

country: Singapore

institute: Nanyang Technological University

data_processing:
Pre-processing of RNAseq data was performed on the Gekko high‐performance computing cluster at Nanyang Technological University. Illumina adapters were trimmed and reads with quality score <15 or length <30 bp were removed using Trimmomatic (v0.39; Bolger et al, 2014). Alignment and quantification of paired‐end reads to the mouse genome were performed using STAR (v2.7.1a; Dobin et al, 2013) and HTseq (v0.11.2; Anders et al, 2015).
Downstream analyses were conducted in R 4.2.1 (R Core Team, 2022). First, the dataset was filtered to genes with minimum 1 log2 count per million (CPM) in at least 3 samples (N=11,404).
Differential expression analyses were conducted on TMM-normalised counts using the quasi-likelihood method with robust dispersion estimation in edgeR comparing DCN, EC and LPS conditions to D-PBS control, and comparing paired samples stimulated with EC and DCN homogenates from the same mouse brain (Robinson et al, 2010; Zhou et al, 2014; Lun et al, 2016). Thresholds for differentially expressed genes were false discovery rate (FDR) < 10% and LFC > ±1.
Assembly: GRCm39, annotation vM28
Supplementary files format and content: Raw count files generated by HTseq with Ensembl gene IDs

molecule: polyA RNA

growth_protocol: BV2 microglial cell lines were maintained in DMEM (Nacalai Tesque) containing 10% fetal bovine serum (Gibco) and 1% penicillin-streptomycin (Gibco). One day before treatment, 5x104 cells were seeded per well in a 24-well plate.

extract_protocol:
Cells were washed with ice-cold D-PBS, and total RNA was harvested using Arcturus® PicoPure® RNA Isolation Kit (Applied Biosystems).
PolyA-enriched libraries were prepared for RNAseq and sequenced on an Illumina NovaSeq 6000 platform by NovogeneAIT to obtain 20M 150bp paired-end reads per sample. All samples had RNA integrity number (RIN) > 9.

treatment_protocol: Cells were treated with either 50 μg EC or DCN protein extracts homogenised in D-PBS from N=8 wildtype male mice aged 12-13 months, an equivalent volume of D-PBS as negative control, or 10 ng/ml of lipopolysaccharide (Sigma Aldrich) as a positive control for induction of inflammatory gene expression. Cells were then incubated for 4 hours at 37°C.

value: microglia

value: LPS

value: 4 hours


title: Fob from naïve FoxP3-Cre-BCL6fl/fl [FU-1]


title: BV2, EC, rep2

value: EC homogenate


title: BV2, DCN, rep3

value: DCN homogenate


title: BV2, EC, rep1


title: Fob from Naïve BCL6fl/fl [WU-4]


title: Fob from naïve FoxP3-Cre-BCL6fl/fl [FU-2]


title: BV2, D-PBS, rep2

value: D-PBS


title: mm_input_spreb_WT.2

city: Chicago

first: Mark

last: Maienschein-Cline

address: 900 S Ashland Ave, Rm 1058, M/C 937

department: Research Resources Center

institute: University of Illinois at Chicago

description: Primary flow purified WT small pre-B cells from mouse bone marrow

data_processing:
Genome alignment and peak calling, for processed files 1 and 2: The sequences were aligned to the mm9 reference genome (National Center for Biotechnology Information build mm9_NCBI_build_37.1) with BWA MEM and PCR duplicates were removed using Picard MarkDuplicates (Version 1.107). Peaks for ChIP-seq samples were called using MACS2. Normalized bedgraph tracks were generated using the SPMR flag and converted to bigwig using the UCSC tool bedGraphToBigWig. Peaks with a score >5 were retained.
For processed files 3 to 6: Quantification steps were carried out separately for each ChIP-seq mark; we did not perform these steps on the ATPneg genotype samples. First, peak calls from replicates in both WT and Brwd1-/- groups were merged using bedtools merge. Peak and input enrichment counts in merged peaks was computed using featureCounts; replicate inputs were combined prior to quantification. Input counts were subtracted from peak counts after adjusting for differences in sequencing depth for each library. Normalized enrichment was computed using edgeR as CPM with TMM normalization factors.
Assembly: mm9
Supplementary files format and content: BED file of peak calls from Macs2 with Q<1e-5
Supplementary files format and content: BigWig file of normalized enrichment from Macs2, normalized with --SPMR (signal per million reads)
Supplementary files format and content: BED file of merged peak calls over all ChIP samples of the same mark, merged using bedtools merge
Supplementary files format and content: Read counts per merged peak for all ChIP samples of the same mark plus input sample(s), quantified using featureCounts. Peak IDs match the coordinates provided in merged bed files (processed data file 3). Input replicates were combined prior to quantification: mm_input_spreb_BRWD1KO is the sum of mm_input_spreb_BRWD1KO.1 and mm_input_spreb_BRWD1KO.2, and mm_input_spreb_WT is the sum of mm_input_spreb_WT.1 and mm_input_spreb_WT.2. mm_input_spreb.2 is the counts from previously-submitted input sample GSM2753125.
Supplementary files format and content: Read counts per merged peaks for all ChIP samples of the same mark, after subtracting input counts from the matched input sample. Input counts were up- or down-sampled stochastically to account for differences in the total number of alignments between input and ChIP samples.
Supplementary files format and content: Normalized counts per merged peak for all ChIP samples of the same mark, units of counts per million and including TMM normalization with edgeR.

growth_protocol: No cultured cells were used. All cells used are primary small pre-B cells isolated from bone marrow of WT or BRWD knock out mice.

extract_protocol:
Chromatin from flow-sorted small pre-B cells (2x10^6) from WT and Brwd1-/- mice, and WT small pre-cells treated with Oligomycin A, were used for each ChIP experiment with  anti-H3K4me1 (07-436, Millipore-Sigma), anti-H3K27Ac (07-360, Millipore-Sigma), anti-CTCF (Millipore Sigma, 07-729) , anti-RAD21 (Abcam, ab154769), anti-SMC3 (Abcam, ab9263), anti-NIPBL (Proteintech, 18792-1-AP) and anti-WAPL (Proteintech, 16370-1-AP) antibodies.
Libraries were prepered by University of Chicago Core facility using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.

treatment_protocol: For ATPneg (ATP depleted) sampleas small pre-B cells were isolated from WT mouse bone marrow and cultured in  presence of 126nM of Oligomycin A for 2hrs before performimg ChIP sample preparation

tag: matched input_for_chip_samples


title: mm_input_spreb_WT.1


title: BV2, D-PBS, rep1


title: Fob from Naïve BCL6fl/fl [WU-2]


title: Fob from Naïve BCL6fl/fl [WU-1]


title: mm_chip_spreb_WAPL-WT.2

value: WAPL


title: BV2, LPS, rep2


title: BV2, DCN, rep2


title: BV2, LPS, rep1


title: BV2, DCN, rep1


title: BV2, D-PBS, rep3


title: mm_chip_spreb_SMC3-BRWD1KO.1

description: Primary flow purified small pre-B cells from BRWD1 knock-out mouse bone marrow


title: mm_chip_spreb_SMC3-WT.1


title: mm_chip_spreb_SMC3-BRWD1KO.2


title: mm_chip_spreb_SMC3-ATPneg.2

description: Primary flow purified small pre-B cells from WT mouse bone marrow treated with ologomycin for 2hrs

value: ATPneg


title: mm_input_spreb_BRWD1KO.2


title: BV2, EC, rep3


title: mm_chip_spreb_WAPL-BRWD1KO.1


title: mm_chip_spreb_WAPL-BRWD1KO.2


title: mm_chip_spreb_RAD21-WT.2


title: mm_chip_spreb_WAPL-ATPneg.1


title: mm_chip_spreb_WAPL-WT.1


title: mm_chip_spreb_RAD21-ATPneg.2


title: mm_chip_spreb_RAD21-WT.1


title: mm_chip_spreb_RAD21-BRWD1KO.2


title: mm_input_spreb_BRWD1KO.1


title: mm_chip_spreb_h3k27ac_brwd1ko.2


title: mm_chip_spreb_NIPBL-WT.2

value: NIPBL


title: mm_chip_spreb_h3k27ac_brwd1ko.1


title: mm_chip_spreb_CTCF-WT.2

value: CTCF


title: mm_chip_spreb_RAD21-ATPneg.1


title: mm_chip_spreb_CTCF-WT.1


title: mm_chip_spreb_SMC3-WT.2


title: mm_chip_spreb_RAD21-BRWD1KO.1


title: mm_chip_spreb_NIPBL-BRWD1KO.2


title: mm_chip_spreb_NIPBL-BRWD1KO.1


title: mm_chip_spreb_SMC3-ATPneg.1


title: mm_chip_spreb_NIPBL-ATPneg.1


title: mm_chip_spreb_h3k4me1_brwd1ko.1


title: mm_chip_spreb_h3k27ac.2


title: wt colonic organoid +TNF, H3K27me3

city: Maebashi

first: Naoko

last: Hattori

state: Gunma

address: 3-39-15 Showa-mach

department: Institute for Molecular and Cellular Regulation

country: Japan

institute: Gunma University

data_processing:
Fastp (version 0.20.0) was used for sequencing QC and adapter trimming.
All reads were aligned to the mouse genome GRCm38/mm10 using bwa-mem (version 2.2) with default parameters.
The resultant SAM file was converted into a BAM file, duplicates were removed using SAMtools (version 1.11), and blacklisted regions were filtered.
Peak calling was performed with the input control using MACS2 (version 2.1.0) with default parameters
Assembly: GRCm38
Supplementary files format and content: Peak files in bed format

source_name: colon

extract_protocol:
Organoids were cross-linked with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a ultrasonicator, and histone-DNA complexes were isolated with antibody. 5 ng of DNA was used as starting material for input and ip samples.
Sequencing library was prepared with GenNext NGS Library Prep Kit (Toyobo, LPK-101) from 5 ng for a final sequencing depth of 40, 40, and 60 million reads per input, H3K4me3, and H3K27me3, respectively.

treatment_protocol: wt colonic organoids were treated with TNFa (40 ng/ml) for 3 wks.

value: colon

value: organoid

value: epithelial cells


title: mm_chip_spreb_h3k4me1_brwd1ko.2

value: WT


title: mm_chip_spreb_h3k4me1.2


title: mm_chip_spreb_CTCF-BRWD1KO.2


title: mm_chip_spreb_h3k4me1.1


title: mm_chip_spreb_NIPBL-ATPneg.2


title: mm_chip_spreb_CTCF-BRWD1KO.1


title: CRISPRko-TFome-withBATF3-IL7R-Low-D2

city: Durham

first: Sean

last: McCutcheon

state: NC

address: 101 Science Drive, CIEMAS Rm. 2323

department: Biomedical Engineering

institute: Duke University

description: human CD8 T cells, CRISPRko TFome with BATF3, IL7R low bin

data_processing:
FASTQ files were aligned to custom indexes for each gRNA library (generated from the bowtie2-build function) using Bowtie.
Counts for each gRNA were extracted and used for further analysis in R.
Individual gRNA enrichment was determined using DESeq2 to compare gRNA counts between low and high sorted populations for each screen.
Assembly: hg38
Supplementary files format and content: Comma-separated files containing gRNA counts, grouped by individual screens

source_name: CD8 T cells

extract_protocol:
genomic DNA was harvested using Qiagen's Dneasy Blood and Tissue Kit
gRNA libraries were amplified from genomic DNA. All genomic DNA was split across 100 μL PCR reactions (25 cycles at 98C for 10s, 60C for 30s, and 72C for 20s) with Q5 2X Master Mix and up to 1 μg of genomic DNA per reaction. PCRs were pooled together for each sample and purified using double-sided SPRI selection at 0.6x and 1.8x. Libraries were run on a High Sensitivity D1000 tape (Agilent) to confirm amplicon size and quantified using Qubit’s dsDNA High Sensitivity assay.
Standard gRNA library construction

value: CD8 T cells

value: BATF3 overexpression + CRISPRko TFome gRNA library

value: CD3/CD28 dynabead activation + lentiviral transduction + electroporation


title: mm_chip_spreb_h3k27ac.1


title: SpreB-Brwd1KO.2

data_processing:
Hi-C processing was performed using Juicer 6 with default values, aligning to reference genome mm9; MboI fragment sizes were downloaded for mm9 from https://aryeelab.github.io/hichipper/RestrictionFragmentFiles/. Analysis was performed using the juicer.sh pipeline script.
Assembly: mm9
Supplementary files format and content: .hic file from JUICER

extract_protocol:
In situ Hi-C was performed as previously described (Rao Et. al. Cell 2014). Briefly, WT and Brwd1-/- small pre-B and WT immature B cells (5x10^6 for each stage) were crosslinked with 1% formaldehyde following a wash with ice cold PBS. Membranes were lysed to keep nuclei intact followed by restriction digestion with 100U of MboI (NEB R0147). The DNA ends were marked with biotin, ligated proximally and crosslinks were reversed. DNA shearing and size selection were then performed for fragments 300-500 bp. The amount of DNA was quantified with the Qubit dsDNA High Sensitivity Assay (Life technologies, Q32854), and biotin pull down was done to prepare the final in-situ Hi-C libraries (in duplicate).
Libraries were prepered  using Immumina Library preparation kit and sequenced on the Illumina NovaSeq 6000.

treatment_protocol: No treatment was performed


title: mm_chip_spreb_NIPBL-WT.1


title: wt colonic organoid, H3K4me3

value: H3K4me3 (#05-745R, Millipore)


title: ImmatureB.2

source_name: Immuture B cell

value: Immuture B cell


title: CRISPRa-TF-CCR7-High-D3

description: human CD8 T cells, CRISPRa TF, CCR7 high bin

value: CRISPRa TF gRNA library

value: CD3/CD28 dynabead activation + lentiviral transduction


title: CRISPRko-TFome-withBATF3-IL7R-High-D2

description: human CD8 T cells, CRISPRko TFome with BATF3, IL7R high bin


title: CRISPRa-TF-CCR7-High-D2


title: CRISPRko-TFome-withBATF3-IL7R-High-D1


title: 12-week TH Grin2a WT snRNA-seq Sample1

city: Cambridge

first: Ally

last: Nicolella

state: MA

address: 75 Ames St

department: Stanley Center for Psychiatric Research

institute: Broad Institute

description:
10x Genomics
grin2a_12wTH_snRNAseq_meta.csv

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, including introns
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Thalamus

extract_protocol:
Brain tissue dissection and nuclei extraction were performed on the same day to avoid freeze-thaw cycles which would result in poor quality nuclei. A gentle, detergent-based dissociation was used to extract the nuclei, according to a previously published protocol available at protocols. io (https://www.protocols.io/view/frozen-tissue-nuclei-extraction-bbseinbe).
Extracted nuclei were loaded into the 10x Chromium V3.1 system (10x Genomics) and library preparation was performed according to the manufacturer’s protocol.
snRNA-seq

value: Thalamus

tag: age


title: wt colonic organoid +TNF, H3K4me3


title: CRISPRa-TF-CCR7-High-D1


title: 12-week TH Grin2a -/- snRNA-seq Sample4

value: Grin2a -/-


title: 12-week TH Grin2a -/- snRNA-seq Sample2


title: wt colonic organoid +TNF, Input

value: Input


title: CRISPRa-TF-CCR7-Low-D2

description: human CD8 T cells, CRISPRa TF, CCR7 low bin


title: CRISPRa-TF-CCR7-Low-D1


title: CRISPRi-TF-CCR7-High-D2

description: human CD8 T cells, CRISPRi TF,  CCR7 high bin

value: CRISPRi TF gRNA library


title: 12-week TH Grin2a +/- snRNA-seq Sample3

value: Grin2a +/-


title: CRISPRko-TFome-withBATF3-IL7R-Low-D1


title: SpreB-WT.2


title: CRISPRko-TFome-noBATF3-IL7R-High-D1

description: human CD8 T cells, CRISPRko TFome without BATF3, IL7R high bin

value: CRISPRko TFome gRNA library


title: wt colonic organoid, Input

value: colon


title: CRISPRko-TFome-noBATF3-IL7R-Low-D1

description: human CD8 T cells, CRISPRko TFome without BATF3, IL7R low bin


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-High-R3

description: Jurkats, CRISPRa VP64-dSaCas9-VP64, IL2RA high bin

source_name: Jurkats

value: Jurkats

value: Immortalized T cells

value: CRISPRa VP64-dSaCas9-VP64 + IL2RA gRNA library

value: lentiviral transduction


title: 12-week TH Grin2a +/- snRNA-seq Sample1


title: 12-week TH Grin2a WT snRNA-seq Sample2

value: WT


title: CRISPRi-TF-CCR7-Low-D1

description: human CD8 T cells, CRISPRi TF, CCR7 low bin

value: CD8 T cells


title: wt colonic organoid, H3K27me3

value: organoid

value: epithelial cells


title: 12-week ST Grin2a WT snRNA-seq Sample3

description:
10x Genomics
grin2a_12wST_snRNAseq_meta.csv

source_name: Striatum

value: Striatum


title: 12-week TH Grin2a -/- snRNA-seq Sample3


title: 12-week TH Grin2a +/- snRNA-seq Sample4


title: CRISPRko-TFome-noBATF3-IL7R-High-D2

value: CD3/CD28 dynabead activation + lentiviral transduction


title: 12-week TH Grin2a WT snRNA-seq Sample3

value: Thalamus


title: 12-week ST Grin2a WT snRNA-seq Sample2


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-High-R1


title: CRISPRko-TFome-noBATF3-IL7R-Low-D2


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-Low-R3

description: Jurkats,  CRISPRa VP64-dSaCas9-VP64, IL2RA low bin


title: 12-week ST Grin2a WT snRNA-seq Sample1


title: CRISPRi-TF-CCR7-High-D1


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-Low-R2


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-Low-R1


title: 12-week ST Grin2a -/- snRNA-seq Sample4

value: Grin2a -/-


title: 12-week ST Grin2a -/- snRNA-seq Sample3


title: CRISPRi-TF-CCR7-Low-D2


title: 12-week TH Grin2a +/- snRNA-seq Sample2


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-High-R3

description: Jurkats, CRISPRa dSaCas9-VP64, IL2RA high bin

value: CRISPRa dSaCas9-VP64 + IL2RA gRNA library


title: CRISPRa-TF-CCR7-Low-D3

value: CRISPRa TF gRNA library


title: 12-week ST Grin2a -/- snRNA-seq Sample1


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-High-R2


title: 12-week TH Grin2a -/- snRNA-seq Sample1


title: 12-week ST Grin2a WT snRNA-seq Sample4


title: CRISPRa-VP64-dSaCas9-VP64-tiling-IL2RA-High-R2


title: 12-week ST Grin2a +/- snRNA-seq Sample4

value: Grin2a +/-


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-Low-R1

description: Jurkats,  CRISPRa dSaCas9-VP64, IL2RA low bin


title: 12-week ST Grin2a -/- snRNA-seq Sample2


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-High-R3

description: human CD8 T cells, CRISPRi, B2M high bin

value: CRISPRi B2M gRNA library


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-High-R1


title: 12-week ST Grin2a +/- snRNA-seq Sample3


title: 12-week SSC Grin2a WT snRNA-seq Sample4

description:
10x Genomics
grin2a_12wSSC_snRNAseq_meta.csv

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: 12-week SSC Grin2a WT snRNA-seq Sample2


title: mm_chip_spreb_WAPL-ATPneg.2

description: Primary flow purified small pre-B cells from WT mouse bone marrow treated with ologomycin for 2hrs

value: ATPneg

value: WAPL


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-Low-R3

value: Jurkats

value: Immortalized T cells


title: CRISPRa-dSaCas9-VP64-tiling-IL2RA-Low-R2

value: lentiviral transduction


title: 12-week ST Grin2a +/- snRNA-seq Sample2


title: 12-week ST Grin2a +/- snRNA-seq Sample1


title: 12-week SSC Grin2a -/- snRNA-seq Sample3


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-Low-R2

description: human CD8 T cells, CRISPRi, B2M low bin

value: CD8 T cells


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-High-R2


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-Low-R3

description: human CD8 T cells, CRISPRi, B2M low bin


title: 12-week SSC Grin2a WT snRNA-seq Sample3

value: WT


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-High-R1


title: 12-week SSC Grin2a -/- snRNA-seq Sample1


title: CRISPRi-dSaCas9-KRAB-tiling-CD2-Low-R2

description: human CD8 T cells, CRISPRi, CD2 low bin

value: CRISPRi CD2 gRNA library


title: CRISPRi-dSaCas9-KRAB-tiling-CD2-Low-R3

description: human CD8 T cells, CRISPRi, CD2 low bin


title: 12-week SSC Grin2a +/- snRNA-seq Sample4


title: 12-week SSC Grin2a WT snRNA-seq Sample1


title: 12-week SSC Grin2a -/- snRNA-seq Sample4


title: 12-week SSC Grin2a -/- snRNA-seq Sample2


title: CRISPRi-dSaCas9-KRAB-tiling-B2M-Low-R1

description: human CD8 T cells, CRISPRi, B2M low bin


title: 12-week SSC Grin2a +/- snRNA-seq Sample1


title: CRISPRi-dSaCas9-KRAB-tiling-CD2-High-R3

description: human CD8 T cells, CRISPRi, CD2 high bin


title: HS360-Day20-P200-rep4 [33-sc2-D20-P200-B]

type: genomic

city: Oslo

first: Ragnhild

last: Eskeland

address: Sognsvannsveien 9

department: Institute of Basic Medical Sciences

country: Norway

institute: University of Oslo

description: Day 20", "male", "maturated NPCs", "paracetamol", "P200

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip v-1-0_B3 using standard Illumina protocol

scan_protocol: Arrays were imaged using Illumina iScan System using standard recommended Illumina scanner settings

data_processing:
R software, Minfi package v 1.36.0m Background correction was performed using NOOB method and β values were normalized using functional normalization. Probes with detection p values >0.01 (n = 12538) and cross-reactive probes (n = 42844) were removed, resulting in a final data set consisting of 810477
Normalized Average Beta (functional normalization)
Unmethylated and methylated signal intensities
"rgSet_paracetamol.Rdata". Minfi object with all data except SNP probes, removed due to data sensitivity.

label: Cy3, Cy5

source_name: HS360, day 20, past stage III maturation, exposed to 200μM paracetamol

label_protocol: Standard Illumina Protocol

growth_protocol: Human embryonic stem cells HS360 (Karolinska Institutet, Sweden, RRID:CVCL_C202) were maintained in Essential 8™ Medium, in feeder-free conditions on Geltrex™ Matrix solution pre-coated culture plates.Culture media were replaced daily and cells were routinely passaged at 75-85% confluency using 0.5 mM EDTA in ratios between 1:3 to 1:6.

extract_protocol: Genomic DNA was extracted from cultured cells using Norgen RNA/DNA purification kit according to the manufacturer's instructions

treatment_protocol: In brief, at Day 0 HS360 hESCs grown in E8 were collected with Accutase and seeded in Geltrex precoated 12 well dishes. Single-cell suspensions were transferred to E8 medium containing 10 µM Rock inhibitor and at Day 1, the culture medium was switched to neural induction medium (NIM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2). During days 2 to 6, media were changed daily and the LSX combo (LDN-193189, SB431542, XAV939) was added fresh to NIM. Cells were collected at Day 7 for passaging into the self patterning phase, counted and seeded on 12 well plates sequentially precoated with polyornithine (PO), fibronectin (F) and Geltrex. At Day 7 the Stage II neural self-patterning (NSPM) medium (Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 1% B27) was supplemented with 10 µM Rock inhibitor. Culture medium was changed daily till day 13. At Day 13, cells were collected for passaging into the maturation phase, counted and seeded on precoated PO+F+Geltrex 12 well dishes and Stage III Neural maturation medium (NMM; Advanced DMEM/F12, 1% GlutaMAX, 1% Penicillin/Streptomycin, 1% N2, 0.5% B27, 10 ng/ml FGF2, 10 ng/ml EGF) was changed daily till Day 20, where cells were collected. For cells that were exposed to either 100 or 200 μM paracetamol, fresh media with paracetamol was added every day from Day 1 until collection day (Day 7 or Day 20)

tag: gender

value: male

value: maturated NPCs

value: Day 20 200 μM paracetamol


title: HS360-Day20-P200-rep3 [32-sc1-D20-P200-B]


title: HS360-Day20-P200-rep2 [17-sc2-D20-P200-A]


title: HS360-Day20-P200-rep1 [16-sc1-D20-P200-A]


title: CRISPRi-dSaCas9-KRAB-tiling-CD2-High-R2

value: CD3/CD28 dynabead activation + lentiviral transduction


title: 12-week PFC Grin2a WT snRNA-seq Sample2

description:
10x Genomics
grin2a_12wPFC_snRNAseq_meta.csv

source_name: Prefrontal Cortex

tag: tissue

value: Prefrontal Cortex


title: 12-week PFC Grin2a WT snRNA-seq Sample1


title: 12-week SSC Grin2a +/- snRNA-seq Sample3


title: 12-week PFC Grin2a WT snRNA-seq Sample4


title: 12-week PFC Grin2a WT snRNA-seq Sample3


title: 12-week SSC Grin2a +/- snRNA-seq Sample2


title: 12-week PFC Grin2a -/- snRNA-seq Sample5

value: Grin2a -/-


title: 12-week PFC Grin2a -/- snRNA-seq Sample3


title: 12-week PFC Grin2a -/- snRNA-seq Sample4


title: HS360-Day20-P100-rep3 [30-sc1-D20-P100-B]

description: Day 20", "male", "maturated NPCs", "paracetamol", "P100

source_name: HS360, day 20, past stage III maturation, exposed to 100μM paracetamol

value: Day 20 100 μM paracetamol


title: HS360-Day20-P100-rep6 [190-D20-P100-B]


title: HS360-Day20-P100-rep4 [31-sc2-D20-P100-B]


title: HS360-Day20-P100-rep5 [189-D20-P100-A]


title: 12-week PFC Grin2a -/- snRNA-seq Sample2


title: HS360-Day20-P100-rep2 [15-sc2-D20-P100-A]


title: 12-week PFC Grin2a +/- snRNA-seq Sample5

value: Grin2a +/-


title: HS360-Day20-rep5 [186-D20-Ctr-A]

description: Day 20", "male", "maturated NPCs", "control

source_name: HS360, day 20, past stage III maturation

value: Day 20 control


title: HS360-Day20-P100-rep1 [14-sc1-D20-P100-A]


title: 4-week PFC Grin2a WT snRNA-seq Sample2

description:
10x Genomics
grin2a_P28PFC_snRNAseq_meta.csv


title: 12-week PFC Grin2a -/- snRNA-seq Sample1


title: HS360-Day20-rep6 [187-D20-Ctr-B]


title: 4-week PFC Grin2a -/- snRNA-seq Sample2


title: 4-week PFC Grin2a WT snRNA-seq Sample1


title: 12-week PFC Grin2a +/- snRNA-seq Sample3


title: HS360-Day13-rep1 [10-sc1-D13-ctrl-A]

description: Day 13", "male", "self-patterning", "NPCs", "control

source_name: HS360, day 13, past stage II self-patterning

value: self-patterning NPCs

value: Day 13 control


title: 12-week PFC Grin2a +/- snRNA-seq Sample4


title: HS360-Day20-rep4 [29-sc2-D20-ctrl-B]


title: HS360-Day13-rep2 [11-sc2-D13-ctrl-A]


title: 12-week PFC Grin2a +/- snRNA-seq Sample2


title: HS360-Day20-rep3 [28-sc1-D20-ctrl-B]


title: HS360-Day7-P200-rep4 [24-sc2-D7-P200-B]

description: Day 7", "male", "neural rosettes", "neural induction", "paracetamol", "P200

source_name: HS360, day 7, past stage I neural induction, exposed to 200μM paracetamol

value: neural rosettes

value: Day 7 200 μM paracetamol


title: 4-week PFC Grin2a +/- snRNA-seq Sample3


title: HS360-Day20-rep1 [12-sc1-D20-ctrl-A]


title: HS360-Day20-rep2 [13-sc2-D20-ctrl-A]


title: HS360-Day7-P100-rep6 [4-d7-p100-2]

description: Day 7", "male", "neural rosettes", "neural induction", "paracetamol", "P100

source_name: HS360, day 7, past stage I neural induction, exposed to 100μM paracetamol

value: Day 7 100 μM paracetamol


title: HS360-Day7-P200-rep1 [8-sc1-D7-P200-A]


title: 12-week PFC Grin2a +/- snRNA-seq Sample1


title: HS360-Day13-rep3 [25-sc1-D13-ctrl-B]


title: 4-week PFC Grin2a WT snRNA-seq Sample3


title: HS360-Day13-rep4 [26-sc2-D13-ctrl-B]


title: 4-week PFC Grin2a -/- snRNA-seq Sample3


title: HS360-Day7-P100-rep5 [3-d7-p100-1]


title: 12-week HP Grin2a WT snRNA-seq Sample3

description:
10x Genomics
grin2a_12wHP_snRNAseq_meta.csv

source_name: Hippocampus

value: Hippocampus


title: HS360-Day7-P100-rep1 [6-sc1-D7-P100-A]


title: HS360-Day7-P200-rep5 [7-d7-p200]


title: HS360-Day7-P200-rep3 [23-sc1-D7-P200-B]


title: 12-week HP Grin2a -/- snRNA-seq Sample5


title: 12-week HP Grin2a -/- snRNA-seq Sample4


title: 4-week PFC Grin2a -/- snRNA-seq Sample1


title: 4-week PFC Grin2a +/- snRNA-seq Sample2


title: HS360-Day7-P200-rep2 [9-sc2-D7-P200-A]


title: 12-week HP Grin2a WT snRNA-seq Sample2

value: WT


title: 12-week HP Grin2a WT snRNA-seq Sample1


title: 12-week HP Grin2a -/- snRNA-seq Sample2


title: 4-week PFC Grin2a +/- snRNA-seq Sample1


title: 12-week HP Grin2a +/- snRNA-seq Sample5


title: 12-week HP Grin2a WT snRNA-seq Sample4


title: 12-week HP Grin2a +/- snRNA-seq Sample4


title: HS360-Day7-rep4 [248-D7-CTRL]

description: Day 7", "male", "neural rosettes", "neural induction", "control

source_name: HS360, day 7, past stage I neural induction

value: Day 7 control


title: 12-week HP Grin2a WT snRNA-seq Sample5


title: HS360-Day7-P100-rep4 [22-sc2-D7-P100-B]

value: male


title: HS360-Day7-P100-rep3 [21-sc1-D7-P100-B]


title: HS360-Day7-P100-rep2 [7-sc2-D7-P100-A]


title: HS360-Day0-rep6 [2-d0-2]

description: Day 0", "male", "hESCs", "control

source_name: HS360, day 0, hESCs undifferentiated

value: hESCs

value: Day 0 control


title: HS360-Day0-rep4 [18-sc1-D0-ctrl-C]

description: Day 0", "male", "hESCs", "control


title: 12-week HP Grin2a +/- snRNA-seq Sample2


title: HS360-Day7-rep6 [6-d7-ctr-2]


title: 4-week HP Grin2a WT snRNA-seq Sample3

description:
10x Genomics
grin2a_P28HP_snRNAseq_meta.csv


title: 4-week HP Grin2a WT snRNA-seq Sample2


title: 12-week HP Grin2a -/- snRNA-seq Sample3


title: HS360-Day0-rep1 [1-sc1-D0-ctrl-A]

description: Day 0", "male", "hESCs", "control


title: HS360-Day0-rep2 [2-sc1-D0-ctrl-B]

description: Day 0", "male", "hESCs", "control


title: HS360-Day7-rep5 [5-d7-ctr-1]


title: 4-week HP Grin2a -/- snRNA-seq Sample3


title: HS360-Day7-rep3 [20-sc1-D7-ctrl-B]


title: 12-week HP Grin2a -/- snRNA-seq Sample1


title: 4-week HP Grin2a -/- snRNA-seq Sample1


title: HS360-Day7-rep2 [5-sc2-D7-ctrl-A]


title: HS360-Day7-rep1 [4-sc1-D7-ctrl-A]


title: 4-week HP Grin2a +/- snRNA-seq Sample2


title: 4-week HP Grin2a +/- snRNA-seq Sample1


title: HS360-Day0-rep5 [1-d0-1]

description: Day 0", "male", "hESCs", "control


title: 12-week HP Grin2a +/- snRNA-seq Sample3


title: 12-week HP Grin2a +/- snRNA-seq Sample1


title: 20-week TH Grin2b WT Bulk RNA-seq Sample3

data_processing:
Reads were aligned to RefSeq M25/GRCm38.p6 and gene and isoform level expression values were estimated using RSEM v1.3.0
Assembly: RefSeq M25
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
Brain dissection was performed in the cryostat using frozen brain tissues collected from Grin2a and Grin2b mutant mice. RNA was prepared from microdissected tissues using RNeasy Mini Kit (Qiagen). 200 ng of isolated total RNA from each sample was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using an Illumina TruSeq Stranded mRNA Kit (Illumina) following the manufacturer’s instructions.
rna

value: Thalamus


title: 20-week TH Grin2b WT Bulk RNA-seq Sample2


title: HS360-Day0-rep3 [3-sc2-D0-ctrl-A]

description: Day 0", "male", "hESCs", "control


title: 4-week HP Grin2a WT snRNA-seq Sample1


title: 4-week HP Grin2a -/- snRNA-seq Sample4


title: 20-week TH Grin2b WT Bulk RNA-seq Sample1


title: Living_body_peripheral_blood_CON_D7 [mRNA]

city: Shanghai

first: Xiaoqiang

last: Chai

state: Shanghai

address: No.130 Dongan Road

department: Institutes of Biomedical Sciences

institute: Fudan University

description:
Gene expression in whole blood from healthy controls
CON_D7

hyb_protocol: Each Slide was hybridized with 1.65μg Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat#5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat#G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat#121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat#5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions。

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=5μm, PMT 100%, 10%, 16bit.

data_processing:
Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).
With a total of 37 samples, the raw data from all of the 37 samples was handled within the R statistical computing framework version 3.0.2 (http://www.R-project.org) to obtain the processed data. As for miRNA raw data, R package AgiMicroRna providing useful functionality for the following processing, quality assessment for Agilent microRNA array data was employed used. In AgiMicroRna, the processed microRNA signal can be obtained using total Gene Signal (TGS) computed by the AFE and RMA algorithm. There were altogether 499 probes with corresponding miRNA in subsequent analysis after the normalization. As well as for mRNA, R package Agi4x44PreProcess was used for background correction, normalization and filtering probes according to different quality flags during the microarray standardization in our study. Ultimately, total 28155 probes mapping 14507 genes denoted by ENTREZ ID were obtained between arrays.

source_name: peripheral blood, CON, D7

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions.

extract_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat#5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany).

treatment_protocol: Morning fasting venous blood samples from donors were collected for RNA extraction. Peripheral blood mononuclear cells (PBMCs) were isolated from the blood by Ficoll gradient separation. In order to achieve lysis and inactivate endogenous, RNAses Cells were mixed with mirVana RNA lysis buffer (Ambion, Austin, Texas, USA). Then the lysates were frozen at -80°C until RNA purification.

tag: individual

value: healthy control

value: control

value: whole blood


title: 4-week HP Grin2a -/- snRNA-seq Sample2

tag: genotype

value: Grin2a -/-


title: 4-week HP Grin2a +/- snRNA-seq Sample3

value: Grin2a +/-


title: 20-week TH Grin2b +/- Bulk RNA-seq Sample4

value: Grin2b +/-


title: Living_body_peripheral_blood_LVL_B14 [mRNA]

description:
Gene expression in whole blood from patient B14 with low viral load
LVL_B14

source_name: peripheral blood, LVL, B14

value: patient B14

value: low viral load

value: female


title: 20-week TH Grin2b WT Bulk RNA-seq Sample5


title: Living_body_peripheral_blood_CON_D4 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D4

source_name: peripheral blood, CON, D4


title: 20-week TH Grin2b +/- Bulk RNA-seq Sample3

source_name: Thalamus


title: Living_body_peripheral_blood_CON_D2 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D2

source_name: peripheral blood, CON, D2


title: 20-week TH Grin2b WT Bulk RNA-seq Sample4


title: Living_body_peripheral_blood_CON_D5 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D5

source_name: peripheral blood, CON, D5


title: Living_body_peripheral_blood_LVL_B9 [mRNA]

description:
Gene expression in whole blood from patient B9 with low viral load
LVL_B9

source_name: peripheral blood, LVL, B9

value: patient B9


title: Living_body_peripheral_blood_CON_D1 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D1

source_name: peripheral blood, CON, D1


title: Living_body_peripheral_blood_CON_D6 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D6

source_name: peripheral blood, CON, D6


title: 12-week TH Grin2b WT Bulk RNA-seq Sample5


title: 12-week TH Grin2b WT Bulk RNA-seq Sample4


title: Living_body_peripheral_blood_LVL_B8 [mRNA]

description:
Gene expression in whole blood from patient B8 with low viral load
LVL_B8

source_name: peripheral blood, LVL, B8

value: patient B8


title: Living_body_peripheral_blood_CON_D3 [mRNA]

description:
Gene expression in whole blood from healthy controls
CON_D3

source_name: peripheral blood, CON, D3


title: Living_body_peripheral_blood_LVL_B7 [mRNA]

description:
Gene expression in whole blood from patient B7 with low viral load
LVL_B7

source_name: peripheral blood, LVL, B7

value: patient B7


title: Living_body_peripheral_blood_LVL_B13 [mRNA]

description:
Gene expression in whole blood from patient B13 with low viral load
LVL_B13

source_name: peripheral blood, LVL, B13

value: patient B13


title: 12-week TH Grin2b WT Bulk RNA-seq Sample3

value: WT


title: Living_body_peripheral_blood_LVL_B5 [mRNA]

description:
Gene expression in whole blood from patient B5 with low viral load
LVL_B5

source_name: peripheral blood, LVL, B5

value: patient B5

value: male


title: Living_body_peripheral_blood_LVL_B6 [mRNA]

description:
Gene expression in whole blood from patient B6 with low viral load
LVL_B6

source_name: peripheral blood, LVL, B6

value: patient B6


title: Living_body_peripheral_blood_LVL_B12 [mRNA]

description:
Gene expression in whole blood from patient B12 with low viral load
LVL_B12

source_name: peripheral blood, LVL, B12

value: patient B12


title: Living_body_peripheral_blood_LVL_B11 [mRNA]

description:
Gene expression in whole blood from patient B11 with low viral load
LVL_B11

source_name: peripheral blood, LVL, B11

value: patient B11


title: Living_body_peripheral_blood_LVL_B10 [mRNA]

description:
Gene expression in whole blood from patient B10 with low viral load
LVL_B10

source_name: peripheral blood, LVL, B10

value: patient B10

value: whole blood


title: 20-week TH Grin2b +/- Bulk RNA-seq Sample2

value: Thalamus


title: 12-week TH Grin2b +/- Bulk RNA-seq Sample4

value: Grin2b +/-


title: 20-week TH Grin2b +/- Bulk RNA-seq Sample1


title: 12-week TH Grin2b +/- Bulk RNA-seq Sample3


title: 12-week TH Grin2b +/- Bulk RNA-seq Sample2


title: 12-week TH Grin2b WT Bulk RNA-seq Sample2


title: 12-week TH Grin2b +/- Bulk RNA-seq Sample1


title: Living_body_peripheral_blood_LVL_B4 [mRNA]

description:
Gene expression in whole blood from patient B4 with low viral load
LVL_B4

source_name: peripheral blood, LVL, B4

value: patient B4


title: 12-week TH Grin2b WT Bulk RNA-seq Sample1


title: Living_body_peripheral_blood_HVL_A15 [mRNA]

description:
Gene expression in whole blood from patient A15 with high viral load
HVL_A15

source_name: peripheral blood, HVL, A15

value: patient A15

value: high viral load


title: 12-week TH Grin2b +/- Bulk RNA-seq Sample5

source_name: Thalamus


title: Living_body_peripheral_blood_LVL_B3 [mRNA]

description:
Gene expression in whole blood from patient B3 with low viral load
LVL_B3

source_name: peripheral blood, LVL, B3

value: patient B3

value: low viral load

value: female


title: Living_body_peripheral_blood_HVL_A13 [mRNA]

description:
Gene expression in whole blood from patient A13 with high viral load
HVL_A13

source_name: peripheral blood, HVL, A13

value: patient A13


title: Living_body_peripheral_blood_HVL_A14 [mRNA]

description:
Gene expression in whole blood from patient A14 with high viral load
HVL_A14

source_name: peripheral blood, HVL, A14

value: patient A14


title: Living_body_peripheral_blood_LVL_B2 [mRNA]

description:
Gene expression in whole blood from patient B2 with low viral load
LVL_B2

source_name: peripheral blood, LVL, B2

value: patient B2


title: 4-week TH Grin2b WT Bulk RNA-seq Sample5

value: WT


title: Living_body_peripheral_blood_LVL_B1 [mRNA]

description:
Gene expression in whole blood from patient B1 with low viral load
LVL_B1

source_name: peripheral blood, LVL, B1

value: patient B1

value: male


title: Living_body_peripheral_blood_HVL_A16 [mRNA]

description:
Gene expression in whole blood from patient A16 with high viral load
HVL_A16

source_name: peripheral blood, HVL, A16

value: patient A16


title: 4-week TH Grin2b WT Bulk RNA-seq Sample4


title: 4-week TH Grin2b WT Bulk RNA-seq Sample2


title: 4-week TH Grin2b +/- Bulk RNA-seq Sample4


title: 4-week TH Grin2b WT Bulk RNA-seq Sample3


title: Living_body_peripheral_blood_HVL_A12 [mRNA]

description:
Gene expression in whole blood from patient A12 with high viral load
HVL_A12

source_name: peripheral blood, HVL, A12

value: patient A12


title: 4-week TH Grin2b WT Bulk RNA-seq Sample1


title: 4-week TH Grin2b +/- Bulk RNA-seq Sample1


title: 4-week TH Grin2b +/- Bulk RNA-seq Sample2


title: 2-week TH Grin2b WT Bulk RNA-seq Sample5


title: Living_body_peripheral_blood_HVL_A9 [mRNA]

description:
Gene expression in whole blood from patient A9 with high viral load
HVL_A9

source_name: peripheral blood, HVL, A9

value: patient A9

value: whole blood


title: Living_body_peripheral_blood_HVL_A11 [mRNA]

description:
Gene expression in whole blood from patient A11 with high viral load
HVL_A11

source_name: peripheral blood, HVL, A11

value: patient A11


title: 2-week TH Grin2b WT Bulk RNA-seq Sample4

value: Thalamus


title: Living_body_peripheral_blood_HVL_A8 [mRNA]

description:
Gene expression in whole blood from patient A8 with high viral load
HVL_A8

source_name: peripheral blood, HVL, A8

value: patient A8


title: 2-week TH Grin2b WT Bulk RNA-seq Sample2


title: Living_body_peripheral_blood_HVL_A3 [mRNA]

description:
Gene expression in whole blood from patient A3 with high viral load
HVL_A3

source_name: peripheral blood, HVL, A3

value: patient A3

value: high viral load


title: Living_body_peripheral_blood_HVL_A6 [mRNA]

description:
Gene expression in whole blood from patient A6 with high viral load
HVL_A6

source_name: peripheral blood, HVL, A6

value: patient A6


title: Living_body_peripheral_blood_HVL_A7 [mRNA]

description:
Gene expression in whole blood from patient A7 with high viral load
HVL_A7

source_name: peripheral blood, HVL, A7

value: patient A7

value: female


title: 4-week TH Grin2b +/- Bulk RNA-seq Sample3

value: Grin2b +/-


title: 2-week TH Grin2b WT Bulk RNA-seq Sample3


title: Living_body_peripheral_blood_HVL_A5 [mRNA]

description:
Gene expression in whole blood from patient A5 with high viral load
HVL_A5

source_name: peripheral blood, HVL, A5

value: patient A5


title: 2-week TH Grin2b +/- Bulk RNA-seq Sample4


title: 2-week TH Grin2b +/- Bulk RNA-seq Sample3


title: Living_body_peripheral_blood_HVL_A2 [mRNA]

description:
Gene expression in whole blood from patient A2 with high viral load
HVL_A2

source_name: peripheral blood, HVL, A2

value: patient A2


title: 2-week TH Grin2b WT Bulk RNA-seq Sample1

value: WT


title: 2-week TH Grin2b +/- Bulk RNA-seq Sample5


title: 2-week TH Grin2b +/- Bulk RNA-seq Sample1


title: Living_body_peripheral_blood_HVL_A4 [mRNA]

description:
Gene expression in whole blood from patient A4 with high viral load
HVL_A4

source_name: peripheral blood, HVL, A4

value: patient A4

value: male


title: Living_body_peripheral_blood_HVL_A10 [mRNA]

description:
Gene expression in whole blood from patient A10 with high viral load
HVL_A10

source_name: peripheral blood, HVL, A10

value: patient A10


title: 2-week TH Grin2b +/- Bulk RNA-seq Sample2

source_name: Thalamus


title: Living_body_peripheral_blood_HVL_A1 [mRNA]

description:
Gene expression in whole blood from patient A1 with high viral load
HVL_A1

source_name: peripheral blood, HVL, A1

value: patient A1


title: wildtype cocaine biological replicate 6

city: Paris

first: Matthias

last: Groszer

address: 17, rue du Fer à Moulin

department: Developmental Neuroscience

country: France

institute: INSERM U839

description: wildtype cocaine replicate 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Illumina BeadArray Reader used to capture images with default setting.

data_processing: Illumina GenomeStudiov2011.1 were used to obtain raw signal intensities.  Background substracted signal intensity for the detected probes (Detection Pval<0.05) were used for analysis.   Probes detected in one array and not in others were not considered for analysis.  Furthermore outlier probes were removed and data were quantile normalized (Bolstad BM et al., 2003)

label: biotin

source_name: brain (nucleus accumbens)

label_protocol: Biotinylated cRNA were prepared by using Illumina TotalPrep-96 RNA Amplification kit from Ambion # 4393543

extract_protocol: Total RNA was extracted from nucleus accumbens (tissue punch) by using mirVanaTM kit (Ambion) following manufacturer's protocol

treatment_protocol: Animals were given i.p. injection of either saline or cocain (15mg/Kg) 1 hour before extraction of nucleus accumbens.

tag: Sex

tag: treatment

value: cocaine

value: nucleus accumbens

tag: strain


title: 20-week ST Grin2b WT Bulk RNA-seq Sample4

source_name: Striatum

value: Striatum


title: 20-week ST Grin2b +/- Bulk RNA-seq Sample5


title: 20-week ST Grin2b WT Bulk RNA-seq Sample2


title: 20-week ST Grin2b WT Bulk RNA-seq Sample1


title: 20-week ST Grin2b +/- Bulk RNA-seq Sample4


title: wildtype cocaine biological replicate 5

description: wildtype cocaine replicate 5


title: heterozygote cocaine biological replicate 5

description: heterozygote cocaine replicate 5


title: heterozygote saline biologicalreplicate 4

description: heterozygote saline replicate 4

value: Saline


title: wildtype saline biological replicate 5

description: wildtype saline replicate 5


title: heterozygote saline biological replicate 5

description: heterozygote saline replicate 5


title: heterozygote cocaine biological replicate 4

description: heterozygote cocaine replicate 4


title: wildtype saline biological replicate 6

description: wildtype saline replicate 6


title: heterozygote saline biological replicate 3

description: heterozygote saline replicate 3


title: heterozygote cocaine biological replicate 6

description: heterozygote cocaine replicate 6


title: 20-week ST Grin2b +/- Bulk RNA-seq Sample3


title: 20-week ST Grin2b WT Bulk RNA-seq Sample3


title: 20-week ST Grin2b +/- Bulk RNA-seq Sample1


title: 12-week ST Grin2b WT Bulk RNA-seq Sample4


title: wildtype saline biological replicate 4

description: wildtype saline replicate 4


title: wildtype cocaine biological replicate 3

description: wildtype cocaine replicate 3


title: heterozygote cocaine biological replicate 3

description: heterozygote cocaine replicate 3


title: wildtype cocaine biological replicate 2

description: wildtype cocaine replicate 2


title: heterozygote cocaine biological replicate 2

description: heterozygote cocaine replicate 2


title: wildtype cocaine biological replicate 4

description: wildtype cocaine replicate 4


title: 12-week ST Grin2b WT Bulk RNA-seq Sample2


title: 20-week ST Grin2b +/- Bulk RNA-seq Sample2


title: 12-week ST Grin2b WT Bulk RNA-seq Sample5


title: 12-week ST Grin2b WT Bulk RNA-seq Sample3


title: 12-week ST Grin2b WT Bulk RNA-seq Sample1


title: 12-week ST Grin2b +/- Bulk RNA-seq Sample4


title: wildtype saline biological replicate 3

description: wildtype saline replicate 3


title: wildtype saline biological replicate 2

description: wildtype saline replicate 2


title: wildtype cocaine biological replicate 1

description: wildtype cocaine replicate 1


title: 12-week ST Grin2b +/- Bulk RNA-seq Sample3


title: heterozygote saline biological replicate 2

description: heterozygote saline replicate 2


title: 12-week ST Grin2b +/- Bulk RNA-seq Sample2


title: 12-week ST Grin2b +/- Bulk RNA-seq Sample1


title: heterozygote cocaine biological replicate 1

description: heterozygote cocaine replicate 1


title: 4-week ST Grin2b WT Bulk RNA-seq Sample5


title: 4-week ST Grin2b WT Bulk RNA-seq Sample4


title: 4-week ST Grin2b WT Bulk RNA-seq Sample2


title: Sputum COPD_19458

city: New Lambton Heights

first: Katherine

last: Baines

state: NSW

address: Hunter Medical Research Institute, Level 2 East, Lot 1, Kookaburra Cct

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

scan_protocol: Standard Illumina scanning protocol

data_processing: The data were log transformed, normalised and baseline converted to the median of all samples.

source_name: Induced sputum

label_protocol: Biotinylated cRNA were prepared with the Ambion TotalPrep RNA Amplification kit for Illumina arrays

extract_protocol: RNA was extracted from sputum samples using the Rneasy Mini Kit (Qiagen) as per manufacturers instructions.

value: sputum

tag: disease group

value: Healthy Control

tag: gold stage

value: Female


title: Sputum COPD_19513

value: Male


title: wildtype saline biological replicate 1

description: wildtype saline replicate 1


title: Sputum COPD_12554


title: 4-week ST Grin2b +/- Bulk RNA-seq Sample5


title: 4-week ST Grin2b WT Bulk RNA-seq Sample3


title: 4-week ST Grin2b +/- Bulk RNA-seq Sample4


title: Sputum COPD_19518


title: 4-week ST Grin2b +/- Bulk RNA-seq Sample3


title: heterozygote saline biological replicate1

description: heterozygote saline replicate1


title: 2-week ST Grin2b WT Bulk RNA-seq Sample5


title: Sputum COPD_14981


title: 4-week ST Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_19556


title: Sputum COPD_11944


title: Sputum COPD_11803


title: Sputum COPD_11384


title: Sputum COPD_11403


title: Sputum COPD_21957

value: COPD


title: 4-week ST Grin2b +/- Bulk RNA-seq Sample2

value: Grin2b +/-


title: Sputum COPD_12152


title: Sputum COPD_10689


title: Sputum COPD_20648


title: 4-week ST Grin2b +/- Bulk RNA-seq Sample1


title: 2-week ST Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_21802


title: 2-week ST Grin2b WT Bulk RNA-seq Sample2


title: 2-week ST Grin2b WT Bulk RNA-seq Sample3


title: 2-week ST Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_20798


title: Sputum COPD_19451


title: Sputum COPD_19942


title: Sputum COPD_12578


title: 2-week ST Grin2b +/- Bulk RNA-seq Sample3


title: 20-week SSC Grin2b +/- Bulk RNA-seq Sample4

source_name: Somatosensory Cortex

value: Somatosensory Cortex


title: Sputum COPD_22315


title: 20-week SSC Grin2b +/- Bulk RNA-seq Sample3


title: Sputum COPD_21413


title: 2-week ST Grin2b +/- Bulk RNA-seq Sample1


title: Sputum COPD_12443


title: 2-week ST Grin2b +/- Bulk RNA-seq Sample2


title: 20-week SSC Grin2b WT Bulk RNA-seq Sample5


title: Sputum COPD_20215


title: 20-week SSC Grin2b +/- Bulk RNA-seq Sample1


title: 20-week SSC Grin2b WT Bulk RNA-seq Sample4


title: 20-week SSC Grin2b WT Bulk RNA-seq Sample3


title: Sputum COPD_20683


title: 20-week SSC Grin2b +/- Bulk RNA-seq Sample5


title: 20-week SSC Grin2b WT Bulk RNA-seq Sample1


title: 12-week SSC Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_21739


title: 20-week SSC Grin2b +/- Bulk RNA-seq Sample2


title: 12-week SSC Grin2b WT Bulk RNA-seq Sample4


title: 20-week SSC Grin2b WT Bulk RNA-seq Sample2


title: 12-week SSC Grin2b +/- Bulk RNA-seq Sample4


title: Sputum COPD_23146


title: 12-week SSC Grin2b WT Bulk RNA-seq Sample3


title: Sputum COPD_23450


title: 12-week SSC Grin2b +/- Bulk RNA-seq Sample1


title: 12-week SSC Grin2b WT Bulk RNA-seq Sample2


title: 12-week SSC Grin2b +/- Bulk RNA-seq Sample5


title: Sputum COPD_12023


title: Sputum COPD_12760


title: Sputum COPD_20688


title: Sputum COPD_20234


title: Sputum COPD_12607


title: Sputum COPD_19019


title: Sputum COPD_20074


title: Sputum COPD_10863


title: Sputum COPD_11261


title: Sputum COPD_12955


title: 4-week SSC Grin2b +/- Bulk RNA-seq Sample5


title: 12-week SSC Grin2b +/- Bulk RNA-seq Sample3


title: 12-week SSC Grin2b +/- Bulk RNA-seq Sample2


title: 4-week SSC Grin2b WT Bulk RNA-seq Sample5


title: Sputum COPD_19802


title: 4-week SSC Grin2b +/- Bulk RNA-seq Sample4


title: Sputum COPD_11641


title: 4-week SSC Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_12741


title: 4-week SSC Grin2b WT Bulk RNA-seq Sample3


title: 4-week SSC Grin2b +/- Bulk RNA-seq Sample2


title: Sputum COPD_11935


title: Sputum COPD_12200


title: Sputum COPD_11815


title: Sputum COPD_12299


title: 4-week SSC Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_14078


title: Sputum COPD_11208


title: Sputum COPD_13240


title: 2-week SSC Grin2b WT Bulk RNA-seq Sample3


title: Sputum COPD_14162


title: Sputum COPD_19070


title: Sputum COPD_12079


title: 2-week SSC Grin2b +/- Bulk RNA-seq Sample3


title: 4-week SSC Grin2b WT Bulk RNA-seq Sample2


title: 4-week SSC Grin2b +/- Bulk RNA-seq Sample1


title: 4-week SSC Grin2b +/- Bulk RNA-seq Sample3


title: Sputum COPD_13561


title: Sputum COPD_12006


title: 2-week SSC Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_11019


title: 2-week SSC Grin2b WT Bulk RNA-seq Sample5


title: 2-week SSC Grin2b WT Bulk RNA-seq Sample4


title: 2-week SSC Grin2b +/- Bulk RNA-seq Sample2


title: 20-week PFC Grin2b WT Bulk RNA-seq Sample2

source_name: Prefrontal Cortex

value: Prefrontal Cortex


title: Sputum COPD_12816


title: Sputum COPD_12893


title: 2-week SSC Grin2b +/- Bulk RNA-seq Sample5


title: Sputum COPD_9978


title: Sputum COPD_12148


title: 2-week SSC Grin2b +/- Bulk RNA-seq Sample4


title: 2-week SSC Grin2b WT Bulk RNA-seq Sample2

value: WT


title: 2-week SSC Grin2b +/- Bulk RNA-seq Sample1


title: Sputum COPD_11351


title: Sputum COPD_13700


title: Sputum COPD_11704


title: 20-week PFC Grin2b +/- Bulk RNA-seq Sample3


title: Sputum COPD_11985


title: 20-week PFC Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_13641


title: 12-week PFC Grin2b WT Bulk RNA-seq Sample3


title: 20-week PFC Grin2b WT Bulk RNA-seq Sample3


title: 12-week PFC Grin2b WT Bulk RNA-seq Sample1


title: 20-week PFC Grin2b WT Bulk RNA-seq Sample1


title: 20-week PFC Grin2b +/- Bulk RNA-seq Sample4


title: 12-week PFC Grin2b +/- Bulk RNA-seq Sample2


title: 12-week PFC Grin2b +/- Bulk RNA-seq Sample3


title: 20-week PFC Grin2b +/- Bulk RNA-seq Sample2


title: 20-week PFC Grin2b +/- Bulk RNA-seq Sample1


title: 12-week PFC Grin2b WT Bulk RNA-seq Sample5


title: 4-week PFC Grin2b WT Bulk RNA-seq Sample2


title: Sputum COPD_23065


title: Sputum COPD_22873


title: Sputum COPD_23507


title: 4-week PFC Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_22604


title: Sputum COPD_22027


title: Sputum COPD_12735


title: 12-week PFC Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_22295


title: Sputum COPD_23357


title: 4-week PFC Grin2b +/- Bulk RNA-seq Sample4


title: 12-week PFC Grin2b WT Bulk RNA-seq Sample2


title: 12-week PFC Grin2b +/- Bulk RNA-seq Sample4


title: 12-week PFC Grin2b +/- Bulk RNA-seq Sample1


title: 4-week PFC Grin2b +/- Bulk RNA-seq Sample2


title: Sputum COPD_23977


title: 4-week PFC Grin2b WT Bulk RNA-seq Sample3


title: Sputum COPD_23005


title: 2-week PFC Grin2b WT Bulk RNA-seq Sample4


title: Sputum COPD_23772


title: GATA3-KO-D3

description: human CD8 T cells, GATA3 KO, day9

data_processing:
Consistent quality validation using FastQC v0.11.2 (Babraham Institute).
Raw reads were trimmed to remove adapters and bases with average quality score (Q; Phred33) of 20 using a 4-bp sliding window (SlidingWindow:4:20) with Trimmomatic v0.32 (Bolger et al., 2014).
Trimmed reads were aligned to the primary assembly of the GRCh38 human reference genome using STAR v2.4.1a removing alignments containing noncanonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical).
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using featureCounts (v1.4.6-p4) with default settings.
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1)
Assembly: hg38
Supplementary files format and content: Tab-delimited text file (single table) including TPM values and ENSEMBL IDs for all samples and genes in Gencode v22

source_name: CD8 T cells

growth_protocol: CD8 T cells were cultured in PRIME-XV T cell expansion XSFM (FujiFilm) supplemented with 5% human platelet lysate (Compass Biomed), 100 units/mL of penicilllin, 100 units/mL of streptomycin, and 100 units/mL human IL-2 (Peprotech).

extract_protocol:
RNA was harvested using Norgen's Total RNA Purification Kit.
RNA libraries for RNA-seq were prepared by Azenta Life Sciences.

treatment_protocol:
Cells were activated with 1:1 ratio of CD3/CD28 dynabeads to cells. Cells transduced with lentivirus encoding for NT, ZNF217, or GATA3 gRNA at 24 hours post activaton and then electroporated with Cas9 protein at 48 hours activation.
T cells were maintained at a concentration of 1-2e6 per mL for 9 days before RNA-sequencing.

tag: cell type

value: CD8 T cells

value: GATA3 KO

value: CD3/CD28 dynabead activation


title: 4-week PFC Grin2b WT Bulk RNA-seq Sample1


title: Sputum COPD_23938


title: Sputum COPD_19682


title: Sputum COPD_20000


title: 4-week PFC Grin2b +/- Bulk RNA-seq Sample5


title: Sputum COPD_22132


title: Sputum COPD_21012


title: Sputum COPD_22800


title: 2-week PFC Grin2b +/- Bulk RNA-seq Sample5


title: Sputum COPD_20134


title: Sputum COPD_21134


title: 2-week PFC Grin2b +/- Bulk RNA-seq Sample4


title: Sputum COPD_19568


title: ZNF217-KO-D1

description: human CD8 T cells, ZNF217 KO, day9

value: ZNF217 KO


title: 4-week PFC Grin2b +/- Bulk RNA-seq Sample3


title: Sputum COPD_21782


title: 4-week PFC Grin2b +/- Bulk RNA-seq Sample1


title: control-nt-D2

description: human CD8 T cells, nt control, day9

value: control (nt)


title: 2-week PFC Grin2b WT Bulk RNA-seq Sample5


title: Sputum COPD_21327


title: control-nt-D1

description: human CD8 T cells, nt control, day9


title: 2-week PFC Grin2b WT Bulk RNA-seq Sample3


title: GATA3-KO-D2

description: human CD8 T cells, GATA3 KO, day9


title: 20-week HP Grin2b WT Bulk RNA-seq Sample5

source_name: Hippocampus

value: Hippocampus


title: 20-week HP Grin2b WT Bulk RNA-seq Sample4


title: 20-week HP Grin2b WT Bulk RNA-seq Sample2


title: 2-week PFC Grin2b WT Bulk RNA-seq Sample2


title: GATA3-KO-D1

description: human CD8 T cells, GATA3 KO, day9


title: Sputum COPD_20987


title: Sputum COPD_21144


title: Sputum COPD_21170


title: 2-week PFC Grin2b WT Bulk RNA-seq Sample1


title: ZNF217-KO-D3

description: human CD8 T cells, ZNF217 KO, day9


title: ZNF217-KO-D2

description: human CD8 T cells, ZNF217 KO, day9


title: T640_WT

first: Elisa

last: Moutin

address: Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Reads were aligned to the genome (GRCh380) using HISAT2.
Gene expression was quantified using salmon.
Counts were normalised using the rlog function from DESeq2.
Assembly: GRCh38
Supplementary files format and content: Table of normalised counts against gene IDs in tab separated value format

source_name: sigmoid colon

growth_protocol: Frozen organoids were thawed at the same time and expanded for 1 week. They were single cell dissociated and RNA was extracted 7 days later.

extract_protocol:
RNA was extracted using the Arcturus PicoPure RNA extraction kit (Thermofisher, KIT0204) according to manufacturer’s instructions.
Library prep was performed using the Illumina Stranded mRNA Prep kit (Illumina, 20040532) according to the manufacturer’s instructions.

value: sigmoid colon

tag: cell line

value: primary derived intestinal organoids

value: intestinal epithelial cells

value: PTEN WT


title: T474_KO

value: PTEN KO


title: T561_KO


title: 2-week PFC Grin2b +/- Bulk RNA-seq Sample3


title: control-nt-D3

description: human CD8 T cells, nt control, day9


title: T474_WT


title: iCtrl, DAN-D1, 30d

city: Belvaux

first: Claudia

last: Saraiva

state: Luxembourg

address: 6, avenue du Swing

department: Luxembourg Centre for Systems Biomedicine

country: Luxembourg

institute: University of Luxembourg

data_processing:
Raw read quality was assessed by FastQC (v0.11.9)
Adapters are removed using AdapterRemoval (v2.3.2), minimum length of the remaining reads set to 35 bp
Reads were mapped to hg38 (GRCh38.p13) using STAR (v.2.7.9a)
featureCounts from the R package Rsubread (2.8.1) used to count reads
Assembly: GRCh38.p13

growth_protocol: Neurons differentiated after Reinhardt et al.

extract_protocol:
RNA extraction was performed using the RNeasy Kit from Qiagen according to manufacturer’s instructions. RNA quality was assessed using the Agilent 2100 Bioanalyzer, RNA integrity (RIN) values were >8.
Libraries were prepared using the TruSeq Stranded mRNA library prep kit and sequenced on a NextSeq2000. For all samples paired reads of 51 bp length were generated.

value: dopaminergic neurons (iPSC-derived)

value: 30 days culture


title: 20-week HP Grin2b +/- Bulk RNA-seq Sample5

value: Grin2b +/-


title: 2-week PFC Grin2b +/- Bulk RNA-seq Sample1


title: PD, DAN-D2, 30d


title: T640_KO


title: 20-week HP Grin2b WT Bulk RNA-seq Sample3


title: 20-week HP Grin2b +/- Bulk RNA-seq Sample4


title: T427_WT


title: PD, DAN-D1, 30d


title: iCtrl, DAN-D4, 30d


title: Mo_CTL_rep3

first: Frederic

last: Blond

address: 17 rue Moreau

institute: Institut de la Vision

data_processing:
Raw reads were filtered with Trimmomatic to obatin Pass-filtered reads
Pass-filtered reads were mapped using HiSAT2 and aligned to human reference genome GRCh38.95
The count table of the gene features was obtained using HTSeq
Normalization and differential expression analysis values were computed with DESeq2
TPM were determined using Libinorm using htseq mode
Assembly: GRCh38
Supplementary files format and content: Tab-separated file including raw counts for all Samples
Supplementary files format and content: Tab-separated file containing all Samples metadata

source_name: monocytes

extract_protocol:
Total RNA were extracted from hiMGCs and pMGCs using the Nucleospin RNA II kit (Macherey-Nagel) according to the manufacturer’s protocol, RNA quality and quantity were evaluated using BioAnalyzer 2100 (Agilent Technologies,) with the RNA 6000 Nano Kit (Agilent Technologies)
RNA sequencing libraries were constructed from 1 μg of total RNA using a modified TruSeq RNA Sample preparation kit protocol

value: monocytes

value: healthy donor

value: DMEM


title: 2-week PFC Grin2b +/- Bulk RNA-seq Sample2

value: Prefrontal Cortex


title: iCtrl, DAN-D3, 30d


title: SG#45, day 7 spinoid#2

city: PARIS

first: Stephane

last: NEDELEC

address: 17 rue du fer a moulin

institute: Institut du Fer à Moulin

data_processing:
library strategy: spatial transcriptomic study (Tomo-sequecing)
data was processed according to code available on https://github.com/anna-alemany/humanGastruloids_tomoseq
Assembly: Human - GRCh38

source_name: hiPSC derived spinoid

extract_protocol:
Fresh spinoids (n = 2) at day 7 were washed in cold PBS and then transferred in plastic mold pre-filled with ice-cooled OCT cryosolution (TissueTek, Leica), snap-frozen on dry ice and stored at −80 °C until sectioning using a cryotome.
Sections of 20 µm were collected in the wells of a hard-shell PCR low-profile, semi-skirted 96-well plate (Bio-rad, HSL9601) that were prefilled with mineral oil (Sigma, M8410-1L) and CEL-seq2 primers.
For each well, a unique, barcoded CEL-seq2 primer was used, which allowed us to pool the content of the wells after second-strand synthesis. To sequence the mRNA content of the wells, SORT-seq (robotized CEL-seq2-based scRNA-seq) was performed using a Nanodrop II liquid handling platform (GC biotech).
DNA libraries were prepared using Cel-Seq2 protocol and Illumina TruSeq small RNA adapters (RPI series).
Illumina TruSeq small RNA

value: hiPSC derived spinoid

value: hiPSC, WTS2 cell line

value: wild type


title: 20-week HP Grin2b WT Bulk RNA-seq Sample1

value: WT


title: SG#45, day 7 spinoid#1


title: PD, DAN-D4, 30d


title: iCtrl, DAN-D2, 30d


title: SG#45_26 x day 7 spinoids

data_processing:
cell-ranger to generate fastQ files
R (v4.1.0) Seurat (v4.1.0 ) for data processing

extract_protocol:
For single cell preparation 26 spinoids at day 7 derived from WTS2 were dissociated frozen and stored at -80. Frozen cells were thawed in 37°C water bath, resuspended in culture medium (N2B27) and spun at 500g for 7 minutes at R/T
Cells were resuspended in N2B27 medium with 10µM Y-27632 at density of 700-1200cells/µl and processed for single cell RNA sequencing according to 10X Chromium Next GEM Single cell 3' v3.1 protocol
Libraries were prepared following 10X Chromium Next GEM Single cell 3' v.3.1 manufacturer protocol
10X Chromium Next GEM Single cell 3' v.3.1


title: Mo_PA_rep3

value: Palmitate 500 µM  +  0,88% w/v of BSA in DMEM


title: Batf2-/-, biol rep 4

city: Pittsburgh

first: Rick

last: van der Geest

state: PA

address: 3459 Fifth Avenue

institute: University of Pittsburgh

data_processing:
CLC Genomics Workbench (Qiagen)
Sequence reads were trimmed for adapter sequences and low quality sequences (limit = 0.01)
Trimmed sequences were mapped to GRCm38/mm10 v86 (mismatch cost: 2; insertion cost: 3; deletion cost: 3; length fraction: 0.8; similarity fraction 0.8)
Read count extraction was performed using CLC genomics workbench
Assembly: GRCm38/mm10 v86
Supplementary files format and content: tab-delimited excel file lists raw counts for each sample

source_name: primary cells

growth_protocol: Alveolar macrophages were maintained in DMEM supplemented with 10% newborn calf serum, 100 units/mL penicillin and 100 ug/mL streptomycin in a cell culture incubator with 5% CO2 at 37C

extract_protocol:
RNA was isolated using RNeasy Plus Micro Kit (Qiagen)
Library preparation was performed using TruSeq Stranded mRNA Library Prep kit (Illumina) according to manufacturer instruction

treatment_protocol: M1-like macrophage polarization was induced by treating the cells with IFNg (10 ng/mL) for 4 hours, followed by stimulation with 20% K. pneumoniae supernatant for 6 hours

value: primary cells

value: alveolar macrophages

value: IFNg + K. pneumoniae supernatant


title: T427_KO

value: sigmoid colon

value: primary derived intestinal organoids

value: intestinal epithelial cells


title: Batf2-/-, biol rep 3


title: PD, DAN-D3, 30d

value: dopaminergic neurons (iPSC-derived)

value: 30 days culture


title: Mo_PA_rep2

value: monocytes


title: 12-week HP Grin2b WT Bulk RNA-seq Sample2

value: Hippocampus


title: Batf2-/-, biol rep 1


title: Mo_PA_rep1

value: healthy donor


title: 20-week HP Grin2b +/- Bulk RNA-seq Sample3

value: Grin2b +/-


title: WT, DAN-D4, 30d


title: WT, DAN-D3, 30d


title: 12-week HP Grin2b WT Bulk RNA-seq Sample1


title: 20-week HP Grin2b +/- Bulk RNA-seq Sample2


title: WT, biol rep 3


title: Mo_CTL_rep2

value: DMEM


title: Mo_CTL_rep1


title: Mo_BSA_rep2

value: 0,88% w/v of BSA in DMEM


title: 12-week HP Grin2b +/- Bulk RNA-seq Sample5


title: 20-week HP Grin2b +/- Bulk RNA-seq Sample1


title: WT, DAN-D1, 30d


title: 12-week HP Grin2b WT Bulk RNA-seq Sample4


title: 12-week HP Grin2b +/- Bulk RNA-seq Sample3


title: WT, biol rep 1


title: Mo_BSA_rep1


title: WT, DAN-D2, 30d


title: TgSPI1Fanca.ko  leukemic_26

city: VILLEJUIF

first: Christel

last: GUILLOUF

address: 114 rue Edouard vaillant

institute: Gustave Roussy

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.17.1.14.
Sequence reads were mapped onto mm10/GRCm38 assembly of mouse genome using STAR v2.5.3a [1].
Gene expression was quantified using htseq-count v0.6.1p1 [2] with gene annotations from Ensembl release 98.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count (htseq-count) for each Sample

source_name: leukemic erythroid blasts

growth_protocol: cells were maintained in culture with EPO, diluted two days before RNA extraction

extract_protocol:
RNA was extracted using Qiagen Reasy Mini kit
Protocol1: RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.
Protocol2:  RNA-Seq libraries were generated from 400 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: leukemic

tag: library protocol

value: Protocol 2


title: 12-week HP Grin2b WT Bulk RNA-seq Sample3

value: WT


title: Batf2-/-, biol rep 2

value: primary cells