title: 2_S2_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ6-BS

value: Healthy Control


title: 7_S7_L003_R1_001

status: Public on Dec 31 2024

type: SRA

city: Baltimore

first: Kenneth

middle: W

last: Witwer

state: Maryland

address: 733 N. Broadway

department: Molecular and Comparative Pathobiology

country: USA

institute: Johns Hopkins University

description: Library name: EXR-KWITW1LPPFRACD7-BS

library_source: transcriptomic

data_processing:
All FASTQ files were processed uniformly through the extra-cellular RNA processing toolkit (exceRpt). Information about exceRpt is available at https://github.gersteinlab.org/exceRpt/.
Assembly: hg19
Supplementary files format and content: Each processed data file is a core results archive generated by exceRpt. The core results archive contains read counts for alignments to the different transcriptome libraries used by exceRpt (miRNA / piRNA / tRNA / GENCODE annotations / circRNA), taxonomy trees for exogenous rRNA and genomic reads aligned by exceRpt, and a variety of other files generated by exceRpt.

molecule: total RNA

organism: Homo sapiens

source_name: Plasma

extract_protocol:
RNA Isolation method was Trizol-LS. RNA Isolation kit was Trizol + spin column.
Library construction kit was BioLiqX small RNA Library Kit. Samples were multiplexed. Type of Starting Material was total RNA.

tag: tissue

value: Plasma

tag: condition

tag: anatomical location

value: Entire body system

tag: rna source

tag: rna isolation kit

value: Trizol + spin column


title: WT: CSP-TTK21 (R3)

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
BCL to FASTq files were obtained using CASAVA Pipeline
NFCORE-RNASEq pipeline was used to process the FASTQ to obtain Read Count Files
Read Count data was TPM normalized for further downstream analysis
Assembly: Hg19
Supplementary files format and content: TPM Normalized data of expressed transcripts in .xlsx format

organism: Mus musculus

source_name: Hippocampus

extract_protocol:
Trizol method. Briefly, Mice were sacrificed by cervical dislocation; the dorsal hippocampus was dissected out and chopped finely with a razor blade. All reagents and instruments used for RNA isolation were DEPC treated. Samples were homogenized in TRIzol reagent (Invitrogen). RNA was isolated by the traditional phenol: chloroform method. After phenol-chloroform treatment, the aqueous phase was collected, and ethanol precipitated using absolute ethanol. The pellets were washed twice with 70% ethanol and air-dried. RNA pellets were resuspended in RNase-free water.  DNase treatment was done for 30 min at 37 ºC. RNA samples were further purified by chloroform/phenol extraction and ethanol precipitated. Pellets were washed twice with 70% ethanol and resuspended in RNase-free water at 65 ºC for 10 mins. RNA concentration was determined by Nano-drop
As per Illumina recommended Protocol

treatment_protocol: Mice were treated with 3 dose (20mg/Kg) of CSP/CSP-TTK21 (1 dose/ week). After 1 week, MWM training was performed for 4 days and mice were sacrificed after 2 hours.

value: Hippocampus

tag: cell line

tag: cell type

value: Male

tag: genotype

value: WT

tag: treatment


title: 3_S3_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACQ9-BS

value: protein-lipid-RNA complex


title: WholeBlood-Control-M-140

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

country: France

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

data_processing:
raw reads were trimmed with bbduk
raw reads were aligned using STAR v2.5.3a and Gencode v29 annotations
gene expression (raw counts) were quantified using HTSeq v0.11.2
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Whole blood

growth_protocol: Not applicable

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
libraries were prepared from 500 ng of total RNA, using poly-A capture and the QIAseq Stranded mRNA Select kit (Qiagen) in Females (F) OR the TruSeq Stranded mRNA LT Sample Preparation Kit (Illumina, San Diego, CA) in males (M)

treatment_protocol: Not applicable

value: Whole blood

tag: group

value: Control

tag: Sex


title: C9_Line3_2_2

city: Philadelphia

first: Aaron

last: Haeusler

address: 900 Walnut Street, JHN-Suite 410

department: Neuroscience

institute: Thomas Jefferson University

data_processing:
Data was generated by Novogene and subjected to QC analysis according to their established protocols. Cleaned reads were obtained by removing raw reads with adapters, poly_N, and low quality.
Cleaned reads were aligned to hg38 using STAR(v.2.7.10b)
Read summarization was performed on .bam files to obtain a featurecounts file using the R package Rsubread (v.2.12.3)
Differential Expression analysis was conducted with DESeq2(v.1.36.0)
Assembly: hg38
Supplementary files format and content: LTG_KCL_featurecounts.txt: tab-delimited file includes feature counts from Rsubread(v.2.12.3)
Supplementary files format and content: LTG_TEA_featurecounts.txt: tab-delimited file includes feature counts from Rsubread(v.2.12.3)

extract_protocol:
RNA was isolated using RNeasy Plus Mini Kit (Qiagen), and cDNA was synthesized from 500 ng RNA using a QuantiTect Reverse Transcription Kit (Qiagen)
Library preparation and RNA-sequencing were performed by third-party company, Novogene. RNA libraries for RNA-seq were prepared following Novogene's protocols and sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.

value: KCL


title: WholeBlood-Control-M-143


title: C9_Line3_2_0


title: C9_Line3_1_6


title: 4_S4_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ14-BS


title: 2_S2_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ8-BS


title: WholeBlood-Control-M-138


title: Syngap1+/-: Saline (R2)

value: Saline


title: WT: Saline (R3)


title: C9_Line3_1_2


title: WholeBlood-Control-M-135


title: WT: CSP-TTK21 (R2)


title: 3_S3_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACQ10-BS


title: C9_Line3_1_0


title: C9_Line2_2_6


title: WholeBlood-Control-M-133


title: Syngap1+/-: Saline (R1)


title: 3_S3_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ12-BS


title: WholeBlood-Control-M-122


title: 6_S6_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD1-BS


title: C9_Line2_2_2


title: 8_S8_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD12-BS


title: WholeBlood-Control-M-116


title: WholeBlood-Control-M-106


title: WholeBlood-Control-M-104


title: Syngap1+/-: CSP-TTK21 (R3)


title: 9_S9_L002_R1_001

description: Library name: EXR-KWITW1LPPFRACD14-BS


title: C9_Line2_1_2


title: Syngap1+/-: CSP-TTK21 (R2)


title: WholeBlood-Control-M-103


title: 9_S9_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACD16-BS


title: C9_Line2_1_0


title: 12_S12_L004_R1_001

description: Library name: EXR-KWITW1LPPFRACQ7R2-BS


title: WT: CSP-TTK21 (R1)


title: C9_Line1_2_6


title: Syngap1+/-: CSP-TTK21 (R1)


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580+100 nM Calcitriol, MED1 ChIP-seq, replicate 3

city: DEBRECEN

first: LAJOS

last: SZELES

address: NAGYERDEI KRT 98

country: Hungary

institute: UNIVERSITY OF DEBRECEN

library_source: genomic

data_processing:
alignment with bwa using default parameters
bam generation with Picard tools using SortSam, AddOrreplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with HOMER makeTagDirectory
Model-based analysis of ChIP-seq version 2 (MACS2) was used for predicting summits of the peaks using q value cutoff (q) = 0.001.
Assembly: hg38
Supplementary files format and content: bedgraph

molecule: genomic DNA

source_name: THP-1 human leukemia monocytic cell line

extract_protocol:
The cells were cross-linked with 2 mM disuccinimidyl glutarate for 40 minutes and 1% methanol-free formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared using a Diagenode Bioruptor sonicator. Precipitated and washed samples were purified using NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel).
Indexed libraries were prepared from ChIP-DNA using a TruSeq ChIP Sample Preparation Kit (Illumina).

tag: stimulation

value: phorbol-12-myristate-13-acetate (PMA) for 16h

value: 100 nM AM580+100 nM Calcitriol

tag: time

value: wt

tag: antibody


title: WholeBlood-Control-M-102


title: WT: Saline (R2)


title: 7_S7_L001_R1_001

description: Library name: EXR-KWITW1LPPFRACD5-BS


title: Syngap1+/-: CSP  (R1)

value: CSP


title: C9_Line2_2_0


title: C9_Line1_2_0


title: WholeBlood-Control-M-101


title: Mouse_eCCA_16

city: Rochester

first: Jessica

last: Hohenstein

state: MN

address: 200 1st St SW

institute: Mayo Clinic

data_processing:
The raw RNA sequencing paired-end reads were processed through the Mayo RNA-Seq bioinformatics pipeline, MAP-RSeq version 3.1.4.
STAR v2.6.1c for alignment
FeatureCounts to quantify expression
edgeR 3.40.2 for defining differentially expressed genes
Assembly: mm10
Supplementary files format and content: tsv format containg raw gene counts and FPKM normalize expression values

source_name: bile duct

extract_protocol: Mouse RNA was extracted from bile duct tissue

value: bile duct


title: Mouse_eCCA_17


title: WT: Saline (R1)


title: C9_Line1_2_2


title: D80, 2, CMZ, bulk RNA

city: Wenzhou

first: Chenghao

last: Li

state: Zhejiang

address: Wenzhou Medical University, Xueyuan Xi Road

country: China

institute: Wenzhou Medical University

data_processing:
Sequence reads were mapped to the hg38 genome and transcriptome by STAR (2.7.10a) and RSEM (1.3.3).
Assembly: hg38
Supplementary files format and content: Gene expression results(TPM, FPKM) from RSEM

source_name: retina

extract_protocol:
Wash the samples twice with PBS, add 0.5 ml of digestion solution (containing 0.25% Trypsin-EDTA, 50 μg/ml DNase I, 20 μg/ml Y-27632), and digest at 37°C for 10 minutes. Add 1 ml of culture medium to neutralize the digestion, filter through a mesh filter, centrifuge at 1000 rpm for 5 minutes, remove the supernatant, and resuspend in an appropriate volume of suspension solution (containing PBS, 50 μg/ml DNase I, 20 μg/ml Y-27632). Count and calculate the proportion of viable cells (≥90%), adjust the cell concentration to 1000 cells/μL, and keep on ice for further testing
For each sample, total RNA was extracted using TRIzol reagent and further purified using the RNeasy Mini Kit (Qiagen), following the manufacturer's instructions. The quality and quantity of the RNA were evaluated using a NanoDrop 2000 spectrophotometer, Agilent 2100 Bioanalyzer, and Agilent RNA 6000 Nano Kit. Annoroad Gene Technology conducted the RNA library construction and RNA sequencing (RNA Seq). To generate the sequencing libraries, the NEB Next Ultra RNA Library Prep Kit for Illumina (NEB) was used, and library clustering was performed with the HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer's recommendations. Following cluster generation, the libraries were sequenced on an Illumina platform, generating 150 bp paired-end reads.

value: retina

value: organoids derived from hPSCs

tag: time point

value: Day 80


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580+100 nM Calcitriol, MED1 ChIP-seq, replicate 1

value: THP-1 human leukemia monocytic cell line


title: C9_Line2_1_6


title: C9_Line1_1_6


title: Mouse_eCCA_15


title: PMA-stimulated THP1 cells, 2h, 100 nM Calcitriol, MED1 ChIP-seq, replicate 3

value: 100 nM Calcitriol


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580+100 nM Calcitriol, MED1 ChIP-seq, replicate 2


title: D80, 3, CMZ, bulk RNA


title: PMA-stimulated THP1 cells, 2h, 100 nM Calcitriol, MED1 ChIP-seq, replicate 2


title: Mouse_eCCA_14


title: D20, 3, NR, bulk RNA

value: Day 20


title: C9_Line1_1_0


title: PMA-stimulated THP1 cells, 2h, 100 nM Calcitriol, MED1 ChIP-seq, replicate 1


title: Mouse_eCCA_13


title: D20, 2, NR, bulk RNA


title: Mouse_eCCA_12


title: AstroCapsule, ITC treatment, Rep3

city: Houston

first: Robert

last: Krencik

state: TX

address: 6670 Bertner Ave

institute: Houston Methodist Research Institute

description: Performed by Novogene

data_processing:
DESeq2
Assembly: Homo sapiens(GRCh38/hg38)
Supplementary files format and content: Excel worksheet. Differential expression analysis, Read Count, FPKM

source_name: Cell culture

growth_protocol: Cells cultured as floating aggregates, within alginate capsules, floating in a flask and fed with Neural Media

extract_protocol:
Direct-zol RNA kit (Zymo) with on-column Dnase treatment
Novogene Eukaryotic RNA-seq (cDNA library), NEB poly-A selected

treatment_protocol: With or without 48 treatment with interleukin 1alpha, TNFalpha, and Complement c1q

value: Cell culture

value: Parental line WTC11

value: Astrocytes

value: Wild-type

value: ITC


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580, MED1 ChIP-seq, replicate 3


title: AstroCapsule, ITC treatment, Rep2

description: Performed by Novogene


title: Mouse_eCCA_10


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580, MED1 ChIP-seq, replicate 2


title: AstroCapsule, ITC treatment, Rep1

description: Performed by Novogene


title: D20, 1, NR, bulk RNA


title: AstroCapsule, Vehicle, Rep3

description: Performed by Novogene

value: Vehicle


title: PMA-stimulated THP1 cells, 2h, 100 nM AM580, MED1 ChIP-seq, replicate 1

value: phorbol-12-myristate-13-acetate (PMA) for 16h


title: Mouse_eCCA_11


title: PMA-stimulated THP1 cells, 2h, vehicle (DMSO:EtOH), MED1 ChIP-seq, replicate 3

value: vehicle (DMSO:EtOH)


title: Mouse_eCCA_9


title: Mouse_eCCA_8


title: IMR90_AA_mRNAseq

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: mRNA

data_processing:
Reads were mapped to the Human genome (hg19) and to spike-in reference sequences using default parameters of TopHat. SAMMate software was used to determine the transcript RPKM (reads per kilobase of exon per million of reads) for mRNA-seq libraries. The sums of RPKM values from the spike-in controls were used to normalize across samples and to adjust transcripts RPKM.
Genome_build: hg19
Supplementary_files_format_and_content: Excel workbook with normalized RPKM values for all samples except the chromRNAseq samples. For chromRNAseq samples, we used mapped counts around the gene regions to illustrate newly synthesized transcripts.   Therefore, processed data for those two libraries are mapped read coverage in wig format (available on the sample records).

source_name: Cell line

growth_protocol: HeLa cells were maintained in DMEM (Cellgro #10-013-CV) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher HyClone #SV30014.03).

extract_protocol:
Total RNA was extracted using the Trizol reagents (Ambion #15596026) and treated with TURBO DNase (Ambion #AM2239).
1 μg of total RNA was used to prepare sequencing library using the Illumina TruSeq RNA sample preparation kit. A mixture of external RNA spike-in controls (Ambion #4456740) was added to total RNA prior to library preparation. Libraries were sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads. No spike-in control was added to biological replicate 2, and 100 bp-long reads were obtained from those two libraries.  For chromatin RNA-seq, chromatin subcellular fractionation was isolated. Total RNA-seq libraries were prepared and sequenced with Illumina Hi-seq platforms to obtain 50 bp-long reads.

treatment_protocol: Media containing complete amino acids (AA) were made from DMEM powder (US Biological #D9802) and supplemented with an additional 3.5 g/L D-glucose (for a total of 4.5 g/L), 1 mM sodium pyruvate (Gibco #11360070), 3.7 g/L sodium bicarbonate, and 0.0159 g/L sodium phenol red (US Biological #P4040). Media without AA were made from DMEM without amino acids powder (US Biological #D9800-013) and supplemented with an additional 3.5 g/L D-glucose, 1 mM sodium pyruvate (Gibco #11360070), and 3.7 g/L sodium bicarbonate. pH of media was adjusted to 7.2 by the addition of HCl before being filter sterilized and supplemented with 10% dialyzed FBS (Gibco #26400-044).

value: AA

tag: sirna mediated knockdown and plasmid


title: D80, 1, CMZ, bulk RNA


title: C9_Line1_1_2

value: KCL


title: IMR90_NOAA_mRNAseq

description: mRNA

value: without AA


title: HBTEC_NOAA_mRNAseq

description: mRNA

value: HBTEC


title: AstroCapsule, Vehicle, Rep1

description: Performed by Novogene


title: HBTEC_AA_mRNAseq

description: mRNA


title: PMA-stimulated THP1 cells, 2h, vehicle (DMSO:EtOH), MED1 ChIP-seq, replicate 1

value: wt


title: Mouse_eCCA_7

value: bile duct


title: HeLa_AA_Setd8KD+MYC_mRNAseq

description: mRNA

value: HeLa


title: PMA-stimulated THP1 cells, 1h, 100 nM AM580, ATAC-seq, replicate 1

extract_protocol:
Cells were counted and 50,000 cells were collected in ice-cold PBS. The nuclei were isolated with ATAC lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1% IGEPAL). Tagmentation of the nuclei was performed using the Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina). Indexing was performed using Nextera DNA library preparation kit (Illumina). DNA was purified with NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). Indexed DNA was amplified for nine PCR cycles with Kapa Hifi Hot Start Kit (Kapa Biosystems). Amplified libraries were purified again with NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel).
Indexed libraries were prepared from tagmented DNA, using Nextera DNA library preparation kit (Illumina)

value: THP-1 human leukemia monocytic cell line


title: MCF7_shATF3_H

city: Bhopal

first: Sanjeev

last: Shukla

state: Madhya Prades

address: Bhopal Bypass Road, Bhauri Bhopal 462 066 Madhya Pradesh, INDIA

department: Biological Sciences

institute: Indian Institute of Science Education and Research Bhopal

data_processing:
Quality control of raw RNA-seq reads was performed using Fastqc.
RNA-seq paired-end sequencing fastq files were mapped to human hg38 genome using STAR aligner
Feature Counts was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: tab delimited text files with raw counts for each sample

molecule: polyA RNA

growth_protocol: MCF7 cells were cultured in media recommended by American Type Cell Culture in a humidified incubator at 37 ⁰C and 5% CO2

extract_protocol:
TRIzol (Invitrogen, 15596026) was used to extract Total RNA. RNA was also subjected to rDNase treatment.
mRNA enrichment method was used as the library preparation strategy . Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®
150 bp paired-end sequencing using Illumina NovaSeq 6000

treatment_protocol: MCF7 shControl or shATF3 cells were kept under Hypoxia (1% oxygen) for 24 hours before performing RNA-seq

value: Breast cancer cell line (luminal)

value: ATF3 Knockdown

value: Hypoxia (1% oxygen)


title: Mouse_eCCA_6


title: sample5_endoderm_day14

city: Ann Arbor

first: Shiyu

last: Sun

state: Michigan

address: G.G. Brown Building, 2350 Hayward St

department: Mechanical Engineering

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
Illumina NovaSeq-6000 for basecalling
10x Genomics Cell Ranger pipeline (version 3.1.0) for barcoding, alignment, filtering
Assembly: GRCh38
Supplementary files format and content: TSV and MTX files are generated by Cell Ranger pipeline, including barcodes, features and matrix. RD file is generated using Seurat.

source_name: H9 hESC

growth_protocol: The samples were generated according to published manuscript.

extract_protocol:
The embryoids were dissociated into single cells. Dissociated cells were then lysed and barcoded with 10x Chromium Controller Instrument (10x Genomics).
cDNA library was constructed according to the standard 10x Genomics scRNA-seq library construction protocol (Single Cell 3' v2). The libraries were sequenced on Illumina NovaSeq-6000 with paired-end sequencing (One sample per flow cell).

value: H9 hESC

value: human embryonic stem cell (hESC)

value: wildtype

value: hESC-derived PTED embryoids with promoted endoderm differentiation


title: HeLa_AA_controlKD+MYC_mRNAseq

description: mRNA

value: Control+c-MYC


title: PMA-stimulated THP1 cells, 2h, vehicle (DMSO:EtOH), MED1 ChIP-seq, replicate 2

value: phorbol-12-myristate-13-acetate (PMA) for 16h

value: vehicle (DMSO:EtOH)


title: AstroCapsule, Vehicle, Rep2

description: Performed by Novogene

value: Cell culture

value: Parental line WTC11

value: Astrocytes

value: Wild-type

value: Vehicle


title: Mouse_eCCA_5

value: bile duct


title: HeLa_AA_Setd8KD_mRNAseq

description: mRNA

value: HeLa

value: AA


title: Mouse_eCCA_4


title: F36P NT, bio rep 3

city: Minato-ku

first: Wenyu

last: ZHANG

state: Tokyo

address: 4-6-1 Shirokanedai

department: Computational Biology and Medical Sciences

country: Japan

institute: The University of Tokyo

data_processing:
The sequencing reads were aligned to the human reference genome (hg38) using Rsubread (v2.4.3). Raw counts were obtained from read alignments using refGene for gene counts or RepeatMasker annotation for transposable elements, and then further transferred to CPM using edgeR (v3.32.1). After filtering out low-expression genes with CPM < 1, all CPM values were performed with log2 transformed for further analysis.
Assembly: hg38
Supplementary files format and content: xlsm files include CPM values for each Sample

extract_protocol:
Total RNA of 2 x10^6 cultured sgHDAC7 or sgNT F36P cells in each sample was extracted by RNeasy Mini Kit (QIAGEN).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: WT


title: HeLa_AA_controlKD_mRNAseq

description: mRNA

value: Control


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), ATAC-seq, replicate 2

value: THP-1 human leukemia monocytic cell line

value: wt


title: HeLa_NOAA_mRNAseq_biological-replicate1

description: mRNA

value: without AA


title: F36P NT, bio rep 2


title: Mouse_eCCA_3


title: Mouse_eCCA_2


title: Donor 3

city: Muenster

first: Markus

last: Fehrholz

address: Mendelstr. 17

country: Germany

institute: Monasterium Laboratory GmbH

data_processing:
Sequencing was performed on a NextSeq 500 system using 1x75 bp read length with an output of approximately 25 M clusters per sample.
Adapters were trimmed with Trimmomatic (version 0.36). Trimmed raw reads were aligned to a hg19 using HISAT2 (version 2.0.5).
The quality of the FASTQ files was analyzed with FastQC and reads were counted in features using HTSeq (version 0.9.1).
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: LCM isolated Melanocytes from human belly skin

extract_protocol:
Total RNA was isolated from 4-5 skin sections per skin sample with 90-180 cells (melanocytes) per section and amplified using the Ovation® RNA-Seq System V2 (NuGEN).
Amplified cDNA was sheared using a Covaris shearing device to obtain approximately 300bp sized fragments. Afterwards rRNA depletion and library preparation were performed using an adapted protocol of the Trio RNA-Seq kit (NuGEN) for low-input samples.

value: untreated


title: HeLa_AA_mRNAseq_biological-replicate1

description: mRNA


title: Mouse_eCCA_1


title: GLU condition, timepoint S2, RNA-seq, replicate 2

first: Lydia

last: Freddolino

state: MI

address: 1150 W. Medical Center Dr., MSRB 3 room 3315

data_processing:
The end-to-end IPOD analysis pipeline from (Freddolino et al., PLoS Biology 19(6): e3001306, 2021) was used
Assembly: E. coli MG1655 U00096.3
Supplementary files format and content: Bedgraph files: position-level information on sequencing read depths, either normalized according to the IPOD-HR pipeline (v6rz scores), z-scored ChIP:input ratios (chip_vs_inp), or read abundances normalized by overall sample read depth (RNA)

organism: Escherichia coli str. K-12 substr. MG1655

source_name: Planktonic cells

growth_protocol: E. coli K-12 MG1655 cells were grown overnight in the respective media (either Glu or Cas). For the Glu medium samples, 1 mL of overnight sample was seeded into 200 mL fresh Glu medium and grown shaking at 37°C to the different time points: 6 hours for mid-logarithmic (OD600 ~0.25), 10 hours for stationary (OD600 ~1.7) and 18 hours for late stationary. For the Cas medium samples, 134 μL of overnight sample was seeded into 200 mL fresh Cas medium and grown shaking at 37°C to the different time points: 2.5 hours for early stationary (OD600 ~0.1), 4.5 hours for mid-logarithmic (OD600 ~0.5), 6.33 hours for late logarithmic (OD600 ~1.4), 10 hours for stationary (OD600 ~4), and 18 hours for late stationary (OD600 ~5.5

extract_protocol:
Detailed instructions for IPOD‐HR interface extraction, RNA polymerase chromatin immunoprecipitation, and crosslinking reversal and recovery of DNA have been previously published (Freddolino et al., PLoS Biology 19(6): e3001306, 2021), and were followed precisely here
Illumina sequencing libraries for DNA samples were prepared using a NebNext Ultra DNA kit, following the manufacturer’s instructions except that a Qiaquick Nucleotide Removal Kit was used for pre-ligation cleanup to avoid loss of low molecular weight fragments. RNA-seq samples were prepared using an Epicentre ScriptSeq v2 kit following the manufacturer’s instructions

treatment_protocol: Samples were treated with 150 μg/mL rifampicin for 10 minutes at 37°C with continuous shaking to stall RNA polymerase at active promoters and allow transcriptional runoff for already- elongating polymerase. Formaldehyde to 1% final concentration was added for crosslinking and incubated at room temperature for 5 minutes shaking. Excess glycine was then added to quench the crosslinking reaction (final concentration 0.333M) for 5 minutes at room temperature, with shaking. Cultures were then chilled on ice and washed twice using phosphate-buffered saline.  Final cross-linked cell pellets were stored at -80°C until ready for extraction

value: Planktonic cells

value: GLU condition. timepoint S2


title: F36P HDAC7 KO, bio rep 3

value: HDAC7 knockout


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 7

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

data_processing:
The pipeline used to process the transcriptomic data is available from Github (https://github.com/bihealth/seasnap-pipeline/). Quality control was performed using a variety of tools, including FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), dupradar , qualimap  and summarised using MultiQC. For adapter trimming, we used the trimadap tool available from https://github.com/lh3/trimadap. Reads were mapped to human genome GRCh38, version p7 using the STAR program, version 2.7.8a .
ounts were produced by the STAR program using the Gencode GRCh38 annotation version 25. For differential gene expression, the R package DESeq2, version 1.38 was used . Gene set enrichment used the R package tmod, v. 0.50.13 , with gene sets included in the MSigDB through the msigdbr package, v. 7.5.1 .
Gene sets used included Gene Ontology Biological Process gene sets, Hallmark gene sets, REACTOME gene sets and transcriptional modules contained in the tmod package. Results, reports, pipeline output and additional files were stored and managed using the SODAR system .
Assembly: GRCh38, version p7
Supplementary files format and content: CSV file with raw count data

source_name: lung

extract_protocol:
Human lung tissue explants were stored in RNAlater™ Stabilization Solution (ThermoFisher) at 4°C overnight (to allow the solution to thoroughly penetrate the tissue). For total RNA isolation the RNeasy Mini Kit (Qiagen) was used according to manufacturer`s instructions. Human lung tissue was transferred to Lysing Matrix D tubes (MP Biomedicals) in 500 μl RLT lysis buffer supplemented with β-mercaptoethanol. Tissue was lysed using FastPrep®-24 (MP Biomedicals) applying 3 rounds of tissue lysis at default settings (6 m/s, 30 s). Homogenates were centrifuged and RNA was purified from the supernatant. 0.5 μg RNA was reverse transcribed and quantitative PCR was performed using TaqMan assays on an ABI 7300 instrument. RNA from infected samples was purified as described above. 0.5 μg RNA was used for RNA-Seq libraries preparation. RNA-Seq libraries were constructed using Illumina TruSeqTM Stranded Total RNA Library Prep Gold kit (New England Biolabs) according to the manufacturer’s instruction, with rRNA depletion and 11 PCR cycles in the amplification step. Sequencing was performed on a NextSeq 500 platform using 1x76 cycles single-end sequencing and aiming at 10-20 mln reads per sample.
RNA from infected samples was purified as described above. 0.5 μg RNA was used for RNA-Seq libraries preparation. RNA-Seq libraries were constructed using Illumina TruSeqTM Stranded Total RNA Library Prep Gold kit (New England Biolabs) according to the manufacturer’s instruction, with rRNA depletion and 11 PCR cycles in the amplification step. Sequencing was performed on a NextSeq 500 platform using 1x76 cycles single-end sequencing and aiming at 10-20 mln reads per sample.

value: lung

value: titrated with HCl to pH6

tag: agent

value: without HEPES

tag: individual

value: donor no. 7


title: GLU condition, timepoint S2, RNA-seq, replicate 1


title: Donor 1

tag: tissue

value: LCM isolated Melanocytes from human belly skin


title: PMA-stimulated THP1 cells, 1h, 100 nM AM580, ATAC-seq, replicate 2

value: phorbol-12-myristate-13-acetate (PMA) for 16h


title: P14 CKO;scRNAseq

city: Nanjing

first: Yuanlin

last: He

address: 101Longmian Avenue, Jiangning District

institute: Nanjing medical university

description: 10x Genomics

data_processing:
Raw reads were processed to generate gene expression profiles using Cell Ranger v.3.0.2. Reads from the 10x library were mapped to mm10. Reads with the same cell barcode, UMI and gene were grouped together to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis. We used the package Seurat (V4.1.3) for quality control and downstream analysis of our single cell RNA-seq data.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrirx files

source_name: cerebellum

extract_protocol:
The entire cerebellum is separated from the entire brain with tweezers and the meninges are removed. The sample was then cut in 1×Hank equilibrium salt solution (HBSS) and digested in 0.25% trypsin solution (Thermo Fisher Scientific) for 15-20 minutes. The dissociated cells were filtered through a 22 μm cell filter (Millipore), centrifuged at 300 g for 3 min, and then suspended in a solution containing 0.04% BSA (Sigma) at a concentration of 2000-3000 cells /ml (without calcium and magnesium). Trypan Blue staining was used to detect cell health status and cell number. The dissociated cells in each sample were segmented into nanoscale gel bead emulsions (GEMs) at limited dilution to reduce the multiplication rate. Single-cell GEMs are then incubated with reverse transcription reagents, including several primers for cell and transcript barcoding in cDNA synthesis, followed by cDNA amplification and library construction. All procedures follow the guidelines provided by 10x Genomics, Inc.
Single-cell suspensions were converted to barcoded scRNA-seq libraries by using the Chromium Single Cell Library, Gel Bead & Multiplex Kit (10x Genomics), and following the manufacturer’s instructions. Briefly, cells were partitioned into Gel Beads in Emulsion in the ChromiumTM Controller instrument where cell lysis and barcoded reverse transcription of RNA occurred. Libraries were prepared using 10x Genomics Library Kits and sequenced on Illumina Nova6000（Illumina）with 150 bp paired end reads.

value: cerebellum

value: Eftud2 cKO

tag: age

value: postnatal day 14


title: MCF7_shControl_H

value: Breast cancer cell line (luminal)

value: WT

value: Hypoxia (1% oxygen)


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 6

value: donor no. 6


title: PMA-stimulated THP1 cells, 1h, vehicle (DMSO:EtOH), ATAC-seq, replicate 1

value: THP-1 human leukemia monocytic cell line

value: vehicle (DMSO:EtOH)

value: wt


title: GLU condition, timepoint S1, RNA-seq, replicate 2

value: Planktonic cells

value: GLU condition. timepoint S1


title: P14 WT;scRNAseq

description: 10x Genomics


title: P10 CKO;scRNAseq

description: 10x Genomics

value: postnatal day 10


title: F36P NT, bio rep 1


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 5

value: lung

value: titrated with HCl to pH6

value: without HEPES

value: donor no. 5


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 4

value: donor no. 4


title: F36P Vector, bio rep 3

data_processing:
The sequencing reads were aligned to the human reference genome (hg38) using Rsubread (v2.4.3). Raw counts were obtained from read alignments using refGene for gene counts or RepeatMasker annotation for transposable elements, and then further transferred to CPM using edgeR (v3.32.1). After filtering out low-expression genes with CPM < 1, all CPM values were performed with log2 transformed for further analysis.
Assembly: hg38
Supplementary files format and content: xlsm files include CPM values for each sample

extract_protocol:
Total RNA of 2 x10^6 cultured ERG overexpression or vector F36P cells in each sample was extracted by RNeasy Mini Kit (QIAGEN).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.


title: P10 WT;scRNAseq

description: 10x Genomics

value: cerebellum


title: GLU condition, timepoint L, RNA-seq, replicate 2

value: GLU condition. timepoint L


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 3

value: donor no. 3


title: GLU condition, timepoint S1, RNA-seq, replicate 1

value: WT


title: F36P Vector, bio rep 1


title: F36P HDAC7 KO, bio rep 2

value: HDAC7 knockout


title: YAP1, replicate 2

city: Suzhou

first: Shuhong

last: Hu

address: No.188 Shizi Street

institute: The First Affiliated Hospital of Soochow University

data_processing:
Cell Ranger (3.0.0) was used to perform alignment, filtering, barcode and unique molecular identifier (UMI) counting to generate feature-barcode-UMI matrices
The cDNA insert was aligned to the GRCm38/mm10 reference genome.
Seurat (4.3.0) R tool kit was used to perform quality control and unsupervised clustering. Cells whose gene number was less than 200 or more than 6300; UMI number was more than 40000 and mitochondrial gene ratio was more than 10 % were regarded as abnormal and filtered out.
In order to reduce batch effect of the samples, we performed data integration using the Harmony method
The screening criteria for upregulated genes are: 1. In the target or control subgroup, genes are expressed in over 25% of cells. 2. P value ≤ 0.01; 3. The gene expression fold log2FC is ≥ 0.36, which means the fold of gene upregulation is ≥ 1.28.
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: bone marrow

extract_protocol:
BM cells from WT, YAP1 heterozygote mice were flow-sorted. Cells were loaded onto the Chromium single cell controller (10x Genomics) to generate single-cell gel beads in the emulsion according to the manufacturer’s protocol.
Captured cells were lysed and the released RNA were barcoded through reverse transcription in individual gel-bead-in-emulsions (GEMs). Single-cell RNA-seq libraries were constructed using Single Cell 3’ Library and Gel Bead Kit V3.1.

value: bone marrow

value: primary cells

value: Nucleated BM cells

value: YAP1 heterozygote

value: 10-week old


title: F36P Vector, bio rep 2


title: GLU condition, timepoint L, RNA-seq, replicate 1

value: Planktonic cells


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 2

value: donor no. 2


title: YAP1, replicate 1


title: CAS condition, timepoint S2, RNA-seq, replicate 2

value: CAS condition. timepoint S2


title: CAS condition, timepoint S1, RNA-seq, replicate 2

value: CAS condition. timepoint S1


title: WT, replicate 2


title: Human lung tissue, titrated with HCl to pH6, without HEPES, donor no. 1

value: lung

value: titrated with HCl to pH6

value: without HEPES

value: donor no. 1


title: F36P ERG, bio rep 3

value: ERG overexpression


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 6

value: Streptococcus pneumoniae D39 infected

value: donor no. 6


title: F36P ERG, bio rep 1


title: F36P HDAC7 KO, bio rep 1

value: HDAC7 knockout


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 7

value: donor no. 7


title: F36P ERG, bio rep 2


title: CAS condition, timepoint S1, RNA-seq, replicate 1

value: WT


title: F36P AM-ERG H3K27ac ChIP

data_processing:
Pair-end sequencing FASTQ files were aligned to the human reference genome (hg38) using Bowtie2 on Galaxy platform (https://usegalaxy.org). Mapped reads were transformed by bamCoverage with the parameter “normalize using RPKM” from the deepTools. Peak calling was performed with MACS2 callpeak.
Assembly: hg38
Supplementary files format and content: bed

extract_protocol:
All samples were carried out using SimpleChIP® Enzymatic Chromatin IP Kit (CST, 9003) following the manufacturer’s instructions. 10^7 cultured F36P cells per sample were fixed with 1% formaldehyde and then quenched with glycine. After washing and cell lysis, the chromatin was fragmented with 0.7 µl of micrococcal nuclease (MNase) at 37oC for 20 min and nuclei were completely lysed by sonication. The 10 µg of chromatin in each reaction was incubated with 10 µl of Acetyl-Histone H3 (Lys27) antibody overnight at 4oC with rotation. Immunoprecipitation was performed with protein G magnetic beads. Following elution, reverse-crosslinks, and purification, DNA was used for further sequencing.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

tag: chip antibody


title: NOR

city: tianjin

first: siyi

last: liu

state: province

institute: tianjin medical university eye hospital

data_processing:
Illumina Hiseq platform
Raw data of fastq format were firstly processed through in-house perl scripts. In this step, clean data were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based onthe clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome  website directly. Index of the reference genome was built using Bowtie v2.2.3 and  paired-end clean reads were aligned to the reference genome using TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: mm10
Supplementary files format and content: tab delimited text file includes reads_count and FPKM values for each sample

source_name: eyeball

extract_protocol:
RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer. RNA concentration was measured using Qubit® RNA Assay Kit in Qubit® 2.0 Flurometer.
A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA)following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: eyeball

tag: disease state

value: control

tag: strain


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 3

value: donor no. 3


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 5

value: donor no. 5


title: F36P Vector H3K27ac ChIP

tag: cell line


title: F36P Vector ChIP

data_processing:
Pair-end sequencing FASTQ files were aligned to the human reference genome (hg38) using Bowtie2 on Galaxy platform (https://usegalaxy.org). Mapped reads were transformed by bamCoverage with the parameter “normalize using RPKM” from the deepTools. Peak calling was performed with MACS2 callpeak and Vector group as the peak calling control group.
Assembly: hg38
Supplementary files format and content: bed

extract_protocol:
All samples were carried out using SimpleChIP® Enzymatic Chromatin IP Kit (CST, 9003) following the manufacturer’s instructions. 10^7 cultured F36P cells per sample were fixed with 1% formaldehyde and then quenched with glycine. After washing and cell lysis, the chromatin was fragmented with 0.7 µl of micrococcal nuclease (MNase) at 37oC for 20 min and nuclei were completely lysed by sonication. The 10 µg of chromatin in each reaction was incubated with 10 µl of AM-Tag antibody overnight at 4oC with rotation. Immunoprecipitation was performed with protein G magnetic beads. Following elution, reverse-crosslinks, and purification, DNA was used for further sequencing.
The DNA fragments were repaired, A-tailed and further ligated with Illumina adapter. The final DNA library was obtained by size selection and PCR amplification.

tag: genotype


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 4

tag: treatment

value: donor no. 4


title: F36P AM-ERG ChIP


title: CAS condition, timepoint S2, RNA-seq, replicate 1

tag: cell type

value: Planktonic cells

value: CAS condition. timepoint S2


title: SHAM rep. 3 d7

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen

data_processing:
Demutliplexing and FASTQ extraction was performed using bcl2fastq v2.20.0.422.
Primary processing of FASTQ data including quality control, filtering, trimming,alignment of reads and counting of gene-sprecific genes was done using nf-core RNA-seq pipeline v3.7
Assembly: mm10
Supplementary files format and content: RNA-seq read counts per gene (csv)

source_name: Lung

extract_protocol:
RNeasy Micro Kit
NEBNext single cell/low input kit

value: Lung

value: Sham

value: Mesenchymal cells


title: CAS condition, timepoint P3, RNA-seq, replicate 1

value: CAS condition. timepoint P3


title: SHAM rep. 2 d7


title: Normal human astrocytes, uninfected, rep1

city: New York

first: Ziyu

last: Lu

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: sequencing parameters: 28X10X10X90

data_processing:
The demultiplexing, barcode processing, gene counting were made using software cellranger-5.0.0
Assembly: GRCh38
Supplementary files format and content: Processed data files are in txt format including a cell annotation file, gene annotation file, and a gene count sparse matrix.

source_name: Primary human astrocytes

growth_protocol: Primary human astrocytes (Creative Biolabs; NCC20-9PZ01; Lot NR34) at passage number 3 were plated in 6-wells (Corning; #3516) and cultured in AGMTM Astrocyte Growth Medium from Lonza (BulletKit CC-3186). 24h after plating, astrocytes were either left uninfected or were infected with JCV diluted in Astrocyte Growth Medium as described in material and methods. 12h after infection, the medium was replaced by fresh Astrocyte Growth Medium. The medium was exchanged every 3 days until day 10, when cells were collected for single cell RNA-Seq library generation using 10xGenomics technology.

extract_protocol:
In vitro cultured astrocytes were collected by trypsinization to generate a single cell suspension before filtering the cells through a 70um cell stainer. The signgle cell solution was used for single cell RNA-Seq library generation using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (16 rxns; PN-1000075) according to manufacturer’s instructions using a 10x Chromium controller.
Single cell RNA-Seq libraries were generated using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 (16 rxns; PN-1000075) according to manufacturer’s instructions using a 10x Chromium controller.

treatment_protocol: Primary human astrocytes were either left uninfected (NHA_uninfected_D10) or were infected with JC virus (NHA_JCV-WT_D10) or Agno-deficient JC virus (NHA_JCV-deltaAgno_D10) diluted in Astrocyte Growth Medium for 12h at an MOI of 0.6. After 12h, the medium was replaced by fresh Astrocyte Growth Medium.

value: Primary human astrocytes

value: wild type

value: uninfected, cultured and collected at the same time as infected cells


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 2

value: lung

value: Streptococcus pneumoniae D39 infected

value: without HEPES

value: donor no. 2


title: CAS condition, timepoint P2, RNA-seq, replicate 1

value: WT

value: CAS condition. timepoint P2


title: WT, replicate 1

value: bone marrow

value: primary cells

value: Nucleated BM cells

value: 10-week old


title: Human lung tissue, Streptococcus pneumoniae D39 infected, without HEPES, donor no. 1

value: donor no. 1


title: OIR

value: eyeball

value: mouse model of oxygen-induced retinopathy (OIR)


title: CAS condition, timepoint P1, RNA-seq, replicate 2

value: Planktonic cells

value: CAS condition. timepoint P1


title: SHAM rep. 1 d7

value: Lung

value: Sham

value: Mesenchymal cells


title: SHAM rep. 1 d14


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 7

value: lung

value: Streptococcus pneumoniae D39 infected

value: with HEPES added

value: donor no. 7


title: CAS condition, timepoint P3, RNA-seq, replicate 2

value: WT

value: CAS condition. timepoint P3


title: CAS condition, timepoint P1, RNA-seq, replicate 1


title: Normal human astrocytes, JCVdeltaAgno infected, rep1

description: sequencing parameters: 28X10X10X90

value: Primary human astrocytes

value: wild type

value: infected with Agno-deficient JC virus, collected 10 days after infection


title: Normal human astrocytes, JCV infected, rep1

description: sequencing parameters: 28X10X10X90

value: JC virus infected, collected 10 days after infection


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 6

value: donor no. 6


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 4

value: donor no. 4


title: H128-Con-2

city: Guangzhou

first: Hong

last: Wang

address: 132, Waihuandonglu, Daxue Cheng

department: School Of Pharmaceutical Sciences

institute: Sun Yat-sen University

data_processing:
ATAC-Seq high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, raw data were generated after sequencing, image analysis, base calling and quality filtering on sequencer. Use fastp software (v 0.23.4) to remove joints and low quality reads to obtain high quality clean reads; And clean reads alignment to the reference genome using bowtie2 software (v2.2.4); The reads aligned to the chrM were removed using the samtools software (v1.9), PCR duplicates were removed using getk-picard software (v4); open chromatin regions (Peak Calling) using MACS2 software (v2.1.1); differential enriched regions were identified using diffReps software; and enrichment peaks were annotated using ChIPseeker software (v1.2.6).GO and KEGG pathway analysis were performed for genes associated with differentially enriched peaks.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: Homo sapiens

growth_protocol: SCLC cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
sample 1-2: ATAC sequencing service was provided by CloudSeq Biotech (Shanghai, China) with GenSeq® ATAC kit (GenSeq Inc.). Briefly, cells were lysed using cold lysis buffer. After lysis, nuclei were collected by centrifuging at 500 g for 10 min at 4℃. The pellet was transposed with transposome and add tags on the both sides of fragmented genomic DNA according to the manufacturer’ s instruction. After tagmentation, the purified tagged DNA was used for PCR amplification with Genseq® 2× HiFi PCR Mix (GenSeq Inc.). The libraries were quantified using Qubit fluorometric assay (ThermoFisher) and then sequenced. in a NovaSeq platform (Illumina).
sample 1-2: ATAC sequencing service was provided by CloudSeq Biotech (Shanghai, China) with GenSeq® ATAC kit (GenSeq Inc.).

treatment_protocol: H128 cells were treated with HX531 for 48 h. (Control group, we named Con-2; treated group, we named H10-2)

value: Homo sapiens

value: tumor cells

value: control


title: PNX rep. 3 d7

value: Lung

value: PNX


title: PNX rep. 2 d7

value: Mesenchymal cells


title: CAS condition, timepoint P2, RNA-seq, replicate 2

value: Planktonic cells

value: CAS condition. timepoint P2


title: H128-HX531-H3K27ac, ChIP

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01.bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
sample 1-4:Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
sample 1-4:ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: H128 cells were treated with HX531 for 48 h.


title: GLU condition, timepoint S1, IPOD sample, replicate 2

description: judith_glu_s1_merged_v6rz_chipsub.bedgraph

data_processing:
The end-to-end IPOD analysis pipeline from (Freddolino et al., PLoS Biology 19(6): e3001306, 2021) was used
Assembly: E. coli MG1655 U00096.3
Supplementary files format and content: Bedgraph files: position-level information on sequencing read depths, either normalized according to the IPOD-HR pipeline (v6rz scores), z-scored ChIP:input ratios (chip_vs_inp), or read abundances normalized by overall sample read depth (RNA)
Library strategy: IPOD

value: GLU condition. timepoint S1


title: GLU condition, timepoint S2, IPOD sample, replicate 2

description: judith_glu_s2_merged_v6rz_chipsub.bedgraph

value: WT

value: GLU condition. timepoint S2


title: H128-H10-2

value: HX531 for 48 h


title: SHAM rep. 2 d14

value: Sham


title: GLU condition, timepoint L, IPOD sample, replicate 2

description: judith_glu_1_merged_v6rz_chipsub.bedgraph

value: GLU condition. timepoint L


title: H128-0-H3K27ac, ChIP


title: H128-0-Input


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 5

value: lung

value: Streptococcus pneumoniae D39 infected

value: with HEPES added

value: donor no. 5


title: Human lung tissue, control sample, without HEPES, donor no. 7

value: control sample

value: without HEPES

value: donor no. 7


title: CAS condition, timepoint S2, IPOD sample, replicate 2

description: judith_cas_s2_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint S2


title: PNX rep. 3 d14

value: Lung

value: PNX

value: Mesenchymal cells


title: PNX rep. 2 d14


title: GLU condition, timepoint S2, IPOD sample, replicate 1

value: Planktonic cells


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 3

value: donor no. 3


title: CAS condition, timepoint S2, IPOD sample, replicate 1

value: WT


title: P7 SMA

data_processing:
For demultiplexing and the subsequent FASTQ file generation we used Illumina’s bcl2fastq (2.19.0.316)
Sequencing reads were aligned to the mouse mm10 reference genome (refdata-gex-mm10-2020-A downloaded from 10xGenomics) using STAR solo (2.7.9a)
STAR was run in Velocyto mode in order to allow for downstream velocity analysis.
Droplet filtering was done using the EmptyDrops_CR parameter setting.
Resulting UMI count matrices were pre-processed for further analyses using Scanpy (1.7.2) in a Python (3.8.10) environment
Assembly: mm10
Supplementary files format and content: h5ad of imported read count matrices

extract_protocol: Library preparation was carried out using the Chromium Next GEM Single-Cell 3ʹ Reagent Kit v3.1 (10x Genomics) according to manufacturer’s instructions.

value: tdTom+ cells

value: Acta2-Cre-ERT2; tdTomatoflox

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P7


title: GLU condition, timepoint S1, IPOD sample, replicate 1

value: GLU condition. timepoint S1


title: macro, RIP, rep2

first: Chenguang

address: 1500E Medical Center Dr, Room 4411

department: Department of Internal Medicine

data_processing:
Trimmed reads were mapped to GRCh38 using STAR (v2.7.8a) and binding peaks were identified by MACS (version 1.4.1) and visualized by IGVtools (v2.8.0).
Assembly: GRCh38
Supplementary files format and content: bigwig

source_name: PBMC

growth_protocol: RPMI, 10%FBS, 1×Penicillin/Streptomycin, cells are incubated at 37°C, 5% CO2

extract_protocol:
1×107 cells/IP were resuspended in 1X ChIP Sonication Cell Lysis Buffer (Cell Signaling #56383). After centrifugation at 500 g for 3 min, Pellet (nuclear fraction) were suspended in 1X ChIP Sonication Nuclear Lysis Buffer (Cell Signaling #56383). Cell suspension were sonicated by Qsonica Q800R3 sonicator (Qsonica L.L.C, Newtown, CT) for 20 min. Chromatin was clarified (16,000× g, 4°C, 10 min) and incubated with DNase at 37°C for 20 min. 10 μg eIF4e and IgG antibody were incubated with chromatin overnight and then incubated with 30 µL Dynabeads Protein G (Invitrogen #10004D) for 4 hours and washed with low-salt washing buffer five times and high-salt washing buffer once. Elution and de-crosslinking were performed overnight in 150 µL elution buffer (300 mM NaCl, 5 mM DTT and 1% SDS in TE buffer, pH8.0) at 65 °C. RNA was extracted from chromatin by Trizol (ThermoFisher, #15596018) and processed according to the manufacturer’s instructions.
RNA was assessed for quality using the TapeStation (Agilent, Santa Clara, CA). Samples were prepared using the NEBNext rRNA Depletion Kit (NEB, E6310) and xGen Broad-range RNA Library Prep (IDT, 1009813) with xGen Normalase UDI Primers (IDT, various). Final libraries were checked for quality and quantity by TapeStation (Agilent) and Qubit (Thermo Fisher Scientific). This pool was subjected to 151bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq). Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.

value: PBMC

value: monocyte-derived macrophage

tag: rip antibody


title: H128-HX531-Input

value: Homo sapiens

value: tumor cells


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 2

value: lung

value: Streptococcus pneumoniae D39 infected

value: with HEPES added

value: donor no. 2


title: PNX rep. 1 d14

value: Lung

value: PNX


title: CAS condition, timepoint S1, IPOD sample, replicate 2

description: judith_cas_s1_merged_v6rz_chipsub.bedgraph

value: Planktonic cells

value: CAS condition. timepoint S1


title: macro, input, rep1


title: P365 SMA

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P365


title: PNX rep. 1 d7

value: Mesenchymal cells


title: Human lung tissue, Streptococcus pneumoniae D39 infected, with HEPES added, donor no. 1

value: donor no. 1


title: CAS condition, timepoint S1, IPOD sample, replicate 1

value: WT


title: Human lung tissue, control sample, without HEPES, donor no. 3

value: control sample

value: without HEPES

value: donor no. 3


title: GLU condition, timepoint L, IPOD sample, replicate 1

value: GLU condition. timepoint L


title: SUP-T1, input, rep2

value: T-cell acute lymphblastic leukemia


title: CAS condition, timepoint P3, IPOD sample, replicate 2

description: judith_cas_p3_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint P3


title: Human lung tissue, control sample, without HEPES, donor no. 5

value: lung

value: donor no. 5


title: macro, input, rep2

value: PBMC

value: monocyte-derived macrophage


title: Human lung tissue, control sample, without HEPES, donor no. 6

value: donor no. 6


title: Human lung tissue, control sample, without HEPES, donor no. 4

value: donor no. 4


title: P28 SMA

value: Lung

value: tdTom+ cells

value: Acta2-Cre-ERT2; tdTomatoflox

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P28


title: Gli1Cre d14 before

value: Gli1Cre-ERT2; tdTomatoflox

value: Tamoxifen injections (three i.p.) 2 weeks before PR8 infection. Lungs were harvested at day 14


title: P7 Gli

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P7


title: macro, RIP, rep1


title: CAS condition, timepoint P1, IPOD sample, replicate 2

description: judith_cas_p1_merged_v6rz_chipsub.bedgraph

value: Planktonic cells

value: WT

value: CAS condition. timepoint P1


title: H9, input, rep2

value: cutaneous T cell lymphoma


title: P365 Gli1

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P365


title: Human lung tissue, control sample, without HEPES, donor no. 2

value: lung

value: control sample

value: without HEPES

value: donor no. 2


title: P28 GLI


title: Human lung tissue, control sample, without HEPES, donor no. 1

value: donor no. 1


title: P182 Gli

value: Lung

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P182


title: SUP-T1, RIP, rep2

value: T-cell acute lymphblastic leukemia


title: CAS condition, timepoint P3, IPOD sample, replicate 1

value: CAS condition. timepoint P3


title: P182 SMA

value: tdTom+ cells

value: Acta2-Cre-ERT2; tdTomatoflox


title: CAS condition, timepoint P2, IPOD sample, replicate 2

description: judith_cas_p2_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint P2


title: SUP-T1, input, rep1


title: GLU condition, timepoint S2, RNA polymerase ChIP sample, replicate 2

description: judith_glu_s2_merged_chip_vs_inp_lograt.bedgraph

value: Planktonic cells

value: GLU condition. timepoint S2


title: Human lung tissue, control sample, with HEPES added, donor no. 2

value: with HEPES added


title: H9, RIP, rep1

value: cutaneous T cell lymphoma


title: Bone marrow-derived macrophage-BMDM_pIL4-1_4

city: Stanford

first: Andy

last: Chen

address: 240 Pasteur Rd

institute: Stanford University

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2 and BLAT aligner
Aligned reads were processed with published MCC pipeline
Assembly: mm10
Supplementary files format and content: normalized bigwig files of contact
Library strategy: MCC

source_name: Bone marrow

growth_protocol: Wild type, 2-3 months old female C57Bl6 mice were purchased from Jackson laboratories. Mice were sacrificed and bone marrow was isolated form the tibiae and femora of the animals. Red blood cell lysis was carried out and cells were plated in differentiation media containing 10% FBS, Dulbecco’s Modified Eagle’s Medium (DMEM) and 20ng/ml mouse M-CSF (Peprotech). On the third day of differentiation, media was replaced with fresh differentiation media. Cytokine treatments sorting procedures were carried out on the 6th day of differentiation.

extract_protocol: Micro-Capture C (MCC) was performed as previously described with the following differences17. Macrophages were scraped and crosslinked in the presence of 1% formaldehyde (in PBS) for 10-minutes in suspension followed by the addition of 1.5ml Glycine (1M) and further incubation for 5-minutes at room temperature. Cells were washed in ice-cold PBS, counted, and 3x106 aliquots were prepared for nuclei isolation with the following MCC lysis buffer: 10mM Tris-HCl pH 7.5, 10mM NaCl, 3mM MgCl2, 0.1% Twee-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin and 1% BSA in nuclease-free H2O. Each cell aliquot of 3x106 were resuspended in 500ul MCC lysis buffer and incubated on ice for 5-minutes. Cells were spun down, washed in ice-cold PBS, and washed in nuclease-free H2O before proceeding to MNase digestion with 1-2U of MNase for 3x106 cells that went on for 1-hour at 37C while shaking in a thermomixer (Eppendorf) at 550rcf. MNase was stopped by the addition of EGTA. At this point, nuclei were split into two tubes, and end-repair and proximity ligation were performed overnight. On the next day, nuclei were spun and subjected to proteinase K digestion at 65C overnight. DNA was column purified (Minelute, Qiagen) and eluted in 130ul H2O for sonication with Covaris E220 model using the following settings: Fill Level – 10, Duty Cycle – 5, PIP – 140, Cycles/Bursts – 200; sonicated for 4-minutes. DNA was cleaned up with Minelute, quantified and subjected to library preparation with Ovation Ultralow V2 Library Systems (Tecan) using 100ng DNA and 8 PCR cycles. Amplified libraries were subjected to hybridization with biotinylated oligonucleotide pools that were designed by the HyperDesign Team (Roche) and synthesized by Roche. All hybridization reagents were purchased from Roche as part of the KAPA Hyper Prep kit, and hybridization, pull-down, and washes were performed per manufacturer’s instructions. Bead-bound libraries were amplified with the PCR reagents from the Ovation Ultralow Library V2 Kit (Tecan). Libraries were quantified and sequenced on a Novaseq 6000 with 2x150bp configuration.

treatment_protocol: Macrophages were treated with either IL-4 (20ng/ml) or IFNG (20ng/ml) (Peprotech). For polarization we used 24 hours of IL-4 polarization and 3 hours of IFNG polarization in differentiation media that contained 10% FBS, 1% penicillin/streptomycin and M-CSF (20ng/ml). IL-4 priming was performed as follows: macrophages were polarized with IL-4 (20ng/ml) for 24 hours. Cell were washed three times with serum-free DMEM, then differentiation media was replaced, and cells were rested for an additional 24 hours. Repolarization was performed at this point for 3 hours with IFNG (20ng/ml). Macrophage polarization for cell cycle experiments used 3 hours of polarization with either IL-4 or IFNG (both at a 20ng/ml concentration).

value: Bone marrow-derived macrophage

tag: Sex

value: female

value: Bone marrow

value: wild type


title: Human lung tissue, control sample, with HEPES added, donor no. 7

value: lung

value: control sample

value: donor no. 7


title: Human lung tissue, control sample, with HEPES added, donor no. 6

value: donor no. 6


title: CAS condition, timepoint P2, IPOD sample, replicate 1

value: WT


title: GLU condition, timepoint S1, RNA polymerase ChIP sample, replicate 2

description: judith_glu_s1_merged_chip_vs_inp_lograt.bedgraph

value: GLU condition. timepoint S1


title: SUP-T1, RIP, rep1

value: T-cell acute lymphblastic leukemia


title: P547 SMA

value: Lung

value: tdTom+ cells

value: Acta2-Cre-ERT2; tdTomatoflox

value: Tamoxifen injection (single s.c.) at P4 and harvesting at P547


title: Human lung tissue, control sample, with HEPES added, donor no. 5

value: with HEPES added

value: donor no. 5


title: Human lung tissue, control sample, with HEPES added, donor no. 1

value: donor no. 1


title: Skin biopsy from AA female_5

city: Chicago

first: Irina

last: Budunova

state: Illinois

address: 303 E Chicago Ave, Ward Bldg, #9-132

department: Dermatology

institute: Northwestern University

data_processing:
Cutadapt[1] and perl scripts were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases
HISAT2 was used to map reads to the genome of homo sapiens (Version: v107)
The mapped reads of each sample were assembled using StringTie
All individual transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare
StringTie[3] and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts
StringTie[ was used to perform expression level for mRNAs and lncRNAs by calculating FPKM.
mRNAs/lncRNAs differential expression analysis was performed by DESeq2 software between two different groups (AA and WNH). The genes/mRNAs/lncRNAs with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes/mRNAs/lncRNAs.
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: normal  skin

extract_protocol:
skin was homogenized by Qiagen Tissue PowerLyzer, RNA was extracted by TRIzol reagent
Illumina’s TruSeq-stranded-total-RNA-sample preparation protocol

value: normal  skin


title: Bone marrow-derived macrophage-BMDM_pIL4_2

value: Bone marrow-derived macrophage

value: female

value: Bone marrow


title: WholeBlood-Control-M-1100

city: Strasbourg

first: Pierre-Eric

last: Lutz

address: 8 allée du général Rouvillois

institute: Institut des Neurosciences Cellulaires et Intégratives, INCI CNRS UPR3212

data_processing:
reads were trimmed using cutadapt v1.18
reads were aligned following the QuickMIRseq pipeline [26] using bowtie v1.2.2 at default parameters
read counts were quantified using HTSeq-count
Assembly: GRCh38.p12
Supplementary files format and content: csv file includes raw counts for each sample

source_name: Whole blood

extract_protocol:
Venous blood passed through LeukoLOCK™ filters (Life Technologies, Ambion), followed by total RNA extraction using ethanol precipitation
MiRNA libraries were prepared using the Bioo Scientific NEXTflex Small RNA-Seq kit v3 (Bioo Scientific), following the manufacturer’s instructions, using 500 ng of total RNA

value: Whole blood

tag: group

value: Control

value: Male


title: CAS condition, timepoint P1, IPOD sample, replicate 1

extract_protocol:
Detailed instructions for IPOD‐HR interface extraction, RNA polymerase chromatin immunoprecipitation, and crosslinking reversal and recovery of DNA have been previously published (Freddolino et al., PLoS Biology 19(6): e3001306, 2021), and were followed precisely here
Illumina sequencing libraries for DNA samples were prepared using a NebNext Ultra DNA kit, following the manufacturer’s instructions except that a Qiaquick Nucleotide Removal Kit was used for pre-ligation cleanup to avoid loss of low molecular weight fragments. RNA-seq samples were prepared using an Epicentre ScriptSeq v2 kit following the manufacturer’s instructions

value: Planktonic cells

value: WT

value: CAS condition. timepoint P1


title: Bone marrow-derived macrophage-BMDM_pIL4_1

value: wild type


title: Human lung tissue, control sample, with HEPES added, donor no. 4

data_processing:
The pipeline used to process the transcriptomic data is available from Github (https://github.com/bihealth/seasnap-pipeline/). Quality control was performed using a variety of tools, including FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), dupradar , qualimap  and summarised using MultiQC. For adapter trimming, we used the trimadap tool available from https://github.com/lh3/trimadap. Reads were mapped to human genome GRCh38, version p7 using the STAR program, version 2.7.8a .
ounts were produced by the STAR program using the Gencode GRCh38 annotation version 25. For differential gene expression, the R package DESeq2, version 1.38 was used . Gene set enrichment used the R package tmod, v. 0.50.13 , with gene sets included in the MSigDB through the msigdbr package, v. 7.5.1 .
Gene sets used included Gene Ontology Biological Process gene sets, Hallmark gene sets, REACTOME gene sets and transcriptional modules contained in the tmod package. Results, reports, pipeline output and additional files were stored and managed using the SODAR system .
Assembly: GRCh38, version p7
Supplementary files format and content: CSV file with raw count data

extract_protocol:
Human lung tissue explants were stored in RNAlater™ Stabilization Solution (ThermoFisher) at 4°C overnight (to allow the solution to thoroughly penetrate the tissue). For total RNA isolation the RNeasy Mini Kit (Qiagen) was used according to manufacturer`s instructions. Human lung tissue was transferred to Lysing Matrix D tubes (MP Biomedicals) in 500 μl RLT lysis buffer supplemented with β-mercaptoethanol. Tissue was lysed using FastPrep®-24 (MP Biomedicals) applying 3 rounds of tissue lysis at default settings (6 m/s, 30 s). Homogenates were centrifuged and RNA was purified from the supernatant. 0.5 μg RNA was reverse transcribed and quantitative PCR was performed using TaqMan assays on an ABI 7300 instrument. RNA from infected samples was purified as described above. 0.5 μg RNA was used for RNA-Seq libraries preparation. RNA-Seq libraries were constructed using Illumina TruSeqTM Stranded Total RNA Library Prep Gold kit (New England Biolabs) according to the manufacturer’s instruction, with rRNA depletion and 11 PCR cycles in the amplification step. Sequencing was performed on a NextSeq 500 platform using 1x76 cycles single-end sequencing and aiming at 10-20 mln reads per sample.
RNA from infected samples was purified as described above. 0.5 μg RNA was used for RNA-Seq libraries preparation. RNA-Seq libraries were constructed using Illumina TruSeqTM Stranded Total RNA Library Prep Gold kit (New England Biolabs) according to the manufacturer’s instruction, with rRNA depletion and 11 PCR cycles in the amplification step. Sequencing was performed on a NextSeq 500 platform using 1x76 cycles single-end sequencing and aiming at 10-20 mln reads per sample.

value: lung

value: control sample

value: donor no. 4


title: H9, RIP, rep2

value: cutaneous T cell lymphoma


title: WholeBlood-MDD-M-913

value: MDD


title: Bone marrow-derived macrophage-BMDM_IL4-31_2


title: Bone marrow-derived macrophage-BMDM_pIL4-1_3


title: H9, input, rep1


title: Skin biopsy from WNH female_4


title: WholeBlood-MDD-F-911

value: Female


title: Bone marrow-derived macrophage-BMDM_IL4-3_4


title: Bone marrow-derived macrophage-BMDM_IL4-31_1


title: Bone marrow-derived macrophage-BMDM_pIL4-1_2


title: GLU condition, timepoint S2, RNA polymerase ChIP sample, replicate 1

data_processing:
The end-to-end IPOD analysis pipeline from (Freddolino et al., PLoS Biology 19(6): e3001306, 2021) was used
Assembly: E. coli MG1655 U00096.3
Supplementary files format and content: Bedgraph files: position-level information on sequencing read depths, either normalized according to the IPOD-HR pipeline (v6rz scores), z-scored ChIP:input ratios (chip_vs_inp), or read abundances normalized by overall sample read depth (RNA)

value: GLU condition. timepoint S2


title: Skin biopsy from WNH female_6

value: normal  skin


title: Skin biopsy from AA female_2


title: Bone marrow-derived macrophage-BMDM_pIL4-1_1

value: Bone marrow-derived macrophage

value: female


title: GLU condition, timepoint S1, RNA polymerase ChIP sample, replicate 1

value: GLU condition. timepoint S1


title: GLU condition, timepoint L, RNA polymerase ChIP sample, replicate 2

description: judith_glu_1_merged_chip_vs_inp_lograt.bedgraph

value: GLU condition. timepoint L


title: Skin biopsy from AA female_1


title: WholeBlood-MDD-F-914

value: Whole blood


title: Bone marrow-derived macrophage-BMDM_IL4-3_2

value: Bone marrow


title: Skin biopsy from AA female_3


title: CAS condition, timepoint P3, RNA polymerase ChIP sample, replicate 2

description: judith_cas_p3_merged_chip_vs_inp_lograt.bedgraph

value: Planktonic cells

value: WT

value: CAS condition. timepoint P3


title: GLU condition, timepoint L, RNA polymerase ChIP sample, replicate 1


title: Skin biopsy from WNH female_5


title: WholeBlood-MDD-F-912


title: Bone marrow-derived macrophage-BMDM_IL4-3_1

value: wild type


title: CAS condition, timepoint S2, RNA polymerase ChIP sample, replicate 1

description: judith_cas_s2_merged_chip_vs_inp_lograt.bedgraph

value: CAS condition. timepoint S2


title: CAS condition, timepoint P3, RNA polymerase ChIP sample, replicate 1


title: Bone marrow-derived macrophage-BMDM_IL4-2_2


title: Skin biopsy from AA female_4


title: CAS condition, timepoint S1, RNA polymerase ChIP sample, replicate 2

description: judith_cas_s1_merged_chip_vs_inp_lograt.bedgraph

value: CAS condition. timepoint S1


title: WholeBlood-MDD-F-910


title: Bone marrow-derived macrophage-BMDM_IL4-3_3


title: CAS condition, timepoint S1, RNA polymerase ChIP sample, replicate 1


title: WholeBlood-MDD-F-904


title: CAS condition, timepoint S2, RNA polymerase ChIP sample, replicate 2


title: Skin biopsy from WNH female_3


title: WholeBlood-MDD-F-908


title: WholeBlood-MDD-F-903


title: CAS condition, timepoint P1, RNA polymerase ChIP sample, replicate 2

description: judith_cas_p1_merged_chip_vs_inp_lograt.bedgraph

value: CAS condition. timepoint P1


title: Bone marrow-derived macrophage-BMDM_IL4-1_1


title: Skin biopsy from WNH female_2


title: REH_KO_InO_rep2

city: Memphis

first: Carolin

last: Escherich

state: Tennessee

address: 262 Danny Thomas Place

institute: St. Jude Children's Research Hospital

description:
2545335_REH_DNTT_KO_Ino_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

data_processing:
BAM file with duplicate reads marked by GATK, after sequencing reads were mapped to the human genome (GRCh38/hg38) by STAR (version 2.6.0b) and annotation file derived from GENCODE (v31).
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample

source_name: B-ALL

growth_protocol: RPMI1640 containg 10% FBS

extract_protocol:
total RNA was extracted using Rneasy Mini Kit (Qiagen)
Total RNA library was constructed using an Illumina TrueSeq stranded mRNA library prep kit

treatment_protocol: Inotuzumab Ozogamicin or vehicle control

value: B-ALL

value: REH

value: B-lymphoblast

value: DNTT KO

value: InO


title: REH_KO_InO_rep1

description:
2545334_REH_DNTT_KO_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: CAS condition, timepoint P2, RNA polymerase ChIP sample, replicate 2

description: judith_cas_p2_merged_chip_vs_inp_lograt.bedgraph

value: CAS condition. timepoint P2


title: WholeBlood-MDD-F-906

value: MDD

value: Female


title: Skin biopsy from WNH female_1

value: normal  skin


title: REH_KO_Contr_rep3

description:
2545333_REH_DNTT_KO_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: control


title: WholeBlood-MDD-F-905

value: Whole blood


title: WholeBlood-MDD-M-901

value: Male


title: WholeBlood-MDD-M-823


title: Bone marrow-derived macrophage-BMDM_IL4-2_1

value: Bone marrow-derived macrophage

value: female

value: Bone marrow


title: Bone marrow-derived macrophage-BMDM_CTR-31_1

value: wild type

value: CTR


title: WholeBlood-MDD-F-909


title: REH_KO_Contr_rep2

description:
2545332_REH_DNTT_KO_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL


title: WholeBlood-MDD-F-822


title: CAS condition, timepoint P2, RNA polymerase ChIP sample, replicate 1

value: Planktonic cells

value: WT


title: REH_KO_InO_rep3

description:
2545336_REH_DNTT_KO_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: REH

value: B-lymphoblast

value: DNTT KO


title: GLU condition, timepoint S1, input sample, replicate 2

description: judith_glu_s1_merged_v6rz_chipsub.bedgraph

value: GLU condition. timepoint S1


title: Bone marrow-derived macrophage-BMDM_CTR-31_2


title: GLU condition, timepoint S2, input sample, replicate 2

description: judith_glu_s2_merged_v6rz_chipsub.bedgraph

value: GLU condition. timepoint S2


title: Human lung tissue, control sample, with HEPES added, donor no. 3

value: lung

value: control sample

value: with HEPES added

value: donor no. 3


title: Bone marrow-derived macrophage-BMDM_CTR-3_4

value: Bone marrow-derived macrophage


title: Bone marrow-derived macrophage-BMDM_IL4-1_2

value: female


title: WholeBlood-MDD-F-820

value: Whole blood

value: MDD

value: Female


title: REH_WT_InO_rep3

description:
2545330_REH_WT_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL

value: InO


title: GLU condition, timepoint S2, input sample, replicate 1

value: Planktonic cells

value: WT


title: Bone marrow-derived macrophage-BMDM_CTR-3_2

value: Bone marrow

value: wild type

value: CTR


title: CAS condition, timepoint P1, RNA polymerase ChIP sample, replicate 1

value: CAS condition. timepoint P1


title: REH_WT_InO_rep2

description:
2545329_REH_WT_Ino_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: REH

value: B-lymphoblast


title: GLU condition, timepoint L, input sample, replicate 2

description: judith_glu_1_merged_v6rz_chipsub.bedgraph

value: GLU condition. timepoint L


title: WholeBlood-MDD-M-813

value: Male


title: GLU condition, timepoint L, input sample, replicate 1


title: REH_KO_Contr_rep1

description:
2545331_REH_DNTT_KO_baseline_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: DNTT KO

value: control


title: WholeBlood-MDD-F-811

value: Whole blood


title: REH_WT_InO_rep1

description:
2545328_REH_WT_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: WholeBlood-MDD-F-817

value: MDD


title: REH_WT_Contr_rep2

description:
2545327_REH_WT_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: Bone marrow-derived macrophage-BMDM_CTR-3_1

value: Bone marrow-derived macrophage

value: female


title: CAS condition, timepoint S2, input sample, replicate 2

description: judith_cas_s2_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint S2


title: Bone marrow-derived macrophage-BMDM_CTR_2


title: Bone marrow-derived macrophage-BMDM_CTR_1


title: WholeBlood-MDD-F-806

value: Female


title: CAS condition, timepoint S2, input sample, replicate 1

value: Planktonic cells

value: WT


title: REH_WT_Contr_rep1

description:
2545326_REH_WT_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL


title: WholeBlood-MDD-F-804


title: Bone marrow-derived macrophage-BMDMpreIL4IFNG_Rep2

data_processing:
Reads were trimmed for quality and adapter sequences using fastQC.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were processed with HiC-Pro pipeline
Contact matrices were created with Juicer
Loop calling was performed with Homer
Assembly: mm10
Supplementary files format and content: Normalized contact matrices and chromatin interaction loops

extract_protocol: Hi-C was performed by following the reported HiChIP protocol and omitting the protein immunoprecipitation step42. Briefly, 106 bone marrow-derived macrophages were crosslinked with 1% formaldehyde for 10-minutes. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated in lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0) by rotating the cells for 1-hour at 4C. Nuclear pellet was resuspended in 0.5% SDS solution and incubated at 62C for 10 minutes. SDS was quenched by the addition of 10% Triton-X. Chromatin was digested with 8U of MboI enzyme overnight at 37C. Biotin fill-in was performed for 1-hour at 37C, followed by proximity ligation for 6-hours at room temperature. After proximity ligation, nuclei were subjected to Proteinase K digestion and decrosslinking overnight at 68C. DNA was column purified (Minelute, Qiagen), and sonicated to a size distribution of 200-500bp. DNA was subjected to streptavidin bead binding to pull-down biotinylated DNA that represents ligation junctions. Tn5 was used to create libraries by on bead tagmentation with sequencing adapters, followed by PCR. Libraries were quantified by Qubit and size distribution was assessed with Bioanalyzer.

value: Bone marrow

value: wild type


title: Bone marrow-derived macrophage-BMDM_CTR-3_3

value: CTR


title: RS411_KO_InO_rep2

description:
2379072_RS411_DNTT_KO_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-lymphoblast

value: InO


title: GLU condition, timepoint S1, input sample, replicate 1

value: GLU condition. timepoint S1


title: CAS condition, timepoint S1, input sample, replicate 2

description: judith_cas_s1_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint S1


title: WholeBlood-MDD-F-802


title: CAS condition, timepoint S1, input sample, replicate 1


title: RS411_KO_InO_rep1

description:
2379070_RS411_DNTT_KO_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: DNTT KO


title: Bone marrow-derived macrophage-BMDMpreIL4_Rep2


title: Bone marrow-derived macrophage-BMDMpreIL4IFNG_Rep1


title: CAS condition, timepoint P3, input sample, replicate 2

description: judith_cas_p3_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint P3


title: WholeBlood-MDD-M-633

value: Whole blood

value: MDD

value: Male


title: Bone marrow-derived macrophage-BMDMpreIL4_Rep1

value: Bone marrow-derived macrophage

value: female


title: RS411_WT_InO_rep3

description:
2379069_RS411_WT_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: RS411_WT_InO_rep2

description:
2379068_RS411_WT_Ino_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: Bone marrow-derived macrophage-BMDMIL4_Rep2


title: WholeBlood-MDD-M-631


title: RS411_WT_InO_rep1

description:
2379067_RS411_WT_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: WholeBlood-MDD-F-629

value: Female


title: CAS condition, timepoint P2, input sample, replicate 2

description: judith_cas_p2_merged_v6rz_chipsub.bedgraph

value: Planktonic cells

value: WT

value: CAS condition. timepoint P2


title: CAS condition, timepoint P3, input sample, replicate 1


title: Bone marrow-derived macrophage-BMDMIL4_Rep1

value: Bone marrow

value: wild type


title: RS411_KO_Contr_rep3

description:
2379066_RS411_DNTT_KO_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL

value: B-lymphoblast

value: control


title: Bone marrow-derived macrophage-BMDMIFNG_Rep2

value: IFNG


title: WholeBlood-MDD-F-623


title: CAS condition, timepoint P2, input sample, replicate 1


title: RS411_KO_Contr_rep2

description:
2379065_RS411_DNTT_KO_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: DNTT KO


title: WholeBlood-MDD-M-621


title: Bone marrow-derived macrophage-BMDMIFNG_Rep1


title: CAS condition, timepoint P1, input sample, replicate 1

description: judith_cas_p1_merged_v6rz_chipsub.bedgraph

value: CAS condition. timepoint P1


title: WholeBlood-MDD-F-801

value: Whole blood


title: WholeBlood-MDD-F-620

value: MDD


title: Bone marrow-derived macrophage-BMDMCTR_Rep2

value: CTR


title: RS411_WT_Contr_rep3

description:
2379063_RS411_WT_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: LD, Yorkshire(P0), scRNA-seq

first: Delin

last: Mo

address: Xingang Road

data_processing:
The CellRanger (10x Genomics) analysis pipeline was employed to generate a Digitak Gene Expression (DGE) matrix. To ensure high-quality filtering and clustering, the raw DGE matrix (UMI counts per cell per gene) was processed using R software version 3.5.2 (https://www.r-project.org/).
Supplementary files format and content: Tab-separated values files and matrix files

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
The longissimus dorsi muscle (LD) was isolated and obtained for 1g per piglet. Single-cell RNA sequencing (scRNA-seq) was performed on the 2.5IW cells obtained from the LD. To eliminate red blood cells and dead cells, the single cells were treated with Red Blood Cell Lysis Buffer and then subjected to magnetic bead separation. The viability of the filtered single cells was assessed using trypan blue staining (Thermo Fisher Scientific, Waltham, MA, USA) and haemocytometry (Thermo Fisher Scientific).
library preparation for reverse transcription was performed using the 10x Genomics Single Cell v2 kit, following the specified protocol. The library was sequenced in a single lane on an Illumina NextSeq-500 system using the high-output (400 M) kit.

value: longissimus dorsi muscle

value: intramuscular vascular stem cells (IVSC)

tag: breed

value: Yorkshire


title: WholeBlood-MDD-M-619

value: Male


title: LD GDSS(P0), scRNA-seq

value: Guangdong small-eared spotted pig


title: RS411_WT_Contr_rep2

description:
2379062_RS411_WT_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: WT


title: WholeBlood-MDD-F-618

value: Female


title: Bone marrow-derived macrophage-BM_pIL4_SMC1A_rep2

data_processing:
Reads were trimmed for quality and adapter sequences using fastp.
Trimmed reads were aligned to the mm10 reference genome using bowtie2.
Aligned reads were deduplicated using Picard.
Peakswere called using MACS2 from the paired endbed file (bedpe) using a false discovery thresh-old of 0.05 (-q 0.05).
Normalized bigwig files were created by normalizing the coverage track of the bedpe file by reads in peaks.
Assembly: mm10
Supplementary files format and content: Normalized bigwig files.

extract_protocol:
Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 12 PCR cycles.

value: Bone marrow-derived macrophage

value: Bone marrow

value: wild type

tag: antibody

value: female


title: RS411_WT_Contr_rep1

description:
2379061_RS411_WT_baseline_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL

value: B-lymphoblast

value: control


title: Nalm6_KO_InO_rep3

description:
2379060_Nalm6_DNTT_KO_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: DNTT KO

value: InO


title: Rat,saline2-TMJ,14days

city: Chongqing

first: Haixia

last: Deng

state: Chongqing

address: No. 426, Songshi North Road, Yubei District, Chongqing, China

department: Department of Anesthesiology

institute: Stomatological Hospital of Chongqing Medical University, Chongqing, China.

description:
Readcount_TPM.txt
DEcircRNAs.txt
N_D2

data_processing:
clean data (clean reads) were obtained by removing reads containing adapter, reads 1 containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
Novel gene prediction using StringTie (1.3.3b) and featureCounts (1.5.0-p3) is used to calculate the number of reads mapped to each gene
Known and new circRNAs in each sample were counted and normalized by TPM. Formula: Normalized expression = (readCount*1,000,000)/libsize Note: libsize: sum of circRNA readcount of samples.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed.
Assembly: ensembl_97
Supplementary files format and content: tab-delimited text file includes TPM readcont for each Sample
Supplementary files format and content: tab-delimited text file includes CFAvsCON DEcircRNAs

organism: Rattus norvegicus

source_name: thalamus

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies,CA,USA)
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: thalamus

value: Bilateral TMJ 50uL saline Injection


title: WholeBlood-MDD-F-611

value: Whole blood

value: MDD


title: Bone marrow-derived macrophage-BM_pIL4_NIPBL_rep2

value: NIPBL


title: Rat,saline1-TMJ,14days

description:
Readcount_TPM.txt
DEcircRNAs.txt
N_D1


title: CAS condition, timepoint P1, input sample, replicate 2

value: Planktonic cells

value: CAS condition. timepoint P1


title: Nalm6_KO_InO_rep2

description:
2379059_Nalm6_DNTT_KO_Ino_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: WholeBlood-MDD-F-603

value: Female


title: WholeBlood-MDD-M-608

value: Male


title: Bone marrow-derived macrophage-BM_pIL4_NIPBL_rep1

value: Bone marrow-derived macrophage

value: Bone marrow


title: Nalm6_KO_InO_rep1

description:
2379058_Nalm6_DNTT_KO_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: WholeBlood-MDD-F-516


title: RS411_KO_Contr_rep1

description:
2379064_RS411_DNTT_KO_baseline_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: Rat,CFA2-TMJ,14days

description:
Readcount_TPM.txt
DEcircRNAs.txt
F_C2

value: Bilateral TMJ 50uL CFA Injection


title: Bone marrow-derived macrophage-BM_pIL4_K4M3_rep2

value: wild type

value: female


title: WholeBlood-MDD-M-515


title: Bone marrow-derived macrophage-BM_pIL4_K4M3_rep1


title: Rat,CFA1-TMJ,14days

description:
Readcount_TPM.txt
DEcircRNAs.txt
F_C1


title: WholeBlood-MDD-M-514


title: Nalm6_WT_InO_rep2

description:
2379056_Nalm6_WT_Ino_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL

value: B-lymphoblast

value: WT


title: Rat,saline3-TMJ,14days

description:
Readcount_TPM.txt
DEcircRNAs.txt
N_D3

value: thalamus


title: Bone marrow-derived macrophage-BM_pIL4_K4M1_rep2


title: Bone marrow-derived macrophage-BM_pIL4_SMC1A_rep1


title: Ctrl #7

city: Callaghan

first: Dylan

last: Kiltschewskij

state: NSW

address: Room MS616, Level 6, Medical Sciences Building, University Drive

department: School of Biomedical Sciences and Pharmacy

country: Australia

institute: The University of Newcastle

data_processing:
Raw base calls were demultixplexed, subjected to adapter trimming, and converted to fastq format utilising bcl2fastq2 (v.2.20). Lane data for each sample were merged, and per-base sequence quality was assessed via FastQC (v.0.11.8), after which low quality 3´ bases (Phred33 score < 28) and short reads (< 25 nt) were discarded using cutadapt (v.2.10).
Alignment to the reference genome (Rnor_6.0, NCBI) was conducted via HISAT2 (v.2.1.0) and gene-level read counts were obtained using HTSeq (v.0.12.4).
The EdgeR (v.3.36.0) R library was then used to normalise data to library size (counts per million, CPM) and genes with consistently low expression across all libraries were omitted. Samples were then normalised via the trimmed mean of means (TMM) method, dispersion was estimated and variation amongst biological replicates was assessed using multidimensional scaling (MDS) and biological coefficient of variation (BCV) plots.
Assembly: Rnor_6.0, NCBI
Supplementary files format and content: tab-delimited text file containing normalised gene-level read-counts expressed as counts-per-million.

source_name: Dorsomedial striatum

growth_protocol: Outbred male Sprague Dawley rats (250–300 g at the time of surgery) were obtained from the Animal Resources Centre (ARC) Western Australia. Rats were housed in pairs on a 12 h light/dark cycle, food, and water ad libitum. All experiments were performed in compliance with Australian Code of Practice for the Care and Use of Animals for Scientific Purposes (University of Newcastle Animal Research Authority 2010-147-420).

extract_protocol:
Animals were deeply anaesthetised and then perfused with ice-cold Diethyl pyrocarbonate (DEPC) treated Phosphate-buffered saline (PBS). Brains were rapidly dissected and flash-frozen using isopentane. RNA was extracted and isolated from tissue samples using TRIzol Reagent as according to manufacturer’s guidelines (Invitrogen, Cat. No. 15596026 and 15596018).
mRNA-Seq was conducted using the Illumina (San Diego, CA, USA) Stranded mRNA Prep, Ligation Kit as per the manufacturer’s instructions. Briefly, 50 ng of total RNA per sample was subjected to poly(A) enrichment via oligo-dT magnetic beads, followed by heat fragmentation and denaturation (94°C, 8 min). Samples were then reverse transcribed, single adenine nucleotides were ligated to cDNA 3´ ends and pre-index anchors were ligated in preparation for dual indexing. cDNA fragments were subsequently amplified via 14 PCR cycles utilising unique dual i7 and i5 indexes (UDP0XXX). The successful production of ~200-600 bp amplicons was validated using an Agilent (Santa Clara, CA, USA) High Sensitivity DNA Kit and Bioanalyzer instrument, after which samples were pooled in equal concentrations and volumes, denatured and diluted. The final pooled library was subjected to 2x151 cycles of paired end sequencing using a NovaSeq6000 instrument and SP v1.5 flow cell.

treatment_protocol: Rats were subjected to bilateral stereotaxic injection of lentivirus pre-miR-137 (HIV-1 derived pMIRNA1/pCDH vector, System Biosciences, 2.97 x 106 Tu/ml) or Control (pCDH empty backbone vector, 7.2 x 106 Tu/ml) into the dorsomedial striatum (AP: -0.3; ML: 2.6; DV: 4.0).

value: Sprague-Dawley rat

value: Dorsomedial striatum

value: pCDH empty vector lentivirus (dorsomedial striatum)

tag: gender

value: male


title: Nalm6_WT_InO_rep3

description:
2379057_Nalm6_WT_Ino_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: InO


title: Ctrl #6


title: Rat,CFA3-TMJ,14days

description:
Readcount_TPM.txt
DEcircRNAs.txt
F_A2


title: WholeBlood-MDD-F-511

value: Whole blood

value: MDD


title: Nalm6_WT_InO_rep1

description:
2379055_Nalm6_WT_Ino_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: Nalm6_KO_Contr_rep3

description:
2379054_Nalm6_DNTT_KO_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: DNTT KO

value: control


title: Nalm6_KO_Contr_rep1

description:
2379052_Nalm6_DNTT_KO_baseline_1
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment


title: Bone marrow-derived macrophage-BM_pIL4_K36M3_rep2

value: Bone marrow-derived macrophage

value: Bone marrow

tag: agent


title: Ctrl #5


title: miR137OE #7

value: pre-miR-137 lentivirus (dorsomedial striatum)


title: WholeBlood-MDD-F-510

value: Female


title: Nalm6_WT_Contr_rep3

description:
2379051_Nalm6_WT_baseline_3
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-ALL


title: Nalm6_KO_Contr_rep2

description:
2379053_Nalm6_DNTT_KO_baseline_2
RNA-seq is performed for B-ALL cell lines with WT or DNTT knockout genotype and with or without InO treatment

value: B-lymphoblast