title: SMN_0M_1

city: Baltimore

first: Natalie

last: Joe

state: MD

address: 1550 Orleans Street, Suite 2-103

institute: Johns Hopkins University School of Medicine

data_processing:
Preliminary analysis was performed by Novogene. The reads were then mapped to Homo Sapiens(GRCh38/hg38) using STAR (v2.5) with the parameter mismatch =2.
Quantification was done using HTSeq (v0.6.1) software with the parameter -m union.
Differentially expressed genes were identified using EdgeR (v3.16.5) with padj<0.005 and [log2(FoldChange)]>1.
Supplementary_files_format_and_content: Comma delimited text file containing gene-level counts

source_name: human cell line

growth_protocol: MDA-MB-231 cells obtained directly from the ATCC and SUM159 cell line given as a gift from Dr. Sara Sukumar's laboratory.

extract_protocol:
Total RNA was extracted from cells using TRIzol (Invitrogen) and purified using Direct-zol RNA mini kit (Zymo Research) with DNase I treatment.
Following RNA purification, samples were confirmed to have a RIN value >9.0 when measured on an Agilent Bioanalyzer. Total RNA qualification, mRNA enrichment, double-stranded cDNA synthesis, end repair, poly-A and adaptor addition, fragments selection and PCR, library quality assessment and Illumina sequencing. Sequencing was performed on a NovaSeq 6000 system with 150-bp paired-end run by Novogene (Sacramento, CA).

treatment_protocol: Cell lines were treated with 1 uM of Mebendazole or DMSO vehicle control for 72 hrs.

tag: mbz treated

value: 0 uM MBZ

value: 72 hrs


title: D8_Pulse [220113_3d_pulse_1_S35_L002]

status: Public on Feb 28 2022

type: SRA

city: South San Francisco

first: Jacob

middle: Cameron

last: Kimmel

state: CA

address: 1170 Veterans Blvd

department: Computing

country: USA

institute: Calico Life Sciences, LLC

library_source: transcriptomic

data_processing:
base calling: bcl2fastq
alignment: kallisto quant
differential expression: sleuth
normalization: kallisto quant
Genome_build: mm10
Supplementary_files_format_and_content: h5ad [Samples, Genes] matrix of TPM values.

molecule: total RNA

organism: Mus musculus

growth_protocol: Cells grown in 6-well plates in DMEM supplemented with 10%FBS and 1% Pen/Strep.

extract_protocol:
RNAlater, TRIzol, Zymo DirectZol columns
NEB Ultra II Directional RNA Library Prep Kit

treatment_protocol: Doxcycline at 0 or 4 ug/mL in media

tag: cell line background

tag: day

tag: reprogramming treatment

value: Pulse


title: Tulipa gesneriana 'Ad Rem' bulb stage 4 rep1

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

country: China

institute: Huazhong Agricultural University

data_processing:
Illumina Casava1.7 software used for base calling.
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis of two stages was performed using the DESeq R package (1.18.0). DESeq provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .  Genes with |fold change| >2 and P-value<0.05 were assigned as differentially expressed.

organism: Tulipa gesneriana

source_name: bulb

extract_protocol:
The bulbs of Tulipa gesneriana at different stages were collected for RAN isolation using plant RNA purification kit (Tiangen, Beijing, China). RNA purity and integrity were assessed using the NanoPhotometer® Spectrophotometer (IMPLEN, CA, USA) and the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), respectively.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: bulb

tag: treatment time

value: 'Ad Rem' bulb development stage 4

tag: genotype

value: Ad Rem


title: MDN_1M_1

organism: Homo sapiens

tag: cell line

value: 1 uM MBZ


title: SMN_1M_1


title: D8_Pulse [220113_3d_pulse_3_S9_L002]


title: MDN_0M_1


title: 28h_1299_4_Scr_100nM_PD

city: London

first: Silvia

last: Marino

address: 4, Newark St

country: United Kingdom

institute: Queen Mary University of London

data_processing:
[trimming and alignment]  Quality control was performed with FastQC and adapter sequences were removed using Trimgalore v0.6.5. Reads were then aligned to the Ensembl  GRCh38 human reference genome using STAR v2.6.1 with gene count quantification mode, retaining only uniquely mapped reads.
[post-processing and filtering]  Lowly expressed genes (CPM < 1) were filtered out via a custom-made script in R and further biotype filtering was performed in R with the Bioconductor packages NOISeq and biomaRt, removing residual highly expressed mitochondrial and ribosomal RNA. Trimmed mean of M-values (TMM) normalization was applied to the dataset prior to differential expression (DE) analysis, performed using the Bioconductor package edgeR.
Genome_build: hg38
Supplementary_files_format_and_content: raw, unfiltered gene counts

source_name: Medulloblastoma

growth_protocol: ICb1299 were cultured in DMEM (high glucose, GlutaMAX™, ThermoFisher) supplemented with 10% foetal bovine serum (FBS, Gibco) and 1% Penicillin-Streptomycin (Gibco). CHLA-01-Med MB cells were grown in DMEM-F12 (Gibco) supplemented with B27 (Gibco), 20 ng/mL human epidermal growth factor (EGF, Peprotech) and 10 ng/mL human basic fibroblast growth factor (FGF, Peprotech)

extract_protocol:
Total RNA was extracted with RNA/DNA/Protein Purification Plus kit (Norgen), polyA mRNA was selected and library prepared using the NEBNext Ultra II Directional RNA Library Prep kit.
Libraries were size selected, multiplexed and 75bp paired-end sequences were obtained with HiSeq4000 (Illumina)

treatment_protocol: Cells were treated with 1uM PTC-209 (PTC, Tocris), 100nM PD325901 (PD, Tocris) or DMSO for the reported time.

tag: knockdown

value: Scramble

tag: treatment

value: 28h of PD325901 100nM treatment


title: D8_Pulse [220113_3d_pulse_1_S35_L001]


title: 28h_1299_4_Scr_1uM_PTC

value: 28h of PTC-209 1uM treatment


title: Tulipa gesneriana 'Ad Rem' bulb stage 3 rep2

value: 'Ad Rem' bulb development stage 3


title: Tulipa gesneriana 'Ad Rem' bulb stage 3 rep1


title: 28h_1299_4_Scr_DMSO

value: 28h of DMSO treatment


title: Tulipa gesneriana 'Ad Rem' bulb stage 2 rep2

value: 'Ad Rem' bulb development stage 2


title: Tulipa gesneriana 'Ad Rem' bulb stage 2 rep1


title: D8_Pulse [220113_3d_pulse_3_S9_L001]


title: Tulipa gesneriana 'Ad Rem' bulb stage 1 rep1

value: 'Ad Rem' bulb development stage 1


title: liver (mouse M00249)

city: Cologne

first: Lisa

last: Werr

address: Kerpener Str. 62

country: Germany

institute: University Hospital of Cologne

description:
genes_CPM; genes_CPM
M00249_T1

data_processing:
Sequencing data was aligned to the mouse genome and quantified prior to differential gene expression analysis.
Data analysis was performed with R using the following packages AnnotationDbi, org.Mm.eg.db, fgsea, ggpubr und stringr.
Supplementary_files_format_and_content: genes_count
Supplementary_files_format_and_content: genes_CPM

source_name: liver

extract_protocol:
Fresh frozen tissue was cut with a cryostat and tissue sections were used for RNA isolation-
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Total extracted RNA fulfilled the following sample requirements for sequencing: RIN >8, DNA free, OD260/280 = 1,8-2,1 and OD260/230 >1,5.
3’ UTR mRNA libraries were generated from total RNA (Lexogen QuantSeq Kit) according to the manufacturers protocol and sequenced on Illumina HiSeq4000.

tag: mouse line

value: Rosa26CD74-NRG1/Flp mice

tag: cell type/tissue

value: tissue

tag: tissue of origin

value: liver

tag: group (t=tumor, n=normal)

value: T


title: 28h_1299_4_shC_100nM_PD


title: muscle (mouse M00249)

description:
genes_CPM; genes_CPM
M00249_N4

source_name: muscle

value: muscle

value: N


title: spleen (mouse M00249)

description:
genes_CPM; genes_CPM
M00249_N1

source_name: spleen

value: spleen


title: sarcoma (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_T2

source_name: sarcoma

value: sarcoma


title: N4

city: Jinan

first: Yujing

last: Sun

state: Shandong Province

address: No. 107, Wenhua West Road, Lixia District

department: Department of Endocrinology

institute: Qilu Hospital, Cheeloo college of medicine, Shandong University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using FASTX-Toolkit  version 0.0.13 and Perl version 5.8.8
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: human GRCh38
Supplementary_files_format_and_content: raw counts

source_name: Human thyroid tissue

extract_protocol:
Total RNA was isolated using theRNeasy mini kit (cat#Qiagen, Germany), after which the RNAconcentration and quality were determined by the Qubit ® 2 .0 Fluorometer (Life Technologies,USA) and the Nanodrop One spectrophotometer (Thermo Fisher Scientific Inc., USA). Integrityoftotal RNA was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., USA),and samples with RNA integrity number (RIN) values above 7.0 were used for sequencing. Onemicrogram of RNA were used as input material for the RNA sample preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Thyroid tissue was removed by fine needle aspiration, rinsed in fresh tissue stock solution,

tag: subject status

value: papillary thyroid carcinoma (PTC) patient

value: The adjacent normal tissues


title: lung (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_N4

source_name: lung

value: lung


title: liver tumour (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_T1


title: muscle (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_N3


title: T4

value: Human papillary thyroid carcer


title: spleen (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_N2


title: N3


title: T3


title: intestine (mouse M00247) T2

description:
genes_CPM; genes_CPM
M00247_T2

source_name: intestine

value: intestine


title: kidney (mouse M00249)

description:
genes_CPM; genes_CPM
M00249_N3

source_name: kidney

value: kidney


title: lung (mouse M00247)

description:
genes_CPM; genes_CPM
M00247_N3


title: N1


title: N2


title: Tulipa gesneriana 'Ad Rem' bulb stage 1 rep2

value: bulb

value: Ad Rem


title: spleen (mouse M00247)

description:
genes_CPM; genes_CPM
M00247_N2


title: liver  (mouse M00247)

description:
genes_CPM; genes_CPM
M00247_N1


title: T1


title: muscle (mouse M00246)

description:
genes_CPM; genes_CPM
M00246_N3


title: lung (mouse M00249)

description:
genes_CPM; genes_CPM
M00249_N2


title: lung (mouse M00246)

description:
genes_CPM; genes_CPM
M00246_N4


title: S41_low_EX_RNA-seq

city: Amherst

last: Pilsner

state: Massachusetts

address: 686 N PLEASANT

department: Environmental Health Sciences

institute: University of Massachusetts Amherst

data_processing:
RRBS data was trimmed using TrimGalore, mapping and methylation calling were performed with Bowtie2 and Bismark respectively. Differential methylation analysis was performed with methylkit R package.
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
RNA-seq data was trimmed with TrimGalore, mapping, SNP calling and differention expression analysed were performed tophat, samtools and edgeR respectively
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include beta and CPM values for each sample .
Supplementary_files_format_and_content: Matrix table with raw beta values and gene counts for every region/gene and every sample

source_name: Extra-embryo

growth_protocol: Exposures were 2.5 and 25mg/kg/day for low and high groups respectively

extract_protocol: DNA and RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: DNA(Sperm and embryo) isolation was performed using rapid extraction protocol involving homogenization with beeds in lyisis buffer mixture of guanidine thyiocyanate and TCEP; total RNA (embryo) was isolated  using the Roche High Pure RNA Isolation Kit

tag: strain

value: C57BL/6 * DBA/2J

value: Extra-embryo

tag: age

value: Embryonic day 7.5

value: wild type

tag: gender

value: male

value: Low DEHP (2.5mg/kg/day)


title: S40_high_EX_RNA-seq

value: High DEHP (25mg/kg/day)


title: S42_low_EX_RNA-seq


title: spleen (mouse M00246)

description:
genes_CPM; genes_CPM
M00246_N2

value: Rosa26CD74-NRG1/Flp mice

value: tissue

value: spleen

value: N


title: liver (mouse M00246)

description:
genes_CPM; genes_CPM
M00246_N1

value: liver


title: sarcoma (mouse M00245) T2

description:
genes_CPM; genes_CPM
M00245_T2

value: sarcoma

value: T


title: S37_control_EX_RNA-seq

value: Unexposed


title: liver (mouse M00248)

description:
genes_CPM; genes_CPM
M00248_N1


title: sarcoma (mouse M00245) T1

description:
genes_CPM; genes_CPM
M00245_T1


title: intestine (mouse M00247) T1

description:
genes_CPM; genes_CPM
M00247_T1

value: intestine


title: T2

value: papillary thyroid carcinoma (PTC) patient

value: Human papillary thyroid carcer


title: S38_control_EX_RNA-seq

value: C57BL/6 * DBA/2J

value: Extra-embryo


title: muscle (mouse M00245)

description:
genes_CPM; genes_CPM
M00245_N3

value: muscle


title: spleen (mouse M00245)

description:
genes_CPM; genes_CPM
M00245_N2


title: sarcoma (mouse M00238)

description:
genes_CPM; genes_CPM
M00238_T01


title: S33_high_EM_RNA-seq

source_name: Embryo

value: Embryo

value: Embryonic day 7.5

value: wild type

value: male


title: liver (mouse M00245)

description:
genes_CPM; genes_CPM
M00245_N1

value: Rosa26CD74-NRG1/Flp mice

value: tissue


title: brain (mouse M00238)

description:
genes_CPM; genes_CPM
M00238_N04

source_name: brain

value: brain

value: N


title: S35_low_EM_RNA-seq

value: Low DEHP (2.5mg/kg/day)


title: S32_control_EM_RNA-seq


title: S39_high_EX_RNA-seq

value: High DEHP (25mg/kg/day)


title: liver (mouse M00238)

description:
genes_CPM; genes_CPM
M00238_N01

value: liver


title: lung (mouse M00238)

description:
genes_CPM; genes_CPM
M00238_N03

value: lung


title: sarcoma (mouse M00237)

description:
genes_CPM; genes_CPM
M00237_T01

value: sarcoma

value: T


title: muscle (mouse M00238)

description:
genes_CPM; genes_CPM
M00238_N02


title: 8 days after surgery control (sham) sample 5 [8dSham624]

city: Torino

first: Raffaele

middle: A

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

country: Italy

institute: University of Torino

data_processing:
Trimming performed with cutadapt embedded  docker4seq package v 2.4.2
Mapping performed with STAR embedded  docker4seq package v 2.4.2
miRNA quantitification performed with SHRIMP embedded  docker4seq package v 2.4.2
Genome_build: mirbase 21
Supplementary_files_format_and_content: tab deliment counts table

source_name: 8 days after surgery control (sham)_liver

extract_protocol:
Blood was collected into K2 EDTA-coated S-Monovette® by cardiac puncture. Plasma was prepared within 1 hour of blood sampling by centrifuging at 1000g for 10 mins at 4°C followed by a second centrifugation of the supernatant at 2000 rpm for 15 mins and frozen at -80°C till further processing. Circulating EVs were collected from 250 µl of plasma. Briefly, plasma was thawed on ice and 63 µl of ExoquickTM (System Biosciences) was added to EV preparation according to the maunfacturer’s instructions. For total RNA purification, EVs pellets were resuspended in 200 µl PBS and 1 ml of QIAzol Lysis reagent (Qiagen) added. RNA was extracted using miRNeasy serum/plasma kit (Qiagen) in an automated way using the QIAcube instrument (Qiagen), thus preventing operator-depending variability. Total RNA was estimated quantitatively with Qubit RNA HS kit (ThermoFisher Scientific) and then stored at -80°C till further use.
Small RNA libraries were prepared using Small RNA Library Preparation Kit NebNext (New England Biolabs) according to manufacturer instructions starting from 40 ng of EV-derived RNA and using 15 PCR cycles. Each library was analysed with the High Sensitivity DNA chip (Agilent) using Agilent 2100 Bioanalyzer. Pools of 12 libraries were concentrated with AMPure XP magnetic beads (Beckman Coulter) and eluted in 40 µl of nuclease free water. The eluate from each pool was loaded onto a 6% precast gel (Life Technologies) and a ≈146 bp band was cut and put in 300 µl of nuclease free water overnight in 2ml low bind eppendorf tube. Gel debris were removed with Qiaquick gel extraction kit (Qiagen) and cDNA was precipitated using 3M NaOAc, 100% cold ethanol and glycogen, centrifuged at 20 000g for 20 mins at 4°C. After one wash with 70% ethanol, cDNA was resuspended in 10 µl nuclease free water and quantified using the Qubit DNA HS (Life Technologies). Pool was analysed with the High Sensitivity DNA chip (Agilent) using Agilent 2100 Bioanalyzer. Two pools (2 x 12 samples purified indexed libraries) were run at the concentration of 1.6 pM on the NextSeq500 sequencer (Illumina) according to the manufacturer’s instructions, in 75 nts single end sequencing mode.

treatment_protocol: bile duct ligation

tag: Sex

value: control (sham)

tag: site

value: Extracellular vesicles


title: brain (mouse M00237)

description:
genes_CPM; genes_CPM
M00237_N04


title: 8 days after surgery control (sham) sample 2 [8dSham426]


title: lung (mouse M00237)

description:
genes_CPM; genes_CPM
M00237_N03


title: lung (mouse M00245)

description:
genes_CPM; genes_CPM
M00245_N5


title: S36_low_EM_RNA-seq

value: C57BL/6 * DBA/2J


title: 8 days after surgery control (sham) sample 1 [8dSham424]


title: muscle (mouse M00237)

description:
genes_CPM; genes_CPM
M00237_N02

value: muscle


title: S34_high_EM_RNA-seq

value: Embryo

value: Embryonic day 7.5


title: liver (mouse M00237)

description:
genes_CPM; genes_CPM
M00237_N01


title: liver tumour (mouse M00236)

description:
genes_CPM; genes_CPM
M00236_T02


title: S31_control_EM_RNA-seq

value: wild type

value: male

value: Unexposed


title: 8 days after surgery bile duct ligation (BDL) sample 5 [8dBDL324]

source_name: 8 days after surgery bile duct ligation (BDL)_liver

value: bile duct ligation (BDL)


title: sarcoma (mouse M00236)

description:
genes_CPM; genes_CPM
M00236_T01

value: Rosa26CD74-NRG1/Flp mice

value: tissue


title: 8 days after surgery control (sham) sample 6 [8dSham626]


title: liver (mouse M00236)

description:
genes_CPM; genes_CPM
M00236_N02

value: N


title: spleen (mouse M00236)

description:
genes_CPM; genes_CPM
M00236_N01

value: spleen


title: 8 days after surgery bile duct ligation (BDL) sample 2 [8dBDL126]

value: liver


title: sarcoma (mouse M00235)

description:
genes_CPM; genes_CPM
M00235_T01

value: sarcoma


title: 8 days after surgery control (sham) sample 3 [8dSham524]


title: 8 days after surgery control (sham) sample 4 [8dSham526]


title: 8 days after surgery control (sham) sample 6 [8dsham6]

data_processing:
Trimming performed skewer embedded  docker4seq package v 2.4.2
Mapping performed with STAR embedded  docker4seq package v 2.4.2
Transcripts/genes quantitification performed with RSEM embedded  docker4seq package v 2.4.2
Genome_build: hg38
Supplementary_files_format_and_content: tab deliment counts table

extract_protocol:
Blood was collected into K2 EDTA-coated S-Monovette® by cardiac puncture. Plasma was prepared within 1 hour of blood sampling by centrifuging at 1000g for 10 mins at 4°C followed by a second centrifugation of the supernatant at 2000 rpm for 15 mins and frozen at -80°C till further processing. Circulating EVs were collected from 250 µl of plasma. Briefly, plasma was thawed on ice and 63 µl of ExoquickTM (System Biosciences) was added to EV preparation according to the maunfacturer’s instructions. For total RNA purification, EVs pellets were resuspended in 200 µl PBS and 1 ml of QIAzol Lysis reagent (Qiagen) added. RNA was extracted using miRNeasy serum/plasma kit (Qiagen) in an automated way using the QIAcube instrument (Qiagen), thus preventing operator-depending variability. Total RNA was estimated quantitatively with Qubit RNA HS kit (ThermoFisher Scientific) and then stored at -80°C till further use.
To detect coding and long non-coding RNAs present in EVs, the TruSeq stranded mRNA library preparation kit (Illumina) was used, following the manufacturer’s instructions but skipping the depletion of ribosomal RNAs and purification of the polyA+ fraction phases. Briefly, 40 ng of total RNA extracted from EVs were fragmentated for 8 min at 94°C. First strand and second strand cDNA were synthetized, a single A nucleotide was added to the 3’ ends of the blunt fragments, and multiple indexing adapters were ligated at the end of the double strand cDNA. A 15 cycles PCR was performed to selectively enrich those DNA fragments with adapter molecules on both ends. Each library was analysed with the DNA 1000 chip (Agilent) using Agilent 2100 Bioanalyzer and quantified using the Qubit DNA HS kit (Life Technologies). A pool of 12 libraries (pooled at equimolar concentration) was generated, quantified with Qubit DNA HS kit and run at the concentration of 1.6 pM on the NextSeq500 (Illumina) sequencer in 75 nts paired end sequencing mode following the manufacturer’s instructions.


title: liver (mouse M00235)

description:
genes_CPM; genes_CPM
M00235_N01


title: MEF Embryo 8 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E8 p3

source_name: Rosa26CD74-NRG1/Flp mouse embryos

extract_protocol:
Murine embryonic fibroblasts were generated according to standard procedures. On cell culture passage 1 and after cell culture passage 3 RNA was isolated.
RNA was extracted using the RNeasy Mini Kit (Qiagen).
Total extracted RNA fulfilled the following sample requirements for sequencing: RIN >8, DNA free, OD260/280 = 1,8-2,1 and OD260/230 >1,5.
3’ UTR mRNA libraries were generated from total RNA (Lexogen QuantSeq Kit) according to the manufacturers protocol and sequenced on Illumina HiSeq4000.

value: murine embryonic fibroblasts

value: embryo

value: CD74-NRG1 negative (Passage 3)


title: KO3

city: xi'an

first: xin

last: wang

address: yanta west road 76

institute: xi'an jiaotong university

data_processing:
Illumina Hiseq 6000 sequencer software used for basecalling.
The double-stranded cDNA library was finished through PCR enrichment and size selection. The prepared cDNA library was sequenced with the Illumina Hiseq 2000 sequencer (Illumina HiSeq 6000 v4 Single-Read 50 bp) after pooling according to its expected data volume and effective concentration.
Firstly, the bulk RNA-seq data were filtered by using SAOPnuke (version 1.5.6) with parameters “-l 15 -q 0.2 -n 0.05 -Q 2”. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10) by using HISAT2 with parameters “-k 1 -p 4 -q --no-unal --dta --un-conc-gz”. Then the expression levels of each gene were calculated by the transcripts per kilobase of exon model per million mapped reads (TPM) by using StringTie3 with parameters “-t -C -e -B -A -p 1”.
The final TPM matrix of all samples was used for subsequent analysis. A 1.5-fold variance in expression levels, a P value less than 0.05, and an adjusted P value less than 0.1 were used as cutoffs to define differentially expressed genes. The P value and adjusted P value were calculated using R software (DESeq2)
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: lymph nodes Tregs from the spleen of Zfp335 deficient mice

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA concentration was detected by the Qubit RNA broad range assay in the Qubit Fluorometer (Invitrogen). After quality control by RNase free agarose gel and Agilent 2100 (Agilent Technologies, Palo Alto, CA, USA), RNA-Seq libraries were prepared using 200ng total RNA with the TruSeq RNA sample prep kit according to manufacturer’s instructions (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: YFP+CD25+ Tregs were sorted from the lymph nodes of YFP+Foxp3cre+Zfp335f/f mice and wild-type littermates

tag: tag

value: Zfp335 deficient

tag: cell type

value: lymph nodes_Tregs


title: MEF Embryo 8 Passage 2

description:
all_samples.mm.genes.count.2018-02-13
E8 p1

value: CD74-NRG1 negative (Passage 1)


title: KO2

tag: tissue


title: 8 days after surgery control (sham) sample 3 [8dsham3]

value: control (sham)

value: Extracellular vesicles


title: MEF Embryo 5 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E5 p3


title: 8 days after surgery bile duct ligation (BDL) sample 6 [8dBDL326]

value: male


title: KO1

tag: genotype


title: MEF Embryo 5 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E5 p1


title: 8 days after surgery bile duct ligation (BDL) sample 4 [8dBDL226]


title: 8 days after surgery control (sham) sample 1 [8dsham1]


title: 8 days after surgery bile duct ligation (BDL) sample 6 [8dBDL6]


title: 8 days after surgery control (sham) sample 4 [8dsham4]


title: 8 days after surgery bile duct ligation (BDL) sample 3 [8dBDL224]


title: WT2

source_name: lymph nodes Tregs from the spleen of WT mice

value: wild type


title: MEF Embryo 3 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E3 p1

value: CD74-NRG1 homozygous (Passage 1)


title: MEF Embryo 3 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E3 p3

value: Rosa26CD74-NRG1/Flp mice

value: CD74-NRG1 homozygous (Passage 3)


title: 8 days after surgery bile duct ligation (BDL) sample 1 [8dBDL124]

value: bile duct ligation (BDL)


title: WT3

value: spleen


title: 8 days after surgery bile duct ligation (BDL) sample 5 [8dBDL5]

value: liver


title: WT1


title: MEF Embryo 6 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E6 p1

value: CD74-NRG1 heterozygous (Passage 1)


title: 8 days after surgery bile duct ligation (BDL) sample 3 [8dBDL3]


title: MEF Embryo 4 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E4 p3

value: murine embryonic fibroblasts

value: CD74-NRG1 heterozygous (Passage 3)


title: 8 days after surgery control (sham) sample 5 [8dsham5]


title: 8 days after surgery bile duct ligation (BDL) sample 4 [8dBDL4]


title: MEF Embryo 6 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E6 p3

value: embryo


title: JQ1.no3

city: New York

first: Jinyang

last: Li

state: New York

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
Transcript quantification using Salmon
Genome_build: hg38
Supplementary_files_format_and_content: txt file of transcript per million (TPM)

growth_protocol: DMEM with 10% FBS

extract_protocol:
Qiagen’s RNeasy Mini kit
library was prepared by a commercial company, Novegene

treatment_protocol: 5 uM FIDAS-5 for 48 hour, or treated with 0.5 uM JQ1 for 48 hour.

tag: cell line

value: human hepatocellular carcinoma cells


title: 8 days after surgery bile duct ligation (BDL) sample 2 [8dBDL2]


title: KO2_untreat [CBW8]

city: shanghai

first: Baiwen

last: Chen

address: south  chongqing road

department: Shanghai Institute of Immunology

institute: Shanghai Jiao Tong University School of Medicine

description:
processed data file:
KO_vs_Con_untreat.txt

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Genome_build: mm9
Supplementary_files_format_and_content: txt files including coutsummary

source_name: MC38 cells

extract_protocol:
Cells were harvested on ice, and RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: MC38 cells were treated with or without IFNγ  (20 ng/ml for 4 h)

value: DENR KO

value: none (untreated)


title: MEF Embryo 4 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E4 p1


title: JQ1.no2


title: JQ1.no1


title: 8 days after surgery control (sham) sample 2 [8dsham2]

value: control (sham)


title: 8 days after surgery bile duct ligation (BDL) sample 1 [8dBDL1]

value: Extracellular vesicles


title: KO1_untreat [CBW7]


title: MEF Embryo 2 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E2 p3


title: Con2_untreat [CBW6]

value: control; wild type


title: FIDAS5.no3


title: 15 days after surgery control (sham) sample 6 [15dsham6]

source_name: 15 days after surgery control (sham)_liver

value: male


title: MEF Embryo 2 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E2 p1


title: 15 days after surgery control (sham) sample 5 [15dsham5]


title: KO2_IFN [CBW4]

description:
processed data file:
KO_vs_Con_IFN.txt

value: IFNγ-treated


title: Con1_untreat [CBW5]


title: MEF Embryo 10 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E10 p3

value: Rosa26CD74-NRG1/Flp mice


title: 15 days after surgery control (sham) sample 4 [15dsham4]


title: FIDAS5.no2


title: 15 days after surgery control (sham) sample 3 [15dsham3]


title: FIDAS5.no1


title: MEF Embryo 10 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E10 p1

value: CD74-NRG1 homozygous (Passage 1)


title: 15 days after surgery control (sham) sample 2 [15dsham2]


title: Con2_IFN [CBW2]

description:
processed data file:
KO_vs_Con_IFN.txt


title: KO1_IFN [CBW3]

description:
processed data file:
KO_vs_Con_IFN.txt


title: MEF Embryo 7 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E7 p3

value: CD74-NRG1 homozygous (Passage 3)


title: MEF Embryo 7 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E7 p1


title: Con1_IFN [CBW1]

description:
processed data file:
KO_vs_Con_IFN.txt


title: Vehicle.no2

value: Vehicle


title: Vehicle.no3


title: 15 days after surgery control (sham) sample 1 [15dsham1]

value: liver


title: MEF Embryo 1 Passage 3

description:
all_samples.mm.genes.count.2018-02-13
E1 p3

value: CD74-NRG1 negative (Passage 3)


title: 15 days after surgery bile duct ligation (BDL) sample 6 [15dBDL6]

source_name: 15 days after surgery bile duct ligation (BDL)_liver

value: bile duct ligation (BDL)


title: MEF Embryo 1 Passage 1

description:
all_samples.mm.genes.count.2018-02-13
E1 p1

value: murine embryonic fibroblasts

value: CD74-NRG1 negative (Passage 1)


title: shIKZF2_2

city: Beijing

first: Bufang

last: Xu

address: No.8 Xishiku Street, Xicheng District

institute: Peking University

data_processing:
Cell line sequencing data produced by Illumina NovaSeq 6000 called as Raw Data, is subjected to quality control (QC) that determine if a resequencing step is needed.
After filtering raw reads via Perl script, Bowtie2 v2.2.3 was used for building the genome index, clean Data was then aligned to the human hg38 reference genome using HISAT2 v2.1.0.
For sequence data of cell lines,clean data were aligned to the reference gene sequence using Bowtie2 and gene expression levels were calculated by FPKM（fragments per kilobase million）.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for 4 CTCL cell-line samples

source_name: CTCL cell line (Hut78)

growth_protocol: Hut78 cells were cultured in RPMI 1640 medium with 10% fetal bovine serum , containing 100 U/mL penicillin and 0.1 mg/mL streptomycin

extract_protocol:
200ng total RNA samples were extracted from lesional skin biopsies obtained from control Hut78 cells and IKZF2-silienced Hut78 cells  using RNeasy Mini kit  (Qiagen-74104) ,respectively.
RNA libraries were prepared for sequencing using standard Illumina protocol

treatment_protocol: Hut78 cells  were subjected with lentivirus-mediated transfection of vectors expressing IKZF2-shRNA(shIKZF2)  or scrambled shRNA(sh0), and then cultured  to produce stable IKZF2 knockdown cell line.

tag: tumor

value: CTCL

value: peripheral blood

tag: dissease state

value: Sézary Syndrome


title: shIKZF2_1


title: 15 days after surgery bile duct ligation (BDL) sample 5 [15dBDL5]

tag: treatment


title: DIA69Con8wk

city: Memphis

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

description: mock injected 8 weeks replicate 4

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes TPM values for all 62 samples

source_name: diaphragm skeletal muscle from female C57BL/6J mice

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from the  time points of 3 week post LLC cell injection
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina NovaSeq 6000 platform.

value: female

value: diaphragm skeletal muscle

value: 2 months

value: mock injected

tag: time

value: 8 weeks


title: DIA70Con8wk

description: mock injected 8 weeks replicate 5


title: DIA68Con8wk

description: mock injected 8 weeks replicate 3


title: 15 days after surgery bile duct ligation (BDL) sample 4 [15dBDL4]

value: male

value: Extracellular vesicles


title: srsf1_eclip_input_hepatocyte_2

city: Urbana

first: Waqar

last: Arif

state: IL

address: 506 S. Mathews Avenue

department: Biochemistry

institute: UIUC

description: eCLIP input for srsf1_eclip_hepatocyte_2

data_processing:
Takes output from raw files.  Run to trim off both 5’ and 3’ adapters on both reads. Command: quality-cutoff 6  -m 18  -a NNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC  -g CTTCCGATCTACAAGTT -g CTTCCGATCTTGGTCCT  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGT  AGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.metrics
Takes output from cutadapt round 1. Run to trim off the 3’ adapters on read 2, to control for double ligation events. Command: cutadapt -f fastq --match-read-wildcards  --times 1  -e 0.1  -O 5  --quality-cutoff 6  -m 18  -A AACTTGTAGATCGGA -A AGGACCAAGATCGGA -A ACTTGTAGATCGGAA -A GGACCAAGATCGGAA -A CTTGTAGATCGGAAG -A GACCAAGATCGGAAG -A TTGTAGATCGGAAGA -A ACCAAGATCGGAAGA -A TGTAGATCGGAAGAG -A CCAAGATCGGAAGAG -A GTAGATCGGAAGAGC -A CAAGATCGGAAGAGC -A TAGATCGGAAGAGCG -A AAGATCGGAAGAGCG -A AGATCGGAAGAGCGT -A GATCGGAAGAGCGTC -A ATCGGAAGAGCGTCG -A TCGGAAGAGCGTCGT -A CGGAAGAGCGTCGTG -A GGAAGAGCGTCGTGT  -o /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz  -p /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.fastq.gz  /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.fastq.gz > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.metrics
Takes output from cutadapt round 2.  Maps to human specific version of RepBase used to remove repetitive elements, helps control for spurious artifacts from rRNA (& other) repetitive reads.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir /path/to/RepBase_human_database_file --genomeLoad LoadAndRemove  --readFilesIn /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.fastq.gz /full/path/to/files/file_R2.C01.fastq.gz.adapterTrim.round2.fastq.gz --outSAMunmapped Within  --outFilterMultimapNmax 30  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam --outSAMattributes All  --readFilesCommand zcat  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bam
Takes output from STAR rmRep.  Maps unique reads to the mouse genome.  Command: STAR  --runMode alignReads  --runThreadN 16  --genomeDir  /path/to/STAR_database_file --genomeLoad LoadAndRemove  --readFilesIn  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate1  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rep.bamUnmapped.out.mate2  --outSAMunmapped Within  --outFilterMultimapNmax 1  --outFilterMultimapScoreRange 1  --outFileNamePrefix /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --outSAMattributes All  --outStd BAM_Unsorted  --outSAMtype BAM Unsorted  --outFilterType BySJout  --outReadsUnmapped Fastx  --outFilterScoreMin 10  --outSAMattrRGline ID:foo  --alignEndsType EndToEnd > /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam
takes output from STAR genome mapping.  Custom random-mer-aware script for PCR duplicate removal. Command: barcode_collapse_pe.py  --bam /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.bam  --out_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  --metrics_file /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.metrics
Takes output from barcode collapse PE.  Sorts resulting bam file for use downstream.  Command: java  -Xmx2048m  -XX:+UseParallelOldGC  -XX:ParallelGCThreads=4  -XX:GCTimeLimit=50  -XX:GCHeapFreeLimit=10  -Djava.io.tmpdir=/full/path/to/files/.queue/tmp  -cp /path/to/gatk/dist/Queue.jar  net.sf.picard.sam.SortSam  INPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.bam  TMP_DIR=/full/path/to/files/.queue/tmp  OUTPUT=/full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  VALIDATION_STRINGENCY=SILENT  SO=coordinate  CREATE_INDEX=true
Takes output from sortSam, makes bam index for use downstream.  Command: samtools index  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam.bai
Takes inputs from multiple final bam files.  Merges the two technical replicates for further downstream analysis.  Command: samtools  merge  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/file_R1.C01.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam /full/path/to/files/file_R1.D08.fastq.gz.adapterTrim.round2.rmRep.rmDup.sorted.bam
Takes output from sortSam, makes bam index for use downstream.  Command: samtools  index  /full/path/to/files/CombinedID.merged.bam  /full/path/to/files/CombinedID.merged.bam.bai
Takes output from sortSam.  Only outputs the second read in each pair for use with single stranded peak caller.  This is the final bam file to perform analysis on.  Command: samtools view -hb -f 128  /full/path/to/files/CombinedID.merged.bam  >  /full/path/to/files/CombinedID.merged.r2.bam
Takes results from samtools view.  Calls peaks on those files.  Command: clipper  -b /full/path/to/files/CombinedID.merged.r2.bam  -s mm9  -o /full/path/to/files/CombinedID.merged.r2.peaks.bed  --bonferroni  --superlocal  --threshold-method binomial  --save-pickle
Genome_build: mm9
Supplementary_files_format_and_content: bed format, contains clusters of predicted RBP binding

source_name: hepatocytes

growth_protocol: Organisms were housed in flow cages, following the standard 12 hour light/dark cycle

extract_protocol:
Samples were lysed in iCLIP lysis buffer, followed by limited digestion with RNase I (Ambion), immunoprecipitation of RBP-RNA complexes with a specific antibody of interest (Protein G sheep anti-rabbit Dynabeads), and stringent washes.
After dephosphorylation with FastAP (Thermo Fisher) and T4 PNK (NEB), a barcoded RNA adapter is ligated to the 3’ end (T4 RNA Ligase, NEB) (at this step, multiple replicates of the same RBP, or potentially RBPs of similar size and bound RNA amount, can be uniquely barcoded and pooled after ligation to simplify downstream steps - see Supplementary Fig. 2A). Ligations are performed on-bead (to allow washing away unincorporated adapter) in high concentration of PEG8000, which improves ligation efficiency to > 90%. Samples are then run on standard protein gels and transferred to nitrocellulose membranes, and a region 75 kDa (~150 nt of RNA) above the protein size is isolated and proteinase K (NEB) treated to isolate RNA. RNA is reverse transcribed with AffinityScript (Agilent), and treated with ExoSAP-IT (Affymetrix) to remove excess oligonucleotides. A second DNA adapter (containing a random-mer of 5 (N5) or 10 (N10) random bases at the 5’ end) is then ligated to the cDNA fragment 3’ end (T4 RNA Ligase, NEB), performed with high concentration of PEG8000 (to improve ligation efficiency) and DMSO (to decrease inhibition of ligation due to secondary structure). After cleanup (Dynabeads MyOne Silane, ThermoFisher), an aliquot of each sample is first subjected to qPCR (to identify the proper number of PCR cycles), and then the remainder is PCR amplified (Q5, NEB) and size selected via agarose gel electrophoresis.

treatment_protocol: No treatment

tag: strain background

value: 1 month

value: wildtype

value: hepatocyte

tag: rip antibody


title: sh0_1


title: sh0_2


title: DIA67Con8wk

description: mock injected 8 weeks replicate 2


title: 15 days after surgery bile duct ligation (BDL) sample 3 [15dBDL3]

value: liver


title: DIA66Con8wk

description: mock injected 8 weeks replicate 1


title: srsf1_eclip_input_hepatocyte_1

description: eCLIP input for srsf1_eclip_hepatocyte_1


title: DIA49NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 4

value: non-cachectic melanoma cells


title: Vehicle.no1

value: human hepatocellular carcinoma cells

value: Vehicle


title: srsf1_eclip_hepatocytes_2

value: Protein G sheep anti-rabbit Dynabeads


title: DIA48NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 3


title: Mutant 2 [Mut4_S9]

city: Los Angeles

first: Tingwei

last: Guo

address: 2250 Alcazar St

department: CCMB

institute: usc

data_processing:
Illumina Casava1.8 software used for basecalling.
Raw reads were trimmed and aligned using TopHat (Version 2.0.8) with the mm10 genome
RPKM was used to normalize the data and differential expression was calculated by selecting transcripts that changed with p < 0.05
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include lognormal with shrinkage mean value for each feature in individual sample.

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol:
Palate samples from Kdm6bfl/+ (control) and Wnt1-Cre;Kdm6bfl/fl (mutant) mice were collected at E12.5 for RNA isolation with RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol
cDNA library preparation and sequencing were performed at the USC Molecular Genomics Core.

treatment_protocol: Not applicable

value: Palate


title: Mutant 1 [Mut2_S8]


title: Dxr 3 -ATc

city: Dallas

first: Charley

last: Gruber

state: TX

address: 6000 Harry Hines

department: Microbiology

institute: UTSW

data_processing:
Single-end RNASeq reads were used to quantify gene expression by aligning against the E. coli MG1655 (ASM584v2) genome with Salmon (version 1.1.0)
The resulting counts and transcript per million (TPM) counts were assembled using the tximport package (version 1.12.0)
TPM counts were transformed to log2 space with an offset of 1 and the summarized integer counts were imported into DESeq2 (version 1.24.0) and then conducted differential analysis with apeglm log fold change shrinkage
We filtered the results that had a p-value less than or equal to 0.05 and a log-fold change greater than 1 or less than -1 to identify upregulated and downregulated genes, respectively
We identify enriched pathways by using DAVID Bioinformatics Resources (version 6.8) to identify functionally enriched pathways
Genome_build: MG1655 ASM584v2
Supplementary_files_format_and_content: counts and relative expression
Supplementary_files_format_and_content: GO enrichment

organism: Escherichia coli

source_name: cells

growth_protocol: Aerobic growth in LB Lennox

extract_protocol:
Qiagen Rneasy extraction kit
rRNA was removed using 1/2 reagent of Ribozero G- bacterial kit (Illumina) and then 1/2 of the ribodepleted material was processed with with 1/3rd reagent of NEBNext II ultra mRNA kit

treatment_protocol: Designated samples were treated with 50ng/ml anhydrotetracycline

value: degron tagged Dxr

value: + anhydrotetracycline

tag: time point

value: 3 hours


title: 15 days after surgery bile duct ligation (BDL) sample 1 [15dBDL1]

tag: strain

value: bile duct ligation (BDL)


title: 15 days after surgery bile duct ligation (BDL) sample 2 [15dBDL2]


title: srsf1_eclip_hepatocytes_1

tag: age


title: Dxr 3 +ATc


title: Mutant 3 [Mut8_S10]


title: DIA47NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 2

value: female

value: diaphragm skeletal muscle

value: 2 months


title: Dxr 2 +ATc

value: - anhydrotetracycline

value: 2 hours


title: Control 3 [Ctl2_S1]

value: wild type


title: Dxr 2 -ATc


title: DIA46NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 1

value: 8 weeks


title: Control 1 [Ctl6_S6]


title: Dxr 1 -+ATc

value: 1 hours


title: Control 2 [Ctl11_S7]


title: DIA30CAC8wk

description: cachectic melanoma cells 8 weeks replicate 7

value: cachectic melanoma cells


title: DIA28CAC8wk

description: cachectic melanoma cells 8 weeks replicate 6


title: Dxr 1 -ATc


title: RNA_NPC_d5_Mll34dCD_rep2

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Dr., CMM-East, Admin Area/Rm 2071

institute: University of California, San Diego School of Medicine

data_processing:
fastq: Illumina's HiSeq Control Software
RNA-seq reads were aligned against the mouse mm10 genome assembly using STAR (Dobin et al., 2013). The processed data was created using HTseq (Anders et al., 2015) and used for differential expression analysis by edgeR (Robinson et al., 2010).
Genome_build: mm10
Supplementary_files_format_and_content: The processed file include all sample data of the number of read counts in each gene that were calculated using HTseq (Anders et al., 2015).

source_name: neural precursor cells

growth_protocol: Cells were grown in DMEM supplemented with 100 U/mL penicillin, 100 mg/mL streptomycin, 15% KnockOut Serum Replacement (ThermoFisher, 10828028), Glutamax (Gibco, 35050), 0.1 mM non-essential amino acid, 0.1mM beta-mercaptoethanol, and 500 U/ml LIF at 37°C and 5% CO2

extract_protocol: RNA-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

treatment_protocol: To deplete CTCF, 1 ul 500 mM auxin per 1 ml medium was added, and medium with auxin was changed every 24 hours. Cells were harvested 24, 48 or 96 hours after stating auxin treatment. Neural progenitor cell differentiation treatment was performed with or without auxin treatment, and harvested on day 2, 4, 6 and 2 days after washing out auxin from day 4 and day 6 samples.

value: E14 mouse neural precursor cell


title: DIA27CAC8wk

description: cachectic melanoma cells 8 weeks replicate 5


title: RNA_NPC_d5_Mll34dCD_rep1


title: Dxr 0

value: 0 hours


title: DIA24CAC8wk

description: cachectic melanoma cells 8 weeks replicate 4


title: DapB 3 +ATc

value: degron tagged DapB


title: DapB 3 -ATc


title: DIA21CAC8wk

description: cachectic melanoma cells 8 weeks replicate 2


title: RNA_NPC_d5_WT_rep2


title: DIA23CAC8wk

description: cachectic melanoma cells 8 weeks replicate 3


title: DapB 2 +ATc


title: RNA_NPC_d5_WT_rep1


title: RNA_NPC_d2.5_Mll34dCD_rep1


title: DapB 2 -ATc


title: RNA_NPC_d2.5_WT_rep2


title: DIA50NCAC8wk

description: non-cachectic melanoma cells 8 weeks replicate 5

value: non-cachectic melanoma cells


title: DIA19CAC8wk

description: cachectic melanoma cells 8 weeks replicate 1


title: RNA_NPC_d2.5_Mll34dCD_rep2


title: DIA65Con6wk

description: mock injected 6 weeks replicate 5

value: mock injected

value: 6 weeks


title: RNA_NPC_d2.5_WT_rep1


title: DIA62Con6wk

description: mock injected 6 weeks replicate 2


title: DIA63Con6wk

description: mock injected 6 weeks replicate 3


title: RNA_ESC_Mll34dCD_rep2

source_name: embryonic stem cells

value: E14 mouse embryonic stem cell


title: RNA_ESC_Mll34dCD_rep1


title: DapB 0


title: DIA61Con6wk

description: mock injected 6 weeks replicate 1


title: DapB 1 -ATc


title: DIA64Con6wk

description: mock injected 6 weeks replicate 4


title: RNA_ESC_WT_rep2


title: Low-beads

city: Shen Zhen

first: Shaohua

last: Ma

state: Guangdong Sheng

address: nanshan street

institute: Tsinghua University

data_processing:
Bcl2fastq(v2.17.1.14) used for base calling
FastQC(v0.10.1) used for evaluating quality,  data were processed by Cutadapt (V1.9.1) to be high quality clean data.
clean data were aligned to reference genome via software Hisat2
HTSeq (v0.6.1) estimated gene and isoform  expression levels from the pair-end clean data, which calculated FPKM（Fragments Per Kilo bases per Million reads）values（Mortazavi, 2008）
Genome_build: hg38
Supplementary_files_format_and_content: xls file include raw counts and FPKM values for each sample

molecule: polyA RNA

source_name: mesenchymal stem cells

extract_protocol:
Total RNA of each sample was extracted using TRIzol Reagent kits.
Next generation sequencing library preparations were constructed  according to the Illumina protocol.

value: umbilical cord tissues

value: mesenchymal stem cells


title: Bulk-gel


title: DIA45NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 5

value: female

value: diaphragm skeletal muscle


title: DIA44NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 4

value: 2 months


title: DapB 1 +ATc

value: + anhydrotetracycline


title: DIA42NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 2


title: Input_ChIP_NPC_WT_rep2

library_source: genomic

data_processing:
fastq: Illumina's HiSeq Control Software
Each fastq file was mapped to mouse genom (mm10) with BWA -aln (Li and Durbin, 2009) and PCR duplicates were removed using Picard MarkDuplicate. The bigWig files were created using deepTools (Ramírez et al., 2016).
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (bigWig) were created using deepTools (Ramírez et al., 2016).

molecule: genomic DNA

extract_protocol:
ChIP and input library preparation were carried out as described in ENCODE experiments (“Ren Lab ENCODE Chromatin Immunoprecipitation Protocol” in https://www.encodeproject.org/documents/)
ChIP-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 or HiSeq2500 protocols (Illumina, San Diego, CA).

tag: chip antibody


title: Input_ChIP_NPC_Mll34dCD_rep1


title: Input_ChIP_NPC_Mll34dCD_rep2


title: DIA15CAC6wk

description: cachectic melanoma cells 6 weeks replicate 5

tag: Sex


title: Input_ChIP_NPC_WT_rep1


title: DIA14CAC6wk

description: cachectic melanoma cells 6 weeks replicate 4


title: Input_ChIP_ESC_Mll34dCD_rep2


title: DIA41NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 1


title: DIA43NCAC6wk

description: non-cachectic melanoma cells 6 weeks replicate 3


title: Input_ChIP_ESC_WT_rep1


title: DIA11CAC6wk

description: cachectic melanoma cells 6 weeks replicate 1


title: H3K27me3_ChIP_NPC_Mll34dCD_rep2

value: H3K27me3 (Active Motif, 61017)


title: DIA12CAC6wk

description: cachectic melanoma cells 6 weeks replicate 2


title: K562_WT_ERRBS_R3

city: Boston

first: Eva

middle: Johanna

last: Schaefer

state: MASSACHUSETTS

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Raw RNA-seq reads were mapped to the GRCh38 build of the human genome by STAR (Dobin et al., 2013). Gene counts were obtained using featureCounts (Liao et al., 2014). Normalization and differential gene expression analysis was performed using the R package DESeq2 (Love et al., 2014). Genome build: Hg38.
ChIP-seq and ATAC-seq alignments and peak calling were performed using the ChiLin pipeline (Qin et al., 2016). Reads were mapped to the hg19 human reference genome with BWA (Li and Durbin, 2009). Mapped reads were indexed and sorted using samtools (Li et al., 2009). Peaks were called with MACS2 (Version 2.1.1, https://github.com/macs3-project/MACS; (Zhang et al., 2008)) at -q 0.01. The --SPMR option was used to generate bedgraph and bigwig files normalized to 1 million reads. Genome build: Hg19.
mERRBS FASTQ files were generated by using the Illumina pipeline. Adapter sequences were filtered out using the FAR software (Dodt, M, Ahmed R, Dieterich C. FAR -- flexible adapter remover. FAR project website (2011)) (http://sourceforge.net/projects/theflexibleadap/). Reads were aligned to the hg19 genome using the bismark (http://www.bioinformatics.babraham.ac.uk/projects/bismark/) alignment tool. Genome build: Hg19.
Supplementary_files_format_and_content: matrix of raw RNA-seq counts; gene counts were obtained using featureCounts (Liao et al., 2014). Genome build: Hg38.
Supplementary_files_format_and_content: ChIP-seq and ATAC-seq bw files normalized to 1 million reads; bw files  were generated using the MACS2 --SPMR option  (Version 2.1.1, https://github.com/macs3-project/MACS; (Zhang et al., 2008)). Genome build: Hg19.
Supplementary_files_format_and_content: methylation call file (myCpG.txt); tab-delimited text file that contains the location of the CpG, total read coverage on the C base, percentage of bisulfite-converted Cs (representing unmethylated Cs) and non-converted Cs (representing methylated Cs). The column headers are: chrBase, chr, base, strand, coverage, freqC, freqT. Genome build: Hg19.

source_name: K562 cell line

growth_protocol: K562 , KG1, MV4-11, and OCI-AML3 cells were cultured in RPMI-1640 medium (Gibco™) with 10% fetal bovine serum (FBS, Sigma-Aldrich) and 1% penicillin-streptomycin-glutamine (PSG, Gibco™) at 37°C and 5% CO2. Primary AML samples were obtained with informed consent from patients with newly diagnosed or relapsed acute myeloid leukemia. Leukemic blasts were isolated from whole blood using CD3 depletion and ficoll density gradient separation. Cell viability and sample purity was determined by trypan blue staining and FACS analyses.

extract_protocol:
High-molecular genomic DNA from K562 cells (n=3) was extracted using the DNA Isolation Kit for Cells and Tissues from Roche (Cat#118147700011).
Multiplexed enhanced reduced-representation bisulfite sequencing (mERRBS) was performed as previously described by the University of Michigan Epigenomics Core (Garrett-Bakelman et al., 2015). Libraries were sequenced on a NovaSeq 6000 with 100bp single-end reads.

value: WT


title: High-beads


title: Input_ChIP_ESC_Mll34dCD_rep1


title: Input_ChIP_ESC_WT_rep2


title: K562_WT_ERRBS_R1


title: H3K27me3_ChIP_NPC_Mll34dCD_rep1


title: DIA60Con4wk

description: mock injected 4 weeks replicate 5

value: 4 weeks


title: DIA59Con4wk

description: mock injected 4 weeks replicate 4


title: RNA-seq AML_BCORPUFDTr_R2

source_name: primary AML cells

extract_protocol:
Total RNA was extracted according to the manufacturer’s recommendations using RNeasy Plus Mini Kit (Qiagen, Cat#74134) or High Pure RNA Isolation Kit (Roche, Cat#11828665001).
Libraries were prepared using Roche Kapa mRNA HyperPrep strand specific sample preparation kits from 200ng of purified total RNA according to the manufacturer’s protocol on a Beckman Coulter Biomek i7. The finished dsDNA libraries were quantified by Qubit fluorometer, Agilent TapeStation 2200, and RT-qPCR using the Kapa Biosystems library quantification kit according to manufacturer’s protocols. Uniquely dual indexed libraries were pooled in equimolar ratios and sequenced on an Illumina NextSeq 550 with single-end 75bp reads or a NovaSeq 6000 with 50bp read pairs.

value: BCORPUFDTr


title: K562_WT_ERRBS_R2


title: RRBS_Patient Derived Xenografts UPN01 at diagnosis, rep 3

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Reads were trimmed using trimmomatic and aligned against the hg38 reference genome using BsMAP.
Bisulfite conversion rate of CpG islands was computed using the biseqMethCalling.py script.
Differential methylation analysis was performed using RnBeads.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated count file

source_name: AML

extract_protocol:
Genomic DNA was extracted using the Wizard SV Genomic DNA purification system, following manufacturer’s instruction and including a step of protein lysis using Proteinase K.
Genomic DNA was digested using methylation-insensitive restriction enzymes to generate short fragments enriched for CpG dinucleotides at the extremities. After end-repair, A-tailing and ligation to methylated adapters, the CpG-rich DNA fragments were subjected to size selection, bisulfite conversion, and PCR amplification.

tag: condition

value: Diagnosis

tag: patient

tag: origin

value: PDX


title: DIA58Con4wk

description: mock injected 4 weeks replicate 3

tag: tissue


title: RRBS_Patient Derived Xenografts UPN01 at relapse, rep 2

value: Relapse


title: RRBS_Patient Derived Xenografts UPN01 at relapse, rep 3


title: RNA-seq AML_BCORPUFDTr_R1

tag: genotype


title: RRBS_Patient Derived Xenografts UPN01 at diagnosis, rep 2


title: DIA57Con4wk

description: mock injected 4 weeks replicate 2


title: H3K4me3_ChIP_NPC_WT_rep1

tag: cell type

value: E14 mouse neural precursor cell

value: H3K4me3 (Millipore, 04-745)


title: RNA-seq AML_BCORWT_R1

value: BCORWT


title: RRBS_Patient Derived Xenografts UPN01 at relapse, rep 1


title: DIA56Con4wk

description: mock injected 4 weeks replicate 1

value: mock injected


title: H3K4me3_ChIP_NPC_WT_rep2


title: RNA-seq AML_BCORWT_R2


title: DIA13CAC6wk

description: cachectic melanoma cells 6 weeks replicate 3

value: cachectic melanoma cells

value: 6 weeks


title: DIA40NCAC4wk

description: non-cachectic melanoma cells 4 weeks replicate 5

value: female

value: non-cachectic melanoma cells


title: H3K4me3_ChIP_ESC_Mll34dCD_rep1

value: E14 mouse embryonic stem cell


title: H3K4me3_ChIP_ESC_Mll34dCD_rep2


title: RNA-seq K562_BCORPUFDTr_BCORL1KO_R2


title: RRBS_Patient Derived Xenografts UPN01 at diagnosis, rep 1


title: H3K4me3_ChIP_ESC_WT_rep2


title: DIA39NCAC4wk

description: non-cachectic melanoma cells 4 weeks replicate 4

value: diaphragm skeletal muscle

value: 2 months


title: RNA-seq K562_BCORPUFDTr_BCORL1KO_R1


title: RRBS_AML patient UPN01 at relapse (post transpantation)

value: Primary


title: RNA_ESC_WT_rep1


title: H3K4me3_ChIP_ESC_WT_rep1


title: DIA38NCAC4wk

description: non-cachectic melanoma cells 4 weeks replicate 3

value: 4 weeks


title: RRBS_AML patient UPN01 at diagnosis


title: H3K27ac_ChIP_NPC_Mll34dCD_rep2

value: H3K27ac (Active Motif, 39133)


title: DIA37NCAC4wk

description: non-cachectic melanoma cells 4 weeks replicate 2


title: RNA-seq K562_BCORPUFDTr_R1

value: BCORPUFDTr


title: RNA_Patient Derived Xenografts UPN01 at relapse, rep 3

description:
UPN01_PDX-R3_Rel
Primary_PDX_RNAseq_counts.tsv

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using HISAT2 and gene abundance estimation using featurecounts
Differential gene expression computed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated count file

extract_protocol:
Total RNA was extracted by using the Rneasy Plus Mini or Micro Kits, following the manufacturers' indications
Full-length RNA-seq libraries were prepared using the TruSeq Stranded mRNA library preparation kit

value: PDX


title: RNA-seq K562_BCORKO_BCORL1KO_R3


title: H3K27ac_ChIP_NPC_WT_rep2


title: RNA_Patient Derived Xenografts UPN01 at diagnosis, rep 3

description:
UPN01_PDX-D3_Diagn
Primary_PDX_RNAseq_counts.tsv

value: Diagnosis


title: H3K27ac_ChIP_NPC_Mll34dCD_rep1

value: E14 mouse neural precursor cell


title: RNA_Patient Derived Xenografts UPN01 at relapse, rep 2

description:
UPN01_PDX-R2_Rel
Primary_PDX_RNAseq_counts.tsv

value: Relapse


title: DIA10CAC4wk

description: cachectic melanoma cells 4 weeks replicate 5


title: RNA-seq K562_BCORKO_BCORL1KO_R2


title: RNA-seq K562_BCORKO_BCORL1KO_R1


title: RNA_Patient Derived Xenografts UPN01 at diagnosis, rep 2

description:
UPN01_PDX-D2_Diagn
Primary_PDX_RNAseq_counts.tsv


title: DIA8CAC4wk

description: cachectic melanoma cells 4 weeks replicate 3


title: RNA_Patient Derived Xenografts UPN01 at relapse, rep 1

description:
UPN01_PDX-R1_Rel
Primary_PDX_RNAseq_counts.tsv


title: RNA-seq K562_BCORKO_R7

value: BCORKO


title: H3K27ac_ChIP_ESC_Mll34dCD_rep1


title: DIA7CAC4wk

description: cachectic melanoma cells 4 weeks replicate 2


title: H3K27ac_ChIP_ESC_Mll34dCD_rep2


title: RNA_Patient Derived Xenografts UPN01 at diagnosis, rep 1

description:
UPN01_PDX-D1_Diagn
Primary_PDX_RNAseq_counts.tsv


title: RNA-seq K562_BCORKO_R6


title: RNA-seq K562_BCORPUFDTr_R2


title: DIA6CAC4wk

description: cachectic melanoma cells 4 weeks replicate 1


title: RNA_Patient Derived Xenografts UPN03 at relapse + EPZ-6438

description:
UPN03_EZH2i
EZH2i_DMSO_RNAseq_counts.tsv

value: Relapse + EPZ-6438


title: H3K27ac_ChIP_ESC_WT_rep2


title: RNA-seq K562_BCORL1KO_R3


title: H3K27ac_ChIP_ESC_WT_rep1


title: RNA_Patient Derived Xenograft UPN03 at relapse + DMSO

description:
UPN03_DMSO
EZH2i_DMSO_RNAseq_counts.tsv

value: Relapse + DMSO


title: DIA55Con2wk

description: mock injected 2 weeks replicate 5

value: mock injected

value: 2 weeks


title: DIA36NCAC4wk

description: non-cachectic melanoma cells 4 weeks replicate 1

value: female

value: non-cachectic melanoma cells


title: H3K27ac_ChIP_NPC_WT_rep1


title: H3K4me1_ChIP_NPC_Mll34dCD_rep2

value: H3K4me1 (abcam, ab8895)


title: H3K4me1_ChIP_NPC_Mll34dCD_rep1


title: RNA-seq K562_BCORL1KO_R2


title: DIA54Con2wk

description: mock injected 2 weeks replicate 4

value: diaphragm skeletal muscle

value: 2 months


title: RNA_Patient Derived Xenografts UPN02 at relapse + EPZ-6438

description:
UPN02_EZH2i
EZH2i_DMSO_RNAseq_counts.tsv

value: Primary


title: DIA9CAC4wk

description: cachectic melanoma cells 4 weeks replicate 4

value: cachectic melanoma cells

value: 4 weeks


title: RNA-seq K562_WT_R7

value: WT


title: DIA53Con2wk

description: mock injected 2 weeks replicate 3


title: RNA_Patient Derived Xenograft UPN02 at relapse + DMSO

description:
UPN02_DMSO
EZH2i_DMSO_RNAseq_counts.tsv


title: H3K4me1_ChIP_NPC_WT_rep2


title: DIA52Con2wk

description: mock injected 2 weeks replicate 2


title: RNA_Patient Derived Xenografts UPN01 at relapse + EPZ-6438

description:
UPN01_EZH2i
EZH2i_DMSO_RNAseq_counts.tsv


title: RNA-seq K562_WT_R6


title: H3K4me1_ChIP_NPC_WT_rep1


title: RNA_Patient Derived Xenograft UPN01 at relapse + DMSO

description:
UPN01_DMSO
EZH2i_DMSO_RNAseq_counts.tsv


title: H3K4me1_ChIP_ESC_Mll34dCD_rep2

value: E14 mouse embryonic stem cell


title: DIA35NCAC2wk

description: non-cachectic melanoma cells 2 weeks replicate 5


title: DIA51Con2wk

description: mock injected 2 weeks replicate 1


title: RNA-seq MV411_parental_R1

source_name: MV411 cell line


title: RNA_AML patient UPN010 at relapse (post chemotherapy)

description:
UPN10CT_Rel
Rel_Diagn_CT_RNAseq_counts.tsv


title: H3K4me1_ChIP_ESC_Mll34dCD_rep1


title: DIA34NCAC2wk

description: non-cachectic melanoma cells 2 weeks replicate 4


title: RNA_AML patient UPN010 at diagnosis

description:
UPN10CT_Diagn
Rel_Diagn_CT_RNAseq_counts.tsv

value: Diagnosis


title: RNA-seq KG1_parental_R2

source_name: KG1 cell line


title: DIA33NCAC2wk

description: non-cachectic melanoma cells 2 weeks replicate 3


title: H3K4me1_ChIP_ESC_WT_rep2


title: RNA_AML patient UPN09 at relapse (post chemotherapy)

description:
UPN09CT_Rel
Rel_Diagn_CT_RNAseq_counts.tsv

value: Relapse


title: RNA-seq K562_BCORL1KO_R1


title: H3K4me1_ChIP_ESC_WT_rep1


title: RNA-seq KG1_parental_R1


title: RNA_AML patient UPN09 at diagnosis

description:
UPN09CT_Diagn
Rel_Diagn_CT_RNAseq_counts.tsv


title: DIA32NCAC2wk

description: non-cachectic melanoma cells 2 weeks replicate 2


title: RNA-seq OCIAML3_parental_R2

source_name: OCIAML3 cell line


title: DIA31NCAC2wk

description: non-cachectic melanoma cells 2 weeks replicate 1


title: PLAC_H3K4me3_NPC_Mll34dCD_rep2

data_processing:
Library strategy: PLAC-seq
fastq: Illumina's HiSeq Control Software
PLAC-seq reads were aligned as single end reads using BWA with default parameters. Uniquely mapping reads were manually paired using in an in house pipeline. PCR duplicate reads were removed using Picard MarkDuplicates.
Genome_build: mm10
Supplementary_files_format_and_content: The processed files (pgl) were generated useing MAPS (Juric and Yu et al., 2019) and FitHiChIP (Bhattacharyya et al., 2019). Significant MAPS peaks: FDR < 0.01 for Broad Peak,  FDR<1.0E-04 for Singleton. Significant FitHiChIP peaks: FDR < 0.01.

extract_protocol:
PLAC-seq experiments were performed according to previous publication (Fang and Yu et al., 2014, Juric and Yu et al., 2019).
PLAC-seq library sequencing procedures were carried out as previously described according to Illumina HiSeq4000 protocols (Illumina, San Diego, CA).

value: E14 mouse neural precursor cell


title: PLAC_H3K4me3_NPC_Mll34dCD_rep1


title: RNA-seq K562_KDM2BKO_R4


title: RNA-seq MV411_parental_R2


title: DIA4CAC2wk

description: cachectic melanoma cells 2 weeks replicate 4


title: RNA_AML patient UPN08 at diagnosis

description:
UPN08CT_Diagn
Rel_Diagn_CT_RNAseq_counts.tsv


title: PLAC_H3K4me3_NPC_WT_rep2


title: RNA-seq K562_KDM2BKO_R3


title: RNA_AML patient UPN07 at relapse (post chemotherapy)

description:
UPN07CT_Rel
Rel_Diagn_CT_RNAseq_counts.tsv


title: RNA_AML patient UPN07 at diagnosis

description:
UPN07CT_Diagn
Rel_Diagn_CT_RNAseq_counts.tsv


title: RNA-seq K562_KDM2BKO_R2


title: DIA2CAC2wk

description: cachectic melanoma cells 2 weeks replicate 2


title: PLAC_H3K4me3_ESC_Mll34dCD_rep2


title: RNA-seq K562_KDM2BKO_R1


title: RNA_AML patient UPN06 at diagnosis

description:
UPN06CT_Diagn
Rel_Diagn_CT_RNAseq_counts.tsv


title: RNA-seq K562_BCORKO_R5

value: BCORKO


title: RNA_AML patient UPN08 at relapse (post chemotherapy)

description:
UPN08CT_Rel
Rel_Diagn_CT_RNAseq_counts.tsv


title: RNA_AML patient UPN05 at relapse (post transpantation)

description:
UPN05_Rel
Rel_Diagn_RNAseq_counts.tsv


title: PLAC_H3K4me3_ESC_WT_rep1


title: RNA_AML patient UPN05 at diagnosis

description:
UPN05_Diagn
Rel_Diagn_RNAseq_counts.tsv


title: DNT cells, UDCA-3

first: Chunpan

last: Zhang

address: No. 95 Yong-An Road

institute: Beijing Friendship Hospital

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 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: mm8
Supplementary_files_format_and_content: processed_data .xlsx (raw counts)

source_name: DNT cells, UDCA

extract_protocol:
Preparing DNT cells by in vitro conversion of wild type mouse-derived CD4+ cells, then these converted DNT cells (CD3+NK1.1-CD4-CD8-) were sorted using FACS Aria II, and then stimulated with or without UDCA (60uM) for 2 days. And then 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 libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: DNT cells

tag: developmental stage

value: adult

value: UDCA stimulation


title: PLAC_H3K4me3_ESC_Mll34dCD_rep1


title: DIA5CAC2wk

description: cachectic melanoma cells 2 weeks replicate 5

value: female

value: 2 weeks


title: RNA-seq K562_BCORKO_R3


title: DNT cells, UDCA-1


title: DIA3CAC2wk

description: cachectic melanoma cells 2 weeks replicate 3

value: diaphragm skeletal muscle


title: RNA_AML patient UPN06 at relapse (post chemotherapy)

description:
UPN06CT_Rel
Rel_Diagn_CT_RNAseq_counts.tsv


title: PLAC_H3K4me3_NPC_WT_rep1


title: RNA-seq K562_BCORKO_R4


title: 20WN17_FRRB202411725-1r

city: Wuhan

first: Nai

last: Wu

state: Hubei

address: No.1, Shizishan Street, Hongshan District

institute: HZAU

data_processing:
use fastp (0.20.1) for quality control with default parameters.
Align reads to NIP genome  to using HISAT2 (2.1.0) with default parameters
Transcript assembly and quantification with StringTie (1.3.3b) with default parameters
DESeq2 R package was used to differential expression gene analysis with
Supplementary_files_format_and_content: raw count

organism: Oryza sativa

source_name: leaf of seedling

growth_protocol: each transgenic lines and wild type ZH11 were planted in pots (d=19.5cm, h=25cm) for normal growth until four leaf stage

extract_protocol:
Total RNA were extracted using Trizol reagent(AmbionTM) according to manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: At four leaf stage, the half of the pots were treated with 42℃ for 0.5 hours and half of the pots were grown at normal condition. And then harvested the leaf tissue for total RNA extraction.

value: leaf

tag: development stage

value: 4-leaf seedling stage

value: HS for 0.5 h


title: 20WN18_FRRB202411726-1r

tag: treatment


title: RNA_AML patient UPN04 at diagnosis

description:
UPN04_Diagn
Rel_Diagn_RNAseq_counts.tsv

value: Primary


title: 20WN16_FRRB202411724-1r


title: DNT cells, UDCA-2


title: DNT cells, Contro-3

source_name: DNT cells, Contro

value: Without UDCA stimulation


title: DIA1CAC2wk

description: cachectic melanoma cells 2 weeks replicate 1

value: 2 months

value: cachectic melanoma cells

tag: time


title: RNA-seq K562_WT_R3

value: WT


title: RNA-seq K562_WT_R4


title: RNA-seq K562_WT_R5


title: PLAC_H3K4me3_ESC_WT_rep2

value: E14 mouse embryonic stem cell


title: DNT cells, Contro-1


title: 20WN15_FRRB202411723-1r


title: 20WN12_FRRB202411720-1r


title: SiEs08_colon_CITE

city: San Diego

first: Pandurangan

last: Vijayanand

state: California

address: 9420 Athena Circle

department: Vaccine Discovery

institute: La Jolla Institute for Immunology

description:
Single-cell RNA-seq with 10x Genomics 5' v2 Cell Surface Protein
078_SiEs08_Mo_colon_5v20_CITE

data_processing:
mkfastq (Cell Ranger 3.1.0) was used to generate FASTQ files with default parameters
count (Cell Ranger 3.1.0) was used to generate the filtered UMI matrix with default parameters
Seurat (3.1.5) was used to filter, normalize and scale the UMI matrix
Genome_build: GRCm38 (mm10-3.0.0 from Cell Ranger); GRCm38 (alts-ensembl-3.1.0 from Cell Ranger)
Supplementary_files_format_and_content: murine_tissue_annotation.txt.gz metadata for 9181 cells
Supplementary_files_format_and_content: murine_tissue_umi.txt.gz count data matrix for 9181 cells

source_name: Colon

extract_protocol:
CD4+FoxP3+ TREG cells were sorted into 1.5ml collection tubes containing 500ul of a 1:1 solution of PBS and FBS and a 1:100 dilution of Rnase inhibitor. Subsequent processing was performed as to manufacturers (10x Genomics) instructions
10x scRNA-seq; RNA libraries were constructed following the manufacturers instructions

tag: strain background

value: Colon

value: FoxP3+CD4+ T cells

tag: sorted fraction


title: RNA_AML patient UPN04 at relapse (post transpantation)

description:
UPN04_Rel
Rel_Diagn_RNAseq_counts.tsv

value: Relapse


title: RNA-seq OCIAML3_parental_R1


title: RNA_AML patient UPN02 at relapse (post transpantation)

description:
UPN02_Rel
Rel_Diagn_RNAseq_counts.tsv


title: RNA_AML patient UPN03 at diagnosis

description:
UPN03_Diagn
Rel_Diagn_RNAseq_counts.tsv

value: Diagnosis


title: 20WN11_FRRB202411719-1r


title: RNA_AML patient UPN02 at diagnosis

description:
UPN02_Diagn
Rel_Diagn_RNAseq_counts.tsv


title: Duo.HV 69_S69

city: Rochester

first: Ting

last: Wei

state: MN

address: 507 3rd St SW

institute: Mayo Clinic

description: Duo.HV

data_processing:
Image data and base calling were processed using the Illumina Standard Pipeline.
Fastq data were analyzed by Mayo Analysis Pipeline for RNA Sequencing (MAPRSeq v3.1.3) with STAR (2.6.1) for reads alignment to the human genome reference GRCh38 (hg38) and RSeqQC for gene expression.
After read counts and library size filtration, normalized counts and RPKM for samples were calculated by edgeR (v4.0.1) and differentially expressed genes between groups were determined
Gene set enrichment analysis (GSEA, v4.0.1) was conducted using preranked module based on gene expression ranks
Genome_build: hg38
Supplementary_files_format_and_content: Raw counts and RPKM (merged)

source_name: Duodenum

extract_protocol:
RNA extracted using Qiagen miRNeasy kit for total RNA (Cat# 217004)
Illumina NovaSeq 6000 S2 flow cell (paired-end libraries 2×50bp)

treatment_protocol: Biopsies were collected, immediately placed in Qiagen Allprotect Tissue Reagent (Cat# 76405) and flash frozen in LN2. Storage at -80°C.

value: Duodenum

value: Healthy

tag: gender

value: M

tag: bmi


title: 20WN10_FRRB202411718-1r


title: RNA_AML patient UPN01 at relapse (post transpantation)

description:
UPN01_Rel
Primary_PDX_RNAseq_counts.tsv, Rel_Diagn_RNAseq_counts.tsv


title: SiEs08_colon_Gex

description:
Single-cell RNA-seq with 10x Genomics 5' v2 GEX
076_SiEs08_Mo_colon_5v20_Gex


title: RNA_AML patient UPN03 at relapse (post transpantation)

description:
UPN03_Rel
Rel_Diagn_RNAseq_counts.tsv


title: 20WN09_FRRB202411717-1r

value: untreated


title: DNT cells, Contro-2

tag: strain

value: spleen

value: DNT cells

value: adult


title: Jej.HV 66_S6

description: Jej.HV

source_name: Jejunum

value: Jejunum


title: Duo.IBSD 67_S67

description: Duo.IBSD

value: IBS-D


title: SiEs08_tumor_TCR

description:
Single-cell RNA-seq with 10x Genomics 5' v2 V(D)J
074_SiEs08_Mo_tumor_5v20_TCR

source_name: Tumor

value: Tumor


title: 20WN08_FRRB202411716-1r

value: leaf

value: 4-leaf seedling stage


title: RNA_AML patient UPN01 at diagnosis

description:
UPN01_Diagn
Primary_PDX_RNAseq_counts.tsv, Rel_Diagn_RNAseq_counts.tsv

value: Primary


title: Duo.IBSD 64_S65

description: Duo.IBSD


title: Duo.IBSC 65_S66

description: Duo.IBSC

value: IBS-C

value: F


title: SiEs08_tumor_Gex

description:
Single-cell RNA-seq with 10x Genomics 5' v2 GEX
073_SiEs08_Mo_tumor_5v20_Gex

value: FoxP3+CD4+ T cells


title: Patient Derived Xenografts UPN01 at diagnosis, rep 3

description:
UPN01_PDX-D3_Diagn
Primary_PDX_ATACseq_counts.tsv

data_processing:
Basecalling using blc2fastq and trimming using cutadapt
Alignment using BWA and abundance estimation using bedtools multicov against GeneHancer database
Differential gene expression computed using DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-separated count file

extract_protocol:
Sorted AML samples were lysed with digitonin and tagmented with an engineered Tn5 transposase, following a protocol optimized for blood cells.
Tagmented DNA was purified and amplified with 10 cycles of PCR. Before the sequencing, fragments with a 1-5 kbp size range were removed by magnetic separation with AMPure XP beads.

value: Diagnosis

value: PDX


title: Duo.IBSC 63_S5

description: Duo.IBSC

value: Duodenum


title: Duo.HV 68_S68

description: Duo.HV

value: Healthy

value: M


title: SiEs08_colon_TCR

description:
Single-cell RNA-seq with 10x Genomics 5' v2 V(D)J
077_SiEs08_Mo_colon_5v20_TCR

value: Colon


title: Patient Derived Xenografts UPN01 at relapse, rep 2

description:
UPN01_PDX-R2_Rel
Primary_PDX_ATACseq_counts.tsv

value: Relapse


title: Duo.HV 62_S64

description: Duo.HV


title: SiEs08_spleen_TCR

description:
Single-cell RNA-seq with 10x Genomics 5' v2 V(D)J
071_SiEs08_Mo_spleen_5v20_TCR

source_name: Spleen

value: Spleen


title: 20WN03_FRRB202411711-1r

value: WT

value: untreated


title: Patient Derived Xenografts UPN01 at diagnosis, rep 2

description:
UPN01_PDX-D2_Diagn
Primary_PDX_ATACseq_counts.tsv


title: Duo.HV 61_S63

description: Duo.HV


title: SiEs08_spleen_Gex

description:
Single-cell RNA-seq with 10x Genomics 5' v2 GEX
070_SiEs08_Mo_spleen_5v20_Gex


title: 20WN02_FRRB202411710-1r


title: SiEs08_tumor_CITE

description:
Single-cell RNA-seq with 10x Genomics 5' v2 Cell Surface Protein
075_SiEs08_Mo_tumor_5v20_CITE

value: Tumor


title: 20WN01_FRRB202411709-1r

value: leaf


title: Duo.IBSD 60_S62

description: Duo.IBSD

value: IBS-D


title: Patient Derived Xenografts UPN01 at relapse, rep 1

description:
UPN01_PDX-R1_Rel
Primary_PDX_ATACseq_counts.tsv


title: Patient Derived Xenografts UPN01 at diagnosis, rep 1

description:
UPN01_PDX-D1_Diagn
Primary_PDX_ATACseq_counts.tsv


title: Patient Derived Xenografts UPN01 at relapse, rep 3

description:
UPN01_PDX-R3_Rel
Primary_PDX_ATACseq_counts.tsv


title: mouse embryonic stem cells p300 knock-in rep1

first: Yihan

last: Lin

address: No.5 Yiheyuan Road, Haidian

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequencing adapters were trimmed using Trim_galore with the following parameters :-q 12 --phred33 --stringency 3 --length 20 -e 0.1 --paired.
Reads were aligned using STAR (version STAR-2.5.3a) against mm10 (Mus_musculus.GRCm38). With parameter --quantMode TranscriptomeSAM GeneCounts, ReadsPerGene.out.tab file for each sample were obtained.
Genome_build: mm10
Supplementary_files_format_and_content: ReadsPerGene.out.tab files with 4 columns correspond to different strandedness options: column 1: gene ID; column 2: counts for unstranded RNA-seq; column 3: counts for the 1st read strand aligned with RNA; column 4: counts for the 2nd read strand aligned with RNA.

source_name: embryo

growth_protocol: Mouse embryonic stem cells were matained on gelatin-coated dishes at 37°C with 5% CO2. The culture medium for mouse embryonic stem cells includes Dulbecco’s Modified Eagle Medium (GIBCO), 15% fetal bovine serum (FBS, GIBCO), 1% penicillin-streptomycin (Sigma-Aldrich), 1% Non-Essential Amino Acids (NEAA), 0.1 mM β-mercaptoethanol (Sigma), and 1000 U/ml LIF (Leukemia Inhibitory Factor, EMD Millipore).

extract_protocol:
Cells were washed twice with DPBS after digestion. RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: E14 cells (E14Tg2a.4)

value: p300 knock-in


title: Duo.HV 59_S61

description: Duo.HV


title: 20WN07_FRRB202411715-1r

value: 4-leaf seedling stage


title: Duo.HV 58_S60

description: Duo.HV

value: F


title: Patient Derived Xenografts UPN03 at relapse + EPZ-6438

description:
UPN03_EZH2i
EZH2i_DMSO_ATACseq_counts.tsv

value: Relapse + EPZ-6438

value: Primary


title: mouse embryonic stem cells WT rep2


title: Duo.HV 57_S59

description: Duo.HV

value: Duodenum


title: Patient Derived Xenografts UPN02 at relapse + EPZ-6438

description:
UPN02_EZH2i
EZH2i_DMSO_ATACseq_counts.tsv


title: Duo.HV 56_S58

description: Duo.HV

value: Healthy


title: 20WN06_FRRB202411714-1r


title: mouse embryonic stem cells WT rep1


title: SiEs08_spleen_CITE

description:
Single-cell RNA-seq with 10x Genomics 5' v2 Cell Surface Protein
072_SiEs08_Mo_spleen_5v20_CITE

value: FoxP3+CD4+ T cells


title: SOL_NONCACMEL_5

description: bearing a non-cachectic (NONCAC) melanoma replicate 5

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and low-quality sequence, then mapped to mm10 whole genome using CLC Genomic Workbench RNA seq tool. TPM for transcripts were reported.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include TPM values for all 59 samples

source_name: soleus (SOL) muscles from 4-month-old female NCI Ath/nude mice

extract_protocol:
Tissues were homogenized in Trizol and RNA extracted by isopropanol precipitation from the aqueous phase. RNA sequencing was performed as previously described from UBR4 mKO tibialis anterior muscle at 6 and 24 months of age.
For sequencing, biological replicates were prepared with the TruSeq stranded mRNA library prep kit (Illumina) and sequenced on the Illumina HiSeq 2000 platform.

value: NCI Ath/nude

value: soleus muscles

tag: age

value: 4 months

value: female


title: Patient Derived Xenografts UPN01 at relapse + EPZ-6438

description:
UPN01_EZH2i
EZH2i_DMSO_ATACseq_counts.tsv


title: Duo.HV 55_S57

description: Duo.HV


title: Patient Derived Xenograft UPN02 at relapse + DMSO

description:
UPN02_DMSO
EZH2i_DMSO_ATACseq_counts.tsv

value: Relapse + DMSO


title: Duo.HV 54_S56

description: Duo.HV

value: M


title: SOL_NONCACMEL_3

description: bearing a non-cachectic (NONCAC) melanoma replicate 3

tag: Sex


title: Patient Derived Xenograft UPN01 at relapse + DMSO

description:
UPN01_DMSO
EZH2i_DMSO_ATACseq_counts.tsv

tag: condition


title: mouse embryonic stem cells p300 knock-in rep2


title: Duo.IBSD 52_S54

description: Duo.IBSD


title: SOL_NONCACMEL_1

description: bearing a non-cachectic (NONCAC) melanoma replicate 1


title: Jej.IBSD 53_S55

description: Jej.IBSD

value: Jejunum


title: AML patient UPN010 at diagnosis

description:
UPN10CT_Diagn
Rel_Diagn_CT_ATACseq_counts.tsv

value: Diagnosis

tag: patient


title: SOL_CACMEL_5

description: bearing a cachectic (CAC) melanoma replicate 5

value: bearing a cachectic (CAC) melanoma


title: Jej.IBSD 51_S53

description: Jej.IBSD

value: IBS-D


title: SOL_NONCACMEL_2

description: bearing a non-cachectic (NONCAC) melanoma replicate 2


title: AML patient UPN09 at diagnosis

description:
UPN09CT_Diagn
Rel_Diagn_CT_ATACseq_counts.tsv

tag: origin


title: Jej.IBSD 49_S51

description: Jej.IBSD

tag: tissue


title: AML patient UPN09 at relapse (post chemotherapy)

description:
UPN09CT_Rel
Rel_Diagn_CT_ATACseq_counts.tsv

value: Relapse


title: Patient Derived Xenograft UPN03 at relapse + DMSO

description:
UPN03_DMSO
EZH2i_DMSO_ATACseq_counts.tsv


title: SOL_CACMEL_3

description: bearing a cachectic (CAC) melanoma replicate 3


title: Duo.IBSD 48_S50

description: Duo.IBSD

tag: genotype


title: SOL_CACMEL_2

description: bearing a cachectic (CAC) melanoma replicate 2


title: AML patient UPN08 at diagnosis

description:
UPN08CT_Diagn
Rel_Diagn_CT_ATACseq_counts.tsv


title: AML patient UPN08 at relapse (post chemotherapy)

description:
UPN08CT_Rel
Rel_Diagn_CT_ATACseq_counts.tsv


title: SOL_NONCACMEL_4

description: bearing a non-cachectic (NONCAC) melanoma replicate 4


title: SOL_CACMEL_1

description: bearing a cachectic (CAC) melanoma replicate 1


title: AML patient UPN07 at relapse (post chemotherapy)

description:
UPN07CT_Rel
Rel_Diagn_CT_ATACseq_counts.tsv


title: AML patient UPN07 at diagnosis

description:
UPN07CT_Diagn
Rel_Diagn_CT_ATACseq_counts.tsv


title: TA_NONCACMEL_5

description: bearing a non-cachectic (NONCAC) melanoma replicate 5

source_name: tibilias anterior (TA) muscles from 4-month-old female NCI Ath/nude mice

value: tibilias anterior muscles


title: Duo.IBSD 45_S47

description: Duo.IBSD


title: TA_NONCACMEL_4

value: bearing a non-cachectic (NONCAC) melanoma


title: Duo.IBSD 46_S48

description: Duo.IBSD


title: AML patient UPN06 at relapse (post chemotherapy)

description:
UPN06CT_Rel
Rel_Diagn_CT_ATACseq_counts.tsv

value: Primary


title: Jej.IBSC 44_S46

description: Jej.IBSC

value: IBS-C


title: Human_CD23CAR+1L

type: RNA

city: Monza

first: Sarah

last: Tettamanti

address: via Pergolesi, 33

institute: M.Tettamanti Research Center

description: CD23.CAR transduced T cells treated with Lenalidomide

hyb_protocol: Following manifacturer instructions, 70ul of hybridization buffer and 28ul of Report plus (cointaining custom probes) were added to Reporter CodeSet tube (42uL) to create a hybridization Master Mix. Then, in every tube of a 12-well PCR strip tube, 10uL of Master Mix,  5ul of sample cointaining 50ng of RNA, 3ul of Master Capture (composed by Capture Plus and Capture ProbeSet) are mixed, spinned and hybridized for 22 hours in a pre-heated 65 C thermal cycler, followed by 4 C incubation. The PCR strip was then moved to a nCounter FLEX platform (Nanostring) to load hybridized samples on cartridge.

scan_protocol: nCounter Digital Analyzer was used to scan the cartridge. High sensitivity protocol was selected in order to acquire up to 555 Field of View (FOV) for each sample.

data_processing: Nanostring nCounter was used to quantify expression of 780 CAR-T transcripts (Human CAR-T Characterization Panel v1) and 16 additional transcripts in a custom panel plus. The lower limit of detection is 20 counts, thus counts below 25 were considered background signal and samples with counts below 100 were considered to be semi-quantitative. Transcripts in which more than 30% of samples had counts under 100 were excluded from subsequent analysis. Gene expression normalization was performed relative to housekeeping genes using the gNorm algorithm. Of ten housekeeping genes included on the panel, eight with the lowest standard deviations after normalization were used (SD < 0.40). Mean Square Error analysis was used to identify potential samples of low data quality, and no samples were removed. All normalized data was then transformed on a log2 scale to undergo further analysis.

source_name: Chronic Lymphocytic leukemia patient

growth_protocol: RPMI Advanced + 10% FBS+ 1% P/S+ 1% L-Glu. IL-2 (50ng/ml) has been added every 3 days.

extract_protocol:
5x106 cells were lysed with RLT Buffer (160 μL/106 cells) (Qiagen, Valencia, CA) and lysates were frozen at -80°C.
RNA sample quality were analyzed via Agilent Bioanalyzer 2100 with a RNA 6000 Pico Kit (Agilent), following manifacturer instructions.

treatment_protocol: NT and CD23.CAR+ T cells either untreated or treated for 48 hours with 1μM lenalidomide

tag: disease state

value: Chronic Lymphocytic leukemia

tag: cell type

value: T cells

tag: genotype/variation

value: CD23.CAR transduced

value: treated with Lenalidomide


title: Human_CD23CAR-L

description: CD23.CAR transduced T cells without Lenalidomide

tag: treatment

value: without Lenalidomide


title: TA_NONCACMEL_3

description: bearing a non-cachectic (NONCAC) melanoma replicate 3

value: NCI Ath/nude

value: 4 months

value: female


title: Duo.IBSD 50_S52

description: Duo.IBSD

value: Duodenum

value: F


title: Human_NT-L

description: Not tranduced T cells without Lenalidomide

value: untransduced


title: AML patient UPN06 at diagnosis

description:
UPN06CT_Diagn
Rel_Diagn_CT_ATACseq_counts.tsv

value: Diagnosis


title: TA_NONCACMEL_2

description: bearing a non-cachectic (NONCAC) melanoma replicate 2


title: Duo.IBSC 43_S45

description: Duo.IBSC

value: M


title: cca1 lhy_CL_12h_3

city: Berlin

first: Anne

last: Cortleven

address: Albrecht-Thaer-Weg 5

department: Institut fur Biologie

institute: FU Berlin

data_processing:
base-calling was done with BGISEQ500, version 1.1.2.29164
After removal of adaptors and low quality reads, the obtained clean reads (approximately 23 million) were stored as FASTQ format   SOAPnuke, version v1.5.2, parameters: -I15 -q 0.5 -n0.1
The clean reads were mapped to the reference genome (TAIR10) using HISAT, version v2.0.4, parameters: -p8 --phred64 --sensitive -I 1 -X10000
For gene expression analysis clean reads were mapped to reference using Bowtie2, v2.2.5, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k  200
Gene expression levels based on the FPKM method were quantified using RSEM v1.2.12, Parameters: default
Genome_build: TAIR10
Supplementary_files_format_and_content: txt file includes FPKM values for each Sample

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis plants were grown for 5 weeks on soil under short day (SD) conditions (8 h light/16 h dark) in a growth chamber with light intensities of 100 to 150 µmol m-2 s-1, using a combination of Philips Son-T Agros 400W and Philips Master HPI-T Plus, 400W/645 lamps, at 22°C and 60% relative humidity.

extract_protocol:
Total RNA was extracted from leaf material, flash-frozen in liquid nitrogen using the NucleoSpin® RNA plant kit (Machery and Nagel, Düren, Germany) as described in the user’s manual.
RNA libraries were prepared by the BGISEQ-500 RNA-Seq Library Preparation Protocol. In brief, mRNA was purified with oligo(dt) magnetic beads, mRNA was chemically fragmented and cDNA was generated using random hexamer-primed reverse transcription. End-repair and 3'adenylation was done and adapters were ligated to the adenylated cDNA. adapter-ligated was amplified via PCR and purified with Ampure XP Beads (Agencourt). The library was validated on the Agilent Technologies 2100 bioanalyzer and the double stranded PCR products were denaturated and circularized.

treatment_protocol: 5-weeks-old plants were exposed to a light period of 32 h (CL) or remained under control conditions (SD).

value: cca1 lhy

value: 32 h light

tag: sampling time point

value: leaf


title: Duo.IBSC 42_S4

description: Duo.IBSC

value: IBS-C


title: cca1 lhy_CL_12h_2


title: TA_NONCACMEL_1

description: bearing a non-cachectic (NONCAC) melanoma replicate 1

value: tibilias anterior muscles


title: AML patient UPN05 at relapse (post transpantation)

description:
UPN05_Rel
Rel_Diagn_ATACseq_counts.tsv

value: Relapse

value: Primary


title: AML patient UPN05 at diagnosis

description:
UPN05_Diagn
Rel_Diagn_ATACseq_counts.tsv


title: Jej.HV 40_S3

description: Jej.HV

value: Jejunum

value: Healthy


title: Jej.IBSC 41_S44

description: Jej.IBSC


title: AML patient UPN04 at relapse (post transpantation)

description:
UPN04_Rel
Rel_Diagn_ATACseq_counts.tsv


title: AML patient UPN04 at diagnosis

description:
UPN04_Diagn
Rel_Diagn_ATACseq_counts.tsv


title: cca1 lhy_CL_12h_1


title: TA_CACMEL_4

description: bearing a cachectic (CAC) melanoma replicate 4

value: NCI Ath/nude

value: bearing a cachectic (CAC) melanoma


title: ahk2 ahk3_CL_12h_2

value: ahk2 ahk3


title: TA_CACMEL_3

description: bearing a cachectic (CAC) melanoma replicate 3

value: 4 months

value: female


title: ahk2 ahk3_CL_12h_3


title: ahk2 ahk3_CL_12h_1


title: Human_NT+1L

description: Not tranduced T cells treated with Lenalidomide

value: Chronic Lymphocytic leukemia

value: T cells

value: untransduced

value: treated with Lenalidomide


title: Jej.HV 39_S43

description: Jej.HV

value: F


title: Duo.HV 38_S42

description: Duo.HV

value: Duodenum


title: AML patient UPN03 at relapse (post transpantation)

description:
UPN03_Rel
Rel_Diagn_ATACseq_counts.tsv


title: AML patient UPN010 at relapse (post chemotherapy)

description:
UPN10CT_Rel
Rel_Diagn_CT_ATACseq_counts.tsv


title: TA_CACMEL_2

description: bearing a cachectic (CAC) melanoma replicate 2


title: WT_CL_12h_3

value: WT

value: 32 h light

value: leaf


title: AML patient UPN02 at relapse (post transpantation)

description:
UPN02_Rel
Rel_Diagn_ATACseq_counts.tsv

value: Relapse

value: Primary


title: AML patient UPN03 at diagnosis

description:
UPN03_Diagn
Rel_Diagn_ATACseq_counts.tsv

value: Diagnosis


title: Jej.HV 35_S39

description: Jej.HV

value: Jejunum

value: Healthy

value: M


title: WT_CL_12h_1


title: WT_CL_12h_2


title: Jej.HV 37_S41

description: Jej.HV


title: AML patient UPN01 at relapse (post transpantation)

description:
UPN01_Rel
Primary_PDX_ATACseq_counts.tsv, Rel_Diagn_ATACseq_counts.tsv


title: Dia_NONCACMEL_9

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 9

source_name: diaphragm muscles (Dia) from 4-month-old female NCI Ath/nude mice

value: NCI Ath/nude

value: diaphragm muscles

value: 4 months


title: Jej.IBSD 47_S49

description: Jej.IBSD

value: IBS-D


title: TA_CACMEL_1

description: bearing a cachectic (CAC) melanoma replicate 1

value: tibilias anterior muscles

value: female

value: bearing a cachectic (CAC) melanoma


title: AML patient UPN02 at diagnosis

description:
UPN02_Diagn
Rel_Diagn_ATACseq_counts.tsv

source_name: AML


title: Jej.HV 34_S38

description: Jej.HV


title: Jej.IBSD 36_S40

description: Jej.IBSD


title: AML patient UPN01 at diagnosis

description:
UPN01_Diagn
Primary_PDX_ATACseq_counts.tsv, Rel_Diagn_ATACseq_counts.tsv


title: Dia_NONCACMEL_8

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 8


title: cca1 lhy_control_12h_2

value: cca1 lhy

value: control (SD conditions)


title: IMD-0354-treated 2

city: Grand Rapids

first: Bin

last: Chen

state: Michigan

address: 400 Monroe Ave NW

department: Department of Pediatrics and Human Development

institute: MICHIGAN STATE UNIVERSITY

description: Total RNA was isolated form Calu-3 cells

data_processing:
RNA-Seq reads were mapped on Hg38 transcriptome using the ENSEMBL GRCh38.p3 annotation with the STAR aligner
Normalized count was obtained from the STAR aligner
Genome_build: UCSC human reference genome (hg38)
Supplementary_files_format_and_content: CSV file includes human ensembl_gene_id and normalized counts (TPM) for each gene in individual samples

growth_protocol: Equal number of Calu-3 cells were grown for 30 min.

extract_protocol:
The total RNA was extracted using KAPA RNA HyperPrep Kit as per manufacturer instructions. Quality and quantity of RNA were checked using a 2100 Bioanalyzer (Agilent Technologies, CA, USA) and the samples with an RNA integrity number ≥ 7 were sequenced.
Ribo-depleted RNA was used for Library preparation and paired end sequencing was performed using Illumina platform (Nextera sequencing) and sequencing chemistry according to the manufacturer’s instructions (Life Technologies, USA).

treatment_protocol:
Cells were grown for 24h without any infection or treatment
For control, no treatment was given to the cells, and they were grown for 24h. For infection, after 30 min of growth a MOI of 0.1 of SARS-CoV-2 was used to infect the cells followed by culture till 24h. For drug treatment groups, cells along with IMD-0354 were grown for 30 min followed by addition of MOI of 0.1 of SARS-CoV-2 and culture them for 24h.

tag: cell line

value: SARS-CoV-2 treated IMD-0354 treated

tag: time

tag: replicates


title: SOL_CACMEL_4

value: soleus muscles


title: Jej.IBSC 30_S35

description: Jej.IBSC

value: IBS-C

tag: gender

tag: bmi


title: Dia_NONCACMEL_7

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 7

tag: strain

tag: age


title: Jej.HV 33_S37

description: Jej.HV


title: Dia_NONCACMEL_6

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 6

tag: Sex


title: Duo.IBSC 29_S34

description: Duo.IBSC

value: Duodenum


title: IMD-0354-treated 3


title: Jej.HV 32_S2

description: Jej.HV


title: Duo.IBSC 28_S33

description: Duo.IBSC


title: SARS-CoV-2-infected 2


title: cca1 lhy_control_12h_1

value: leaf


title: cca1 lhy_control_12h_3


title: Dia_NONCACMEL_5

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 5


title: Duo.IBSC 31_S36

description: Duo.IBSC


title: Dia_NONCACMEL_4

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 4


title: ahk2 ahk3_control_12h_3

value: ahk2 ahk3


title: Dia_NONCACMEL_3

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 3


title: SARS-CoV-2-infected 3


title: IMD-0354-treated 1


title: ahk2 ahk3_control_12h_1


title: Dia_NONCACMEL_2

description: bearing a non-cachectic (NONCAC) melanoma without rFibcd1 treated replicate 2


title: ahk2 ahk3_control_12h_2


title: WT_control_12h_3

value: WT