title: PSR1-expressing plants-rep3

city: Shanghai

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw reads were firstly processed to obtain clean reads.
Clean reads were mapped to mosue genome (TAIR10 version) by Hisat2.
FeatureCounts v1.6.3 was used to count the reads numbers mapped to each gene.
Gene abundance (FPKM/TPM) were calculated using stringtie.
Genome_build: TAIR10
Supplementary_files_format_and_content: FPKM, TPM

organism: Arabidopsis thaliana

source_name: whole plant

extract_protocol:
RNA was harvested using Trizol reagent
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: ecotype

tag: development stage/tissue

value: 6-week-old seedings


title: L8

status: Public on Jul 22 2022

type: SRA

city: Solna

first: Hong

last: Yang

state: Stockholm

address: Tomtebodavägen 23A

department: Systems Biology

country: Sweden

institute: KTH Royal Institute of Technology/Science For Life Laboratory

description:
108_HSD (Liver)
P13605_108_S8

library_source: transcriptomic

data_processing:
Kallisto
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited Raw counts for every gene and samples
Supplementary_files_format_and_content: Tab-delimited TPM counts for every gene and samples

molecule: total RNA

organism: Mus musculus

source_name: Liver

extract_protocol: At the age of 16 weeks, all mice are sacrificed and necropsies from liver, muscle, WAT and heart tissue were taken for RNA sequencing and lipid quantification.

treatment_protocol: Eight male C57BL/6J mice wild-type mice and eight Pklr-/- mutant mice were fed a standard mouse chow diet and housed in a 12‐h light–dark cycle. From the age of 8 weeks, both the wild-type and mutant mice were then divided into two groups of 4 mice fed with chow diet, high-sucrose diet for another 8 weeks, respectively.

tag: strain

tag: Sex

value: male

tag: genotype

value: KO

tag: tissue

value: Liver

tag: diet

value: HSD


title: PSR1-expressing plants-rep2

country: China

molecule: polyA RNA

tag: treatment


title: COV_NPC_26

city: New York

first: Shan

last: Jiang

department: Taub Institute for Research on Alzheimer’s Disease and the Aging Brain

country: USA

institute: Columbia University Irving Medical Center

data_processing:
Paired-end sequencing reads were processed using STAR (v. 2.7.3a). We aligned sequencing reads to reference genome in chimeric mode.
Genome_build: GRCh38.Gencode.v30

organism: Homo sapiens

source_name: Neural progenitor cells

growth_protocol: hNPCs were cultured in DMEM/F12 supplemented with 1x N-2, 1x B-27-RA and 20ng/mL FGF2 on matrigel until transduction. O the 4th day after transduction and selection, media was changed to Brainphys neuron medium plus 1ug/mL dox.

extract_protocol:
Cells were collected in QIAzol (cat. No. 79306) and RNA was isolated using standard methods recommended by the manufacturer. Isolated RNA was cleaned up using the Qiagen Rneasy Mini Kit (cat. No. 74106).
Libraries were prepared from RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR).  Libraries were prepared for SARS-CoV-2 detection using the AmpliSeq for SARS-CoV-2 by Illumina.

treatment_protocol: NPCs stably expressing dCas9-VPR were infected with the gRNA viruses and NGN2 virus and then activated with doxycycline, selected with antibiotics and differentiated for 7 days until SARS-CoV-2 infection. NPC-derived neurons were infected with SARS-CoV-2 (MOI of 0.1) for 24hrs before collection in lysis buffer.

tag: cell type

value: Neural progenitor cells

tag: infection state

value: CoV+

tag: treatment category

value: CRISPRa

value: Scramble gRNA


title: COV_NPC_7

value: shRNA

value: Scramble shRNA


title: Wild type mice 2

city: Guangzhou

first: Wenlong

last: Zhang

address: Yuexiu

institute: The First Affiliated Hospital of Guangzhou Medical University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Mus

source_name: brain; basolateral amygdala

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: brain; basolateral amygdala

tag: gender

value: Wild type


title: COV_NPC_6

value: CoV-

value: IL10RB-1 gRNA


title: L10

description:
110_Chow (Liver)
P13605_110_S10

value: CTRL

value: Chow


title: 331-c IRF5-_2

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

data_processing:
Illumina Bcl2fastq2 (2.18)  software used for basecalling.
Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded
Reads were then aligned against Homo sapiens genome from Ensembl version 91 using STAR (version 2.5.2b)
Alignments from reads matching more than once on the reference genome were removed using Java version of samtools
To compute gene expression, Homo sapiens GTF genome annotation version 91 from Ensembl was used
All overlapping regions between alignments and referenced exons were counted using HTSeq-count 0.5.3
The sample counts were normalized using DESeq2 1.8.1
Statistical treatments and differential analyses were also performed using DESeq2 1.8.1
Genome_build: Homo sapiens Ensembl version 91
Supplementary_files_format_and_content: tsv files containing raw counts

source_name: venous blood

extract_protocol:
Cells were FACS sorted into RNA extraction buffer and flash frozen until extraction with the Qiagen RNEasy kit
20 ng of total RNA were amplified and converted to cDNA using SMART-Seq v4 Ultra Low Input RNA kit (Clontech).
Afterwards an average of 150 pg of amplified cDNA was used to prepare library following Nextera XT DNA kit (Illumina).
Libraries were multiplexed by 12 on a high-output flowcells.

tag: disease state

value: Type-2 diabetes

value: Blood

tag: age

value: Adult

tag: sorted cells


title: L7

description:
107_HSD (Liver)
P13605_107_S7

value: male

value: KO

value: Liver


title: 332-a IRF5-_3


title: L6

description:
106_HSD (Liver)
P13605_106_S6

value: HSD


title: 331-b IRF5-_2


title: PINP1-silenced plants-rep3

value: 6-week-old seedings


title: L5

description:
105_HSD (Liver)
P13605_105_S5


title: COV_NPC_5

value: Neural progenitor cells

value: CRISPRa


title: PINP1-silenced plants-rep1


title: 330-d IRF5-_1


title: PINP1-silenced plants-rep2


title: COV_NPC_3

value: CoV+


title: COV_NPC_4


title: Control ChIP-seq from HepG2 (ENCLB713MSO)

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

description:
https://www.encodeproject.org/experiments/ENCSR032BUQ/
***************
biological replicate number: 1
technical replicate number: 1
description: HepG2 immortalized cell line stably expressing C-terminal eGFP-RAD21 fusion protein.
experiment encode accession: ENCSR032BUQ
assay title: Control ChIP-seq
assembly: GRCh38
encode release date: 2022-01-20
lab: Michael Snyder, Stanford
library encode accession: ENCLB713MSO
size range: 450-650

library_source: genomic

data_processing: See GSM*_README.txt supplementary file linked below

molecule: genomic DNA

source_name: Homo sapiens HepG2 cell line genetically modified (insertion) using CRISPR targeting H. sapiens RAD21

tag: line

value: cell line

tag: description

value: HepG2 cell line stably expressing a C-terminal LAP-tag containing eGFP, fused to RAD21.

tag: biosample encode accession

value: 15 year

tag: health state

value: hepatocellular carcinoma

tag: dev stage

value: child

tag: lab

value: Michael Snyder, Stanford

tag: source

value: Michael Snyder

tag: link

value: ENCBS084JXC at ENCODE; https://www.encodeproject.org/ENCBS084JXC/

value: Derived from ENCODE donor ENCDO000AAC; https://www.encodeproject.org/ENCDO000AAC/


title: L3

description:
103_Chow (Liver)
P13605_103_S3

tag: strain

tag: Sex

value: male

tag: genotype

tag: tissue

tag: diet

value: Chow


title: WT-rep3

tag: ecotype

tag: development stage/tissue

tag: treatment

value: untreated


title: 330-b IRF5-_1

tag: disease state

value: Type-2 diabetes

value: Blood

tag: age

value: Adult

tag: sorted cells


title: COV_NPC_2

tag: cell type

value: Neural progenitor cells

tag: infection state

tag: treatment category

value: CRISPRa

value: IL10RB-1 gRNA


title: 330-c IRF5-_1


title: 333+a IRF5+_4


title: PSR1-expressing plants-rep1

value: 6-week-old seedings


title: COV_NPC_11

value: CoV-

value: shRNA

value: Scramble shRNA


title: WT-rep2


title: 330-a IRF5-_1


title: 331-a IRF5-_2


title: WT-rep1


title: L1

description:
101_Chow (Liver)
P13605_101_S1

value: KO

value: Liver


title: L4

description:
104_Chow (Liver)
P13605_104_S4


title: 512_8

status: Public on Jul 21 2022

city: Singapore

first: Lih Feng

last: Cheow

address: 4 Engineering Drive 3

department: Biomedical Engineering

country: Singapore

institute: National University of Singapore

library_source: other

data_processing:
Adapter trimming was done using Cutadapt
Alignment and determination of methylation status was done using Bismark
Deduplication was done using Picard tools
Assembly: hg38
Supplementary files format and content: Methylation extractor output file for CpG context

molecule: other

source_name: CRC Plasma

extract_protocol:
cell-free DNA was extracted using Qiagen QiaAmp Circulating Nucleic Acids kit
5-10 ng of cfDNA was used as input for library construction using Kapa hyper prep kit
End repair and A-tailing using Kapa hyper prep kit and methylated Truseq nano adapters. Bisulfite conversion was done using Zymo EZ DNA Methylation-Gold kit

value: CRC Plasma

value: CRC


title: 512_2


title: 512_6


title: 512_5


title: 512_7


title: 809_8


title: 809_7


title: 512_1


title: 809_4


title: COV_NPC_1

value: CoV+


title: 809_5


title: L2

description:
102_Chow (Liver)
P13605_102_S2

value: male

value: Chow


title: H0063

source_name: Healthy Plasma

value: Healthy Plasma

value: healthy


title: 809_2


title: H0086


title: 809_3


title: H0051


title: H0083


title: 519_1


title: 897


title: H0070


title: 575_1


title: 809_1


title: 69


title: 476


title: 575_2


title: 809_6


title: 519_8


title: Inflamed tissue from patient 23

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

country: Italy

institute: University of Florence

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 23 affected by Crohn's disease

data_processing:
Library strategy: paired-end amplicon sequencing
demultiplexing: from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
pair merging: micca mergepairs -i pair1.fastq -r pair2.fastq -o out.joined.fastq -l 30 -d 3
primer check and trimming: micca trim -i out.joined.fastq -o out.trimmed.fastq -w CCTACGGGNBGCWSCAG -r GACTACHVGGGTATCTAATCC -W -R -c
quality check: micca filter -i out.trimmed.fastq -o out.hiqual.fastq -e 0.5 -m 350 -f fastq
read merging: micca merge -i *.hiqual.fastq -o merged.fastq -f fastq
OTU table creation by clustering: micca otu -m denovo_greedy -i merged.fasta -o otudata -d 0.97 -c -t 20
taxonomic assignment (RDP): micca classify -m rdp -i otudata/otus.fasta -o otudata/taxa.txt
further analyses: R phyloseq package (see https://github.com/matteoramazzotti/papers/tree/main/2022crohn)
Supplementary files format and content: OTU table

source_name: gut tissue

extract_protocol:
deparaffinatin with xylene followed by DNA extration with QIAamp DNA FFPE tissue kit (QIAGEN)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

treatment_protocol: isolation of 8 slices of 10 um from paraffin embedded gut tissue for each sample

tag: sample id

tag: surgery

value: first

tag: disease

value: Inflamed

tag: patientid


title: Inflamed tissue from patient 22

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 22 affected by Crohn's disease

value: relapse


title: 575_3


title: Inflamed tissue from patient 20

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 20 affected by Crohn's disease


title: Inflamed tissue from patient 21

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 21 affected by Crohn's disease


title: 1179


title: 986_1


title: Inflamed tissue from patient 6

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 6 affected by Crohn's disease


title: Inflamed tissue from patient 8

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 8 affected by Crohn's disease


title: Inflamed tissue from patient 19

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 19 affected by Crohn's disease


title: Inflamed tissue from patient 18

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 18 affected by Crohn's disease


title: Inflamed tissue from patient 4

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 4 affected by Crohn's disease


title: 512_4


title: 512_3


title: Inflamed tissue from patient 1

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 1 affected by Crohn's disease


title: Notinflamed tissue from patient 23

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 23 affected by Crohn's disease

value: Notinflamed


title: Inflamed tissue from patient 3

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 3 affected by Crohn's disease


title: 986_2


title: Notinflamed tissue from patient 22

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 22 affected by Crohn's disease


title: Inflamed tissue from patient 2

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 2 affected by Crohn's disease


title: Notinflamed tissue from patient 8

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 8 affected by Crohn's disease


title: Notinflamed tissue from patient 9

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 9 affected by Crohn's disease


title: Notinflamed tissue from patient 6

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 6 affected by Crohn's disease


title: Notinflamed tissue from patient 2

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 2 affected by Crohn's disease


title: Notinflamed tissue from patient 18

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 18 affected by Crohn's disease


title: Notinflamed tissue from patient 3

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 3 affected by Crohn's disease


title: Notinflamed tissue from patient 19

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 19 affected by Crohn's disease


title: Notinflamed tissue from patient 21

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 21 affected by Crohn's disease


title: Notinflamed tissue from patient 4

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 4 affected by Crohn's disease


title: 201B7_5hr_delta Met

type: RNA

city: Yokohama

first: nobuaki

last: shiraki

address: 4259-B-25 Nagatsuta-cho, Midori-ku

department: School of Life Science and Technology

country: Japan

institute: Tokyo Institute of Technology

description: undifferentiated human iPS cells cultured with methionine deprived medium for 5hr

hyb_protocol: Following fragmentation, 5.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Transcriptome Array 2.0. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G.

data_processing: The data were analyzed with Affymetrix Transcriptome Analysis console (TAC) software using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: undifferentiated human ES cells cultured with Leucine deprived medium for 5hr

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (WT PLUS Reagent, P/N 902309, Affymetrix).

growth_protocol: Before the following assay, human iPS cells (201B7) are grown in human ES media to 70-80% confluent.

extract_protocol: Total RNA was extraced using RNeasy Mini Kit, according to the manufacturer's instructions.

treatment_protocol: 201B7 cells are cultured in the complete media for 5hr, or in the abesence of  extracellular threonine, valine, isoleucine, leucine, lysine, histidine, phenylalanine, tryptophane or methionine for 5hr.

value: human iPS cells

tag: cell line


title: 201B7_5hr_deltaTrp

description: undifferentiated human iPS cells cultured with tryptophane deprived medium for 5hr


title: Notinflamed tissue from patient 20

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 20 affected by Crohn's disease


title: 201B7_5hr_delta Lys

description: undifferentiated human iPS cells cultured with lysine deprived medium for 5hr


title: Inflamed tissue from patient 9

description: 16S V3-V4 sequencing of a FFPE specimen from an inflamed gut portion of patient 9 affected by Crohn's disease


title: 201B7_5hr_deltaThr

description: undifferentiated human iPS cells cultured with threonine deprived medium for 5hr


title: 201B7_5hr_delta Phe

description: undifferentiated human iPS cells cultured with phenylalanine deprived medium for 5hr


title: Notinflamed tissue from patient 1

description: 16S V3-V4 sequencing of a FFPE specimen from an not inflamed gut portion of patient 1 affected by Crohn's disease


title: 201B7_5hr_delta Leu

description: undifferentiated human iPS cells cultured with leucine deprived medium for 5hr


title: 201B7_5hr_delta Val

description: undifferentiated human iPS cells cultured with valine deprived medium for 5hr


title: 201B7_5hr_delta Ile

description: undifferentiated human iPS cells cultured with isoleucine deprived medium for 5hr


title: 201B7_5hr_delta His

description: undifferentiated human iPS cells cultured with histidine deprived medium for 5hr


title: 201B7_5hr_Compl

description: undifferentiated human iPS cells cultured with complete medium for 5hr

source_name: undifferentiated human ES cells cultured with complete medium for 5hr


title: WT8OC_3

city: wuhan

first: Yong

last: Liu

address: Bayi road

department: College of Life Sciences

institute: Wuhan university

data_processing:
Illumina RTA used for base calling and converting into raw FASTQ files with Bcl2Fastq conversion software
quality control using fastQC version 0.11.3
mRNA-seq reads were aligned to the mm10 genome assembly using TopHat2 version 2.0.14 with the default parameters.
FPKM (fragments per kilobase of exon per million fragments mapped) were calculated using Cufflinks version 2.2.1 .
Genome_build: mm10
Supplementary_files_format_and_content: Gene_Count: FPKM value for each sample
Supplementary_files_format_and_content: IRE1α-regulated gene at 8OC and 30OC: genes regulated by IRE1a at 8OC or 30OC and its FPKM

source_name: inguinal white adipose tissue

growth_protocol: The mice were maintained at room tempurature for 4 weeks prior to 6 weeks of thermal-neutrality (30oC) accumulation, then challenged with cold stress (8oC) or 30oC for another 3 days.

extract_protocol:
Adipose tissue were isolated and flash frozen on liquid nitrogen, then the RNAs were extracted with TRIzol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: inguinal white adipose tissue

tag: strain

value: 10 Weeks

tag: genotype

value: WT

tag: stress


title: Lung, normal epithelial cells

first: Yan

last: Gu

address: 800 Xiangyin Road

department: Immunology

institute: Second Miilitary Medical University

data_processing:
Raw data (raw reads) were processed using Trimmomatic. The reads containing poly-N and the low quality reads were removed to obtain the clean reads.
Clean reads were mapped to reference sequences and/or reference gene set using SOAPaligner/SOAP2. No more than 2 mismatches were allowed in the alignment.
The expression level for each gene is determined by the numbers of reads uniquely mapped to the specific gene and the total number of uniquely mapped reads in the _x000D_sample
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads),
We use "FDR ≤0.001 and the absolute value of log2Ratio ≥1" as the_x000D_threshold to judge the significance of gene expression difference.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized RPKM values for each Sample

source_name: Lung epithelial cells

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Total RNA was quantified using a NanoDrop ND-2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA)
The total RNA samples are first treated with DNase I to degrade any possible DNA contamination. Then the mRNA is enriched by using the oligo(dT) magnetic beads (for_x000D_eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments (about 200 bp). Then the first strand of cDNA is synthesized by using random_x000D_hexamer-primer. Buffer, dNTPs, RNase H and DNA polymerase I are added to synthesize the second strand. The double strand cDNA is purified with magnetic beads. End_x000D_reparation and 3'-end single nucleotide A (adenine) addition is then performed. Finally, sequencing adaptors are ligated to the fragments. The fragments are enriched by PCR_x000D_amplification. During the QC step, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used to qualify and quantify of the sample library.

treatment_protocol: In spontaneous lung metastatic models, 1×10^6 luciferase-labeled LLC cells were subcutaneously injected on the dorsum of mice. Lung tissues were digested into single-cell suspensions and Sftpc+ epithelial cells were purified by FASC, followed by transcriptome sequencing. Wild type mouse without tumor-bearing was as a control.

tag: tissue

value: Lung

value: lung epithelial cells

value: 6-8 weeks

value: control


title: AKO8OC_1


title: AKO8OC_2


title: Lung, tumor epithelial cells

value: LLC cells subcutaneously injected in the dorsum of mice

value: spontaneous lung metastatic model


title: AKO8OC_3


title: WT8OC_1


title: WT8OC_2


title: WT30OC_2


title: WT30OC_3


title: AKO30OC_2


title: AKO30OC_1


title: Ch12 Zbtb7a, Zfp580 Knockout rep1

city: Bethesda

first: Yongbing

last: Zhao

state: Maryland

address: 10 Center Drive RooM 13C101A

department: NIAMS

institute: National Institutes of Health

description: library: RNACh12Zbtb7aZfp580KoA7Rep1

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: Ch12 cell line

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
mRNA-seq: Total RNA was extracted from 0.5 million cultured cells using RNAqueous™ Total RNA Isolation Kit (AM1912). mRNA was then isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB E7490).
mRNA-seq: Standard RNA-Seq library preparation was performed following Illumina's RNA-Seq protocol v2. 50 cycles of sequencing data were acquired on HiSeq 3000 (Illumina).

treatment_protocol: CRISPR Cas9 engineering of CH12 B-cells: For complete deletion of respective transcription factor gene, two sgRNA were used per target gene. (a)sgRNA design: sgRNA targets were dresigned by the sgRNA online tool (https://crispr.zhaopage.com). Selected sgRNAs were cloned into px458 (Addgene #48138). (b) Nucleofection and cell sorting: Cultured CH12 B cells were nucleofected with 1 ug of plasmid per 1 million cells, using the SF Cell line 4D-Nucleofector X kit with the 4D-Nucleofector device (Pulse code: CM150). Cells were single cell-sorted for GFP expression into 96-well plates and allowed to recover for 7-10 days. Grown colonies were genotyped using respective primers, and clones with homozygous deletion were expanded for further experiments and analysis.

value: Ch12 cell line

value: Zbtb7a, Zfp580 Knockout

tag: experimental type

value: mRNA-Seq


title: WT30OC_1


title: Ch12 Zbtb7a, Zfp580 Knockout rep2

description: library: RNACh12Zbtb7aZfp580KoD10Rep2

tag: treatment


title: Ch12 Klf16, Zfp580 Knockout rep3

description: library: RNACh12Klf16Zfp580KoG4Rep3

value: Klf16, Zfp580 Knockout


title: Ch12 Klf16, Sp1, Zbtb7a, Zfp580 Knockout rep1

description: library: RNACh12Klf16Sp1Zbtb7aZfp580KoRep1

value: Klf16, Sp1, Zbtb7a, Zfp580 Knockout


title: Ch12 Klf16, Zfp580 Knockout rep2

description: library: RNACh12Klf16Zfp580KoB7Rep2


title: Ch12 Klf16, Zfp580 Knockout rep1

description: library: RNACh12Klf16Zfp580KoB3Rep1


title: Ch12 Zbtb7a, Zfp580 Knockout rep3

description: library: RNACh12Zbtb7aZfp580KoE8Rep3


title: Ch12 WT rep3

description: library: RNACh12CtlRep3


title: Ch12 WT rep1

description: library: RNACh12CtlRep1


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout rep3

description: library: RNACh12Klf16MazSp1Zbtb7aKoE11Rep3

value: Klf16, Maz, Sp1, Zbtb7a Knockout


title: Ch12 Klf16, Sp1, Zbtb7a, Zfp580 Knockout rep3

description: library: RNACh12Klf16Sp1Zbtb7aZfp580KoRep3


title: AKO30OC_3


title: Ch12 Klf16, Sp1, Zbtb7a, Zfp580 Knockout rep2

description: library: RNACh12Klf16Sp1Zbtb7aZfp580KoRep2


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout rep1

description: library: RNACh12Klf16MazSp1Zbtb7aKoE11Rep1


title: Ch12 WT rep2

description: library: RNACh12CtlRep2


title: Ch12 WT TGFb 6h rep1

description: library: RNACH12WTTGFb6hS1Rep2

value: TGFb 6h


title: Ch12 WT TGFb 6h rep2

description: library: RNACH12WTTGFb6hS1Rep3


title: Ch12 WT TGFb 24h rep2

description: library: RNACH12WTTGFb24hS1Rep3

value: TGFb 24h


title: Ch12 WT TGFb 24h rep1

description: library: RNACH12WTTGFb24hS1Rep2


title: Ch12 WT TGFb 1h rep2

description: library: RNACH12WTTGFb1hS1Rep2

value: TGFb 1h


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout rep2

description: library: RNACh12Klf16MazSp1Zbtb7aKoE11Rep2


title: Ch12 WT TGFb 1h rep3

description: library: RNACH12WTTGFb1hS1Rep3


title: Ch12 WT TGFb 1h rep1

description: library: RNACH12WTTGFb1hS1Rep1


title: Ch12 WT control, DMSO rep2

description: library: RNACH12WTDMSOS1Rep2

value: control, DMSO


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 24h rep2

description: library: RNACH12QKOTGFb24hS1Rep3


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 6h rep1

description: library: RNACH12QKOTGFb6hS1Rep2


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 24h rep1

description: library: RNACH12QKOTGFb24hS1Rep2


title: Ch12 WT control, DMSO rep3

description: library: RNACH12WTDMSOS1Rep3

value: WT


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 6h rep2

description: library: RNACH12QKOTGFb6hS1Rep3


title: Ch12 WT control, DMSO rep1

description: library: RNACH12WTDMSOS1Rep1


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 1h rep1

description: library: RNACH12QKOTGFb1hS1Rep1


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 1h rep3

description: library: RNACH12QKOTGFb1hS1Rep3


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout TGFb 1h rep2

description: library: RNACH12QKOTGFb1hS1Rep2


title: aB Sp1

description: library: aBSp1

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Genome_build: mm10

source_name: activated B cells

growth_protocol: Mature B cells were isolated from C57BL/6J mouse spleen by negative selection (StemCell Technologies)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen). 50 cycles of sequencing data were acquired on Illumina HiSeq 3000.

treatment_protocol: activated B cells were treated with mithramycin with 10nM, 50nM, and 100nM.

value: activated B cells

tag: target

value: ChIP-Seq


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout control, DMSO rep2

description: library: RNACH12QKODMSOS1Rep2


title: activated B cells (LPS+IL4+aCD180 72h) treated with 100nM mithramycin rep2

description: library: RNA1027S11R2

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Genome_build: mm10

source_name: activated B cells (LPS+IL4+aCD180 72h)

value: activated B cells (LPS+IL4+aCD180 72h)

value: treated with 100nM mithramycin


title: Ch12 biotag Pax5

description: library: ChIP1905Pax5BirAS1


title: aB Rela

description: library: aBP65

value: Rela


title: aB Spi1

description: library: aBPu1


title: aB Input

description: library: ChIPaB24hInputS1

value: Input


title: Ch12 Nrf1

description: library: ChIPCh12WtAntiNrf1S1R1

value: Ch12 cell line


title: aB Irf4

description: library: aBIrf4


title: activated B cells (LPS+IL4+aCD180 72h) treated with 10nM mithramycin (1 sample)

description: library: RNA1027S9R1

value: treated with 10nM mithramycin


title: activated B cells (LPS+IL4+aCD180 72h) treated with 50nM mithramycin rep2

description: library: RNA1027S10R2

value: treated with 50nM mithramycin

value: mRNA-Seq


title: activated B cells (LPS+IL4+aCD180 72h) treated with 100nM mithramycin rep1

description: library: RNA1027S11R1


title: activated B cells (LPS+IL4+aCD180 72h) no treatment rep2

description: library: RNA1027S8R2

value: no treatment


title: activated B cells (LPS+IL4+aCD180 72h) treated with 50nM mithramycin rep1

description: library: RNA1027S10R1


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout control, DMSO rep1

description: library: RNACH12QKODMSOS1Rep1

value: Klf16, Maz, Sp1, Zbtb7a Knockout


title: activated B cells (LPS+IL4+aCD180 48h) treated with 100nM mithramycin rep2

description: library: RNA1027S7R2

source_name: activated B cells (LPS+IL4+aCD180 48h)

value: activated B cells (LPS+IL4+aCD180 48h)


title: activated B cells (LPS+IL4+aCD180 72h) no treatment rep3

description: library: RNA1027S8R3


title: activated B cells (LPS+IL4+aCD180 48h) treated with 50nM mithramycin rep1

description: library: RNA1027S6R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 10nM mithramycin rep1

description: library: RNA1027S5R1


title: activated B cells (LPS+IL4+aCD180 72h) no treatment rep1

description: library: RNA1027S8R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 100nM mithramycin rep1

description: library: RNA1027S7R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 50nM mithramycin rep2

description: library: RNA1027S6R2


title: activated B cells (LPS+IL4+aCD180 48h) no treatment rep1

description: library: RNA1027S4R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 10nM mithramycin rep2

description: library: RNA1027S5R2


title: activated B cells (LPS+IL4+aCD180 72h) treated with 50nM mithramycin

description: library: ATAC1027S9R1

data_processing:
Base calling: Illumina CASAVA 1.8.2
ATAC-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ATAC-Seq: Remove duplicates with picard.
ATAC-Seq: Remove mitochondria reads.
ATAC-Seq: Keep high-quality reads with MAPQ>=30.
ATAC-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ATAC-Seq: Call peak with MACS2.
Genome_build: mm10

extract_protocol:
ATAC-seq: To prepare nuclei for tagmentation, 100,000 cells were centrifuged at 500 × g for 5 minutes, then washed with 50 μL of cold 1x PBS and centrifugated at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were centrifuged at 500 × g for 10 minutes using a refrigerated centrifuge. Immediately following the nuclei prep, the pellets were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Zymo Clean and Concentrator kit. After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 4 cycles at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR, the PCR reaction was monitored using qPCR in order to stop amplification prior to saturation. A 5 μl aliquot of the PCR reaction was mixed with 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x, and a 20-cycles qPCR was run to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were then purified using the Zymo Clean and Concentrator kit.
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the Illumina HiSeq 3000.

value: ATAC-Seq


title: activated B cells (LPS+IL4+aCD180 72h) no treatment

description: library: ATAC1027S7R1


title: activated B cells (LPS+IL4+aCD180 48h) no treatment rep3

description: library: RNA1027S4R3


title: activated B cells (LPS+IL4+aCD180 72h) treated with 10nM mithramycin

description: library: ATAC1027S8R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 100nM mithramycin

description: library: ATAC1027S6R1


title: activated B cells (LPS+IL4+aCD180 48h) treated with 50nM mithramycin

description: library: ATAC1027S5R1


title: activated B cells (LPS+IL4+aCD180 48h) no treatment

description: library: ATAC1027S3R1


title: Ch12 wt S3

description: library: RNAch12WtS3r1

value: wt


title: activated B cells (LPS+IL4+aCD180 48h) treated with 10nM mithramycin

description: library: ATAC1027S4R1


title: Ch12 wt S2

description: library: RNAch12WtS2r1


title: Ch12 wt S5

description: library: RNAch12WtS5r1


title: Ch12 wt S1

description: library: RNAch12WtS1r1


title: Ch12 Zfp580 Zbtb7a Klf16 Ko G5

description: library: RNAch12Zfp580Zbtb7aKlf16KoG5

value: Zfp580 Zbtb7a Klf16 Knockout


title: Ch12 Zfp580 Zbtb7a Klf16 Ko G4

description: library: RNAch12Zfp580Zbtb7aKlf16KoG4


title: Ch12 Zfp580 Zbtb7a Klf16 Ko E3

description: library: RNAch12Zfp580Zbtb7aKlf16KoE3


title: Ch12 Zfp580 Sp3 Ko E6r2

description: library: RNAch12Zfp580Sp3KoE6r2

value: Zfp580 Sp3 Knockout


title: Ch12 Zfp580 Sp3 Ko E6r1

description: library: RNAch12Zfp580Sp3KoE6r1


title: activated B cells (LPS+IL4+aCD180 48h) no treatment rep2

description: library: RNA1027S4R2


title: activated B cells (LPS+IL4+aCD180 72h) treated with 100nM mithramycin

description: library: ATAC1027S10R1


title: Ch12 Zfp580 Sp1 Ko B7

description: library: RNAch12Zfp580Sp1KoB7

value: Zfp580 Sp1 Knockout


title: Ch12 Zfp580 Sp3 Ko B10

description: library: RNAch12Zfp580Sp3KoB10


title: Ch12 Zfp580 Ko C11r3

description: library: RNAch12Zfp580KoC11r3

value: Zfp580 Knockout


title: Ch12 Zfp580 Ko C11r1

description: library: RNAch12Zfp580KoC11r1


title: Ch12 Zfp580 Ko C11r2

description: library: RNAch12Zfp580KoC11r2


title: Ch12 Zbtb7a Sp1 Ko F7r3

description: library: RNAch12Zbtb7aSp1KoF7r3

value: Zbtb7a Sp1 Knockout


title: Ch12 Zbtb7a Sp1 Ko F7r1

description: library: RNAch12Zbtb7aSp1KoF7r1


title: Ch12 wt S4

description: library: RNAch12WtS4r1


title: Ch12 Zbtb7a Sp1 Ko F7r2

description: library: RNAch12Zbtb7aSp1KoF7r2


title: Ch12 Zbtb7a Ko G4

description: library: RNAch12Zbtb7aKoG4

value: Zbtb7a Knockout


title: Ch12 Zbtb7a Klf16 Ko F12r2

description: library: RNAch12Zbtb7aKlf16KoF12r2

value: Zbtb7a Klf16 Knockout


title: Ch12 Zbtb7a Klf16 Ko F12r3

description: library: RNAch12Zbtb7aKlf16KoF12r3


title: Ch12 Sp3 Ko C4r2

description: library: RNAch12Sp3KoC4r2

value: Sp3 Knockout


title: Ch12 Zbtb7a Klf16 Ko F12r1

description: library: RNAch12Zbtb7aKlf16KoF12r1

value: Ch12 cell line


title: Ch12 Zbtb7a Ko F6r2

description: library: RNAch12Zbtb7aKoF6r2


title: Ch12 Sp3 Ko D11

description: library: RNAch12Sp3KoD11


title: Ch12 Zbtb7a Ko F6r1

description: library: RNAch12Zbtb7aKoF6r1


title: Ch12 Sp1 Zbtb7a Klf16 Ko C11r1

description: library: RNAch12Sp1Zbtb7aKlf16KoC11r1

value: Sp1 Zbtb7a Klf16 Knockout


title: Ch12 Sp3 Ko C4r1

description: library: RNAch12Sp3KoC4r1


title: Ch12 Zfp580 Sp1 Ko F3

description: library: RNAch12Zfp580Sp1KoF3


title: Ch12 Sp1 Zbtb7a Klf16 Ko C11r2

description: library: RNAch12Sp1Zbtb7aKlf16KoC11r2


title: Ch12 Sp1 Zbtb7a Klf16 Ko C11r3

description: library: RNAch12Sp1Zbtb7aKlf16KoC11r3


title: Ch12 Maz Ko C3

description: library: RNAch12MazKoC3

value: Maz Knockout


title: Ch12 Maz Ko G4r2

description: library: RNAch12MazG4S1r2

value: mRNA-Seq


title: Ch12 Klf16 Ko D3r3

description: library: RNAch12Klf16KoD3r3

value: Klf16 Knockout


title: Ch12 Zfp580 Sp1 Ko E5

description: library: RNAch12Zfp580Sp1KoE5


title: Ch12 Klf16 Ko D3r1

description: library: RNAch12Klf16KoD3r1


title: Ch12 Klf13 Ko A6

description: library: RNAch12Klf13KoA6

value: Klf13 Knockout


title: Ch12 Klf13 Ko E11

description: library: RNAch12Klf13KoE11


title: Ch12 Klf16 Ko D3r2

description: library: RNAch12Klf16KoD3r2


title: Ch12 Klf13 Ko E6

description: library: RNAch12Klf13KoE6


title: Ch12 Egr1 Ko A5

description: library: RNAch12Egr1KoA5

value: Egr1 Knockout


title: Ch12 Egr1 Ko F10

description: library: RNAch12Egr1KoF10


title: Ch12 Egr1 Ko F9

description: library: RNAch12Egr1KoF9


title: ATAC1905A|CH12 B cells clone bc5

data_processing:
Base calling: Illumina CASAVA 1.8.2
ATAC-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ATAC-Seq: Remove duplicates with picard.
ATAC-Seq: Remove mitochondria reads.
ATAC-Seq: Keep high-quality reads with MAPQ>=30.
ATAC-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ATAC-Seq: Call peak with MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: CH12 B cells

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).  Mature B cells were isolated from C57BL/6J mouse spleen by negative selection (StemCell Technologies). Mouse ES cells (E14) were cultured in Knock-out DMEM (Thermo Fisher Scientific) supplemented with 10% FBS (ES Cell qualified, ATCC), 1% Penicillin-Streptomycin, 1% Glutamax, 1% Non-Essential Amino Acids and 1% b-mercaptoethanol (Thermo Fisher Scientific).

extract_protocol:
ATAC-seq: To prepare nuclei for tagmentation, 100,000 cells were centrifuged at 500 × g for 5 minutes, then washed with 50 μL of cold 1x PBS and centrifugated at 500 × g for 5 minutes. Cells were lysed using cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2 and 0.1% IGEPAL CA-630). Immediately after lysis, nuclei were centrifuged at 500 × g for 10 minutes using a refrigerated centrifuge. Immediately following the nuclei prep, the pellets were resuspended in the transposase reaction mix (25 μL 2x TD buffer, 2.5 μL Transposase (Illumina) and 22.5 μL of nuclease free water). The transposition reaction was carried out for 30 minutes at 37 °C. Directly following transposition the sample was purified using a Zymo Clean and Concentrator kit. After purification, library fragments were amplified using 1x NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers, using the following PCR conditions: 72°C for 5 minutes, 98°C for 30 seconds, followed by 4 cycles at 98°C for 10 seconds, 63°C for 30 seconds and 72°C for 1 minute. To reduce GC and size bias in our PCR, the PCR reaction was monitored using qPCR in order to stop amplification prior to saturation. A 5 μl aliquot of the PCR reaction was mixed with 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6x, and a 20-cycles qPCR was run to determine the additional number of cycles needed for the remaining 45 μL reaction. The libraries were then purified using the Zymo Clean and Concentrator kit.
ATAC-seq: DNA was prepared for single-end Illumina sequencing. 50 cycles of sequencing data were acquired on the HiSeq 3000 or Illumina NovaSeq 6000 (Illumina).

value: CH12 B cells


title: ATAC1158|Th2 T cells (Nippostronglysus infected)

source_name: Th2 T cells (Nippostronglysus infected)

value: Th2 T cells (Nippostronglysus infected)


title: Ch12 Maz Ko G4r1

description: library: RNAch12MazG4S1r1


title: ATAC1100|Long Term HSCs

source_name: Long Term HSCs

value: Long Term HSCs


title: ATAC1102|gamma delta TCR

source_name: gamma delta TCR

value: gamma delta TCR


title: ATAC1157|ILC2


title: ATAC1099|B cells aBCD180-activated

source_name: B cells aBCD180-activated

value: B cells aBCD180-activated


title: ATAC1103|gamma delta TCR Marco

source_name: gamma delta TCR Marco

value: gamma delta TCR Marco


title: ATAC1096|Sensorimotor Cortex

source_name: Sensorimotor Cortex

value: Sensorimotor Cortex


title: ATAC1095|Medulla Oblongata

source_name: Medulla Oblongata

value: Medulla Oblongata


title: ATAC1104|gamma delta TCR M/S -/-

source_name: gamma delta TCR M/S -/-

value: gamma delta TCR M/S -/-


title: ATAC1101|Short Term HSCs

source_name: Short Term HSCs

value: Short Term HSCs


title: ATAC1150|NK (IL2-IL12-activated)

source_name: NK (IL2-IL12-activated)

value: NK (IL2-IL12-activated)


title: ATAC1098|splenic B cells sample 2

source_name: splenic B cells

value: splenic B cells


title: ATAC1097|Cerebellum

source_name: Cerebellum

value: Cerebellum


title: ATAC1094|Putamen

source_name: Putamen

value: Putamen


title: ATAC1093|Frontal Cortex

source_name: Frontal Cortex

value: Frontal Cortex


title: ATAC1092|Olfactory Bulb

source_name: Olfactory Bulb

value: Olfactory Bulb


title: ATAC1905B|CH12 B cells clone bc12


title: ATAC1091|Optic nerve

source_name: Optic nerve

value: Optic nerve


title: ATAC1083|Placenta

source_name: Placenta

value: Placenta


title: ATAC1090|Neural retina

source_name: Neural retina

value: Neural retina


title: ATAC1087|Pancreas

source_name: Pancreas

value: Pancreas


title: ATAC1084|Spinal cord

source_name: Spinal cord

value: Spinal cord


title: ATAC1085|Stomach

source_name: Stomach

value: Stomach


title: Ch12 Klf16, Maz, Sp1, Zbtb7a Knockout control, DMSO rep3

description: library: RNACH12QKODMSOS1Rep3

source_name: Ch12 cell line

value: Ch12 cell line

value: Klf16, Maz, Sp1, Zbtb7a Knockout

value: control, DMSO

value: mRNA-Seq


title: ATAC1155|NCR+ILC3 IL23-treated

source_name: NCR+ILC3 IL23-treated

value: NCR+ILC3 IL23-treated


title: ATAC1080|Adrenal gland

source_name: Adrenal gland

value: Adrenal gland


title: ATAC1079|Mammary tissue

source_name: Mammary tissue

value: Mammary tissue


title: ATAC1077|Heart sample 2

source_name: Heart

value: Heart


title: ATAC1076|Muscle

source_name: Muscle

value: Muscle


title: ATAC1078|Adipose tissue sample 2

source_name: Adipose tissue

value: Adipose tissue


title: ATAC1075|Lung sample 3

source_name: Lung

value: Lung


title: ATAC1071|Small Intestine

source_name: Small Intestine

value: Small Intestine


title: ATAC1072|Large Intestine sample 2

source_name: Large Intestine

value: Large Intestine


title: ATAC1069|ES cells (E14)

source_name: ES cells (E14)

value: ES cells (E14)


title: ATAC1070|MEFs

source_name: MEFs

value: MEFs


title: Control rep1

city: New Delhi

first: Jyothish

middle: Madambikattil

last: Sasi

state: Delhi

address: BenitoJuarez Marg

department: Department of Plant Molecular Biology

country: India

institute: University of Delhi

data_processing:
NGS QC Toolkit software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Oryza sativa Japonica Group assembly Build 4.0 whole genome using TopHat.
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cuffdiff.
Assembly: NCBI Oryza sativa Japonica Group assembly Build 4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryza sativa

source_name: Coleoptile

growth_protocol: Rice seeds were surface sterilized and submerged for seven days in sterile water.

extract_protocol:
Coleoptiles were harvested, flash frozen on liquid nitrogen, and RNA was extracted using GITC method. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The seeds with coleoptile was transferred to aerobic condition

value: Coleoptile

tag: age

value: 7 days post germination

value: wild type

value: submergence


title: Control rep2


title: day 2 rep2

value: 9 days post germination


title: day 2 rep1


title: ATAC1082|Testis

source_name: Testis

value: Testis


title: ATAC1066|ISP (Immature single positive)

source_name: ISP (Immature single positive)

value: ISP (Immature single positive)


title: ATAC1065|DN3b


title: ATAC1064|DN3a


title: ATAC1063|DP

source_name: DP

value: DP


title: ATAC1062|Erythroblasts sample 2

source_name: Erythroblasts

value: Erythroblasts


title: Whole Blood, mixed, scRNAseq

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

country: Germany

institute: Helmholtz Institute for RNA-based Infection Research

description:
3 different individuals, paired with A6
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw sequencing data (bcl) were processed using Cell Ranger software (v3.1.0, 10x Genomics).
Raw sequencing data were converted to FASTQs with the command “cellranger mkfastq” and default parameters.
Read mapping to ERB genome, UMI counting and generating the count matrix were performed with the command “cellranger count” and default parameters.
Assembly: mRouAeg1.p + mitochondrial genome (GenBank: CM024382.1) after annotation
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rousettus aegyptiacus

source_name: Blood

growth_protocol: ERBs were kept in captive breeding colonies under quarantine conditions, according to current German Animal Welfare Regulations.

extract_protocol:
Peripheral blood was drawn from sedated animals. After whole blood or PBMC preparation, cells were filtered through 70µm Flowmi® cell strainers. Platelets were depleted by cell sorting using a 100µm nozzle, the lowest flow rate and the single cell setting of the cell sorter FACSAria Fusion (Becton Dickinson). Sorted cells were centrifuged at 400×g and 4°C for 15min. After centrifugation, the cell count was set at 1000cells/µl in 1x PBS + 20µg/ml UltraPure™ BSA. Samples were loaded on separated wells of a Chromium Next GEM Chip G before running on a Chromium controller.
Reverse transcription and cDNA library preparation were performed according to the manufacturer's instructions (GEM Single Cell 3’ Reagents Kits v3.1, 10x Genomics).

treatment_protocol: Whole Blood: Collected blood was immediately subjected to Red Blood Cell (RBC) lysis using 10X RBC lysis buffer (Biolegend) diluted 1:10 with endotoxin-free water. RBC lysis was performed twice. Washing steps were carried out in 1x PBS without calcium and magnesium, supplemented with 20µg/ml UltraPure™ BSA.

value: Blood

value: Circulating leukocytes

tag: library name

value: Mixed (1 adult and 2 subadults)


title: PBMCs, mixed, scRNAseq

description:
3 different individuals, paired with A5
10x Genomics

treatment_protocol: PBMCs: 400 µl of whole blood was each diluted in PBS with 20 µg/ml BSA. Diluted blood was added to 3 ml Ficoll-Paque PLUS (1.077 g/ml, Cytiva) and centrifuged at 760 ×g for 30 min without brakes or acceleration. PMBCs were collected and washed with PBS with 20 µg/ml BSA.

tag: cell type

value: Circulating leukocytes from PBMC fraction


title: Whole Blood, juveniles, scRNAseq

description:
3 different individuals
10x Genomics

value: Juveniles (approx. 1 year old)


title: ATAC1060|bone marrow-derived macrophages sample 2

source_name: bone marrow-derived macrophages

value: bone marrow-derived macrophages


title: ATAC1059|bone marrow-derived dendritic cells

source_name: bone marrow-derived dendritic cells

value: bone marrow-derived dendritic cells


title: Whole Blood, adults, scRNAseq

description:
3 different individuals
10x Genomics

value: Adults (older than 3 years old)


title: ATAC1056|CD4+CD8-TCRhiCD25-Foxp3+ T cells

source_name: CD4+CD8-TCRhiCD25-Foxp3+ T cells

value: CD4+CD8-TCRhiCD25-Foxp3+ T cells


title: ATAC1054|CD4-CD8+TCRhiCD69loCD24lo (MHCII-/- mice)


title: ATAC1055|CD4+CD8-TCRhiCD25+Foxp3- T cells

source_name: CD4+CD8-TCRhiCD25+Foxp3- T cells

value: CD4+CD8-TCRhiCD25+Foxp3- T cells


title: PHH_GenX_Control_Batch2

city: Kansas City

first: Dakota

last: Robarts

state: KS

address: 3901 Rainbow Blvd

institute: University of Kansas Medical Center

description: Gene expression after 96hr after GenX exposure

hyb_protocol: 45C, 17hr plus or minus 1hr, 60rpm using GeneChip Hybridization oven 645

scan_protocol: Single Scan using Affymetrix GeneChip Scanner 3000 7G with autoloader

data_processing: The data were analyzed withAffymetrix Standard GeneChip using Affymetrix default analysis settings and global scaling as normalization method. The scaling parameter was set to 500.

source_name: Cultured Hepatocytes

label_protocol: TdT terminal labeling with the GeneChip WT Plus Labeling Kit

growth_protocol: PHH were cultured at 37C and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: GenX was dissolved in Media for the concentrations of 0.1, 10, and 100 uM and were used on the PHH.

value: Untreated


title: ATAC1052|CD4+CD8intTCRhiCD69hiCD24hi T cells (MHCII-/- mice)


title: PHH_GenX_0.1uM_Batch2

value: GenX Treated


title: PHH_GenX_Control_Batch1


title: PHH_GenX_10uM_Batch2


title: ATAC1053|CD4-CD8+TCRhiCD69hiCD24hi T cells (MHCII-/- mice)


title: ATAC1057|CD4+CD8-TCRhiCD25+Foxp3+ T cells

source_name: CD4+CD8-TCRhiCD25+Foxp3+ T cells

value: CD4+CD8-TCRhiCD25+Foxp3+ T cells


title: ATAC1050|CD4+CD8-TCRhiCD69hiCD24hiCD25- T cells (Beta-2 microglobulin-/- mice)


title: PHH_GenX_100uM_Batch1


title: ATAC1048|CD4+CD8+CD69lo small DP precursors

source_name: CD4+CD8+CD69lo small DP precursors

value: CD4+CD8+CD69lo small DP precursors


title: ATAC1051|CD4+CD8-TCRhiCD69loCD24loCD25- T cells (Beta-2 microglobulin-/- mice)


title: ATAC1047|CD4+CD8+CD69lo large DP precursors

source_name: CD4+CD8+CD69lo large DP precursors

value: CD4+CD8+CD69lo large DP precursors


title: ATAC1045|CD4+ T cells sample 3

source_name: CD4+ T cells

value: CD4+ T cells


title: Ferret_Lung_Native_1717

city: Seattle

first: kathie

last: walters

state: WA

address: 401 Terry Ave N

institute: Institute for Systems Biology

description: Gene expression profiling of lung tissue from control ferrets

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
processed data file contains: normalized intensity values

organism: Mustela putorius furo

source_name: Day 5_PBS

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.3 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA was isolated from lung tissue using RNAeasy (Qiagen) according to manufacturer's instructions.RNA quality was assessed using Agilent Bioanalyzer.

treatment_protocol: Lung tissue collected from mice and stored in RNAlater  according to manufacturer's instructions.

value: Lung

tag: virus strain

value: PBS

tag: day p.i.

value: Day 5

tag: vaccination status

value: not vaccinated


title: Ferret_Lung_H10N7_IM_E6176

description: Gene expression profiling of lung tissue from influenza infected ferrets

source_name: Day 5_H10N7_IM

value: vaccinated


title: ATAC1046|CD4+ T cells MUT

source_name: CD4+ T cells MUT

value: CD4+ T cells MUT


title: ATAC1043|Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)

source_name: Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)

value: Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)


title: ATAC1042|non-Tfh T cells (CD4+CD44+CXCR5-PD1-CD25-) activated MUT


title: ATAC1040|Tfhs Mut

source_name: Tfhs Mut

value: Tfhs Mut


title: ATAC1041|non-Tfh T cells (CD4+CD44+CXCR5-PD1-CD25-) activated


title: Ferret_Lung_H10N7_IM_E6177


title: ATAC1039|Tfhs

source_name: Tfhs

value: Tfhs


title: Ferret_Lung_H10N7_Mock_E6182

source_name: Day 5_H10N7_PBS


title: ATAC1037|Tfhs from LCMV-infected mice

source_name: Tfhs from LCMV-infected mice

value: Tfhs from LCMV-infected mice


title: Ferret_Lung_Native_1716


title: ATAC1049|CD4+CD8intTCRhiCD69hiCD24hi T cells (Beta-2 microglobulin-/- mice)


title: Ferret_Lung_Native_1715


title: Ferret_Lung_H10N7_Mock_E6184


title: Ferret_Lung_H10N7_Mock_E6183


title: ATAC1036|neutrophils

source_name: neutrophils

value: neutrophils


title: ATAC1035|eosinophils (from spleens)

source_name: eosinophils (from spleens)

value: eosinophils (from spleens)


title: Ferret_Lung_H1N1_(SW31)_Mock_E5467

source_name: Day 5_H1N1 (SW31)_PBS


title: ATAC1034|eosinphils (ex-vivo-derived)

source_name: eosinphils (ex-vivo-derived)

value: eosinphils (ex-vivo-derived)


title: ATAC1033|basophils

source_name: basophils

value: basophils


title: Ferret_Lung_H10N7_Mock_E6185


title: Ferret_Lung_H1N1_(SW31)_IN_E5456

source_name: Day 5_H1N1 (SW31)_IN


title: ATAC1031|B cells aCD40+IL4-activated

source_name: B cells aCD40+IL4-activated

value: B cells aCD40+IL4-activated


title: Ferret_Lung_H2N7_Mock_E6703_replicate

source_name: Day 5_H2N7_PBS


title: ATAC1032|mast cells

source_name: mast cells

value: mast cells


title: ATAC1029|B cells LPS+a-d-dextran-activated

source_name: B cells LPS+a-d-dextran-activated

value: B cells LPS+a-d-dextran-activated


title: ATAC1028|B cells LPS+IL21-activated

source_name: B cells LPS+IL21-activated

value: B cells LPS+IL21-activated


title: Ferret_Lung_H1N1_(SW31)_IM_E5462

source_name: Day 5_H1N1 (SW31)_IM

value: Lung


title: Ferret_Lung_H3N2_(Port_Chambers)_IN_E5485

source_name: Day 5_H3N2 (Port_Chambers)_IN

value: H3N2 (Port_Chambers)

value: Day 5


title: ATAC1027|B cells LPS+IL4-activated

source_name: B cells LPS+IL4-activated

value: B cells LPS+IL4-activated


title: ATAC1026|B cells LPS-activated

source_name: B cells LPS-activated

value: B cells LPS-activated


title: ATAC1025|plasma cells

source_name: plasma cells

value: plasma cells


title: Ferret_Lung_H10N7_IN_E6170

source_name: Day 5_H10N7_IN

value: vaccinated


title: Ferret_Lung_H10N7_IN_E6168


title: Ferret_Lung_H2N7_Mock_E6705

value: not vaccinated


title: ATAC1023|B1 B cells

source_name: B1 B cells

value: B1 B cells


title: Ferret_Lung_H2N7_IM_E6695

source_name: Day 5_H2N7_IM


title: Ferret_Lung_H3N2_(Port_Chambers)_Mock_E5497

source_name: Day 5_H3N2 (Port_Chambers)_PBS


title: Ferret_Lung_H2N7_IM_E6694


title: Ferret_Lung_H2N7_Mock_E6703


title: Ferret_Lung_H2N7_IN_E6687

source_name: Day 5_H2N7_IN


title: ATAC1022|MZ B cells

source_name: MZ B cells

value: MZ B cells


title: ATAC1021|mature B cells

source_name: mature B cells

value: mature B cells


title: Ferret_Lung_H1N1_(SW31)_IM_E5461


title: Ferret_Lung_H2N7_IM_E6697


title: ATAC1019|preB cells sample 2

source_name: preB cells

value: preB cells


title: Ferret_Lung_H1N1_(SW31)_IN_E5455

source_name: Day 5_H1N1 (SW31)_IN


title: ATAC1044|Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+) MUT


title: ATAC1020|immature B cells

source_name: immature B cells

value: immature B cells


title: ATAC1024|GC B cells

source_name: GC B cells

value: GC B cells


title: ATAC1017|NK cells (from spleen)

source_name: NK cells (from spleen)

value: NK cells (from spleen)


title: ATAC1010|Th17


title: Ferret_Lung_H3N2_(Port_Chambers)_IM_E5492

source_name: Day 5_H3N2 (Port_Chambers)_IM


title: ATAC1018|proB cells

source_name: proB cells

value: proB cells


title: Ferret_Lung_H10N7_IM_E6175

source_name: Day 5_H10N7_IM


title: ATAC1009|CD4+ memory T cells (CD25-CCR6-)

source_name: CD4+ memory T cells (CD25-CCR6-)

value: CD4+ memory T cells (CD25-CCR6-)


title: Ferret_Lung_H2N7_IN_E6689

value: Lung


title: Ferret_Lung_H3N2_(Port_Chambers)_IN_E5486

source_name: Day 5_H3N2 (Port_Chambers)_IN

value: H3N2 (Port_Chambers)


title: Ferret_Lung_H3N2_(Port_Chambers)_Mock_E5498

value: Day 5


title: ATAC1004|CD8+ T cells

source_name: CD8+ T cells

value: CD8+ T cells


title: ATAC1002|MPP HSCs

source_name: MPP HSCs

value: MPP HSCs


title: Ferret_Lung_H2N7_Mock_E6704

source_name: Day 5_H2N7_PBS


title: Ferret_Lung_H2N7_IM_E6696

source_name: Day 5_H2N7_IM


title: RNA1905S5|CH12 B cells clone bc5

data_processing:
Base calling: Illumina CASAVA 1.8.2
mRNA-Seq: Align raw reads to the reference genome with STAR.
mRNA-Seq: Quantify transcript and gene abundances with RSEM.
mRNA-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig, RSEM output

source_name: CH12 B cells clone bc5

growth_protocol: CH12 B lymphoma cells were cultured in RPMI-1640 media supplemented with 10% FBS (Gemini), 1% Penicillin-Streptomycin and 50 µM of b-mercaptoethanol (Thermo Fisher Scientific).  Mature B cells were isolated from C57BL/6J mouse spleen by negative selection (StemCell Technologies).

value: CH12 B cells clone bc5


title: control_lung_Mock_d8_rep1

description: Gene expression profiling of lung tissue from control mice

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

extract_protocol: Total RNA was isolated from lung tissue using RNAeasy (Qiagen) according to manufacturer's instructions.  RNA quality was assessed using Agilent Bioanalyzer.

value: Mock


title: RNA1231A|CD4+ T cells (ConA-activated)

source_name: CD4+ T cells (ConA-activated)

value: CD4+ T cells (ConA-activated)


title: control_lung_Mock_d8_rep3

value: not vaccinated


title: Ferret_Lung_H1N1_(SW31)_Mock_E5468

source_name: Day 5_H1N1 (SW31)_PBS


title: RNA1289A|Back skin

source_name: Back skin

value: Back skin


title: RNA1098A|splenic B cells

source_name: splenic B cells

value: splenic B cells


title: Ferret_Lung_H2N7_Mock_E6702


title: control_lung_Mock_d8_rep4


title: Ferret_Lung_H10N7_IM_E6174

value: vaccinated


title: RNA1096A|Sensorimotor Cortex

source_name: Sensorimotor Cortex

value: Sensorimotor Cortex


title: Ferret_Lung_H10N7_IN_E6169

source_name: Day 5_H10N7_IN


title: Ferret_Lung_H2N7_IN_E6686

source_name: Day 5_H2N7_IN


title: RNA1095A|Medulla Oblongata

source_name: Medulla Oblongata

value: Medulla Oblongata


title: RNA1094A|Putamen

source_name: Putamen

value: Putamen


title: H6N1_6dpc_Mock_F_564_LP

description: Gene expression profiling of lung tissue from influenza infected mice


title: Ferret_Lung_H3N2_(Port_Chambers)_IM_E5491

source_name: Day 5_H3N2 (Port_Chambers)_IM


title: H6N1_6dpc_Mock_F_564_DP


title: RNA1046A|CD4+ T cells MUT

source_name: CD4+ T cells MUT

value: CD4+ T cells MUT


title: RNA1044A|Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+) MUT


title: Ferret_Lung_H10N7_IN_E6171


title: Ferret_Lung_H2N7_IN_E6688


title: H6N1_6dpc_IM_F_563_DP


title: RNA1045A|CD4+ T cells

source_name: CD4+ T cells

value: CD4+ T cells


title: H6N1_6dpc_Mock_F_566_RP

value: Lung


title: H6N1_6dpc_IM_F_563_LP


title: RNA1043A|Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)

source_name: Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)

value: Tfrs T cells (CD4+CD44+CXCR5+PD1+CD25+)


title: RNA1042A|non-Tfh T cells (CD4+CD44+CXCR5-PD1-CD25-) activated MUT


title: RNA1041A|non-Tfh T cells (CD4+CD44+CXCR5-PD1-CD25-) activated


title: H6N1_6dpc_IN_F_560_LP


title: RNA1040A|Tfhs Mut

source_name: Tfhs Mut

value: Tfhs Mut


title: RNA1039A|Tfhs

source_name: Tfhs

value: Tfhs


title: RNA1031C|B cells aCD40+IL4-activated

source_name: B cells aCD40+IL4-activated

value: B cells aCD40+IL4-activated


title: H6N1_6dpc_Mock_F_564_NP


title: RNA1033B|basophils

source_name: basophils

value: basophils


title: H6N1_6dpc_IM_F_563_2RP


title: RNA1029C|B cells LPS+a-d-dextran-activated

source_name: B cells LPS+a-d-dextran-activated

value: B cells LPS+a-d-dextran-activated


title: RNA1028A|B cells LPS+IL21-activated

source_name: B cells LPS+IL21-activated

value: B cells LPS+IL21-activated


title: H6N1_6dpc_IN_F_560_DP


title: RNA1027A|B cells LPS+IL4-activated

source_name: B cells LPS+IL4-activated

value: B cells LPS+IL4-activated


title: H6N1_6dpc_IN_F_560_2RP


title: H6N1_3dpc_Mock_F_565_RP

value: not vaccinated


title: H6N1_6dpc_IM_F_563_NP


title: RNA1026C|B cells LPS-activated

source_name: B cells LPS-activated

value: B cells LPS-activated


title: H6N1_6dpc_IN_F_560_NP

value: vaccinated


title: H6N1_3dpc_Mock_F_565_2RP


title: H6N1_3dpc_IM_F_562_RP


title: H6N1_3dpc_Mock_F_565_LP


title: H6N1_3dpc_Mock_F_565_DP


title: H6N1_3dpc_IM_F_562_LP


title: H6N1_3dpc_IM_F_562_DP


title: 215_3

source_name: CRC Plasma

value: CRC Plasma

tag: disease state

value: CRC


title: 215_2


title: 53_5


title: control_lung_Mock_d8_rep2

value: Mock


title: H6N1_3dpc_IN_F_559_RP


title: H6N1_3dpc_IM_F_562_2RP


title: H6N1_3dpc_IN_F_559_LP


title: 53_4


title: 53_3


title: 215_4


title: H6N1_3dpc_IN_F_559_DP


title: H6N1_3dpc_IN_F_559_2RP


title: H10N7_3dpc_IN_F_603_RP


title: H7N1_6dpc_Mock_F_600_2RP


title: H7N1_6dpc_Mock_F_600_NP


title: 53_2


title: 53_1


title: 1798_4


title: 1798_5


title: 1798_3


title: 1798_2


title: 1409_5


title: RNA1099C|B cells aBCD180-activated

source_name: B cells aBCD180-activated

value: B cells aBCD180-activated


title: 1798_1


title: H7N1_6dpc_IM_F_596_NP


title: 1409_3


title: 215_1


title: H7N1_6dpc_IM_F_597_NP


title: 1409_1


title: 1409_2


title: H7N1_3dpc_Mock_F_600_DP


title: H7N1_6dpc_IN_F_594_NP


title: H7N1_6dpc_Mock_F_599_NP


title: 1014_6


title: H7N1_6dpc_IN_F_594_2RP


title: H7N1_6dpc_IM_F_597_2RP


title: 1014_4


title: 1014_5


title: 1014_2


title: 1014_1


title: 1014_3


title: 1066_5


title: H7N1_3dpc_IM_F_597_LP


title: H7N1_6dpc_IN_F_593_NP


title: H7N1_3dpc_IM_F_597_DP


title: H7N1_3dpc_IN_F_594_RP


title: H7N1_3dpc_IN_F_594_LP


title: H7N1_3dpc_IN_F_594_DP


title: H7N1_3dpc_Mock_F_600_RP


title: 1066_4


title: H7N1_3dpc_Mock_F_600_LP


title: H10N7_6dpc_IM_F_607_NP


title: 1066_1


title: 507_5


title: 1066_3


title: H10N7_6dpc_IM_F_607_2RP


title: H10N7_6dpc_Mock_F_610_LP


title: 507_1


title: H10N7_6dpc_Mock_F_610_DP


title: H10N7_6dpc_IN_F_604_NP


title: H10N7_6dpc_IM_F_607_DP


title: H10N7_6dpc_Mock_F_610_2RP


title: 507_3


title: H10N7_6dpc_IN_F_604_2RP


title: 507_2


title: H10N7_6dpc_IM_F_607_LP


title: 839_5


title: 839_6


title: 1409_4


title: H10N7_6dpc_Mock_F_610_2RP_replicate


title: 839_3


title: H10N7_6dpc_Mock_F_610_NP


title: 507_4


title: 839_4


title: 839_1


title: 839_2


title: H10N7_3dpc_Mock_F_609_2RP


title: H10N7_3dpc_Mock_F_609_DP


title: H10N7_6dpc_Mock_F_610_NP_replicate


title: 519_7


title: 519_6


title: H10N7_6dpc_IN_F_604_DP


title: 519_5


title: 519_4


title: 519_3


title: H10N7_6dpc_IN_F_604_LP


title: H10N7_3dpc_IM_F_606_DP


title: H10N7_3dpc_IM_F_606_2RP


title: 1176_3


title: H10N7_3dpc_IN_F_603_DP


title: 1176_1


title: aPD1_PDL1-il2v_6

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

data_processing:
Aligned with Hisat2 to mm10
Reads counted with subread/featurecounts
normalization and differential expression with DEseq2

source_name: Spleen

extract_protocol:
Direct-zol RNA Microprep kit
library contruction protocol: Clontech SMART-seq v4 Ultra Low Input RNA

value: Spleen

value: DbGP33+ CD8+ T cells

value: muPD-L1 + muPD1-IL2v


title: aPD1_PDL1-il2v_5


title: H10N7_3dpc_IM_F_606_RP

value: Lung


title: H10N7_3dpc_IN_F_603_2RP


title: H10N7_3dpc_Mock_F_609_LP


title: PD1-IL2v_4


title: PD1-IL2v_5


title: H10N7_3dpc_IM_F_606_LP


title: 386_5

data_processing:
Adapter trimming was done using Cutadapt
Alignment and determination of methylation status was done using Bismark
Deduplication was done using Picard tools
Assembly: hg38
Supplementary files format and content: Methylation extractor output file for CpG context


title: aPDL1_PD1-il2v_4


title: aPD1_PDL1-il2v_3

extract_protocol:
Rneasy Micro kit
library contruction protocol: Clontech SMART-seq v4 Ultra Low Input RNA


title: H10N7_3dpc_Mock_F_609_RP


title: 519_2


title: 386_4


title: 1176_5


title: 1066_2


title: 386_3


title: aPDL1_PD1-il2v_1


title: aPD1_PDL1-il2v_2


title: 1176_4


title: PD1-IL2v_3


title: PD1-IL2v_2


title: 386_1


title: 1176_2


title: 357_6


title: aPDL1_2


title: 357_5


title: aPDL1_1


title: 357_3


title: untreated_1

value: untreated


title: 357_2


title: 357_1


title: PD1-IL2v_1


title: naïve_1

value: CD44lo CD8+ T cells

value: uninfected


title: naïve_2


title: muPDL1_PD1IL2v_2

description: Batch1-same batch as GSE206722

extract_protocol:
Rneasy Micro kit
library contruction protocol: Nugen Ovation V2


title: muPDL1_PD1IL2v_3

description: Batch1-same batch as GSE206722


title: Inner ear organoid WT d20 PAX2nG- 7AAD-

city: Indianapolis

first: Tsubasa

last: Saeki

state: IN

address: 980 W Walnut St

department: Otolaryngology-Head and Neck Surgery

institute: Indiana University School of Medicine

description: 10x Genomics

data_processing:
Illumina's Real Time Analysis software was used to generate a BCL file, which was subsequently de-multiplexed and converted to a FASTQ file by the bcl2fastq Conversion Software (Illumina).
The Cell Ranger pipeline was used to process the FASTQ file as follows: De-multiplexed reads were mapped to the GRCh38/hg38 human reference genome with the STAR (Spliced Transcripts Alignment to a Reference) aligner, mapped reads were grouped by cell barcode, and single-cell gene expression was quantified using unique molecular identifiers (UMIs).
The resulting filtered gene-barcode (count) matrix was used as input for downstream analysis.
Assembly: GRCh38/hg38

source_name: Inner ear organoids

growth_protocol: Human inner ear organoids were derived from hESCs following our previous protocol with modifications. Briefly, to start differentiation, hESCs cultured on 6-well plates were washed three times with DPBS (Thermo Fisher) followed by dissociation with accutase (Thermo Fisher) for 8 min at 37°C. Dissociated cells were pelleted by centrifuging for 3 min at 100×g and were resuspended in E8fn medium containing 20 µM Y-27632 (Stemcell Technologies) to a final concentration of 35,000 cells/mL. 100 µL of cells were added to each well (3,500 cells per well) of Nunclon Sphera low-binding 96-well U-bottom plate(s) (Thermo Fisher) and were centrifuged to the bottom of the wells at 120×g for 5 min. After ≥4 h of incubation at 37˚C 5% CO2, 100 µL of E8fn were added to each well to decrease the concentration of Y-27632 to 10 µM. Following a 48 h incubation after cell seeding, the aggregates were transferred to fresh low-binding 96U plates in 180 µL of chemically defined medium (CDM) containing 2% Matrigel (Corning), 10 µM SB-431542 (Stemcell Technologies), 4 ng/mL FGF-2 (Stemcell Technologies), and 100 pg/mL BMP-4 (ReproCell) to initiate non-neural induction – that is, differentiation day 0 (d0). CDM contained a 1:1 mixture of F-12 Nutrient Mixture with GlutaMAX (Thermo Fisher) and Iscove’s Modified Dulbecco’s Medium with GlutaMAX (IMDM; Thermo Fisher), additionally supplemented with 0.5% Bovine Serum Albumin (BSA, Sigma), 1× Chemically Defined Lipid Concentrate (Thermo Fisher), 7 µg/mL Insulin (Sigma), 15 µg/mL Transferrin (Sigma), 450 µM Mono-Thioglycerol (Sigma), and 100 µg/mL Normocin (Invivogen). On day 4 of differentiation culture, 45 µL of CDM containing 250 ng/mL FGF-2 (50 ng/mL final concentration) and 1 µM LDN-193189 (200 nM final concentration; ReproCell) was added to the pre-existing 180 µL of media in each well. On day 8 of differentiation culture, 45 µL of CDM containing 18 µM CHIR-99021 (3 µM final concentration; Stemcell Technologies) was added to the pre-existing 225 µl of media in each well. On differentiation day 11, the aggregates were pooled together, washed with DMEM:F12 with HEPES (Thermo Fisher), and resuspended in freshly prepared Organoid Maturation Medium (OMM) supplemented with 1% Matrigel and 3 µM CHIR-99021. The OMM medium contains a 1:1 mixture of Advanced DMEM:F12 (Thermo Fisher) and Neurobasal Medium (Thermo Fisher) supplemented with 0.5× N2 Supplement (Thermo Fisher), 0.5× B27 without Vitamin A (Thermo Fisher), 1× GlutaMAX (Thermo Fisher), 0.1 mM β-Mercaptoethanol (Thermo Fisher), and 100 µg/mL Normocin. Starting from day 11, the aggregates were cultured stationary on non-coated 100 mm dishes. On day 13 and day 15, medium was changed with OMM supplemented with 3 µM CHIR-99021. Starting on day 18, the aggregates were cultured in OMM without additional supplements. OMM medium change were performed twice a week or when the color of the medium start to turn orange or slightly yellow. Aggregates can be gently washed off the dishes and transferred to new 100 mm dishes during medium change to get rid of the migrating cells growing adherently on the dishes, which may compete with the aggregates to consume the culture medium. To start differentiation of the WT-CHD7KO/KO chimeric cultures, WT (AAVS1mT) and CHD7KO/KO hESCs were separately dissociated and resuspended to a final concentration of 35,000 cells/mL. Equal volume of WT and CHD7KO/KO hESCs were mixed in a fresh tube, followed by seeding of 100 µL of the cell mixture to each well of low-binding 96U plates (3,500 cells per well). The rest of the culture procedures were the same as regular organoid cultures.

extract_protocol:
For d20 WT vs. CHD7KO/KO scRNA-seq, 30 WT aggregates (PAX2nG) and 30 CHD7KO/KO aggregates (CHD7KO/KO PAX2nG) (as well as 10 WA25 control aggregates dissociated in separate tubes and wells) were washed three times with DPBS, three times with 1.1 mM EDTA, followed by resuspension in an accutase solution. 10–15 aggregates were transferred to each well of a Nunclon Sphera low-binding 6-well plate (Thermo Fisher) along with 3 mL of accutase. The plates were incubated at 37˚C 5% CO2 for 90 min with gentle trituration every 5–10 min with a wide-bore P1000 pipet tip. Dissociated cells were filtered through a 100 µm cell strainer and then a 40 µm cell strainer (Corning), and then centrifuged in 2 mL round-bottom tubes at 100 × g for 3 min. Cell pellets were resuspended in a DMEM:F12 solution (with HEPES, no phenol red; Thermo Fisher) supplemented with 10% FBS (Thermo Fisher) and 1:500 propidium iodide (Thermo Fisher) cell viability dye. GFP+ propidium iodide- cells were sorted into a DMEM:F12 (with HEPES, no phenol red) solution supplemented with 10% FBS on a SORP Aria FACS machine (BD Biosciences) for 1 h at Indiana University Flow Cytometry Resource Facility, using dissociated cells from d20 WA25 aggregates as negative control for gating. For d20 WT PAX2nG+ and PAX2nG– scRNA-seq, the cell dissociation and FACS sorting were performed similarly, with the exception that 1:500 7-AAD (BioLegend) was used as a viability dye, and that both GFP+ and GFP– populations were separately collected for downstream scRNA-seq experiments. To enrich hair cells and supporting cells from d70 WT (POU4F3nT PAX2nG) and CHD7KO/+ (CHD7KO/+ POU4F3nT PAX2nG) organoids, tissues containing vesicle structures harboring the POU4F3nT-positive hair cells were micro-dissected from the rest of the d70 aggregates with fine tweezers (Dumont) under a fluorescence stereomicroscope. The dissected d70 organoid tissues were dissociated and FACS sorted in a similar way as d20 organoids, with the exception that no viability dye was used. tdTomato+ and tdTomato– cell populations were collected in separate tubes for separate downstream scRNA-seq reactions. For d70 WT (POU4F3nT PAX2nG) vs. CHD7KO/KO (CHD7KO/KO PAX2nG) scRNA-seq, the POU4F3nT FACS sorting strategy can no longer be used to enrich the otic epithelial cell types, as the CHD7KO/KO organoids do not generate any POU4F3nT+ hair cells. Therefore, while POU4F3nT fluorescence signals was still used as a guide for micro-dissection for the WT organoids, phase contrast live imaging was used for micro-dissection of the CHD7KO/KO organoids to enrich tissues containing vesicle morphological structures. After tissue dissociation, cells were stained with 1:100 PE-conjugated EPCAM antibody (BioLegend) by nutating at 4˚C for 40 min in dark. No viability dye was co-stained. After antibody staining, cells were washed twice prior to FACS sorting. Both PE-EPCAM+ and PE-EPCAM– populations were collected in separate tubes for separate downstream scRNA-seq reactions. For WT samples, as the POU4F3nT+ hair cells also express EPCAM on their cell surface, the hair cells exhibit both tdTomato and PE fluorescence signals, both of which are red. As such, the WT hair cells were FACS-isolated as a sub-population of PE-EPCAM+ cell. The POU4F3nT reporter is highly specific to the EPCAM-expressing hair cells, and the PE-EPCAM– population does not contain any POU4F3nT signals.
Sorted single cells were captured, lysed, and cDNA libraries were generated using a Chromium Controller and Single Cell 3' Reagent Kits V3 (10X Genomics) following the manufacturer's instructions. cDNA library quality was verified using a bioanalyzer (Agilent Technologies), followed by sequencing using the NovaSeq 6000 sequencing system (Illumina) at Indiana University School of Medicine Center for Medical Genomics.

value: Inner ear organoids

tag: facs isolation_strategy

value: PAX2nG negative; 7AAD negative

value: WA25 human ESCs

tag: developmental stage

value: day 20


title: Inner ear organoid WT d70 EPCAM-

description: 10x Genomics

tag: cell line

value: EPCAM-PE negative

value: day 70


title: HFEXT7-IP

city: beijing

first: wenhao

last: ju

state: chaoyang

address: yabaolu

institute: shouduerkeyanjiusuo

data_processing:
3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3)
clean reads of all libraries were aligned to the reference genome by Hisat2 software (v2.0.4)
Methylated sites on RNAs (peaks) were identified by exomePeak software
Differentially methylated sites were identified by diffReps
Assembly: mm10
Supplementary files format and content: excel format

source_name: exercise group IP for m6A

extract_protocol:
Total RNA was extracted by Trizol reagent
RNA immunoprecipitation was performed with the m6A antibody.Both the input sample without immunoprecipitation and the m6A IP samples were used for RNA-seq library generation with NEBNext® Ultra™ RNA Library Prep Kit . Library sequencing was performed on an illumina NovaSeq 6000 instrument with 150bp paired-end reads

tag: strain

value: heart

tag: condition

value: exercise group


title: HFEXT14-input

source_name: exercise group input for m6A


title: HFEXT14-IP


title: Inner ear organoid CHD7-/- d70 EPCAM-

description: 10x Genomics


title: Inner ear organoid WT d70 EPCAM+

description: 10x Genomics

value: EPCAM-PE positive


title: Inner ear organoid WT d20 PAX2nG+ 7AAD-

description: 10x Genomics

value: PAX2nG positive; 7AAD negative


title: HFEXT7-input


title: muPDL1_PD1IL2v_1

description: Batch1-same batch as GSE206722

value: Spleen


title: Inner ear organoid CHD7-/+ d70 POU4F3nT+

description: 10x Genomics

value: POU4F3nT positive


title: 357_4

extract_protocol:
cell-free DNA was extracted using Qiagen QiaAmp Circulating Nucleic Acids kit
5-10 ng of cfDNA was used as input for library construction using Kapa hyper prep kit
End repair and A-tailing using Kapa hyper prep kit and methylated Truseq nano adapters. Bisulfite conversion was done using Zymo EZ DNA Methylation-Gold kit

value: CRC Plasma

value: CRC


title: Inner ear organoid CHD7-/+ d70 POU4F3nT-

description: 10x Genomics

value: POU4F3nT negative


title: untreated_2

value: DbGP33+ CD8+ T cells

value: untreated


title: HFEXT6-input


title: HF43-IP

source_name: control IP for m6A

value: control


title: HFEXT6-IP


title: Inner ear organoid WT d70 POU4F3nT-

description: 10x Genomics

value: Inner ear organoids


title: HF37-IP


title: Inner ear organoid CHD7-/- d20 PAX2nG+ PI-

description: 10x Genomics

value: PAX2nG positive; PI negative

value: WA25 human ESCs


title: HF37-input

source_name: control input for m6A


title: Inner ear organoid WT d20 PAX2nG+ PI-

description: 10x Genomics

value: day 20


title: Inner ear organoid WT d70 POU4F3nT+

description: 10x Genomics

value: day 70


title: Inner ear organoid CHD7-/- d70 EPCAM+

description: 10x Genomics


title: HF43-input

value: heart


title: HF36-IP


title: HF36-input


title: Arid1b P120 PFC vehicle wildtype 3

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.4.1.1) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file include normalized read count metrix calculated by using DESeq2.

source_name: Brain

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage and the pups are weaned on P21.

extract_protocol:
RNA samples were prepared for sequencing using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Fluoxetine hydrochloride (0.1 mg/ml in 0.2 % saccharin-based drinking water) was delivered to dams to treat fluoxetine to pups via mammary milks. Dams in the vehicle group were fed with 0.2% saccharin water without fluoxetine. Drug treatment was done from postnatal day 3 to postnatal day 21. At postnatal day 21, mice were weaned and co-housed in cages with 3–6 mice in the same genetic background. After weaning, mice were fed with normal drinking water. Brain samples were collected at postnatal day 120.

value: prefrontal cortex

value: Postnatal day 120

tag: Sex

value: male


title: PP2A WT CD4+T Cell 2

city: HangZhou

first: Jiang

last: Yu

address: Yuhangtang road 866

institute: Zhejiang University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp. We used HISAT2 (https://ccb.jhu.edu/software/hisat2) to map reads to the reference genome of Mus musculus GRCm38
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters.
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/). After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: GRCm38
Supplementary files format and content: Excel file includes FPKM values and counts for each Sample

source_name: spleen

growth_protocol: Primary CD4+T cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS), penicillin and streptomycin, HEPES, sodium pyruvate  2-mercaptoethanol  antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using RNAeasy Plus Mini kit (Qiagen).
The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Naive CD4+ T cell was stimulated with 2ug/ml plate-bound anti-CD3/28

tag: tissue

value: spleen

value: primary CD4+ T cell

tag: genotype

value: PP2A WT

value: TCR Stimulation


title: PP2A CKO CD4+T Cell 3

value: PP2A CKO

tag: treatment


title: H7N1_3dpc_IM_F_597_RP

value: Lung

value: vaccinated


title: PP2A CKO CD4+T Cell 2


title: PP2A CKO CD4+T Cell 1


title: PP2A WT CD4+T Cell 1


title: PP2A WT CD4+T Cell 3


title: Arid1b P120 PFC fluoxetine wildtype 1


title: Arid1b P120 PFC fluoxetine wildtype 2


title: Arid1b P120 PFC vehicle wildtype 2


title: Arid1b P120 PFC fluoxetine wildtype 4


title: Arid1b P120 PFC fluoxetine wildtype 3


title: Arid1b P120 PFC vehicle hetero 2


title: Arid1b P120 PFC vehicle hetero 4


title: Arid1b P120 PFC vehicle hetero 1


title: Arid1b P120 PFC vehicle hetero 3


title: H10N7_3dpc_IN_F_603_LP


title: Arid1b P120 PFC fluoxetine hetero 3


title: Arid1b P120 PFC fluoxetine hetero 2


title: Arid1b P10 wildtype replicate 4

data_processing:
Transcript abundance was estimated with Salmon(v1.1.0) in Quasi-mapping-based mode onto the Mus musculus genome (GRCm38) with GC bias correction (--gcBias).
Quantified gene-level abundance data was imported to R (v.4.1.1) with tximport package and differential gene expression analysis was carried out using R/Bioconductor DEseq2 (v1.30.1).
The normalized read counts were computed by dividing the raw read counts by size factors and fit to a negative binomial distribution.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file includes normalized read count matrix calculated by using DESeq2.

growth_protocol: Mice were fed ad libitum under a 12-h dark/light cycle. A mother mouse reared two to eight wild-type and knock-out mouse pups in one cage.

value: Postnatal day 10

value: Arid1b wildtype


title: Arid1b P10 wildtype replicate 2


title: Arid1b P120 PFC vehicle wildtype 4


title: Arid1b P120 PFC vehicle wildtype 1


title: Arid1b P10 heterozygous replicate 5

value: Arid1b heterozygote


title: Arid1b P3 wildtype replicate 5

value: WT

value: whole brain

value: Postnatal day 3


title: Arid1b P3 wildtype replicate 3


title: Arid1b P10 wildtype replicate 5


title: Arid1b P10 heterozygous replicate 1


title: Arid1b P3 wildtype replicate 1


title: Arid1b P10 heterozygous replicate 2


title: Arid1b P10 heterozygous replicate 4


title: Arid1b P3 heterozygous replicate 3

value: Arid1b heterozygous


title: Arid1b P120 PFC fluoxetine hetero 4

value: prefrontal cortex


title: Arid1b P120 PFC fluoxetine hetero 1

value: Postnatal day 120


title: Arid1b P10 wildtype replicate 3

value: male


title: CAST/EiJ x BALB/c F1 T Cells Input Rep3

description: library:ChIPCastXBalbcF1TCellS2InputRep3

data_processing:
Base calling: Illumina CASAVA 1.8.2
ChIP-Seq: Align raw reads to the reference genome with bowtie2 (default parameters).
ChIP-Seq: Remove duplicates with picard.
ChIP-Seq: Keep high-quality reads with MAPQ>=30.
ChIP-Seq: Make bigwig track with bedtools and bedGraphToBigWig.
ChIP-Seq: Call peak with MACS2.
Assembly: mm10

source_name: T Cells

growth_protocol: Mature B and T cells were isolated by negative selection (StemCell Technologies)

extract_protocol:
ChIP-Seq: Cultured cells were fixed with 1% formaldehyde (Sigma) for 10’ at 37°C. Fixation was quenched by addition of glycine (Sigma) at a final concentration of 125 mM. Twenty million fixed cells were washed with PBS and stored at −80°C until further processing or resuspended in 800 uL of RIPA buffer (10 mM Tris pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% sodium deoxycholate, 1% Triton X-100, 1 × Complete Mini EDTA free proteinase inhibitor (Roche)). Sonication was performed using Bioruptor sonicator, 30 cycles of 30” sonication and 30” of pause. Five microgram of respective antibody was incubated with 40 μL of Dynabeads Protein A (or G) for 40 min at room temperature. Antibody-bound beads were added to 500 μL of sonicated chromatin, incubated at 4°C overnight, and washed twice with RIPA buffer, twice with RIPA buffer containing 0.3M NaCl, twice with LiCl buffer (0.25 M LiCl, 0.5% Igepal-630, 0.5% sodium deoxycholate), once with TE (pH 8.0) plus 0.2% Triton X-100, and once with TE (pH 8.0). Crosslinking was reversed by incubating the beads at 65°C for 4 hr in the presence of 0.3% SDS and 1 mg/mL Proteinase K. ChIP DNA was purified by ChIP DNA clean and concentrator column (Zymo research).
ChIP-Seq: Library was prepared in Ovation SP Ultralow library system (Nugen).

value: T Cells

tag: background

value: CAST/EiJ x BALB/c F1

tag: experimental type

value: ChIP-Seq


title: CAST/EiJ x BALB/c F1 T Cells Input Rep2

description: library:ChIPCastXBalbcF1TCellS2InputRep2


title: Arid1b P10 wildtype replicate 1

tag: age


title: CAST/EiJ x BALB/c F1 T Cells Yy1 Rep1

description: library:ChIPCastXBalbcF1TCellS2AntiYy1Rep1

tag: cell type


title: CAST/EiJ x BALB/c F1 T Cells Input Rep1

description: library:ChIPCastXBalbcF1TCellS2InputRep1


title: CAST/EiJ x BALB/c F1 T Cells Yy1 Rep3

description: library:ChIPCastXBalbcF1TCellS2AntiYy1Rep3


title: CAST/EiJ x BALB/c F1 T Cells Yy1 Rep2

description: library:ChIPCastXBalbcF1TCellS2AntiYy1Rep2


title: Arid1b P3 wildtype replicate 4


title: CAST/EiJ x BALB/c F1 T Cells Sp1 Rep2

description: library:ChIPCastXBalbcF1TCellS2AntiSp1Rep2


title: Arid1b P10 heterozygous replicate 3


title: CAST/EiJ x BALB/c F1 T Cells Sp1 Rep1

description: library:ChIPCastXBalbcF1TCellS2AntiSp1Rep1


title: Arid1b P3 heterozygous replicate 4


title: CAST/EiJ x BALB/c F1 T Cells Nrf1 Rep3

description: library:ChIPCastXBalbcF1TCellS2AntiNrf1Rep3


title: Arid1b P3 heterozygous replicate 2


title: Arid1b P3 heterozygous replicate 1


title: CAST/EiJ x BALB/c F1 T Cells Nrf1 Rep1

description: library:ChIPCastXBalbcF1TCellS2AntiNrf1Rep1


title: CAST/EiJ x BALB/c F1 T Cells Irf4 Rep3

description: library:ChIPCastXBalbcF1TCellAntiIrf4Rep3


title: CAST/EiJ x BALB/c F1 T Cells Input S1 Rep2


title: CAST/EiJ x BALB/c F1 T Cells Input S1 Rep3


title: CAST/EiJ x BALB/c F1 T Cells Input S1 Rep1


title: CAST/EiJ x BALB/c F1 T Cells Irf4 Rep2

description: library:ChIPCastXBalbcF1TCellAntiIrf4Rep2


title: CAST/EiJ x BALB/c F1 T Cells Irf4 Rep1

description: library:ChIPCastXBalbcF1TCellAntiIrf4Rep1


title: C57BL/6 x BALB/c F1 aB Input Rep1

source_name: aB

value: aB

value: C57BL/6 x BALB/c F1


title: CAST/EiJ x BALB/c F1 T Cells Ikfz1 Rep3

description: library:ChIPCastXBalbcF1TCellAntiIkfz1Rep3


title: CAST/EiJ x BALB/c F1 T Cells Ikfz1 Rep1

description: library:ChIPCastXBalbcF1TCellAntiIkfz1Rep1


title: CAST/EiJ x BALB/c F1 T Cells Ikfz1 Rep2

description: library:ChIPCastXBalbcF1TCellAntiIkfz1Rep2


title: C57BL/6 x BALB/c F1 aB YY1 Rep3


title: C57BL/6 x BALB/c F1 aB YY1 Rep1


title: C57BL/6 x BALB/c F1 aB YY1 Rep2


title: CAST/EiJ x BALB/c F1 T Cells Nrf1 Rep2

description: library:ChIPCastXBalbcF1TCellS2AntiNrf1Rep2


title: C57BL/6 x BALB/c F1 aB SP1 Rep2


title: C57BL/6 x BALB/c F1 aB NRF1 Rep3


title: C57BL/6 x BALB/c F1 aB SP1 Rep3


title: C57BL/6 x BALB/c F1 aB NRF1 Rep2


title: C57BL/6 x BALB/c F1 aB IRF4 Rep1


title: C57BL/6 x BALB/c F1 aB IRF4 Rep2


title: C57BL/6 x BALB/c F1 aB NRF1 Rep1


title: C57BL/6 x BALB/c F1 aB IRF4 Rep3


title: C57BL/6 x BALB/c F1 aB Input Rep2


title: C57BL/6 x BALB/c F1 aB Input Rep3


title: C57BL/6 x BALB/c F1 aB Ikfz Rep3


title: C57BL/6 x BALB/c F1 aB Ikfz Rep1


title: Arid1b P3 wildtype replicate 2


title: C57BL/6 x BALB/c F1 aB SP1 Rep1


title: CAST/EiJ x BALB/c F1 aB InputS3R2


title: CAST/EiJ x BALB/c F1 aB InputS3R3


title: CAST/EiJ x BALB/c F1 aB InputS3R1


title: C57BL/6 x BALB/c F1 aB Ikfz Rep2


title: Lung, IL17AKO, Naive 9SR35155A_B11

city: New Haven

first: Govindarajan

last: Rajagopalan

state: CT

address: 300 Cedar Street

institute: Yale University

description:
Lung, IL17AKO, Naive
Gene expression profiling in the lungs

hyb_protocol: Hynridized with Mouse clariom S chips as per standard protocol

scan_protocol: GeneChips were scanned using GeneArray Scanner

data_processing: CEL data files were exported into Transcriptome Analysis Console (TAC, Applied Biosystems) software and analyzed as per recommended procedure.

label: Biotin

source_name: HLA-DR3.IL-17AKO, Lung

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Mice were mainted in the vivarium as per standard procedure

extract_protocol: RNA were extracted using TRIZOL, cleaned using Qiagen RNA purification kit. Frozen RNAs were sent to THermoFisher Scienfitific Microarray lab for subsequent processing.

treatment_protocol: HLA-DR3, HLA-DR3.IL17A knockout and HLA-DR3.IFN-gamma knockout (KO) mice were challenged intraperitoneally with 10 microgram of staphylococcal enterotoxin B. 4 and 24 hours later mice were euthanized, lungs harvested, RNA extracted and processed for gene expression analysis using Clariom s arrays

tag: sample type

value: Lung, IL17AKO, Naive


title: CAST/EiJ x BALB/c F1 aB Rreb1S1R3


title: Lung, WT, SEB, 24 hrs 9SR35155A_B04

description:
Lung, WT, SEB, 24 hrs
Gene expression profiling in the lungs

source_name: HLA-DR3,WT, Lung

value: Lung, WT, SEB, 24 hrs


title: CAST/EiJ x BALB/c F1 aB Rreb1S1R2


title: Lung, WT, Naive 9SR35155A_B07

description:
Lung, WT, Naive
Gene expression profiling in the lungs

value: Lung, WT, Naive


title: Lung, IL17AKO, SEB, 24 hrs 9SR35155A_B06

description:
Lung, IL17AKO, SEB, 24 hrs
Gene expression profiling in the lungs

value: Lung, IL17AKO, SEB, 24 hrs


title: Lung, IL17AKO, SEB, 24 hrs 9SR35155A_B08


title: Lung, IFNgKO, Naive 9SR35155A_B09

description:
Lung, IFNgKO, Naive
Gene expression profiling in the lungs

source_name: HLA-DR3.IFNgKO, Lung

value: Lung, IFNgKO, Naive


title: Lung, IL17AKO, SEB, 24 hrs 9SR35155A_B05


title: Lung, IFNgKO, SEB, 4 hrs 9SR35155A_B01

description:
Lung, IFNgKO, SEB, 4 hrs
Gene expression profiling in the lungs

value: Lung, IFNgKO, SEB, 4 hrs


title: CAST/EiJ x BALB/c F1 aB Rreb1S1R1


title: Lung, IFNgKO, SEB, 24 hrs 9SR35155A_B02

description:
Lung, IFNgKO, SEB, 24 hrs
Gene expression profiling in the lungs

value: Lung, IFNgKO, SEB, 24 hrs


title: Lung, IL17AKO, Naive 9SR35155A_B10


title: CAST/EiJ x BALB/c F1 aB MazS3R3


title: Lung, IFNgKO, SEB, 4 hrs 9SR35155A_A11


title: 386_2

value: CRC Plasma

value: CRC


title: Lung, IFNgKO, SEB, 24 hrs 9SR35155A_B03


title: Lung, WT, SEB, 24 hrs 9SR35155A_A10


title: Lung, WT, SEB, 24 hrs 9SR35155A_A09


title: Lung, IFNgKO, SEB, 4 hrs 9SR35155A_A07


title: Lung, WT, SEB, 24 hrs 9SR35155A_A08


title: Lung, IFNgKO, Naive 9SR35155A_A06


title: Lung, IL17AKO, Naive 9SR35155A_A05


title: CAST/EiJ x BALB/c F1 aB MazS3R2


title: Lung, IFNgKO, Naive 9SR35155A_A04


title: CAST/EiJ x BALB/c F1 aB Input Rep3


title: CAST/EiJ x BALB/c F1 aB MazS3R1


title: CAST/EiJ x BALB/c F1 aB Input Rep2


title: CAST/EiJ x BALB/c F1 aB Input Rep1


title: Lung, WT, Naive 9SR35155A_A03


title: Lung, WT,Naive 9SR35155A_A02

description:
Lung, WT,Naive
Gene expression profiling in the lungs

value: Lung, WT,Naive


title: Lung, WT, SEB, 4 hrs 9SR35154B_H11

description:
Lung, WT, SEB, 4 hrs
Gene expression profiling in the lungs

value: Lung, WT, SEB, 4 hrs


title: CAST/EiJ x BALB/c F1 aB YY1 Rep2


title: Lung, IL17AKO, SEB, 4 hrs 9SR35155A_A01

description:
Lung, IL17AKO, SEB, 4 hrs
Gene expression profiling in the lungs

value: Lung, IL17AKO, SEB, 4 hrs


title: CAST/EiJ x BALB/c F1 aB YY1 Rep3