title: naïve CD4+ T cells sample 2 protected_V(D)J sequence

city: Bronx

first: Gregoire

middle: S

last: Lauvau

state: NY

address: 1301 Morris park

department: M&I

institute: Albert Einstein College of Medicine

description: FACS sorted naïve CD4+ T cells  (live CD3+ CD4+ CD45RO- CD27+)

data_processing:
Cell Ranger Pipeline v2.2.0
Genome_build: hg38
Supplementary_files_format_and_content: HDF5 Feature Barcode Matrix Format (Gene expression matrix)
Supplementary_files_format_and_content: .vloupe (Clonotype information)

source_name: naïve CD4+ T cells (PBMC)

extract_protocol:
Frozen vials of PBMCs were placed a 37°C water bath and gently agitated until ~90% thawed. The vials were transferred to a tissue culture hood and 1mL of sterile warmed media (RPMI/20%FBS) was added to the PBMCs for 5 minutes before transferring drop-wise to a 10ml volume of warmed media (RPMI/20%FBS) containing 200U/ml of DNase I (Roche, Switzerland). After 10 minutes at room temperature, the PBMCs were centrifuged at 300g, at room temperature for 5 minutes. The pellets were washed twice with room temperature media (RPMI/20%FBS) before staining with Live/dead Fixable Aqua (Thermofisher Scientific) for 30 minutes at room temperature. Cells were then washed and incubated with antibodies against CD3, CD4, CD19, IgD, IgM, CD45RO, CD27 and CXCR3 on ice for 30 minutes in MACS buffer (PBS, 2% BSA, 2mM EDTA). Cells were washed, resuspended in a solution of 50% MACS buffer and 50% FBS, and run on the BD Aria III with the 100μm nozzle. Up to 19,000 live naïve CD4+ T cells (CD19- CD3+ CD4+ CD45RO- CD27+) or memory CD4+ T cells (CD19- CD3+ CD4+ CD45RO+) were sorted into solution of 50% MACS buffer and 50% FBS. Sorted cells were applied to the 10x genomics single-cell RNA-seq platform for cell barcoding, cDNA synthesis and 5’ gene expression library and V(D)J library preparation following the manufacturer’s protocols. 5’ gene expression and V(D)J libraries were sequenced on the Hi-seq Illumina platform (2x150bp paired-end, Genewiz).
Chromium Next GEM Single Cell V(D)J v1
Single cell RNAseq + Single Cell Immune Profiling

treatment_protocol: Whole blood samples were collected in at in ethylenediaminetetraacetic acid (EDTA) coated tubes at enrollment, during each subsequent episodes of clinical malaria and day 30 post infection. Within 6 hours of collection, the blood sample was centrifuged to collect plasma aliquots and PBMCs were isolated using ACK lysis buffer (Crystalgen) using standard methods (96) and stored in 5% DMSO and 95% FBS (Fisher Scientific) in liquid nitrogen.  Samples were shipped to Albert Einstein College of Medicine in liquid nitrogen gas and preserved as such.

value: Plasmodium falciparum infection

tag: gender

value: female

value: 18.4 years


title: CRCGN008_HEPG2_24H:F24

status: Public on Aug 28 2021

type: RNA

city: Boston

first: Stefano

last: Monti

state: MA

address: 25 Buick Street

department: Computational Medicine

country: USA

institute: Boston University

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F24.lxb
CRCGN008_HEPG2_24H_X3_B29_F24.lxb
Broad Institute Human L1000 epsilon

scan_protocol: Following treatment and lysis, the gene expression of the HepG2 and MCF10A cells was profiled using the L1000 platform, a high-throughput assay that measures the expression of ∼1,000 landmark genes and computationally infers the expression of nonmeasured transcripts.

data_processing: For each perturbation and landmark gene, we computed the change in gene expression following the perturbation using a moderated z-score procedure as described in the CMap–L1000 workflow. Differential expression values were calculated as moderated z-scores for each landmark gene and each unique perturbation (chemical and dose combination) perturbation, collapsed to a single value across replicates (Subramanian et al. 2017).

label: biotin

molecule: polyA RNA

organism: Homo sapiens

source_name: Liver Carcinogenicity

label_protocol: Each chemical perturbation for the HEPG2 screen was administered at six doses in triplicate wells per dose and chemical combination, starting from 40μM maximum dose (40 mM stock diluted 1:1,000) for NTP chemicals and 20μM for chemicals procured from Sigma-Aldrich, in series of two-fold dilutions. The sole exception to the standard dosage was 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), which had a starting dose of 50 nM due to its extreme potency. Each chemical perturbation for the MCF10A was administered at three doses (100, 33, 10μM) in triplicate wells. The vehicle control used was DMSO with final dose of 14.1 mM. Four positive controls were used (vorinostat, geldanamycin, mitoxantrone, withaferin-a) each in final doses of 10, 3.33, and 1.00μM, respectively.

growth_protocol: HepG2 (ATCC® HB-8,065™), MCF10A parental and TP53-/- (Horizon, cat# HD 101-005), were used with medium RPMI1640 (10040CV; Mediatech) supplemented with 10% v/v fetal bovine serum (F4135; Sigma-Aldrich), 1× penicillin-streptomycin-glutamine (Invitrogen 10378016), and incubated at humidified 5% CO2 atmosphere at 37°C. Cell cultures were plated with 4,000 cells (45μL of growth medium) per well on 384-well plates (3707; Corning) and incubated for 24 h before treatment.

treatment_protocol: Cells were treated with 5μL of 1:100 diluted 1,000× stock compound plates to final volume of 50μL and incubated for 24 h before lysis

tag: tissue

tag: treatment


title: naïve CD4+ T cells sample 3 protected_V(D)J sequence

type: SRA

library_source: transcriptomic

molecule: total RNA

tag: disease state

tag: age

value: 34 years


title: CRCGN008_HEPG2_24H:F22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F22.lxb
CRCGN008_HEPG2_24H_X3_B29_F22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:G02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G02.lxb
CRCGN008_HEPG2_24H_X3_B29_G02.lxb
Broad Institute Human L1000 epsilon


title: memory CD4+ T cells sample 3 protected_V(D)J sequence

description: FACS sorted memory CD4+ T cells  (live CD3+ CD4+ CD45RO+)

source_name: memory CD4+ T cells (PBMC)


title: Donor 2_CD73+ memory CD4 T cells (ATACseq)

city: Palo Alto

first: Fengqin

last: Fang

state: CA

address: 3801 Miranda Avenue

department: Rheumatology&Immunology

institute: Stanford University

library_source: genomic

data_processing:
Reads were trimmed for adaptor sequence, then mapped to UCSC hg19 using bowtie2, duplicate fragments were then removed using Picard.
peaks alled using MACS2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files

molecule: genomic DNA

source_name: Peripheral blood

growth_protocol: Directly sorted from human peripheral blood

extract_protocol:
Around 50,000 cells were used for each transposition reaction. Nuclei were prepared prior to transposition.
Sequencing libraries were constructed using a modified version of the Illumina Nextera DNA Sample prep kit.

treatment_protocol: no treatment

tag: cell type

value: Resting memory CD4 T cells

tag: cell subset

value: no treatment

value: Healthy donor


title: mouse_MeCP2_T158M_RNA-seq_rep2

city: Shanghai

first: Xing

last: Fu

address: 3888 Chenhua Road

country: China

institute: Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences

data_processing:
We cleaned the paired-end reads by Trimimomatic (version 0.36). After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
The genome sequence and gene annotation of human (GRCh38) and mouse (GRCm38) were downloaded from GENCODE. Cleaned reads were mapped to the genome sequence by HISAT (version 2.1.0) with default parameters. Number of reads that were mapped to each gene was calculated with the htseq-count script in HTSeq (version 0.9.1)
EdgeR was used to identify genes that were differentially expressed between control and experiment samples. Genes with at least two-fold change in expression and had a FDR < 0.05 were considered differentially expressed genes (DEGs).
The barcode regions in the iCLIP reads are filtered by FASTX-Toolkit.The demultiplexing and adapter trimming are performed by Flexbar. Only trimmed reads with at least 15 nt are kept for further analysis.
The individual FASTQ files for each sample are mapped to human reference genome (GRCh38) by STAR. The technical duplicates are removed using UMI-tools.
After deduplication, the crosslink events are transformed from the mapped reads by extracting the position upstream of the 5’end of the reads with BEDTools.
The crosslink sites with significantly enriched crosslink events are identified by PureCLIP and post-processed by custom scripts.
Genome_build: human (GRCh38) and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, log2Fold change and FDR for each gene.
Supplementary_files_format_and_content: bed files include the chromosome, start/end position and strand of each binding site.
Supplementary_files_format_and_content: bigWig files were generated by bedtools and bedGraphToBigWig, the scores represent the read coverage on the genome.

organism: Mus musculus

source_name: mouse cerebral cortex

growth_protocol: HEK293T cells were maintained in Dulbecco's Modified Eagle's medium supplemented with 10% fetal bovine serum.

extract_protocol:
For RNA-seq, total RNAs were isolated using TRIzol (Invitrogen, USA).
RNA-seq libraries were prepared according to the manufacturer’s instructions (Illumina). iCLIP-seq libraries were prepared as previously described (Buchbender et al., Methods, 2019).

treatment_protocol: Mouse cerebral cortex tissues were obtained from 6-week-old male mice.

tag: genotype

value: MeCP2 T158M

value: mouse cerebral cortex


title: CRCGN008_HEPG2_24H:F20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F20.lxb
CRCGN008_HEPG2_24H_X3_B29_F20.lxb
Broad Institute Human L1000 epsilon


title: mouse_MeCP2_T158M_RNA-seq_rep1


title: CRCGN008_HEPG2_24H:F19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F19.lxb
CRCGN008_HEPG2_24H_X3_B29_F19.lxb
Broad Institute Human L1000 epsilon


title: memory CD4+ T cells sample 2 protected_V(D)J sequence


title: naïve CD4+ T cells sample 1 protected_V(D)J sequence

value: 24.6 years


title: CRCGN008_HEPG2_24H:F17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F17.lxb
CRCGN008_HEPG2_24H_X3_B29_F17.lxb
Broad Institute Human L1000 epsilon


title: mouse_WT_RNA-seq_rep6

value: WT


title: memory CD4+ T cells sample 1 protected_V(D)J sequence

description: FACS sorted memory CD4+ T cells (live CD3+ CD4+ CD45RO+)


title: CRCGN008_HEPG2_24H:F16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F16.lxb
CRCGN008_HEPG2_24H_X3_B29_F16.lxb
Broad Institute Human L1000 epsilon


title: mouse_WT_RNA-seq_rep5


title: CRCGN008_HEPG2_24H:F18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F18.lxb
CRCGN008_HEPG2_24H_X3_B29_F18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:F15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F15.lxb
CRCGN008_HEPG2_24H_X3_B29_F15.lxb
Broad Institute Human L1000 epsilon


title: mouse_WT_RNA-seq_rep4


title: naïve CD4+ T cells sample 3 protected_whole gene expression


title: CRCGN008_HEPG2_24H:G01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_G01.lxb
CRCGN008_HEPG2_24H_X3_B29_G01.lxb
Broad Institute Human L1000 epsilon


title: memory CD4+ T cells sample 3 protected_whole gene expression


title: CRCGN008_HEPG2_24H:F06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F06.lxb
CRCGN008_HEPG2_24H_X3_B29_F06.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:F21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F21.lxb
CRCGN008_HEPG2_24H_X3_B29_F21.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:F05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F05.lxb
CRCGN008_HEPG2_24H_X3_B29_F05.lxb
Broad Institute Human L1000 epsilon


title: naïve CD4+ T cells sample 2 protected_whole gene expression


title: mouse_MeCP2_KO_RNA-seq_rep3

value: MeCP2 KO


title: CRCGN008_HEPG2_24H:F04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F04.lxb
CRCGN008_HEPG2_24H_X3_B29_F04.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:F03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F03.lxb
CRCGN008_HEPG2_24H_X3_B29_F03.lxb
Broad Institute Human L1000 epsilon


title: memory CD4+ T cells sample 2 protected_whole gene expression


title: CRCGN008_HEPG2_24H:F02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F02.lxb
CRCGN008_HEPG2_24H_X3_B29_F02.lxb
Broad Institute Human L1000 epsilon


title: mouse_MeCP2_KO_RNA-seq_rep1


title: naïve CD4+ T cells sample 1 protected_whole gene expression

description: FACS sorted naïve CD4+ T cells  (live CD3+ CD4+ CD45RO- CD27+)


title: mouse_WT_RNA-seq_rep3


title: CRCGN008_HEPG2_24H:F13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F13.lxb
CRCGN008_HEPG2_24H_X3_B29_F13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E23.lxb
CRCGN008_HEPG2_24H_X3_B29_E23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:F14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F14.lxb
CRCGN008_HEPG2_24H_X3_B29_F14.lxb
Broad Institute Human L1000 epsilon


title: memory CD4+ T cells sample 1 protected_whole gene expression


title: CRCGN008_HEPG2_24H:F01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_F01.lxb
CRCGN008_HEPG2_24H_X3_B29_F01.lxb
Broad Institute Human L1000 epsilon


title: 24888_2181DN

city: Rochester

first: Cameron

last: Baker

address: 601 Elmwood Ave

institute: University of Rochester

data_processing:
Data Formatting - bcltofastq-2.19.0
Data Cleaning - Trimmomatic-0.36, TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35
Genome Alignment - STAR_2.6.0c, --twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical
Read Quantification - subread-1.6.1, featurecounts, -M -s 0 -t exon -g gene_name
Genome_build: hg38/gencode28

source_name: Whole blood

extract_protocol:
Total RNA was isolated using the RNeasy Plus Micro Kit (Qiagen, Valencia, CA) per manufacturer’s recommendations.
RNA concentration was determined with the NanopDrop 1000 spectrophotometer (NanoDrop, Wilmington, DE) and RNA quality assessed with the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 1ng of total RNA was pre-amplified with the SMARTer Ultra Low Input kit v4 (Clontech, Mountain View, CA) per manufacturer’s recommendations. The quantity and quality of the subsequent cDNA was determined using the Qubit Flourometer (Life Technnologies, Carlsbad, CA) and the Agilent Bioanalyzer 2100 (Agilent, Santa Clara, CA). 150pg of cDNA was used to generate Illumina compatible sequencing libraries with the NexteraXT library preparation kit (Illumina, San Diego, CA) per manufacturer’s protocols. The amplified libraries were hybridized to the Illumina single end flow cell and amplified using the cBot (Illumina, San Diego, CA). Single end reads of 100nt were generated by the HiSeq2500 (Illumina, San Diego, CA).

tag: flow sort selection

value: SLE


title: CRCGN008_HEPG2_24H:E24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E24.lxb
CRCGN008_HEPG2_24H_X3_B29_E24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E20.lxb
CRCGN008_HEPG2_24H_X3_B29_E20.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E22.lxb
CRCGN008_HEPG2_24H_X3_B29_E22.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E21.lxb
CRCGN008_HEPG2_24H_X3_B29_E21.lxb
Broad Institute Human L1000 epsilon


title: 24888_2182Naive


title: mouse_WT_RNA-seq_rep1


title: mouse_WT_RNA-seq_rep2


title: CRCGN008_HEPG2_24H:E19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E19.lxb
CRCGN008_HEPG2_24H_X3_B29_E19.lxb
Broad Institute Human L1000 epsilon


title: Cultured Brain Cell-type Mixture_100

city: Adelaide

first: Urwah

last: Nawaz

state: SA

address: 4 North Terrace

department: Adelaide Medical Science

country: Australia

institute: UNIVERSITY OF ADELAIDE

data_processing:
Reads were mapped using STAR with parameters --outSJfilterOverhangMin 15 15 15 15 --alignSJoverhangMin 15 --alignSJDBoverhangMin 15 --outFilterMultimapNmax 1 --outFilterScoreMin 1 --outFilterMatchNmin 1 --outFilterMismatchNmax 2  --chimSegmentMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --chimJunctionOverhangMin 15 --bamRemoveDuplicatesType UniqueIdenticalNotMulti
Gene counts were normalised to Reads Per Kilobase of exon per Million mapped reads (RPKM) using total exonic length from GENCODE v19.
Genome_build: hg19 (samples 1:7); hg38 (samples 8:17)
Supplementary_files_format_and_content: rpkm

source_name: RNA from cultured human neurons and astrocytes

extract_protocol:
RNA was extracted from cells using a Qiagen miRNeasy kit, and prepared for sequencing using an Illumina TruSeq stranded kit
Standard Illumina protocols

tag: sample type

value: Human primary astrocytes (Lonza, #CC-2565) and 2-week differentiated human neural progenitors

tag: mixing ratio

value: 100:0 Neurons:Astrocytes

tag: molecule subtype

value: Total RNA


title: mouse_MeCP2_KO_RNA-seq_rep2


title: Cultured Brain Cell-type Mixture_50

value: 50:50 Neurons:Astrocytes


title: CGACGG_CTRL

city: Munich

first: Irmela

last: Jeremias

address: Feodor-Lynenstr. 21

department: Research Unit Apoptosis in Hematopoietic Stem Cells

country: Germany

institute: Helmholtz Zentrum München, German Center for Environmental Health (HMGU), Munich, Germany

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned toa combined Human Genome (hg38) and Mouse Genome (mm10) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: UMI_counts.txt:  cell (columns) and gene (rows) -wise UMI expression table

source_name: ALL PDX line

growth_protocol: PDX cells were injected into NSG mice

extract_protocol:
prime-seq
Library was constructed using the prime-seq protocol

treatment_protocol: Mice were treated with 100 mg/kg tamoxifen 7 and 8 days after injection to induce recombination and shRNA expression

value: patient derived xenograft (PDX) cells

value: acute lymphoblastic leukemia

tag: protocol

value: PDX cells injected into NSG mice

value: mice treated with shCTRL_TAM

value: control PDX cells isolated from murine bone marrow after treatment


title: TTGTTA_DUX4

value: mice treated with shDUX4_TAM

value: DUX4 KD PDX cells isolated from murine bone marrow after treatment


title: CRCGN008_HEPG2_24H:E17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E17.lxb
CRCGN008_HEPG2_24H_X3_B29_E17.lxb
Broad Institute Human L1000 epsilon


title: 24888_2179DN


title: ACTAAA_CTRL


title: Cultured Brain Cell-type Mixture_45

value: 45:55 Neurons:Astrocytes


title: CRCGN008_HEPG2_24H:E16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E16.lxb
CRCGN008_HEPG2_24H_X3_B29_E16.lxb
Broad Institute Human L1000 epsilon


title: Cultured Brain Cell-type Mixture_40

value: 40:60 Neurons:Astrocytes


title: CRCGN008_HEPG2_24H:E15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E15.lxb
CRCGN008_HEPG2_24H_X3_B29_E15.lxb
Broad Institute Human L1000 epsilon


title: AATGTA_DUX4


title: 24888_2184DN


title: CRCGN008_HEPG2_24H:E18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E18.lxb
CRCGN008_HEPG2_24H_X3_B29_E18.lxb
Broad Institute Human L1000 epsilon


title: Cultured Brain Cell-type Mixture_0 Rep3

value: 0:100 Neurons:Astrocytes


title: AAATCA_DUX4


title: 24888_2179Naive


title: 24888_2183Naive


title: CRCGN008_HEPG2_24H:E13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E13.lxb
CRCGN008_HEPG2_24H_X3_B29_E13.lxb
Broad Institute Human L1000 epsilon


title: Cultured Brain Cell-type Mixture_0 Rep1


title: 24888_1369DN

value: HC


title: Cultured Brain Cell-type Mixture_0 Rep2


title: 35323 TS_MCL1_GAAGAC

data_processing:
Fastq reads were processed with the zUMIs pipeline (Parekh et al., 2017)
cDNA reads were aligned to a combined Human Genome (hg38) and Mouse Genome (mm10) with STAR 2.6.0a
Quantification was done with ENSEMBL gene models (Homo_sapiens:GRCh38.84, Mus_musculus:GRCm38.85)
Mouse reads were excluded for further analysis
Genome_build: hg38
Supplementary_files_format_and_content: cell (columns) and gene (rows) -wise UMI expression table (raw counts)

source_name: AML PDX line_sh-MCL1 24h TAM

value: patient derived xenograft cells

tag: disease

value: acute myeloid leukemia

tag: genotype/treatment

value: sh-MCL1 24h TAM


title: 35323 GFP_MCL1_TGTATT


title: 24888_2185DN

value: SLE


title: 24888_2182CD14pos


title: 36856_MCL1_TCGCGG

source_name: AML PDX line_sh-CTRL without TAM

value: sh-CTRL without TAM


title: CRCGN008_HEPG2_24H:E12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E12.lxb
CRCGN008_HEPG2_24H_X3_B29_E12.lxb
Broad Institute Human L1000 epsilon


title: 42091_MCL1_GCGCCA

source_name: AML PDX line_sh-MCL1 7days TAM

value: sh-MCL1 7days TAM


title: CRCGN008_HEPG2_24H:E10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E10.lxb
Broad Institute Human L1000 epsilon


title: 42086_MCL1_CGGAGC


title: CRCGN008_HEPG2_24H:E09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E09.lxb
CRCGN008_HEPG2_24H_X3_B29_E09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E14.lxb
CRCGN008_HEPG2_24H_X3_B29_E14.lxb
Broad Institute Human L1000 epsilon


title: 24888_1369CD14pos


title: 24888_2184Naive


title: BEC_8

city: Portland

first: Bin

last: Li

state: OR

address: 3181 SW Sam Jackson Pk Rd

department: Oregon Stem Cell Center

institute: Oregon Health and Science University

description: FACS sort with DHIC-4D9

data_processing:
Base calling - using Illumina RTA version 1.13.48.
Conversion to FASTQ using CASAVA v1.8.2
We trimmed all reads to 44 bases and aligned to mm9/hg19 with Bowtie version 1.0.0 (Allowed up to 3 mismatches, but required unique best matches.)
Used R scripts to count tags that aligned to the exons of UCSC RefSeq gene models and calculate FPKM values.
Genome_build: mm9 and hg19

source_name: normal human cholangiocytes

extract_protocol:
RNA lysis buffer is TRIzol reagent
RNA libraries were prepared with standard Illumina protocols

value: normal human cholangiocytes

value: uncultured, FACS sorted cholangiocytes

tag: passage number

tag: diagnosis

value: normal

value: 60 year

tag: Sex

value: Male


title: CRCGN008_HEPG2_24H:E08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E08.lxb
CRCGN008_HEPG2_24H_X3_B29_E08.lxb
Broad Institute Human L1000 epsilon

tag: tissue


title: AAGTTA_CTRL

value: patient derived xenograft (PDX) cells

value: acute lymphoblastic leukemia

value: PDX cells injected into NSG mice

tag: treatment

value: mice treated with shCTRL_TAM

value: control PDX cells isolated from murine bone marrow after treatment


title: BEC_7

description: FACS sort with DHIC-4D9

value: 57 year

value: Female


title: CRCGN008_HEPG2_24H:E07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:E11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E11.lxb
CRCGN008_HEPG2_24H_X3_B29_E11.lxb
Broad Institute Human L1000 epsilon


title: 24888_1368Naive

tag: disease state

value: HC


title: BEC_10

description: FACS sort with DHIC-4D9

value: normal, metastasis of colorectal cancer

tag: age

value: 46 year


title: BEC_6

description: FACS sort with DHIC-4D9

tag: cell type


title: CRCGN008_HEPG2_24H:E06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E06.lxb
CRCGN008_HEPG2_24H_X3_B29_E06.lxb
Broad Institute Human L1000 epsilon


title: 42070_MCL1_CATCAG

source_name: AML PDX line_sh-CTRL 7days TAM

value: patient derived xenograft cells

value: acute myeloid leukemia

value: sh-CTRL 7days TAM


title: BEC_9

description: FACS sort with DHIC-4D9

value: normal human cholangiocytes

value: uncultured, FACS sorted cholangiocytes


title: 24888_1367Naive


title: BEC_5

description: FACS sort with DHIC-4D9

value: normal

value: missing


title: 24888_1369Naive


title: 24888_1368CD14pos


title: 42079_MCL1_TCTAAT


title: CRCGN008_HEPG2_24H:E05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E05.lxb
CRCGN008_HEPG2_24H_X3_B29_E05.lxb
Broad Institute Human L1000 epsilon


title: BEC_4

description: FACS sort with DHIC-4D9


title: 42080_MCL1_GAATAT


title: CRCGN008_HEPG2_24H:E04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E04.lxb
CRCGN008_HEPG2_24H_X3_B29_E04.lxb
Broad Institute Human L1000 epsilon


title: 24888_1367CD14pos


title: 42085_MCL1_AGTATA

source_name: AML PDX line_sh-MCL1  72h TAM

value: sh-MCL1  72h TAM


title: 42102_MCL1_CACCGG

value: sh-MCL1 7days TAM


title: 24888_2181CD14pos

value: SLE


title: 24888_1368DN


title: BEC_3

description: FACS sort with DHIC-4D9

value: 49 year


title: 42071_MCL1_GCCTGC

source_name: AML PDX line_sh-CTRL 72h TAM

value: sh-CTRL 72h TAM


title: CRCGN008_HEPG2_24H:E02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E02.lxb
CRCGN008_HEPG2_24H_X3_B29_E02.lxb
Broad Institute Human L1000 epsilon


title: BEC_1

description: FACS sort with DHIC-4D9

value: 23 year

value: Male


title: 42077_MCL1_GTGGGG


title: CRCGN008_HEPG2_24H:E03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E03.lxb
CRCGN008_HEPG2_24H_X3_B29_E03.lxb
Broad Institute Human L1000 epsilon


title: BEC_2

description: FACS sort with DHIC-4D9

value: young

value: Female


title: 24888_1367DN

value: HC


title: huHC_3

source_name: normal human hepatocytes

value: normal human hepatocytes

value: normal, unclutured


title: CRCGN008_HEPG2_24H:E01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_E01.lxb
CRCGN008_HEPG2_24H_X3_B29_E01.lxb
Broad Institute Human L1000 epsilon


title: 42087_MCL1_CGCGTG

source_name: AML PDX line_sh-MCL1  52h TAM

value: patient derived xenograft cells

value: acute myeloid leukemia

value: sh-MCL1  52h TAM


title: 24888_2184CD14pos


title: CRCGN008_HEPG2_24H:D24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D24.lxb
CRCGN008_HEPG2_24H_X3_B29_D24.lxb
Broad Institute Human L1000 epsilon


title: 42082_MCL1_AGGCGG


title: 42073_MCL1_ATCGAG


title: 24888_2181Naive


title: huHC_2

value: normal

value: 7 month


title: 24888_2179CD14pos


title: huHC_1

value: missing


title: 24888_1365DN


title: CRCGN008_HEPG2_24H:D22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D22.lxb
CRCGN008_HEPG2_24H_X3_B29_D22.lxb
Broad Institute Human L1000 epsilon


title: SZIPSC2

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

institute: University of Texas Health Science Center at Houston

data_processing:
Raw mRNA sequence reads were pre-processed using cutadapt (v.1.15) to remove bases with quality scores < 20 and adapter sequences, followed by alignment of clean RNA-seq reads to GRCh38.83 with STAR (v2.5.3a).
Uniquely mapped reads overlapping genes were counted by htseq-count with default parameter using annotation from ENSEMBL v83.
Genome_build: Genome Reference Consortium Human Build 38
Supplementary_files_format_and_content: Raw counts matrices obtained from htseq-count used in determining the scientific conclusions from the manuscript Stertz et al 2020 are provided. Columns include the Ensembl Gene ID for each gene and raw unnormalized counts for each sample.

source_name: hiPSC Lines of Pooled Schizophrenia Patients: 416, 486, 624, 352, 413

growth_protocol: Reprogramming of human LCLs with episomal vectors:   LCLs (n = 13) were reprogrammed into hiPSCs using the Epi5™ Episomal iPSC reprogramming Kit (Thermo Fisher Scientific, Waltham, MA), containing Oct4, Sox2, Klf4, L-Myc, and Lin28. Nucleofection was conducted using the Cell Line Optimization Nucleofector™ X Kit for the 4D-Nucleofector™ System (program EW113, Lonza, Basal, Switzerland). Briefly, 2 × 106 cells from each subject were nucleofected with Epi5™, stabilized in RPMI1640 medium with 10% FBS (Gibco) and 1x Penicillin Streptomycin (PenStrep, Gibco-Thermo Fisher Scientific, Waltham, MA) for 3 days, and then transferred to 60 mm dishes coated with Membrane Matrix (Corning Matrigel hESC-Qualified Matrix (Corning) or Geltrex™ LDEV-Free Reduced Growth Factor Basement Membrane Matrix (Gibco-Thermo Fisher Scientific, Waltham, MA)). RPMI medium was then replaced by TeSR™-E8™ (StemCell Technologies, Vancouver, Canada) and 1x PenStrep (Gibco) every day until the appearance of colonies (15–30 days), at which time clones were manually chosen and expanded.  Neuronal precursor cells (NPC) differentiation:   One clone from each subject (n = 13) was differentiated into hiPSC–NPC using AggreWell™ methodology (StemCell Technologies), that involves the formation of embryoid bodies (EB) using STEMdiff™ Neural Induction Medium, according to manufacture instructions. After 5 days, EBs were plated in six-well plates coated with Membrane Matrix. Rosette selection was performed after 7 days using STEMdiff Rosette Selection Reagent (StemCell Technologies) and plated on Membrane Matrix-coated wells. STEMdiff™ Neural Induction Medium was changed every day. When confluent, hiPSC–NPC were lifted using Accutase (Innovative Cell Technologies, Inc.) and expanded on Membrane Matrix-coated plates in Neurobasal medium 50/50 (50% DMEM/F12 (Corning), 50% Neurobasal Medium (Gibco), 1x GlutaMAX (Gibco), 1x NEAA (Gibco), 1x PenStrep (Gibco), 1x N-2 Supplement (Gibco), 1x B27 minus vitamin A (Gibco)) supplemented with 20 ng/ml FGF-Basic (AA 1–155) Recombinant Human Protein (Gibco) until passage 3. Cortical neuron differentiation  Differentiation of hiPSC–NPCs into cortical neurons: (hiPSC–neuron) was performed as previously described, with a few modifications. Briefly, NPCs were cultivated in pre-coated Laminin/Poly-L-Ornithine plates in Neurobasal Medium 50/50 supplemented with 20 ng/ml BDNF (PeproTech), 20 ng/ml GDNF (PeproTech), 1 mM dibutyryl-cyclic AMP (Sigma), 200 nM ascorbic acid (Sigma), 10 ng/mL IGF-1 (PeproTech), and 10 ng/ml WNT-3A (R&D).

extract_protocol:
Total RNA was extracted and purified using the RNeasy Plus Mini kit (Qiagen, Hilden Germany).
A total of 1 μg RNA per sample was used for mRNA-seq library construction using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (Illumina Inc., San Diego, CA).

value: hiPSC

tag: phenotype

value: Schizophrenia

value: mixed

tag: subject


title: 42064_MCL1_GTCGCG

source_name: AML PDX line_sh-CTRL 24h TAM

value: sh-CTRL 24h TAM


title: 24888_2185CD14pos

tag: flow sort selection

value: SLE


title: 24888_2183CD14pos


title: 42072_MCL1_TCAAAA

source_name: AML PDX line_sh-CTRL 52h TAM

value: sh-CTRL 52h TAM


title: 42069_MCL1_CTTAAT


title: SZLCL2

source_name: Limphoblastoid Cell Line of Pooled Schizophrenia Patients: 416, 486, 624, 352, 413

value: Limphoblastoid Cells

value: Male


title: CRCGN008_HEPG2_24H:D21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D21.lxb
CRCGN008_HEPG2_24H_X3_B29_D21.lxb
Broad Institute Human L1000 epsilon

source_name: Liver Carcinogenicity


title: CRCGN008_HEPG2_24H:D18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D18.lxb
CRCGN008_HEPG2_24H_X3_B29_D18.lxb
Broad Institute Human L1000 epsilon


title: 24888_1366Naive

source_name: Whole blood

value: HC


title: HCIPSC2

source_name: hiPSC Cell Line of Pooled Healthy Controls: 353, 419, 357

value: Healthy Control

value: Pooled Male and Female


title: SZLCL1

source_name: Limphoblastoid Cell Line of Pooled Schizophrenia Patients: 418, 414


title: CRCGN008_HEPG2_24H:D20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D20.lxb
CRCGN008_HEPG2_24H_X3_B29_D20.lxb
Broad Institute Human L1000 epsilon


title: HCIPSC1

source_name: hiPSC Cell Line of Pooled Healthy Controls: 417, 354, 412

value: Female


title: 42063_MCL1_GCCGCA

value: patient derived xenograft cells

value: acute myeloid leukemia


title: CRCGN008_HEPG2_24H:D17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D17.lxb
CRCGN008_HEPG2_24H_X3_B29_D17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D16.lxb
CRCGN008_HEPG2_24H_X3_B29_D16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D23.lxb
CRCGN008_HEPG2_24H_X3_B29_D23.lxb
Broad Institute Human L1000 epsilon


title: 24888_2182DN


title: SZIPSC1

source_name: hiPSC Lines of Pooled Schizophrenia Patients: 418, 414


title: HCLCL2

source_name: Limphoblastoid Cell Line of Pooled Healthy Controls: 353, 419, 357


title: 42092_MCL1_TTGGAT

source_name: AML PDX line_sh-MCL1 24h TAM

value: sh-MCL1 24h TAM


title: 42099_MCL1_AGCCGC


title: 24888_1365Naive


title: 24888_1365CD14pos


title: 24888_1366CD14pos


title: NSC624

source_name: Cortical Neuron derived from hiPSC of subject 624

value: Cortical Neuron


title: CRCGN008_HEPG2_24H:D13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D13.lxb
CRCGN008_HEPG2_24H_X3_B29_D13.lxb
Broad Institute Human L1000 epsilon


title: 42094_MCL1_CTAAAA


title: CRCGN008_HEPG2_24H:D15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D15.lxb
CRCGN008_HEPG2_24H_X3_B29_D15.lxb
Broad Institute Human L1000 epsilon


title: HCLCL1

source_name: Limphoblastoid Cell Line of Pooled Healthy Controls: 417, 354, 412


title: CRCGN008_HEPG2_24H:D10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D10.lxb
CRCGN008_HEPG2_24H_X3_B29_D10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D19.lxb
CRCGN008_HEPG2_24H_X3_B29_D19.lxb
Broad Institute Human L1000 epsilon


title: WL-F-2-1d-gonad

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

country: South Korea

institute: Seoul National University

data_processing:
The raw reads were trimmed by filtering out adaptor-only nucleotides with 75 bp minimum length, using Trimmomatic.
Trimmed reads were aligned to the reference genome (Gallus gallus 6.0a) using HISAT2.
Mapped reads were quantified in gene units using FeatureCounts.
Genome_build: galGal6.0a
Supplementary_files_format_and_content: Tab-delimited text files include mapped counts for each sample.

organism: Gallus gallus

source_name: Gonad

extract_protocol:
Total RNA was isolated from the gonadal tissues of DMRT1 gene-disrupted male and female chickens along with control male and female chickens using Maxwell (Promega) based method. Total RNA integrity was checked using an Agilent Technologies 2100 Bioanalyzer and RiboGreen dye (Invitrogen), and quantified using a Trinean DropSense96 spectrophotometer. 1 mg of total RNA was processed for preparing mRNA sequencing library using MGIEasy RNA Directional Library Prep Kit (MGI) according to manufacturer’s instruction.
The double stranded library was quantified using QauntiFluor ONE dsDNA System and equals 330 ng in a total volume of 60 ml or less. The library was cyclized at 37 °C for 60 min, and then digested at 37 °C for 30 min, followed by cleanup of circularization product. To make DNA nanoball, the library was incubated at 30 °C for 25 min using DNB enzyme. Finally, Library was quantified by QauntiFluor ssDNA System (Promega). Sequencing of the prepared DNB was conducted on the MGIseq system with 100 bp paired-end reads.

value: Control

value: Ovary

tag: time


title: 42095_MCL1_TATTAC


title: WL-F-3-1d-gonad


title: 24888_2187Naive


title: 24888_2185Naive


title: WL-F-1-1d


title: NSC486

source_name: Cortical Neuron derived from hiPSC of subject 486

value: Schizophrenia


title: 24888_2183DN


title: NSC419

source_name: Cortical Neuron derived from hiPSC of subject 419


title: NSC418

source_name: Cortical Neuron derived from hiPSC of subject 418


title: NSC416

source_name: Cortical Neuron derived from hiPSC of subject 416


title: NSC417

source_name: Cortical Neuron derived from hiPSC of subject 417


title: 24888_2187DN


title: CRCGN008_HEPG2_24H:D12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D12.lxb
CRCGN008_HEPG2_24H_X3_B29_D12.lxb
Broad Institute Human L1000 epsilon


title: 24888_2189CD14pos


title: CRCGN008_HEPG2_24H:D08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D08.lxb
CRCGN008_HEPG2_24H_X3_B29_D08.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:D14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D14.lxb
CRCGN008_HEPG2_24H_X3_B29_D14.lxb
Broad Institute Human L1000 epsilon


title: DMRT1-KI-F-3-1d-gonad

value: Case


title: 24888_2187CD14pos


title: CRCGN008_HEPG2_24H:D07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D07.lxb
CRCGN008_HEPG2_24H_X3_B29_D07.lxb
Broad Institute Human L1000 epsilon


title: DMRT1-KI-F-2-1d-gonad


title: NSC413

source_name: Cortical Neuron derived from hiPSC of subject 413


title: NSC412

source_name: Cortical Neuron derived from hiPSC of subject 412


title: 24888_2189DN

source_name: Whole blood


title: CRCGN008_HEPG2_24H:D06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D06.lxb
CRCGN008_HEPG2_24H_X3_B29_D06.lxb
Broad Institute Human L1000 epsilon

source_name: Liver Carcinogenicity


title: 42103_MCL1_CGCCTC


title: 24888_2189Naive


title: DMRT1-KI-F-1-1d-gonad


title: WL-M-3-1d

value: Testis


title: NSC357

source_name: Cortical Neuron derived from hiPSC of subject 357


title: CRCGN008_HEPG2_24H:D05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D05.lxb
CRCGN008_HEPG2_24H_X3_B29_D05.lxb
Broad Institute Human L1000 epsilon


title: 24888_1366DN


title: WL-M-2-1d-gonad


title: CRCGN008_HEPG2_24H:D04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D04.lxb
CRCGN008_HEPG2_24H_X3_B29_D04.lxb
Broad Institute Human L1000 epsilon


title: NSC353

source_name: Cortical Neuron derived from hiPSC of subject 353


title: CA9KO-B4_T11_Rep2

city: Saskatoon

first: Franco

middle: J

last: Vizeacoumar

state: Saskatchewan

address: 4D40 Health Sciences Building, 107 Wiggins Road

department: Oncology

country: Canada

institute: University of Saskatchewan

data_processing:
Library strategy: amplicon sequencing
Sequenced files were demultiplexed from illumina
Read counts were calculated using the package from Li, et al. Genome Biology 15:554 (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: triple negative breast cancer cells

growth_protocol: 7x10^8 cells were infected at an MOI of 0.3 with a viral library (lentiCRISPRv2_A) containing 65,000 sgRNAs to yield a library coverage of 300x.  Infected cells were selected for with puromycin.  T0 replicates (x2) of 2.5x10^7 cells were collected and triplicate replicates for culture in hypoxia were plated at 2x10^7 per replicate.

extract_protocol:
genomic DNA was extracted using the QIAamp Blood Maxi kit (Qiagen #51194)
libraries were constructed following the previously described method in Shalem O et al Science 2014

treatment_protocol: Cells were cultured in 1% oxygen and passaged every 72 hours for a period of 20 generations.  2x10^7 cells were collected from each replicate following each passage.  2x10^7 cells were maintained in culture for each replicate for the subsequent generation to maintain 300x library coverage

tag: cell line

value: derived from primary tumour of anaplastic carcinoma of the breast

value: 1% oxygen

tag: condition

value: CA9 knock-out


title: CRCGN008_HEPG2_24H:D03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D03.lxb
CRCGN008_HEPG2_24H_X3_B29_D03.lxb
Broad Institute Human L1000 epsilon


title: DMRT1-KI-M-3-1d-gonad


title: NSC352

source_name: Cortical Neuron derived from hiPSC of subject 352

value: Male


title: DMRT1-KI-M-2-1d-gonad


title: NPCSC624

source_name: Neural Progenitor Cell from subject 624

value: Neural Progenitor Cell


title: DMRT1-KI-M-1-1d-gonad


title: CA9KO-B4_T0_Rep1


title: CRCGN008_HEPG2_24H:C18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C18.lxb
CRCGN008_HEPG2_24H_X3_B29_C18.lxb
Broad Institute Human L1000 epsilon


title: WT-E6-F3


title: CRCGN008_HEPG2_24H:C17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C17.lxb
CRCGN008_HEPG2_24H_X3_B29_C17.lxb
Broad Institute Human L1000 epsilon


title: CA9KO-B4_T0_Rep2


title: WL-M-1-1d


title: NTC_T11_Rep1

value: non-targeting control


title: NPCSC419

source_name: Neural Progenitor Cell from subject 419

value: Healthy Control


title: WT-E6-F2


title: NPCSC418

source_name: Neural Progenitor Cell from subject 418


title: CRCGN008_HEPG2_24H:D02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D02.lxb
CRCGN008_HEPG2_24H_X3_B29_D02.lxb
Broad Institute Human L1000 epsilon


title: WT-E6-F1

source_name: Gonad


title: NTC_T0_Rep2


title: CA9KO-B4_T11_Rep1


title: NPCSC417

source_name: Neural Progenitor Cell from subject 417

value: Female


title: CRCGN008_HEPG2_24H:C16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C16.lxb
CRCGN008_HEPG2_24H_X3_B29_C16.lxb
Broad Institute Human L1000 epsilon


title: NTC_T0_Rep1


title: NPCSC416

source_name: Neural Progenitor Cell from subject 416


title: CRCGN008_HEPG2_24H:C15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C15.lxb
CRCGN008_HEPG2_24H_X3_B29_C15.lxb
Broad Institute Human L1000 epsilon


title: NPCSC486

source_name: Neural Progenitor Cell from subject 486


title: DMRT1-E6-F3


title: CRCGN008_HEPG2_24H:C14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C14.lxb
CRCGN008_HEPG2_24H_X3_B29_C14.lxb
Broad Institute Human L1000 epsilon


title: NPCSC414

source_name: Neural Progenitor Cell from subject 414


title: DMRT1-E6-F2


title: CRCGN008_HEPG2_24H:D01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_D01.lxb
CRCGN008_HEPG2_24H_X3_B29_D01.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:C13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C13.lxb
CRCGN008_HEPG2_24H_X3_B29_C13.lxb
Broad Institute Human L1000 epsilon


title: NTC_T11_Rep2


title: NPCSC413

source_name: Neural Progenitor Cell from subject 413


title: DMRT1-E6-F1


title: Quantseq_ST-Dox_MSX2_iOX_r2

city: Vienna

first: Andreas

last: Lackner

address: Schwarzspanierstrasse 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_ST-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_ST-d_2

data_processing:
RNA-seq
read trimming: TrimGalore! (0.6.5)
alignment: STAR (2.7.3a)
alignment processing: samtools (1.10)
read counting: Rsubread (2.0.0)
ChIP-seq:
read trimming: CUTADAPT (2.8)
alignment: bowtie 2 (2.3.5.1)
alignment processing: samtools (1.10)
peak calling: MACS2 (2.2.7.1)
idr analysis: idr (1.2)
bigwig files: bamCoverage (3.5.0)
Genome_build: hg38
Supplementary_files_format_and_content: read counts, bigwig

growth_protocol: hTSC line CT30 were cultured in the basal media (DMEM/F12 (11320074, Thermo Fisher), 1x ITS-X (51500056, Thermo Fisher), 0.2% FBS (PAA), 1.5 µg/mL L-ascorbic acid (A4403, Sigma) supplemented with 2 µM CHIR99021, 50ng/mL EGF, 0.5 µM A83-01 and 5µM Y27632. Cells were passaged every 3-4 days using TrypLE (12605036, Thermo Scientific).

extract_protocol:
RNAseq. RNA was extracted using RNeasy mini kit (Qiagen) and treated with DNaseI (Qiagen). Indexed libraries were prepared with 500 ng RNA using QuantSEQ 3’ mRNA-Seq Library Prep Kit FWD for Illumina (015.96, Lexogen) according to manufacturer’s recommendations. The libraries were pooled and sequenced with a 100-base-pair single-end (MSX2_iOX) and 50-base-pair single-end protocol on Illumina HiSeq 2500 sequencer. ChIPseq. Cells (1-2x108) were fixed in 2mM Di(N-succinimidyl) glutarate (DSG) (80424, Sigma) in PBS at room temperature (RT) for 45 min. After washing in PBS, cells were fixed again in 1% formaldehyde (28908, Sigma) in TS base media at RT for 12 min. Fixation was stopped by adding glycine to a final concentration of 0.125 M. Cells were washed twice in PBS and resuspended in wash buffer 1 (10mM Hepes pH7.5, 10mM EDTA, 0.5mM EGTA and 0.75% Triton X-100) and incubated at 4C for 10min. After pelleting, cells were resuspended in wash buffer 2 (10mM Hepes pH7.5, 200mM NaCl, 1mM EDTA and 0.5mM EGTA) and incubated at 4C for 10min. After pelleting, cells were lysed in the lysis/sonication buffer (150mM NaCl, 25mM Tris pH 7.5, 5mM EDTA, 0.1%Triton, 1% SDS and 0.5% sodium deoxycholate) with complete protease inhibitors (11873580001, Sigma) on ice for 30min. Chromatin was sonicated 15s on /30s off for 23-25 cycles using the UW2070 sonicator (Bandelin) to the average 300-bp fragments. Chromatin was diluted 1/10 with the dilution buffer (150mM NaCl, 25mM Tris pH 7.5, 5mM EDTA, 1% Triton X-100, 0.1% SDS and 0.5 % sodium deoxycholate) containing complete protease inhibitors. Protein G magnetic Dynabeads (10004D, Invitrogen) were blocked with 1mg/ml BSA and tRNA at 4C for 1h and washed with buffer A (150mM NaCl, 25mM Tris pH 8.0, 1mM EDTA, 1% NP-40, 0.1 % SDS and 0.5 % sodium deoxycholate). Chromatin was pre-cleared with pre-blocked beads at 4C for 1h. Four hundred micrograms of chromatin and seven micrograms of antibody (rabbit anti-MSX2 (HPA005652, Sigma) and rabbit normal IgG (NI01, Sigma) were used per each IP. IP was performed overnight at 4C with rotation. Pre-blocked magnetic beads were added next morning for 7-8 h. Beads were washed at 4C with buffer A three times, buffer B (50mM Tris pH 8.0, 500mM NaCl, 0.1% SDS, 0.5 % sodium deoxycholate, 1% NP-40 and 1mM EDTA), buffer C (50mM Tris pH 8.0, 250mM LiCl, 0.5% sodium deoxycholate, 1% NP-40 and 1mM EDTA) and rinsed with TE buffer. DNA was eluted from beads in the elution buffer (1% SDS, 0.1M NaHCO3). Samples were treated with RNAse A and Proteinase K and reverse-crosslinked overnight by incubation for 2h at 37C, followed by 12h at 65C. DNA was purified on the PCR purification columns (Qiagen).
Quantseq libraries were generated using the Quantseq 3' FWD kit according to the maunfacturers recommendations. ChIPseq libraries were generated using the NEBnext ultra II DNA library prep kit according to the standard protocol.

treatment_protocol: To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G418

value: hTSC-derived syncytiotrophoblast

tag: differentiation state

value: syncytiotrophoblast (ST)

tag: modification

value: inducible MSX2

tag: dox induction

value: no dox

tag: modification protocol

value: To generate the inducible MSX2 expression construct, the coding sequence of MSX2 including the 3xFlag tag was cloned into PiggyBac-Tre-Dest-rTA-HSV-neo. After transfection, the hTSC were selected with 300 μg/ml G418 and expression was induced with 1 μg/ml doxycycline.


title: NPCSC412

source_name: Neural Progenitor Cell from subject 412


title: CRCGN008_HEPG2_24H:C12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C12.lxb
CRCGN008_HEPG2_24H_X3_B29_C12.lxb
Broad Institute Human L1000 epsilon


title: WT-E6-M2

value: Control


title: NPCSC357

source_name: Neural Progenitor Cell from subject 357


title: CRCGN008_HEPG2_24H:C11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C11.lxb
CRCGN008_HEPG2_24H_X3_B29_C11.lxb
Broad Institute Human L1000 epsilon


title: Quantseq_ST+Dox_MSX2_iOX_r3

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_ST+Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_ST+d_3

value: dox


title: Quantseq_ST-Dox_MSX2_iOX_r3

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_ST-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_ST-d_3


title: WT-E6-M1


title: WT-E6-M3


title: Quantseq_ST-Dox_MSX2_iOX_r1

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_ST-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_ST-d_1


title: CRCGN008_HEPG2_24H:C10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C10.lxb
CRCGN008_HEPG2_24H_X3_B29_C10.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:C08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C08.lxb
CRCGN008_HEPG2_24H_X3_B29_C08.lxb
Broad Institute Human L1000 epsilon


title: DMRT1-KI-E6-M3

value: Case


title: Quantseq_ST+Dox_MSX2_iOX_r2

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_ST+Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_ST+d_2


title: CRCGN008_HEPG2_24H:C09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C09.lxb
CRCGN008_HEPG2_24H_X3_B29_C09.lxb
Broad Institute Human L1000 epsilon


title: DMRT1-KI-E6-M2

value: Testis


title: Quantseq_SR_-Dox_MSX2_iOX_r3

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_SR_-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_SR_-d_3

value: human trophoblast stem cells

value: self-renewal (SR)


title: DMRT1-KI-E6-M1


title: NPCSC353

source_name: Neural Progenitor Cell from subject 353


title: NPCSC352

source_name: Neural Progenitor Cell from subject 352

value: Schizophrenia


title: Quantseq_SR_-Dox_MSX2_iOX_r2

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_SR_-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_SR_-d_2


title: Quantseq_SR_-Dox_MSX2_iOX_r1

description:
processed data file:
MSX2_iOX_counts.txt
Quantseq_SR_-Dox_MSX2_iOX
CE83TANXX_5#114175_MSX2iOX_SR_-d_1


title: CRCGN008_HEPG2_24H:C06

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C06.lxb
CRCGN008_HEPG2_24H_X3_B29_C06.lxb
Broad Institute Human L1000 epsilon

source_name: Liver Carcinogenicity


title: CRCGN008_HEPG2_24H:C07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C07.lxb
CRCGN008_HEPG2_24H_X3_B29_C07.lxb
Broad Institute Human L1000 epsilon


title: HEK293T_MeCP2_ChIP-seq_rep2

description: ChIP-seq

data_processing:
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2 version 2.4.1 with the default parameters.
The aligned reads with multiple positions and mapping quality less than 30 were filtered using samtools version 1.9.
Peaks were called using MACS version 1.4 with the default parameters.
Read coverage were calculated and normalized to reads per million (RPM) using BedTools version 2.29.2.
Genome_build: hg38
Supplementary_files_format_and_content: BedGraph files were generated using BedTools; Scores represent normalized coverage: reads per million (RPM)

extract_protocol:
For RNA-seq, total RNAs were isolated using TRIzol (Invitrogen, USA).
RNA-seq and ChIP-seq libraries were prepared according to the manufacturer’s instructions (Illumina). iCLIP-seq libraries were prepared as previously described (Buchbender et al., Methods, 2019).

treatment_protocol: HEK293T cells were maintained in Dulbecco's Modified Eagle's medium supplemented with 10% fetal bovine serum.

tag: genotype

value: WT

tag: antibody


title: HEK293T_MeCP2_ChIP-seq_rep1

description: ChIP-seq


title: Quantseq_SR_MSX2_KD2_hTSC_r1

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_MSX2_KD2_1

value: LV transduction with shMSX2-2

value: To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G421


title: CRCGN008_HEPG2_24H:C05

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C05.lxb
CRCGN008_HEPG2_24H_X3_B29_C05.lxb
Broad Institute Human L1000 epsilon

tag: tissue


title: NPCSC354

source_name: Neural Progenitor Cell from subject 354

value: Neural Progenitor Cell

value: Healthy Control

tag: Sex

value: Male


title: H3K9me3_MSX2_KD_hTSC_r2

description:
processed data file:
H3K9me3_KDMSX2_SR_IDR.bed

data_processing:
RNA-seq
read trimming: TrimGalore! (0.6.5)
alignment: STAR (2.7.3a)
alignment processing: samtools (1.10)
read counting: Rsubread (2.0.0)
ChIP-seq
read trimming: CUTADAPT (2.8)
alignment: bowtie 2 (2.3.5.1)
alignment processing: samtools (1.10)
peak calling: MACS2 (2.2.7.1)
idr analysis: idr (1.2)
bigwig files: bamCoverage (3.5.0)
Genome_build: hg38
Supplementary_files_format_and_content: read counts, bigwig

source_name: human trophoblast stem cells (hTSCs)

growth_protocol: hTSCs were cultured in basal media (DMEM/F12 (11320074, Thermo Fisher), 1x ITS-X (51500056, Thermo Fisher), 0.2% FBS (PAA), 1.5 µg/mL L-ascorbic acid (A4403, Sigma) supplemented with 2 µM CHIR99021, 50ng/mL EGF, 0.5 µM A83-01 and 5µM Y27632. Cells were passaged every 3-4 days using TrypLE (12605036, Thermo Scientific).

treatment_protocol:
ST differentiation was induced in basal medium supplemented with 2 µM Forskolin (6652995, Peprotech), 5 µM Y27632 and 4% KnockOut Serum Replacement (10828010, Thermo Scientific).
To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G418.

value: human trophoblast stem cells (hTSCs)

value: LV transduction with shMSX2-1


title: HEK293T_input DNA

description: ChIP-seq


title: CRCGN008_HEPG2_24H:C04

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C04.lxb
CRCGN008_HEPG2_24H_X3_B29_C04.lxb
Broad Institute Human L1000 epsilon

tag: treatment


title: Quantseq_SR_MSX2_KD1_hTSC_r3

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_MSX2_KD1_3

value: LV transduction with shMSX2

value: To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G420


title: Quantseq_SR_MSX2_KD1_hTSC_r2

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_MSX2_KD1_2

value: To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G419


title: H3K9me3_hTSC_r2

description:
processed data file:
H3K9me3_WT_SR_IDR.bed

value: not transduced


title: H3K9me3_MSX2_KD_hTSC_r1


title: H3K9me3_hTSC_r1


title: H3K27me3_MSX2_KD_hTSC_r2

description:
processed data file:
H3K27me3_KDMSX2_SR_IDR.bed


title: CRCGN008_HEPG2_24H:C03

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C03.lxb
CRCGN008_HEPG2_24H_X3_B29_C03.lxb
Broad Institute Human L1000 epsilon


title: Quantseq_SR_MSX2_KD1_hTSC_r1

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_MSX2_KD1_1

value: To deplete MSX2, cells were transduced with pLKO.1-based lentiviral particles containing either shRNA against MSX2 (TRCN0000234848 and TRCN0000234849) or a shRNA against GFP as a control for 16h and selected for integrations by treatment with 300µg/ml G418


title: Xiap-/-  2

first: Monica

last: Yabal

address: Ismaninger straße 22

institute: Technical University of Munich

data_processing:
Dropseq tools v1.12 was used for mapping the raw sequence reads to the reference genome and to generate transcript counts
Differential expression analysis with DESeq2 v1.18.1 was utilized to identify differentially expressed genes
Genome_build: GRCm38.p6

source_name: small intestinal crypts

extract_protocol:
Isolation of RNA from liver was performed using NucleoSpin RNA Kit from Macherey-Nagel.
Library preparation for bulk 3’-sequencing of poly(A)-RNA was done as described previously in Drop-Seq pipeline. Briefly, barcoded cDNA of each sample was generated with a Maxima RT polymerase (Thermo Fisher) using oligo-dT primer containing barcodes, unique molecular identifiers (UMIs) and an adapter. 5’ ends of the cDNAs were extended by a template switch oligo (TSO) and after pooling of all samples full-length cDNA was amplified with primers binding to the TSO-site and the adapter. cDNA was tagmented with the Nextera XT kit (Illumina) and 3’-end-fragments finally amplified using primers with Illumina P5 and P7 overhangs. The P5 and P7 sites were exchanged to allow sequencing of the cDNA in read1 and barcodes and UMIs in read2 to achieve a better cluster recognition. The library was sequenced on a NextSeq 500 (Illumina) with 75 cycles for the cDNA in read1 and 16 cycles for the barcodes and UMIs in read2.

tag: strain

value: small intestine

tag: genotype/variation

value: Xiap-/-


title: Xiap-/-  4


title: Quantseq_SR_shGFP_hTSC_r2

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_CTRL_2

tag: cell type

value: human trophoblast stem cells

value: self-renewal (SR)

value: LV transduction with shGFP


title: Xiap-/-  3


title: Quantseq_SR_shGFP_hTSC_r3

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_CTRL_3


title: CRCGN008_HEPG2_24H:C02

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C02.lxb
CRCGN008_HEPG2_24H_X3_B29_C02.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B24.lxb
CRCGN008_HEPG2_24H_X3_B29_B24.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:C01

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_C01.lxb
CRCGN008_HEPG2_24H_X3_B29_C01.lxb
Broad Institute Human L1000 epsilon


title: Xiap-/-  1


title: Quantseq_SR_shGFP_hTSC_r1

description:
processed data file:
MSX2_KD_counts.txt
CE9U2ANXX_6#126005_CTRL_1


title: H3K27me3_hTSC_r2

description:
processed data file:
H3K27me3_WT_SR_IDR.bed


title: WT 6

value: WT


title: WT 5


title: H3K27me3_hTSC_r1


title: WT 4


title: hTSC_Input_r2

description:
processed data file:
INmerge_128077_130125.bw
INPUT_hTSC_3_130125_GATCAG


title: CRCGN008_HEPG2_24H:B22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B22.lxb
CRCGN008_HEPG2_24H_X3_B29_B22.lxb
Broad Institute Human L1000 epsilon


title: hTSC_Input_r1

description:
processed data file:
INmerge_128077_130125.bw
INPUT_hTSC_128077x2_TGACCA


title: CRCGN008_HEPG2_24H:B21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B21.lxb
CRCGN008_HEPG2_24H_X3_B29_B21.lxb
Broad Institute Human L1000 epsilon


title: H3K27ac_MSX2_KD_hTSC_r2

description:
processed data file:
H3K27ac_KDMSX2_SR_IDR.bed


title: WT 3


title: CRCGN008_HEPG2_24H:B20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B20.lxb
CRCGN008_HEPG2_24H_X3_B29_B20.lxb
Broad Institute Human L1000 epsilon


title: H3K27ac_MSX2_KD_hTSC_r1


title: H3K27me3_MSX2_KD_hTSC_r1


title: WT 2


title: CRCGN008_HEPG2_24H:B23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B23.lxb
CRCGN008_HEPG2_24H_X3_B29_B23.lxb
Broad Institute Human L1000 epsilon


title: H3K27ac_hTSC_r2

description:
processed data file:
H3K27ac_WT_SR_IDR.bed


title: MSX2_hTSC_ChIPseq_r2

description:
processed data file:
M2_128246_129321_130126.bw
MSX2_WT_SR_all_IDR_CPA.bed
MSX2_hTSC_2_129321_ACTTGA


title: H3K27ac_hTSC_r1


title: Cohoused WT 5


title: SMARCA4_MSX2_KD_hTSC_r1

description:
processed data file:
SMARCA4_KDMSX2_SR_IDR.bed


title: WT 1


title: HEK293T_MeCP2_KO_RBFOX2 iCLIP-seq_rep3

data_processing:
Library strategy: iCLIP-seq
We cleaned the paired-end reads by Trimimomatic (version 0.36). After trimming the adapter sequence, removing low quality bases and filtering short reads, clear read pairs were retained for further analysis.
The genome sequence and gene annotation of human (GRCh38) and mouse (GRCm38) were downloaded from GENCODE. Cleaned reads were mapped to the genome sequence by HISAT (version 2.1.0) with default parameters. Number of reads that were mapped to each gene was calculated with the htseq-count script in HTSeq (version 0.9.1)
EdgeR was used to identify genes that were differentially expressed between control and experiment samples. Genes with at least two-fold change in expression and had a FDR < 0.05 were considered differentially expressed genes (DEGs).
The barcode regions in the iCLIP reads are filtered by FASTX-Toolkit.The demultiplexing and adapter trimming are performed by Flexbar. Only trimmed reads with at least 15 nt are kept for further analysis.
The individual FASTQ files for each sample are mapped to human reference genome (GRCh38) by STAR. The technical duplicates are removed using UMI-tools.
After deduplication, the crosslink events are transformed from the mapped reads by extracting the position upstream of the 5’end of the reads with BEDTools.
The crosslink sites with significantly enriched crosslink events are identified by PureCLIP and post-processed by custom scripts.
Genome_build: human (GRCh38) and mouse (GRCm38)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values, log2Fold change and FDR for each gene.
Supplementary_files_format_and_content: bed files include the chromosome, start/end position and strand of each binding site.
Supplementary_files_format_and_content: bigWig files were generated by bedtools and bedGraphToBigWig, the scores represent the read coverage on the genome.

value: MeCP2 KO

value: HEK293T cell line


title: Cohoused WT 4


title: CRCGN008_HEPG2_24H:B18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B18.lxb
CRCGN008_HEPG2_24H_X3_B29_B18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B16.lxb
CRCGN008_HEPG2_24H_X3_B29_B16.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B17.lxb
CRCGN008_HEPG2_24H_X3_B29_B17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B19.lxb
CRCGN008_HEPG2_24H_X3_B29_B19.lxb
Broad Institute Human L1000 epsilon


title: Cohoused WT 3


title: SMARCA4_hTSC_r2

description:
processed data file:
SMARCA4_WT_SR_IDR.bed


title: Cohoused WT 2


title: HEK293T_MeCP2_KO_RBFOX2 iCLIP-seq_rep1


title: HEK293T_WT_RBFOX2 iCLIP-seq_rep3


title: CRCGN008_HEPG2_24H:B14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B14.lxb
CRCGN008_HEPG2_24H_X3_B29_B14.lxb
Broad Institute Human L1000 epsilon


title: SMARCA4_hTSC_r1


title: CRCGN008_HEPG2_24H:B15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B15.lxb
CRCGN008_HEPG2_24H_X3_B29_B15.lxb
Broad Institute Human L1000 epsilon


title: Cohoused WT 1


title: MSX2_hTSC_ChIPseq_r3

description:
processed data file:
M2_128246_129321_130126.bw
MSX2_WT_SR_all_IDR_CPA.bed
MSX2_hTSC_3_130126_TAGCTT


title: HEK293T_WT_RBFOX2 iCLIP-seq_rep2


title: SMARCA4_MSX2_KD_hTSC_r2


title: CRCGN008_HEPG2_24H:B13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B13.lxb
CRCGN008_HEPG2_24H_X3_B29_B13.lxb
Broad Institute Human L1000 epsilon


title: Cohoused Xiap-/-  5


title: HEK293T_MeCP2_KO_RBFOX2 iCLIP-seq_rep2


title: ARID1A_MSX2_KD_hTSC_r1

description:
processed data file:
ARID1A_KDMSX2_SR_IDR.bed


title: CRCGN008_HEPG2_24H:B12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B12.lxb
CRCGN008_HEPG2_24H_X3_B29_B12.lxb
Broad Institute Human L1000 epsilon


title: HEK293T_WT_RBFOX2 iCLIP-seq_rep1


title: Cohoused Xiap-/-  4


title: ARID1A_hTSC_r1

description:
processed data file:
ARID1A_WT_SR_IDR.bed


title: HEK293T_WT_RBFOX2 iCLIP-seq ctrl


title: Cohoused Xiap-/-  3


title: HEK293T_RBFOX2_KI_RNA-seq_rep2

value: RBFOX2 KI


title: Cohoused Xiap-/-  2


title: CRCGN008_HEPG2_24H:B10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B10.lxb
CRCGN008_HEPG2_24H_X3_B29_B10.lxb
Broad Institute Human L1000 epsilon


title: HEK293T_RBFOX2_KI_RNA-seq_rep1


title: MSX2_KD_hTSC_Input_r1


title: CRCGN008_HEPG2_24H:B09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B09.lxb
CRCGN008_HEPG2_24H_X3_B29_B09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B08.lxb
CRCGN008_HEPG2_24H_X3_B29_B08.lxb
Broad Institute Human L1000 epsilon


title: Cohoused Xiap-/-  1


title: HEK293T_MeCP2_KO_RNA-seq_rep2


title: ARID1A_MSX2_KD_hTSC_r2


title: HEK293T_MeCP2_KO_RNA-seq_rep1


title: hTSC_Input_r2_163150


title: CRCGN008_HEPG2_24H:B07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B07.lxb
CRCGN008_HEPG2_24H_X3_B29_B07.lxb
Broad Institute Human L1000 epsilon


title: ARID1A_hTSC_r2


title: hTSC_Input_r1_163149


title: HEK293T_WT_RNA-seq_rep1


title: CRCGN008_HEPG2_24H:A24

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A24.lxb
CRCGN008_HEPG2_24H_X3_B29_A24.lxb
Broad Institute Human L1000 epsilon


title: HEK293T_WT_RNA-seq_rep2


title: MSX2_KD_hTSC_Input_r2


title: Brain Whole Cells 5381

source_name: Bulk post-mortem adult human brain tissue

extract_protocol:
RNA was extracted by a Qiagen mini RNA prep kit, following the manufacturer's instructions, including a DNAse treatment step. Libraries were prepared using the TruSeq Stranded mRNA library prep kit.
Standard Illumina protocols

tag: sample type

value: Frozen human brain tissue

tag: mixing ratio

tag: molecule subtype

value: PolyA+ RNA


title: S6-B-HPC

city: Baltimore

first: XIAOLEI

last: ZHU

state: MD

address: 417 old trail rd

institute: JHU

data_processing:
Original BAM files were converted into FASTQ format using picard tools (SamToFastq command). Reads shorter than 15 nt were removed from the raw FASTQ data using cutadapt software v1.18. The size-selected reads were aligned to mouse reference transcriptomes using Bowtie software (1 mismatch tolerance) in a sequential manner.
Specifically, reads were first mapped to rRNA, tRNA, RN7S, snRNA, snoRNA, scaRNA, VT-RNA, Y-RNA as well as the mitochondrial genome. All reads which did not map to the above RNA species were aligned to mouse miRNA references (miRBase 22 release). The remaining reads were further aligned to protein-coding mRNAs and long non-coding RNA (lncRNA) references (GENCODE Release 29). The numbers of reads mapped to each RNA type were extracted using eXpress software based on a previous publication. Differential gene expression was quantified using R/Bioconductor packages DESeq or DESeq2 as described. RefFinder is used for evaluating and screening internal reference genes from small RNA sequencing datasets.
Genome_build: mm9
Supplementary_files_format_and_content: Excel file contains all mapped reads

source_name: Brain

extract_protocol:
RNA was purified by miRNeasy Mini Kit solutions and Zymo-Spin I Columnsaccording to the manufacturer’s instructions.
Small RNA libraries were constructed from 8 μl of RNA extracted from bdEVs using the CATS Small RNA-seq Kit (Diagenode C05010040).

value: HPC

value: Brain tissue derived EVs

value: Ctr + PDDC


title: S7-C-HPC

value: EcoHIV + Vehicle


title: S5-A-HPC

value: Ctr + Vehicle


title: Xbp1 rep-3

city: Daejeon

first: Kwang-Soo

last: Shin

department: Life Science

institute: Daejeon University

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using bbmap), then mapped to hg19 whole genome using Bowtie2
Read count extraction and nomalization were performed using edgeR.
Genome_build: Aspergillus fumigatus Af293
Supplementary_files_format_and_content: tab-delimited text files include read count values for each Sample

organism: Aspergillus fumigatus Af293

source_name: Asexual spore and mycelium

growth_protocol: Incubate 2 days in liquid media

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: Freeze-dry

value: xbp1 deletion mutant

value: conidia and mycelium


title: S4-D-PFC

value: PFC

value: EcoHIV + PDDC


title: Brain Whole Cells 5144


title: CRCGN008_HEPG2_24H:A21

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A21.lxb
CRCGN008_HEPG2_24H_X3_B29_A21.lxb
Broad Institute Human L1000 epsilon

data_processing: For each perturbation and landmark gene, we computed the change in gene expression following the perturbation using a moderated z-score procedure as described in the CMap–L1000 workflow. Differential expression values were calculated as moderated z-scores for each landmark gene and each unique perturbation (chemical and dose combination) perturbation, collapsed to a single value across replicates (Subramanian et al. 2017).


title: Brain Whole Cells 5006


title: Xbp1 rep-2


title: S8-D-HPC


title: Brain Whole Cells 4899


title: S3-C-PFC


title: Xbp1 rep-1


title: CRCGN008_HEPG2_24H:A20

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A20.lxb
CRCGN008_HEPG2_24H_X3_B29_A20.lxb
Broad Institute Human L1000 epsilon


title: Brain Whole Cells 1541


title: S2-B-PFC


title: S1-A-PFC


title: Brain Nuclear 5381

extract_protocol:
RNA was extracted by a hot Trizol extraction method. Nuclei were washed in PBS and resuspended in Trizol at 65°C and incubated on a shaker at 1,300 rpm for 15 min. RNA was enriched using a guanidinium HCl buffer and silica-coated magnetic beads with a DNAse I treatment step. Libraries were prepared using the TruSeq Stranded mRNA library prep kit.
Standard Illumina protocols

value: PolyA+ Nuclear RNA


title: CRCGN008_HEPG2_24H:A19

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A19.lxb
CRCGN008_HEPG2_24H_X3_B29_A19.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A23

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A23.lxb
CRCGN008_HEPG2_24H_X3_B29_A23.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A22

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A22.lxb
CRCGN008_HEPG2_24H_X3_B29_A22.lxb
Broad Institute Human L1000 epsilon


title: Afp1 rep-2

value: afp1 deletion mutant


title: Afp1 rep-1


title: Brain Nuclear 5144


title: CRCGN008_HEPG2_24H:A17

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A17.lxb
CRCGN008_HEPG2_24H_X3_B29_A17.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A16

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A16.lxb
Broad Institute Human L1000 epsilon


title: Ngn4 rep-3

value: ngn4 deletion mutant


title: Brain Nuclear 4899


title: Brain Nuclear 5006


title: Liver PSC_14

city: Paris

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

country: France

institute: GenoSplice technology

description:
Liver from PSC mouse 14
Deseq2_normalized_gene_expression_with_annotations.txt

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.4.0
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text file includes deseq2 normalized expression values for each gene and for each sample. Annotations from Mouse FAST DB v2018_1 were also provide

source_name: Liver

extract_protocol:
Mouse livers were collected at day 35 post-cholangitis induction and stored directly in RNAprotect Tissue Reagent solution (Qiagen) and stored at 4°C. Total RNA extraction and purification were performed using the RNeasy plus mini kit (Qiagen) and the Qiashredder homogenizer columns (Qiagen), according to the supplier’s instructions. Lysis and homogenization of the tissues was formerly achieved thanks to the Precellys 24 Tissue Homogenizer (Bertin Instruments) and hard tissue homogenizing CK28-R 2 mL tubes (Bertin Instruments) in the lysis buffer supplied in the RNeasy plus mini kit, at 5 000 rpm for 20 seconds (twice). RNA concentration in samples was then measured using a NanoDropTM 1000 (Thermo Fisher Scientific).
The libraries were prepared following the Tru-seq mRNA protocol from Illumina, starting from 1 µg of high-quality total RNA. Paired end (2 × 75) sequencing was performed on an Illumina Nextseq 500 platform. Fluorometric Qubit RNA HS assay (Life Technologies, Grand Island, New York, USA) was applied to measure RNA concentration. RNA quality (RNA integrity number) was assessed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA). To build libraries, 1 µg of high-quality total RNA sample (RIN >8) was processed using TruSeq stranded mRNA kit (Illumina) according to manufacturer’s instructions. Briefly, after purification of poly-A containing mRNA molecules, nucleic acids were fragmented and reverse-transcribed using random primers. Replacement of dTTP by dUTP during the second strand synthesis permitted to achieve strand specificity. Addition of a single A base to the cDNA was followed by ligation of adapters. Libraries were quantified by Qubit DNA HS Assay (Life Technologies, Grand Island, CA, USA) and library profiles were assessed using the DNA High Sensitivity LabChip kit on an Agilent Bioanalyzer. Libraries were sequenced on an Illumina Nextseq 500 instrument using 75 base-length read V2 chemistry in a paired-end mode. After sequencing, a primary analysis based on AOZAN software (ENS, Paris) was applied to demultiplexed and control the quality of the raw data (based of FastQC modules / version 0.11.5) (Perrin et al., 2017).

treatment_protocol: Autoimmune primary biliary cholangitis (PBC) was induced in C57Bl/6 mice as described before: Chang et al., 2014; Wakabayashi et al., 2008. Briefly, mice were immunized with 100 µg of 2-octynoic acid BSA conjugate (2OA-BSA) intraperitoneally (i.p.) in a mix of PBS and complete Freund’s adjuvant (CFA, Sigma-Aldrich) at day 0 and were reboosted at days 14 and 28 with 2OA-BSA and incomplete Freund’s Adjuvant (IFA, Sigma Aldrich). Concomitantly with the two first injections of 2OA-BSA, mice were also injected intravenously (i.v.) with 2 μg of α-galactosylceramide (α-GalCer, Abcam) in PBS.   Non-autoimmune primary sclerosing cholangitis model (PSC) was induced in C57Bl/6 mice as previously published: Fickert et al., 2007; Ikenaga et al., 2017. They were fed the SAFE A04 diet (SAFE™) containing 0.089% (in weight) of 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC, Sigma-Aldrich) for 2 weeks (from day 0 to 14). After one week of recovery with the regular diet, mice were fed again with the DDC-supplemented diet for one more week.

value: Liver

value: Wild type

tag: time (day of liver collection)

value: Day 35 post cholangitis induction


title: Liver PSC_11

description:
Liver from PSC mouse 11
Deseq2_normalized_gene_expression_with_annotations.txt


title: Liver PSC_13

description:
Liver from PSC mouse 13
Deseq2_normalized_gene_expression_with_annotations.txt


title: Brain Nuclear 1541

value: Frozen human brain tissue


title: Afp1 rep-3


title: CRCGN008_HEPG2_24H:A15

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A15.lxb
CRCGN008_HEPG2_24H_X3_B29_A15.lxb
Broad Institute Human L1000 epsilon


title: Liver PBC_9

description:
Liver from PBC mouse 9
Deseq2_normalized_gene_expression_with_annotations.txt

value: 2-octynoic acid BSA conjugate + α-galactosylceramide


title: Liver PBC_8

description:
Liver from PBC mouse 8
Deseq2_normalized_gene_expression_with_annotations.txt


title: Elp3 rep-3

value: elp3 deletion mutant


title: CRCGN008_HEPG2_24H:A14

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A14.lxb
CRCGN008_HEPG2_24H_X3_B29_A14.lxb
Broad Institute Human L1000 epsilon


title: Liver PBC_7

description:
Liver from PBC mouse 7
Deseq2_normalized_gene_expression_with_annotations.txt


title: CRCGN008_HEPG2_24H:A18

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A18.lxb
CRCGN008_HEPG2_24H_X3_B29_A18.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A12

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A12.lxb
CRCGN008_HEPG2_24H_X3_B29_A12.lxb
Broad Institute Human L1000 epsilon


title: Liver Control_4

description:
Liver from mouse control 4
Deseq2_normalized_gene_expression_with_annotations.txt

value: Untreated


title: Elp3 rep-1


title: CRCGN008_HEPG2_24H:A11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A11.lxb
CRCGN008_HEPG2_24H_X3_B29_A11.lxb
Broad Institute Human L1000 epsilon


title: Ngn4 rep-2


title: CRCGN008_HEPG2_24H:A10

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A10.lxb
CRCGN008_HEPG2_24H_X3_B29_A10.lxb
Broad Institute Human L1000 epsilon


title: Ngn4 rep-1


title: Wild type rep-2


title: Wild type rep-3


title: Liver Control_3

description:
Liver from mouse control 3
Deseq2_normalized_gene_expression_with_annotations.txt


title: CRCGN008_HEPG2_24H:A09

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A09.lxb
CRCGN008_HEPG2_24H_X3_B29_A09.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A07

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A07.lxb
CRCGN008_HEPG2_24H_X3_B29_A07.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:A08

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A08.lxb
CRCGN008_HEPG2_24H_X3_B29_A08.lxb
Broad Institute Human L1000 epsilon


title: Wild type rep-1


title: Elp3 rep-2


title: Liver Control_1

description:
Liver from mouse control 1
Deseq2_normalized_gene_expression_with_annotations.txt


title: Serum of healthy human LncRNA 3

city: Harbin

first: qichang

last: gao

state: Heilongjiang

address: youzheng street, Nangang district

department: orthopedics departmnet

institute: First Affiliated Hospital of Harbin Medical University

description: LncRNA expression data from Homo sapiens serum

hyb_protocol: 1.Add 500 μL of nuclease-free water to the vial containing lyophilized 10X Blocking Agent. Mix by gently vortexing.  2. Equilibrate water bath to 60°C.  3. For each microarray, add each of the components as indicated in the tables as below to a 1.5 mL nuclease-free microfuge tube  4. Mix well but gently on a vortex mixer.  5. Incubate at 60°C for exactly 30 minutes to fragment RNA.   6. Add 2x GEx Hybridization Buffer HI-RPM to the array to stop the fragmentation reaction.  7. Mix well by careful pipetting. Take care to avoid introducing bubbles. Do not mix on a vortex mixer; mixing on a vortex mixer introduces bubbles.  8. Spin for 1 minute at room temperature at 13,000 rpm in a microcentrifuge to drive the sample off the walls and lid and to aid in bubble reduction.  9. Place sample on ice and load onto the array as soon as possible.   10. Load a clean gasket slide into the Agilent SureHyb chamber base with the label facing up and aligned with the rectangular section of the chamber base. Ensure that the gasket slide is flush with the chamber base and is not ajar.  11. Slowly dispense the volume of hybridization sample onto the gasket well in a “drag and dispense” manner.  12. Slowly place an array “active side” down onto the SureHyb gasket slide, so that the “Agilent”-labeled barcode is facing down and the numeric barcode is facing up. Verify that the sandwich-pair is properly aligned.   13. Place the SureHyb chamber cover onto the sandwiched slides and slide the clamp assembly onto both pieces.  14. Hand-tighten the clamp onto the chamber.  15. Vertically rotate the assembled chamber to wet the gasket and assess the mobility of the bubbles.  16. Place assembled slide chamber in rotisserie in a hybridization oven set to 65°C. Set your hybridization rotator to rotate at 10 rpm.  17. Hybridize at 65°C for 17 hours.

scan_protocol: 1. Assemble the slides into an slide holder.   2. Place assembled slide holders into scanner carousel.  3. Verify scan settings for one-color scans.  4. Click Scan Slot m-n on the Scan Control main window where the letter m represents the Start slot where the first slide is located and the letter n represents the End slot where the last slide is located.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The LncRNAs that at least 3 out of 6 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed LncRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: Serum of healthy human

label_protocol: 1. Add 1ug of total RNA to a 1.5-mL microcentrifuge tube.   2. Add 1.2 μL of T7 Promoter Primer.   3. Use nuclease-free water to bring the total reaction volume to 11.5 μL.  4. Denature the primer and the template by incubating the reaction at 65°C in a circulating water bath for 10 minutes.  5. Place the reactions on ice and incubate for 5 minutes.  6. Immediately prior to use, gently mix the components listed in the following table for the cDNA Master Mix by adding in the order indicated, and put on ice.  7. Briefly spin each sample tube in a microcentrifuge to drive down the contents from the tube walls and the lid. Return the tubes to ice.  8. Add 8.5 μL of cDNA Master Mix to each sample tube and mix by pipetting up and down.  9. Incubate samples at 40°C in a circulating water bath for 2 hours.  10. Move samples to a 65°C circulating water bath and incubate for 15 minutes.  11. Move samples to ice. Incubate for 5 minutes.  12. Spin samples briefly in a microcentrifuge to drive down tube contents from the tube walls and lid.  13. Immediately prior to use, gently mix the components listed in the following table in the order indicated for the Transcription Master Mix by pipetting at room temperature.  14. Add 60 μL of Transcription Master Mix to each sample tube. Gently mix by pipetting.  15. Incubate samples in a circulating water bath at 40°C for 2 hours.   16. Add 20 μL of nuclease-free water to sample, for a total volume of 100 μL.  17. Add 350 μL of Buffer RLT and mix well by pipetting.  18. Add 250 μL of ethanol (100% purity) and mix thoroughly by pipetting. Do not centrifuge.  19. Transfer the 700 μL of the cRNA sample to an RNeasy mini column in a 2 mL collection tube. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through and collection tube.  20. Transfer the RNeasy column to a new collection tube and add 500 μL of buffer RPE (containing ethanol) to the column. Centrifuge the sample at 4°C for 30 seconds at 13,000 rpm. Discard the flow-through. Re-use the collection tube.  21. Add another 500 μL of buffer RPE to the column. Centrifuge the sample at 4°C for 60 seconds at 13,000 rpm. Discard the flow-through and the collection tube.  22. Elute the cleaned cRNA sample by transferring the RNeasy column to a new 1.5 mL collection tube. Add appropriate RNase-free water (Passed-please see report ”Labeling Efficiency-QC”) directly onto the RNeasy filter membrane. Wait 60 seconds, then centrifuge at 4°C for 30 seconds at 13,000 rpm.  23. Maintain the cRNA sample-containing flow-through on ice. Discard the RNeasy column.  24.  Take 1.5 μl of each sample to determine the yield and specific activity by using the NanoDrop ND-1000

extract_protocol: 1. Open the Agilent Feature Extraction (FE) software.  2. Add the images (.tif) to be extracted to the FE Project.  3. Set FE Project Properties.  4. Check the Extraction Set Configuration.  5. Save the FE Project (.fep) by selecting File > Save As and browse for desired location.  6. Select Project > Start Extracting and export data to txt.

treatment_protocol: Collect 2ml of serum from Alzheimer’s patients and healthy controls to extract total RNA.

tag: disease state

value: healthy control

tag: gender

value: female

value: serum


title: Serum of healthy human LncRNA 1

value: male


title: Serum of healthy human LncRNA 2


title: Serum of Alzheimer's patients LncRNA 1

source_name: Serum of Alzheimer’s patients

value: Alzheimer's patient


title: Serum of Alzheimer's patients LncRNA 3


title: Serum of Alzheimer's patients LncRNA 2


title: Liver Control_2

description:
Liver from mouse control 2
Deseq2_normalized_gene_expression_with_annotations.txt


title: CRCGN008_HEPG2_24H:A13

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_A13.lxb
CRCGN008_HEPG2_24H_X3_B29_A13.lxb
Broad Institute Human L1000 epsilon


title: CRCGN008_HEPG2_24H:B11

description:
raw data information:
CRCGN008_HEPG2_24H_X2_B29_B11.lxb
CRCGN008_HEPG2_24H_X3_B29_B11.lxb
Broad Institute Human L1000 epsilon


title: Peripheral blood_CN_rep2

status: Public on Aug 27 2021

city: Ningbo

first: Jin

last: Xu

address: 818 Fenghua Road

institute: Ningbo University

description: circRNA expression in healthy control pregnant woman

hyb_protocol: Arrays were hybridized was preformed in a Agilent Hybridization Oven overnight at a rotation speed of 20 rpm and a temperature of 42℃ and washed with two consecutive solutions (0.2% SDS, 2× SSC at 42℃ for 5 min, and 0.2× SSC for 5 min at room temperature).

scan_protocol: The microarrays were scanned using the Agilent chip scanner (G2565CA).

data_processing: The circRNA array data were analyzed using the GeneSpring software V13.0 (Agilent). The Significance Analysis of Microarrays (SAM)  method was used to correct, normalize and summarize the probe level information.

source_name: Control pregnant woman peripheral blood,replicate 2

label_protocol: cDNA labeled with a fluorescent dye (Cy3-dCTP) was produced by Eberwine’s linear RNA amplification method and subsequent enzymatic reaction. This procedure has been improved by using CapitalBio cRNA Amplification and Labeling Kit (CapitalBio) for producing higher yields of labeled cDNA.

extract_protocol: HP total RNA extraction kit was used to extract total RNA from 1mL PBMCs according to the manufacturer's instructions.

treatment_protocol: Peripheral blood was delaminated with Ficoll separation solution and centrifuged at 1500rpm for 40 minutes. The second layer of white flocs was absorbed in the obtained separation solution, and PBS buffer was added to 6ml. After centrifuging at 1700rpm for 10 minutes, the lowest white precipitate was collected, 1mL TRIzol pyrolysis solution was added to make it completely dissolve.

value: Healthy Control/Pregnant

value: Peripheral blood mononuclear cells

tag: age


title: Peripheral blood_CN_rep1

source_name: Control pregnant woman peripheral blood,replicate 1


title: Peripheral blood_CN_rep6

source_name: Control pregnant woman peripheral blood,replicate 6


title: WT CD8 T cell_post act 96h_Biological repeats_ W3

city: Stockholm

first: Joanna

last: Rorbach

state: Not Applicable (Outside of US and Canada)

address: Solnavägen 9, 9d 171 77 Stockholm, Sweden

department: Department of Medical Biochemistry and Biophysics

country: Sweden

institute: karolinska institute

hyb_protocol: Hybridisation processed under 'High Sensitivity' settings.

scan_protocol: High Sensitivity'  FOV 555 in nCounter Digital Analyzer

data_processing: Data normalization was performed in nSolver 4.0 (NanoString)

source_name: WT CD8 T cell_post act 96h

label_protocol: nCounter® mice Metabolic Pathways Panel, see manufacturer's website http://www.nanostring.com

growth_protocol: Negative selected splenic naive CD8 T cell from 4 WT and 4 C5024T mice. Mice were age (2-month-old) and sex matched. Been cultured and activated in RPMI1640 with 10% FBS, 2.05 mM L-glutamine, 1% penicillin/streptomycin and 55 μM 2-ME.

extract_protocol: Total RNA was extracted using Trizol LS reagent (Invitrogen) and RNA concentrations determined using a NanoDrop ND-1000 UV-Vis Spectrophotometer (ThermoFisher Scientific)

treatment_protocol: for each mouse, freshly purified (negative selection) splenic naïve CD8+ T cells were seeded at a density of 200,000 cells/well and activated using a 1:1 ratio(beads to cell) with Dynabeads Mouse T-Activator CD3/CD28 for 6 and 96 hr at 37oC (5% CO2). 200,000 ex vivo purifyed naïve CD8+ T cells were collected for baseline (0 hr) measurement.

value: 8 weeks

value: splenic CD8 T cell

value: WT

tag: group

value: CD8 T cell_post act 96h


title: Peripheral blood_CN_rep3

source_name: Control pregnant woman peripheral blood,replicate 3


title: C5024T(Ala) CD8 T cell_post act 6h_Biological repeats_ A4

source_name: C5024T(Ala) CD8 T cell_post act 6h

value: CD8 T cell_post act 6h


title: WT naive CD8 T cell_Biological repeats_ W4

source_name: WT naive CD8 T cell

value: naive CD8 T cell


title: C5024T(Ala) CD8 T cell_post act 6h_Biological repeats_ A3


title: WT naive CD8 T cell_Biological repeats_ W3


title: WT CD8 T cell_post act 6h_Biological repeats_ W3

source_name: WT CD8 T cell_post act 6h


title: C5024T(Ala) naive CD8 T cell_Biological repeats_ A4

source_name: C5024T(Ala) naive CD8 T cell


title: WT CD8 T cell_post act 96h_Biological repeats_ W4


title: C5024T(Ala) CD8 T cell_post act 96h_Biological repeats_ A4

source_name: C5024T(Ala) CD8 T cell_post act 96h


title: C5024T(Ala) naive CD8 T cell_Biological repeats_ A3


title: WT CD8 T cell_post act 6h_Biological repeats_ W4


title: Peripheral blood_GDM_rep6

description: circRNA expression in GDM woman

source_name: Gestational diabetes mellitus peripheral blood,replicate 6

value: Gestational diabetes mellitus


title: C5024T(Ala) CD8 T cell_post act 96h_Biological repeats_ A3


title: WT CD8 T cell_post act 96h_Biological repeats_ W2


title: WT CD8 T cell_post act 6h_Biological repeats_ W2


title: Peripheral blood_GDM_rep5

description: circRNA expression in GDM woman

source_name: Gestational diabetes mellitus peripheral blood,replicate 5


title: Peripheral blood_GDM_rep4

description: circRNA expression in GDM woman

source_name: Gestational diabetes mellitus peripheral blood,replicate 4


title: Peripheral blood_GDM_rep2

description: circRNA expression in GDM woman

source_name: Gestational diabetes mellitus peripheral blood,replicate 2


title: Naive

city: Lausanne

first: Tania

last: Wyss

address: Rue du Bugnon 25A

country: Switzerland

institute: SIB Swiss Institute of Bioinformatics

description: Naive

data_processing:
Single cells were processed using 10x Genomics Single Cell 3' v3 chemistry. Sequencing performed at the Gene Expression Core Facility (EPFL, Lausanne, Switzerland). Conventional Sanger / Illumina 1.9 score encoding. Fastq files were processed with Cell Ranger v.3.0.1, with cell detection setting expect=5000
Alignment and counts per genes were processed using the Cell Ranger v.3.0.1 pipeline
The Cell Ranger output matrix containing filtered features and barcodes was imported into R v.3.5.1. and normalized using the Seurat package v.3.1.5
Genome_build: Mus musculus mm10
Supplementary_files_format_and_content: tab-separated text file of raw counts, gene x cell matrix. The first column contains gene symbols. The sample origin of each cell is contained within each cell's name (column names)

source_name: Total P14 cells from naive mice

extract_protocol:
Cell lysis and RNA capture was performed according to the 10x Genomics protocol (Single Cell 3' v3 chemistry)
The cDNA libraries were generated according to the manufacturer’s protocol (Illumina) and further sequenced (paired-end) with HiSeq2500 technology (Illumina) at the Gene Expression Core Facility (GECF) of the School of Life Sciences EPFL.
10x Genomics single-cell RNA sequencing

treatment_protocol: Total P14 cells were flow sorted from the spleen of naive mice based as CD62L+ CD8+ cells  (Naive) or from the spleens of LCMV infected mice based on CD8+ CD45.2+ CD45.1-.

value: CD8 T cells expressing a P14 TCR and a Tcf7GFP reporter

value: B6;D2-Tg(TcrLCMV)327Sdz/JDvsJ   B6-Tg(Tcf7GFP)WHe


title: Peripheral blood_CN_rep4

source_name: Control pregnant woman peripheral blood,replicate 4


title: c13

source_name: Total P14 cells at day 32 of LCMV cl13 infection


title: WT CD8 T cell_post act 6h_Biological repeats_ W1


title: WT CD8 T cell_post act 96h_Biological repeats_ W1


title: WT naive CD8 T cell_Biological repeats_ W1


title: WT naive CD8 T cell_Biological repeats_ W2


title: C5024T(Ala) naive CD8 T cell_Biological repeats_ A1


title: C5024T(Ala) naive CD8 T cell_Biological repeats_ A2


title: C5024T(Ala) CD8 T cell_post act 96h_Biological repeats_ A1


title: Peripheral blood_CN_rep5

source_name: Control pregnant woman peripheral blood,replicate 5


title: C5024T(Ala) CD8 T cell_post act 6h_Biological repeats_ A2


title: ATACseq_mESC_46C

city: Berlin

first: Alexander

last: Kukalev

address: Hannoversche Str., 28

department: Berlin Institute for Medical Systems Biology

institute: Max-Delbrueck Center for Molecular Medicine

data_processing:
For bulk mESC ATAC-seq, paired-end reads were mapped to the mouse genome (mm10) using Bowtie with the following parameters: --minins 25 --maxins 2000 --no-discordant --dovetail --soft-clipped-unmapped-tlen. Low quality mapped reads (MQ < 30) and mitochondrial reads were removed. Duplicated reads were removed with Sambamba115 (version 0.6.8). Reads passing quality checks were converted to BAM format for further analyses. Next, dimensionality reduction was performed using the Latent semantic indexing (LSI) dimensionality reduction method from ArchR, with default parameters (except: iterations = 10, resolution =0.2, varFeatures = 60000). The ArchR addHarmony function was ysed to run the Harmony algorithm for batch correction with default parameters, followed by clusters calling. Gene scores were determined as specified by ArchR116. DNs were identified as the cluster with higher gene scores for Th, a well-known DN marker, and confirmed by additional DN marker expression (e.g. Lmx1b, Foxa2, Foxa1, Slc6a3). The DN cluster is composed of 216 cells in total (113 from VTA-1 and 103 from the VTA-2). UMI duplicates were collapsed to one fragment. To visualize an approximation for gene expression, gene scores were calculated using the createArrowFiles (addGeneScoreMat = TRUE) function in ArchR.
For VTA snATAC-seq, paired-end reads were demultiplexed and mapped to the mouse genome (mm10) using the 10X Genomics Cellranger software. The two VTA snATAC-seq libraries were analyzed using ArchR software116. Doublets were removed following default parameters in ArchR. Next, low-quality cells (identified as TSS enrichment score < 4 and < 2500 unique fragments per cell) were removed for further analyses. Next, dimensionality reduction was performed using the Latent semantic indexing (LSI) dimensionality reduction method from ArchR, with default parameters (except: iterations = 10, resolution =0.2, varFeatures = 60000). The ArchR addHarmony function was ysed to run the Harmony algorithm for batch correction with default parameters, followed by clusters calling. Gene scores were determined as specified by ArchR116. DNs were identified as the cluster with higher gene scores for Th, a well-known DN marker, and confirmed by additional DN marker expression (e.g. Lmx1b, Foxa2, Foxa1, Slc6a3). The DN cluster is composed of 216 cells in total (113 from VTA-1 and 103 from the VTA-2). UMI duplicates were collapsed to one fragment. To visualize an approximation for gene expression, gene scores were calculated using the createArrowFiles (addGeneScoreMat = TRUE) function in ArchR.
Genome_build: mm10

source_name: mouse embryonic stem cells

extract_protocol: ATACseq libraries were generated from ~75,000 mESC nuclei following the Omni ATAC protocol114 with a modified transposition reaction: TAPS-DMF buffer (50 mM TAPS-NaOH, pH 8.5, 25 mM MgCl2, 50% DMF), 0.1 % Tween-20, 0.1% Digitonin, in PBS. 3 uL of the a Tn5 mix (5.6 g Tn5 and 0.143 volume of 100uM adapter mix) were added to the transposition reaction mix. Libraries were prepared as described in the Omni ATAC protocol. The final library was sequenced with an Illumina NextSeq 500 machine, according to manufacturer’s instructions, using paired-end 75 bp reads (150 cycles).

value: M

value: mouse embryonic stem cells


title: Arm

source_name: Total P14 cells at day 32 of LCMV Arm infection