title: FB_TAC_8Weeks_RNA_seq_rep3

first: Joerg

last: Heineke

address: Ludolf-Krehl-Str. 7-11

institute: Medizinische Fakultät Mannheim

data_processing:
Trim Galore! wrapper tool. Reads shorter 20nt were removed from FASTQ files.
Trimmed reads were aligned to the reference using the short read aligner STAR (https://code.google.com/p/rna-star/).
Genes were quantified by the use of featurecounts in R. Differential expression analysis was performed using EdgeR from R. Differentially expressed Genes were selected with (0.75<FC>1.5 and FDR<0.05).).
Gene ontology biological processes and KEGG pathway analysis from different groups of genes was performed by compareCluster using the enrichGO and enrichKEGG databases with a P-value <0.05 Bonferroni as a method to correct the p-value.
Genome_build: mm10
Supplementary_files_format_and_content: excel

source_name: isolated cardiac fibroblast cells

growth_protocol: Mice were anesthetized with 4% isoflurane in an induction chamber and placed on a heating pad to keep body temperature at 37°C. Anesthesia was maintained with 1-2% isoflurane via mask. Non-invasive echocardiography was performed in parasternal long- and short axis with a 30MHz transducer (Vevo 770, Visualsonics), as previously described

extract_protocol:
The RNA sequencing library was generated from 100ng total RNA using Dynabeads® mRNA DIRECT™ Micro Purification Kit (Thermo Fisher)
TruSeq SBS Kit v3-HS

treatment_protocol: TAC or sham surgery was performed by subjecting the aorta to a defined 26-gauge constriction in 8-9 week old mice as described previously (Appari M, et al and Grund A et al 2019) Mice were subcutaneously (s.c.) injected with 0.02 mg/kg atropine and 0.1 mg/kg buprenorphine. Anesthesia was induced with 3-4% isoflurane in an induction chamber. After oral intubation, mice were connected to a small animal ventilator (MiniVent Type 845, Harvard Apparatus), and anesthesia was maintained with 1.5-2% isoflurane. A left sternal thoracotomy was performed, and the transverse aorta was tied around a 26G needle. In sham-operated control mice, the same procedure was conducted, but no ligature was placed around the aorta. During surgery, the animals were placed on a heating pad connected to a temperature controller (Föhr Medical Instruments) to maintain body temperature at 37 °C.

tag: gender

value: Male

value: C57Bl6N mice (Charles River)

value: isolated cardiac fibroblast cells

value: 8-10 weeks

value: TAC


title: 45 days old, wild type, JIB-04, replicate 3

status: Public on Feb 08 2022

type: SRA

city: Dallas

first: Elisabeth

last: Martinez

state: Texas

address: 6000 Harry Hines Blvd

department: Hamon Center for Therapeutic Oncology Research

country: USA

institute: UT Southwestern Medical Center

library_source: transcriptomic

data_processing:
Illumina sequencer (NovaSeq 6000 or HiSeq X Ten) was used at Novogene Corp.
fastq files were aligned to GRCm38 mouse reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2FPKM values for each sample

molecule: total RNA

organism: Mus musculus

source_name: 45 days old, wild type, JIB-04

extract_protocol:
RNA were extract using Trizol.
Libraries were prepared using eukaryotic non-directional mRNA library prep kits, compatible with Illumina sequencing.

treatment_protocol: Mice were treated with JIB-04 starting from 4 or 5 weeks of age at 50 mg/Kg, 3 times per week, and hearts were collected at indicated age.

tag: strain

tag: mouse reference

tag: age

value: postnatal day 45

tag: genotype

value: wild type

tag: treatment

tag: tissue

value: heart


title: N81-S1

city: Shenzhen

first: Yulin

last: Huang

state: Guangdong

address: 628 Zhenyuan Road, Xinhu Street, Guangming District

department: Department of Orthopedics Surgery

country: China

institute: The Seventh Affiliated Hospital of Sun Yat-sen University

data_processing:
Illumina NovaSeq 6000 was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
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: GRCh37
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: Homo sapiens

source_name: nucleus pulposus cells

growth_protocol: The NP tissues were digested in 0.2% type II collagenase (9001-12-1, BioFroxx) for 4h at 37°C. After washing with PBS, the digested tissues were transferred to DMEM/F12 (C11330500BT, Gibco, Life technologies) containing 10% fetal bovine serum (P30-3306, PAN Biotech) and 1% penicillin / streptomycin (15140-122, Gibco, Life technologies) in the incubator at 5% CO2 and 37°C.

extract_protocol:
Total RNAs were extract with Trizol reagent,according to the manufacturer’s instruction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The transfection using riboFECT™ CP (C10502-05, Robobio) was performed as the manufacturer’s instruction. The si-02569 and si-NC was purchased from RiboBio Company. NPCs were seeded in 6-well plates and incubated in 2 mL of medium for 24 h. Subsequently, the medium was replaced by fresh medium and then the siRNA- riboFECT complexes were added in the plates. After incubation for 6 h, the cells were washed with PBS solution and further incubated in fresh medium for another 48 h.

tag: cell type

value: nucleus pulposus cells

value: nucleus pulposus


title: 45 days old, wild type, JIB-04, replicate 2


title: A50_R2_P2

type: RNA

city: Montpellier

first: Virginie

last: Galeote

address: 2, place Pierre Viala

country: France

institute: UMR SPO, INRAE

description: Gene expression in sample from EC1118 strain, after addition of nitrogen at 50g/L of CO2 released, sampling 2h after addition

hyb_protocol: Agilent gene expression microarrays 8x15k was used for the micro array hybridization, with one-color method. Array design is based on ID 038619 completed with the regions A, B and C + KHR1 + MPR1 from the new regions of EC1118  (Agilent Technologies, Santa Clara, CA, USA). A quantity of 600ng of labeled cRNA were hybridized for 17h in 65°C in a rotative hybridization oven (Corning) using the Expression Hybridization kit (Agilent Technologies, 5188-5242). Plates were washed with expression wash buffer kit (Agilent Technologies, 5188-5325 5188-5326).

scan_protocol: The array pictures were analyzed on a GenePix 4000B laser Scanner (Axon Instruments) and with the GenePix software Pro7.

data_processing: Data normalization and statistical analysis were performed using R 4.0.2 software and the limma package. Normalization was done by the quantile method considering all arrays.

organism: Saccharomyces cerevisiae

label_protocol: Cy3-labeled cRNA was synthesized with the One color RNA Spike-In kit (Agilent Technologies) and purified with RNeasy kit (Qiagen). Quality and quantity of RNA were controlled at each step by spectrometry (NanoDrop 1000, Thermo Scientific).

growth_protocol: The cells were grown in a medium containing 180 g/l glucose, 140 mg/l of assimilable nitrogen (amino acids and ammonium) at 24°C.

extract_protocol: Total RNA extraction was perform with Trizol reagent, and purified with RNeasy kit (Qiagen).

treatment_protocol: 109 cells were harvested by filtration and frozen at -80°C.

tag: nitrogen (g/l)

tag: batch


title: MEC1_crispred_ALT_ATACseq_rep1

city: Lausanne

first: Bart

last: Deplancke

address: EPFL SV IBI-SV UPDEPLA

country: Switzerland

institute: ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE

library_source: genomic

data_processing:
Base call files were converted to fastq and adaptor sequences trimmed with bcl2fastq v2.20.0.
Fastq files were aligned to hg19 with BWA-MEM67 v.0.7.17-r1188.
Duplicates were removed with Picard v22.2.9 (http://broadinstitute.github.io/picard/).
BigWig files were generated with bamCoverage62 v3.5.0 (10-bp bin size and RPKM normalized).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig of merged BAM files from the three MEC1 cirspred ALT replicates
Supplementary_files_format_and_content: BigWig of merged BAM files from the three MEC1 cirspred REF replicates

molecule: genomic DNA

growth_protocol: Cells were grown in IMDM GlutaMAX HEPES (Gibco) media supplemented with 10% fetal bovine serum (Gibco) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
50,000 cells were washed with PBS, resuspended in 50 μl RSB buffer (10 mM Tris-HCL pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween20) and incubated on ice for 3 min. Cells were spun down, supernatant was discarded, cells were resuspended in 1 ml RBS buffer without NP40, inverted three times and spun down. Supernatant was discarded, cells were resuspended in 25 μl 2X Tagmentation buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl2, 20% Dimethyl Formamide), 0.5 μl 10% Tween20, 16.5 μl PBS, 1 μl of homemade 24.5 μM Tn5 and 7 μl H2O and incubated 30 min at 37ºC rotating at 1000 rpm. DNA was then purified with a DNA Clean & Concentrator-5 (Zymo Research).
Tagmented and amplified 11 cycles.

tag: cell line

value: Chronic lymphocytic leukemia cell line

value: ALT


title: N81-NC

value: si-NC


title: MEC1_Axin2_RNAseq_rep3

data_processing:
Base call files were converted to fastq and adaptor sequences trimmed with bcl2fastq v2.20.0.
Reads were aligned to hg19 using STAR v2.7.3a (--outSAMmapqUnique 60 --outFilterMultimapNmax 1).
Read counts per transcript were assessed using htseq-count v0.12.4 (-s reverse -m union) with the gtf file downloaded from Ensembl, GRCh37 release 75.
Raw read counts were normalized by library size and exon length sum using edgeR 3.28.1 (rpkm function).
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited table with raw gene counts for every gene and every sample.
Supplementary_files_format_and_content: Tab delimited table with normalized transcript abundance values (FPKM) for each sample.

extract_protocol:
RNA from 500.000 cells was extracted using the Direct-zol RNA Miniprep kit (Zymo Research) with 15min on column DNase digestion.
800ng of total RNA were used to synthesise the libraries with Truseq Stranded mRNA LT kit (Illumina).

value: Chronic lymphocytic leukemia

tag: overexpression


title: N79-S1


title: FB_TAC_8Weeks_RNA_seq_rep1

city: Mannheim

state: Baden Wuttemberg

department: – Department of Cardiovascular Research (HKF)

country: Germany

molecule: polyA RNA


title: 45 days old, wild type, JIB-04, replicate 1


title: 77 days old, wild type, JIB-04, replicate 3

source_name: 77 days old, wild type, JIB-04

value: postnatal day 77


title: MEC1_Axin2_RNAseq_rep2


title: N79-NC


title: FB_TAC_1Week_RNA_seq_rep1


title: FB_TAC_1Week_RNA_seq_rep2


title: 77 days old, wild type, JIB-04, replicate 1


title: 77 days old, wild type, JIB-04, replicate 2


title: Acan-Cre+/Cre;Stat3fl/fl

city: Los Angeles

first: Denis

last: Evseenko

state: CA

address: 1450 Biggy St

department: Orthopaedic Surgery

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software (build version 10.0.21.0602). Briefly, raw reads were checked for their quality, trimmed and reads with an average base quality score per position >30 were considered for alignment. Trimmed reads were aligned to the mouse genome version mm10 using STAR-2.7.3a with default parameters. Reads with alignment percentage >75% were de-duplicated based on their unique molecular identifiers (UMIs). Reads mapping to the same chromosomal location with duplicate UMIs were removed. Thereafter ‘Knee’ plot was constructed using the cumulative fraction of reads/UMIs for all barcodes. Barcodes below the cut-off defined by the location of the knee were assigned as true cell barcodes and quantified. Further noise filtration was done by removing cells having >5% mitochondrial counts and total read counts >24,000. Ambient mRNAs were removed using the R package SoupX. Genes not expressed in any cell were also removed as an additional clean-up step. Cleaned-up reads were normalized using counts per million (CPM) method followed by log-transformation generating count matrices for each sample. Samples were batch-corrected on the basis of expressed genes and mitochondrial reads percent. Count matrices were used to visualize and explore the samples in further details by generating tSNE plots, a non-linear dimensional reduction technique. This algorithm learns the underlying manifold of the data and places similar cells together in a low-dimensional space. Dot plots were generated in R (v 4.0.3) using ggplot2 (v3.3.3).
Genome_build: mm10-Gencode Genes- release M25
Supplementary_files_format_and_content: Sparse matrix files with genes in columns and cells in rows

source_name: STAT3KO female mice

extract_protocol:
Single cell samples were prepared using Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 and chip Kit (10X Genomics) according to the manufacturer’s protocol. Briefly samples were FACS sorted using DAPI to select live cells followed by resuspension in 0.04% BSA-PBS. Nearly 1200 cells/µl were added to each well of the chip with a target cell recovery estimate of 10,000 cells. Thereafter Gel bead-in Emulsions (GEMs) were generated using GemCode Single-Cell Instrument. GEMs were reverse transcribed, droplets were broken and single stranded cDNA was isolated. cDNAs were cleaned up with DynaBeads and amplified. Finally, cDNAs were ligated with adapters, post-ligation products were amplified, cleaned-up with SPRIselect and purified libraries were sequenced on Novaseq at the UCLA Technology Center for Genomics and Bioinformatics.
Single Cell 3' Library & Gel Bead Kit v3.1

tag: genotype/variation

tag: Sex

value: female


title: MEC1_ctr_RNAseq_rep3

value: control


title: U87MG_Si461

city: Taipei

first: Wen-Bin

last: Yang

address: 250 Wu-Hsing Street

country: Taiwan

institute: Taipei Medical University

data_processing:
Illumina official tool, bcl2fastq2 conversion Software v2.20 was used to convert BCL files from all Illumina sequencing systems.
Both adaptor clipping and sequence quality trimming were accomplished by Trimmomatic Ver 0.36, and sequencing reads were mapped to GRCh38.p13 using HISAT2, which is based on the hierarchical graph FM index (GFM index).
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated to quantify expression levels for each transcript.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample

source_name: glioblastoma cell line

extract_protocol:
Total RNA was extracted using Trizol® Reagent (Invitrogen, USA) according to the instruction manual. Purified RNA was quantified at OD260nm by using a ND-1000 spectrophotometer (Nanodrop Technology,USA) and qualitated by using a Bioanalyzer 2100 (Agilent Technology, USA) with RNA 6000 LabChip kit (Agilent Technologies, USA).
All RNA Sample preparation procedures were carried out according to the official Illumina protocol.


title: Stat3fl/fl

source_name: Control female mice


title: VVGM-CTLA4 -treated tumours D18 rep10

city: Illkirch-Graffenstaden

first: Jules

last: Deforges

address: Boulevard Gonthier d'Andernach

institute: Transgene SA

description:
489
Table_readcount.txt

data_processing:
The 3 first bases from read 2 were trimmed using Trimmomatic (3 extra G added by the library preparation protocol).
PCR duplicates were removed using Unique molecular identifiers (UMIs) using the program dedup from the package UMI-tools.
Reads were aligned using STAR to an artificial genome containing the whole mouse genome (GRCm38) and mBT-001 viral genome.
Read count for each murine and viral gene was quantified using HTSeq-count.
Genome_build: GRCm38
Supplementary_files_format_and_content: Table_readcount.txt: Raw read count table.

source_name: CT26-induced tumour

extract_protocol:
Total RNA was extracted from whole tumours using the Qiagen kit RNeasy Plus Mini.
Strand specific 3' mRNA sequencing libraries were prepared by Integragen, SA.

value: BALB/c

value: CT26-induced tumour

tag: tumor harvesting time (days)


title: TMZ-resistant U87MG_SiHDAC6

value: TMZ-resistant U87MG


title: FB_TAC_8Weeks_RNA_seq_rep2

value: Male

value: C57Bl6N mice (Charles River)

value: isolated cardiac fibroblast cells

value: 8-10 weeks


title: FB_Sham_RNA_seq_rep3

value: sham


title: MEC1_ctr_RNAseq_rep2


title: FB_Sham_RNA_seq_rep2


title: VVGM-CTLA4 -treated tumours D18 rep9

description:
865
Table_readcount.txt


title: TMZ-resistant U87MG_Non-targeting Control

value: Non-targeting Control siRNAs


title: FB_TAC_1Week_RNA_seq_rep3

value: TAC


title: MEC1_ctr_RNAseq_rep1


title: VVGM-CTLA4 -treated tumours D18 rep8

description:
428
Table_readcount.txt


title: FB_Sham_RNA_seq_rep1


title: M605

city: Duarte

first: Debbie

last: Thurmond

address: City of Hope Beckman Research Institue

department: Molecular and Cellular Endocrinology

institute: City of Hope

description: RNA-Seq data, Pak1Loxp-Dox, replicate 3

data_processing:
Real Time Analysis (RTA, v1.18.64) was used for base calling, and bcl2fastq v2.18 was used to generate FASTQ files
Reads aligned using TopHat2 (v2.0.14), with --no-coverage-search --library-type fr-firststrand
Unique reads quantified using htseq-count (version 0.6.0), with database generated from TxDb.Mmusculus.UCSC.mm10.knownGene (Bioconductor annotations, downloaded 12/22/2016).
Genome_build: mm10
Supplementary_files_format_and_content: FPKM normalized expression (using aligned reads and TxDb annotations in R) and read counts (calculated using htseq-count)

source_name: mouse skeletal muscle

growth_protocol: Inducible skeletal muscle specific PAK1 knock out and over expression mouse were driven by doxycyclin

extract_protocol:
RNAs were isolated by TRIZol method
KAPA Stranded RNA-Seq Kit
stranded polyA RNA-Seq

treatment_protocol: 2 mg/mL of doxycyclin conferring skeletal muscle specific over expression or knocking out of PAK1

tag: group

tag: dox

value: -Dox

tag: pak1 status


title: MEC1_Axin2_RNAseq_rep1


title: Kidney Medulla-RNA-seq-Donor3

city: Seattle

first: Shreeram

last: Akilesh

state: Washington

address: 1959 NE Pacific St, Box 356100

institute: University of Washington

data_processing:
PEx150 sequence reads were trimmed to remove adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step.
Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. The hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads that fell within exon regions were counted. Since a strand-specific library preparation was performed, the reads were strand-specifically counted
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: bam; bigwig; RNA-seq reads
Supplementary_files_format_and_content: csv; raw gene counts (not normalized)

source_name: Kidney Medulla

extract_protocol:
Kidney cortex and medulla tissues were stabilized overnight at 4°C in RNALater before long term storage at -80°C
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: rin

value: Kidney Medulla

tag: donor number


title: EC_TAC_8Weeks_RNA_seq_rep3

source_name: isolated cardiac endothelial cells

tag: gender

tag: strain

value: isolated cardiac endothelial cells

tag: age


title: VVGM-CTLA4 -treated tumours D18 rep6

description:
858
Table_readcount.txt

tag: tissue

tag: treatment


title: EC_TAC_8Weeks_RNA_seq_rep2


title: P5_rep2

city: Napoli

first: Annamaria

last: Carissimo

address: via Castellino

country: Italy

institute: Tigem

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files including raw counts

source_name: fibroblast

growth_protocol: culture medium for fibroblasts cells: D-MEMF12 plus 10% fetal bovine serum and 1% penicillin and streptomycin

extract_protocol:
Service Ngdx: RNA> Extraction - R015.2
3'DGE mRNA-seq (research*/clinical**/diagnostic***) grade sequencing service (Next Generation Diagnostics srl)
3'DGE mRNA-seq

treatment_protocol: no

value: TAB2 patient


title: VVGM-CTLA4 -treated tumours D18 rep5

description:
490
Table_readcount.txt


title: Kidney Medulla-RNA-seq-Donor1


title: Kidney Medulla-RNA-seq-Donor2


title: U87MG_Non-targeting Control


title: P5_rep1


title: P6_rep1


title: EC_TAC_8Weeks_RNA_seq_rep1


title: Kidney Cortex-RNA-seq-Donor3

source_name: Kidney Cortex

value: Kidney Cortex


title: EC_TAC_1Week_RNA_seq_rep3


title: VVGM-CTLA4 -treated tumours D18 rep4

description:
431
Table_readcount.txt


title: EC_TAC_1Week_RNA_seq_rep2


title: P4_rep2


title: Kidney Cortex-RNA-seq-Donor2


title: P4_rep1


title: VVGM-CTLA4 -treated tumours D18 rep2

description:
794
Table_readcount.txt


title: Kidney Cortex-RNA-seq-Donor1


title: VVGM-CTLA4 -treated tumours D18 rep7

description:
978
Table_readcount.txt


title: EC_TAC_1Week_RNA_seq_rep1


title: P3_rep2


title: IgG_Control

city: Bethesda

first: Christophe

middle: E

last: Redon

state: MD

address: 37 Convent Drive

institute: NIH

description:
Rabbit IgG control
ChIP-Seq reads from Ntera2

data_processing:
Aligned fastq file of each sample to human reference genome (version hg19) with novoalign (novocraft version 3.08.00), sorted by coordinate with novosort (novocraft version 3.08.00), removed duplicates with MarkDuplicates (Picard tools version 2.9.4).
Peak calling using MACS2.0, band width = 300, model fold = [5, 50], qvalue cutoff = 1.00e-02, Range for calculating regional lambda is: 1000 bps and 10000 bps, Broad region calling on
HiSeq 4000 paired read 100 nucleotides sequencing, Illumina Genome Analyzer.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: Bed file format of ChipSeq.

source_name: Embryonic Carcinoma

growth_protocol: Cancer cells were grown in DMEM medium, 10% FBS.

extract_protocol:
Chromatin immunoprecipitation was performed using chromatin isolated from NTera2 cell line as explained in Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):8338-43. doi: 10.1073/pnas.1424705112. Anti-BEND3 (S3242-2) and rabbit IgG antibodies were used to pull the chromatin. The ChIPseq libraries were prepared with the Hyper Library Construction Kit from Kapa Biosystems with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 10 cycles. The libraries were quantitated by PCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1. Fasta files were generated and demultiplexed with the bcl2fast v2.17.1.14 Conversion Software (Illumina). Adaptors have been trimmed from the 3'-end of the reads. Construction of ChIP-Seq libraries and sequencing on the HiSeq 4000 was carried out at the Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign (UIUC).
Hyper Library Construction Kit from Kapa Biosystems.
HiSeq 4000 paired-end sequencing.

tag: cell type

value: Cultured cancer cell line

tag: chip antibody

value: Rabbit IgG


title: BEND3_Chip2

description:
Anti-BEND3 antibody (S3242-2, In house)
ChIP-Seq reads from Ntera2

tag: cell line

value: Anti-BEND3 Rabbit


title: VVGM-CTLA4 -treated tumours D18 rep1

description:
486
Table_readcount.txt

value: BALB/c

value: CT26-induced tumour


title: EC_Sham_RNA_seq_rep3

value: Male


title: P3_rep1


title: VV empty-treated tumours D18 rep10

description:
859
Table_readcount.txt

value: VV empty


title: BEND3_Chip1


title: EC_Sham_RNA_seq_rep1

value: C57Bl6N mice (Charles River)


title: P2_rep1


title: CM_TAC_8Weeks_RNA_seq_rep3

source_name: isolated cardiac myocytes cells

value: heart cardiomyocytes

value: 8-10 weeks


title: P2_rep2


title: cranial NCC ATAC prdm16 mutant rep2

city: Easton

first: Ezra

last: Lencer

state: PA

address: 746 High Street

department: Department of Biology

institute: Lafayette College

data_processing:
RNA-seq:
Sequenced reads were trimmed for adaptor sequence and mapped to the danRer11 genome using TopHat v2.1.1
Differential gene expression was calculated using Cufflinks
ATAC-seq:
Adapters and barcodes were removed from paired end reads using Cutadapt.
Trimmed paired-end sequencing reads were aligned to the zebrafish genome (danRer11) with Bowtie2 (v2.4.4) with default parameters (--end-to-end, --sensitive).
Peaks were called using the Genrich peak calling program (https://github.com/jsh58/Genrich), with the following parameters: -r, -p0.01, -a200, -j, -e MT
Genome_build: danRer11
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each sample and differentially expressed gene differences between wildtype and each mutant across replicates. All replicates are included in one file for each mutant.
Supplementary_files_format_and_content: bigwig files were generated using bedtools v2.30.0
Supplementary_files_format_and_content: narrowPeak files were generated from Genrich peak calling program.

organism: Danio rerio

source_name: sox10:GFP cranial NCC

extract_protocol:
sox10:GFP positive cranial NCC were isolated via FAC-sorting from dissociated pooled zebrafish embryos, nuclei were collected by centrifugation and subjected to tagmentation with the Nextera Tagmentation DNA enzyme and buffer from Illumina. Tagmented DNA was purified using Zymogen Clean and Concentrator kit
libraries were amplified and indexed using NEBNext High Fidelity2x PCR master mix and custom primers

value: cranial NCCs

value: 48 hours post fertilization

tag: genotype

value: sox10:GFP positive cells

tag: molecule subtype

value: Tagmented DNA


title: cranial NCC ATAC prdm16 mutant rep1


title: VVGM-CTLA4 -treated tumours D18 rep3

description:
705
Table_readcount.txt


title: P1_rep1


title: CM_TAC_8Weeks_RNA_seq_rep2

value: TAC


title: CM_TAC_8Weeks_RNA_seq_rep1


title: cranial NCC ATAC prdm16 wt rep2

value: wildtype


title: VV empty-treated tumours D18 rep7

description:
427
Table_readcount.txt


title: P1_rep2

value: TAB2 patient


title: VV empty-treated tumours D18 rep8

description:
722
Table_readcount.txt


title: cranial NCC ATAC prdm16 wt rep1


title: C5_rep2

value: unaffected individual


title: VV empty-treated tumours D18 rep5

description:
915
Table_readcount.txt


title: CM_TAC_1Week_RNA_seq_rep3


title: C5_rep1


title: CM_TAC_1Week_RNA_seq_rep2


title: EC_Sham_RNA_seq_rep2

value: isolated cardiac endothelial cells

value: sham


title: cranial NCC ATAC prdm3 mutant rep2


title: VV empty-treated tumours D18 rep4

description:
977
Table_readcount.txt

value: BALB/c


title: VV empty-treated tumours D18 rep9

description:
996
Table_readcount.txt

value: CT26-induced tumour


title: cranial NCC ATAC prdm3 mutant rep1


title: VV empty-treated tumours D18 rep6

description:
998
Table_readcount.txt


title: C4_rep2


title: P6_rep2


title: CM_TAC_1Week_RNA_seq_rep1

value: Male


title: VV empty-treated tumours D18 rep3

description:
488
Table_readcount.txt

value: VV empty


title: VV empty-treated tumours D18 rep2

description:
999
Table_readcount.txt


title: cranial NCC ATAC prdm3 wt rep2


title: CM_Sham_RNA_seq_rep3

value: C57Bl6N mice (Charles River)


title: C3_rep2


title: CM_Sham_RNA_seq_rep2

value: heart cardiomyocytes


title: cranial NCC mRNA prdm16 mutant rep3

description:
processed data file: PRDM16_DEG.txt
4_prdm16_mutant_S31_L003

extract_protocol:
sox10:GFP positive cranial NCC were isolated via FAC-sorting from dissociated pooled zebrafish embryos and RNA was havested using Trizol reagent and the Zymogen Direct-zol RNA miniprep kit
cDNA libraries were generated using the Clonetech Pico Library Prep kit and standard Illumina protocols


title: CM_Sham_RNA_seq_rep1

value: 8-10 weeks


title: VV empty-treated tumours D18 rep1

description:
460
Table_readcount.txt


title: untreated tumours D18 rep5

description:
857
Table_readcount.txt

value: untreated


title: C3_rep1


title: C2_rep2


title: cranial NCC mRNA prdm16 mutant rep2

description:
processed data file: PRDM16_DEG.txt
3_prdm16_mutant_cleaned_S33_L003

value: cranial NCCs

value: 48 hours post fertilization


title: Patient9_Normal [p031n]

city: Berlin

first: Philip

last: Bischoff

address: Charitéplatz 1

department: Institute of Pathology

institute: Charité - Universitätsmedizin Berlin

description: single-cell RNA sequencing

data_processing:
raw reads were assigned and count matrices produced by cellranger, version 3.0.2, reference GRCh38
raw data was loaded, merged and filtered in R using Seurat v4
Genome_build: GRCh38
Supplementary_files_format_and_content: meta data (epithelial_metadata.tsv.gz, immune_metadata.tsv.gz, stromal_metadata.tsv.gz): Meta data of the cells, one row per cell, contains information about cell type clusters, signature scores, etc. Tab delimited files.
Supplementary_files_format_and_content: cellranger files (p0XXt/n.h5): contain filtered cellranger output files.
Supplementary_files_format_and_content: count matrices (p0XXt/n.tsv.gz): contain the raw expression counts for all cells of a sample. Each row is a gene, each column is a cell. Cell ids correspond to the cell ids in the meta data table.

source_name: C34.3 (Lung, lower lobe)

extract_protocol:
drop seq
10x genomics 3' v3

treatment_protocol: surgical resection

tag: tissue type

value: Normal Lung

tag: tnm stage

tag: histological subtype


title: RNA-Seq small pre-B cells KO rep2

first: Guixin

last: Ruan

address: 1088 Xueyuan Avenue

department: Biology

institute: Southern University of Science and Technology

description: RNA-Seq small pre-B cells KO

data_processing:
RNA-Seq: Sequence reads were trimmed using Trimmomatic to remove adaptors. Reads were then mapped to mouse GRCm38 genome using Hisat2 (version 2.1.0) with default parameters. Gene expression mapped to exons was estimated using featureCounts (version 1.6.1) with default parameters. Data were calculated to TPM for normalization to control the variation. DESeq2 was used to calculate differential gene expression. Statistically significant genes (adjusted P-value < 0.05 by Benjamini and Hochberg’s approach) with > 2-fold change were considered as differentially expressed genes. The results were only considered for genes expressed above 1 TPM.
Hi-C-Seq: Analysis of the sequencing data was truncated, aligned and filtered using HiCUP (version 0.7.4) pipeline by applying Bowtie2 and Samtools (version 1.9). Juicer tools (version 1.22.01) were used to generate normalized contact matrices. The resolution of the Hi-C data was calculated according to reference(Rao et al., 2014) using the calculate_map_resolution script in Juicer. Chromatin interactions were called using HiCCUPS and were visualized at the resolution of 5-kb using Juicebox (version 1.11.08).
Genome_build: GRCm38
Supplementary_files_format_and_content: txt files contain the raw counts generated using featureCounts; hic files are binary outputs generated by HiCUP pipeline

source_name: small pre-B

extract_protocol:
Small pre-B cells were sorted using flow cytometry. The total RNA of each sample was extracted using the RNeasy Mini Kit (Qiagen), quantified and qualified by Agilent 2100 Bioanalyzer. The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer protocol.

value: Usp39 fl/fl cd19-cre

tag: cell preparation

value: FACS sorted from bone marrow

value: small pre-B


title: cranial NCC mRNA prdm16 mutant rep1

description:
processed data file: PRDM16_DEG.txt
2_prdm16-mutant_cleaned_S32_L003

value: sox10:GFP positive cells


title: untreated tumours D18 rep4

description:
793
Table_readcount.txt

tag: tumor harvesting time (days)


title: untreated tumours D18 rep3

description:
871
Table_readcount.txt


title: C2_rep1

tag: group

value: unaffected individual


title: RNA-Seq small pre-B cells KO rep1

description: RNA-Seq small pre-B cells KO


title: cranial NCC mRNA prdm3 mutant rep3

description:
processed data file: PRDM3_DEG.txt
4_prdm3_mutant_S28_L003


title: C1_rep2


title: untreated tumours D18 rep2

description:
860
Table_readcount.txt


title: RNA-Seq small pre-B cells WT rep1

description: RNA-Seq small pre-B cells WT

value: Usp39 fl/fl


title: C4_rep1


title: untreated tumours D18 rep1

description:
701
Table_readcount.txt

value: BALB/c


title: RNA-Seq small pre-B cells WT rep2

description: RNA-Seq small pre-B cells WT


title: C1_rep1


title: cranial NCC ATAC prdm3 wt rep1

value: wildtype

value: Tagmented DNA


title: NCI-H460 cells, PRMT5kd3

city: shanghai

first: bingqian

last: zhou

state: 上海

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome,(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for all Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and all sample

source_name: Human lung adenocarcinoma cell line

growth_protocol: NCI-H460 cells were routinely cultured in RPMI-1640.

extract_protocol:
Medium was removed. Cells were washed by sterile PBS, and RNA was harvested using Trizol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Lentivirus infection for shRNA against GFP or PRMT5.

value: PRMT5 knockdown

value: lentivirus infection NCI-H460 for shRNA against PRMT5


title: cranial NCC mRNA prdm3 mutant rep1

description:
processed data file: PRDM3_DEG.txt
1_prdm3_mutant_S29_L003


title: RNA-Seq pre-pro-B cells KO rep2

description: RNA-Seq pre-pro-B cells KO

source_name: pre-pro-B

extract_protocol:
Pre-pro-B cells were sorted using flow cytometry. The total RNA of each sample was extracted using the RNeasy Mini Kit (Qiagen), quantified and qualified by Agilent 2100 Bioanalyzer. The poly(A) mRNA isolation was performed using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB).
Libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina according to the manufacturer protocol.

value: Usp39 fl/fl mb1-cre

value: pre-pro-B


title: VVGM-CTLA4 -treated tumours D11 rep10

description:
721
Table_readcount.txt

value: CT26-induced tumour


title: cranial NCC mRNA wt rep3

value: cranial NCCs


title: NCI-H460 cells, PRMT5kd2

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院


title: VVGM-CTLA4 -treated tumours D11 rep9

description:
791
Table_readcount.txt


title: cranial NCC mRNA wt rep2

value: 48 hours post fertilization


title: VVGM-CTLA4 -treated tumours D11 rep8

description:
856
Table_readcount.txt


title: NCI-H460 cells, GFPkd3

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院

value: control

value: lentivirus infection NCI-H460 for shRNA against GFP


title: cranial NCC mRNA wt rep1


title: RNA-Seq pre-pro-B cells WT rep2

description: RNA-Seq pre-pro-B cells WT

value: FACS sorted from bone marrow


title: VVGM-CTLA4 -treated tumours D11 rep7

description:
723
Table_readcount.txt


title: VVGM-CTLA4 -treated tumours D11 rep6

description:
980
Table_readcount.txt


title: cranial NCC mRNA prdm3 mutant rep2

description:
processed data file: PRDM3_DEG.txt
3_prdm3_mutant_cleaned_S30_L003


title: SPF sample 4

city: Amsterdam

first: Hein

middle: te

last: Riele

address: Plesmanlaan 121

department: Tumor Biology & Immunology

country: Netherlands

institute: The Netherlands Cancer Institute

data_processing:
The 65 bp single end reads were mapped to the aligned against the mouse reference genome (Ensembl build 38) using TopHat (version 2.1.0).
TopHat was supplied with a known set of gene models based on Ensembl GTF version 77 and was guided to use the first-strand as the library-type. As additional parameters --prefilter-multihits and –no coverage were used.
In order to count the number of reads per gene, a custom script, Itreecount (https://github.com/NKI-GCF/itreecount), has been used. This script is based on the same ideas as HTSeq-count. A list of the total number of uniquely mapped sequencing reads for each gene that is present in the provided Gene Transfer Format (GTF) file was generated.
Genome_build: Ensembl GRCm38
Supplementary_files_format_and_content: Tab-separated file with number of reads per gene/sample. Qlucore Omics explorer 3.6

source_name: whole jejunum

growth_protocol: intestines were isolated and flash frozen

extract_protocol:
Samples were crushed under cryogenic conditiones, RNA was extracted using the Qiagen Rneasy mini kit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: jejunum

tag: condition

value: SPF


title: RNA-Seq pre-pro-B cells WT rep1

description: RNA-Seq pre-pro-B cells WT

value: Usp39 fl/fl


title: NCI-H460 cells, GFPkd2

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院


title: HVEMfloxCD4 rep 4

city: San Diego

first: John

last: Sedy

address: 10770 Wateridge Cir

institute: AnaptysBio

description:
Whoie bacteria isolated from mouse fecal pellets
Bacterial DNA

data_processing:
Raw data files were processed and analyzed with the CLC Microbial Genomics Module
Taxonomy assigned using BLAST against NCBI 16S Bacteria and Archea database
Genome_build: NCBI Bacteria and Archea database

organism: mouse gut metagenome

source_name: Fecal pellet DNA

extract_protocol:
DNA was extracted using QIAmp Fast DNA stool mini kit.
Library constructed using Illunina protocol for bacterial 16S ribosomal DNA gene sequencing

treatment_protocol: Treated animals were administered antibodies i.p.

tag: background

value: HVEMflox

value: CD4 cre


title: HVEMfloxCD4 rep 2


title: HVEMfloxCD4 rep 3


title: conventional sample 4

tag: strain

value: conventional


title: NCI-H460 cells, GFPkd1

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院


title: HVEMfloxCD4 rep 1


title: scATAC-Seq StageII-JNKIN8

city: Beijing

last: Lyu

address: No.5 Yiheyuan Road Haidian District

department: School of Life Sciences

institute: Peking University

data_processing:
The single-cell ATAC-seq reads were mapped to human reference genome hg19 using Cell Ranger ATAC v1.2.0.
Genome_build: hg19
Supplementary_files_format_and_content: gzipped .tsv files of cellrangerATAC output containing fragment data of each cell and their .tbi index file.

source_name: human somatic cells during chemical reprogramming stage II without JNKIN8

growth_protocol: Human embryonic fibroblasts (HEFs) were cultured in high glucose DMEM supplemented with 15% Fetal Bovine Serum (FBS), 1% GlutaMAX™, 1% MEM Non-Essential Amino Acids Solution (NEAA), 1% Penicillin-Streptomycin and 0.055 mM 2-mercaptoethanol under 21% O2, 5% CO2 at 37 ℃.

extract_protocol:
The nuclei were isolated and washed according to the method supplied by 10X Gemomis: Nuclei Isolation for Single Cell ATAC Sequencing (CG000169). Then the nucleus were resuspend by chilled Diluted Nuclei Buffer (10xGenomics; 2000153). The volume of Diluted Nuclei Buffer used to resuspend nuclei was based on the number of starting cells and the final target nuclei concentration. Countstar (Rigel S2) was used to count the nuclei. The nuclei were then immediately proceed to single cell ATAC-seq libraries.
Following the 10x Genomics single cell ATAC solution, by using Chromium Chip E Single Cell Kit(Product Code 1000156 ) and Chromium Single Cell ATAC Library & Gel Bead Kit (Product Code 1000110), the nucleus in bulk sample are partitioned into nanoliter-scale Gel Beads-inemulsion (GEMs), a pool of ~750,000 10x Barcodes is sampled to separately and uniquely index the transposed DNA of each individual nucleus, and libraries are generated (performed by CapitalBio Technology, Beijing). The libraries was sequenced using an Illumina Novaseq sequencer with a sequencing depth of at least 25k read pairs per nucleus with pair-end 50 bp (PE50) reading strategy (performed by CapitalBio Technology, Beijing).
single cell ATAC-seq

treatment_protocol: Human somatic cells were treated with different small molecule combinations during human chemical reprogramming.


title: scATAC-Seq StageII-5azac

source_name: human somatic cells during chemical reprogramming stage II without 5azac


title: conventional sample 3


title: VVGM-CTLA4 -treated tumours D11 rep3

description:
724
Table_readcount.txt

source_name: CT26-induced tumour

value: BALB/c


title: VVGM-CTLA4 -treated tumours D11 rep4

description:
874
Table_readcount.txt


title: scATAC-Seq StageII

description: StageII

source_name: human somatic cells during chemical reprogramming stage II


title: HVEMfloxCD19 rep 3

value: CD19 cre


title: RNA-Seq pre-pro-B cells KO rep1

city: Shenzhen

description: RNA-Seq pre-pro-B cells KO

value: Usp39 fl/fl mb1-cre


title: conventional sample 2


title: NCI-H460 cells, PRMT5kd1

address: 上海市杨浦区控江路新华医院

institute: 上海交大医学院附属新华医院

value: PRMT5 knockdown

value: lentivirus infection NCI-H460 for shRNA against PRMT5


title: HVEMfloxCD19 rep 2


title: HVEMfloxCD19 rep 1


title: scATAC-Seq fibroblast

description: fibroblast

source_name: human embryonic fibroblasts


title: SPF sample 2


title: VVGM-CTLA4 -treated tumours D11 rep1

description:
461
Table_readcount.txt

value: CT26-induced tumour


title: VV empty-treated tumours D11 rep10

description:
702
Table_readcount.txt

value: VV empty


title: Sh60_S2_ATGTCAGA_L006_R1_001

city: Urbana

first: Supriya

middle: G

last: Prasanth

state: Illinois

address: 601S Goodwin Avenue

department: Cell and Developmental Biology

institute: University of Illinois Urbana-Champaign

data_processing:
Base calling was performed by FASTQC
Alignment using STAR v2.7.6a using UCSC iGenomes hg19 release gene annotation, genes.gtf:          STAR --runThreadN 8 \        --genomeDir hg19 \        --readFilesIn <FASTQ> \        --sjdbGTFfile genes.gtf \        --outFileNamePrefix <SAMPLE_NAME>_ \        --sjdbGTFtagExonParentGene gene_id \        --outSAMtype BAM SortedByCoordinate \        --quantMode GeneCounts \        --outSAMmultNmax 1 \        --outMultimapperOrder Random \        --outFilterMultimapNmax 200 \        --limitGenomeGenerateRAM 40000000000
Then aligned (using UCSC iGenomes hg19 release gene annotation, genes.gtf):          STAR --runThreadN 8 \        --genomeDir hg19 \        --readFilesIn <FASTQ> \        --sjdbGTFfile genes.gtf \        --outFileNamePrefix <SAMPLE_NAME>_ \        --sjdbGTFtagExonParentGene gene_id \        --outSAMtype BAM SortedByCoordinate \        --quantMode GeneCounts \        --outSAMmultNmax 1 \        --outMultimapperOrder Random \        --outFilterMultimapNmax 200 \        --limitGenomeGenerateRAM 40000000000
Gene counts using featureCounts, from the Subreads v2.0.0 release:        featureCounts -T 8 -s 2 -g \      gene_id -t $params.countFeature \      -o <SAMPLE_NAME>_featCounts.txt -a genes.gtf <SAMPLE_BAM>
Genome_build: GRCh37
Supplementary_files_format_and_content: Individual files include gene count information are presented in txt format

source_name: Ntera-2 cell line

growth_protocol: NTERA2 cells were periodically propagated in media plate filled with DMEM high glucose cell culture media, supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotic

extract_protocol:
Total RNA was extracted using RNeasy minikit from Qiagen
4 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 using Illumina TruSeq Stranded mRNA Library Prep and single-end sequencing.

tag: genotype/variation

value: BEND3 sh60

value: ES-derived human lung carcinoma cell line

tag: clone


title: HVEMflox rep 3

value: WT

tag: treatment


title: SPF sample 1

value: FVB

tag: tissue


title: VV empty-treated tumours D11 rep9

description:
725
Table_readcount.txt


title: conventional sample 1

value: jejunum


title: Sh60_S1_GATCAGAT_L006_R1_001

tag: cell type


title: VV empty-treated tumours D11 rep8

description:
997
Table_readcount.txt


title: HVEMflox rep 2


title: BTLAfloxCD4 rep 5

value: BTLAflox


title: VV empty-treated tumours D11 rep7

description:
868
Table_readcount.txt


title: HVEMflox rep 1


title: IDD_3.miRNA

city: Nanning

first: Zhimin

last: Li

address: Shuangyong Road

institute: School

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, then mapped to hg38 whole genome using STAR v2.7.1a.
Use the StringTie 2.0.4 to assemble RNA-Seq alignments into potential transcripts. Under the guidance of the gtf gene annotation file, filter out known lncRNA and potential novel lncRNA.
Use the featureCounts v2.0.0 to obtain the reads count of each samples. Then, use  and DESeq2 v1.26.0 to calculate TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value of the transcript level LncRNA as the expression profile of the LncRNA, the fold change and p-value between two/group samples to screen for differential expression of LncRNA and mRNA.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to known miRNA and genome using bowtie v1.2.3.
Use custom perl script to obtain the reads count of each samples from alignment, Reads Per Megabase of library size (RPM) were calculated using a protocol from Chepelev et al.
Use DEseq2 to call differential expression miRNA
Genome_build: HG38
Supplementary_files_format_and_content: TPM values for each Sample.

source_name: IDD_nucleus pulposus

extract_protocol:
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..
RNA labraries were prepared for sequencing using standard protocols

treatment_protocol: Samples of nucleus pulposus (NP) tissue were obtained from IDD patients and those with spinal cord injury who had undergone surgery. NP tissue was shock-frozen immediately in liquid nitrogen after isolated.

tag: subject status

value: intervertebral disc degeneration (IDD) patient

tag: age

value: nucleus pulposus (NP)


title: P93

city: Winston-Salem

first: Jeff

last: Chou

state: NC

address: Medical Center Blvd

institute: Atrium Health Wake Forest Baptist

description: Sample 25

data_processing:
Adapter contamination was cleaned with Trimmomatic V0.32.
Reads were aligned to the reference human genome GRCh38 using the STAR sequence aligner, and gene counts determined using featureCounts software version 2.0.3.
Counts were normalized for gene length and sequencing depth using the Transcripts Per Million (TPM) method. To account for differences between the Phase 1 samples (paired-end sequenced) and Phase II samples (single-end sequenced), log2 normalized counts were mean-centered within Phase groups. Reads were annotated with Ensembl identifiers resulting in a gene matrix of 57,820 genes. This matrix was filtered to exclude those genes having >50% zero values in either the Phase I or Phase II datasets.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with counts normalized using the Transcripts Per Million (TPM) method and annotated with Ensembl IDs.

source_name: Bone Marrow-Derived Mononuclear Cells

extract_protocol:
Bone marrow biopsies were performed within 2 weeks of enrollment. Mononuclear cells were isolated by Ficoll gradient separation and stored at −80°C until use. Total RNA was isolated using the Qiagen RNeasy RNA isolation kit per the manufacturer’s instructions. RNA samples were assessed for quality by electrophoretic tracing (Agilent Bioanalyzer).
cDNA libraries were generated using the Illumina TruSeq Stranded Total RNA kit with Ribo-Zero rRNA depletion according to the manufacturer’s instructions. Library size distributions were inspected for quality using an Agilent 2100 Bioanalyzer. Library quantity was measured on a Qubit 3.0 (Thermo Fisher, USA). Indexed libraries were pooled and sequenced to a target read depth of 30-50M reads per library using 150 bp paired-end sequencing or 100 bp single-end sequencing on an Illumina NextSeq 500 high-output flow cell.

tag: patient age (yrs)

tag: patient gender

value: female

tag: clinical trial phase

value: II

tag: inclusion criteria

value: histologically or cytological documented relapsed and/or refractory AML

tag: ecog performance status

value: less than or equal to 3

tag: treatment response status

value: Responder


title: P96

description: Sample 13

value: male

value: I

value: Failure


title: P88

description: Sample 12


title: LacZ_S1_CAGATCAT_L006_R1_001

value: BEND3 LacZ


title: VVGM-CTLA4 -treated tumours D11 rep2

description:
976
Table_readcount.txt

extract_protocol:
Total RNA was extracted from whole tumours using the Qiagen kit RNeasy Plus Mini.
Strand specific 3' mRNA sequencing libraries were prepared by Integragen, SA.

value: BALB/c

value: CT26-induced tumour

tag: tumor harvesting time (days)


title: IDD_3.mRNA_lncRNA


title: BTLAfloxCD4 rep 4

tag: genotype

value: CD4 cre


title: VV empty-treated tumours D11 rep5

description:
1000
Table_readcount.txt

value: VV empty


title: SPF sample 3

value: FVB

value: jejunum

tag: condition

value: SPF


title: BTLAfloxCD4 rep 3

tag: background

value: BTLAflox


title: VVGM-CTLA4 -treated tumours D11 rep5

description:
873
Table_readcount.txt

tag: strain


title: P86

description: Sample 24


title: P85B2

description: Sample 17

value: female


title: VV empty-treated tumours D11 rep4

description:
867
Table_readcount.txt


title: BTLAfloxCD4 rep 2


title: IDD_2.mRNA_lncRNA

value: intervertebral disc degeneration (IDD) patient

value: nucleus pulposus (NP)


title: VV empty-treated tumours D11 rep3

description:
430
Table_readcount.txt


title: LacZ_S3_ACTTGAAT_L006_R1_001

tag: genotype/variation

value: ES-derived human lung carcinoma cell line

tag: clone


title: P79

description: Sample 23

value: II

value: histologically or cytological documented relapsed and/or refractory AML

value: less than or equal to 3

value: Responder


title: BTLAfloxCD4 rep 1

tag: treatment


title: IDD_1.miRNA

tag: tissue


title: P72

description: Sample 22

value: male

value: Failure


title: VV empty-treated tumours D11 rep1

description:
462
Table_readcount.txt

value: BALB/c

value: CT26-induced tumour


title: VV empty-treated tumours D11 rep2

description:
914
Table_readcount.txt

value: VV empty


title: BTLAfloxCD19 rep 4

value: CD19 cre


title: P6

description: Sample 18


title: IDD_1.mRNA_lncRNA

tag: subject status


title: BTLAfloxCD19 rep 5


title: VV empty-treated tumours D11 rep6

description:
866
Table_readcount.txt


title: untreated tumours D11 rep5

description:
487
Table_readcount.txt

value: untreated


title: control_3.miRNA

source_name: control_nucleus pulposus

value: control

tag: age


title: BTLAfloxCD19 rep 3

value: BTLAflox


title: P50

description: Sample 21

tag: patient age (yrs)

value: female


title: control_3.mRNA_lncRNA


title: P40

description: Sample 20

tag: patient gender


title: IDD_2.miRNA

value: intervertebral disc degeneration (IDD) patient


title: control_2.miRNA

value: nucleus pulposus (NP)


title: untreated tumours D11 rep4

description:
913
Table_readcount.txt


title: BTLAfloxCD19 rep 2


title: BTLAfloxCD19 rep 1


title: control_2.mRNA_lncRNA


title: untreated tumours D11 rep2

description:
458
Table_readcount.txt


title: P33

description: Sample 5

tag: clinical trial phase

value: I


title: BTLAflox rep 5

value: WT


title: control_1.miRNA


title: untreated tumours D11 rep1

description:
795
Table_readcount.txt


title: P27

description: Sample 19

value: II

tag: inclusion criteria

value: histologically or cytological documented relapsed and/or refractory AML


title: BTLAflox rep 4


title: control_1.mRNA_lncRNA


title: P203B2

description: Sample 16

tag: ecog performance status

value: less than or equal to 3

value: Responder


title: 45 days old, CnaTg, JIB-04, replicate 3

city: Dallas

first: Elisabeth

last: Martinez

address: 6000 Harry Hines Blvd

institute: UT Southwestern Medical Center

data_processing:
Illumina sequencer (NovaSeq 6000 or HiSeq X Ten) was used at Novogene Corp.
fastq files were aligned to GRCm38 mouse reference genome using STAR v2.7.1a
bam files were processed to remove read duplicates using Picard MarkDuplicates from GATK v4.1.2
FPKM values were obtained using Cufflinks v2.2.1
FPKM values were upper-quartile normalized, then log-transformed
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include log2FPKM values for each sample

source_name: 45 days old_CnaTg_JIB-04_heart

extract_protocol:
RNA were extract using Trizol.
Libraries were prepared using eukaryotic non-directional mRNA library prep kits, compatible with Illumina sequencing.

treatment_protocol: Mice were treated with vehicle or JIB-04 starting from 4 or 5 weeks of age at 50 mg/Kg, 3 times per week, and hearts were collected at indicated age.

tag: mouse reference

value: postnatal day 45

value: calcineurin transgenic

value: heart


title: 45 days old, CnaTg, JIB-04, replicate 2


title: P198B2

description: Sample 11

tag: treatment response status

value: Failure


title: BTLAflox rep 2

tag: genotype


title: P194B2

description: Sample 10

value: male


title: P181B2

description: Sample 9


title: untreated tumours D11 rep3

description:
869
Table_readcount.txt

value: BALB/c

value: CT26-induced tumour

value: untreated

tag: tumor harvesting time (days)


title: 45 days old, CnaTg, JIB-04, replicate 1


title: Serum_7day_371901

data_processing:
Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).
Reads aligned to  reference genome (GENCODE human release 30 GRCh38) using STAR (v2.6.1d)
Aligned data were read into R and summarized as counts per gene using the Bioconductor GenomicAlignments package
Differential analysis was performed by voom method in the Bioconductor limma package.
Genome_build: GRCh38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of gene counts, with Ensembl IDs in the first column, and the sample names in the header

source_name: 3D human kidney proximal tubule MPS

growth_protocol: Nortis Triplex™ devices were filled with 6 mg/mL of rat tail collagen I, and left overnight at room temperature to allow the collagen I matrix to solidify.  The mandrels of the MPS platforms were removed, leaving behind hollow channels through the collagen I matrix.  Cell chambers were coated with a 5 µg/mL mouse collagen IV to facilitate human PTECs adhesion.  T-flask cultures of PTECs were trypsinized to obtain single cell suspensions.  The cells were resuspended with PTEC maintenance media at a concentration of ~20 ×10^6 cells/mL and 2-2.5 µL were injected into the collagen IV-coated channels of the MPS.  The cells were allowed to attach for 3 hours before starting perfusion at a rate of 1.0 µL/min.  PTECs were cultured under flow for at least 7 days to form the tubule cell structures.  Only kidney MPS that exhibited tubules with >90% channel coverage and continuous media flow characteristics were selected for use in functional experiments.

extract_protocol:
Cells cultured in the kidney MPS were isolated by injecting 100 uL buffer RLT (Qiagen, 79216) and the lysate was collected at the outflow port into an additional 900 uL of buffer RLT then frozen at -80°C until extraction. Total RNA was isolated using the Qiagen RNeasy Micro Kit.
Total RNA was normalized to 2ng in a total volume of 9ul and then transcribed to cDNA in a dedicated PCR clean workstation using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Bio, Mountain View, CA).  Sequencing libraries were constructed from cDNA using the SMARTer ThruPLEX DNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).

treatment_protocol: Kidney MPS were exposed to maintenance media or maintenance media spiked with 2% normal human serum or 720 ug/mL albumin for either 8 hours or 7 days.

value: 3D human kidney proximal tubule MPS

value: Serum

tag: donor

tag: exposure time


title: Anti-BTLA 6A6 rep 5

tag: background

value: Anti-BTLA 6A6


title: 45 days old, CnaTg, Vehicle, replicate 3

source_name: 45 days old_CnaTg_Vehicle_heart

tag: strain

value: Vehicle


title: P34

description: Sample 6

value: I


title: 45 days old, CnaTg, Vehicle, replicate 2

tag: treatment


title: Serum_7day_371900

tag: tissue


title: Serum_7day_371899


title: Control_7day_371898

value: Control


title: Anti-BTLA 6A6 rep 4

value: WT


title: P169B2

description: Sample 4

value: histologically or cytological documented relapsed and/or refractory AML

value: less than or equal to 3


title: P17B2

description: Sample 8

value: female

value: Responder


title: Anti-BTLA 6A6 rep 3


title: 45 days old, CnaTg, Vehicle, replicate 1

value: postnatal day 45

value: calcineurin transgenic

value: heart


title: P154

description: Sample 7


title: BTLAflox rep 3

value: BTLAflox


title: 45 days old, wild type, Vehicle, replicate 3

source_name: 45 days old_wild type_Vehicle_heart

value: wild type


title: Anti-BTLA 6A6 rep 2


title: Control_7day_371896


title: Serum_8hr_371895


title: P138

description: Sample 2

value: male


title: 45 days old, wild type, Vehicle, replicate 2


title: BTLAflox rep 1


title: Serum_8hr_371894

value: 3D human kidney proximal tubule MPS


title: Anti-BTLA 6A6 rep 1


title: 45 days old, wild type, Vehicle, replicate 1


title: IgG control rep 4

value: Control Ig


title: Control_7day_371897


title: P137or39

description: Sample 15


title: P116B2

description: Sample 3


title: P109B2

description: Sample 14

value: Failure


title: Control_8hr_371891


title: Serum_8hr_371893

value: Serum


title: Control_8hr_371892


title: P1

description: Sample 1

value: I


title: 77 days old, CnAtg, JIB-04, replicate 2

source_name: 77 days old_CnAtg_JIB-04_heart

value: postnatal day 77


title: IgG control rep 2

value: WT


title: Control_8hr_371890

value: Control


title: Serum_7day_371889


title: BTLAfloxFoxP3+/- rep 5


title: Serum_7day_371888


title: BTLAfloxFoxP3+/- rep 4


title: 77 days old, CnAtg, JIB-04, replicate 4


title: 77 days old, CnAtg, Vehicle, replicate 3

source_name: 77 days old_CnAtg_Vehicle_heart

value: Vehicle


title: 77 days old, CnAtg, JIB-04, replicate 3


title: 77 days old, CnAtg, Vehicle, replicate 2


title: BTLAfloxFoxP3+/- rep 3


title: Albumin_7day_371886

value: Albumin


title: CPPS (Chronic pelvic pain syndrome) patients 1

city: Guangzhou

first: Bin

last: Ouyang

address: No. 1, Panfu Rd

department: Department of Andrology

institute: Guangzhou First People's Hospital,School of Medicine,South China University of Technology

data_processing:
Cutadapt (v2.5) was used to trim adapters and filter for sequences.
BWA was used to alignment.
Genome_build: hg38
Supplementary_files_format_and_content: read_counts.txt

source_name: Extracellular vesicles from prostatic fluid

extract_protocol:
Total RNA was isolated from samples using TRIzol reagent.
For smallRNA-seq: Libraries were constructed using QIAseq® miRNA Library Kit (331502).

value: Extracellular vesicles

tag: disease

value: CPPS (Chronic pelvic pain syndrome)


title: CPPS (Chronic pelvic pain syndrome) patients 2


title: healthy men 3

value: healthy


title: CPPS (Chronic pelvic pain syndrome) patients 3


title: Albumin_7day_371885


title: BTLAfloxFoxP3+/- rep 2

source_name: Fecal pellet DNA


title: 77 days old, CnAtg, Vehicle, replicate 1

tag: age

value: calcineurin transgenic

value: heart


title: healthy men 1


title: Hi-C-Seq pre-pro-B cells KO

description: Hi-C-Seq pre-pro-B cells KO

source_name: pre-pro-B

extract_protocol:
Pre-pro-B cells were sorted using flow cytometry.
Hi-C libraries were prepared from the merge of three to four biological replicates as described previously(Niu et al., 2019; Rao et al., 2014).

value: Usp39 fl/fl mb1-cre

tag: cell preparation

value: FACS sorted from bone marrow

tag: cell type

value: pre-pro-B


title: IgG control rep 5

value: Control Ig


title: IgG control rep 1


title: healthy men 2


title: BTLAfloxFoxP3+/- rep 1

value: BTLAflox


title: 77 days old, CnAtg, JIB-04, replicate 1


title: 77 days old, CnAtg, Vehicle, replicate 4


title: Albumin_7day_371884

value: 3D human kidney proximal tubule MPS


title: BTLAfloxFoxP3+/+ rep 5

value: FoxP3 +/+


title: Hi-C-Seq pre-pro-B cells WT

description: Hi-C-Seq pre-pro-B cells WT

value: Usp39 fl/fl


title: REH_SCM

city: Atlanta

first: Chris

last: Scharer

state: GA

address: 1510 Clifton Rd, Suite 3086A

department: Microbiology and Immunology

institute: Emory University

data_processing:
Fastq reads were mapped to the hg38 reference genome using STAR with the default parameters.
Reads mapping to exons for unique ENTREZ genes were annotated and normalized using the GenomicRanges package in R/Bioconductor.
Genome_build: hg38
Supplementary_files_format_and_content: RPKM normalized gene expression counts for all detected genes.

source_name: B-ALL cell line

growth_protocol: Human B-ALL cell lines (REH and RCH-AcV) were grown in 10% RPMI until cultured for 48 hours in uncondtioned medium (10% RPMI), bone marrow stromal cell conditioned medium, or adipocyte conditioned medium.

extract_protocol:
After the treatment conditions, RNA was extracted using the RNAeasy mini kit (cat. no. 74104) from Qiagen.
200-1000 ng of total RNA was used with the KAPA mRNA HyperPrep kit with polyA selection beads and 10 rounds of PCR to generate RNA-seq libraries.

treatment_protocol: Human B-ALL cells were treated with vehicle or methotrexate (50 nM) for 24 hours prior to extracting RNA for sequencing.  Note:  We performed sequencing on 1 replicate per conditon.

value: B-cell acute lymphoblastic leukemia

tag: treament

value: No treatment

tag: mutation

value: ETV6-RUNX1 gene fusion

tag: origin

value: 74% European + 21% African + 5% Asian (peripheral blood sample)


title: Control_7day_371883

value: Control


title: Serum_7day_371887

value: Serum


title: REH_SCM_Pos_MTX

value: Methotrexate


title: BTLAfloxFoxP3+/+ rep 4


title: 2564 Wt_Ve_rep4

source_name: heart

treatment_protocol: Mice were treated with vehicle or JIB-04 starting from 4 weeks of age at 50 mg/Kg, 3 times per week, and hearts were collected at indicated age.

value: post natal day 158

value: wild type

value: Vehicle

tag: mouse reference


title: Control_7day_371882


title: REH_RPMI


title: BTLAfloxFoxP3+/+ rep 3


title: 2543 Wt_Ve_rep3

value: heart


title: REH_RPMI_Pos_MTX


title: 2200 Wt_Ve_rep2

value: post natal day 125


title: BTLAfloxFoxP3+/+ rep 1


title: REH_ACM


title: Serum_8hr_371880


title: 2199 Wt_Ve_rep1


title: Serum_8hr_371879


title: Control_7day_371881


title: RCHAcV_RA_SCM

value: chromosome translocation 1;19 and trisomy 8

value: >96% European (bone marrow sample)


title: 2565 CnAtg JIB-04_rep_2

value: calcineurin transgenic


title: 2566 CnAtg Ve_rep_3


title: 2197 CnAtg JIB-04: rep_1


title: Albumin_8hr_371877

value: 3D human kidney proximal tubule MPS

value: Albumin


title: Serum_8hr_371878


title: Albumin_8hr_371876


title: RCHAcV_RA_SCM_Pos_MTX

value: B-cell acute lymphoblastic leukemia


title: RCHAcV_RA_RPMI

value: No treatment


title: RCHAcV_RA_RPMI_Pos_MTX


title: 2542 CnAtg Ve_rep_2


title: RCHAcV_RA_ACM


title: Control_8hr_371873


title: BTLAfloxFoxP3+/+ rep 2

value: BTLAflox

value: FoxP3 +/+


title: Control_8hr_371872

value: Control


title: RCHAcV_RA_ACM_Pos_MTX


title: REH_ACM_Pos_MTX

value: ETV6-RUNX1 gene fusion

value: 74% European + 21% African + 5% Asian (peripheral blood sample)


title: Kidney Medulla-ATAC-seq-Donor3

data_processing:
The paired-end 42 bp sequencing reads (PE42) generated by Illumina sequencing (using NextSeq 500) are mapped to the genome (hg38) using the BWA algorithm with default settings. Alignment information for each read is stored in the BAM format. Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Genomic regions with high levels of transposition/tagging events are determined using the MACS2 peak calling algorithm (Zhang et al., Genome Biology 2008, 9:R137). Since both reads (tags) from paired-end sequencing represent transposition events, both reads are used for peak-calling but treated a single, independent reads. Note that we use the generic term “Interval” to describe the genomic regions identified by MACS2. Intervals are defined by the chromosome number and a start and end coordinate.
To identify the density of transposition events along the genome, the genome is divided into 32 bp bins and the number of fragments in each bin is determined. For this purpose, reads are extended to 200 bp, which is close to the average length of the sequenced library inserts. In silico extension also helps to smooth the data. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file.
Genome_build: GRCh38 (hg38)
Supplementary_files_format_and_content: bam, bigwig; frequency histogram of Tn5 transposition events
Supplementary_files_format_and_content: csv; MACS interval calls for all 6 samples

source_name: Kidney Medulla

extract_protocol:
Snap frozen tissue
Tn5 transposition and ATAC-seq was performed by ActiveMotif (Carlsbad, CA)

value: Kidney Medulla

tag: donor number


title: Serum_7day_371869

value: Serum


title: Serum_7day_371871


title: Serum_7day_371870


title: STAT3_control_rep2

city: Los Angeles

first: Denis

last: Evseenko

address: 1450 Biggy St

institute: University of Southern  California

data_processing:
Raw sequencing reads were processed using Partek Flow Analysis Software. Briefly, raw unaligned reads were quality checked, trimmed and reads with a Phred quality score >20 were used for alignment. Trimmed reads were aligned to human genome version hg38 with Gencode release 29 annotations using STAR aligner (2.5.3a) with default parameters. Transcript levels were quantified to the annotation model using Partek’s optimization of the expectation-maximization algorithm using default parameters. Transcript counts were normalized using reads per kilobase million (RPKM) approach and transformed to log2(RPKM+1). Differential expression gene expression analysis was performed by the DESeq2 R package.
Genome_build: hg38-Gencode-release 29
Supplementary_files_format_and_content: Normalized counts

source_name: Human fetal chondrocytes treated with scrambled lentiviral particles

extract_protocol:
Human fetal chondrocytes from the interzone were isolated from de-identified material from anonymous donors following informed consent. Passage 0 chondrocytes were cultured in vitro for 2-3 days before being infected with doxycycline inducible STAT3 shRNA or scrambled lentiviral particles (Dharmacon). One day later, doxycycline treatment commenced for a total of three days; fresh doxycycline was added daily. After three days, cells were sorted for RFP and mRNA was isolated with the RNeasy kit (Qiagen). Libraries (KAPA LTP kit, Roche) were prepared after RNA quality validation (Agilent Bioanalyzer 2100) and sequenced on a HiSeq3000 (Illumina).
KAPA LTP kit, Roche

value: Human fetal chondrocytes

value: scrambled lentiviral particles


title: STAT3_KD_rep3

source_name: Human fetal chondrocytes treated with STAT3 shRNA lentiviral particles

value: STAT3 shRNA lentiviral particles


title: STAT3_KD_rep2


title: Albumin_7day_371868

city: Seattle

last: Akilesh


title: 2198 CnAtg Ve_rep_1

value: heart

value: post natal day 125

tag: genotype

value: Vehicle


title: Kidney Cortex-ATAC-seq-Donor2

source_name: Kidney Cortex

value: Kidney Cortex


title: intestinal CD45+ cells - D6 - S8

city: Zhunan

first: Cheng-Yuan

last: Kao

address: 35 Keyan Road

department: Immunology Research Center

institute: National Health Research Institutes

data_processing:
raw base call files generated using RTA version 2.7.7.
cellranger mkfastq demultiplexes raw base call files into FASTQ files. It is a wrapper around Illumina's bcl2fastq, with additional features that are specific to 10x libraries and a simplified sample sheet format.
cellranger count takes FASTQ files from cellranger mkfastq and performs alignment, filtering, barcode/cell counting, and UMI/gene counting.

source_name: intestinal CD45+ cells from Dusp6 knockout mice

extract_protocol:
The cells living in the epithelial layer and laminar propria of the small intestine were isolated via a Lamina Propria Dissociation Kit (130-097-410, Miltenyi Biotec) and the procedures were according to the manufacturer's instructions. Three male D6KO mice and three littermate male WT mice at 11 weeks of age were euthanized by CO2 inhalation, and perfused with 4°C Hank’s Balanced Salt Solution without calcium and magnesium salts (HBSS w/o) containing 5% fetal bovine serum (FBS) to remove the blood leukocytes. Approximately 20 cm of intestine was harvested, and the luminal content was removed by flushing with HBSS w/o. Peyer’s patches were also removed to exclude the leukocytes of secondary gut-associated lymphoid tissue. The intestine was longitudinally slit, washed by HBSS w/o, and laterally cut into pieces of around 0.5 cm in length. The intestinal pieces were incubated with predigestion solution (HBSS w/o containing 5 mM EDTA, 5% FBS, and 1 mM DTT) for 20 mins at 37°C on a shaker at 220 rpm, and the solution was passed through the 100 μm strainer. The flow-through fraction was placed on ice for 10 mins, and the supernatant containing the suspended intraepithelial leukocytes was collected. The intestinal pieces were conducted with the above procedures thrice to obtain the cells from the epithelial layer and to remove the entire epithelial layer. For the isolation of cells from laminar propria, the remaining pieces were further incubated with enzymes for 20 mins at 37°C on a shaker at 220 rpm, churned by gentleMACS Dissociator, and passed through the 100 μm strainer. All fractions were centrifugated at 300 rcf for 5 mins at 4°C, and the pellet was resuspended in 4°C PB buffer. The cells isolated from the epithelial layer and laminar propria were pooled together, passed through the 70 μm strainer, and washed with 4°C PB buffer once. The live cells were isolated using a Dead Cell Removal Kit (130-090-101, Miltenyi Biotec). The CD45+ cells were selected through a MACS column with CD45 MicroBeads (130-052-301, Miltenyi Biotec). To increase the purity of live CD45+ intestinal cells, the cells were further stained with Live/Dead fluorescent reactive dye (L34957, Invitrogen) and PE anti-mouse CD45 antibody (103105, BioLegend) and sorted by BD Influx™ Cell Sorter (BD Biosciences) in 100% FBS. The sorted cells were centrifugated at 300 rcf for 5 mins at 4°C, and finally resuspended in 4°C PBS. Due to low sorting efficacy, one D6KO sample was abandoned. Ultimately, three WT samples and two D6KO samples were chosen for following single-cell RNA sequencing.
The isolated intestinal CD45+ cells were counted by Cellometer Auto T4 (Nexcelom Bioscience). Three WT samples and two D6KO samples were pooled separately. Subsequently, WT and D6KO samples were processed by BIOTOOLS Co., Ltd through the GemCode Single Cell Platform using the GemCode Gel Bead, Chip and 3’-Library v2 Kits (10X Genomics, Pleasanton) according to the manufacturer’s instructions. In brief, cell suspensions were loaded onto a Chromium Single-Cell Chip along with the reverse transcription master mix and single cell 3′ gel beads, aiming for 5,000 cells per channel. Following generation of single-cell gel bead-in-emulsions, reverse transcription was carried out in a Mastercycler ep gradient S thermocycler (Eppendorf). The amplified cDNA was subsequently purified using SPRIselect beads and sequenced on an Illumina HiSeq X Ten PE150 platform. The raw data contained the following read regions: 26 bp Read 1 (16 bp single cell barcode, 10x barcode; 10 bp Unique molecular identifier, UMI), 98 bp Read 2 (transcript insert), 8 bp i7 Index (sample index). The Cell Ranger software pipeline (version 2.0.1, 10X Genomics) was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts (27,998 genes) versus cells (3,996 cells in WT and 3,908 cells in D6KO).
Single cell RNA-seq

value: small intestine

value: Dusp6 knockout

value: 11 weeks old

tag: Sex

value: male

tag: sample barcode


title: Kidney Cortex-ATAC-seq-Donor3

first: Shreeram

address: 1959 NE Pacific St, Box 356100

institute: University of Washington


title: Kidney Cortex-ATAC-seq-Donor1


title: STAT3_KD_rep1


title: Albumin_7day_371866

value: 3D human kidney proximal tubule MPS

value: Albumin

tag: donor

tag: exposure time


title: Kidney Medulla-ATAC-seq-Donor1


title: Control_7day_371865

value: Control


title: intestinal CD45+ cells - D6 - S7

tag: strain


title: IgG control rep 3

tag: background

value: WT

tag: treatment

value: Control Ig


title: intestinal CD45+ cells - D6 - S6

tag: tissue


title: Control_B82_Ctrl.301292

data_processing:
Reads were aligned to the hg38 genome using STAR v2.5.3a
The number of reads aligned to each exon (feature) was counted using featureCounts from subread package using annotation file Homo_sapiens.GRCh38.100.gtf downloaded from Ensembl database.
Differential expression of genes and read count normalization was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: The processed data file is a tab-delimited matrix of raw gene counts, with gene symbols in the rows, and the samples in the columns.

extract_protocol:
Cells cultured in the kidney MPS were isolated by injecting 100 uL detergent (Abcam, part 8206000) and the lysate was collected at the outflow port into 900 uL of Trizol (ThermoFisher, 15596026) then frozen at -80°C until extraction. Total RNA was isolated using the Qiagen RNeasy Micro Kit.
Total RNA was normalized to 12ng in a total volume of 4ul and then rRNA depleted in a dedicated PCR clean workstation using the Ribogone - Mammalian kit (Takara Bio, Mountain View, CA).  RNA was transcribed to cDNA and subsequently converted to NGS sequencing libraries using the SMARTer Stranded RNA-Seq kit (Takara Bio).  Final libraries were quantified and library insert size distribution was checked using the Bioanalyzer (Agilent Technologies, Santa Clara, CA).  Base calls generated in real-time on the NovaSeq 6000 instrument (RTA 3.1.5);demultiplexed, unaligned BAM files produced by Picard ExtractIlluminaBarcodes and IlluminaBasecallsToSam are converted to FASTQ format using SamTools bam2fq (v1.4).

treatment_protocol: Kidney MPS were exposed to maintenance media or maintenance media spiked with 2% normal human serum (~720 ug/mL albumin equivalent) for 48 hours.

value: Female


title: STAT3_control_rep1

value: Human fetal chondrocytes


title: Kidney Medulla-ATAC-seq-Donor2

value: Kidney Medulla


title: STAT3_control_rep3

value: scrambled lentiviral particles


title: Control_7day_371864


title: A1552∆varA (#3812) growth until OD600 2.5, replicate 3

city: Lausanne

first: Melanie

last: Blokesch

address: Station 19 / EPFL-SV-UPBLO

institute: Swiss Federal Institute of Technology Lausanne (EPFL)

data_processing:
Data processing was done by Microsynth (Balgach, Switzerland) using their pipeline "Standard differential prokaryotic gene expression analysis"
Single end reads (1x75bp), which passed Illumina’s chastity filter, were demultiplexed and trimmed off the Illumina adaptors using Illumina’s bcl2fastq software version v2.20.0.422 (no further refinement or selection).
Reads were mapped to the reference genomes (A1552 chromosome 1 [CP028894] and 2 [CP028895]) via bowtie2 (version 2.3.5.1)
Uniquely mapped reads to annotated genes were counted using the software htseq-count (HTSeq version 0.11.2)
Normalization of the raw counts and differential gene expression analysis was carried out with help of the R software package DESeq2 (version 1.22.2)
Genome_build: Reference genomes were A1552 chromosome 1 [CP028894] and 2 [CP028895].
Supplementary_files_format_and_content: .tsv files for normalized counts

organism: Vibrio cholerae

source_name: in vitro bacterial culture

growth_protocol: V. cholerae strains were grown in LB medium until they reached and optical density at 600nm (OD600) of 0.2 or 2.5.

extract_protocol:
RNA was isolated using standard RNA isolation kits. The RNA was cleaned up after DNAse treatment using a RNA clean-up procedure (GenElute Mammalian Total RNA miniprep kit; Sigma). Next, Illumina RNA libraries incl. bacterial Ribo-depletion were prepared.
RNA libraries were prepared with a TruSeq Stranded mRNA sample prep kit (Illumina).

treatment_protocol: The harvested bacteria were washed in pre-chilled PBS buffer, lysed through resuspension in Tri Reagent, and stored at -80C until their processing.

value: varA-deficient mutant of A1552

tag: growth medium

value: LB medium


title: Control_B82_Ctrl.301291


title: Albumin_7day_371867


title: A1552∆varA (#3812) growth until OD600 2.5, replicate 2


title: A1552∆varA (#3812) growth until OD600 2.5, replicate 1


title: intestinal CD45+ cells - D6 - S5

tag: age


title: A1552∆varA (#3812) growth until OD600 0.2, replicate 3


title: Serum_B82_2S.301294


title: Serum_8hr_371862

value: Serum


title: Serum_B82_2S.301295


title: intestinal CD45+ cells - WT - S3

source_name: intestinal CD45+ cells from wild-type mice

value: wild-type


title: A1552∆varA (#3812) growth until OD600 0.2, replicate 2


title: Serum_B82_2S.301293

source_name: 3D human kidney proximal tubule MPS


title: Serum_8hr_371861


title: A1552∆varA (#3812) growth until OD600 0.2, replicate 1


title: Serum_8hr_371860


title: intestinal CD45+ cells - WT - S1

value: small intestine


title: intestinal CD45+ cells - WT - S2


title: A1552 (#1) growth until OD600 2.5, replicate 3

value: wild-type (A1552)


title: Albumin_8hr_371859


title: Control_B76_KL_Ctrl.301297

value: Male


title: Control_B76_KL_Ctrl.301298


title: A1552 (#1) growth until OD600 2.5, replicate 2


title: A1552 (#1) growth until OD600 2.5, replicate 1


title: Albumin_8hr_371858


title: mig1

city: Tianjin

first: Qinhong

last: Wang

address: 32 West 7th Avenue, Tianjin Airport Economic Area

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

description:
Transcriptome profiles of all sequenced strains.xlsx
Differential gene expression_mig1 vs. ScY01a.xlsx

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to reference genome using Bowtie 1.2.0 with default parametres
Abundance measurements by RSEM
Differential gene expression by R package DESeq2, a p-value cutoff of 0.05 or less and an absolute fold-change threshold of 2.0 or greater.
Genome_build: R64
Supplementary_files_format_and_content: Transcriptome profiles of all sequenced strains.xlsx: Windows Excel file include abundance for each sample
Supplementary_files_format_and_content: Differential gene expression_ric1 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_srb2 vs. ScY01a.xlsx: Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_sin3 vs. ScY01a.xlsx:  Windows Excel file include different expression gene list and fold change of two samples
Supplementary_files_format_and_content: Differential gene expression_mig1 vs. ScY01a.xlsx:  Windows Excel file include different expression gene list and fold change of two samples

source_name: Early-log phase cells grown on YP medium containing 200 g/l glucose at 40ºC

extract_protocol:
Sample were grown on YP medium containing 200 g/l glucose at 40ºC at 200 rpm for 10 h to the early-log phase, and harvested in Falcon tubes precooled in liquid N2 by centrifuging for 5 minutes at 4000 rpm (3220 × g). The supernatant was discarded, and the pellet was stored at −80°C until further use. Total RNA extraction, library construction and sequencing were conducted by GENEWIZ Inc. (Suzhou, Jiangsu, China).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: ScY01a (mig1-delta)

value: MIG1 deletion strain


title: intestinal CD45+ cells - WT - S4

value: 11 weeks old

value: male


title: Control_7day_371863

value: 3D human kidney proximal tubule MPS

value: Control


title: sin3

description:
Transcriptome profiles of all sequenced strains.xlsx
Differential gene expression_sin3 vs. ScY01a.xlsx

value: ScY01a (sin3-delta)

value: SIN3 deletion strain


title: Control_B76_KL_Ctrl.301296


title: Serum_B76_KL_2S.301304


title: Albumin_8hr_371857

value: Albumin


title: srb2

description:
Transcriptome profiles of all sequenced strains.xlsx
Differential gene expression_srb2 vs. ScY01a.xlsx

value: ScY01a (srb2-delta)

value: SRB2 deletion strain


title: A1552 (#1) growth until OD600 0.2, replicate 3

value: LB medium


title: Control_8hr_371856


title: ric1

description:
Transcriptome profiles of all sequenced strains.xlsx
Differential gene expression_ric1 vs. ScY01a.xlsx

value: ScY01a (ric1-delta)

value: RIC1 deletion strain


title: Serum_B76_KL_2S.301302


title: ScY01a

description: Transcriptome profiles of all sequenced strains.xlsx

value: wild type strain


title: A1552 (#1) growth until OD600 0.2, replicate 2

value: wild-type (A1552)


title: Serum_B76_KL_2S.301303

value: Male


title: A1552 (#1) growth until OD600 0.2, replicate 1


title: Control_8hr_371854


title: HUVEC_miR-125a-5p_4

status: Public on Feb 07 2022

city: Munich

first: Martin

middle: Bernhard

last: Mueller

address: Marchioninistrasse 15

department: Department of Anaesthesiology

institute: University Hospital, Ludwig-Maximilians-University Munich (LMU)

data_processing:
The RNA-Seq analysis was performed with the CLC Genomics Workbench “RNA-Seq analysis” tool.
The human reference genome (GRCh38.p7) was downloaded from NCBI and used as reference sequence.
For mapping purposes of the generated *.fastq files, reads were mapped according to their similarity to the reference sequences. The following mapping parameters were applied: Mismatch cost: 2; Insertion/Deletion cost: 3; Length fraction: 0.8; Similarity;  fraction: 0.8; Maximum number of hits per read: 5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated occording to the method described by Mortazavi et al. Nat Methods. Juli 2008;5(7):621–8.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include TPM and RPKM values for each sample

source_name: Primary human umbilical vein cells (HUVECS

growth_protocol: Primary Human Umbilical Vein Endothelial Cells (HUVEC) were isolated from umbilical cords of healthy neonates. HUVEC were isolated from umbilical vein vascular wall by collagenase A (Roche) treatment and cultured in Endothelial Cell Basal Medium (ECGM; PromoCell) with SupplementMix (PromoCell), 10% FCS (Biochrom AG) and 1% Penicillin/Streptomycin (Pen/Strep, Gibco). Cells of one single cord at passage 2-4 were used for each of the independent experiments.

extract_protocol:
RNA was isolated using miRNeasy Mini kit (Qiagen)and analyzed by IMGM Laboratories GmbH (Martinsried, Germany). Quality control for all total RNA samples was done on the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano LabChip Kits (Agilent Technologies).
Library preparation was performed with the TruSeq Stranded mRNA HT technology (Illumina), according to the manufacturer's protocol, including fragmentation, a poly-T oligo pulldown and sequencing adapter ligation. RNA sequencing was performed on the Illumina NextSeq 500 next generation sequencing system and its high output mode with 1 x 75 bp single-end read chemistry with >10 million reads per sample.

treatment_protocol: 18 hours after transfection with NEON transfection system cells were TNF stimulation (25 ng/ml) for additional 6 hours

tag: material

value: Cell culture

tag: cell type

tag: transfection

value: transfection with miR-125a-5p

tag: stimulation

value: TNF stimulation (25 ng/ml) for 6h


title: HUVEC_miR-125a-5p_5

value: Primary human umbilical vein cells (HUVECS


title: HUVEC_miR-125a-5p_3


title: HUVEC_miR-125a-5p_2


title: HUVEC_NC_3

value: transfection with negative controle


title: HUVEC_miR-125a-5p_1


title: HUVEC_NC_5


title: HUVEC_NC_1


title: HUVEC_NC_4


title: HUVEC_NC_2


title: Control_8hr_371855

value: 3D human kidney proximal tubule MPS

value: Control


title: SSc_41, classical monocyte

city: Birmingham

first: Peter

middle: Christopher

last: Allen

state: Alabama

address: 1720 University Blvd

department: Graduate Biomedical School

institute: University of Alabama at Birmingham

data_processing:
Data was analyzed by Rosalind (https://rosalind.onramp.bio/), with a HyperScale architecture developed by OnRamp BioInformatics, Inc. (San Diego, CA).
Reads were trimmed using cutadapt.
Quality scores were assessed using FastQC.
Reads were aligned to the Homo sapiens genome build hg19 using STAR.
Individual sample reads were quantified using HTseq.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

source_name: SSc, classical monocyte

extract_protocol:
Total RNA was extracted from classical monocytes isolated from 16 female African American patients and 18 female African American controls using the RNeasy Kits (Qiagen) according to the manufacturers guideline.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Female

tag: race

value: AA

tag: disease status

value: Systemic sclerosis (SSc)

tag: disease subset

value: dcSSc

value: classical monocyte


title: SSc_53, classical monocyte


title: SSc_44, classical monocyte

value: lcSSc


title: SSc_45, classical monocyte


title: SSc_43, classical monocyte


title: SSc_49, classical monocyte


title: SSc_52, classical monocyte


title: SSc_51, classical monocyte


title: SSc_40, classical monocyte

value: ssSSc


title: SSc_32, classical monocyte

value: SSc


title: SSc_30, classical monocyte


title: SSc_31, classical monocyte


title: SSc_28, classical monocyte


title: Control_25, classical monocyte

source_name: Control, classical monocyte


title: Control_24, classical monocyte


title: SSc_39, classical monocyte


title: Control_22, classical monocyte


title: Wouter33

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

institute: UMCG

data_processing:
Data processing was performed with the Lexogen Quantseq 2.3.1 FWD UMI pipeline on the BlueBee Genomics Platform (1.10.18)
Supplementary_files_format_and_content: Countfile where each column is a sample and each row is a gene.

source_name: Cell line

growth_protocol: DMEM + 10% FCS +1% pen/strep

extract_protocol:
Qiagen ALL-PREP
Lexogen QuantSeq 3'mRNA-seq Libray prep kit (FWD with UMI) from Illumina.

treatment_protocol: For U2OS cells: no treatment, 72 hours of growth under normal conditions. For HEK293T cells: 24 hour treatment with camptothecin or vehicle (DMSO), 48 hour recovery, harvest

tag: cell line

tag: treatment/group

value: DMSO-treated


title: Wouter32


title: Control_21, classical monocyte


title: Wouter31


title: Control_23, classical monocyte


title: Control_20, classical monocyte


title: Wouter26

value: Camptothecin-treated


title: Control_19, classical monocyte


title: Wouter28


title: Control_17, classical monocyte


title: Control_16, classical monocyte


title: Control_18, classical monocyte


title: Control_14, classical monocyte


title: Wouter25


title: Control_13, classical monocyte


title: SSc_29, classical monocyte


title: Wouter24


title: Wouter23


title: Control_15, classical monocyte


title: T2H6_0702

city: Singapore

first: Zbynek

last: Bozdech

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

description:
P.falciparum parasite isolate
H6_sample180

data_processing:
Standard Illumina pipeline was used for base calling and demultiplexing
Sequenced reads were trimmed for adapter, primer and low quality bases from 3'-ends using Trimgalore (version 0.4.4)
Trimmed reads then mapped to Plasmodium falciparum 3D7 genome (genedb version 3) using HiSAT2 (version 2.1.0) with parameters --min-intronlen 60 --max-intronlen 2500 --fr
Uniquely mapped and properly oridented reads were extracted using samtools (version: 1.8) and raw count generated by bedtools (v2.27.1)
Normalized count - Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated, except gene length in the formula is replaced with mapped length
Genome_build: Genome_build: Plasmodium falciparum 3D7 geneDB version 3
Supplementary_files_format_and_content: Tab-delimited text file includes Log2 FPKM values for each sample

organism: Plasmodium falciparum

source_name: P.falciparum field isolate from patient

growth_protocol: All samples used in this study (Except ring 3D7 batch controls) were collected from patients involved in Tracking Resistance to Artemisinin Collaboration 2 (TRAC2), a multi-site study that took place between Aug 7, 2015, and Feb 8, 2018. Following collection, blood was subsequently depleted of plasma and buffy coat. Hour 0 samples were additionally purified from white blood cells (WBC) using CF11 columns following the Worldwide Antimalarial Resistance Network (WWARN) protocols. 0.2 to 0.5 mL of packed red blood cells (pRBC) from each sample was homogenized by mixing with 10 volumes of TRIzol (Invitrogen), frozen at -80oC.

extract_protocol:
Total RNA was extracted using Trizol and ZYMO DirectZol96 extraction kit following protocol described in Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020).
Reverse transcription and cDNA synthesis was done following modifed Smart-Seq2 protocol using only oligo(d)T primers to enrich for mRNA transcripts (Kucharski, M., Tripathi, J., Nayak, S. et al. A comprehensive RNA handling and transcriptomics guide for high-throughput processing of Plasmodium blood-stage samples. Malar J 19, 363 (2020)). Purified amplicon (cDNA) was used to generate sequencing libraries using Illumina Nextera XT kit as described in manufacturer’s protocol. Libraries were analyzed on the Bioanalyser High-Sensitivity DNA chips (Agilent, Cat. No.: 5067-4626), subsequently pooled (24 samples per lane) and sequenced on Illumina HiSeq4000 platform generating 150 bp paired end reads with 110 Gb data output generated per lane.

treatment_protocol: In brief, samples were collected from the venous blood of malaria-infected patients at admission to the clinic (Hour 0, 0hr) and 6 hours after their respective treatment (Hour 6, 6hr). Depending on their location, patients were randomly assigned different double or triple Artemisinin Combination Therapy (ACT) as follows: Thailand, Cambodia, Vietnam, and Myanmar - dihydroartemisinin-piperaquine or dihydroartemisinin-piperaquine plus mefloquine; Cambodia - artesunate-mefloquine or dihydroartemisinin-piperaquine plus mefloquine; Laos, Myanmar, Bangladesh - artemether-lumefantrine or artemether-lumefantrine plus amodiaquine.

tag: isolate

value: In vivo, Blood stage

value: After ACT treatment, 6h


title: T2H6_0687

description:
P.falciparum parasite isolate
H6_sample178


title: Wouter22


title: Wouter30


title: T2H6_0674

description:
P.falciparum parasite isolate
H6_sample177


title: Control_7, classical monocyte


title: Wouter20

value: ATM KO


title: T2H6_0659

description:
P.falciparum parasite isolate
H6_sample176


title: Control_9, classical monocyte


title: Wouter27


title: T2H6_0656

description:
P.falciparum parasite isolate
H6_sample175


title: T2H6_0654

description:
P.falciparum parasite isolate
H6_sample174


title: T2H6_0652

description:
P.falciparum parasite isolate
H6_sample173


title: Control_6, classical monocyte


title: Wouter19


title: T2H6_0692

description:
P.falciparum parasite isolate
H6_sample179


title: Control_5, classical monocyte


title: Wouter18


title: T2H6_0651

description:
P.falciparum parasite isolate
H6_sample172


title: T2H6_0649

description:
P.falciparum parasite isolate
H6_sample171


title: C1-sgKMT2D-Epi_ASH2L_CUT&RUN

city: Cambridge

first: Yun

last: Zhang

email: zhangyunbio@gmail.com, barc@wi.mit.edu

state: MA

address: 455 Main Street

institute: Whitehead Institute for Biomedical Research

data_processing:
Library strategy: CUT&RUN
CUT&RUN paired-end reads were aligned using bowtie2 to the human genome (GRCh38), with the parameters: --very-sensitive --no-discordant -X 1000 --phred64
Genome_build: GRCh38
Supplementary_files_format_and_content: bigWig files in counts per million (cpm) were generated using bamCoverage from deepTools

source_name: HMLER

growth_protocol: Cells were cultured in 2:1:1 MEGM (Lonza Bullet kit), DMEM and F12 media, supplemented with insulin (10 μg/ml), EGF (10 ng/ml), hydrocortisone (1 μg/ml), and 1x Pen/Strep (50 I.U./mL penicillin and 50 μg/mL streptomycin, Sigma-Aldrich #P4333).

extract_protocol: Libraries were prepared using Swift Science’s Accel-NGS Library Preparation Kit for Illumina Platforms according to manufacturer’s directions.

tag: genotype

value: HMLER

tag: cut&run antibody


title: T2H6_0613

description:
P.falciparum parasite isolate
H6_sample170

tag: treatment


title: Wouter21


title: T2H6_0605

description:
P.falciparum parasite isolate
H6_sample169


title: T2H6_0603

description:
P.falciparum parasite isolate
H6_sample168


title: HMEC_siSTAG2_3_3

city: Boston

first: Stephen

middle: J

last: Elledge

address: 77 Avenue Louis Pasteur NRB160

institute: Brigham and Women's Hospital | HHMI

data_processing:
For U937 cells, RNA-seq reads were mapped using STAR version 2.4.2a. The STAR genome index was generated from human reference sequence hg19 (FASTA downloaded from UCSC genome browser) and coding transcripts from GENCODE Release 19 (GTF downloaded from http://www.gencodegenes.org/). Reads mapping to genes were quantified with featureCounts from the R package Subread (v2.0.1). Transcripts per million (TPM) were quantified from the count data.
For HMECs, each RNA-seq sample was aligned to the hg19 genome using STAR version 2.7.0a.
For HMECs, reads mapping to genes were quantified with featureCounts.
For HMECs, differential expression was quantified using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts matrix, TPM normalized counts matrix, differential expression output

source_name: HMEC

growth_protocol: U937 cells were grown in RPMI+10%FBS+1%P/S/G, HMEC cells were grown in HuMEC media supplemented with HuMEC supplement kit

extract_protocol:
HMECs Total RNA was purified from 1 million cells using Rneasy plus isolation kit (QIAGEN) following the manufacturer instructions
HMEC RNA-seq libraries were prepared with the NEBnext Ultra II Directional RNA Library kit according to the standard protocol.

treatment_protocol: HMECs were treated with no-targeting siRNAs or STAG2 targeting siRNAs. HMECs were transfected with 5uL per 6-well plate of Lipofectamine RNAiMAX transfection reagent and 40nM siRNA duplex (Dharmacon).

value: HMEC

value: Mammary Epithelial Cells

tag: genotype/variation

value: STAG2-siRNA 2


title: T2H6_0602

description:
P.falciparum parasite isolate
H6_sample167


title: HMEC_siSTAG2_3_2


title: C1-sgEED-Epi_ASH2L_CUT&RUN

value: EED-KO


title: T2H6_0597

description:
P.falciparum parasite isolate
H6_sample165


title: HMEC_siSTAG2_3_1


title: C2-Epi_ASH2L_CUT&RUN

value: wild type