title: RNAseq of G-NHX9-21FGAA_4 [NHX9_21FGAA_R4]

tag: cell surface marker


title: RNAseq of G-NHX9-21FGAA_2 [NHX9_21FGAA_R2]

status: Public on Oct 13 2021

type: SRA

city: MEMPHIS

first: QINGSONG

last: GAO

state: Tennessee

address: 262 DANNY THOMAS PLACE

country: USA

institute: ST JUDE CHILDREN'S RESEARCH HOSPITAL

library_source: transcriptomic

data_processing:
RNA sequencing was performed by the Hartwell Center at St. Jude Children’s Research Hospital. Libraries were prepared using the TruSeq Stranded Total RNA kit (Ilumina). 100 basepair, paired reads were generated by sequencing on the NovaSeq 6000Read alignment to the Mus musculus reference genome (mm10) was performed with STAR software (v2.7.0d). To evaluate gene expression level, the read count for each annotated gene was calculated using HTSeq (version 0.11.2). Differential gene expression and regularized log transformation (rlog) on raw count data were carried out using DESeq2. All the genes were ranked according to the fold-change and significance from differential analysis. GSEA was then performed using molecular signatures database (MSigDB) (version 6.2) C2 genes.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file with raw read count for each gene across the 35 samples.

molecule: total RNA

organism: Mus musculus

source_name: Mouse lineage negative hematopoietic stem and progenitor cells

growth_protocol: Cells were grown in Methocult M3434 with 10 ng/mL GM-CSF for one week

extract_protocol:
RNA was harvested using the Direct-zol RNA MiniPrep or MicroPrep kit and was quantified using the Qubit 2.0 fluorometer prior to library generation
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).
RNAseq: paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

value: Lineage negative

tag: tissue

value: bone marrow

tag: age

value: 8 weeks

tag: genotype

tag: cell line

tag: treatment


title: RNAseq of G-NHX9-21FGAA_1 [NHX9_21FGAA_R1]


title: Subject_7_AlcoholUseDisorder; Human postmortem caudate

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

description: miRNA transcriptome data

data_processing:
The Comprehensive Analysis Pipeline for miRNA Sequencing Data (CAP-miRseq) workflow [BMC Genomics. 2014; 15:423] was used for raw reads (in fastq files) pre-processing, alignment, mature/precursor/novel miRNA qualification and prediction.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
Small RNA-seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) (NEB, Ipswich, MA, USA) with 250 ng of total RNAs.
RNA libraries were prepared for sequencing using the protocol for use with NEBNext Small RNA Library Prep Set for Illumina

value: Human postmortem caudate

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Female

tag: batch

tag: rin

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Current

tag: liverclass

value: Cirrhosis


title: RNAseq of G-NHX9-21FGAA_3 [NHX9_21FGAA_R3]

tag: cell surface marker

tag: tissue


title: Subject_8_Control; Human postmortem caudate

description: miRNA transcriptome data

value: Control

value: Male

value: Left

value: Never

value: Steatosis


title: RNAseq of G-NHX9-8FA_5 [NHX9_8FA_R5]

tag: age

tag: genotype


title: Subject_6_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Respiratory

value: Normal


title: Subject_5_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data


title: Subject_4_AlcoholUseDisorder; Human postmortem caudate

description: miRNA transcriptome data

value: Toxicity


title: Subject_2_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Unknown


title: RNAseq of G-NHX9-8FA_3 [NHX9_8FA_R3]

value: Lineage negative

value: bone marrow

value: 8 weeks

tag: cell line

tag: treatment


title: Subject_3_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Human postmortem caudate

tag: aud status

tag: alcoholdailyuse(gram/day)

value: Female


title: Fibroblasts Thbs4-treated rep1 (Thbs4_1)

city: Tartu

first: Mariliis

last: Klaas

address: Riia 23

department: Institute of Molecular and Cell Biology

country: Estonia

institute: University of Tartu

description: Thbs4 treatment for 4 hours (culture medium from Thbs4-transfected HEK293 cells)

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using CutAdapt 1.16 with Python 3.6.4.
RNA STAR (Galaxy version 2.7.7a) was used for sequence alignment to reference genome GRCh38/h38.87 and featureCounts (Galaxy version 2.0.1) was used to count the number of reads.
Differential gene expression was analysed using DESeq2 package
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: tab-delimited text files include DESeq2 result values for each sample

source_name: Cultured skin fibroblasts

growth_protocol: Primary human fibroblasts were cultured in a growth medium containing 89% DMEM, 10% FBS and 1% Penicillin/Streptomycin solution (all Gibco, Invitrogen) on 60mm-diameter cell culture dishes (Falcon, Corning) until 70-80% confluency.

extract_protocol:
Total RNA was separated using RNeasy Mini Kit (Qiagen) according to manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HEK293 cells were transiently transfected with pcDNA3.1 expression vector containing human Thbs4 sequence. Medium containing secreted Thbs4 protein was collected and used for fibroblast stimulation. Fibroblasts were stimulated with Thbs4-conditioned medium or control medium (from pcDNA mock-transfected HEK293 cells) in 1:4 ratio for 4 h.

value: skin

value: Thbs4 treatment for 4 hours

tag: cell type

value: fibroblasts


title: Fibroblasts Thbs4-treated  rep2 (Thbs4_2)


title: RNAseq of G-NHX9-8FA_4 [NHX9_8FA_R4]


title: RNAseq of G-NHX9_5 [NHX9_R5]


title: Fibroblasts control rep2 (pcDNA_2)

description: control (medium from mock-transfected HEK293 cells)

value: control


title: RNAseq of G-NHX9-8FA_2 [NHX9_8FA_R2]


title: Subject_24_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: AlcoholUseDisorder

tag: Sex

value: Male

tag: batch

tag: rin

value: Cardiovascular

value: Current


title: RNAseq of G-NHX9-8FA_1 [NHX9_8FA_R1]


title: Subject_1_Control ; Human postmortem caudate

description: miRNA transcriptome data

value: Control

tag: brainweight

tag: brainph

tag: pmi

value: Left

value: Cardiac

value: Never

value: MildSteatosis


title: Fibroblasts control rep1 (pcDNA_1)


title: BM41

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

data_processing:
RNA-seq results were aligned to GRCh38.
UCSC Genome assembly GRCh38.p13 (GCA_000001405.28) genome annotation files (around 19,862 mainly protein-encoding genes but not including IGHM).
Reads were quality-checked and processed using the nf-core/rnaseq analysis workflow v1.3 pipeline consisting of Nextflow v19.04.1, FastQC v0.11.8 Cutadapt v2.4, Trim Galore! v0.5.0, STAR vSTAR_2.6.1d, HISAT2 v2.1.0, Picard MarkDuplicates v2.18.27, Samtools v1.9, featureCounts v1.6.4, StringTie v1.3.5, Preseq v2.0.3, deepTools, v3.2.0, RSeQC v3.0.0, MultiQCv1.7 software.
Raw count results were analyzed using edgeR (RNA-seq differential expression analysis, two groups) against hg38 to determine significantly regulated genes (criteria: fold change ≥2; p<0.05; low expression filter rpkm <1.0).
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Gene_rawcounts_BCP.txt

source_name: Mixed-lineage leukemia (MLL) cells

growth_protocol: Cells were not cultured.

extract_protocol:
RNA was extracted from frozen cell pellets using Trizol (ThermO-Fisher 315596026) and further purified using an RNEasy Mini kit (Qiagen #74104). Quality control analysis was done using Bioanalyzer RNA Nano and D1000Chips. Nucleic acid concentrations were determined by Qubit.
The mRNA library was prepared using an Illumina Truseq Stranded mRNA High Throughput Prep kit and samples were sequenced using an Illumina NextSeq 500 Mid-Output Sequencing Reagent kit (v2, 150 cycles), 132 M reads on an Illumina NextSeq 500 instrument.

treatment_protocol: Starting materials for isolation of control healthy precursor B cells were four BM samples (R7B1, R7B3, R7B6 and R7B11) from different donors depleted of CD34+ stem cells. R7B11 was not further processed, whereas R7B6 was enriched in CD19+ B cells, and R7B1 and R7B3 were enriched for both B‑ and T-cells [CD19 and TCRα/β]. To isolate normal CD19+CD10+ precursor B-cells, around 2x10^9  viably frozen normal bone marrow cells from each sample were applied to EasySep™ Release Human CD19 Positive Selection Kit (STEMCELL Technologies, Vancouver, BC, Canada, Cat#17754) and EasySep™ Human CD10 Positive Selection Kit (STEMCELL Technologies, Cat#18358) columns. MLL samples were BM0 [(11q23) relapse sample, 98% blasts], BM37 [(46XY, t(9;11) diagnosis, 98% blasts], and BM41 (60% blasts, MLL rearranged (11q23; t9;11) 46XY]. Ficoll‑Plaque Plus (GE Healthcare, Cat#17-1440-02) centrifugation was used to remove red blood cells, according to manufacturer’s instructions and after washing viably, frozen with DMSO. Viably frozen cells were thawed and washed with twice with ice-cold DPBS (500xg, 4 min, 4°C). Each sample, consisting of 2-3x106 total cells was used for RNA isolation.

value: Bone marrow

value: CD19+ leukemic precursor B cells

tag: disease state

value: leukemia


title: BM37


title: RNAseq of G-NHX9_4 [NHX9_R4]

value: Lineage negative

value: bone marrow

value: 8 weeks


title: RNAseq of G-NHX9_3 [NHX9_R3]


title: R7B11

source_name: Normal bone marrow (BM) pre-B cells

value: CD19+CD10+ precursor B cells

value: normal control


title: BM0


title: Subject_22_Control; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: Female

tag: leftrightbrain

tag: causeofdeathcategory

tag: smoking

tag: liverclass

value: Normal


title: Subject_21_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

tag: tissue

value: AlcoholUseDisorder

value: Male

value: Current

value: Cirrhosis


title: R7B6


title: Subject_23_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Right

value: Toxicity

value: Never

value: Steatosis


title: RNAseq of G-NHX9_1 [NHX9_R1]

tag: cell surface marker

tag: age

value: 11 weeks

tag: genotype

tag: cell line


title: RNAseq of Empty_5 [Empty_R5]

value: Lineage negative

value: 10 weeks

value: Empty

tag: treatment


title: R7B3

value: Bone marrow

tag: cell type

value: CD19+CD10+ precursor B cells


title: Subject_18_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

value: Hepatic


title: RNAseq of G-NHX9_2 [NHX9_R2]

value: bone marrow

value: 8 weeks


title: RNAseq of Empty_3 [Empty_R3]


title: RNAseq of Empty_1 [Empty_R1]


title: Subject_16_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: AlcoholUseDisorder

value: Male

tag: rin

tag: brainweight

tag: brainph

tag: pmi

value: Left


title: Subject_17_Control ; Human postmortem amygdala

description: miRNA transcriptome data

value: Control

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Vascular

tag: smoking

value: Normal


title: SKMEL30 Induced 18hours Rep2

city: London

first: Veronica

last: Kinsler

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Adapter & quality trimmed at sequencing facility prior to release (trimmomatic v0.36, min qual=20, MINLEN=20bp)
Adapter trim with cutadapt 1.5
Align with Star 2.2.2a
Merge lane level bam files with samtools 1.8
Assess expected counts per feature with RSEM 1.3.0
Normalise and call differentially expressed genes with DESeq2
Genome_build: GRCh38-r86
Supplementary_files_format_and_content: DESeq normalised counts in a tab delimited text file

source_name: Melanoma cell lines

growth_protocol: Inducible stable overexpression cell lines, cells seeded in 6 well plates

extract_protocol:
RNA extracted using Qiagen RNeasy
KAPA mRNA HyperPrep Kit

treatment_protocol: doxycycline at 1ul/ul to induce expression of the construct in relevant samples


title: BTSC268, X+0

type: genomic

city: Homburg (Saar)

first: Marc

last: Remke

state: Saarland

address: Kirrberger Straße 100, Gebäude 9

department: Pediatric Translational Oncology Lab

country: Germany

institute: Universitätsklinikum des Saarlandes

description: GBM cell line

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC chip according to standard protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: idat files were imported into Partek Genomic Suite and processed using Functional normalization.

molecule: genomic DNA

source_name: human brain

label_protocol: Standard Illumina Protocol

growth_protocol: BTS cells grown in Neurobasal, other cell lines grown in DMEM+F12 medium

extract_protocol: Genomic DNA was extracted and purified from cell culture samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: samples were harvested at either passage 0 or passage 30

tag: passage

tag: gender

value: male

tag: tissue

value: brain

tag: disease state

value: glioblastoma


title: Subject_15_Control; Human postmortem amygdala

description: miRNA transcriptome data

value: Female

value: Cardiac

value: Current

tag: liverclass


title: BTSC349, X+30

description: GBM cell line

tag: cell line

value: female


title: Huh7-siUPF1-2

city: Seoul

first: Suman

last: Lee

address: FTC, 222 Wangsimni-ro, Seongdong-gu

country: South Korea

institute: Hanyang university

data_processing:
Illumina Pipeline (CASAVA) v1.8.2 used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FastQC v0.11.7 and Trimmomatic v0.38, then mapped to mm10 whole genome using HISAT2 v2.1.0
And then, transcript assembly of known transcripts, novel transcripts, and alternative splicing transcripts was processed by StringTie v1.3.4d (Pertea, Mihaela, et al., 2015, 2016)
Base on the result of that, expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample
The expression profiles are used to do additional analysis such as DEG (Differentially Expressed Genes)
Genome_build: UCSC hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: Human hepatocellular carcinoma

extract_protocol:
RNA was isolated using Trizol® reagent (Thermo Fisher Scientific, Waltham, MA, USA)
Library construction was performed by Macrogen Inc. (Macrogen, Seoul, Korea). 1 µg of total RNA was used to construct cDNA libraries with the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA).

tag: cell type

value: Liver cancer cell line

tag: treatment

value: UPF1 siRNA


title: RNAseq of Empty_4 [Empty_R4]

tag: cell surface marker

value: Lineage negative

value: bone marrow

tag: age

value: 9 weeks

tag: genotype

value: Empty


title: Huh7-siCtrl-2

value: Scrambled siRNA


title: BTSC233, X+30

description: GBM cell line


title: Subject_19_Control; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

tag: batch

tag: rin

tag: brainweight

value: Right

value: Congestion


title: BTSC349, X+0

description: GBM cell line

tag: passage

value: brain


title: R7B1

value: Bone marrow

value: CD19+CD10+ precursor B cells

value: normal control


title: Subject_20_Control; Human postmortem amygdala

description: miRNA transcriptome data

value: Female

tag: brainph

tag: pmi

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Toxicity

tag: smoking

value: Unknown


title: CD34cre_FAI4W

city: Hangzhou

first: Qingbo

last: Xu

state: Zhejiang

address: 79 Qingchun Road

department: Department of Cardiology

country: China

institute: First Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Data were processed following standard protocols using Cell Ranger version 3.1.0.
Cellranger mkfastq was used to demultiplex raw base call files into fastq files.
Cellranger count was used to perform alignment, filtering, barcode counting, UMI counting, and to generate feature-barcode matices.
Genome_build: mm10
Supplementary_files_format_and_content: TSV data for genes and barcodes; MTX data for gene expression matrix

source_name: Femoral artery

extract_protocol:
Mice were euthanized and perfused with PBS and femoral arteries were harvested and placed in a petri dish containing DMEM with 10% fetal bovine serum (FBS) on ice. Perivascular adipose tissues and connective tissues were carefully removed. After collecting all arteries, to obtain single cell suspensions, arteries were washed with PBS for three times, cut into fine pieces and incubated with 1 mg/ml papain digesting solution [1 mg/ml papain (Sigma, P4762), 0.5 mg/ml 1,4-Dithioerythritol (Sigma, D8255), 0.156 mg/ml Taurine (Sigma, T8691), 0.25 mg/ml bovine serum albumin in PBS]. The digestion was performed at 37 ℃ water bath with reciprocal shaking. Detached cells in the supernatant were collected and suspended in DMEM with 10% FBS. Femoral tissues were then incubated with fresh digestion solutions every 10 min. After 3-4 digestions, the remaining tissues were incubated with 1 mg/ml papain digesting solution and 2 mg/ml collagenase I (Gibco, 17018029) and 1 mg/ml dispase II (Sigma, D4693) in Hank’s balanced salt solution containing calcium and magnesium. Detached cells were collected and fresh digestion solutions were added until the tissues dissolved completely. All digested cells from one sample were pooled together at the end of the digestion process. After sufficient digestion, cells were filtered through a 40-μm cell strainer, and the collected cells were centrifuged 8 min at 500 g speed at 4 ℃. Subsequently, cell pellet was suspended in PBS and stained with LIVE/DEAD ™ Fixable Near-IR Dead Cell Stain Kit and Hoechst 33342 for 20 mins on ice. After PBS washing, cells were resuspended in PBS and single nucleated live cells (Hoechst+ & Dead Cell Stain-) were sorted into PBS with 0.04% BSA using a Flow Cytometer. Samples were subjected to scRNA-seq. A ChromiumTM Single Cell 3' Reagent Kit v2 or V3 chemistry (10x Genomics) was used and a standard protocol was followed. The library was generated and sequenced on a Novaseq6000 PE150 platform (Illumina) with paired-end 150 bp sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

tag: tissue

value: Femoral artery

tag: time point

value: 4 weeks post injury


title: GBM-1, X+0

description: GBM cell line

tag: cell line

tag: gender

value: male

tag: disease state

value: glioblastoma


title: SKMEL30 Induced 18hours Rep3

tag: treatment


title: BTSC268, X+30

description: GBM cell line


title: SKMEL30 Induced 18hours Rep1


title: Subject_14_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Current

tag: liverclass

value: Cirrhosis


title: Subject_12_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: Male

tag: batch

tag: rin

tag: brainweight

value: Cardiac

value: Normal


title: Huh7-siUPF1-1

tag: cell type

value: Liver cancer cell line

value: UPF1 siRNA


title: Subject_11_Control ; Human postmortem amygdala

description: miRNA transcriptome data

value: Control

tag: brainph

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Congestion


title: GBM-1, X+30

description: GBM cell line

tag: passage

tag: tissue

value: brain


title: SKMEL30 Induced 6hours Rep3

tag: cell line


title: Subject_13_Control ; Human postmortem amygdala

description: miRNA transcriptome data

value: Left

tag: smoking

value: Never


title: C57_FA

tag: strain

value: Femoral artery

tag: genotype

value: wild type

tag: time point

value: normal


title: Subject_10_Control ; Human postmortem amygdala

description: miRNA transcriptome data

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex


title: Huh7-MYC-1

tag: treatment

value: Control MYC vector


title: JHH520, X+30

description: GBM cell line

tag: gender

value: female

tag: disease state

value: glioblastoma


title: BTSC233, X+0

description: GBM cell line


title: SKMEL30 Induced 6hours Rep2


title: Huh7-MYC-2

tag: cell type


title: JHH520, X+0

description: GBM cell line


title: Huh7-siCtrl-1

value: Scrambled siRNA


title: Huh7-MYC-UPF1-2

value: MYC-UPF1 Overexpression vector


title: Huh7-MYC-UPF1-1


title: Indole 12h Rep3

city: St. Louis

first: Lisa

last: Funkhouser-Jones

state: MO

address: 660 Euclid Ave

data_processing:
Demultiplexed fastq files were imported into Partek Flow (Partek, Inc.) and mapped to the Homo sapiens hg38 genome build (NCBI GenBank assembly ID GCA_000001405.15) using the STAR 2.7.8a aligner.
The number of reads mapping to each gene was quantified based on the human Ensembl Transcripts release 100. Gene expression values were normalized across samples by dividing the number of reads per gene by the total number of reads per sample to obtain counts per million (CPM) values.
A pair-wise comparison of indole-treated (6 total) and DMSO-treated samples (5 total) was performed using the Partek gene-specific analysis (GSA) algorithm using default parameters. Genes were considered significantly differentially expressed if the FDR-corrected P value was less than 0.05 and the absolute fold change was greater than 2.
Genome_build: Homo sapiens hg38 genome build (NCBI GenBank assembly ID GCA_000001405.15)
Supplementary_files_format_and_content: comma-separated values (.csv) file containing CPM values for all genes in each sample

source_name: colon cancer cell line

growth_protocol: HCT-8 cells were plated at 9 x 10^5 cells per well in 12-well culture plates and grown in RPMI 1640 ATCC Modification medium (Thermo Fisher A14091-01) supplemented with 10% fetal bovine serum (Gibco) for ~24h at 37C, 5% CO2.

extract_protocol:
Cells were lysed in RLT buffer (QIAGEN) plus 1% ꞵ-mercaptoethanol (Sigma) and homogenized using a QIAshredder column (QIAGEN). RNA was extracted using the RNeasy Mini kit (QIAGEN) and treated with the DNA-free DNA Removal kit (Thermo Fisher Scientific).
Total RNA from three technical replicates per treatment condition was submitted to the Genome Access Technology Center (Washington University School of Medicine) for library prep and sequencing. RNA integrity was determined using an Agilent Bioanalyzer (all samples had an RIN of 10) and library preparation was performed with 5 – 10 μg of total RNA per sample. Ribosomal RNA was removed by poly-A selection using Oligo-dT beads (mRNA Direct kit, Life Technologies). mRNA was then fragmented and reverse transcriptase buffer by heating to 94 °C for 8 min. mRNA was reverse transcribed using SuperScript III RT enzyme (Life Technologies) and random hexamers, per manufacturer’s instructions. A second strand reaction was performed to yield ds-cDNA, and then cDNA was blunt-ended before adding an A base to the 3’ ends and ligating Illumina sequencing adapters to both ends. Ligated fragments were amplified for 12 – 15 cycles using primers incorporating unique dual index tags, then sequenced on an Illumina NovaSeq 6000 to generate 150 bp, paired-end reads.

treatment_protocol: Cells were infected with ~4 x 10^6 excysted Cryptosporidium parvum sporozoites per well and incubated for 4 h before washing 2X with DPBS to remove extracellular parasites. Cells were then treated with either indole (880 μM) or 1% DMSO in cell culture medium for an additional 4 h or 12 h.

value: indole

tag: treatment duration

value: 12 hours


title: RNAseq of Empty_2 [Empty_R2]

tag: cell surface marker

value: Lineage negative

value: bone marrow

tag: age

value: 8 weeks

value: Empty


title: Subject_8_Control; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: Control

value: Male

tag: batch

tag: rin

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Cardiac

tag: liverclass

value: Steatosis


title: Indole 12h Rep2

institute: Washington University School of Medicine

tag: cell line


title: Indole 12h Rep1


title: SKMEL2 Induced 18hours Rep2


title: BTSC23, X+30

description: GBM cell line

tag: passage

tag: tissue

value: brain


title: SKMEL2 Induced 18hours Rep3

tag: treatment


title: FIBCL biological rep1

city: Nanjing

first: zhen

last: chen

state: Jiangsu

address: 12 Xuefu-Road, Pukou District

department: Model Animal Research Center

institute: Nanjing university

description: small molecules FIBCL induced neuron from SGC sphere

data_processing:
The raw paired end reads were trimmed and quality controlled by SeqPrep (https://github.com/jstjohn/SeqPrep) and Sickle (https://github.com/najoshi/sickle) with default parameters.
RNA-seq reads were separately aligned to reference genome with orientation mode using TopHat (http://tophat.cbcb.umd.edu/, version2.0.0)
The TopHat-Cufflinks pipeline was used to predict gene isoforms from our RNA-seq data.
To identify DEGs (differential expression genes) between two different samples, the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Supplementary_files_format_and_content: the expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) method.

source_name: cultured cells

growth_protocol: Both sexes of the 6-8 postnatal 3 to 21 days (P3-P21) mice spiral ganglia were dissected in HBSS (Invitrogen 14065056) at pH 7.4 on ice for tissue harvesting. The stria vascularis, vestibule and the organ of Corti were removed carefully with forceps (Dumont) to dissect the modiolus. And then the modiolus were digested with Trypsin/EDTA (Sigma 59418C) and DNase I (20 U/ml) at 37°C in a total volume of 50 µl for ~15 min with shaking at 300 rpm/min (Thermo) in 1.5 ml EP tube. Dissociation was terminated by adding 0.4 ml SCM media containing DMEM/F12 (HyClone 36254) supplemented with B27 (Thermo 17504044) and N2 (Thermo 17502048) supplement, 20 ng/ml EGF (Peprotech 315-09), 10 ng/ml bFGF (Peprotech 450-33), 50 ng/ml IGF (Peprotech 250-19) and 50 ng/ml heparan sulfate (MCE HY-101916). The samples were then carefully triturated with 1 ml pipette tips and next with 200 µl tips, followed by suspension with 1ml SCM medium.  The cell suspension was then passed through a 70-µm cell strainer, and spin at 300 g for 5-10 min. A small white ball should be observed at the bottom and then carefully aspirate the supernatant. SCM medium were added to resuspend and count cells, and then the cells were plated in 6-well dish (Corning 3471). For propagation, the cochlear glial spheres were harvested after 5-7 days.

extract_protocol:
The induction media (IM) for small molecule reprogramming contains Neurobasal Medium (Thermo 21103049), supplemented with B27 (Thermo 17504044) and N2 (Thermo 17502048), 50 ng/ml bFGF (Peprotech 450-33), GlutaMax (Thermo 35050061), penicillin-streptomycin and bFGF (100 ng/ml), with small molecules Forskolin (20 µM), ISX9 (20 μM), I-BET (1 μM), Chir99021 (10 μM) (all from Selleck) and LIF (1000 U/ml). Half of the medium was replaced every 2-3 days.  Differentiated cells were analyzed after 14 days.
RNA-seq transcriptome librariy was prepared following TruSeqTM RNA sample preparation Kit from Illumina (San Diego, CA) using 1μg of total RNA. Shortly, messenger RNA was isolated according to polyA selection method by oligo(dT) beads and then fragmented by fragmentation buffer firstly. Secondly double-stranded cDNA was synthesized using a SuperScript double-stranded cDNA synthesis kit (Invitrogen, CA) with random hexamer primers (Illumina).  Then the synthesized cDNA was subjected to end-repair, phosphorylation and ‘A’ base addition according to Illumina’s library construction protocol. Libraries were size selected for cDNA target fragments of 200–300 bp on 2% Low Range Ultra Agarose followed by PCR amplified using Phusion DNA polymerase (NEB) for 15 PCR cycles.

treatment_protocol: To induce neuronal differentiation, cochlear glial spheres were plated on 96-well plate (Thermo 310109008) coated with Poly-L-ornithine (Sigma P4957) and 10ng/ml Laminin (Corning 354232) in SCM for 12-24 h, and then replaced with SCDM containing DMEM/F12 (HyClone 36254) supplemented with B27 (Thermo 17504044) and N2 (Thermo 17502048) supplement, 50 ng/ml BDNF (Stemcell 78005), 50 ng/ml NT3 (Stemcell 78074). Additional control SCDM/FGF is SCDM supplemented with bFGF (100 ng/ml).  The induction media (IM) for small molecule reprogramming contains Neurobasal Medium (Thermo 21103049), supplemented with B27 (Thermo 17504044) and N2 (Thermo 17502048), 50 ng/ml bFGF (Peprotech 450-33), GlutaMax (Thermo 35050061), penicillin-streptomycin and bFGF (100 ng/ml), with small molecules Forskolin (20 µM), ISX9 (20 μM), I-BET (1 μM), Chir99021 (10 μM) (all from Selleck) and LIF (1000 U/ml). Half of the medium was replaced every 2-3 days. Differentiated cells were analyzed after 14 days.

tag: strain

value: mix background of C57Bl6 and FVB/N

value: Cochlea

value: postnatal day 4


title: DMSO 12h Rep3

value: DMSO


title: SKMEL30 Untreated  Rep1

value: Untreated


title: BTSC23, X+0

description: GBM cell line

tag: gender

value: female

tag: disease state

value: glioblastoma


title: SKMEL30 Untreated  Rep2


title: CD34cre_normal_FA

value: Femoral artery

tag: genotype

tag: time point

value: normal


title: SKMEL30 Induced 6hours Rep1


title: CD34cre_FAI2W

value: 2 weeks post injury


title: SKMEL2 Induced 6hours Rep3


title: FIBCL biological rep3

tag: age


title: Subject_4_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Female

tag: batch

tag: rin

value: Right

value: Toxicity

tag: smoking

value: Current

value: Normal


title: SGC SCDM/FGF biological rep1

description: SCDM/FGF induced neuron from SGC sphere


title: SKMEL30 Untreated  Rep3


title: C57_FACS_CD34

value: wild type


title: Subject_9_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: Male

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

tag: liverclass

value: Steatosis


title: SGC SCDM biological rep3

description: SCDM induced neuron from SGC sphere

tag: strain

value: mix background of C57Bl6 and FVB/N

tag: tissue

value: Cochlea

value: postnatal day 4


title: SGC SCDM biological rep2

description: SCDM induced neuron from SGC sphere


title: SKMEL2 Induced 6hours Rep1

tag: cell line

tag: treatment


title: NCH644, X+0

description: GBM cell line

tag: passage

tag: gender

value: female

value: brain

tag: disease state

value: glioblastoma


title: Subject_2_Control ; Human postmortem amygdala

description: miRNA transcriptome data

tag: aud status

value: Control

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Cardiac

value: Unknown


title: SKMEL2 Untreated  Rep3

value: Untreated


title: Indole 4h Rep2

value: indole

tag: treatment duration

value: 4 hours


title: SGC SCDM/FGF biological rep3

description: SCDM/FGF induced neuron from SGC sphere

tag: age


title: SGC SCDM biological rep1

description: SCDM induced neuron from SGC sphere


title: SKMEL2 Induced 18hours Rep1


title: SGC sphere biological rep3

description: SGC sphere from cochlear glial cells


title: miRNA-seq_Ethanol-unexposed rep 2

description:
Ethanol untreated
Sample_4

source_name: hESC-derived neural cells

growth_protocol: hESC-derived cortical interneurons were cultured in the neuronal maturation media

extract_protocol:
hESC-derived neural cells (exposed or unexposed to ethanol) were collected, flash frozen on dry ice, and installed at -80 degree freezer. Total RNAs were extracted using the QIAGEN miReasy Mini Kit.
Small RNA-seq libraries were generated using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Set 1) (NEB, Ipswich, MA, USA) with 250 ng of total RNAs.
RNA libraries were prepared for sequencing using the protocol for use with NEBNext Small RNA Library Prep Set for Illumina

treatment_protocol: Cultured hESC-derived cortical interneurons were exposed (or unexposed) to ethanol at a concentration of around 50-100 mM (equivalent to blood alcohol levels of heavy or intoxicated drinkers) for 7 days.

value: hESC-derived neural cells

value: Cultured for 7 days without ethanol exposure

value: H1 ESC


title: FIBCL biological rep2


title: DMSO 12h Rep1

value: DMSO

value: 12 hours


title: SKMEL2 Untreated  Rep1


title: DMSO 4h Rep2


title: SGC sphere biological rep1

description: SGC sphere from cochlear glial cells

value: mix background of C57Bl6 and FVB/N


title: NCH644, X+30

description: GBM cell line


title: DMSO 12h Rep2


title: Subject_7_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

value: AlcoholUseDisorder

value: Female

tag: batch

tag: rin

tag: brainweight

tag: brainph

value: Right

tag: smoking

value: Current

value: Cirrhosis


title: Subject_6_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

tag: pmi

tag: leftrightbrain

tag: causeofdeathcategory

value: Respiratory

tag: liverclass

value: Normal


title: Subject_3_Control ; Human postmortem amygdala

description: miRNA transcriptome data

tag: tissue

value: Control

value: Left

value: Cardiac


title: Hbo1-KO H3K14ac - replicate 2

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Library strategy: CUT&Tag
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome by Rsubread version 2.0.1
Read counts were summarized by genomic regions - Gene bodies, TSS - 5 kb to TSS regions, and TES to TES + 5 kb regions - using the Rsubread's featureCounts function and mm10 NCBI annotation.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files for gene body counts; columns represent Entrez Gene ID, total gene length (total base count of all exons) and the number of reads mapping to that gene. Tab-delimited text files for other region counts around TSS and TES of genes; columns represent Entrez Gene ID, and the number of reads mapping to that region.

source_name: Bone marrow Haematopoietic stem cells

extract_protocol:
Cells isolated by FACS
Libraires generated using Tn5 transposase during the CUT&Tag protocol

treatment_protocol: mice treated with poly(I:C) to induce Mx1-cre recombinase and generate Hbo1 KO and heterozygous controls

tag: background strain

value: Bone marrow

tag: cell type

value: LSK cells

tag: gender

value: Male

tag: genotype

value: Hbo1def/def; T/+

tag: chip antibody

value: H3K14ac (abcam, ab52946)


title: Hbo1 heterozygous control HBO1 (KAT7)

source_name: Bone marrow Progenitor cells

value: Hbo1def/+; T/+


title: SKMEL2 Induced 6hours Rep2

tag: cell line

tag: treatment


title: SGC SCDM/FGF biological rep2

description: SCDM/FGF induced neuron from SGC sphere

tag: strain

value: mix background of C57Bl6 and FVB/N

value: Cochlea

tag: age

value: postnatal day 4


title: miRNA-seq_Ethanol-unexposed rep 1

description:
Ethanol untreated
Sample_3

value: hESC-derived neural cells

value: Cultured for 7 days without ethanol exposure

value: H1 ESC


title: Subject_5_AlcoholUseDisorder; Human postmortem amygdala

description: miRNA transcriptome data

value: Human postmortem amygdala

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Female

tag: batch

tag: rin

tag: brainweight

value: Right

value: Respiratory

value: Current

value: Cirrhosis


title: Subject_1_Control ; Human postmortem amygdala

description: miRNA transcriptome data

value: Control

value: Male

tag: brainph

tag: pmi

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

tag: smoking

value: Never

tag: liverclass

value: MildSteatosis


title: Hbo1-KO H3K14ac - replicate 1

tag: background strain

tag: tissue

value: Bone marrow

tag: cell type

value: LSK cells

tag: gender

tag: genotype

value: Hbo1def/def; T/+

tag: chip antibody

value: H3K14ac (abcam, ab52946)


title: MLKL_KO_IR_rep2

city: Shanghai

first: Liufu

last: Deng

address: Room 1002, West #5 Building, 280 South Chongqing Road, Shanghai 200025, China

institute: Shanghai Institute of Immunology; Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine

description:
MLKL_KO_IR_8
transfected with Lenti-MLKL-gRNA3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5 with default setting
Stringtie v1.3 was used to calculate the read count for each gene
Genome_build: mm10
Supplementary_files_format_and_content: excel file containing read count for each gene

growth_protocol: MC38 cells were cultured at 37℃ with 5% CO2 in Dulbecco’s modified Eagle’s medium-high glucose media (Hyclone) containing 10% FBS (Gemini), 100 U/mL penicillin (Thermo Fisher Scientific), 100 mg/mL streptomycin (Thermo Fisher Scientific) and 10 mM HEPES (Thermo Fisher Scientific).

extract_protocol:
Total RNA from each sample was extracted using Trizol Reagent (ThermoFisher Scientific) following standard protocols. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: WT and MLKL_KO cells were seeded in 6-well plate overnight, then were subjected to single fraction of X-ray (15 Gy) or not. 60 hours later, total RNA from each sample was extracted using Trizol Reagent following standard protocols.

tag: strain background

tag: cell line

tag: treatment

value: IR

value: MLKL_KO (MLKL-gRNA3)


title: SKMEL2 Untreated  Rep2

value: Untreated


title: miRNA-seq_Ethanol-exposed rep 2

description:
Ethanol treated
Sample_2

value: hESC-derived neural cells

value: Ethanol (50-100 mM) exposure for 7 days

value: H1 ESC


title: Indole 4h Rep3

value: indole

tag: treatment duration

value: 4 hours


title: Ethanol-unexposed rep 1

description: Ethanol untreated

data_processing:
The sequence reads were processed using the RNA-seq processing pipeline Pipeliner [Front Genet. 2019; 10:614] workflow.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
hESC-derived neural cells (exposed or unexposed to ethanol) were collected, flash frozen on dry ice, and installed at -80 degree freezer. Total RNAs were extracted using the QIAGEN miReasy Mini Kit.
The Illumina® TruSeq® Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) was used to construct mRNA-seq libraries with 1 ug of total RNAs as the starting material.

value: Cultured for 7 days without ethanol exposure


title: DMSO 4h Rep1

value: DMSO


title: Indole 4h Rep1


title: Human NODAL-KO embryoids at 48h

city: Syracuse

first: Yi

last: Zheng

state: New York

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

data_processing:
see the associated publication
Genome_build: GRCh38.p13 and Pan_tro_3.0
Supplementary_files_format_and_content: .Rd files are the output of R Studio containing the data anlaysis ressults. The .Rd files can be loaded into RStudio using "load ("file_name.Rd")", and analyzed using the Seurat R package (https://satijalab.org/seurat/). In case of difficulties accessing the data, please contact Dr. Yi Zheng (zhengum@umich.edu)

molecule: polyA RNA

source_name: microfluidic embryoids

growth_protocol: see the associated publication

extract_protocol:
see the associated publication
10x genomics

treatment_protocol: see the associated publication


title: Human microfluidic embryoids at 24, 36 48 hours

value: wildtype


title: MLKL_KO_nonIR_rep2

description:
MLKL_KO_nonIR_6
transfected with Lenti-MLKL-gRNA3

value: nonIR


title: miRNA-seq_Ethanol-exposed rep 1

description:
Ethanol treated
Sample_1


title: Hbo1 heterozygous control H3K14ac - replicate 2

value: Male

value: Hbo1def/+; T/+


title: MLKL_KO_IR_rep1

description:
MLKL_KO_IR_7
transfected with Lenti-MLKL-gRNA3


title: MLKL_KO_nonIR_rep1

description:
MLKL_KO_nonIR_5
transfected with Lenti-MLKL-gRNA3


title: HUVECs, NET4hDF20_3

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

data_processing:
Alignment with STAR (v2.6.1b)
Assigned count estimates to genes with RSEM (v1.3.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: raw counts

source_name: normal human umbilic endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs) purchased from ATCC were cultured in EBM supplemented with EGM-2MV singleQuots (Lonza) without hydrocortisone in 0.2% gelatin-coated tissue culture plates.

extract_protocol:
Total RNA from cells was isolated using RNeasy Plus Mini Kit (74134, Qiagen) according to manufacturer’s instructions. Sequencing was performed by the UM Advanced Genomics Core, with libraries constructed and subsequently subjected to 150 paired-end cycles on the NovaSeq-6000 platform (Illumina).
NEB RNA Ultra II, 151 PE

treatment_protocol: Triplicates treated with vehicle, NETs, or NETs + defibrotide

value: HUVEC

value: normal human umbilic endothelial cells


title: WT_IR_rep2

description:
WT_IR_4
transfected with Lenti-CRISPR-Ctrl

value: WT (CRIPSR-Ctrl)


title: HUVECs, NET4hDF20_2


title: Hbo1 heterozygous control H3K14ac - replicate 1

value: Bone marrow

value: LSK cells

value: H3K14ac (abcam, ab52946)


title: Ethanol-exposed rep 1

description: Ethanol treated

value: hESC-derived neural cells


title: HUVECs, NET4hDF20_1


title: HUVECs, NET4h_3


title: Ethanol-exposed rep 2

description: Ethanol treated

value: Neural cell

value: Ethanol (50-100 mM) exposure for 7 days


title: WT_nonIR_rep2

description:
WT_nonIR_2
transfected with Lenti-CRISPR-Ctrl


title: WT_IR_rep1

description:
WT_IR_3
transfected with Lenti-CRISPR-Ctrl

value: IR


title: SGC sphere biological rep2

description: SGC sphere from cochlear glial cells

tag: strain

value: mix background of C57Bl6 and FVB/N

value: Cochlea

tag: age

value: postnatal day 4


title: HUVECs, NET4h_1


title: Ethanol-unexposed rep 2

description: Ethanol untreated

value: Cultured for 7 days without ethanol exposure

value: H1 ESC


title: HUVECs, NET4h_2


title: HUVECs, NT_2

value: NT


title: HEK293-FlpInTREx-rep2-5hmC

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description: 1971073_SJNORM056733_C214-ActiveMotif_55010_HEK293_FlpInTREx_062820-5hmC-AB2

data_processing:
library strategy: hMeDIP
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP9 (v1.11)
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: bigwig

source_name: HEK293 cells

growth_protocol: Cells were grown in Gibco DMEM medium plus 10% FBS with Pen-Strep, Zeocin and Blasticidin under 37 degree.

extract_protocol:
Genomic DNA of cells was extracted by using the QIAamp DSP DNA Mini Kit (Qiagen, 61304). 20 μg genomic DNA was sonicated to 200-600 bp by using a Bioruptor Plus sonication device (Diagenode, B01020001) in 300 μL 10 nM Tris-HCl pH 8.5 buffer. Set aside 100 ng fragmented DNA for use as input DNA. Set up a 100 μL reaction mixture containing 1 μg sonicated DNA, 1 μL provided Protease Inhibitor Cocktail, 10 μL provided Buffer C, and 4 μL provided 5-hydroxymethylcytidine pAb. Incubate overnight with end-to-end rotation at 4°C. Add 25 μL provided Protein G magnetic beads to each tube and incubate for 2 hours with end-to-end rotation at 4°C. Collect the beads by using the provide magnetic stand. Wash the beads three times with ice cold Buffer C and then two times with the ice cold provided Buffer D. Resuspend the washed beads with 50 μL provided Elution Buffer AM2 and incubate for 15 minutes at room temperature with end-to-end rotation. Add 50 μL provided Neutralization buffer and pipette up and down to mix. Use magnetic stand to pellet the beads and transfer the supernatant to a fresh tube. All the inputs and supernatants are then submitted to DNA purification by using the QIAquick PCR Purification Kit (Qiagen, 28106).
DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay. HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina) was used.

treatment_protocol: No treatmernt before DNA extraction.

tag: cell line full name

value: Flp-In T-REx HEK293 (Invitrogen, R78007)

value: human embryonic kidney cells

tag: antibody

value: hMeDIP Kit (Active Motif, 55010)


title: WT_nonIR_rep1

description:
WT_nonIR_1
transfected with Lenti-CRISPR-Ctrl

value: nonIR

value: WT (CRIPSR-Ctrl)


title: HEK293-PROSER1KO1D3-rep2-5hmC

description: 1971074_SJNORM056733_C215-ActiveMotif_55010_HEK293_PROSER1KO1D3_062820-5hmC-AB2


title: HEK293-FlpInTREx-rep1-5hmC

description: 1955007_SJNORM056733_C183-ActiveMotif_55010_HEK293_FlpInTREx_030920-5hmC-AB2


title: HEK293-PROSER1KO1D3-hMeDIPseq-INPUT

description: 1971072_SJNORM056733_C213-HEK293_PROSER1KO1D3_062820-INPUT


title: PROSER1KO1D3_WGBS_rep2

description: Genome-wide bisulfite sequencing (WGBS)

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore (v0.6.5), with settings: -q 30 --fastqc --phred33 --illumina --stringency 1 -e 0.1 --paired --length 15 -- clip_R1 10 --clip_R2 10 --three_prime_clip_R1 10 --three_prime_clip_R2 10
Duplicated reads were marked with Picard toolkit (v2.0.1)
The methylation ratio in various contexts was extracted by methratio.py from BSMAP (v2.9.0) with settings: -m 17 -x 600 -z 33 -f 5 -g 3 -r 0 -u -R
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: extracted methylation data in tab separated TXT file format; fields are: chr, pos, strand, context, ratio, eff_CT_count, C_count, CT_count, rev_G_count, rev_GA_count, CI_lower, CI_upper

extract_protocol:
Genomic DNA of cells was extracted by using the QIAamp DSP DNA Mini Kit (Qiagen, 61304).
Genomic DNA was bisulfite converted using the EZ-96 DNA Methylation-Gold MagPrep (Zymo Research). Libraries were prepared from converted DNA using the Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences). Libraries were analyzed for insert size distribution on a 2100 BioAnalyzer High Sensitivity kit (Agilent Technologies), 4200 TapeStation D1000 ScreenTape assay, or Caliper LabChip GX DNA High Sensitivity Reagent Kit (PerkinElmer). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies) or low pass sequencing with a MiSeq nano kit (Illumina).

tag: cell full name

tag: genotype/variation

value: PROSER1 KO


title: HUVECs, NT_1

value: HUVEC

value: normal human umbilic endothelial cells


title: HEK293-FlpInTREx-hMeDIPseq-INPUT

description: 1971071_SJNORM056733_C212-HEK293_FlpInTREx_062820-INPUT


title: AGM-WT-2_FKDL192530634-1a

city: Beijing

first: Jia

last: Yu

address: Dong Dan San Tiao 5, Dongcheng District

institute: Peking Union Medical College

description: E10.0 HEC (bulk)

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were firstly trimmed for adaptor sequences and low quality bases using trimmomatic (version 0.36) with parameters ‘LEADING:5 TRAILING:5 SLIDINGWINDOW:4:15 HEADCROP:20 CROP:101 MINLEN:101’, then mapped to GENCODE (vM22) mouse genome (mm10) with STAR (version 2.7.3a) using parameters ‘--outSAMattributes All --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic’.
Isofrorm-level expression was quantified as transcripts per million reads (TPM) with Salmon (version 1.1.0) using aligned transcriptome bam files from STAR output. R package ‘tximport’ was used to map transcripts to gene-level expression.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include TPM at gene and isoform level.

source_name: mouse embryonic cells

growth_protocol: Wildtype AECs and HECs were sorted from the E10 embryonic AGM region of C57 mice. Wildtype (WT) and mutant (KO) HECs were sorted from the E10 embryonic AGM region of Srsf2 conditional knockout mice.

extract_protocol:
Morphologically deformed cells were discarded. Living single cells were rinsed in PBS-BSA, and manually transferred into cell lysis buffer with a mouth pipette; 0.05 μl of 1:200,000 dilution of External RNA Controls Consortium (ERCC) RNA spike-in Mix1 (Ambion) was added to lysis buffer per reaction.
The cDNA libraries from single cells were generated as described previously. "Tang, F. et al. mRNA-Seq whole-transcriptome analysis of a single cell. Nature  Methods, 6, 377–382 (2009)."

treatment_protocol: FACS-sorted cells were kept on ice until lysed and reverse transcribed.

value: AGM

tag: developmental stage

value: wild type


title: AGM-KO-1_FKDL192530630-1a

description: E10.0 HEC (bulk)


title: HEK293-PROSER1KO1D3-rep1-5hmC

description: 1955008_SJNORM056733_C184-ActiveMotif_55010_HEK293_PROSER1KO1D3_030920-5hmC-AB2


title: HUVECs, NT_3


title: AGM-WT-3_FKDL192530635-1a

description: E10.0 HEC (bulk)


title: AGM-KO-2_FKDL192530631-1a

description: E10.0 HEC (bulk)


title: AGM-WT-1_FKDL192530633-1a

description: E10.0 HEC (bulk)


title: HEK293-PROSER1KO1D3-DSG_021221-OGT-AB2

description: 2132551_SJNORM056733_C250-SC_HEK293_PROSER1KO1D3-DSG_021221-OGT-AB2

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000
Duplicated reads were marked with bamsormadup tool from biobambam (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: bigwig

extract_protocol:
After sequential lysis of the crosslinked cells in Lysis Buffer 1 and Lysis Buffer 2, the nuclear pellet was sonicated in Lysis Buffer 3 with a probe sonicator (Fisher Scientific Model 705 Sonic Dismembrator) at output level 55 (27–33 W) for 16 cycles with each cycle constituting of a 30 sec sonication on followed by a 60 sec off. For each ChIP, 100 μL Protein G Dynabeads (Invitrogen, 10003D) slurry and 10 µg of antibody was used. Chromatin incubation with antibody was carried out at 4°C with end-to-end rotation for 4-6 hours.
DNA was quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496). Libraries were prepared with the KAPA HyperPrep Library Kit (Roche, 07962363001) and analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay.   HiSeq 2500, HiSeq 4000, or NovaSeq 6000 System (all from Illumina) was used.

treatment_protocol: Dual crosslinking was performed at room temperature first for 30 min with 2 mM disuccinimidyl glutarate (DSG) in DPBS and then by addition of paraformaldehyde to a final concentration of 1% for another 15 minutes. Crosslinking was quenched with 150 mM glycine for 5 min at room temperature.

value: rabbit α-OGT (Santa Cruz, sc-74546)


title: HEK293-FlpInTREx-control-DSG_021221-OGT-AB2

description: 2132550_SJNORM056733_C249-SC_HEK293_FlpInTREx-DSG_021221-OGT-AB2


title: FlpInTREx_control_WGBS_rep2

description: Genome-wide bisulfite sequencing (WGBS)

value: Mock treated


title: PROSER1KO1D3_WGBS_rep1

description: Genome-wide bisulfite sequencing (WGBS)


title: FlpInTREx_control_WGBS_rep1

description: Genome-wide bisulfite sequencing (WGBS)


title: HEK293-PROSER1KO1D3-DSG_021221-OGT-AB1

description: 2132549_SJNORM056733_C248-AM_HEK293_PROSER1KO1D3-DSG_021221-OGT-AB1

value: rabbit α-OGT (Active Motif, 61355)


title: HE-4-HE-4-6_FKDL202561890-1a-27

description: E10.0 HEC (single-cell)


title: HE-4-HE-4-5_FKDL202561890-1a-25

description: E10.0 HEC (single-cell)


title: Day21_Organoid

city: San Francisco

first: Jaymin

middle: J

last: Kathiriya

state: CA

address: 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

description: Cells were harvested from 21 day old organoid co-culture of HTII-280 and primary human lung mesenchyme

data_processing:
Reads were aligned to GRCh38 human genome and quantified using Cell Ranger Single-Cell Software.The matrix outputs were generated with barcodes (cell IDs), genes (gene names).
Genome_build: GRCh38
Supplementary_files_format_and_content: 10X genomics cellranger output

source_name: Freshly sorted AEC2s co-cultured with primary human mesenchyme and harvested at Day 21 in culture

extract_protocol:
single cells were isolated either from a freshly obtained lung explant or from organoids at several time points.
Libraries were constructed using the Chromium Single-Cell 3' library kit (10X Genomics)


title: HE-4-HE-4-3_FKDL202561890-1a-22

description: E10.0 HEC (single-cell)


title: IPF_All

description: IPF explant tissue was digested and single cell suspension was sorted to collect live/CD45neg cells.

source_name: Freshly sorted Live/CD45neg from IPF explant


title: TCF7L1L2_P0P5_overexpression_scRNAseq

city: Baltimore

first: Seth

last: Blackshaw

state: Maryland

address: 733 N. Broadway Avenue

institute: Johns Hopkins University

description:
P0P5_Overexpression_raw_matrix.mtx
P0P5_Overexpression_cell_annotation.txt
P0P5_Overexpression_gene_annotation.txt

data_processing:
We processed raw scRNA-seq data with the Cell Ranger software for formatting reads, demultiplexing samples, genomic alignment, and generating the cell-by-gene count matrix. The ‘cellranger mkfastq’ function was used to convert BCL files to fastq files. The ‘cellranger count’ function was used to process fastq files for each sample with the mm10 mouse reference index provided by 10x Genomics. The cell-by-gene count matrix is the final output from the Cell Ranger pipeline. We used the cell-by-gene count matrix for all downstream analysis.
We applied the Seurat (Stuart et al., 2019) package to create Seurat objects for each sample with the cell-by-gene count matrix with the function ‘CreateSeuratObject’. After visual checking the violin plot of the total counts for each cell, we filtered out cells with nCount_RNA. We further filtered out the cells with a mitochondrial fraction > 10%. Next, we used Scrublet (Wolock et al., 2019) to identify and remove doublets with default parameters.  After  performing dimensional reduction and clustering analysis through the standard Seurat pipeline, we annotated the cell types for each cluster according to the well-known markers. We filtered out non-neuroretinal cells, such as microglia and astrocytes for each sample. The cleaned data were used for downstream integration and DEG analysis.
Genome_build: mm10
Supplementary_files_format_and_content: cell annotation, gene annotation and raw data matrix files

source_name: retina

growth_protocol: Retinas from CD1 mouse embryos at day 14 (E14) and postnatal day 0 (P0) were used for ex vivo electroporation as described previously (de Melo and Blackshaw, 2011).

extract_protocol:
Retinal cells were dissociated from explants for fluorescence-activated cell sorting (FACS) as described previously (Hoang et al., 2020). GFP+ cells were collected in ice-cold PBS with 10% heat-inactivated fetal bovine serum (FBS).
ScRNA-seq analysis was performed on dissociated retinal cells using 10x Genomics. Briefly, dissociated retinal cells (~10,000 cells per sample) were loaded into a 10x Genomics Chromium Single Cell system using Chromium Single Cell 3’ Reagents Kits v3.1 (10X Genomics, Pleasanton, CA). scRNA libraries were generated by following the manufacturer’s instructions. Libraries were pooled and sequenced on Illumina NextSeq 500 or NovaSeq 6000. Sequencing reads were processed through the Cell Ranger 3.1 pipeline (10x Genomics) using default parameters.

treatment_protocol: For overexpression studies, pCAGIG was used as a control, while pCAGIG-based plasmids encoding full-length ORFs were used for overexpression (see Table). For analysis of NFIA/B/X and TCF7L1/2 function, equal molar amounts of each plasmid were combined prior to electroporation.

tag: condition

value: TCF7L1/L2 overexpression

tag: replicates


title: IPF_All2

tag: cell type

value: IPF explant tissue was digested and single cell suspension was sorted to collect live/CD45neg cells.


title: TBX3_P0P5_overexpression_scRNAseq

value: TBX3 overexpression


title: HEK293-FlpInTREx-control-DSG_021221-INPUT

description: 2132546_SJNORM056733_C245-HEK293_FlpInTREx-DSG_021221-INPUT


title: HEK293-PROSER1KO1D3-DSG_012221-H3K27Ac-AB6

description: 2119060_SJNORM056733_C244-RM172_HEK293_PROSER1KO1D3-DSG_012221-H3K27Ac-AB6

value: rabbit α- H3K27ac (RevMAb, 31-1056-00)


title: HEK293-FlpInTREx-control-DSG_021221-OGT-AB1

description: 2132548_SJNORM056733_C247-AM_HEK293_FlpInTREx-DSG_021221-OGT-AB1

value: Flp-In T-REx HEK293 (Invitrogen, R78007)


title: HEK293-PROSER1KO1D3-DSG_012221-INPUT

description: 2119054_SJNORM056733_C238-HEK293_PROSER1KO1D3-DSG_012221-INPUT

value: human embryonic kidney cells


title: HE-4-HE-4-2_FKDL202561890-1a-21

description: E10.0 HEC (single-cell)

tag: tissue


title: HEK293-FlpInTREx-control-DSG_012221-H3K27Ac-AB6

description: 2119059_SJNORM056733_C243-RM172_HEK293_FlpInTREx-DSG_012221-H3K27Ac-AB6


title: HEK293-PROSER1KO1D3-DSG_021221-INPUT

description: 2132547_SJNORM056733_C246-HEK293_PROSER1KO1D3-DSG_021221-INPUT


title: Day14_Organoid

description: Cells were harvested from 14 day old organoid co-culture of HTII-280 and primary human lung mesenchyme

source_name: Freshly sorted AEC2s co-cultured with primary human mesenchyme and harvested at Day 14 in culture


title: HTII-280pos

description: Freshly sorted HTII-280+ (mature AEC2s) were sequenced

source_name: Freshly sorted distal lung epithelium

value: Freshly sorted HTII-280+ (mature AEC2s)


title: Ctrl_P0P5_overexpression_scRNAseq rep 2

value: Ctrl


title: HEK293-FlpInTREx-control-DSG_012221-INPUT

description: 2119053_SJNORM056733_C237-HEK293_FlpInTREx-DSG_012221-INPUT


title: Day7_Organoid

description: Cells were harvested from 7 day old organoid co-culture of HTII-280 and primary human lung mesenchyme

source_name: Freshly sorted AEC2s co-cultured with primary human mesenchyme and harvested at Day 7 in culture


title: HE-3-HE-3-4_FKDL202561889-1a-16

description: E10.0 HEC (single-cell)

tag: genotype


title: 269_++_Cvs_(MTA-1_0)

type: RNA

city: Duesseldorf

first: Birgit

last: Knebel

address: Auf'm Hennekamp 65

department: Cinical Biochemistry and Pathobiochemistry

institute: German Diabetes Center

hyb_protocol: Amplified cDNA was hybridized on Affymetrix Mouse MTA arrays (Affymetrix)

scan_protocol: Detection of probe intensities was performed using a GeneChip scanner 3000 7G (GDAS 1.4 package, Affymetrix).

data_processing: The data were analyzed with Affymetrix Expression  Console v4.0 using default analysis settings for combined RNA analyses dabg .CHP files.

label: biotin

label_protocol: 150 ng total RNAwas amplified using the  WT Expression Kit and the WT Terminal Labeling Kit (Thermofisher, Darmstadt, Germany).

growth_protocol: Wildtype (WT; FGF21+/+) and Fgf21 knockout  (FGF21KO; FGF21-/-) F17male mice were bred and maintained in a regular 12h light/dark cycle (22°C ± 1°C, 50% ± 5% humidity). All mice were group housed (max. 5 mice per cage) with ad libitum access to standard chow (58% carbohydrates, 9% fat, 33% protein, R/M-H Extrudat, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water. Animal protocols were approved by the Landesamt für Natur, Umwelt und Verbraucherschutz (LANUV), NRW, Germany (81-02.04.2017.A421) and performed according to the ‘Principle of laboratory animal care’ (NIH publication No. 85-23, revised 1996) and the German law on the protection of animals.

extract_protocol: Total RNA extraction from liver tissue was made with RNeasy mini kit (Qiagen, Hilden, Germany) including DNAse digestion according to the manufacturer's instructions. RNA quality was evaluated using an Agilent 2100 Bioanalyzer and only high quality RNA (RIN > 8) was used for microarray analysis.

treatment_protocol: The mice were stressed with our Cvs protocol as previously described (doi:https://doi.org/10.1016/j.molmet.2018.06.012). In brief,  the  Cvs protocol consists of five different stressors (warm swim, cold exposure, shaking, restraint and overnight isolation) applied in a random manner 2 per day for 15 days.

value: Cvs

value: liver


title: HEK293-PROSER1KO1D3-DSG_022420-H3K4me3-AB8

description: 1927824_SJNORM056733_C178-RevMab_RM137_HEK293_PROSER1KO1D3-DSG_022420-H3K4me3-AB8

tag: chip antibody

value: rabbit α-H3K4me3 (RevMAb, 31-1039-00)


title: INSM1_P0P5_overexpression_scRNAseq

value: INSM1 overexpression


title: HE-3-HE-3-3_FKDL202561889-1a-15

description: E10.0 HEC (single-cell)

value: AGM


title: Cas9_ctrl_P0P5_scRNAseq

description:
P0P5_KO_cell_annotation.txt
P0P5_KO_gene_annotation.txt
P0P5_KO_scRNAseq_raw_matrix.mtx

growth_protocol: For somatic CRISPR-mediated gene knockout, the CBh promoter of Cas9-P2A-GFP plasmid (Addgene #48138) was replaced by pCAG promoter (pCAGIG, Addgene #11159) to allow for more robust Cas9-P2A-GFP expression in retinal explants. Dual gRNAs targeting two different exon regions were cloned into a single Cas9 plasmid using PrecisionX™ Multiplex gRNA Cloning Kit with U6 and H1 promoters. gRNAs were designed using the CHOPCHOP tool. For combined Insm1/2 knockout, equal molar amounts  of each gRNA-Cas9 plasmid were mixed prior to electroporation.


title: HEK293-PROSER1KO1D3-DSG_022420-TET2-AB4

description: 1927822_SJNORM056733_C176-CST_18950S_HEK293_PROSER1KO1D3-DSG_022420-TET2-AB4

value: rabbit α-TET2 (Cell Signaling Technology, 18950S)


title: 267_++_Cvs_(MTA-1_0)


title: INSM2_P0P5_overexpression_scRNAseq

value: INSM2 overexpression


title: HE-4-HE-4-4_FKDL202561890-1a-23

description: E10.0 HEC (single-cell)

value: wild type


title: HE-2-HE-2-6_FKDL202561888-1a-12

description: E10.0 HEC (single-cell)


title: HEK293-PROSER1KO1D3-DSG_022420-TET2-AB1

description: 1927820_SJNORM056733_C174-Bethyl_A304-247A_HEK293_PROSER1KO1D3-DSG_022420-TET2-AB1

value: rabbit α-TET2 (Bethyl Laboratories, A304-247A)


title: activated CD4 T-cells, 72 hours after activation, low CD62L [Set1_72_lo_1]

city: Rehovot

first: Roni

last: Rak

address: Herzl 229

department: Animal Science

country: Israel

institute: Agriculture Research Organization

description:
Set1_72_lo_1_S84
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv

data_processing:
library strategy: tRNA-seq
Read were trimmed using homerTool
Alignment was done to the genome concatenate with mature tRNA (Chan, P.P. & Lowe, T.M. (2016) GtRNAdb 2.0: an expanded database of transfer RNA genes identified in complete and draft genomes. Nucl. Acids Res. 44(Database issue):D184-D189.) using Bowtie2 with parameters --very-sensitive-local. Read aligned with equal alignment score to the genome and mature tRNA were annotated as mature tRNA. Reads aligned to multiple tRNA genes were assigned by ratio of valid reads of the possible mapping location.
Read count was done using BedTools-coverage count.
Genome_build: mm10
Supplementary_files_format_and_content: read counts of mature tRNA and sum of read per anticodon of all samples

growth_protocol: Naïve cells were extracted from six spleens of B6 mice using the StemCell CD62L+CD44+ kit (female, 7 weeks, 6-9% naive). Each two spleens were pooled to a total of 3 samples extracted separately. A portion from the naïve state was taken to FASC sorted for live cells followed by RNA extraction. The remaining naive cells were activated by addition of anti-CD3/anti-CD28 activation bead (1:1 bead:cell ratio, thermoFisher Scientific Cat#11131D)    Cells were grown at 0.25 cell/ml in 24 wells, and were collected at 20h, 48h, and 72h after activation. At 20h only live cells were sorted. At 48 and 72 h cells were sorted into CD62L+CD44+ (memory T-cells) and CD62L-CD44+(effector T-cells). The cells were stained as followed, and analyzed using ARIAIII FACS:

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
tRNA sequencing protocol was adapted from Zheng et al., 2015 (Zheng et al., 2015) with minor modification. Small RNA was isolated using SPRI-beads (Agencourt AMPure XP, Beckman Coulter), using dual side size-selection protocol. First RNA and beads were mixed at 1:1.8 ratio, collection the supernatant. The small RNA was isolated by mixing the clear supernatant with bead at 1:0.8 ratio, with addition of X1.34 isopropanol. Small RNA was treated for modification removal using AlkB wt, and D135S, a kind gift from Prof. Tao Pan. Reverse transcription was done using TGIRT™-III Enzyme, with the indicated primers. 3’ adaptor was ligated to the cDNA using T4 ligase (NEB). The cDNA was purified using Dynabeads myOne SILANE (life Technologies) after each step.  The library was amplified using NEBNext PCR mix and cleaned using SPRI-beads. Samples were pooled and sequenced using NextSeq illumina. primers: Reverse-transcription DNA:5’-CACGACGCTCTTCCGATCTT  -3’,  Reverse-transcription RNA:5’-rArGrArUrCrGrGrArArGrArGrCrGrUrCrGrUrG-3’,  3’ adaptor:5’-  CGTCATAGATCGGAAGAGCACA-3’.

treatment_protocol: cells were centrifuged at 12,000 rpm for 1 min, frozen in liquid nitrogen and stored at -80 ̊C until RNA extraction.

tag: activation stage

value: 72 hours

value: CD4 T-cells

tag: molecule subtype

value: tRNA


title: HEK293-FlpInTREx-control-DSG_022420-TET2-AB1

description: 1927819_SJNORM056733_C173-Bethyl_A304-247A_HEK293_FlpInTREx-DSG_022420-TET2-AB1


title: Ctrl_P0P5_overexpression_scRNAseq rep 1

description:
P0P5_Overexpression_raw_matrix.mtx
P0P5_Overexpression_cell_annotation.txt
P0P5_Overexpression_gene_annotation.txt


title: HE-3-HE-3-2_FKDL202561889-1a-14

description: E10.0 HEC (single-cell)


title: HE-3-HE-3-6_FKDL202561889-1a-19

description: E10.0 HEC (single-cell)


title: activated CD4 T-cells, 72 hours after activation, high CD62L [Set1_72_hi_3]

description:
Set1_72_hi_3_S83
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: 299_++_Ctrl_(MTA-1_0)

tag: treatment


title: activated CD4 T-cells, 72 hours after activation, high CD62L [Set1_72_hi_2]

description:
Set1_72_hi_2_S82
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: activated CD4 T-cells, 72 hours after activation, low CD62L [Set1_72_lo_2]

description:
Set1_72_lo_2_S85
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: HE-3-HE-3-1_FKDL202561889-1a-13

description: E10.0 HEC (single-cell)


title: HEK293-PROSER1KO1D3-DSG_022420-TET1-AB4

description: 1927818_SJNORM056733_C172-Invitrogen_GT1462_HEK293_PROSER1KO1D3-DSG_022420-TET1-AB4

value: mouse α-TET1 (Invitrogen, MA5-16312)


title: HEK293-FlpInTREx-control-DSG_022420-TET2-AB4

description: 1927821_SJNORM056733_C175-CST_18950S_HEK293_FlpInTREx-DSG_022420-TET2-AB4

value: Flp-In T-REx HEK293 (Invitrogen, R78007)


title: 298_++_Ctrl_(MTA-1_0)


title: HEK293-FlpInTREx-control-DSG_022420-TET1-AB4

description: 1927817_SJNORM056733_C171-Invitrogen_GT1462_HEK293_FlpInTREx-DSG_022420-TET1-AB4

value: human embryonic kidney cells


title: HEK293-FlpInTREx-control-DSG_022420-H3K4me3-AB8

description: 1927823_SJNORM056733_C177-RevMab_RM137_HEK293_FlpInTREx-DSG_022420-H3K4me3-AB8


title: HE-2-HE-2-3_FKDL202561888-1a-9

description: E10.0 HEC (single-cell)


title: Cas9_Insm12_P0P5_scRNAseq

treatment_protocol: For combined Insm1/2 knockout, equal molar amounts of each gRNA-Cas9 plasmid were mixed prior to electroporation.

value: KO


title: activated CD4 T-cells, 72 hours after activation, high CD62L [Set1_72_hi_1]

description:
Set1_72_hi_1_S81
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: HE-3-HE-3-5_FKDL202561889-1a-18

description: E10.0 HEC (single-cell)


title: 284_++_Ctrl_(MTA-1_0)

value: Ctrl


title: HE-2-HE-2-2_FKDL202561888-1a-8

description: E10.0 HEC (single-cell)


title: activated CD4 T-cells, 72 hours after activation, low CD62L [Set1_72_lo_3]

description:
Set1_72_lo_3_S86
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: activated CD4 T-cells, 48 hours after activation, low CD62L [Set1_48_lo_3]

description:
Set1_48_lo_3_S80
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv

value: 48 hours


title: HEK293-FlpInTREx-control-DSG_022420-INPUT

description: 1927815_SJNORM056733_C169-HEK293_FlpInTREx-DSG_022420-INPUT


title: 300_++_Ctrl_(MTA-1_0)

value: liver


title: HEK293-PROSER1KO1D3-DSG_022420-INPUT

description: 1927816_SJNORM056733_C170-HEK293_PROSER1KO1D3-DSG_022420-INPUT


title: activated CD4 T-cells, 48 hours after activation, low CD62L [Set1_48_lo_2]

description:
Set1_48_lo_2_S79
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: HE-1-HE-1-6_FKDL202561887-1a-6

description: E10.0 HEC (single-cell)


title: HE-4-HE-4-1_FKDL202561890-1a-20

description: E10.0 HEC (single-cell)


title: 268_++_Cvs_(MTA-1_0)

value: Cvs


title: HEK293-PROSER1KO1D3-DSG_021620-H3K4me2-AB5

description: 1921390_SJNORM056733_C164-ActiveMotif_39679_HEK293_PROSER1KO1D3-DSG_021620-H3K4me2-AB5

value: Mouse α-H3K4me2 (Active Motif, 39679)


title: 278_KO_Cvs_(MTA-1_0)


title: activated CD4 T-cells, 48 hours after activation, high CD62L [Set1_48_hi_3]

description:
Set1_48_hi_3_S77
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: 277_KO_Cvs_(MTA-1_0)


title: 276_KO_Cvs_(MTA-1_0)


title: HE-2-HE-2-4_FKDL202561888-1a-10

description: E10.0 HEC (single-cell)

value: AGM


title: 266_++_Cvs_(MTA-1_0)


title: activated CD4 T-cells, 48 hours after activation, high CD62L [Set1_48_hi_1]

description:
Set1_48_hi_1_S75
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: HEK293-FlpInTREx-control-DSG_021620-H3K4me1-AB4

description: 1921387_SJNORM056733_C161-RevMab_RM140_FlpInTREx-DSG_021620-H3K4me1-AB4

value: Rabbit α-H3K4me1 (RevMAb, 31-1046-00)


title: 270_++_Cvs_(MTA-1_0)


title: HEK293-PROSER1KO1D3-DSG_021620-UTX-AB11

description: 1921386_SJNORM056733_C160-CST_33510S_HEK293_PROSER1KO1D3-DSG_021620-UTX-AB11

value: rabbit α-UTX/KDM6A (Cell Signaling Technology, 33510S)


title: 275_KO_Cvs_(MTA-1_0)


title: HE-2-HE-2-5_FKDL202561888-1a-11

description: E10.0 HEC (single-cell)

value: wild type


title: activated CD4 T-cells, 20 hours after activation (sorted for live cells) [set1_20_2]

description:
Set1_20_2_S73
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv

value: 20 hours


title: HEK293-PROSER1KO1D3-DSG_021620-H3K4me1-AB4

description: 1921388_SJNORM056733_C162-RevMab_RM140_HEK293_PROSER1KO1D3-DSG_021620-H3K4me1-AB4


title: HEK293-FlpInTREx-control-DSG_021620-H3K4me2-AB5

description: 1921389_SJNORM056733_C163-ActiveMotif_39679_HEK293_FlpInTREx-DSG_021620-H3K4me2-AB5


title: HE-1-HE-1-4_FKDL202561887-1a-4

description: E10.0 HEC (single-cell)


title: 283_++_Ctrl_(MTA-1_0)


title: HE-1-HE-1-3_FKDL202561887-1a-3

description: E10.0 HEC (single-cell)


title: activated CD4 T-cells, 48 hours after activation, high CD62L [Set1_48_hi_2]

description:
Set1_48_hi_2_S76
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: activated CD4 T-cells, 48 hours after activation, low CD62L [Set1_48_lo_1]

description:
Set1_48_lo_1_S78
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: HEK293-PROSER1KO1D3-DSG_021620-PROSER1-AB3

description: 1921384_SJNORM056733_C158-Herz_34429_HEK293_PROSER1KO1D3-DSG_021620-PROSER1-AB3

value: rabbit α-PROSER1  (Herz Lab, #34429, human aa 302-597)


title: 289_KO_Cvs_(MTA-1_0)


title: 293_KO_Ctrl_(MTA-1_0)


title: HE-2-HE-2-1_FKDL202561888-1a-7

description: E10.0 HEC (single-cell)


title: AEC-2-AEC-2-4_FKDL202561885-1a-18

description: E10.0 AEC (single-cell)


title: HE-1-HE-1-5_FKDL202561887-1a-5

description: E10.0 HEC (single-cell)


title: HE-1-HE-1-2_FKDL202561887-1a-2

description: E10.0 HEC (single-cell)


title: 292_KO_Ctrl_(MTA-1_0)


title: AEC-2-AEC-2-5_FKDL202561885-1a-19

description: E10.0 AEC (single-cell)


title: 255_KO_Ctrl_(MTA-1_0)


title: HEK293-PROSER1KO1D3-DSG_021620-PROSER1-AB7

description: 1921382_SJNORM056733_C156-Herz_34643_HEK293_PROSER1KO1D3-DSG_021620-PROSER1-AB7

value: rabbit α-PROSER1 (Herz Lab, #34643, mouse aa 582-811)


title: 254_KO_Ctrl_(MTA-1_0)


title: HE-1-HE-1-1_FKDL202561887-1a-1

description: E10.0 HEC (single-cell)


title: HEK293-FlpInTREx-control-DSG_021620-PROSER1-AB3

description: 1921383_SJNORM056733_C157-Herz_34429_HEK293_FlpInTREx-DSG_021620-PROSER1-AB3

value: rabbit α-PROSER1 (Herz Lab, #34429, human aa 302-597)


title: HEK293-FlpInTREx-control-DSG_021620-PROSER1-AB7

description: 1921381_SJNORM056733_C155-Herz_34643_HEK293_FlpInTREx-DSG_021620-PROSER1-AB7

value: rabbit α-PROSER1  (Herz Lab, #34643, mouse aa 582-811)


title: HiC.dom-kd.st5.rep2

city: Freiburg

first: Michael

last: Rauer

address: Breisacherstr. 153

department: Medical Faculty

institute: University of Freiburg

data_processing:
mapping, QC, building and balancing matrices: HiC pipeline of snakepipes-v2.1.0 (Bhardwaj et al., 2019)
TAD calling: hicexplorer-v3.4.3 (Woff et al 2020)
Genome_build: dm6
Supplementary_files_format_and_content: hdm5 matrices, bigwig insulation scores

organism: Drosophila melanogaster

source_name: embryos

extract_protocol:
50 µl ice-cold HiC lysis buffer (10 mM Tris-HCl [pH 8], 10 mM NaCl, 0.2% Igepal, 1x Protease Inhibitor Cocktail (Roche, 11836170001)) were added and embryos were crushed with a pestle. Then, nuclei were pelleted by centrifugation (3000g, 5min at 4°C). Next, the pellet was incubated in 50 µl 0.5% SDS for 10 min at room temperature. The reaction was quenched by adding 145 µl of water and 25 µl of 10% Triton X100. For chromatin digestion, 0.7 µl of DpnII (NEB R0543T) and 25 µl of DpnII buffer were added. The reaction was incubated for 90 min at 37°C at 600 rpm and a second instance of 0.7 µl of DpnII was added followed by a second incubation of 90 min. Nuclei were then pelleted and resuspended in 135 µl of 1x CutSmart buffer (NEB B7204S). To biotinylate the free chromatin ends, 0.15mM (final) of dNTP-mix (NEB), 0.05mM (final) of Biotin-14-dATP (Jena Bioscience, NU-835-BIO14-S) and 10 U of Klenow (NEB M0210 L) was added to the reaction and incubated for 60 min at 25 °C. The chromatin free ends were then ligated by adding ligation buffer (NEB B0202S) (1x final concentration), TritonX-100 (0.8% final concentration), 120 µg BSA and 2000 U ligase (NEB M0202S). This reaction was incubated for 2hrs, after which another 2000 U of ligase were added and incubated for another 2hrs. Nuclei were then pelleted and resuspended in 200 µl elution buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 1% SDS). Proteins were digested upon addition of 400 µg Proteinase K for 30 min at 55 °C. The chromatin was reverse crosslinked in the presence of 0.365 M NaCl at 68 °C overnight. DNA was purified using the ChIP DNA Clean&Concentrator Kit (Zymo Research D5205) eluted in 50 µl and biotin was removed from non-ligated fragments by adding NEB buffer 2 (NEB B7002S) (1x final), 12 µg of BSA, dATP and dGTP (0.025 final each), 3 U T4 DNA polymerase (NEB M0203S) in a final volume of 120 µl. The reaction was stopped by adding a final concentration of 13 mM EDTA. Samples were sheared with Covaris E220 (Covaris microTUBE snap cap (520045) with intensifier (50014), duty factor 10%, peak incident power 140, cycle/burst 200, 120 sec) to generate fragments of 200-300bp. Ligated and biotinylated fragments were enriched through biotin pulldown using Dynabeads MyOne Streptavidin C1 (Invitrogen 65001). Afterwards, 2x binding buffer (10 mM Tris-HCl [pH 8], 1 mM EDTA, 2 M NaCl) (1x final concentration) was added to each sample. Subsequently, beads (equilibrated with TWB (5 mM Tris-HCl [pH 8], 0.5 mM EDTA, 1 M NaCl, 0.05% Tween) resuspended in 1x binding buffer were added to each sample. The beads were washed twice for 2 min at 55 °C with TWB, twice with EB-buffer (Qiagen), resuspended in 50 µl of EB-buffer and directly used for library preparation
Libraries were prepared using the NEB Ultra II DNA Library Prep Kit for Illumina (E7645S and E6440) following the manufacturer’s instructions except that the adapter ligation occurred on the biotin beads. The fragments were released from the beads before the PCR reaction (by heating to 98 °C for 10 min) once non-ligated adapters had been removed.

tag: timepoint

tag: assay

value: HiC


title: AEC-2-AEC-2-6_FKDL202561885-1a-20

description: E10.0 AEC (single-cell)

tag: strain


title: Naïve CD4 T-cells (sorted for live cells) [set1_Naive_2]

description:
Set1_Naive_2_S70
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv

value: naïve

value: CD4 T-cells

value: tRNA


title: activated CD4 T-cells, 20 hours after activation (sorted for live cells) [set1_20_1]

description:
Set1_20_1_S72
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: AEC-3-AEC-3-5_FKDL202561886-1a-16

description: E10.0 AEC (single-cell)


title: HEK293-PROSER1KO1D3-DSG_021620-PROSER1-AB5

description: 1921380_SJNORM056733_C154-Herz_34641_HEK293_PROSER1KO1D3-DSG_021620-PROSER1-AB5

tag: cell line full name

value: Flp-In T-REx HEK293 (Invitrogen, R78007)

value: human embryonic kidney cells

value: rabbit α- PROSER1  (Herz Lab, #34641, human aa 2-233)


title: AEC-3-AEC-3-4_FKDL202561886-1a-15

description: E10.0 AEC (single-cell)


title: HiC.dom-kd.st5.rep1


title: AEC-3-AEC-3-3_FKDL202561886-1a-14

description: E10.0 AEC (single-cell)


title: Naïve CD4 T-cells (sorted for live cells) [set1_Naive_1]

description:
Set1_Naive_1_S69
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: activated CD4 T-cells, 20 hours after activation (sorted for live cells) [set1_20_3]

description:
Set1_20_3_S74
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: 291_KO_Ctrl_(MTA-1_0)

value: Ctrl

value: liver


title: 72Low2_activated CD4 T-cells, 72 hours after activation, low CD62L

description: Mars-seq sequencing of  T-cells 48h after in-vitro activation, sorted for low CD62L

data_processing:
library strategy: MARS-seq
Reads were trimmed using cutadapt (DOI: 10.14806/ej.17.1.200) and mapped to genome /shareDB/iGenomes/Mus_musculus/UCSC/mm10/Sequence/STAR_index using STAR (DOI: 10.1093/bioinformatics/bts635) v2.4.2a (default parameters).
The pipeline quantifies the genes annotated in RefSeq (that have expanded with 1000 bases toward 5’ edge and 100 bases toward 3’ bases): /home/labs/bioservices/services/ngs/support/gtf/mm10.genes.3utr.gtf.
Counting was done using htseq-count (DOI: 10.1093/bioinformatics/btu638) (union mode).
Further analysis is done for genes having minimum 5 read in at least one sample.
Normalization of the counts and differential expression analysis was performed using DESeq2 (DOI: 10.1186/s13059-014-0550-8) with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFiltering=FALSE. Raw P values were adjusted for multiple testing using the procedure of Benjamini and Hochberg.
Genome_build: Pipeline was constructed using Snakemake (DOI: 10.1093/bioinformatics/bts480).
Supplementary_files_format_and_content: read counts , RPKM, and DE was calculated using DESeq2.

extract_protocol:
RNA was extracted using TRI-reagent (Sigma-Aldirch), according to standard protocol.
mRNA sequencing for the first biological repeat was preform using MARS-Seq protocol as described  (Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776–9 (2014))

value: 72 hours


title: HEK293-FlpInTREx-control-DSG_021620-UTX-AB11

description: 1921385_SJNORM056733_C159-CST_33510S_HEK293_FlpInTREx-DSG_021620-UTX-AB11

value: rabbit α-UTX/KDM6A (Cell Signaling Technology, 33510S)


title: AEC-3-AEC-3-2_FKDL202561886-1a-13

description: E10.0 AEC (single-cell)

value: AGM

value: wild type


title: HiC.ctrl.st5.rep2


title: HEK293-FlpInTREx-control-DSG_021620-PROSER1-AB5

description: 1921379_SJNORM056733_C153-Herz_34641_HEK293_FlpInTREx-DSG_021620-PROSER1-AB5

value: rabbit α- PROSER1 (Herz Lab, #34641, human aa 2-233)


title: 72Low3_activated CD4 T-cells, 72 hours after activation, low CD62L


title: Naïve CD4 T-cells (sorted for live cells) [set1_Naive_3]

description:
Set1_Naive_3_S71
processed data file:
set1_cytosolictRNAReads_RPM.csv
set1_cytosolictRNA_byAntiCodon_RPM.csv


title: AEC-2-AEC-2-3_FKDL202561885-1a-11

description: E10.0 AEC (single-cell)


title: GROseq.dom-kd.st5.A_rep2

data_processing:
Library strategy: GRO-seq
In order to match the custom GRO-seq protocol, an in-house protocol was developed. The workflow processes GRO-seq single-end library, and retains UMI-like randomers that are part of the custom GRO-seq protocol. First, adapters were trimmed using Cutadapt (version 2.5) (Martin, 2011) (-a “NNNN“ <TGGAATTCTCGGGTGCCAAGG > --overlap=3 --minimum-length=12 --max-n 0). UMI-like tetramers were trimmed and retained using UMI-tools(version 1.0)(Smith et al., 2017). The SE library was mapped afterwards using Botwie2(Langmead and Salzberg, 2012)(version 2.3.3.1) with default parameters and bowtie2 –local alignment. Only alignments with MAPQ3 or higher were kept.
strand-specific read counting per gene using featureCounts (GRO-seq; –s 1 –Q 3, Liao et al., 2014) on non-deduplicated alignments was performed
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs containing signal which is deduplicated, library size corrected and scaled by expression of Zelda-zygotic genes. Table featureCounts table contains the raw counts per transcript

extract_protocol:
The GRO-seq protocol was adapted from Quarato et al., 2020 with modifications in the nuclei extraction protocol as follows: Embryos were resuspended in 1.5 ml nuclei extraction buffer (3 mM CaCl2, 2 mM MgCl2, 10 mM Tris HCl pH 7.5, 0.25 % Np40, 10 % Glycerol, Protease inhibitors and RNase inhibitor 4U/ml) and stroked 60 times. The lysate was centrifuged at 100g and nuclei were pellet at 1000g, and washed afterwards four times with nuclei extraction buffer. Nuclei were washed once with freezing buffer (50 mM Tris HCl pH 8, 5 mM MgCl2, 0.1 mM EDTA) and resuspended in 100 μl of freezing buffer. The Nuclear Run-On (NRO) reaction was performed by addition of 100 µl NRO 2x buffer (10 mM Tris HCl, 5 mM MgCl2, 1 mM DTT, 300 mM KCl, 1 % Sarkosyl, 0.5 mM ATP, CTP and GTP and 0.8 U/µl RNase inhibitor), using 1 mM Bio-11-UTP final concentration, follow by an incubation of 5 min at 30°C. RNA extraction was performed following the manufacturer’s instructions with TRIzol reagent. Purified RNA was fragmented by the addition of reverse transcriptase buffer and 7 minutes incubation at 95°C. Biotinylated nascent RNAs were bound to 30 µl Dynabeads MyOne Streptavidin C1 (Invitrogen), washed and purified. Fragmented RNAs were repaired incubating with Polynucleotide kinase (Thermo scientific) for 30 minutes at 37˚C. RNA was purified with Phenol:Chloroform and precipitated. RNA was then ligated to 3’ end adapter using T4 RNA ligase 2 Truncated KQ (home-made) for 16h at 15˚C. After ligation RNA was purified using SPRI beads and biotinylated RNA was enriched as described above. Purified RNA was ligated at 5’ end using T4 RNA ligase1 for 2 h at 25˚C. Then, RNA was purified using SPRI beads and biotinylated RNA was enriched for a third time as described above.
Purified RNA was reverse transcribed using SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific) following manufacturer conditions except that reaction was incubated for 1h at 50˚C. cDNA was PCR amplified with specific primers using Phusion High fidelity PCR master mix 2x (New England Biolab) for 18-20 cycles.

value: GRO-seq

tag: rna population

value: nuclear RNA


title: HEK293-PROSER1KO1D3-DSG_122419-H3K4me3-AB8

description: 1883843_SJNORM056733_C132-RevMab_RM137_HEK293_PROSER1KO1D3-DSG_122419-H3K4me3-AB8-H3K4me3-AB8

value: rabbit α-H3K4me3 (RevMAb, 31-1039-00)


title: 72hi2_activated CD4 T-cells, 72 hours after activation, high CD62L

description: Mars-seq sequencing of  T-cells 72h after in-vitro activation, sorted for high CD62L


title: HiC.ctrl.st5.rep1

value: HiC


title: 72hi1_activated CD4 T-cells, 72 hours after activation, high CD62L


title: GROseq.ctrl.st5.B_rep2


title: AEC-2-AEC-2-2_FKDL202561885-1a-10

description: E10.0 AEC (single-cell)


title: AEC-1-AEC-1-6_FKDL202561884-1a-6

description: E10.0 AEC (single-cell)


title: 72Low1_activated CD4 T-cells, 72 hours after activation, low CD62L


title: HEK293-PROSER1KO1D3-DSG_021620-INPUT

description: 1921378_SJNORM056733_C152-HEK293_PROSER1KO1D3-DSG_021620-INPUT


title: 48Low1_activated CD4 T-cells, 48 hours after activation, low CD62L

value: 48 hours


title: AEC-2-AEC-2-1_FKDL202561885-1a-9

description: E10.0 AEC (single-cell)


title: HEK293-FlpInTREx-control-DSG_021620-INPUT

description: 1921377_SJNORM056733_C151-HEK293_FlpInTREx-DSG_021620-INPUT


title: C_Input.ctrl.st5.rep2

description: processed data file:

data_processing:
Raw short read sequencing was processed uniformly using default parameters of snakepipes-v2.0.2 (Bhardwaj et al., 2019)). ChIP-seq samples were processed with the DNA-mapping workflow (–trim, --dedup, –properPairs), followed by assay-specific workflow, i.e. ChIP-seq.
Differential Pol II occupancy was determined using the method described in Blythe and Wieschaus, 2015. In brief, reads were countered per transcript using featureCounts (-t transcript -g transcript_id -f -O -Q 3 --primary -s 0). Reads were counted multiple times if they overlap several isoforms. Then, per transcript read counts were processed with edgeR (Robinson et al., 2010) to compute differential Pol2 occupancy. Like in the published method, transcripts spanning less than 125 nucleotides were discarded and only transcripts with read counts across replicates sum more that 10 reads were considered.
Genome_build: dm6, ensembl 96
Supplementary_files_format_and_content: Supplementary files are bigwigs contains library size and input corrected bigwig tracks and the promoter quantification of the Rpb3 (pol2) ChIP-seq.

extract_protocol:
ChIP-seq experiments were performed as in Zenk et al., 2017. Briefly, nuclei were extracted in lysis buffer (140 mM NaCl, 15 mM HEPES [pH 7.6], 1 mM EDTA, 0.5 mM EGTA, 1 % TritonX100, 0.5 mM DTT, 0.1 % Sodium Deoxycholate, 10 mM Sodium Butyrate, 1X Protease Inhibitors) and subsequent ultrasound treatment (Covaris E220, 45 sec, peak power 75, duty factor 10, cycles burst 200). Fixed chromatin was then sheared using Covaris E220 (900 sec, peak power 140, duty factor 5, cycle burst 200) and precleared overnight. Each sample was incubated with the relevant antibody and concentration for at least 4 hrs at 4°C. Samples were then washed, eluted and decrosslinked overnight by incubation at 65°C. Next, samples were treated with RNaseA(50mg/mL final concentration) for 30min at 37°C and ProteinaseK (200mg/mL, final) for 3 hrs at 56°C.
Libraries were prepared according to manufacturer’s instructions using the NEBNext Ultra II DNA Library Prep Kit for Illumina. Libraries were quality controlled by capillary electrophoresis on the Fragment Analyzer system (Advanced Analytical).

value: ChIP-seq

value: none (input)


title: HEK293-FlpInTREx-control-DSG_122419-H3K4me3-AB8

description: 1883842_SJNORM056733_C131-RevMab_RM137_HEK293_FlpInTREx-DSG_122419-H3K4me3-AB8-H3K4me3-AB8

value: Flp-In T-REx HEK293 (Invitrogen, R78007)


title: GROseq.dom-kd.st5.B_rep1


title: GROseq.ctrl.st5.B_rep1


title: 48Low3_activated CD4 T-cells, 48 hours after activation, low CD62L

value: CD4 T-cells


title: AEC-1-AEC-1-8_FKDL202561884-1a-8

description: E10.0 AEC (single-cell)


title: GROseq.dom-kd.st5.A_rep1


title: AEC-1-AEC-1-4_FKDL202561884-1a-4

description: E10.0 AEC (single-cell)


title: 48Low2_activated CD4 T-cells, 48 hours after activation, low CD62L


title: HEK293-PROSER1KO1D3-DSG_122419-INPUT

description: 1883831_SJNORM056733_C122-HEK293_PROSER1KO1D3-DSG_122419-INPUT

value: human embryonic kidney cells


title: C_Input.ctrl.st5.rep1

description: processed data file:


title: 33T48

first: JP

last: Courneya

state: United States of America

address: 685 W Baltimore St., HSF2 Room 480

institute: University of Maryland, Baltimore

data_processing:
gene alignment: STAR
transcript abundance: HTSeq 0.6.1p2
differential gene expression: DESeq2
Genome_build: hg19 / GRCh37
Supplementary_files_format_and_content: counts

source_name: Normal Human Lung Fibroblasts

extract_protocol:
Following treatments cells were flash-frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Total Library Preparation workflow with Ribo-Zero Gold rRNA removal mix (Illumina, Catalog# 20020598), which depletes samples of both cytoplasmic and mitochondrial rRNA.

tag: plasmid

tag: activation

value: TGF-B

tag: activation time


title: HEK293-FlpInTREx-control-DSG_122419-INPUT

description: 1883830_SJNORM056733_C121-HEK293_FlpInTREx-DSG_122419-INPUT


title: AEC-1-AEC-1-5_FKDL202561884-1a-5

description: E10.0 AEC (single-cell)

tag: developmental stage


title: AEC-1-AEC-1-2_FKDL202561884-1a-2

description: E10.0 AEC (single-cell)


title: AEC-1-AEC-1-7_FKDL202561884-1a-7

description: E10.0 AEC (single-cell)


title: GROseq.ctrl.st5.A_rep1


title: AEC-1-AEC-1-1_FKDL202561884-1a-1

description: E10.0 AEC (single-cell)


title: 3348


title: 72hi3_activated CD4 T-cells, 72 hours after activation, high CD62L

description: Mars-seq sequencing of  T-cells 48h after in-vitro activation, sorted for high CD62L


title: 48hi2_activated CD4 T-cells, 48 hours after activation, high CD62L


title: 33T24


title: Testis3

city: Vienna

first: Luis Enrique

last: Cabrera Quio

address: Campus Vienna-Biocenter 1

country: Austria

institute: Research Institute of Molecular Pathology

data_processing:
Libraries were  sequenced on a Illumina Hiseq 2500 on SR100 mode
BAM files containing sequencing reads were converted to fastq files using samtools (v1.9)
Barcoded libraries were demultiplexed using fastx-toolkit (v0.0.14)
Sequencing adapters were trimmed with cutadapt (v1.18) and only reads longer than 25 bases were kept
Reads were aligned to GRCz11 with Hisat2 v2.1.0, using the Ensembl transcriptome release 102. The following parameters were used: hisat2 -q --dta --rna-strandness R -k 12 --no-unal
Quantification at the gene level (to obtain transcript per million (TPM)) was perfomed using Kallisto (v0.43.0)
Genome_build: GRCz11
Supplementary_files_format_and_content: Tab delimited files containing TPM

organism: Danio rerio

source_name: zebrafish testis

growth_protocol: Zebrafish (Danio rerio) were raised according to standard protocols (28°C water temperature; 14/10 hour light/dark cycle)

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol. To obtain polyA+ RNA, the poly(A) selection kit from LEXOGEN was used.
Strand-specific cDNA libraries were generated using NEBNext Ultra Directional RNA Library Prep Kit for Illumina and indexed with NEBNext Multiplex Oligos for Illumina

value: wild-type

value: testis

value: TLAB


title: Naive3_Naïve CD4 T-cells (sorted for live cells)

description: Mars-seq sequencing of naïve T-cells

value: naïve


title: Testis2


title: B48


title: 20h1_activated CD4 T-cells, 20 hours after activation (sorted for live cells)

description: Mars-seq sequencing of  T-cells 20h after in-vitro activation

value: 20 hours


title: 48hi3_activated CD4 T-cells, 48 hours after activation, high CD62L


title: 20h3_activated CD4 T-cells, 20 hours after activation (sorted for live cells)


title: G7dP6-2

city: wuhan

first: wu

middle: xiao

last: man

address: Donghu South Road

institute: Institute of Hydrobiology, Chinese Academy of Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v4-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GCGD:Grass Carp Genome Database http://bioinfo.ihb.ac.cn/gcgd/php/index.php?page=download
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Ctenopharyngodon idella

source_name: grass carp

extract_protocol:
Gills were removed, flash-frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. RNA concentration and purity was measured using NanoDrop 2000(Thermo Fisher Scientific, Wilmington, DE). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X）.First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: gill

tag: age

value: three mouths

value: grass carp were cultured at saline-alkali water with the concentration of 6percent

value: 7 days post infected with Flavobacterium cloumnare